pinecone/core-2020-05-10-deduplication huggingface dataset:
$k$-Schur functions and affine Schubert calculus

This book is an exposition of the current state of research of affine
Schubert calculus and $k$-Schur functions. This text is based on a series of
lectures given at a workshop titled "Affine Schubert Calculus" that took place
in July 2010 at the Fields Institute in Toronto, Ontario. The story of this
research is told in three parts: 1. Primer on $k$-Schur Functions 2. Stanley
symmetric functions and Peterson algebras 3. Affine Schubert calculusComment: 213 pages; conference website:
  http://www.fields.utoronto.ca/programs/scientific/10-11/schubert/, updates
  and corrections since v1. This material is based upon work supported by the
  National Science Foundation under Grant No. DMS-065264
Text mining for drug-drug interaction

In order to understand the mechanisms of drug-drug interaction (DDI), the study of pharmacokinetics (PK), pharmacodynamics (PD), and pharmacogenetics (PG) data are significant. In recent years, drug PK parameters, drug interaction parameters, and PG data have been unevenly collected in different databases and published extensively in literature. Also the lack of an appropriate PK ontology and a well-annotated PK corpus, which provide the background knowledge and the criteria of determining DDI, respectively, lead to the difficulty of developing DDI text mining tools for PK data collection from the literature and data integration from multiple databases.To conquer the issues, we constructed a comprehensive pharmacokinetics ontology. It includes all aspects of in vitro pharmacokinetics experiments, in vivo pharmacokinetics studies, as well as drug metabolism and transportation enzymes. Using our pharmacokinetics ontology, a PK corpus was constructed to present four classes of pharmacokinetics abstracts: in vivo pharmacokinetics studies, in vivo pharmacogenetic studies, in vivo drug interaction studies, and in vitro drug interaction studies. A novel hierarchical three-level annotation scheme was proposed and implemented to tag key terms, drug interaction sentences, and drug interaction pairs. The utility of the pharmacokinetics ontology was demonstrated by annotating three pharmacokinetics studies; and the utility of the PK corpus was demonstrated by a drug interaction extraction text mining analysis.The pharmacokinetics ontology annotates both in vitro pharmacokinetics experiments and in vivo pharmacokinetics studies. The PK corpus is a highly valuable resource for the text mining of pharmacokinetics parameters and drug interactions
Mathematical Modelling of Optical Coherence Tomography

In this chapter a general mathematical model of Optical Coherence Tomography
(OCT) is presented on the basis of the electromagnetic theory. OCT produces
high resolution images of the inner structure of biological tissues. Images are
obtained by measuring the time delay and the intensity of the backscattered
light from the sample considering also the coherence properties of light. The
scattering problem is considered for a weakly scattering medium located far
enough from the detector. The inverse problem is to reconstruct the
susceptibility of the medium given the measurements for different positions of
the mirror. Different approaches are addressed depending on the different
assumptions made about the optical properties of the sample. This procedure is
applied to a full field OCT system and an extension to standard (time and
frequency domain) OCT is briefly presented.Comment: 28 pages, 5 figures, book chapte
Regularity of a kind of marginal functions in Hilbert spaces

We study well-posedness of some mathematical programming problem depending on a parameter that generalizes in a certain sense the metric projection onto a closed nonconvex set. We are interested in regularity of the set of minimizers as well as of the value function, which can be seen, on one hand, as the viscosity solution to a Hamilton-Jacobi equation, while, on the other, as the minimal time in some related optimal time control problem. The regularity includes both the Fréchet differentiability of the value function and the Hölder continuity of its (Fréchet) gradient
Integral closure of rings of integer-valued polynomials on algebras

