cssi/SciSciGPT-SciSciNet huggingface dataset:
Computing Exact p-values for a Cross-correlation Shotgun Proteomics Score Function

The core of every protein mass spectrometry analysis pipeline is a function that assesses the quality of a match between an observed spectrum and a candidate peptide. We describe a procedure for computing exact p-values for the oldest and still widely used score function, SEQUEST XCorr. The procedure uses dynamic programming to enumerate efficiently the full distribution of scores for all possible peptides whose masses are close to that of the spectrum precursor mass. Ranking identified spectra by p-value rather than XCorr significantly reduces variance because of spectrum-specific effects on the score. In combination with the Percolator postprocessor, the XCorr p-value yields more spectrum and peptide identifications at a fixed false discovery rate than Mascot, X!Tandem, Comet, and MS-GF+ across a variety of data sets.
A Hyperactive NAD(P)H:Rubredoxin Oxidoreductase from the Hyperthermophilic Archaeon Pyrococcus furiosus

NAD(P)H:rubredoxin oxidoreductase (NROR) has been purified from the hyperthermophilic archaeon Pyrococcus furiosus. The enzyme is exceedingly active in catalyzing the NADPH-dependent reduction of rubredoxin, a small (5.3-kDa) iron-containing redox protein that had previously been purified from this organism. The apparent Vmax at 80 degrees C is 20,000 micromol/min/mg, which corresponds to a kcat/Km value of 300,000 mM(-1) s(-1). The apparent Km values measured at 80 degrees C and pH 8.0 for rubredoxin, NADPH, and NADH were 50, 5, and 34 microM, respectively. The enzyme did not reduce P. furiosus ferredoxin. NROR is a monomer with a molecular mass of 45 kDa and contains one flavin adenine dinucleotide molecule per mole but lacks metals and inorganic sulfide. The possible physiological role of this hyperactive enzyme is discussed.
Locally optimal soft handoff algorithm

The performance of soft handoff algorithms is studied in terms of the tradeoff between three metrics: rate of handoffs, mean active set size and link quality. A locally optimal (LO) handoff algorithm is derived as an approximation to the optimal handoff algorithm. The LO algorithm is shown to yield a significantly better tradeoff than the static threshold handoff algorithm. A simple dynamic threshold handoff algorithm is shown to be an approximation to the LO algorithm, and result in performance only slightly inferior to the LO algorithm.
Optimal Spectrum Estimation in Statistical Mechanics

In statistical mechanics, spectrum estimation is traditionally done by computing Fourier transforms of time-correlation functions[1]-[3] to find the amplitudes of frequency components that fit best the observed data (assuming each component is the only one present). Examples of important time correlation functions include the van Hove, dipole density, and magnetization correlation functions, whose Fourier transforms are related to the structure factor, infrared lineshape, and NMR signal lineshape, respectively.[4],[5] Although the Fourier transform is extremely general, crucial restrictions limiting its applications in statistical mechanics include assumptions of periodic or stationary time series and a linear system, so that data may be projected onto complex sinusoidal basis functions.[6],[7] These and other limitations of the Fourier transform have spurred a recent search for alternatives, but most options are closely related to the Fourier transform,[7]-[9] make similar assumptions , and share similar limitations. Herein, we present an alternative to Fourier-transform-based methods that finds wide use in fields where signal processing,[10] pattern recognition,[11] or multivariate statistical analysis[12] methods are common. The method, known by various names which include principal component analysis (PCA)[10],[12] and the Karhunen-Love expansion,[10],[11] shares many limitations of Fourier transforms, but is more flexible than Fourier-like methods because it gives data-adaptive basis functionsmore » in addition to the amplitudes of frequency components. In fact, PCA is usually used for data compression to find the smallest set of vectors that reproduce a covariance matrix to desired accuracy and is used most frequently in statistical mechanics to compress molecular dynamics trajectories of proteins to a minimal set of vectors which represent only the large amplitude, low frequency motions.[13]-[15] This contribution states the ability of PCA to give optimal spectral density functions in a mean-square sense,[16] gives analytical proof that PCA gives a more accurate spectrum than Fourier analysis for a fixed, finite number of basis vectors, and demonstrates numerically that PCA gives spectra more accurately than fast Fourier transform (FFT) or maximum-entropy algorithms.[17] The potential utility of PCA is illustrated by calculating vibrational frequencies and modes from dynamics trajectories (time series) for water, but PCA is general and equally valid for estimating other spectral densities,[1],[3]-[5] analyzing distributions generated from Monte Carlo simulations[18] or experimental data, and analyzing quantum-mechanical time-correlation functions.[19]« less
Theoretical Comparison of the Linear and Bent Structures for the Weakly Bound CO2—HF Complex

