Miracle-dz/UniFAR-FTUs huggingface dataset:
Porcine CYP 2 A 19 , CYP 2 E 1 and CYP 1 A 2 forms are responsible for skatole biotransformation in the reconstituted system

OBJECTIVES: To study the contribution of individual purified porcine CYP1A2, 2E1 and 2A19 enzymes to the biotransformation of skatole. METHODS: Individual porcine and human enzymes (CYP1A2, 2E1 or 2A6/19) were used to study their potential involvement in skatole metabolism. Furthermore, the inhibition experiments using specific inhibitors of CYP1A2, 2E1 or 2A6/19, were performed. For determination of skatole biotransformation by individual CYP forms in reconstituted systems, HPLC method with UV detection was used. RESULTS: The data presented in this paper show that porcine and human CYPs are responsible for the formation of indole-3-carbinol and 3-methyloxindole. Whereas in pig CYP2A19 and CYP1A2 seem to be the most important for metabolism of skatole, in man CYP1A2 and CYP2E1 forms are mainly responsible for the production of the metabolites mentioned above. CONCLUSIONS: The porcine and human CYP1A2, 2E1, 2A6/19 forms contribute to formation of 3-methyloxindole and indole-3-carbinol.
Evaluation of Models of the Reading Process.

ABSTRACT A variety of reading process models have been proposed and evaluated in reading research. Traditional approaches to model evaluation specify the workings of a system in a simplified fashion to enable organized, systematic study of the system's components. Following are several statistical methods of model evaluation: (1) empirical research on components, in which the researcher predicts behavior based on an analysis of the model's components; (2) tally sheet summarization of studies addressing particular issues; (3) meta-analytic techniques, a more sophisticated inter-study summarization than the tally sheet approach; and (4) causal modeling, in which researchers go beyond the constraints of correlation analysis to make statistical inferences concerning causation. Comparisons of reading models are often descriptive in nature rather than analytical. Leading texts on reading are generally comprised of key theoretical articles that provide readers with important and original introductory materials on various reading models. English/language arts education has long emphasized philosophical reading theories based on what reading should be, although several attempts have been made to evaluate reading models by constructing classification systems as well. The ultimate test of any reading model rests on whether it can be effectively applied in the classroom. A four-page reference list is provided. (JD)
Sole farming: nearly there but not quite?

That seems to have been the reality of the last few years, but that rather depressing scenario does have to be tempered with the optimism that we will get there in the end! At least that seemed to be the mood of the most recent (the fourth) Workshop on the Cultivation of Soles that was hosted by the CCMAR of the University of the Algarve in Faro from 11-13 November last year. An article summarising the results of the first three workshops was published in Aquaculture Europe in September 2006.
Randomized sketch descent methods for non-separable linearly constrained optimization

In this paper we consider large-scale smooth optimization problems with multiple linear coupled constraints. Due to the non-separability of the constraints, arbitrary random sketching would not be guaranteed to work. Thus, we first investigate necessary and sufficient conditions for the sketch sampling to have well-defined algorithms. Based on these sampling conditions we develop new sketch descent methods for solving general smooth linearly constrained problems, in particular, random sketch descent (RSD) and accelerated random sketch descent (A-RSD) methods. To our knowledge, this is the first convergence analysis of RSD algorithms for optimization problems with multiple non-separable linear constraints. For the general case, when the objective function is smooth and non-convex, we prove for the non-accelerated variant sublinear rate in expectation for an appropriate optimality measure. In the smooth convex case, we derive for both algorithms, non-accelerated and A-RSD, sublinear convergence rates in the expected values of the objective function. Additionally, if the objective function satisfies a strong convexity type condition, both algorithms converge linearly in expectation. In special cases, where complexity bounds are known for some particular sketching algorithms, such as coordinate descent methods for optimization problems with a single linear coupled constraint, our theory recovers the best known bounds. Finally, we present several numerical examples to illustrate the performances of our new algorithms.
Single cell RNAseq uncovers a robust transcriptional 1 response to morphine by glia 2 3