Let $D$ be an integrally closed domain with quotient field $K$. Let $A$ be a
torsion-free $D$-algebra that is finitely generated as a $D$-module. For every
$a$ in $A$ we consider its minimal polynomial $\mu_a(X)\in D[X]$, i.e. the
monic polynomial of least degree such that $\mu_a(a)=0$. The ring ${\rm
Int}_K(A)$ consists of polynomials in $K[X]$ that send elements of $A$ back to
$A$ under evaluation. If $D$ has finite residue rings, we show that the
integral closure of ${\rm Int}_K(A)$ is the ring of polynomials in $K[X]$ which
map the roots in an algebraic closure of $K$ of all the $\mu_a(X)$, $a\in A$,
into elements that are integral over $D$. The result is obtained by identifying
$A$ with a $D$-subalgebra of the matrix algebra $M_n(K)$ for some $n$ and then
considering polynomials which map a matrix to a matrix integral over $D$. We
also obtain information about polynomially dense subsets of these rings of
polynomials.Comment: Keywords: Integer-valued polynomial, matrix, triangular matrix,
  integral closure, pullback, polynomially dense set. accepted for publication
  in the volume "Commutative rings, integer-valued polynomials and polynomial
  functions", M. Fontana, S. Frisch and S. Glaz (editors), Springer 201
Markov chains for promotion operators

We consider generalizations of Schuetzenberger's promotion operator on the
set L of linear extensions of a finite poset. This gives rise to a strongly
connected graph on L. In earlier work (arXiv:1205.7074), we studied
promotion-based Markov chains on these linear extensions which generalizes
results on the Tsetlin library. We used the theory of R-trivial monoids in an
essential way to obtain explicitly the eigenvalues of the transition matrix in
general when the poset is a rooted forest. We first survey these results and
then present explicit bounds on the mixing time and conjecture eigenvalue
formulas for more general posets. We also present a generalization of promotion
to arbitrary subsets of the symmetric group.Comment: 17 pages, includes review of results of arXiv:1205.707
Fomin-Greene monoids and Pieri operations

We explore monoids generated by operators on certain infinite partial orders.
Our starting point is the work of Fomin and Greene on monoids satisfying the
relations $(\u{r}+\u{r+1})\u{r+1}\u{r}=\u{r+1}\u{r}(\u{r}+\u{r+1})$ and
$\u{r}\u{t}=\u{s}\u{r}$ if $|r-t|>1.$ Given such a monoid, the non-commutative
functions in the variables $\u{}$ are shown to commute. Symmetric functions in
these operators often encode interesting structure constants. Our aim is to
introduce similar results for more general monoids not satisfying the relations
of Fomin and Greene. This paper is an extension of a talk by the second author
at the workshop on algebraic monoids, group embeddings and algebraic
combinatorics at The Fields Institute in 2012.Comment: 33 pages, this is a paper expanding on a talk given at Fields
  Institute in 201
Forest landscape ecology and global change: an introduction

Forest landscape ecology examines broad-scale patterns and processes and their interactions in forested systems and informs the management of these ecosystems. Beyond being among the richest and the most complex terrestrial systems, forest landscapes serve society by providing an array of products and services
and, if managed properly, can do so sustainably. In this chapter, we provide an overview of the field of forest landscape ecology, including major historical and present topics of research, approaches, scales, and applications, particularly those concerning edges, fragmentation, connectivity, disturbance, and biodiversity. In addition, we discuss causes of change in forest landscapes, particularly land-use and management changes, and the expected structural and functional consequences that may result from these drivers. This chapter is intended to set the context and provide an overview for the remainder of the book and poses a broad set of questions related to forest landscape ecology and global change that need answers
Forest landscape ecology and global change: what are the next steps?

In this chapter, we summarize current trends and challenges and future research directions in forest landscape ecology and in management related to global change. We discuss the available knowledge in forest landscape ecology and the possibilities of using this knowledge to support management under changing conditions. We also discuss the forest sector’s preparedness to deal with changes in management and how forest landscape ecology can guide this management. Forest landscape ecology has gathered substantial knowledge on patterns, processes, tools, and methods that can support forest and landscape management during changing scenarios. We recognize that existing knowledge is incomplete and that a substantial portion of our knowledge is uncertain, that variability in landscape conditions and various forms of error compound the problem, that we still lack considerable knowledge in some fields, and that there are likely to be knowledge gaps we are not aware of. We nonetheless face the challenge of responding to change based on the available knowledge
Humans as agents of change in forest landscapes.

