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Back-illuminated charged-coupled device (BI-CCD) arrays increase quantum efficiency but also amplify etaloning, a multiplicative, wavelength-dependent fixed-pattern effect. When spectral data from hundreds of BI-CCD rows are combined, the averaged spectrum will generally appear etalon-free. This can mask substantial etaloning at the row level, even if the BI-CCD has been treated to suppress the effect. This paper compares two methods of etalon correction, one with simple averaging and one with row-by-row calibration using a fluorescence standard. Two BI-CCD arrays, both roughened by the supplier to reduce etaloning, were used to acquire Raman spectra of murine bone specimens. For one array, etaloning was the dominant source of noise under the exposure conditions chosen, even for the averaged spectrum across all rows; near-infrared-excited Raman peaks were noticeably affected. In this case, row-by-row calibration improved the spectral quality of the average spectrum. The other CCD’s performance was shot-noise limited and therefore received no benefit from the extra calibration. The different results highlight the importance of checking for and correcting row-level fixed pattern when measuring weak Raman signals in the presence of a large fluorescence background.

Angularly-resolved light scattering has been proven to be an early detector of subtle changes in organelle size due to its sensitivity to scatterer size and refractive index contrast. However, for cells immersed in media with a refractive index close to 1.33, the cell itself acts as a larger scatterer and contributes its own angular signature. This whole-cell scattering, highly dependent on the cell’s shape and size, is challenging to distinguish from the desired organelle scattering signal. This degrades the accuracy with which organelle size information can be extracted from the angular scattering. To mitigate this effect, we manipulate the refractive index of the immersion medium by mixing it with a water-soluble, biocompatible, high-refractive-index liquid. This approach physically reduces the amount of whole-cell scattering by minimizing the refractive index contrast between the cytosol and the modified medium. We demonstrate this technique on live cells adherent on a coverslip, using Fourier transform light scattering to compute the angular scattering from complex field images. We show that scattering from the cell: media refractive index contrast contributes significant scattering at angles up to twenty degrees and that refractive index-matching reduces such low-angle scatter by factors of up to 4.5. This result indicates the potential of refractive index-matching for improving the estimates of organelle size distributions in single cells.

Spatially offset Raman spectroscopy (SORS) is able to detect bone signal transcutaneously and could assist in predicting bone fracture risk. Criteria for optimal source-detector offsets for transcutaneous human measurements, however, are not well-established. Although larger offsets yield a higher percentage of bone signal, the absolute amount of bone signal decreases. Spectral unmixing into bone, adipose, and non-adipose components was employed to quantify changes in bone signal to noise ratio across a range of offsets, and optimal offsets for phalanx and metacarpal measurements were determined. The bone signal to noise ratio was maximized at offsets ranging from 4-6 mm.

We present simulated angular scattering from organelle populations of arbitrary size distribution and spatial location. Simulations will be used to explore the limitations of extracting size information from single cells, motivated by experiments.

To better understand the origin of microplastics in municipal drinking water, we evaluated 50 mL water samples from different stages of the City of Rochester&rsquo, s drinking water production and transport route, from Hemlock Lake to the University of Rochester. We directly filtered samples using silicon nitride nanomembrane filters with precisely patterned slit-shaped pores, capturing many of the smallest particulates (&lt, 20 &micro, m) that could be absorbed by the human body. We employed machine learning algorithms to quantify the shapes and quantity of debris at different stages of the water transport process, while automatically segregating out fibrous structures from particulate. Particulate concentrations ranged from 13 to 720 particles/mL at different stages of the water transport process and fibrous pollution ranged from 0.4 to 8.3 fibers/mL. A subset of the debris (0.2&ndash, 8.6%) stained positively with Nile red dye which identifies them as hydrophobic polymers. Further spectroscopic analysis also indicated the presence of many non-plastic particulates, including rust, silicates, and calcium scale. While water leaving the Hemlock Lake facility is mostly devoid of debris, transport through many miles of piping results in the entrainment of a significant amount of debris, including plastics, although in-route reservoirs and end-stage filtration serve to reduce these concentrations.

Bone fragility and fracture risk are assessed by measuring the areal bone mineral density (aBMD) using dual-energy X-ray absorptiometry (DXA). While aBMD correlates with bone strength, it is a poor predictor of fragility fracture risk. Alternatively, fracture toughness assesses the bone’s resistance to crack propagation and fracture, making it a suitable bone quality metric. Here, we explored how femoral midshaft measurements from DXA, micro-computed tomography (μCT), and Raman spectroscopy could predict fracture toughness. We hypothesized that ovariectomy (OVX) decreases aBMD and fracture toughness compared to controls and we can optimize a multivariate assessment of bone quality by combining results from X-ray and Raman spectroscopy. Female mice underwent an OVX (n=5) or sham (n=5) surgery at 3 months of age. Femurs were excised 3 months after ovariectomy and assessed with Raman spectroscopy, μCT, and DXA. Subsequently, a notch was created on the anterior side of the mid-diaphysis of the femurs. Three-point bending induced a controlled fracture that initiated at the notch. The OVX mice had a significantly lower aBMD, cortical thickness, and fracture toughness when compared to controls (p2=0.71, p2=0.92, p

