cssi/SciSciGPT-SciSciNet huggingface dataset:
Implementing the trajectory-grid transport algorithm in an air quality model

Eulerian-based air quality models encounter a serious numerical problem in solving the advection equation. In addition, mass conservation is often violated when meteorological model output is used as input to air quality models. The Trajectory-Grid algorithm handles the advection and eddy-diffusion in the Lagrangian and Eulerian framework, respectively. It is very accurate and can be used to trivially solve the advection equation for mixing ratios to address (but not correct) the mass conservation issue. We incorporated the algorithm into the state-of-the-science Comprehensive Air Quality Model with Extensions (CAMx). Applications of the model reveal the inaccuracy of the commonly used Bott advection scheme, and the subsequent compensating errors of the model. The results clearly call for a more reliable description of eddy diffusivity and emissions inventory in order to truly improve the reliability and predictive capability of air quality models.
Many Faces of Liquidity and Asset Pricing: Evidence from the U.S. Treasury Securities Market

This paper tests the illiquidity premium hypothesis using U.S. Treasury securities intraday interdealer data. In contrast to the existing literature where notes are matched with bills in terms of maturity date, we compare notes with other notes maturing on the same day. One reason for comparing notes with notes rather than notes with bills is that differences in tax treatment across bills and notes could confront an experiment to measure the illiquidity effect. We find that notes are quoted at essentially identical prices despite substantial differences in their liquidity. This rejection of the hypothesis is in sharp contrast to the result of previous studies (Amihud and Mendelson, 1991). Therefore we reconsider the evidence based on matched bills and notes. We identify cross-sectional variation in bill-note pricing differences that cannot be supported by the illiquidity premium hypothesis. We also show that the pricing difference is smaller for matches with on-the-run bills, although the difference in liquidity between these bills and notes is significantly larger.
Captivity, Citizenship, and the Ethics of Otherwise in the Society-of-Captives Thesis A Commentary on Arrigo

In this engagement with Professor Bruce Arrigo's psychological jurisprudence model, I explore his critique of captivity and risk management. I am particularly interested in his claims that incarceration culminates in society's own captivity, that the most destructive aspect of captivity is its foreclosing of human difference and potentiality, and that a praxis that is both clinical and mindful might point a way out. By way of a case anecdote, I interrogate several of the key terms in Arrigo's formulation-citizenship, reform, revolution, and praxis-in an effort to further conjugate from the ground up such an innovative and important set of possibilities.
Real-time economic optimization for an integrated plant via a dynamic optimization scheme

Conventional real-time optimizers are based on steady-state models and their effectiveness on plants with long-lived dynamics are thus limited. This is particularly true for tightly integrated plants with material recycle loops and other mass/energy integration loops, which tend to show distinct time-scale separation in their dynamic behavior. The use of steady state model limits the execution frequency of the RTO and precludes the utilization of dynamic degrees of freedom, ultimately leading to suboptimal results. Researchers have suggested to combine unit-level controls and plant-wide economic optimization into a single dynamic optimization but the demand for modeling accuracy and computation may be too high for such an approach to be feasible in practice. We propose a two-layer architecture for dynamic plant-wide optimization and control, in which the upper layer performs a dynamic optimization of the integrated plant to determine economically optimal setpoints for the lower layer performing control functions at the unit level. To alleviate the unrealistic modeling and computational requirements, we propose the plant-wide dynamic optimization at a rate significantly lower than those of the controllers. Slow-scale plant-wide models are less "stiff" and therefore thought to be more robust to model errors. We discuss how to obtain a "slow"-scale plant-wide model for a chosen optimization frequency and the interfacing of the slow-running plant-wide dynamic optimizer with the fast running unit controllers. An example is given to compare the various approaches.
Evaluation of biological cell properties using dynamic indentation measurement

Viscoelastic mechanical properties of biological cells are commonly measured using atomic force microscope (AFM) dynamic indentation with spherical tips. A semiempirical analysis based on numerical simulation is built to determine the cell mechanical properties. It is shown that the existing analysis cannot reflect the accurate values of cell elastic/dynamic modulus due to the effects of substrate, indenter tip size, and cell size. Among these factors, substrate not only increases the true contact radius but also interferes the indentation stress field, which can cause the overestimation of cell moduli. Typically, the substrate effect is much stronger than the other two influences in cell indentation; and, thus, the cell modulii are usually overestimated. It is estimated that the moduli can be overestimated by as high as over 200% using the existing analysis. In order to obtain the accurate properties of cells, correction factors that account for these effects are required in the existing analysis.
A new computational method for plasmon resonances of nanoparticles and for wave propagation