Density-functional theory method (DFT) B3LYP/6-311++G(3df,2pd) and Moller-Plesset perturbation method (MP2) MP2/6-311++G(3df,2pd) of Gaussian 03 were selected for the theoretical study of weakly bound CO 2 ---HF complex. In addition to the well-known linear structure, the various bent structure complexes were also found in this work. The self-consistent energy differences were only around 0.02 kJ/mol between the bent structure and linear structure by comparison. From the results of H-bonding distance, d HF elongation and red shift of V HF vibration frequency, all the evidence shows that the H-bonding effect in the bent structure is stronger than the linear structure. However, if one compares the Gibbs energy of the complex formation by temperature variation, it is very easily found that the linear form is favored under the thermal conditions of most temperatures whenever T ≥ 40 K. Such a fact is consistent with the former spectroscopic observed result of Klemperer et al.
Laser Induced Breakdown Spectroscopy for Analysis of Aerosols

LIBS has been successfully applied for analysis of variety of samples including solids, liquids, gases and aerosols. In this chapter the focus will be on the application of LIBS for aerosol analysis. LIBS is well suited for aerosol analysis due to the discrete nature of LIBS plasma volume as well as discrete nature of aerosol particles. This unique sampling nature is advantageous as well as challenging at times. During the past decade various research groups have worked on understanding and solving the fundamental and application related issues associated with aerosol analysis using LIBS which has led to better understanding of the processes as well as development of novel LIBS based instruments. In this chapter the discussion will include aerosol sampling physics, novel sampling approaches, figures of merit and matrix effect in aerosol analysis using LIBS.
Novel Dynamic Representation and Control of Power Systems With FACTS Devices

FACTS devices have been shown to be useful in damping power system oscillations. However, in large power systems, the FACTS control design is complex due to the combination of differential and algebraic equations required to model the power system. In this paper, a new method to generate a nonlinear dynamic representation of the power network is introduced to enable more sophisticated control design. Once the new representation is obtained, a back stepping methodology for the UPFC is utilized to mitigate the generator oscillations. Finally, the neural network approximation property is utilized to relax the need for knowledge of the power system topology and to approximate the nonlinear uncertainties. The net result is a power system representation that can be used for the design of an enhanced FACTS control scheme. Simulation results are given to validate the theoretical conjectures.
Promoting Ethical Reasonings Affect and Behaviour Among High School Students: an evaluation of three teaching strategies

Abstract Ethics education should aim to promote students’ maturity across a broad spectrum of moral functioning, including moral reasoning, moral affect and moral behaviour. To identify the most effective strategy for promoting the comprehensive moral maturity of high school students, we enrolled students in one of four groups: an introductory ethics class, a blended economics‐‐ethics class, a role‐model ethics class taught by graduate students and a non‐ethics comparison class. Pretest and post‐test instruments measured the ways students (a) reason, (b) feel and (c) act with regard to ethical‐normative issues. The results indicated that the approaches to teaching ethics varied considerably in terms of their ability to promote significant positive changes in students’ moral reasoning, empathy and behaviour.
S100A12 in Vascular Smooth Muscle Accelerates Vascular Calcification in Apolipoprotein E–Null Mice by Activating an Osteogenic Gene Regulatory Program

Objective— The proinflammatory cytokine S100A12 is associated with coronary atherosclerotic plaque rupture. We previously generated transgenic mice with vascular smooth muscle–targeted expression of human S100A12 and found that these mice developed aortic aneurysmal dilation of the thoracic aorta. In the current study, we tested the hypothesis that S100A12 expressed in vascular smooth muscle in atherosclerosis-prone apolipoprotein E (ApoE)–null mice would accelerate atherosclerosis. Methods and Results— ApoE-null mice with or without the S100A12 transgene were analyzed. We found a 1.4-fold increase in atherosclerotic plaque size and more specifically a large increase in calcified plaque area (45% versus 7% of innominate artery plaques and 18% versus 10% of aortic root plaques) in S100A12/ApoE-null mice compared with wild-type/ApoE-null littermates. Expression of bone morphogenic protein and other osteoblastic genes was increased in aorta and cultured vascular smooth muscle, and importantly, these changes in gene expression preceded the development of vascular calcification in S100A12/ApoE-null mice. Accelerated atherosclerosis and vascular calcification were mediated, at least in part, by oxidative stress because inhibition of NADPH oxidase attenuated S100A12-mediated osteogenesis in cultured vascular smooth muscle cells. S100A12 transgenic mice in the wild-type background (ApoE+/+) showed minimal vascular calcification, suggesting that S100A12 requires a proinflammatory/proatherosclerotic environment to induce osteoblastic differentiation and vascular calcification. Conclusion— Vascular smooth muscle S100A12 accelerates atherosclerosis and augments atherosclerosis-triggered osteogenesis, reminiscent of features associated with plaque instability.
Holocene strath terraces, climate change, and active tectonics: The Clearwater River basin, Olympic Peninsula, Washington State