Transcutaneous determination of a bone's Raman spectrum is challenging because the type I collagen in the overlying soft tissue is spectroscopically identical to that in bone. In a previous transcutaneous study of murine tibiae, we developed a library-based model called SOLD to unmix spatially offset Raman measurements into three spectra: a bone estimate, a soft tissue estimate, and a residual. Here, we demonstrate the value of combining the bone estimate and the residual to produce a "top layer subtracted" (tls) spectrum. We report superior prediction of two standard bone metrics (volumetric bone mineralization density and maximum torque) using partial least squares regression models based upon tls spectra rather than SOLD bone estimates, implying that the spectral residuals contain useful information. Simulations reinforce experimental in vivo findings. This chemometric approach, which we denote as SOLD/TLS, could have broad applicability in situations where comprehensive spectral libraries are difficult to acquire.

Angle-resolved light scattering microscopy enables the size distribution of scatterers within a cell to be estimated non-invasively. Our group is working towards obtaining quantitative estimates of mean scatterer size in single cells by comparing the angular distribution of scattered light to Mie theory models. Using quantitative phase imaging, we are able to measure multiple cells at a time and still obtain each cell’s scattering pattern individually. We are now acquiring data from macrophages performing antibody-dependent cellular phagocytosis (ADCP) in hopes of relating the size estimates to the different known stages of the process.

Using transcutaneous spatially offset Raman spectroscopy (SORS) and partial least squares regression (PLSR), we recently predicted the areal bone mineral density (aBMD), volumetric bone mineralization density (vBMD) and maximum torque (MT) of tibiae in living mice. Despite the spatial offset geometry, the accuracy of the predictions was still affected by the signal from the overlying soft tissue that, like bone, contains large amounts of Type I collagen. Here we report a way to use SOLD (simultaneous, overconstrained, library-based decomposition) to improve the PLSR accuracy. The SOLD processing generates one bone spectrum estimate, one soft tissue spectrum estimate, and a residual. We combine the bone and residual spectra together for submission to PLSR, discarding only the soft tissue contribution. With the implementation of this soft-tissue-subtracted SOLD processing, we demonstrate that we can predict vBMD and MT more accurately than our previous transcutaneous measurements.

Fracture toughness, a bone’s resistance to breaking, is typically measured via invasive mechanical tests. In this ex vivo study on mouse femurs, four Raman spectral features associated with bone properties were significantly correlated to fracture toughness using a partial least squares regression model. By including parameters measured from dual-energy absorptiometry and micro-computed tomography in the model, fracture toughness predictions on ovariectomized mice were significantly lower than a control cohort’s. This shows that meaningful estimates of fracture toughness can be estimated using input parameters obtained non-destructively.

Angular scattering from wavelength-scale objects can be obtained from quantitative phase images. Using Fourier phase microscopy, excellent fits with Mie theory are obtained for single micron-scale beads, and size distribution estimates are performed for the first time on various single cells.

Spatially offset Raman spectroscopy (SORS) is able to detect bone signal transcutaneously and could assist in predicting bone fracture risk. Criteria for optimal source-detector offsets for transcutaneous human measurements, however, are not well-established. Although larger offsets yield a higher percentage of bone signal, the absolute amount of bone signal decreases. Spectral unmixing into bone, adipose, and non-adipose components was employed to quantify changes in bone signal to noise ratio across a range of offsets, and optimal offsets for phalanx and metacarpal measurements were determined. The bone signal to noise ratio was maximized at offsets ranging from 4-6 mm.

We constructed a microscope system that obtains angular scattering information using dark-field quantitative phase imaging. In this technique, unscattered light acts as a reference for interferometry. We tested the system using polystyrene beads.

We report what is to our knowledge the first use of Fourier phase microscopy (FPM) to estimate diameters of individual single-micrometer beads and to classify cells based upon changes in scatterer size distribution. FPM, a quantitative phase imaging (QPI) method, combines the planar illumination typically used in off-axis QPI (ideal for Mie theory analysis) with the common-path geometry typically used in on-axis QPI (ideal for optimizing angular scattering range). Low-spatial-frequency imaging artifacts inherent to FPM have negligible impact upon these angular-domain applications. The system is simple to align and stable, and requires no external reference beam. Angular scattering patterns obtained from single 1 µm polystyrene beads in glycerol ( Δ n = 0.11 ) display unprecedented fidelity to Mie theory, produce diameter estimates consistent with the manufacturer’s specifications, and offer precision on the scale of tens of nanometers. Measurements of macrophages at different stages of antibody-dependent cellular phagocytosis demonstrate the ability to detect changes in a cell’s scattering caused by the presence of phagocytosed material within.

Scanning confocal Raman microscopy is proposed to measure a gradient index (GRIN) profile at an optical surface. The Raman microscope is calibrated to index of refraction for a binary copolymer GRIN material, and then the index of refraction is mapped on the plano surface of a GRIN polymer lens. The measurement deduces axial shift of 680 μm and identifies lateral tilt or decenter with respect to the nominal position of the GRIN profile. Results suggest that the mapping method is a nondestructive way to measure the GRIN profile of a GRIN lens and its positioning within the lens geometry, to within the sampling precision of the Raman microscope.