Numerical simulation of electromagnetic wave propagation and scattering in nanoscale applications, and in particular photonic crystals and plasmon resonances, faces serious challenges. This paper addresses one of the computational difficulties: the treatment of material interface boundaries. Flexible local approximation methods (FLAME) employ any desired local approximating functions that are seamlessly built into the difference scheme. In particular, this new finite-difference calculus provides an accurate representation of material interfaces on geometrically nonconforming simple Cartesian grids. For instance, in the vicinity of cylindrical or spherical dielectric particles the field can be approximated by cylindrical or spherical harmonics. The new approach achieves the same level of accuracy as the finite element method with two orders of magnitude fewer unknowns.
Geochemistry, petrogenesis, and tectonic implications of central High Cascade mafic platform lavas

Petrographic and multi-element geochemical data for a 37-sample suite representing Oregon9s central High Cascade mafic platform allow the distinction of basalts ( 2 ) from two types of basaltic andesites with associated high-silica basaltic andesites (53–62 wt % SiO 2 ). All units yield fractionated REE and incompatible element-enriched patterns characteristic of continental tholeiitic magmas. Mount Washington (MW)-type basaltic andesites are distinguished from North Sister (NS) types by relatively higher total REE and other LILE abundances, although lithologic similarities prevail. Trace-element signatures of both types do not support their derivation from magmas represented by basalts, but represeint near-primary melts from regions apart from the sources of primary basalt magmas. Normal basalts are modeled with 14% incongruent partial melting and concomitant olivine fractionation of spinel Iherzolite upper mantle in the presence of water-rich fluids derived from a subducted oceanic slab. Basaltic andesites are modeled as 6% to 12% partial melting of fluid-enriched spinel Iherzolite accompanied by olivine (± clinopyroxene ± plagioclase) fractionation. Unusual units, including one with ground-mass biotite and rare quartz xenocrysts, probably resulted from divergent processes of crustal assimilation, crystal fractionation, or melting from alternate sources. Early Pleistocene eruptions were largely diktytaxitic basalt outpourings in response to crustal readjustments and subsidence which occurred prior to 4.5 m.y. ago. The transformation to extensional tectonics abruptly reduced the amount of andesitic and silicic volcanism and allowed tapping of deeper, mafic magma source regions. Chemical and petrographic data support the concept of juxtaposed tectonomagmatic types such that, extension-related basalts erupted within the realm of calc-alkaline basaltic andesites and their silicic derivatives.
Test generation for VLSI chips with embedded memories

An effective approach for generating patterns for testing memories embedded in logic is presented. Through circuit testability analysis, which is a study of the effect of process defects on memory circuits, unique algorithms can be derived for testing the memory. Circuit and logic designs for test features that are required to make the pattern generation process optimal are discussed. An analytical method is described which assesses the performance characteristics of the memory after functional test.
Comparison of capillary column gas chromatographic and AOAC gravimetric procedures for total fat and distribution of fatty acids in foods

Abstract There is increasing interest in the fatty acid composition, including levels of trans fatty acids, of foods. The trans fatty acid content of American diets is increasingly studied because of reported adverse effects of trans fatty acids on risk of coronary heart disease. In this study, total fat content and fatty acid composition of 43 food products were determined after acid hydrolysis by gas chromatography using an SP-2560 flexible fused silica capillary column. Total fat content determined by the gas chromatographic method was compared with fat content determined by AOAC gravimetric method 922.06 for all food products. Total fat, saturated fat and unsaturated fat content of the foods determined by the gas chromatographic method ranged from 0.9 to 96.7, 0.2 to 16.8 and 0.5 to 89.3%, respectively. Trans fatty acids hexadecenoate (t-16:1), elaidic (t-18:1), and octa-decadienoate (t,t-18:2) were identified by comparison of their retention times with those of known standards and quantitated. These fatty acids were present in foods at levels of 0.25 to 1.50 (t-16:1), 0.87 to 268.32 (t-18:1), and 0.23 to 7.92 (t,t-18:2) mg/g.
Bibliography on Automation and Technological Change and Studies of the Future

Abstract : This Bibliography lists works associated with two on-going RAND projects: Automation and Technological Change, and a related informal study of future national and international problems. The listing is by no means exhaustive; it consists largely of materials assembled to date by project members. However, some entries have been included that are relevant to but not in our collection. New entries, which have been added since the last updating of this paper in March 1967, are indicated by asterisks. (Author)
Lymphatic response to depilation-induced inflammation in mouse ear assessed with label-free optical lymphangiography.