The ∼400 km 2 Clearwater River basin, located on the Pacific flank of the actively uplifting Olympic Mountains of western Washington State, contains a well-preserved flight of Holocene fluvial terraces. We have collected a large data set of numeric ages from these terraces that is used to elucidate the geomorphic, fluvial, active tectonic, and climatic processes that operate at Holocene spatial and temporal scales. Detailed field mapping reveals three prominent Holocene straths and their overlying terrace deposits. Terrace ages fall into three broad ranges: ca. 9000–11 000 yr B.P. (Qt4), 4000–8000 yr B.P. (Qt5), and 0–3000 yr B.P. (Qt6). Terrace deposit stratigraphy, sedimentology, and age distributions allow us to consider two alternative models for their genesis. The favored model states that the terrace ages are coincident with lateral incision of the Clearwater channel, emplacement of the terrace alluvium, and the carving of the straths. Vertical incision of the Clearwater channel was primarily relegated to the brief (∼1000 yr) intervals when we have no record of terraces. Alternatively, the straths were carved as the channel incised vertically during the brief time periods between dated terrace deposits, and the terrace ages record a subsequent long time of alluviation atop the straths and concomitant termination of vertical incision. In both models, we envision a Clearwater River channel at or near capacity with a temporally variable rate of both lateral and vertical incision. Small deviations from this at-capacity condition are driven by variations in the liberation and delivery of hillslope sediment to the channel. We consider several causes for variable hillslope sediment flux in this tectonically active setting including Holocene climate change and ground accelerations related to earthquakes. Holocene rates of vertical incision are reconstructed along nearly the entire Clearwater Valley from the wide distribution of dated terraces. Incision rates clearly increase upstream, mimicking a pattern documented for Pleistocene terraces in the same basin; however, the rates are 2–3 times those determined for the Pleistocene terraces. The faster Holocene incision rates may be interpreted in terms of an increase in the rates of rock uplift. However, we favor an alternative explanation in which the Holocene rates represent a channel rapidly reacquiring its stable, graded concavity following protracted periods of time in the Pleistocene when it could not accomplish any vertical incision into tectonically uplifted bedrock because the channel was raised above the bedrock valley bottom by climatically induced alluviation. These results illustrate how, even in tectonically active settings, representative rates of rock uplift inferred from studies of river incision should be integrated over at least one glacial-interglacial cycle.
Nuclear receptors CAR and PXR cross talk with FOXO1 to regulate genes that encode drug-metabolizing and gluconeogenic enzymes

The nuclear receptors CAR and PXR activate hepatic genes in response to therapeutic drugs and xenobiotics, leading to the induction of drug-metabolizing enzymes, such as cytochrome P450. Insulin inhibits the ability of FOXO1 to express genes encoding gluconeogenic enzymes. Induction by drugs is known to be decreased by insulin, whereas gluconeogenic activity is often repressed by treatment with certain drugs, such as phenobarbital (PB). Performing cell-based transfection assays with drug-responsive and insulin-responsive enhancers, glutathione S-transferase pull down, RNA interference (RNAi), and mouse primary hepatocytes, we examined the molecular mechanism by which nuclear receptors and FOXO1 could coordinately regulate both enzyme pathways. FOXO1 was found to be a coactivator to CAR- and PXR-mediated transcription. In contrast, CAR and PXR, acting as corepressors, downregulated FOXO1-mediated transcription in the presence of their activators, such as 1,4-bis[2-(3,5-dichloropyridyloxy)]benzene (TCPOBOP) and pregnenolone 16alpha-carbonitrile, respectively. A constitutively active mutant of the insulin-responsive protein kinase Akt, but not the kinase-negative mutant, effectively blocked FOXO1 activity in cell-based assays. Thus, insulin could repress the receptors by activating the Akt-FOXO1 signal, whereas drugs could interfere with FOXO1-mediated transcription by activating CAR and/or PXR. Treatment with TCPOBOP or PB decreased the levels of phosphoenolpyruvate carboxykinase 1 mRNA in mice but not in Car(-/-) mice. We conclude that FOXO1 and the nuclear receptors reciprocally coregulate their target genes, modulating both drug metabolism and gluconeogenesis.
Data-aware scheduling of legacy kernels on heterogeneous platforms with distributed memory

In this paper, we describe a runtime to automatically enhance the performance of applications running on heterogeneous platforms consisting of a multi-core (CPU) and a throughput-oriented many-core (GPU). The CPU and GPU are connected by a non-coherent interconnect such as PCI-E, and as such do not have shared memory. Heterogeneous platforms available today such as [9] are of this type. Our goal is to enable the programmer to seamlessly use such a system without rewriting the application and with minimal knowledge of the underlying architectural details. Assuming that applications perform function calls to computational kernels with available CPU and GPU implementations, our runtime achieves this goal by automatically scheduling the kernels and managing data placement. In particular, it intercepts function calls to well-known computational kernels and schedules them on CPU or GPU based on their argument size and location. To improve performance, it defers all data transfers between the CPU and the GPU until necessary. By managing data placement transparently to the programmer, it provides a unified memory view despite the underlying separate memory sub-systems.We experimentally evaluate our runtime on a heterogeneous platform consisting of a 2.5GHz quad-core Xeon CPU and an NVIDIA C870 GPU. Given array sorting, parallel reduction, dense and sparse matrix operations and ranking as computational kernels, we use our runtime to automatically retarget SSI [25], K-means [32] and two synthetic applications to the above platform with no code changes. We find that, in most cases, performance improves if the computation is moved to the data, and not vice-versa. For instance, even if a particular instance of a kernel is slower on the GPU than on the CPU, the overall application may be faster if the kernel is scheduled on the GPU anyway, especially if the kernel data is already located on the GPU memory due to prior decisions. Our results show that data-aware CPU/GPU scheduling improves performance by up to 25% over the best data-agnostic scheduling on the same platform.
Turnover rate of phospholipid phosphorus in the liver of the white rat.