3 Denis Avey1,2, Sumithra Sankararaman2, Aldrin K. Y. Yim1, Ruteja Barve3, Jeffrey 4 Milbrandt1*, Robi D. Mitra1,2* 5 1Department of Genetics, Washington University, School of Medicine, St. Louis, MO, 63110, 6 USA 7 2Center for Genome Sciences and Systems Biology, Washington University, School of 8 Medicine, St. Louis, MO 63110, USA 9 3Genome Technology Access Center, Department of Genetics. Washington University, School 10 of Medicine, St. Louis, MO, 63110, USA 11 *Correspondence should be addressed to Jeffrey Milbrandt (jmilbrandt@wustl.edu) or Robi 12 Mitra (rmitra@wustl.edu) 13 14 SUMMARY 15 16 Molecular and behavioral responses to opioids are thought to be primarily mediated by 17 neurons, although there is accumulating evidence that other cell types play a prominent 18 role in drug addiction. To investigate cell-type-specific opioid responses, we performed 19 single-cell RNA sequencing of the nucleus accumbens of mice following acute morphine 20 treatment. Differential expression analysis uncovered unique morphine-dependent 21 transcriptional responses by oligodendrocytes and astrocytes. We examined the 22 expression of selected genes, including Cdkn1a and Sgk1, by FISH, confirming their 23 induction by morphine in oligodendrocytes. Further analysis using RNAseq of FACS24 purified oligodendrocytes revealed a large cohort of morphine-regulated genes. 25 Importantly, the affected genes are enriched for roles in cellular pathways intimately 26 linked to oligodendrocyte maturation and myelination, including the unfolded protein 27 response. Altogether, our data illuminate the morphine-dependent transcriptional 28 response by oligodendrocytes and offer mechanistic insights into myelination defects 29 associated with opioid abuse. 30 31
Nonequilibrium Molecular Dynamics

The development of nonequilibrium molecular dynamics is described, with emphasis on massively-parallel simulations involving the motion of millions, soon to be billions, of atoms. Corresponding continuum simulations are also discussed. field. Nonequilibrium molecular dynamicsl - 3 began around 1970 when Bill Ashurst set out to simulate flows of momentum and energy in nonequilibrium liquids by using boundary heat and momentum reservoirs made up of particles. A typical fluid geometry is illustrated in Figure 1. The methods that Ashurst developed were successfully formalized and generalized about ten years later, in work that is still rapidly developing. He achieved his goal, reproducing the experimental situations leading to nonequilibrium transport. It has turned out that the transport coefficients so deternlined depend only very slightly on the amount of deviation from equilibrium. Thus the necessarily large gradients in the computer simulations are perfectly acceptable for quantitative work. By 1980, following pioneering work of Klimenko and Dremin in Russia4 , a joint effort at Los Alamos and Livermore resulted in the simulation and characterization of a strong dense-fluid shockwave5 using 4800 atoms. The measured structure of that shockwave is compared, in Figure 2, to the predictions of the Navier-Stokes equations, and indicates shear viscosity and heat conductivity coefficients only 30% larger than the small-gradient limits of Newtonian viscosity and Fourier heat con­ duction. The shockwave transport coefficients are a bit bigger because the relatively rigid and disordered shockwave structure is a more efficient medium for transporting momentum and energy.
Dissecting the Role of Folr 1 and Folh 1 Genes in the Pathogenesis of Metabolic Syndrome in Spontaneously Hypertensive Rats

J. ŠILHAVÝ, J. KRIJT, J. SOKOLOVÁ, V. ZÍDEK, P. MLEJNEK, M. ŠIMÁKOVÁ, V. ŠKOP, J. TRNOVSKÁ, O. OLIYARNYK, I. MARKOVÁ, M. HÜTTL, H. MALÍNSKÁ, L. KAZDOVÁ, F. LIŠKA, V. KOŽICH, M. PRAVENEC Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic, Department of Pediatrics and Adolescent Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic, Institute for Clinical and Experimental Medicine, Prague, Czech Republic, Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Prague, Czech Republic
Findings from the Teaching, Learning, and Computing Survey: Is Larry Cuban Right?