Background and Objectives Optical microangiography (OMAG) is a noninvasive technique capable of imaging 3D microvasculature. OMAG-based optical lymphangiography has been developed for 3D visualization of lymphatic vessels without the need for exogenous contrast agents. In this study, we utilize the optical lymphangiography to investigate dynamic changes in lymphatic response within skin tissue to depilation-induced inflammation by using mouse ear as a simple tissue model. Materials and Methods A spectral-domain optical coherence tomography (OCT) system is used in this study to acquire volumetric images of mouse ear. The system operates under the ultrahigh-sensitive OMAG scanning protocol with five repetitions for each B frame. An improved adaptive-threshold-based method is proposed to segment lymphatic vessels from OCT microstructure images. Depilation is achieved by placing hair removal lotion on mouse ear pinna for 5 minutes. Three acquisitions are made before depilation, 3-minute and 30-minute post-depilation, respectively. Results Right after the application of depilation lotion on the skin, we observe that the blind-ended sacs of initial lymphatics are mainly visible in a specific area of the normal tissue. At 5 minutes, more collecting lymphatic vessels start to form, evidenced by their valve structure that only exists in collecting lymphatic vessels. The lymphangiogenesis is almost completed within 8 minutes in the inflammatory tissue. Conclusions Our experimental results demonstrate that the OMAG-based optical lymphangiography has great potential to improve the understanding of lymphatic system in response to various physiological conditions, thus would benefit the development of effective therapeutics. Lasers Surg. Med. 47:669–676, 2015. © 2015 Wiley Periodicals, Inc.
Multiple interactions of aluminum with neurofilament subunits: Regulation by phosphate‐dependent interactions between C‐terminal extensions of the high and middle molecular weight subunits

Exposure of individual purified neurofilament (NF) proteins to AlCl3 alters their electrophoretic properties in a time- and concentration-dependent manner, as visualized by their failure to migrate into SDS gels. Co-incubation of purified high (NF-H) and middle (NF-M) but not low (NF-L) molecular weight NF subunits prevents this AlCl3-induced alteration in electrophoretic migration. This latter finding suggested that specific interactions between NF-H and NF-M other than filament formation influenced their interaction with AlCl3. Co-incubation of the 160 kDa α-chymotryptic cleavage product of NF-H (corresponding to the highly phosphorylated C-terminal sidearm domain) with native NF-M prevented alteration in subunit electrophoretic migration by AlCl3. By contrast, intact, dephosphorylated NF-H subunits were unable to prevent AlCl3-induced alteration of native NF-M electrophoretic migration. Taken together, these findings suggest that phosphate-dependent interactions between the sidearm extensions of NF-H and NF-M diminish the ability of AlCl3 to associate with either subunit in a manner that alters their electrophoretic migration. This interaction of NF-H and NF-M sidearms is SDS-sensitive, while AlCl3-induced alteration in electrophoretic migration of individual subunits is SDS-resistant. Addition of SDS to mixtures of NF-H and NF-M subunits disrupted the protective effect, and promoted AlCl3-induced alterations in subunit electrophoretic migration. These findings support and extend the current hypothesis that the ability of aluminum to interact with NF subunits is a function of subunit phosphorylation, assembly, and extent of neurofilament-neurofilament cross-linking. © 1994 Wiley-Liss, Inc.
An ellipsoid constrained quadratic programming (ECQP) approach to MCE training of MQDF-based classifiers for handwriting recognition

In this study, we propose a novel optimization algorithm for minimum classification error (MCE) training of modified quadratic discriminant function (MQDF) models. An ellipsoid constrained quadratic programming (ECQP) problem is formulated with an efficient line search solution derived, and a subspace combination condition is proposed to simplify the problem in certain cases. We show that under the perspective of constrained optimization, the MCE training of MQDF models can be solved by ECQP with some reasonable approximation, and the hurdle of incomplete covariances can be handled by subspace combination. Experimental results on the Nakayosi/Kuchibue online handwritten Kanji character recognition task show that compared with the conventional generalized probabilistic descent (GPD) algorithm, the new approach achieves about 7% relative error rate reduction.
Understanding the roles of subjective and objective aspects of time in the work-family interface

The experience of time has been posited as an important predictor of work-family conflict; however, few studies have considered subjective and objective aspects of time conjointly. This study examined the reported number of hours dedicated to work and family as indices of objective aspects of time, and perceived time pressure (in the work and family domains respectively) as an important feature of the subjective nature of temporal experiences within the work-family interface. Results indicate that the stress of having insufficient time to fulfill commitments in one domain (i.e., perceived time pressure) predicts work-family conflict, and that perceived time pressures predict the amount of time allocated to a domain. Additionally, findings suggest that domain boundaries are not symmetrical, with work boundaries being more rigidly constructed than family boundaries. Work-to-family and family-to-work conflict were generally related to overall health, turnover intentions, and work performance, as expected.
The Effects of Absence Culture on Individual Absence

This field study provided empirical evidence for the effects of absence culture on individual absenteeism among employees (N = 264) within five clerical units. Absence culture was derived from the aggregation of an individual-level measure of the beliefs about the perceived costs (i.e., deterrent outcomes) and benefits (i.e., encouraging outcomes) of being absent from work. It was hypothesized that these individual beliefs about absence could be aggregated meaningfully to the unit level. In addition, it was hypothesized that absence culture would explain a significant amount of variance in individual absence beyond the effects of demographics and general work attitudes. Paid and unpaid absence data for the 3-month period following collection of the beliefs measures were collected from organizational records. This study demonstrated support for the existence of an absence culture and its impact on individual absence. Implications for managing absence and suggestions for future research are discussed.
INTERACTION OF SALINITY AND TEMPERATURE ON NET PROTEIN SYNTHESIS AND VIABILITY OF VIBRIO MARINUS1,2