ConclusionsThe proportional turnover rate R for hepatic phospholipid P in the white rat is on the average close to 5% per hour, and since the mean concentration of hepatic phospholipid P for both experiments together was 132 mg per 100 g of liver, that r, the mass turnover rate, is about 6 mg P per hour per 100 g of liver, which is 0.2 mg P per 100 g body weight.
Visualization of cortical, subcortical and deep brain neural circuit dynamics during naturalistic mammalian behavior with head-mounted microscopes and chronically implanted lenses

Genetically encoded calcium indicators for visualizing dynamic cellular activity have greatly expanded our understanding of the brain. However, owing to the light-scattering properties of the brain, as well as the size and rigidity of traditional imaging technology, in vivo calcium imaging has been limited to superficial brain structures during head-fixed behavioral tasks. These limitations can now be circumvented by using miniature, integrated microscopes in conjunction with an implantable microendoscopic lens to guide light into and out of the brain, thus permitting optical access to deep brain (or superficial) neural ensembles during naturalistic behaviors. Here we describe steps to conduct such imaging studies using mice. However, we anticipate that the protocol can be easily adapted for use in other small vertebrates. Successful completion of this protocol will permit cellular imaging of neuronal activity and the generation of data sets with sufficient statistical power to correlate neural activity with stimulus presentation, physiological state and other aspects of complex behavioral tasks. This protocol takes 6-11 weeks to complete.
A Power Tool for Sampling Soil for Insects

The Entomology Research Division and the Amalgamated and Utah-Idaho Sugar Companies have conducted a cooperative study of methods of controlling the sugarbeet root maggot, Tetanops myopaeformis (Roder). Taking soil samples to a depth of 12 in. to determine the presence of larval populations was a necessary step in the research. Each soil sample was taken so that it included a sugar-beet plant in the center. For this work, a poweroperated soil digger, or sampler, was constructed and mounted on the rear of a tractor, as shown in Fig. 1.
Observing Single Quantum Trajectories of a Superconducting Qubit

We monitor the quantum trajectory of a superconducting qubit as it evolves under a continuous weak measurement. We verify the trajectory using quantum state tomography and investigate statistical properties of ensembles of trajectories.
A finite difference based scheme for automatic costate calculation

Abs t r ac t A method for the automatic calculation of costates using only results obtained from direct optimization techniques is presented. The approach is based on finite differences and exploits the relation between the costates and certain sensitivities of the cost function. The complete theory for handling free, control constrained, and state constrained optimal control problems is presented in this paper. An important advantage of the method presented here is that it does not require a priori identification of the optimal switching structure. As a numerical example, a state constrained version of the Brachistochrone problem is solved and the results are compared to the optimal solution obtained from Pontryagin's Minimum Principle. The agreement is found to be excellent.
Heirs to forgotten kingdoms: journeys into the disappearing religions of the Middle East

Gerard Russell’s Heirs to Forgotten Kingdoms is an insightful book halfway between an academic work and analytic journalism. Largely based on a series of informal and personal investigations, it ch...
Aetiological study on viral pathogens of diarrhea patients from Taizhou in 2013

Objective To study the aetiology characteristics of virus in diarrhea patients at Taizhou in 2013. Methods A total of 336 stool samples from diarrhea patients were detected by real-time PCR. Results The detection rates of adenovirus, rotavirus, norovirus I, norovirus II, astrovirus and sapovirus were 3.57%, 5.36%, 0.59%, 7.14%, 2.68% and 2.08%, respectively. The rate of viral diarrhea was highest during January-April and November-December. The infection rate in age group of 0-10 years was higher.Conclusion Norovirus II and rotavirus were the main pathogens which induced infectious diarrhea at Taizhou in 2013. We should strengthen the surveillance of viral diarrhea and typing detection, which may provide the evidence for the prevention and control of virus diarrhea.
Chronic Hepatitis in Patients With Hemophilia A: Histologic Studies in Patients With Intermittently Abnormal Liver Function Tests

Recent studies in multiply transfused patients with hemophilia A and persistent liver function abnormalities have shown a high incidence of chronic active hepatitis. The purpose of the present study was to determine the severity of liver disease in multiply transfused patients with intermittent liver enzyme abnormalities. Fifteen patients with elevated enzymes on two or three out of four determinations at 6-mo intervals were studied. None had signs or symptoms of chronic liver disease. Thirteen had serologic evidence of prior exposure to the hepatitis B virus. Liver biopsy performed on these patients after replacement therapy with factor VIII showed chronic persistent hepatitis or other mild forms of liver disease in 14 of the 15 patients. Patients with chronic persistent hepatitis had significantly higher mean liver enzymes at time of biopsy than patients with milder forms of hepatic inflammation, but there was no relationship between liver histology and hepatitis B serology or the amount of factor VIII used in the 6 mo preceding biopsy. These findings support the continued use of factor VIII concentrates in patients with hemophilia.
Protein glycosylation energizes T cells

Nutrient transport is regulated by signaling pathways that together indicate metabolic checkpoints in T cell self-renewal, differentiation and proliferation.
Wearing my disability with pride.