Functional spintronic devices rely on spin-charge interconversion effects, such as the reciprocal processes of electric field-driven spin torque and magnetization dynamics-driven spin and charge flow. Both damping-like and field-like spin-orbit torques have been observed in the forward process of current-driven spin torque and damping-like inverse spin-orbit torque has been well-studied via spin pumping into heavy metal layers. Here we demonstrate that established microwave transmission spectroscopy of ferromagnet/normal metal bilayers under ferromagnetic resonance can be used to inductively detect the AC charge currents driven by the inverse spin-charge conversion processes. This technique relies on vector network analyzer ferromagnetic resonance (VNA-FMR) measurements. We show that in addition to the commonly-extracted spectroscopic information, VNA-FMR measurements can be used to quantify the magnitude and phase of all AC charge currents in the sample, including those due to spin pumping and spin-charge conversion. Our findings reveal that Permalloy/Pt bilayers exhibit both damping-like and field-like inverse spin-orbit torques. While the magnitudes of both the damping-like and field-like inverse spin-orbit torque are of comparable scale to prior reported values for similar material systems, we observed a significant dependence of the damping-like magnitude on the order of deposition. This suggests interface quality plays an important role in the overall strength of the damping-like spin-to-charge conversion. Spin memory loss (SML) [1] and proximity-induced magnetic moments at the FM/NM interface [2] have been invoked to explain the large damping enhancement caused by thin NM films even when the NM thickness is less than its spin diffusion length. In this model, spin loss at the FM/NM interface acts as an additional parallel spin relaxation pathway to that of spin pumping and diffusion into the Pt bulk. From damping measurements alone, the relative contributions of these mechanisms are not resolvable. In this work, we show that a self-consistent fit of Gilbert damping and damping-like iSOT versus Pt thickness—where both sets of data are described by the same spin diffusion length—makes it possible to separate these sources of damping. Furthermore, this data analysis methodology allows for unambiguous determination of the spin-mixing conductance at the FM/NM interface. We therefore can determine the spin Hall conductivity (or spin Hall angle) without having to refer to spin transport parameters, e.g. the spin-mixing conductance and spin diffusion length, as determined from measurements performed on dissimilar samples or theoretical idealized values. For our samples of Pt deposited on Permalloy, only 37 ± 6% of the total damping enhancement from the Pt film is attributable to spin pumping into the Pt layer when the Pt thickness is much greater than the spin diffusion length. The self-consistent fit also results in a spin diffusion of length of (4.2 ± 0.1) nm, and a spin mixing conductance of (130,000 ± 20,000) 1/(μΩ cm^2), which is in good agreement with the maximum theoretical value for Pt of 107,000 1/(μΩ cm^2) [3], given the estimated error, and σ_SH = (2.36 ± 0.04) 1/(μΩ m). This corresponds to a spin Hall angle of 0.387 ± 0.008. While this θ_SH is among the largest reported for Pt [4, 5], it is a necessary logical conclusion that with less spin current driven into the NM (on account of SML), a larger spin-to-charge conversion efficiency is required to fit the data than would be otherwise obtained if the SML were negligible. We furthermore stress that the phenomenological value for the damping-like spin orbit torque is comparable to that measured with other techniques [5-7]. This indicates that the Pt layer in our samples behaves conventionally, and stresses the importance of characterizing spin loss mechanisms to optimize SOT for magnetic switching. REFERENCES [1] J.-C. Rojas-Sanchez, N. Reyren, P. Laczkowski, et al., "Spin Pumping and Inverse Spin Hall Effect in Platinum: The Essential Role of Spin-Memory Loss at Metallic Interfaces," Phys. Rev. Lett., vol. 112, p. 106602 (2014). [2] M. Caminale, A. Ghosh, S. Auffret, et al., "Spin pumping damping and magnetic proximity effect in Pd and Pt spin-sink layers," Physical Review B, vol. 94, p. 014414 (2016). [3] Y. Liu, Z. Yuan, R. J. H. Wesselink, et al., "Interface Enhancement of Gilbert Damping from First Principles," Physical Review Letters, vol. 113, p. 207202 (2014). [4] W. Zhang, W. Han, X. Jiang, et al., "Role of transparency of platinum-ferromagnet interfaces in determining the intrinsic magnitude of the spin Hall effect," Nat Phys, Article vol. 11, pp. 496-502 (2015). [5] C.-F. Pai, Y. Ou, L. H. Vilela-Leao, et al., "Dependence of the efficiency of spin Hall torque on the transparency of Pt/ferromagnetic layer interfaces," Phys. Rev. B, vol. 92, p. 064426 (2015). [6] K. Garello, I. M. Miron, C. O. Avci, et al., "Symmetry and magnitude of spin-orbit torques in ferromagnetic heterostructures," Nat. Nano., vol. 8, pp. 587-593 (2013). [7] M.-H. Nguyen, D. C. Ralph, and R. A. Buhrman, "Spin Torque Study of the Spin Hall Conductivity and Spin Diffusion Length in Platinum Thin Films with Varying Resistivity," Physical Review Letters, vol. 116, p. 126601 (2016).