The relationship of temperature and salinity to protein synthesis was determined for cells of Vibrio marinus. The critical temperature of the lesion in protein synthesis increased with increasing salinity of the growth medium. Protein synthesis was significantly inhibited at 22C at a salinity of 25‰, but not at a salinity of 35‰ until the cells were incubated for 20 min at 24C. The thermal lesion did not involve precursor accumulation mechanisms rather than protein synthesis at salinities between 25 and 35%. At 40‰, the uptake of extracellular proline by whole cells was inhibited at 24C and preceded the inhibition of precursor into protein. Total RNA synthesis continued for 50 min at 22C in growth media at salinities between 15 and 35‰ but at 40‰ decreased after 20 min of cell incubation. At salinities between 15‰ and 30‰, total RNA synthesis continued at 15 and 22C, but cellular protein synthesis was inhibited by either temperature or salinity effects. Loss of cell viability at 22 and 25C at salinities of 25 and 35‰ showed that the onset of cell death occurs simultaneously with thermal inhibition of protein synthesis.
The effect of “robust” integrator dynamics on decision-making performance

The drift-diffusion model of decision-making provides a framework to explain performance statistics of two-alternative perceptual decision-making tasks. In addition, the cortical activity of rhesus monkeys performing these tasks has been observed to stochastically fluctuate until a threshold level of activity is reached, implying a neuronal implementation of this decision-making paradigm [1]. The observed ramping of activity is hypothesized to represent the accumulation of sensory evidence over timescales much longer than those of the underlying cortical hardware. One proposed mechanism to implement this short-term cortical memory is by a self-excitatory recurrent neural integrator [2]. However, it has been observed that naive excitatory recurrent circuits require extremely fine-tuning to accurately integrate an input signal [3]. We investigated the consequences of implementing a short-term evidence accumulation circuit via a recurrent network designed to be robust to mistuning in the global self-excitation parameter [4], [5]. Following the approach of previous work, we derived a firing rate model for the dynamics of the integrator parameterized by biophysically relevant quantities. In particular, a single piecewise-defined ordinary differential equation models the average firing rate activity of a number of bistable sub-populations exhibiting hysteresis. A major consequence of this robust integration scheme is the exclusion of instantaneous sensory evidence that does not sufficiently favor one alternative over the other. In particular, if stimulus is below a certain evidence-exclusion threshold, average integrator activity does not change. This evidence exclusion mechanism reveals a potential performance tradeoff between gaining robustness to mistuning on one hand, but ignoring potentially relevant information on the other. To our surprise, we find that a surprisingly large fraction of sensory evidence can be ignored before decision-making performance is compromised. To explain this observation, we derived equations that describe a hierarchy of sequential hypothesis tests that vary in their evidence-exclusion threshold. These models yield quantitative predictions of how decision-making performance is diminished as model robustness is increased. We conclude that for a fixed task difficulty and a constant decision threshold, a substantial fraction of the stimulus can be ignored before error rates or reaction times increase, if decision boundaries are modified appropriately. This observation implies that an evidence-accumulating neural integrator circuit robust to feedback mistuning might be able to underlie perceptual decision-making, without a strong compromise in performance.
A novel electron gun with an independently addressable cathode array

The design of a novel electron gun with an array of independently addressable cathode elements is presented. Issues relating to operation in a 6.5 Tesla axial magnetic field are discussed. Simulations with the TriComp electromagnetic field code that were used to determine the space charge limited tube characteristic and to model focusing of the electron beam in the magnetic field are reviewed. Foil heating and stress calculations are discussed. The results of CYLTRAN simulations yielding the energy spectrum of the electron beam and the current transmitted through the foil window are presented.
Crystallization conditions of membrane protein CLC-ec1: An example outside the crystallization slot

Many soluble proteins crystallize in conditions where their second virial coefficient takes on slightly negative values, known as the crystallization slot, allowing the possibility to screen for crystallizability by measuring virial coefficients. Here we measure virial coefficients for the membrane protein CLC-ec1, which has been crystallized. These virial coefficients reveal that CLC-ec1 crystallization conditions do not correspond to the crystallization slot found for soluble proteins and certain membrane proteins. Additionally, while some membrane proteins crystallize under conditions that are associated with a phase transition of the solubilizing detergent and with attractive detergent interactions, it is demonstrated that this is not the case for CLC-ec1 crystallization. As with many soluble and membrane proteins, CLC-ec1 has been crystallized by adding the neutral polymer poly(ethylene glycol) (PEG). It is shown that the addition of PEG destabilizes detergent micelles and induces CLC-ec1 aggregation in crystallization conditions. r 2007 Elsevier B.V. All rights reserved. PACS: 87.15.Nn
A characterization of sharing in parallel programs and its application to coherency protocol evaluation