Forest systems play a crucial role in biogeochemical cycling and provide a variety of ecosystem services at multiple scales. Considerable progress has been made in understanding the dynamics of tropical and temperate deforestation and land-use and cover change. However, less attention has been dedicated to understanding the social and biophysical conditions under which reforestation occurs. Recent research documents the experiences of many countries that have undergone transitions from a period of high deforestation to a period of declining deforestation or even net reforestation. However, these transitions take place across a range of temporal and spatial scales. Here, we review global forest-cover trends and social processes affecting forest cover and then focus on a comparison of reforestation in the states of São Paulo, Brazil, and Indiana, United States. Both states have undergone extensive deforestation but now show forest restoration alongside continuing deforestation. Our focus on forest change at the state level permits a detailed examination of deforestation and reforestation dynamics and of the diverse social factors that underlie these changes. Among these factors, human values and attitudes appear most important.201
Video ergo sum: an artist’s thoughts on inventing with computer technology in the creation of artworks

Abstract:\ud
\ud
The computer, while not a new concept, has in its modern form transformed the way we disseminate ideas, interact with one another and enhanced our capacity to acquire information. From the artist’s perspective digital imaging presents opportunities for visual invention and challenges in how visual form is mediated. In my artwork I use the computer as a means to create imagery that would not be possible without its use, and that enables exploration of an artificially created space that enhances spatial awareness and challenges our perception of what we encounter
Visualization of Notch signaling oscillation in cells and tissues.

<Book Title>Notch SignalingThe Notch signaling effectors Hes1 and Hes7 exhibit oscillatory expression with a period of about 2-3 h during embryogenesis. Hes1 oscillation is important for proliferation and differentiation of neural stem cells, whereas Hes7 oscillation regulates periodic formation of somites. Continuous expression of Hes1 and Hes7 inhibits these developmental processes. Thus, expression dynamics are very important for gene functions, but it is difficult to distinguish between oscillatory and persistent expression by conventional methods such as in situ hybridization and immunostaining. Here, we describe time-lapse imaging methods using destabilized luciferase reporters and a highly sensitive cooled charge-coupled device camera, which can monitor dynamic gene expression. Furthermore, the expression of two genes can be examined simultaneously by a dual reporter system using two-color luciferase reporters. Time-lapse imaging analyses reveal how dynamically gene expression changes in many biological events
Remodeling of glycans using glycosyltransferase genes.

Remodeling of glycans on the cell surface is an essential technique to analyze cellular function of lectin-glycan ligand interaction. Here we describe the methods to identify the responsible enzyme (glycosyltransferase) regulating the expression of the glycan of interest and to modulate the glycan expression by overexpressing the glycosyltransferase gene. For the identification of the responsible enzyme, we introduce a new method, CIRES (correlation index-based responsible-enzyme gene screening), that consists of statistical comparison of glycan expression profile obtained by flow cytometry and gene expression profile obtained by DNA microarray
Detection of the glucocorticoid receptors in brain protein extracts by SDS-PAGE

Uncorrected proofGlucocorticoids are steroid hormones vital for organ system homeostasis and for the maintenance of essential biological processes. A significant part of these actions are mediated through glucocorticoid receptor (GR) that belongs to the nuclear receptor superfamily. To cover such variety of processes the different glucocorticoids act through different GR isoforms that are originated due to posttranscriptional and posttranslational mechanisms. For this reason when evaluating the levels of GRs we should preferentially determine protein levels instead of gene expression. Here, we describe the detection by Western blotting of the GR (a and ß isoforms) protein, using macrodissected brain tissue
In vivo axial loading of the mouse tibia