Bone strength is a worldwide health concern. Although multiple techniques have been developed to evaluate bone quality, there are still gaps to be filled. Here we report a non-invasive approach for the prediction of bone strength in vivo using spatially offset Raman spectroscopy. Raman spectra were acquired transcutaneously from the tibiae of mice from 4 to 23 weeks old and subsequently on the exposed bones. Partial least squares regression was applied to generate predictions of the areal bone mineral density (aBMD), volumetric bone mineralization density (vBMD), and maximum torque (MT) of each tibia as quantified by dual-energy X-ray absorptiometry, microCT imaging, and biomechanical tests, respectively. Significant correlations were observed between Raman spectral predictions and the reference values in all three categories. To our knowledge, this is the first demonstration of Raman spectroscopy predicting a biomechanical bone parameter (MT) in vivo with an uncertainty much smaller than the spread in the reference values.

Understanding the evolution of spin-orbit torque (SOT) with increasing heavy-metal thickness in ferromagnet/normal metal (FM/NM) bilayers is critical for the development of magnetic memory based on SOT. However, several experiments have revealed an apparent discrepancy between damping enhancement and dampinglike SOT regarding their dependence on NM thickness. Here, using linewidth and phase-resolved amplitude analysis of vector network analyzer ferromagnetic resonance (VNA-FMR) measurements, we simultaneously extract damping enhancement and both fieldlike and dampinglike inverse SOT in ${\mathrm{Ni}}_{80}{\mathrm{Fe}}_{20}$/Pt bilayers as a function of Pt thickness. By enforcing an interpretation of the data which satisfies Onsager reciprocity, we find that both the damping enhancement and dampinglike inverse SOT can be described by a single spin diffusion length $(\ensuremath{\approx}4\phantom{\rule{0.16em}{0ex}}\mathrm{nm})$, and that we can separate the spin pumping and spin-memory loss contributions to the total damping. This analysis indicates that less than 40% of the angular momentum pumped by FMR through the ${\mathrm{Ni}}_{80}{\mathrm{Fe}}_{20}$/Pt interface is transported as spin current into the Pt. On account of the spin-memory loss and corresponding reduction in total spin current available for spin-charge transduction in the Pt, we determine the Pt spin Hall conductivity $[{\ensuremath{\sigma}}_{\mathrm{SH}}=(2.36\ifmmode\pm\else\textpm\fi{}0.04)\ifmmode\times\else\texttimes\fi{}{10}^{6}\phantom{\rule{0.28em}{0ex}}{\ensuremath{\omega}}^{\ensuremath{-}1}\phantom{\rule{0.16em}{0ex}}{\mathrm{m}}^{\ensuremath{-}1}]$ and bulk spin Hall angle $({\ensuremath{\theta}}_{\mathrm{SH}}=0.387\ifmmode\pm\else\textpm\fi{}0.008)$ to be larger than commonly cited values. These results suggest that Pt can be an extremely useful source of SOT if the FM/NM interface can be engineered to minimize spin loss. Lastly, we find that self-consistent fitting of the damping and SOT data is best achieved by a model with Elliott-Yafet spin relaxation and extrinsic inverse spin Hall effect, such that both the spin diffusion length and spin Hall conductivity are proportional to the Pt charge conductivity.

Angularly resolved elastic scattering microscopy enables the size distribution of cellular organelles to be estimated non-invasively. By comparing the angular distribution of light scattered from a cell to Mie theory models, our group is working towards obtaining quantitative estimates of mean organelle size within single cells and tracking them over time. These estimates can then be used to assess the health of the cell. We are now testing our system’s performance in measuring induced size changes in HeLa cells undergoing apoptosis, or programmed cell death. Apoptosis is induced in these cells by exposing them to a Fas ligand. Because the response of the cell occurs on the scale of a few hours, we can take multiple measurements of many cells individually before they show changes that would be visible with traditional microscopy. Additionally, we take measurements prior to exposing cells to the ligand to establish the baseline fluctuations in the organelle size estimates. Our goal is to find optical signatures that characterize the cellular progression prior to the final, most extreme stages of the apoptotic process. We would then be able to look at the behavior of multiple cells and predict when each cell will die.

Electromagnetic Theory is a required junior-year course for Optics majors at the University of Rochester. This foundational course gives students their first rigorous exposure to electromagnetic vector fields, dipole radiation patterns, Fresnel reflection/transmission coefficients, waveguided modes, Jones vectors, waveplates, birefringence, and the Lorentz model of refractive index.To increase the percentage of class time devoted to student-centered conceptual reasoning and instructor feedback, this course was recently “flipped”. Nearly all of the mathematically-intensive derivations were converted to narrated screencasts (“Khan Academy” style) and made available to students through the course’s learning management system. On average, the students were assigned two 10–15 minute videos to watch in advance of each lecture. An electronic survey after each tutorial encouraged reflection and counted towards the student’s participation grade. Over the past three years, students have consistently rated the videos as being highly valuable.This presentation will discuss the technical aspects of creating tutorial videos and the educational tradeoffs of flipping a mathematically-intensive upper-level course. The most important advantage is the instructor’s increased ability to identify and respond to student confusion, via activities that would consume too much time in a lecture-centered course. Several examples of such activities will be given. Two pitfalls to avoid are the temptation for the instructor not to update the videos from year to year and the tendency of students not to take lecture notes while watching the videos.