In this paper we use trace-driven simulation to analyze the memory reference patterns of write shared data in several parallel applications. We first develop a characterization of write sharing (based on the notion of a write run), and then examine the traces, using metrics derived from the characterization. The results indicate that the amount of write sharing in all programs is small; and that it is characterized by short to medium sequences of per processor references, with little contention for either data or locks.We determine to what extent this analysis can be used to predict the coherency overhead of write-invalidate and write-broadcast protocols. We develop a simple model of write sharing from the write run characterization. By applying the results of the sharing analysis to the model, weighted by machine-specific cycle costs for carrying out coherency-related bus operations, we can estimate relative protocol performance. We compare these results to those from detailed architectural simulations.The simulation results indicate that (1) neither protocol dominates in performance; and that (2) the write run model is a good predictor of protocol performance when the unit of the coherency operations matches that in the sharing analysis. This is the case for the write-broadcast protocols, in which one word is broadcast for each write to shared data. However, in Berkeley Ownership, a write-invalidate protocol, the unit of coherency is an entire cache block. When the block size is large, performance for this protocol is quite sensitive to the memory reference patterns within the block.
Characterization of the second-harmonic response of second-order nonlinear probes

We report the characterization of the second-harmonic response of several types of second-order nonlinear probes, which consist of an optical fiber taper, a single nanowire attached to the taper, and functional second-harmonic micro- or nanocrystals attached to the nanowire. We observed anomalous power dependence in the probe composed of multiwall carbon nanotube (CNT) and BaTiO3 nanocrystals. We attributed this anomaly to the transition of BaTiO3 nanocrystals from the tetragonal to the cubic phase due to the heating of CNT by the ultrashort laser pulses.
Pubertal Assessment Method and Baseline Characteristics in a Mixed Longitudinal Study of Girls

OBJECTIVES: The objective of this study was to describe the assessment methods and maturation status for a multisite cohort of girls at baseline recruitment and at ages 7 and 8 years. METHODS: The method for pubertal maturation staging was developed collaboratively across 3 sites. Girls at ages 6 to 8 years were recruited at 3 sites: East Harlem, New York; greater Cincinnati metropolitan area; and San Francisco Bay area, California. Baseline characteristics were obtained through interviews with caregivers and anthropometric measurements by trained examiners; breast stage 2 was defined as onset of pubertal maturation. The κ statistic was used to evaluate agreement between master trainers and examiners. Logistic regression models were used to identify factors that are associated with pubertal maturation and linear regression models to examine factors that are associated with height velocity. RESULTS: The baseline cohort included 1239 girls. The proportion of girls who had attained breast stage 2 varied by age, race/ethnicity, BMI percentile, and site. At 7 years, 10.4% of white, 23.4% of black non-Hispanic, and 14.9% of Hispanic girls had attained breast stage ≥2; at 8 years, 18.3%, 42.9%, and 30.9%, respectively, had attained breast stage ≥2. The prime determinant of height velocity was pubertal status. CONCLUSIONS: In this multisite study, there was substantial agreement regarding pubertal staging between examiners across sites. The proportion of girls who had breast development at ages 7 and 8 years, particularly among white girls, is greater than that reported from studies of girls who were born 10 to 30 years earlier.
A Critical Race Feminism Empirical Research Project: Sexual Harassment and the Internal Complaints Black Box

A statistical analysis of 120 survey responses from sexual harassment victims suggests that White women and Women of Color may differ in their uses of internal complaint procedures. Specifically, White women in the study informed their supervisors and human resources representatives of their sexual harassment experiences at statistically greater rates than Women of Color in the study. The racial disparity is particularly worrisome in light of recent Supreme Court decisions tying employer liability to the use of internal complaints procedures. If the survey respondents track the general population of Women of Color who are disinclined to use internal complaints procedures, then Women of Color will be more limited by the Supreme Court jurisprudence than White women.
The Journey of Two Latino Educators: Our Collective Resilience.

ABSTRACTThis article represents a journey into education undertaken by two Latino educators from diverse generations. Through the content of the narratives, we emphasize that success was achieved within the presence of oppression. The narratives reveal significant constructs that shaped our journey. For the first author, Pablo, role models, pivotal moments, and resistance had a powerful influence in his journey. Family lessons and self-sacrifice were key to the success of the second author, Yolanda. These constructs contributed to both of our resilience and success. We suggest that the aforementioned constructs have significant implications for Latino youth in the educational system.
Testing phytolith analysis approaches to estimate the prehistoric anthropogenic burning regime on the central California coast