Cuban (1986; 2000) has argued that computers are largely incompatible with the requirements of teaching, and that, for the most part, teachers will continue to reject their use as instruments of student work during class. Using data from a nationally representative survey of 4th through 12th grade teachers, this paper demonstrates that although Cuban correctly characterizes frequent use of computers in academic subject classes as a teaching practice of a small and distinct minority, certain conditions make a big difference in the likelihood of a teacher having her students use computers frequently during class time. In particular, academic subject-matter teachers who have at least five computers present in their classroom, who have at least average levels of technical expertise in their use, and who are in the top quartile on a reliable and extensive measure of constructivist teaching philosophy are very likely to have students make regular use of computers during class. More than 3/4 of such teachers have students use word processing programs regularly during class and a majority are regular users of at least one other type of software besides skill-based games. In addition, other factors-such as an orientation towards depth rather than breadth in their teaching(perhaps caused by limited pressures to cover large amounts of content) and block scheduling structures that provide for long class periods-are also associated with greater use of computers by students during class. Finally, the paper provides evidence that certain approaches to using computers result in students taking greater initiative in using computers outside of class time-approaches consistent with a constructivist teaching philosophy, rather than a standards- based, accountability-oriented approach to teaching. Thus, despite their clear minority status as a primary resource in academic subject classroom teaching, computers are playing a major role in at least one major direction of current instructional reform efforts.
Ecosystem changes in large and shallow Võrtsjärv, a lake in Estonia — evidence from sediment pigments and phosphorus fractions

Palaeopigments, organic matter dissolved in sediment porewater (pDOM) and phosphorus fractions were analysed in a sediment core from large shallow Vortsjarv with the aim to assess whether the trends of climate-driven and anthropogenic changes in lake trophy within the 20th century are reflected in its sediment record. In the first half of the last century, the lake was naturally slightly eutrophic as the accumulation of palaeopigments was low and the load of nutrients stable; investigated variations in palaeoparameters were induced by the regular natural water level fluctuations. Since the mid-1950s eutrophication of Vortsjarv has accelerated — content of fossil pigments, CaCO 3 and nutrients increased, while pDOM revealed high autochthonous matter input. The increase of palaeopigment's concentrations during the last decade may be consistent with regional climate warming. Investigated palaeoindicators and water level changes had a stronger relationship in the second half of the 20th century.
Spatial Variability in Soil Microbial Communities in a Nitrogen-Saturated Hardwood Forest Watershed Forest , Range & Wildland Soils

6 Soil Sci. Soc. Am. J. 75:2011 Posted online 18 Oct. 2010 doi:10.2136/sssaj2010.0172 Received 15 Apr. 2010. *Corresponding author (gilliam@marshall.edu). © Soil Science Society of America, 5585 Guilford Rd., Madison WI 53711 USA All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. Spatial Variability in Soil Microbial Communities in a Nitrogen-Saturated Hardwood Forest Watershed Forest, Range & Wildland Soils
Nanostructured Microelectrodes for High-Activity Electrochemistry in Biosensing and CO 2 Recycling by Tina