The development of spatially offset Raman spectroscopy (SORS) has enabled deep, non-invasive chemical characterization of turbid media. Here, we use SORS to measure subcortical bone tissue and depth-resolved biochemical variability in intact, exposed murine bones. We also apply the technique to study a mouse model of the genetic bone disorder osteogenesis imperfecta. The results suggest that SORS is more sensitive to disease-related biochemical differences in subcortical trabecular bone and marrow than conventional Raman measurements.

Functional spintronic devices rely on spin-charge interconversion effects, such as the reciprocal processes of electric field-driven spin torque and magnetization dynamics-driven spin and charge flow. Both dampinglike and fieldlike spin-orbit torques have been observed in the forward process of current-driven spin torque and dampinglike inverse spin-orbit torque has been well studied via spin pumping into heavy metal layers. Here, we demonstrate that established microwave transmission spectroscopy of ferromagnet/normal metal bilayers under ferromagnetic resonance can be used to inductively detect the ac charge currents driven by the inverse spin-charge conversion processes. This technique relies on vector network analyzer ferromagnetic resonance (VNA-FMR) measurements. We show that in addition to the commonly extracted spectroscopic information, VNA-FMR measurements can be used to quantify the magnitude and phase of all ac charge currents in the sample, including those due to spin pumping and spin-charge conversion. Our findings reveal that ${\mathrm{Ni}}_{80}{\mathrm{Fe}}_{20}\text{/Pt}$ bilayers exhibit both dampinglike and fieldlike inverse spin-orbit torques. While the magnitudes of both the dampinglike and fieldlike inverse spin-orbit torque are of comparable scale to prior reported values for similar material systems, we observed a significant dependence of the dampinglike magnitude on the order of deposition. This suggests interface quality plays an important role in the overall strength of the dampinglike spin-to-charge conversion.

Angularly resolved elastic light scattering is an established technique for probing the average size of organelles in biological tissue and cellular ensembles. Focusing of the incident light to illuminate no more than one cell at a time restricts the minimum forward-scattering angle θmin that can be detected. Series of simulated single-cell angular-scattering patterns have been generated to explore how size estimates vary as a function of θmin. At a setting of θmin=20 deg, the size estimates hop unstably between multiple minima in the solution space as simulated noise (mimicking experimentally observed levels) is varied. As θmin is reduced from 20 deg to 10 deg, the instability vanishes, and the variance of estimates near the correct answer also decreases. The simulations thus suggest that robust Mie theory fits to single-cell scattering at 785 nm excitation require measurements down to at least 15 deg. Notably, no such instability was observed at θmin=20 deg for narrow bead distributions. Accurate sizing of traditional calibration beads is, therefore, insufficient proof that an angular-scattering system is capable of robust analysis of single cells. Experimental support for the simulation results is also presented using measurements on cells fixed with formaldehyde.

Background: Exposure to lead (Pb) from environmental and industrial sources remains an overlooked serious public health risk. Elucidating the effect of Pb on bone cell function is therefore critical for understanding its risk associated with diseases of low bone mass. Objectives: We tested the hypothesis that Pb negatively affects bone mass. We also assessed the underlying mechanisms of Pb on bone signaling pathways. Methods: We used a model of low-level Pb exposure in a rodent beginning before conception and continuing over 18 months. We characterized the effect of Pb on bone quality using dual-energy X-ray absorptiometry (DXA), micro-computed tomography, Raman spectroscopy, and histology. We assessed the effect of Pb on bone and adipocyte formation by mineral deposition, lipid droplet formation, and Western blot and RNA analysis. Results: Pb-exposed animals had decreased bone mass that resulted in bones that were more susceptible to fracture. Pb decreased osteoblastic cell number leading to a depression of bone formation. Accompanying this, Pb exposure elevated sclerostin protein levels in the skeleton, and correspondingly reduced levels of β-catenin and Runx2 in stromal precursor cells. Pb also increased skeletal expression of peroxisome proliferator-activated receptor-γ (PPAR-γ). These results indicate a shift in mesenchymal differentiation wherein Pb promoted enhanced adipogenesis and decreased osteoblastogenesis. Substantial differences in bone marrow composition were observed, highlighted by an increase in adipocytes. Conclusions: The disruption Pb has on bone mass and bone homeostasis is principally explained by inhibition of the Wnt/β-catenin pathway, which may provide a molecular basis for novel therapeutic strategies to combat Pb-induced bone pathologies.

