pinecone/core-2020-05-10-deduplication huggingface dataset:
Cre/loxP, Flp/FRT Systems and Pluripotent Stem Cell Lines

Cre and FLP recombinases are the most widely used site-specific recombinases in genome engineering. Both are members of the tyrosine class of recombinases and catalyze the reversible, site-specific recombination between two identical sequences of 34 bp length in the absence of accessory factors. The substrate sequences for Cre and Flp recombinases are called loxP and FRT sites respectively. Cre recombinase was discovered in the E. coli bacteriophage P1 where it plays a crucial role in the life cycle of P1 while Flp recombinase was originally derived from the 2 μ circle of Saccharomyces cerevisiae and catalyzes recombination between inverted repeats within the 2 μ plasmid. This chapter shall provide a brief historical perspective on the discovery and early development of the Cre/loxP and FRT/FLP systems citing key studies that paved the way for the application of these site-specific recombination technologies to the engineering of mammalian genomes. Also included are discussions on the mechanisms of Cre/loxP and FRT/FLP systems application of these site-specific recombinase technologies to the introduction of transgenes in human pluripotent stem cells. Certain studies using mouse pluripotent stem cells will also be discussed in order to highlight the possibility of adopting the same strategy in their human counterparts. Lastly, future prospects for these two site-specific recombinases will be presented
Design of new vaccines in the genomic and post-genomic era

During the twentieth century, the introduction of vaccines changed the history of mankind, eliminating most of the childhood diseases that used to cause millions of deaths. However, where conventional vaccinology approaches failed, many new and emerging infectious diseases remain a threat to health worldwide. The advent of whole-genome sequencing and innovation in bioinformatic tools radically changed the way to design and develop new and improved vaccines, starting from the genomic information of a single bacterial or viral isolate, with a process named reverse vaccinology. As the genomic era progressed, reverse vaccinology has evolved in combination with different approaches, such as transcriptomics, metabolomics, structural genomics, proteomics, and immunomics, contributing to the design of new and universal vaccines. Furthermore, the genomic information of the host is increasingly being used to aid understanding of the human immune response to vaccines.Full Tex
Asphalt rubber interlayer benefits in minimizing reflective cracking of overlays over rigid pavements

This paper provides an overview of the asphalt rubber interlayer benefits on reflective crack retardation in overlays over rigid pavements. These interlayers are known in California as asphalt rubber absorbing membrane interlayers (SAMI-R) or as asphalt rubber aggregate membrane interlayers (ARAM-I) chip seals. The paper focuses on the performance in terms of field project reviews, laboratory performance tests and finite element analysis. SAMI-R has been given a reflective cracking equivalent thickness of 15 mm of asphalt rubber hot mix overlays or 30 mm of dense graded hot mix overlays. The finite element analysis confirms the quantified reflective cracking benefits of SAMI-R and provides optimum design alternatives to conventional dense grades asphalt concrete overlays. The paper concludes that SAMI-R is effective in minimizing reflective cracking distress and in extending pavement life
The wonders of flap endonucleases: structure, function, mechanism and regulation

Processing of Okazaki fragments to complete lagging strand DNA synthesis requires coordination among several proteins. RNA primers and DNA synthesised by DNA polymerase α are displaced by DNA polymerase δ to create bifurcated nucleic acid structures known as 5′-flaps. These 5′-flaps are removed by Flap Endonuclease 1 (FEN), a structure-specific nuclease whose divalent metal ion-dependent phosphodiesterase activity cleaves 5′-flaps with exquisite specificity. FENs are paradigms for the 5′ nuclease superfamily, whose members perform a wide variety of roles in nucleic acid metabolism using a similar nuclease core domain that displays common biochemical properties and structural features. A detailed review of FEN structure is undertaken to show how DNA substrate recognition occurs and how FEN achieves cleavage at a single phosphate diester. A proposed double nucleotide unpairing trap (DoNUT) is discussed with regards to FEN and has relevance to the wider 5′ nuclease superfamily. The homotrimeric proliferating cell nuclear antigen protein (PCNA) coordinates the actions of DNA polymerase, FEN and DNA ligase by facilitating the hand-off intermediates between each protein during Okazaki fragment maturation to maximise through-put and minimise consequences of intermediates being released into the wider cellular environment. FEN has numerous partner proteins that modulate and control its action during DNA replication and is also controlled by several post-translational modification events, all acting in concert to maintain precise and appropriate cleavage of Okazaki fragment intermediates during DNA replication.Faculty of Science, Environment, Engineering and TechnologyFull Tex
Dynamic Assessment of Narrative Competence