Abstract Expanding on a previous study that used phytolith analysis and other evidence to show that native people within Quiroste Valley on California's Central Coast used frequent fire to actively manage vegetation by arresting succession toward shrubs or forest to maintain open grassland during the Late Holocene, we extracted phytoliths from soils at sites located on a 500 m grid throughout the coastal portion of the watershed. We found that the prehistoric grass-dominated grassland, likely maintained by frequent anthropogenic fire, extended to the landscape scale, well beyond the confines of Quiroste Valley. In a novel attempt to use the proportion of burned phytoliths in the soil to quantitatively estimate prehistoric fire frequency at nearby McCabe Canyon in Pinnacles National Park, we tested three approaches described in the phytolith literature to identify individual burned soil phytoliths and found each approach had serious problems. The first approach, identifying visually darkened phytoliths, was accurate when performed on freshly burned leaf material, but highly problematic when applied to weathered phytoliths extracted from a typical grassland soil. The second approach, using changes in the refractive index caused by heating of phytoliths, was not effective within the temperature range typical of grassland fires, and was prone to rehydration effects in the soil environment. The third approach, using Raman spectroscopy to identify phytoliths with spectral changes caused by heating of carbon occluded in phytoliths, was not able to distinguish heated, non-darkened phytoliths, but was able to distinguish visually darkened phytoliths that had been subjected to an open flame. Each approach was rejected as inadequate; we were unable to use phytoliths to quantitatively estimate prehistoric fire frequency. Additional research quantifying the effects of weathering on soil phytolith coloration and opacity may make the visual approach viable.
A Two-Way Coupled Polydispersed Simulation of Bubbly Flow Beneath a Plunging Liquid Jet

Plunging liquid jets are commonly encountered in nature and are widely used in industrial applications (e.g., in waterfalls, waste-water treatment, the oxygenation of chemical liquids, etc.). Despite numerous experimental studies that have been devoted to this interesting problem, there have been very few two-phase flow simulations. The main difficulty is the lack of a quantitative model to simulate the air entrainment process, which plays a critical role in this problem. In this paper, we present a computational multiphase fluid dynamics (CMFD) approach for solving this problem. The main ingredients of this approach are a comprehensive subgrid air entrainment model that predicts the rate and location of the air entrainment and a two-fluid transport model in which bubbles of different sizes are modeled as a continuum fluid. Using this approach, a Reynolds-averaged Navier Stokes (RaNS) two-way coupled two-phase flow simulation of a plunging liquid jet with a diameter of 24mm and a liquid jet velocity around 3.5m/s was performed. We analyzed the simulated void fraction and bubble count rate profiles at three different depths beneath the average free surface, and compared them with experimental data. We observed good agreement at all locations.© 2010 ASME
Near infrared spectroscopic imaging assessment of cartilage composition: Validation with mid infrared imaging spectroscopy

Abstract Disease or injury to articular cartilage results in loss of extracellular matrix components which can lead to the development of osteoarthritis (OA). To better understand the process of disease development, there is a need for evaluation of changes in cartilage composition without the requirement of extensive sample preparation. Near infrared (NIR) spectroscopy is a chemical investigative technique based on molecular vibrations that is increasingly used as an assessment tool for studying cartilage composition. However, the assignment of specific molecular vibrations to absorbance bands in the NIR spectrum of cartilage, which arise from overtones and combinations of primary absorbances in the mid infrared (MIR) spectral region, has been challenging. In contrast, MIR spectroscopic assessment of cartilage is well-established, with many studies validating the assignment of specific bands present in MIR spectra to specific molecular vibrations. In the current study, NIR imaging spectroscopic data were obtained for compositional analysis of tissues that served as an in vitro model of OA. MIR spectroscopic data obtained from the identical tissue regions were used as the gold-standard for collagen and proteoglycan (PG) content. MIR spectroscopy in transmittance mode typically requires a much shorter pathlength through the sample (≤10 microns thick) compared to NIR spectroscopy (millimeters). Thus, this study first addressed the linearity of small absorbance bands in the MIR region with increasing tissue thickness, suitable for obtaining a signal in both the MIR and NIR regions. It was found that the linearity of specific, small MIR absorbance bands attributable to the collagen and PG components of cartilage (at 1336 and 856 cm−1, respectively) are maintained through a thickness of 60 μm, which was also suitable for NIR data collection. MIR and NIR spectral data were then collected from 60 μm thick samples of cartilage degraded with chondroitinase ABC as a model of OA. Partial least squares (PLS) regression using NIR spectra as input predicted the MIR-determined compositional parameters of PG/collagen within 6% of actual values. These results indicate that NIR spectral data can be used to assess molecular changes that occur with cartilage degradation, and further, the data provide a foundation for future clinical studies where NIR fiber optic probes can be used to assess the progression of cartilage degradation.
Three‐dimensional interstitial space mediates predator foraging success in different spatial arrangements