Nanostructured Microelectrodes for High-Activity Electrochemistry in Biosensing and CO2 Recycling Tina Saberi Safaei Doctor of Philosophy Graduate Department of Electrical and Computer Engineering University of Toronto 2017 Electrochemical biosensors are promising candidates for point-of-care (POC) diagnostics, since they require neither costly instrumentation nor expert operators. However, for them to become widely used in a clinical setting, biosensors must be enhanced in sensitivity without increasing costs or compromising the speed of detection. The goal of this thesis is to realize this vision by promoting high-activity redox reactions via rational design of the size, shape and structure of electrodes. Incorporating nanostructures on the surface of microelectrodes greatly increases their surface area and reaction rates, while maintaining efficient diffusion of analytes to electrode surfaces. Here, by coupling optimized electrode morphology with an enzyme-based assay, I report on a new class of ultra-sensitive biosensors. I showcase the applicability of these sensors for POC diagnostics by incorporating them on a platform designed to isolate rare cells in biological samples. The integrated device is the first example of an electrochemical sensing platform capable of detecting cancer cells with clinically-relevant sensitivity and specificity. Decreasing the cost of POC diagnostic devices is vitally important for their adoption in low-resource settings. To that end, I advance a strategy to decrease the costs associated with the fabrication of nanostructured microelectrodes (NMEs). I present an image-reversal soft lithography (IRSL) technique based on an elastomeric stamping protocol, eliminating the need for costly photolithographic fabrication steps. The distinct morphology of the sensors made
Inverse Problems for the Stationary Transport Equation in the Diffusion Scaling

We consider the inverse problem of reconstructing the optical parameters of the radiative transfer equation (RTE) from boundary measurements in the diffusion limit. In the diffusive regime (the Knudsen number $\mathsf{Kn}\ll 1$), the forward problem for the stationary RTE is well approximated by an elliptic equation. However, the connection between the inverse problem for the RTE and the inverse problem for the elliptic equation has not been fully developed. This problem is particularly interesting because the former one is mildly ill-posed , with a Lipschitz type stability estimate, while the latter is well known to be severely ill-posed with a logarithmic type stability estimate. In this paper, we derive stability estimates for the inverse problem for RTE and examine its dependence on $\mathsf{Kn}$. We show that the stability is Lipschitz in all regimes, but the coefficient deteriorates as $e^{\frac{1}{\mathsf{Kn}}}$, making the inverse problem of RTE severely ill-posed when $\mathsf{Kn}$ is small. In this way we connect the two inverse problems. Numerical results agree with the analysis of worsening stability as the Knudsen number gets smaller.
Multi-Modal Video Summarization

Most previous work on summarization targeted either only on video or on its description of single video document. To efficiently manage huge video documents, this paper addresses a new prototype for summarizing video documents that automatically processes text and key-frames from the given video documents, indexes and provides mechanism for search and retrieval. The system separately summarizes the text and video related information. Both summarizations will enhance the performance as well the quality of the video document retrieval processes. The text summarizer provides a summarized view of a large video document to improve the learning speed and to give a glimpse of the document for better understanding. The video summarization consists of the key frames that effectively express the content and context of the video. This is achieved by quantifying visual attention of each frame in a video. This framework provides meaningful two-way summarization for video documents.
Description of the SSFATE Numerical Modeling System

Abstract : This technical note describes the numerical modeling system SSFATE (Suspended Sediment FATE), which is being developed to compute suspended sediment fields resulting from dredging operations. Both theoretical aspects of the computations made within SSFATE and application aspects of the shell-based personal computer program are discussed. SSFATE was developed in response to a need for tools to assist dredging'project managers confronted by requests for environmental windows. Environmental windows, intended to protect biological resources or their habitats, are requested during the interagency coordination process for dredging projects (Reine, Dickerson, and Clarke 1998). In many cases, decisions regarding environmental windows must be based on limited technical information because potential impacts are linked to a host of site- and project-specific factors. For example, navigation dredging operations in different reaches of the same waterway may pose risks to different resources, or potential impacts may vary dependent on the type of dredge plant involved. Few tools exist to evaluate such concerns early in the environmental window negotiation process. Consequently, a general inability to address "What if" questions associated with given dredging project scenarios tends to ensure that recommended environmental windows are conservative, and perhaps over- restrictive (Reine, Dickerson, and Clarke 1998). Some of the most frequently asked "What if' questions during dredging project coordination are related to resuspension and dispersion of sediments at the dredging site. Suspended sediments are a primary concern of resource agencies, as exposure of aquatic organisms to elevated suspended sediment concentrations is perceived to be a major source of detrimental impact. Likewise, redeposition of suspended sediments can be a significant concern if sensitive bottom-dwelling organisms (e.g., oysters or sea grasses) are present in the vicinity of a dredging project.
The Resultant, the Discriminant, and the Derivative of Generalized Fibonacci Polynomials