In Developmental Education, language plays an essential role as a tool for communication (and thinking). Learning to produce coherent messages (“narratives”) with both cultural and personal value in the context of meaningful socio-cultural practices is considered as an important goal of Developmental Education. Narratives are essential for human action as they function as a tool for giving meaning to reality. Therefore, close observation and assessment of children’s narratives is essential in the context of Developmental Education. Over the past years we have developed a Dynamic Assessment (DA) instrument for assessing children’s narrative competence. This instrument combines two common approaches to DA, namely standardised interventionist DA and interactionist DA. With the help of this instrument, teachers are able to gain insight into children’s actual narrative competence as well as their developmental potential and their receptivity to certain forms of assistance to reach this potential. Our experience up to now shows that it is possible to assess children’s narrative competence in a valid and reliable manner
Motion planning for parallel robots with non-holonomic joints

Designing a robot manipulator with fewer actuators than the dimension of its configuration space —to reduce bulk, weight and cost— becomes feasible by introducing mechanical elements that lead to non-holonomic constraints. Unfortunately,\ud
the mechanical advantages of these non-holonomic designs are usually darkened\ud
by the complexity of their control. This paper deals with motion planning for\ud
parallel robots with non-holonomic joints shedding new light on their control strategies.\ud
As a case study, the motion planning problem is solved for a 3-˘UPU parallel robot,where ˘U stands for a non-holonomic joint whose instantaneous kinematics are equivalent to that of a universal joint. It is thus shown how the three prismatic actuators can maneuver to reach any six-degree-of-freedompose of the moving platform.\ud
The motion planning has been addressed as a control problem in the control system\ud
representation of the robot’s kinematics and a motion planning algorithm has been devised based on a Jacobian inversion of the end-point map of the representation.\ud
Performance of the algorithm is illustrated with numeric computations.Preprin
Simplified Voronoi diagrams for motion planning of quadratically-solvable Gough-Stewart platforms

The obstacles in Configuration Space of quadratically-solvable Gough-Stewart platforms, due to both kinematic singularities and collisions, can be uniformly represented by a Boolean combination of signs of 4×4 determinants involving the homogeneous coordinates of sets of four points. This Boolean combination\ud
induces a measure of distance to obstacles in Configuration Space from which a\ud
simplified Voronoi diagram can be derived. Contrary to what happens with standard Voronoi diagrams, this diagram is no longer a strong deformation retract of free space but, as Canny proved in 1987, it is still complete for motion planning. Its main advantage is that it has lower algebraic complexity than standard Voronoi diagrams based on the Euclidean metric.Postprint (author’s final draft
Kinematic synthesis of multi-fingered robotic hands for finite and infinitesimal tasks

In this paper we present a novel method of designing multi-fingered robotic hands using tasks composed of both finite and infinitesimal motion. The method is based on representing the robotic hands as a kinematic chain with a tree topology. We represent finite motion using Clifford algebra and infinitesimal motion using Lie algebra to perform finite dimensional kinematic synthesis of the multifingered\ud
mechanism. This allows tasks to be defined not only by displacements, but also by the velocity and acceleration at different positions for the design of robotic hands. The additional information enables an increased local approximation of the task at critical positions, as well as contact and curvature specifications. An example task is provided using an experimental motion  capture system and we present the design of a robotic hand for the task using a hybrid Genetic Algorithm/Levenberg-Marquadt solver.Peer ReviewedPreprin
Fast Approximate Implicitization of Envelope Curves using Chebyshev
  Polynomials