Snap, cluck, snap! The noises rang out in the conference hall. Several people turned toward me to see what was causing the disturbance. As I walked down the aisle to join my graduate school labmate, I jerked my head to the left and snapped my fingers in my right ear, continuing to draw attention to
Landscape control of nitrous oxide emissions during the transition from conservation reserve program to perennial grasses for bioenergy

Future liquid fuel demand from renewable sources may, in part, be met by converting the seasonally wet portions of the landscape currently managed for soil and water conservation to perennial energy crops. However, this shift may increase nitrous oxide (N2O) emissions, thus limiting the carbon (C) benefits of energy crops. Particularly high emissions may occur during the transition period when the soil is disturbed, plants are establishing, and nitrate and water accumulation may favor emissions. We measured N2O emissions and associated environmental drivers during the transition of perennial grassland in a Conservation Reserve Program (CRP) to switchgrass (Panicum virgatum L.) and Miscanthus x giganteus in the bottom 3-ha of a watershed in the Ridge and Valley ecoregion of the northeastern United States. Replicated treatments of CRP (unconverted), unfertilized switchgrass (switchgrass), nitrogen (N) fertilized switchgrass (switchgrass-N), and Miscanthus were randomized in four blocks. Each plot was divided into shoulder, backslope, and footslope positions based on the slope and moisture gradient. Soil N2O flux, soil moisture, and soil mineral nitrogen availability were monitored during the growing season of 2013, the year after the land conversion. Growing season N2O flux showed a significant vegetation-by-landscape position interaction (P < 0.009). Switchgrass-N and Miscanthus treatments had 3 and 6-times higher cumulative flux respectively than the CRP in the footslope, but at other landscape positions fluxes were similar among land uses. A peak N2O emission event, contributing 26% of the cumulative flux, occurred after a 10.8-cm of rain during early June. Prolonged subsoil saturation coinciding with high mineral N concentration fueled N2O emission hot spots in the footslopes under energy crops. Our results suggest that mitigating N2O emissions during the transition of CRP to energy crops would mostly require a site-specific management of the footslopes.
A Multi-Compartment Hybrid Computational Model Predicts Key Roles for Dendritic Cells in Tuberculosis Infection

Tuberculosis (TB) is a world-wide health problem with approximately 2 billion people infected with Mycobacterium tuberculosis (Mtb, the causative bacterium of TB). The pathologic hallmark of Mtb infection in humans and Non-Human Primates (NHPs) is the formation of spherical structures, primarily in lungs, called granulomas. Infection occurs after inhalation of bacteria into lungs, where resident antigen-presenting cells (APCs), take up bacteria and initiate the immune response to Mtb infection. APCs traffic from the site of infection (lung) to lung-draining lymph nodes (LNs) where they prime T cells to recognize Mtb. These T cells, circulating back through blood, migrate back to lungs to perform their immune effector functions. We have previously developed a hybrid agent-based model (ABM, labeled GranSim) describing in silico immune cell, bacterial (Mtb) and molecular behaviors during tuberculosis infection and recently linked that model to operate across three physiological compartments: lung (infection site where granulomas form), lung draining lymph node (LN, site of generation of adaptive immunity) and blood (a measurable compartment). Granuloma formation and function is captured by a spatio-temporal model (i.e., ABM), while LN and blood compartments represent temporal dynamics of the whole body in response to infection and are captured with ordinary differential equations (ODEs). In order to have a more mechanistic representation of APC trafficking from the lung to the lymph node, and to better capture antigen presentation in a draining LN, this current study incorporates the role of dendritic cells (DCs) in a computational fashion into GranSim. Results: The model was calibrated using experimental data from the lungs and blood of NHPs. The addition of DCs allowed us to investigate in greater detail mechanisms of recruitment, trafficking and antigen presentation and their role in tuberculosis infection. Conclusion: The main conclusion of this study is that early events after Mtb infection are critical to establishing a timely and effective response. Manipulating CD8+ and CD4+ T cell proliferation rates, as well as DC migration early on during infection can determine the difference between bacterial clearance vs. uncontrolled bacterial growth and dissemination.
Distributed Algorithms for Computing Very Large Thresholded Covariance Matrices