Identifying and quantifying the relevant properties of habitat structure that mediate predator-prey interactions remains a persistent challenge. Most previous studies investigate effects of structural density on trophic interactions and typically quantify refuge quality using one or two-dimensional metrics. Few consider spatial arrangement of components (i.e., orientation and shape) and often neglect to measure the total three-dimensional (3D) space available as refuge. This study tests whether the three-dimensionality of interstitial space, an attribute produced by the spatial arrangement of oyster (Crassostrea virginica) shells, impacts the foraging success of nektonic predators (primary blue crab, Callinectes sapidus) on mud crab prey (Eurypanopeus depressus) in field and mesocosm experiments. Interstices of 3D-printed shell mimics were manipulated by changing either their orientation (angle) or internal shape (crevice or channel). In both field and mesocosm experiments, under conditions of constant structural density, predator foraging success was influenced by 3D aspects of interstitial space. Proportional survivorship of tethered mud crabs differed significantly as 3D interstitial space varied by orientation, displaying decreasing prey survivorship as angle of orientation increased (0° = 0.76, 22.5° = 0.13, 45° = 0.0). Tethered prey survivorship was high when 3D interstitial space of mimics was modified by internal shape (crevice = 0.89, channel = 0.96) and these values did not differ significantly. In mesocosms, foraging success of blue crabs varied with 3D interstitial space as mean proportional survivorship (± SE) of mud crabs was significantly lower in 45° (0.27 ± 0.06) versus 0° (0.86 ± 0.04) orientations and for crevice (0.52 ± 0.11) versus channel shapes (0.95 ± 0.01). These results suggest that 3D aspects of interstitial space, which have direct relevance to refuge quality, can strongly influence foraging success in our oyster reef habitat. Our findings highlight the importance of spatial arrangement in mediating consumptive pathways in hard-structured habitats and demonstrate how quantifying the three-dimensionality of living space captures aspects of habitat structure that have been missing from previous empirical studies of trophic interactions and structural complexity. This article is protected by copyright. All rights reserved.
Rising recreancy: flood control and community relocation in Houston, TX, from an environmental justice perspective

ABSTRACTThis article looks at issues of recreancy, environmental justice, and relocation as they relate to a flood control infrastructure project in inner city Houston. The main research questions were “What forms would recreancy take?” and “Can a project be environmentally just if recreancy is present?” Through the structural coding of 53 semi-structured interviews, recreancy was found even in a project where the sponsors used community cohesion as a guideline. This article illuminates the difficulties flood control project engineers face when working in local communities and argues that engineering issues are also social issues. Further, the relocatees within this flood control project voice some of the same concerns experienced by people relocated in other involuntary infrastructure development projects. The case outlined in this article could be used to better help those involuntarily relocated for flood control.
Regeneration ability of valvular interstitial cells from diseased heart valve leaflets

Regeneration of heart valves depends on the regeneration of cells residing in the heart valve leaflet, i.e., valvular interstitial cells (VICs). In this study, the regeneration capacity of VICs obtained from healthy and diseased valves of patients with various ages and genders were investigated. The cells obtained from the valves were cultured in vitro for 21 days on our developed standalone nanofibrous substrates. The substrates were pliable. Proliferation of cells, their morphologies, collagen deposition, and gene and protein expression were assayed to compare their regeneration capacity. VICs from healthy valves exhibited higher proliferation and cell spreading in comparison to VICs from diseased valves. However, collagen deposition by VICs from diseased valves was higher compared to the deposition by VICs from healthy valves, irrespective of age and gender of the patients. VICs on nanofibrous substrates showed high vimentin and collagen type I expression; expression of α-SMA showed the reverse trend demonstrating the importance of nanofibers in heart valve tissue engineering and regeneration. Although variations in proliferation, gene, and protein expression of VICs from healthy and diseased valves of patients with various ages and genders were observed, they were not statistically significant. Thus, VICs from a diseased valve maintain the potential to regenerate in a non-degenerative environment, providing an opportunity for tissue engineering of diseased valves.
Extremity CTA for penetrating trauma: 10-year experience using a 64-detector row CT scanner

The purpose of this study is to assess the performance of CT angiography (CTA) in the evaluation of penetrating vascular trauma to the extremities in a large cohort of patients at our level I trauma center. A retrospective, IRB-approved review of consecutive CTAs for the evaluation of penetrating trauma to the extremities in 446 patients (M/F = 396:50, mean age = 27 years) from 1/1/2005 to 5/1/2015 was performed. Medical records were reviewed to correlate diagnostic imaging findings with clinical history and subsequent interventions. Image quality was quantified by measurement of CT attenuation coefficients in the major arteries of the extremities. The Fisher’s exact test was used to analyze the relationships between the presence and type of vascular injury and subsequent clinical management. One hundred and thirty-one (29.4 %) of 446 patients with penetrating trauma demonstrated major vascular injury on CTA, 35 (26.7 %) of whom underwent subsequent surgical repair. None of the patients without vascular injury on CTA underwent subsequent vascular intervention. Fisher’s exact test demonstrated a statistically significant difference in management and requirement for vascular repair in those patients with a vascular injury on CTA when compared to those without a vascular injury (p < 0.0001). The mean attenuation values achieved in upper and lower extremity CTAs in this population exceeded 250 HU. Extremity CTA is found to be an accurate tool for surgical triage in patients having sustained penetrating vascular trauma.
Neuregulin1 fine-tunes pre-, post-, and perisynaptic neuromuscular junction development.