Consider a rational family of planar rational curves in a certain region of
interest. We are interested in finding an approximation to the implicit
representation of the envelope. Since exact implicitization methods tend to be
very costly, we employ an adaptation of approximate implicitization to envelope
computation. Moreover, by utilizing an orthogonal basis in the construction
process, the computational times can be shortened and the numerical condition
improved. We provide an example to illustrate the performance of our approach.Comment: 8 pages, 6 figure
Planning singularity-free force-feasible paths on the Stewart platform

This paper provides a method for computing force-feasible paths on the Stewart platform. Given two configurations of the platform, the method attempts to connect them through a path that, at any point, allows the platform to counteract any external wrench lying inside a predefined six-dimensional region. In particular, the Jacobian matrix of the manipulator will be full rank along such path, so that the path will not traverse the forward singularity locus at any point. The path is computed by first characterizing the force-feasible C-space of the manipulator as the solution set of a system of equations, and then using a higher-dimensional continuation technique to explore this set systematically from one configuration, until the second configuration is found. Examples are included that demonstrate the performance of the method on illustrative situations.Preprin
Water transport between mortar and brick: the influence of material parameters

This article deals with the phenomenon of the early water transport between fresh mortar and a dry brick. Two bricks with different transport parameters were considered in combination with two different mortars: a lime hydrate mortar and a cement mortar. Water transport was monitored during the first hour after contact using X-ray imaging and simulated using a commercial control volume (CVM)software tool. Such simulations are made possible by a newly developed method to measure transport parameters of fresh mortars. The amount of water leaving the mortar in 1 h depends mostly on two parameters of the mortar: initial and residual water content. The rate of fl ow across the interface shows a complex behaviour and is larger for cement mortar and for strongly absorbing brick. The accuracy of simulations is somewhat limited by the importance of over-capillary effects in the bricks near the interface. It appears that this over-capillary water is partly distributed over the brick, and partly reabsorbed by the mortar.status: publishe
Teachers' instrumental geneses when integrating spreadsheet software

Published version available at: http://link.springer.com/chapter/10.1007/978-94-007-4638-1_11International audienceThe spreadsheet is not a priori a didactical tool for mathematics education. It may progressively become such an instrument through the process of professional geneses on the part of teachers. This chapter describes the beginning of such a genesis, and presents some results concerning teachers' professional development with ICT by examining the outcomes of two different sets of data. Theoretical notions, such as instrumental distance and double instrumental genesis supported the analysis of data leading to a comparison of a teacher integrating spreadsheets for the first time in her practices with the practices of teachers who are more expert with spread-sheets. The similarities found in the ways they use the tool leads to some hypotheses on the importance of these common elements as key issues in teachers' ICT practices
P2P Web service based system for supporting decision-making in cellular manufacturing scheduling

With the increase of the Internet and Virtual Enterprises (VEs), interfaces for web systems and automated services are becoming an emergent necessity. In this paper we propose a Peer-to-peer (P2P) web-based decision-support system for enabling access to different manufacturing scheduling methods, which can be remotely available and accessible from a distributed knowledge base. The XML-based modeling and communication is applied to manufacturing scheduling. Therefore, manufacturing scheduling problems and methods are modeled using XML. The proposed P2P web-based system works as web services, under the SOAP protocol. The system’s distributed knowledge base enables sharing information about scheduling problems and corresponding solving methods in a widened search space, through a scheduling community, integrating a VE. Running several methods enables different results for a given problem, consequently, contributing for a better decision-making. An important aspect is that this knowledge base can be easily and continuously updated by any contributor through the VE. Moreover, through this system once suitable available methods, for a given problem, are identified, it enables running one or more of them, for enabling a better manufacturing scheduling support, enhanced though incorporated fuzzy decision-making proceduresinfo:eu-repo/semantics/publishedVersio
Spontaneous EEG Activity and Biases in Perception of Supra-Threshold Stimuli