Noninvasive methods to apply controlled, cyclic loads to the living skeleton are used as anabolic procedures to stimulate new bone formation in adults and enhance bone mass accrual in growing animals. These methods are also invaluable for understanding bone signaling pathways. Our focus here is on a particular loading model: in vivo axial compression of the mouse tibia. An advantage of loading the tibia is that changes are present in both the cancellous envelope of the proximal tibia and the cortical bone of the tibial diaphysis. To load the tibia of the mouse axially in vivo, a cyclic compressive load is applied up to five times a week to a single tibia per mouse for a duration lasting from 1 day to 6 weeks. With the contralateral limb as an internal control, the anabolic response of the skeleton to mechanical stimuli can be studied in a pairwise experimental design. Here, we describe the key parameters that must be considered before beginning an in vivo mouse tibial loading experiment, including methods for in vivo strain gauging of the tibial midshaft, and then we describe general methods for loading the mouse tibia for an experiment lasting multiple days
Mitochondrial tRNA Valine in Cardiomyopathies

Mitochondrial respiratory chain disorders are a heterogeneous group of diseases that clinically involve multiple tissues although they tend to mainly affect nervous system and skeletal muscle. The predominance of neurologic and neuromuscular manifestations in mitochondrial diseases has generally masked the presence of other, but not less important, clinical phenotypes, such as cardiac complications. Nowadays, mitochondrial defects are being increasingly recognized to play an important role in the pathogenesis of a subgroup of cardiomyopathies produced by defects in the energetic metabolism (mitochondrial cardiomyopathies). These diseases can result from mutations in either nuclear or mitochondrial encoded genes although mitochondrial DNA mutations are more frequent. In fact, cardiac conduction abnormalities have been associated with different mtDNA rearrangements. In a same way, sporadic or inherited mutations in mitochondrial DNA specifically in the mitochondrial transfer ribonucleic acid genes (mostly in the tRNALeu(UUR) and tRNAIle) have also been associated with hypertrophic and dilated cardiomyopathy. Mitochondrial diseases caused by mutations in the mitochondrial tRNAVal gene (MT-TV) are not very frequent. However, a relatively high percentage of mutations in this gene have been associated with mitochondrial cardiomyopathy. Besides, functional and molecular analyses suggest that the MT-TV gene should be routinely considered in the diagnosis when there is a high suspicion of mitochondrial cardiomyopathy. Finally, the increasingly importance of the role that this gene has begun to play in the pathophysiology of mitochondrial cardiomyopathies indicates that future studies about the molecular mechanisms that could explain why the cardiomyopathy phenotype appears must be carried ouThis work was supported by grants of the Center for Biomedical Research on Rare Diseases
(CIBERER), Instituto de Salud Carlos III (grants PI 07/0167, PI 10/0703 to R.G. and PI06/0205, PS09/00941 to B.B.)
and Comunidad de Madrid (grant number S2010/BMD-2402)
Can we count on you at a distance? The impact of culture on formation of swift trust within global virtual teams

The goal of this chapter is to explore the research question, “How do cultural values impact the formation of swift trust within global virtual teams?” We first introduce the phenomena of global virtual teams and swift trust, and establish a clear understanding of several underlying concepts and definitions such as global virtual teams, swift trust, and in-group and out-group. Next, we look at the concept of in-group vs. out-group based on relevant cultural dimensions from cross-cultural theorists such as Hall (1976), Hofstede (1980), and Trompenaars (1994). Using these theoretical lenses, we examine the impact of cultural values on swift trust formation when people engage in virtual collaboration. We then present several propositions to support the argument that culture does impact the ability to form swift trust within global virtual teams. Finally, we offer some implications and directions for future research
Energy-Aware Algorithms for Task Graph Scheduling, Replica Placement and Checkpoint Strategies

International audienceThe energy consumption of computational platforms has recently become a critical problem, both for economic and environmental reasons. To reduce energy consumption, processors can run at different speeds. Faster speeds allow for a faster execution, but they also lead to a much higher (superlinear) power consumption. Energy-aware scheduling aims at minimizing the energy consumed during the execution of the target application, both for computations and for communications. The price to pay for a lower energy consumption usually is a much larger execution time, so the energy-aware approach makes better sense when coupled with some prescribed performance bound. In other words, we have a bi-criteria optimization problem, with one objective being energy minimization, and the other being performance-related
Probabilistic counterparts of nonlinear parabolic PDE systems