Computation of covariance matrices from observed data is an important problem, as such matrices are used in applications such as principal component analysis (PCA), linear discriminant analysis (LDA), and increasingly in the learning and application of probabilistic graphical models. However, computing an empirical covariance matrix is not always an easy problem. There are two key difficulties associated with computing such a matrix from a very high-dimensional dataset. The first problem is over-fitting. For a p-dimensional covariance matrix, there are p(p − 1)/2 unique, off-diagonal entries in the empirical covariance matrix S for large p (say, p > 105), the size n of the dataset is often much smaller than the number of covariances to compute. Over-fitting is a concern in any situation in which the number of parameters learned can greatly exceed the size of the dataset. Thus, there are strong theoretical reasons to expect that for high-dimensional data—even Gaussian data—the empirical covariance matrix is not a good estimate for the true covariance matrix underlying the generative process. The second problem is computational. Computing a covariance matrix takes O(np2) time. For large p (greater than 10,000) and n much greater than p, this is debilitating. In this article, we consider how both of these difficulties can be handled simultaneously. Specifically, a key regularization technique for high-dimensional covariance estimation is thresholding, in which the smallest or least significant entries in the covariance matrix are simply dropped and replaced with the value 0. This suggests an obvious way to address the computational difficulty as well: First, compute the identities of the K entries in the covariance matrix that are actually important in the sense that they will not be removed during thresholding, and then in a second step, compute the values of those entries. This can be done in O(Kn) time. If K L p2 and the identities of the important entries can be computed in reasonable time, then this is a big win. The key technical contribution of this article is the design and implementation of two different distributed algorithms for approximating the identities of the important entries quickly, using sampling. We have implemented these methods and tested them using an 800-core compute cluster. Experiments have been run using real datasets having millions of data points and up to 40, 000 dimensions. These experiments show that the proposed methods are both accurate and efficient.
Solar Blind Photodetectors Enabled by Nanotextured β-Ga2O3 Films Grown via Oxidation of GaAs Substrates

A simple and inexpensive method for growing Ga2O3 using GaAs wafers is demonstrated. Si-doped GaAs wafers are heated to 1050 °C in a horizontal tube furnace in both argon and air ambients in order to convert their surfaces to β-Ga2O3. The β-Ga2O3 films are characterized using scanning electron micrograph, energy-dispersive X-ray spectroscopy, and X-ray diffraction. They are also used to fabricate solar blind photodetectors. The devices, which had nanotextured surfaces, exhibited a high sensitivity to ultraviolet (UV) illumination due in part to large surface areas. Furthermore, the films have coherent interfaces with the substrate, which leads to a robust device with high resistance to thermo-mechanical stress. The photoconductance of the β-Ga2O3 films is found to increase by more than three orders of magnitude under 270 nm ultraviolet illumination with respect to the dark current. The fabricated device shows a responsivity of ∼292 mA/W at this wavelength.
Echocardiographic Response of the Normal Human Left Ventricle to Wide Variations in Preload

Animal experiments have shown that, at constant heart rates and aortic pressures, variations in preload produce proportional alterations in the ejection phase indices of left ventricular function. Human studies have previously been confined to relatively small uncontrolled alterations in preload.
A model-based systems engineering approach to design automation of SUAS

This paper presents an approach to enabling rapid design and deployment of small unmanned aerial systems (SUAS) using SysML. Recent advances in SUAS technologies have uniquely situated these systems to provide battlefield situational awareness and operational support to the U.S. Army. However, off-design mission performance is often highly degraded due to the small scale of the vehicles. Previous efforts have developed a new approach to SUAS design and deployment in order to improve the capability of these vehicles. The approach, named “Aggregate Derivative Approach to Product Design” (ADAPt Design), uses rigorous systems engineering techniques to form an executable link between input requirements and output design. The result is the capability to automatically synthesize multiple SUAS designs from differing sets of design requirements using a common set of components. Derived designs are compatible with automated manufacturing processes permitting rapid in-situ fabrication. The approach works by extending the notion of a product family so that family members exist as potential designs varying continuously over a fixed design space rather than a finite number of designs occupying discrete points in the space. Executable model-based design tools are then paired with the product family to form the link between requirements and output design. The approach is presented via an application to multirotor SUAS in a model-based systems engineering motivated format using the SysML modeling language. SysML diagrams permit the interconnection of descriptive, behavioral, and process models capturing essential systems engineering processes including verification and validation of requirements, system architecture definition, interface specification, component description, and sequencing of design logic. The implementation of ADAPt Design presented in this paper illustrates that a model-based systems engineering format is useful in documenting the approach, and also highlights the format's drawbacks and limitations.
Cord Blood Processing: Different Bags and Automation

Cord blood (CB) banking is a worldwide resource that primarily supports hematopoietic progenitor cell (HPC) transplantation. Increasingly, CB is used as a source of HPCs, other neonatal cell types, and proteins for biomedical research and new therapies, such as ophthalmological tissue regeneration and platelet lysates for tissue culture. This chapter will review the methods used to prepare a volume-reduced HPC-enriched fraction from the blood collected at birth, from the placenta and umbilical cord of neonates, as well as the methods for its cryopreservation and storage under cryogenic conditions. Initially, a manual procedure allowed the centrifugal separation of a buffy-coat fraction that was cryopreserved with dimethyl sulfoxide (DMSO) and frozen under controlled rate, with aliquots of the product being separated into unattached freezing vials, for use as future test samples. Subsequently, automated methods for withdrawing the buffy coat have been introduced that allow for aliquots of the cord blood unit (CBU) to be segregated into sealed “segments” of its integral plastic tubing, enabling monitoring the identity, viability, and potency of the CBU, including testing at the time of use. The stability of the CBUs and their segments after many years of storage has been established, as well as their safety and effectiveness. Food and Drug Administration (FDA) has determined that the CBUs produced according to established norms are safe and effective and has issued licenses to CBUs produced by a growing number of cord blood banks (CBBs). CBUs that do not meet the required thresholds for use in HPC transplantation are currently either used clinically if met with other criteria or for research in the generation of tissues and cells for regenerative medicine and immunotherapy. However, challenges, including costs and declining CBU utilization, may interfere with the expanding potential for CB clinical and research applications.
Chylothorax as a Risk Factor for Thrombosis in Adults: A Proof-of-Concept Study.