Habitat disturbance from development, resource extraction, off-road vehicle use, and energy development ranks highly among threats to desert systems worldwide. In the Mojave Desert, United States, these disturbances have promoted the establishment of nonnative plants, so that native grasses and forbs are now intermixed with, or have been replaced by invasive, nonnative Mediterranean grasses. This shift in plant composition has altered food availability for Mojave Desert tortoises (Gopherus agassizii), a federally listed species. We hypothesized that this change in forage would negatively influence the physiological ecology, immune competence, and health of neonatal and yearling tortoises. To test this, we monitored the effects of diet on growth, body condition, immunological responses (measured by gene transcription), and survival for 100 captive Mojave tortoises. Tortoises were assigned to one of five diets: native forbs, native grass, invasive grass, and native forbs combined with either the native or invasive grass. Tortoises eating native forbs had better body condition and immune functions, grew more, and had higher survival rates (>95%) than tortoises consuming any other diet. At the end of the experiment, 32% of individuals fed only native grass and 37% fed only invasive grass were found dead or removed from the experiment due to poor body conditions. In contrast, all tortoises fed either the native forb or combined native forb and native grass diets survived and were in good condition. Health and body condition quickly declined for tortoises fed only the native grass (Festuca octoflora) or invasive grass (Bromus rubens) with notable loss of fat and muscle mass and increased muscular atrophy. Bromus rubens seeds were found embedded in the oral mucosa and tongue in most individuals eating that diet, which led to mucosal inflammation. Genes indicative of physiological, immune, and metabolic functions were transcribed at lower levels for individuals fed B. rubens, indicating potential greater susceptibility to disease or other health-related problems. This study highlights the negative indirect effects of invasive grasses, such as red brome, in desert ecosystems, and provides definitive evidence of a larger negative consequence to health, survival, and ultimately population recruitment for Mojave Desert tortoises than previously understood.

The literature contains several reports of Mie-like fits to angular-domain elastic scattering measurements from multiple cells or isolated mitochondria. In these studies, the sampling volume typically contains hundreds or thousands of mitochondria, allowing for the size distribution of mitochondria to be modeled as a smooth function, (e.g. Gaussian or log-normal) with a small number of free parameters. In the case of a single-cell volume containing significantly fewer mitochondria, the true size distribution will no longer be as smooth. Increasing the number of free parameters can lead to unstable fits, however, as the forward-directed angular scattering pattern from such a population illuminated with 785 nm light is a monotonically decaying radial function with few distinct features. Using simulations, we have investigated the limitations of modeling single-cell mitochondrial scattering using smooth population distributions of Mie scatterers. In different instances, the fidelity of the estimated size information can be limited by the number of organelles, the angular detection range, or the non-ideality of the data (both speckle and shot noise). We will describe the conditions under which each of these effects dominates. We will also discuss whether mean and standard deviation are the best sizes to report from such Mie modeling, or if there are other size parameters that have greater fidelity to the true, non-smooth size distributions.

The goal of this project is to estimate non-nuclear organelle size distributions in single cells by measuring angular scattering patterns and fitting them with Mie theory. Simulations have indicated that the large relative size distribution of organelles (mean:width≈2) leads to unstable Mie fits unless scattering is collected at polar angles less than 20 degrees. Our optical system has therefore been modified to collect angles down to 10 degrees. Initial validations will be performed on polystyrene bead populations whose size distributions resemble those of cell organelles. Unlike with the narrow bead distributions that are often used for calibration, we expect to see an order-of-magnitude improvement in the stability of the size estimates as the minimum angle decreases from 20 to 10 degrees. Scattering patterns will then be acquired and analyzed from single cells (EMT6 mouse cancer cells), both fixed and live, at multiple time points. Fixed cells, with no changes in organelle sizes over time, will be measured to determine the fluctuation level in estimated size distribution due to measurement imperfections alone. Subsequent measurements on live cells will determine whether there is a higher level of fluctuation that could be attributed to dynamic changes in organelle size. Studies on unperturbed cells are precursors to ones in which the effects of exogenous agents are monitored over time.

A Matlab based fNIRS visualization and processing GUI developed in order to increase the researcher’s ability to analyze the patient studies. Developed tools: multiple window visualization, regressions, motion artifact detection and database engine.

Objective Glucocorticoid (GC) therapy is associated with increased risk of fracture in patients with rheumatoid arthritis (RA). To elucidate the cause of this increased risk, we examined the effects of chronic erosive inflammatory arthritis and GC treatment on bone quality, structure, and biomechanical properties in a murine model. Methods Mice with established arthritis and expressing human tumor necrosis factor α (TNFα) transgene (Tg) and their wild-type (WT) littermates were continually treated with GC (prednisolone 5 mg/kg/day via subcutaneous controlled-release pellet) or placebo for 14, 28, or 42 days. Microstructure, biomechanical properties, chemical composition, and morphology of the tibiae and lumbar vertebral bodies were assessed by micro–computed tomography, biomechanical testing, Raman spectroscopy, and histology, respectively. Serum markers of bone turnover were also determined. Results TNF-Tg and GC treatment additively decreased mechanical strength and stiffness in both the tibiae and the vertebral bodies. GC treatment in the TNF-Tg mice increased the ductility of tibiae under torsional loading. These changes were associated with significant alterations in the biochemical and structural composition of the mineral and organic components of the bone matrix, a decrease in osteoblast activity and bone formation, and an increase in osteoclast activity. Conclusion Our findings indicate that the concomitant decrease in bone strength and increase in bone ductility associated with chronic inflammation and GC therapy, coupled with the significant changes in the bone quality and structure, may increase the susceptibility of the bone to failure under low-energy loading. This may explain the mechanism of symptomatic insufficiency fractures in patients with RA receiving GC therapy who do not have radiographic manifestations of fracture.