We extend the results of the FBSDE theory in order to construct a
probabilistic representation of a viscosity solution to the Cauchy problem for
a system of quasilinear parabolic equations. We derive a BSDE associated with a
class of quailinear parabolic system and prove the existence and uniqueness of
its solution. To be able to deal with systems including nondiagonal first order
terms along with the underlying diffusion process we consider its
multiplicative operator functional. We essentially exploit as well the fact
that the system under consideration can be reduced to a scalar equation in a
enlarged phase space. This allows to obtain some comparison theorems and to
prove that a solution to FBSDE gives rise to a viscosity solution of the
original Cauchy problem for a system of quasilinear parabolic equations
Design and Cloning of Short HairpinRNAs (shRNAs) into a Lentiviral Silencing Vector to Study the Function of Selected Proteins in Neuronal Apoptosis

Double-stranded RNA-mediated interference (RNAi) is a new simple and fast research tool for shutting 7 down genes and characterizes function of their respective proteins. Many strategies for design and delivery of 8 siRNA to target cells are available. Here, we describe the use of lentiviral short hairpin RNA (shRNA) RNA 9 silencing to identify the involvement of d-serine racemase (SR)- an enzyme that syntheses d-serine to modu- 10 late glutamate-N-methyl-d-aspartate receptor- in regulating rat cerebellar granule neurons (CGN) apoptosis. 11 Apoptosis is induced by serum and KCl withdrawal and is detected with fluorometric caspase 3 assay
RNA Antisense Purification (RAP) for Mapping RNA Interactions with Chromatin

RNA-centric biochemical purification is a general approach for studying the functions and mechanisms of noncoding RNAs. Here, we describe the experimental procedures for RNA antisense purification (RAP), a method for selective purification of endogenous RNA complexes from cell extracts that enables mapping of RNA interactions with chromatin. In RAP, the user cross-links cells to fix endogenous RNA complexes and purifies these complexes through hybrid capture with biotinylated antisense oligos. DNA loci that interact with the target RNA are identified using high-throughput DNA sequencing
Computational Design of Artificial RNA Molecules For Gene Regulation

This volume provides an overview of RNA bioinformatics methodologies, including basic strategies to predict secondary and tertiary structures, and novel algorithms based on massive RNA sequencing. Interest in RNA bioinformatics has rapidly increased thanks to the recent high-throughput sequencing technologies allowing scientists to investigate complete transcriptomes at single nucleotide resolution. Adopting advanced computational technics, scientists are now able to conduct more in-depth studies and present them to you in this book. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and equipment, step-by-step, readily reproducible bioinformatics protocols, and key tips to avoid known pitfalls.Authoritative and practical, RNA Bioinformatics seeks to aid scientists in the further study of bioinformatics and computational biology of RNA
Drawing and Editing the Secondary Structure(s) of RNA.

International audienceSecondary structure diagrams are essential, in RNA biology, to communicate functional hypotheses and summarize structural data, and communicate them visually as drafts or finalized publication-ready figures. While many tools are currently available to automate the production of such diagrams, their capacities are usually partial, making it hard for a user to decide which to use in a given context. In this chapter, we guide the reader through the steps involved in the production of expressive publication-quality illustrations featuring the RNA secondary structure. We present major existing representations and layouts, and give precise instructions to produce them using available free software, including jViz.RNA, the PseudoViewer, RILogo, R-chie, RNAplot, R2R, and VARNA. We describe the file formats and structural descriptions accepted by popular RNA visualization tools. We also provide command lines and Python scripts to ease the user's access to advanced features. Finally, we discuss and illustrate alternative approaches to visualize the secondary structure in the presence of probing data, pseudoknots, RNA-RNA interactions, and comparative data