BACKGROUND Neuromuscular junction (NMJ) development is a multistep process mediated by coordinated interactions between the nerve terminal, target muscle, and perisynaptic Schwann cell that require constant back-and-forth communication. Retrograde and anterograde growth and differentiation factors have been postulated to participate in this communication. While neuregulin1 (NRG1) has been shown to be potent anterograde signal that activates acetylcholine receptor (AChR) transcription and clustering in vitro, its roles in NMJ development in vivo remain elusive. RESULTS Using the model of chicken embryo, we measured the effects of NRG1 signaling during NMJ development in ovo using quantitative, sequential measures of AChR cluster size and density, pre- and postsynaptic apposition, and the alignment of perisynaptic Schwann cells. Using in ovo electroporation at early stages and a targeted soluble neuregulin antagonist through all developmental stages, we found soluble NRG1 regulates AChR cluster density and size at the earliest stage prior to nerve-AChR cluster contact. Once the nerve contacts with muscle AChRs, NRG1 has pronounced effects on presynaptic specialization and on the alignment of perisynaptic Schwann cells at endplates. CONCLUSION These findings suggest that, while NRG1 may not be critical for overall development, it appears to be important in fine-tuning pre-, post-, and perisynaptic development of the NMJ. Developmental Dynamics 246:368-380, 2017. © 2017 Wiley Periodicals, Inc.
Introduction to Negative Theology

From a very particular angle of view, attempting to talk about ultimate reality is just plain silly. I do not refer to the perspective furnished by critiques of religion as a kind of fantasy discourse. Rather I refer to a religious and theological perspective affirming that ultimate reality, whatever else it may be, must be beyond human cognitive grasp.
Medical genetics and genomics education: how do we define success? Where do we focus our resources?

Medical genetics and genomics education: how do we define success? Where do we focus our resources?
Dementia Risk in Posttraumatic Stress Disorder: the Relevance of Sleep-Related Abnormalities in Brain Structure, Amyloid, and Inflammation.

Purpose of Review Posttraumatic stress disorder (PTSD) is associated with increased risk for dementia, yet mechanisms are poorly understood.
Clinical Fractures Among Older Men With Diabetes Are Mediated by Diabetic Complications.

Introduction Type 2 diabetes mellitus among older women has been associated with increased bone mineral density, but paradoxically with increased fracture risk. Findings among older men have varied, and potential mechanisms have not been fully elucidated. Methods A retrospective study of male veterans 65 to 99 years of age who received primary care in the Veterans Health Administration from 2000 to 2010, using administrative data from all 146 Veterans Health Administration medical centers linked to Centers for Medicare and Medicaid Services Medicare fee-for-service data. Potential mediating factors of the diabetes-associated risk were evaluated using negative binomial regression models with the outcomes of any clinical fracture and hip fracture. Results Of 2,798,309 Veterans included in the cohort, 900,402 (32.3%) had a diagnosis of diabetes. After adjusting for age, race, ethnicity, body mass index, alcohol and tobacco use, rheumatoid arthritis, and corticosteroid use, the risk of any clinical fracture associated with diabetes was 1.22 (95% confidence interval, 1.21 to 1.23) and that of hip fracture was 1.21 (95% confidence interval, 1.19 to 1.23). Significant mediating factors included peripheral neuropathy, cardiovascular disease, and congestive heart failure, with 45.5% of the diabetes-associated fracture risk explained by these diagnoses. Conclusions Older male Veterans with diabetes have a 22% increased risk of incident clinical fracture compared with those without. A significant portion of this risk is explained by diabetes-related comorbidities, specifically peripheral neuropathy and congestive heart failure. Identification of these mediating factors suggests possible mechanisms, as well as potential interventions.
The Birth of the "Polak-Katolik"

The Birth of the Polak-Katolik The concept of the Polak-Katolik emerged in the form we know it today only at the very end of the 19th century. While there were many earlier ways to express the complicated relationship between Polish national belonging and Roman Catholicism, the distinctive pairing of two hyphenated nouns signified a new stage in the history of this entanglement. Geneza pojecia Polak katolik Pojecie Polak katolik w postaci, ktorą znamy dzisiaj, wylonilo sie dopiero pod sam koniec XIX wieku. Choc skomplikowany związek pomiedzy przynaleznością do narodu polskiego a rzymskim katolicyzmem wyrazany byl wcześniej na wiele sposobow, to jednak zestawienie i polączenie obu tych rzeczownikow w jednej parze wyznaczylo nowy etap w dziejach tego splotu.