Functional near-infrared spectroscopy (fNIRS) research to date has tended to publish group-averaged rather than individual infant data due to normative basic research goals. Acquisition of individual infant time courses holds interest, however, both for cognitive science and particularly for clinical applications. Infants are more difficult to study than adults as they cannot be instructed to remain still. In addressing this, upright infants pose several associated complications for the researcher. We identified and optimized the factors that affect the quality of fNIRS data from individual 6- to 9-month-old infants exposed to a visual stimulation paradigm. The fNIRS headpiece was reconfigured to reduce inertia, increase comfort, and improve conformity to the head, while preserving fiber density to avoid missing the visual cortex activation. The visual-stimulation protocol was modified to keep the attention of infants throughout the measurement, thus helping to reduce motion artifacts. Adequate optical contact was verified by checking power levels before each measurement. By revising our experimental process and our data rejection criteria to prioritize good optical contact, we report for the first time usable hemodynamic data from 83% of infants and that two-thirds of infants produced a statistically significant fNIRS response.

Functional near-infrared spectroscopy (fNIRS) records hemodynamic changes in the cortex arising from neurovascular coupling. However, (noninvasive) fNIRS recordings also record surface vascular signals arising from noncortical sources (e.g., in the skull, skin, dura, and other tissues located between the sensors and the brain). A current and important focus in the fNIRS community is determining how to remove these noncortical vascular signals to reduce noise and to prevent researchers from erroneously attributing responses to cortical sources. The current study is the first to test a popular method for removing signals from the surface vasculature (removing short, 1 cm, channel recordings from long, 3 cm, channel recordings) in human infants, a population frequently studied using fNIRS. We find evidence that this method does remove surface vasculature signals and indicates the presence of both local and global surface vasculature signals. However, we do not find that the removal of this information changes the statistical inferences drawn from the data. This latter result not only questions the importance of removing surface vasculature responses for empiricists employing this method, but also calls for future research using other tasks (e.g., ones with a weaker initial result) with this population and possibly additional methods for removing signals arising from the surface vasculature in infants.

In near-infrared spectroscopy (NIRS) of human cerebral hemodynamics, detection of stimulus-related responses is confounded by the presence of unrelated trends in both the brain and the overlying scalp. A proposed strategy for reducing hemodynamic noise has been to record “scalp only” trends simultaneously via a second shorter-separation detector (~5 mm rather than ~30 mm) and perform a subtraction (C-NIRS, for “corrected near-infrared spectroscopy”). To compare the single- and dual-detector strategies, a 21-volunteer study of visual stimulation responses (6 stimulation blocks and 8 recording channels per measurement run) has been conducted. Activation-flagged channels were defined based upon (a) the significance (p-value) of the average rise in oxyhemoglobin concentration and (b) the average signal-to-noise over 6 stimulation epochs. At reasonable thresholds (p 1), the C-NIRS method increased the number of activation-flagged channels from 47 to 66, an increase of 40%, adding 24 channels and eliminating only 5. Of the 71 channels that were activation-flagged by at least one modality, the C-NIRS time series exhibited more significant oxyhemoglobin rise in 80% of such channels, and better signal-to-noise in 73%. In addition, single-subject C-NIRS stimulus responses were more consistent than NIRS over the six stimulation epochs, with significantly lower coefficients of variation in both amplitude and latency (i.e. time between stimulus onset and maximum hemoglobin rise). These results demonstrate that two-detector C-NIRS provides a straightforward way of (a) removing hemodynamic interference from NIRS data, (b) increasing the detection rate of cerebrally-unique responses, and (c) improving the quality of those recorded responses. Parallel insights regarding deoxyhemoglobin trends could not be drawn from this data set but should be attainable in future studies with higher signal to noise ratios.

A key design parameter in spatially offset Raman spectroscopy (SORS) is the choice of offset distance between the illumination and collection areas. To investigate this choice, we performed SORS measurements on a simple two-layer chemical phantom. We show that while the SORS ratio, or the ratio of signal from the bottom layer to the top layer, monotonically increases with spatial offset, the signal-to-noise ratio (SNR) does not. Specifically, we show that there exists a specific spatial offset that yields the best SNR for signal originating in the bottom layer of a two-layer sample. We also show that this SNR-optimal offset depends upon the strength of the particular Raman band. This work presents the considerations that should be taken into account when designing optical probes for use in SORS.