A second order polynomial sequence is of \emph{Fibonacci-type} (\emph{Lucas-type}) if its Binet formula has a structure similar to that for Fibonacci (Lucas) numbers. Known examples of these type of sequences are: Fibonacci polynomials, Pell polynomials, Fermat polynomials, Chebyshev polynomials, Morgan-Voyce polynomials, Lucas polynomials, Pell-Lucas polynomials, Fermat-Lucas polynomials, Chebyshev polynomials. The \emph{resultant} of two polynomials is the determinant of the Sylvester matrix and the \emph{discriminant} of a polynomial $p$ is the resultant of $p$ and its derivative. We study the resultant, the discriminant, and the derivatives of Fibonacci-type polynomials and Lucas-type polynomials as well combinations of those two types. As a corollary we give explicit formulas for the resultant, the discriminant, and the derivative for the known polynomials mentioned above.
Dynamics of Adaptation and Evolutionary Branching

We present a formal framework for modeling evolutionary dynamics with special emphasis on the generation of diversity through branching of the evolutionary tree. Fitness is defined as the long term growth rate which is influenced by the biotic environment leading to frequency-dependent selection. Evolution can be described as a dynamics in space with variable number of dimensions corresponding to the number of different types present. The dynamics within a subspace is governed by the local fitness gradient. Entering a higher dimensional subspace is possible only at a particular type of attractors where the population undergoes evolutionary branching.
Global and Local Persistence of Influenza A ( H 5 N 1 ) Virus

highly pathogenic avian influenza A(H5N1) virus is helpful for surveillance and disease prevention. To characterize the migration network of this virus, we used genetic analysis, which supported a global persistence model in which each of 9 regions acts to some extent as a source. Siberia is the major hub for the dispersal of the virus. Southeast Asia and Africa are major sources of genetically and antigenically novel strains. We found evidence of local persistence of the virus in Southeast Asia and Africa, which is rare for human influenza A viruses. The differences in migration dynamics between avian and human influenza viruses might help with the design of region-specific surveillance efforts and the selection of vaccine candidates.
Life Insurance Demand Under Health Shock Risk

This paper studies the life cycle consumption-investment-insurance problem of a family. The wage earner faces the risk of a health shock that significantly increases his probability of dying. The family can buy term life insurance with realistic features. In particular, the available contracts are long term so that decisions are sticky and can only be revised at significant costs. Furthermore, a revision is only possible as long as the insured person is healthy. A second important and realistic feature of our model is that the labor income of the wage earner is unspanned. We document that the combination of unspanned labor income and the stickiness of insurance decisions reduces the insurance demand significantly. This is because an income shock induces the need to reduce the insurance coverage, since premia become less affordable. Since such a reduction is costly and families anticipate these potential costs, they buy less protection at all ages. In particular, young families stay away from life insurance markets altogether.
Clinical utility of antiemetics and complementary therapies in the prevention of postoperative nausea and vomiting

License. The full terms of the License are available at http://creativecommons.org/licenses/by-nc/3.0/. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Ltd, provided the work is properly attributed. Permissions beyond the scope of the License are administered by Dove Medical Press Ltd. Information on how to request permission may be found at: http://www.dovepress. com/permissions.php Clinical Audit 2013:5 67–76 Clinical Audit Dovepress