Background Postoperative chylothorax in children is associated with an increased risk of vascular thrombosis, hypothesized to be from loss of antithrombin into chylous fluid resulting in a hypercoagulable state. In adults, an increased thrombotic risk with chylothorax has not been described. Adults undergoing Ivor-Lewis esophagogastrectomy have two strong thrombotic risk factors—active malignancy and postoperative state—allowing for relative homogeneity in baseline thrombotic risk; therefore, we studied the association of chylothorax with thrombosis in this population. Methods We performed a single-center retrospective cohort study at a tertiary care academic center. Patients included adults undergoing Ivor-Lewis esophagogastrectomy between January 1, 2006, and December 31, 2012. We collected demographics, pleural fluid characteristics, and relevant imaging within 30 days after the operation. Using nominal logistic regression, we studied the effects of chylothorax, age, sex, body mass index, American Society of Anesthesiologists Physical Status Classification, operative duration, and hospital length of stay on the incidence of postoperative thrombosis. Results We identified 608 patients who underwent Ivor-Lewis esophagogastrectomy. Of these, 524 (86.2%) had no pleural fluid analysis, 48 (7.9%) had nonchylous effusions, and 36 (5.9%) had chylothoraces, with incident acute vascular thrombosis within 30 days postoperatively occurring in 22 of 524 (4.2%), 2 of 48 (4.2%), and 8 of 36 (22.2%), respectively ( p = 0.001). In multivariate analyses, after adjusting for the above factors, chylothorax was associated with significantly higher odds of any vascular thrombosis (odds ratio, 5.46; p = 0.0013) and deep venous thrombosis/pulmonary embolism (odds ratio, 6.76; p = 0.0016). Conclusions Chylothorax is associated with a significantly higher incidence of vascular thrombosis in adults undergoing Ivor-Lewis esophagogastrectomy. Vascular thrombosis was associated with a significantly higher 90-day mortality rate.
Developing a Framework for Financial Achievability of Department of Transportation Research and Development Projects

A financial analysis framework was developed to allow departments of transportation to assess research projects better. The framework recognizes that the research process contains multiple stages of decision making, and the framework details the information needed at each stage. The framework is described as it applies to each step in the research process: identifying potential research projects, evaluating research proposals, monitoring ongoing research projects, and evaluating final research reports. The framework also considers the decision to implement the research and its potential effects on employees. The application of the framework is illustrated with several Florida Department of Transportation research projects that involve the development of a multipurpose survey vehicle for evaluation of Florida roadways. This illustration allows for an explanation of each step in the framework with actual data from research reports and other internal or external sources. Although the framework is flexible an...
Blood gas sample spiking with total parenteral nutrition, lipid emulsion, and concentrated dextrose solutions as a model for predicting sample contamination based on glucose result.

Abstract Objective Evaluate the effects of blood gas sample contamination with total parenteral nutrition (TPN)/lipid emulsion and dextrose 50% (D50) solutions on blood gas and electrolyte measurement; and determine whether glucose concentration can predict blood gas sample contamination with TPN/lipid emulsion or D50 . Design and methods Residual lithium heparin arterial blood gas samples were spiked with TPN/lipid emulsion (0 to 15%) and D50 solutions (0 to 2.5%). Blood gas (pH, pCO2, pO2), electrolytes (Na+, K+ ionized calcium) and hemoglobin were measured with a Radiometer ABL90. Glucose concentration was measured in separated plasma by Roche Cobas c501. Chart review of neonatal blood gas results with glucose >300 mg/dL (>16.65 mmol/L) over a seven month period was performed to determine whether repeat (within 4 h) blood gas results suggested pre-analytical errors in blood gas results. Results were used to determine whether a glucose threshold could predict contamination resulting in blood gas and electrolyte results with greater than laboratory-defined allowable error. Results Samples spiked with 5% or more TPN/lipid emulsion solution or 1% D50 showed glucose concentration >500 mg/dL (>27.75 mmol/L) and produced blood gas (pH, pO2, pCO2) results with greater than laboratory-defined allowable error. TPN/lipid emulsion, but not D50, produced greater than allowable error in electrolyte (Na+,K+,Ca++ ,Hb) results at these concentrations. Based on chart review of 144 neonatal blood gas results with glucose >250 mg/dL received over seven months, four of ten neonatal intensive care unit (NICU) patients with glucose results >500 mg/dL and repeat blood gas results within 4 h had results highly suggestive of pre-analytical error. Only 3 of 36 NICU patients with glucose results 300–500 mg/dL and repeat blood gas results within 4 h had clear pre-analytical errors in blood gas results. Conclusion Glucose concentration can be used as an indicator of significant blood sample contamination with either TPN/lipid emulsion or D50 solution. NICU blood gas samples with glucose ≥300 mg/dL should be considered potentially contaminated, and samples with glucose >500 mg/dL have a risk for contamination.
Aggressive Renal Angiomyolipoma in a Patient With Tuberous Sclerosis Resulting in Pulmonary Tumor Embolus and Pulmonary Infarction