Understanding the complex properties of electronic and spintronic devices at the micro- and nano-scale is a topic of intense current interest as it becomes increasingly important for scientific progress and technological applications. In operando characterization of such devices by scanning probe techniques is particularly well-suited for the microscopic study of these properties. We have developed a scanning probe microscope (SPM) which is capable of both standard force imaging (atomic, magnetic, electrostatic) and simultaneous electrical transport measurements. We utilize flexible and inexpensive FPGA (field-programmable gate array) hardware and a custom software framework developed in National Instrument's LabVIEW environment to perform the various aspects of microscope operation and device measurement. The FPGA-based approach enables sensitive, real-time cantilever frequency-shift detection. Using this system, we demonstrate electrostatic force microscopy of an electrically biased graphene field-effect transistor device. The combination of SPM and electrical transport also enables imaging of the transport response to a localized perturbation provided by the scanned cantilever tip. Facilitated by the broad presence of LabVIEW in the experimental sciences and the openness of our software solution, our system permits a wide variety of combined scanning and transport measurements by providing standardized interfaces and flexible access to all aspects of a measurement (input and output signals, and processed data). Our system also enables precise control of timing (synchronization of scanning and transport operations) and implementation of sophisticated feedback protocols, and thus should be broadly interesting and useful to practitioners in the field.

Using simultaneous magnetic force microscopy (MFM) and transport measurements of a graphene spin valve, we correlate the non-local spin signal with the magnetization of the device electrodes. The imaged magnetization states corroborate the influence of each electrode within a one-dimensional spin transport model and provide evidence linking domain wall pinning to additional features in the transport signal., Comment: The following article has been submitted to Applied Physics Letters. If it is published, it will be found online at http://apl.aip.org

Raman scattering from aqueous liquids can be collected with high efficiency by enclosing the liquid within a suitable waveguide, as several groups have reported. Here, we present a quantitative model that predicts the relative strength of signals collected from (a) a tubular waveguide and (b) a flat-walled cuvette. Experimental measurements of Raman scattering from aqueous ethanol are made using two geometries, a Teflon®-AF waveguide and a standard quartz cuvette. The model correctly predicts the enhancements in several ethanol Raman bands provided by the waveguide geometry. This model should be useful in aligning and characterizing liquid core waveguides, whose manufacture is still undergoing refinements. In particular, the model shows that absorption and scattering losses affect the enhancement factor in different ways.

Four different species of bacteria (streptococcus mutans, s. sanguis, s. intermedius and s. oralis) important in the field of oral biology were studied using spontaneous Raman scattering spectroscopy. Spectra of several bacterial colonies of each type were acquired using a Raman microscope system. After correction for system background and fluorescence, the Raman spectra were grouped using a blind clustering algorithm. The clusters thus generated were found to correspond closely to the four species of bacteria, with 5 misclassifications out of 80 samples. The clustering may be due to differences in the concentrations of amino acids and nucleic bases in the various bacterial species. The results suggest that Raman spectroscopy may be used as a rapid means of identifying the species of bacterial colonies of oral streptococci.

Background Motor learning is associated with changes in synchronized oscillatory activity at alpha (8–12 Hz) and beta (12–30 Hz) frequencies. Numerous studies demonstrated that tACS can entrain ongoing oscillatory activity ( Antal and Herrmann, 2016 ) and modulate motor behavior ( Pollok et al., 2015 , Wach et al., 2013 ). However, the neurophysiological mechanisms underlying tACS ( Antal and Paulus, 2013 ) and its modulatory effect on motor learning remain ambiguous. Thus, the purpose of the study was to investigate the effects of tACS on the learning of a bimanual visuomotor coordination task and the accompanied oscillatory activity. Methods Up to now, 19 right-handed healthy volunteers participated in the study and performed the task which is divided into three different levels of complexity (easy, moderate, difficult). Concurrent to motor practice, participants received either 10 Hz tACS, 20 Hz tACS or a sham stimulation over the parietal cortex (P3/P4) for 20 min via small gel electrodes (3,14 cm2 Ag/AgCl, amperage = 1 mA). Before and after tACS (immediately, 30 min, 1 day, 4 days, 7 days), movement speed and accuracy of the visuomotor coordination were assessed. Oscillatory activity was measured by electroencephalography (EEG, Starstim-Neuroelectrics, P3/P4/Fpz/Fz/Cz/Pz/Oz/VEOG). Results Analyzing motor performance, a three-way ANOVA (GROUPxTIMExCOMPLEXITY) revealed a significant main effect for TIME (F(5, 80) = 13.285; p η 2 = 0.454), a significant main effect for COMPLEXITY (F(2, 32) = 195.087; p η 2 p = 0.924) and a significant TIMExCOMPLEXITY interaction (F10, 160) = 7.095; p η 2 p = 0.307). Bonferroni-corrected post hoc t-tests yielded a significant difference from pre to post-test immediately after tACS for all groups indicating an improvement in the task. The comparison of 10 Hz tACS and 20 Hz tACS revealed a significant difference in visuomotor coordination performance at the moderate level 30 min after stimulation (p Conclusions The present study suggests that 10 Hz tACS and 20 Hz tACS increase EEG alpha activity which is in line with the theory of entrainment where synchronization can also occur at harmonics or subharmonics ( Antal and Herrmann, 2016 ). Nevertheless, while both tACS frequencies entrain alpha activity they seem to have a different effect on motor behavior, 10 Hz tACS slows down while 20 Hz tACS speeds up the visuomotor execution.