Renal angiomyolipoma (AML) is the most commonly encountered mesenchymal tumor of the kidney which can present spontaneously or in association with tuberous sclerosis complex. Rarely, renal AMLs may demonstrate aggressive features such as renal vein invasion. This common entity and its uncommon complications are diagnosed based on physical examination and computed tomography results. Here we report imaging findings of a renal AML with renal vein and inferior vena cava invasion resulting in pulmonary tumor embolus and pulmonary infarction.
Higgs scalars and vacuum instability in SU(2) L ⊗SU(2) R ⊗U(1)

The ${\mathrm{SU}(2)}_{L}\ensuremath{\bigotimes}{\mathrm{SU}(2)}_{R}\ensuremath{\bigotimes}\mathrm{U}(1)$ model of weak and electromagnetic interactions requires a minimum of two Higgs multiplets, $\ensuremath{\Phi}$ and $P$, to have the residual electromagnetic U (1) symmetry after the spontaneous symmetry breaking. With this minimum number of Higgs multiplets, we study the existence of a metastable vacuum and the corresponding limits on the masses of Higgs bosons using the effective potential in the one-loop approximation. Demanding that this model have the same neutrino neutral-current interactions as those of the Weinberg-Salam model and using the available phenomenological information, we get the minimum value for the sum of the squares of masses, ${M}_{\ifmmode\pm\else\textpm\fi{}}$, of two of the neutral Higgs bosons in terms of a parameter which involves the mixing of $\ensuremath{\Phi}$ and $P$, assuming a stable asymmetric vacuum exists. Under the assumption that the ${(\mathrm{mass})}^{2}$ matrix of the Higgs bosons is diagonal, we obtain ${(M_{+}^{}{}_{}{}^{2}+M_{\ensuremath{-}}^{}{}_{}{}^{2})}^{\frac{1}{2}}g11.4$ Gev. No limit can be placed on the other Higgs bosons with the presently available information.
Direct-acting antiviral treatment of acute hepatitis C virus infections.

ABSTRACTIntroduction: Hepatitis C contributes to significant morbidity and mortality worldwide. AHCV is defined as documented infection within 6 months of exposure. Treating acute hepatitis C virus...
A Comparative Analysis of Academic and Nonacademic Hospitals on Outcome Measures and Patient Satisfaction

Academic hospitals contribute to health care through patient care, research, and teaching; however, their outcomes may not be equivalent to nonacademic hospitals. Multivariate analysis of variance is used to compare publicly reported data on patient satisfaction, readmission rates, mortality rates, and hospital-acquired injury scores between 1906 academic and nonacademic hospitals, while controlling for hospital-level covariates. Results show that academic hospitals have higher levels of patient satisfaction on 7 of the 11 measures and are equivalent to nonacademic hospitals on the remaining 4 measures. Academic hospitals have lower pneumonia mortality rates than nonacademic hospitals, with no difference for other mortality or disease-specific readmissions. However, academic hospitals have a slightly higher overall readmission rate. Infection rates were equivalent between academic and nonacademic hospitals for central line-associated bloodstream infections, pressure ulcers, and wound dehiscence for abdominal and pelvic injuries, but academic hospitals have higher catheter-associated urinary tract infection rates.
Speech and Debate As Civic Education

Speech and Debate as Civic Education emphasizes the need for integrating more speech and debate training into education as a means for civic engagement to “sustain our democratic republic” (20). Th...
A Performance Comparison of Centralized and Distributed Spectrum Management Techniques in Elastic Optical Networks

Elastic optical networks (EONs) have emerged to provide higher spectrum efficiency than traditional Dense Wavelength-Division-Multiplexing (DWDM) by utilizing enabling technologies such as flexible spectrum grid, Orthogonal Frequency Division Multiplexing (OFDM), and distance adaptive rate and modulation. The choice of the control-plane is an important consideration when deploying any new technology, especially in optical networks. This paper considers generic distributed and centralized spectrum assignment policies in conjunction with the accompanying connection set-up signaling protocols in EONs. A network simulator for Generalized Multiprotocol Label Switching (GMPLS) was developed with Forward Reservation Protocol and Backward Reservation Protocol signaling methods. These signaling techniques are used with the First Fit (FF) and Random Fit (RF) Routing and Spectrum Allocation (RSA) algorithms. The paper discusses control elements (central and distributed architectures) decisions under busy hour and normal network conditions and presents a comprehensive performance analysis of key performance metrics such as connection success rate, connection establishment time, and capacity requirement.