Human perception of oriented visual stimuli is biased: some orientations are seen more often than others. We studied how the orientation bias is represented in the electrical brain activity that preceded presentation of ambiguous supra-threshold visual stimuli. We examined scalp EEG over the parieto-occipital regions during 1 sec before stimulus presentation. The alpha activity of pre-stimulus EEG was associated with the orientation bias: the preference for vertical orientation in most observers corresponded to low pre-stimulus alpha power. The results indicate that the orientation bias is encoded in intrinsic properties of ongoing cortical dynamics, forming spontaneous orientation-specific patterns of activity.status: publishe
Transformation elastodynamics and active exterior acoustic cloaking

This chapter consists of three parts. In the first part we recall the
elastodynamic equations under coordinate transformations. The idea is to use
coordinate transformations to manipulate waves propagating in an elastic
material. Then we study the effect of transformations on a mass-spring network
model. The transformed networks can be realized with "torque springs", which
are introduced here and are springs with a force proportional to the
displacement in a direction other than the direction of the spring terminals.
Possible homogenizations of the transformed networks are presented, with
potential applications to cloaking. In the second and third parts we present
cloaking methods that are based on cancelling an incident field using active
devices which are exterior to the cloaked region and that do not generate
significant fields far away from the devices. In the second part, the exterior
cloaking problem for the Laplace equation is reformulated as the problem of
polynomial approximation of analytic functions. An explicit solution is given
that allows to cloak larger objects at a fixed distance from the cloaking
device, compared to previous explicit solutions. In the third part we consider
the active exterior cloaking problem for the Helmholtz equation in 3D. Our
method uses the Green's formula and an addition theorem for spherical outgoing
waves to design devices that mimic the effect of the single and double layer
potentials in Green's formula.Comment: Submitted as a chapter for the volume "Acoustic metamaterials:
  Negative refraction, imaging, lensing and cloaking", Craster and Guenneau
  ed., Springe
Viral integration and consequences on host gene expression

Upon cell infection, some viruses integrate their genome into the host
chromosome, either as part of their life cycle (such as retroviruses), or incidentally.
While possibly promoting long-term persistence of the virus into the cell, viral
genome integration may also lead to drastic consequences for the host cell, including
gene disruption, insertional mutagenesis and cell death, as well as contributing to
species evolution. This review summarizes the current knowledge on viruses integrating
their genome into the host genome and the consequences for the host cell
Hierarchical Needs, Income Comparisons and Happiness Levels

The cornerstone of the hierarchical approach is that there are some basic human needs which must be satisfied before non-basic needs come into the picture. The hierarchical structure of needs implies that the satisfaction of primary needs provides substantial increases to individual happiness compared to the subsequent satisfaction of secondary needs. This idea can be combined with the concept of comparison income which means that individuals compare rewards with individuals with similar characteristics.  These two notions could provide additional explanations   of empirical findings indicating a positive relationship between income and happiness up to certain level of income
Nonlinear thermoelectric response of quantum dots: renormalized dual
  fermions out of equilibrium

The thermoelectric transport properties of nanostructured devices continue to
attract attention from theorists and experimentalist alike as the spatial
confinement allows for a controlled approach to transport properties of
correlated matter. Most of the existing work, however, focuses on
thermoelectric transport in the linear regime despite the fact that the
nonlinear conductance of correlated quantum dots has been studied in some
detail throughout the last decade. Here, we review our recent work on the
effect of particle-hole asymmetry on the nonlinear transport properties in the
vicinity of the strong coupling limit of Kondo-correlated quantum dots and
extend the underlying method, a renormalized superperturbation theory on the
Keldysh contour, to the thermal conductance in the nonlinear regime. We
determine the charge, energy, and heat current through the nanostructure and
study the nonlinear transport coefficients, the entropy production, and the
fate of the Wiedemann-Franz law in the non-thermal steady-state. Our approach
is based on a renormalized perturbation theory in terms of dual fermions around
the particle-hole symmetric strong-coupling limit.Comment: chapter contributed to 'New Materials for Thermoelectric
  Applications: Theory and Experiment' Springer Series: NATO Science for Peace
  and Security Series - B: Physics and Biophysics, Veljko Zlatic (Editor), Alex
  Hewson (Editor). ISBN: 978-9400749863 (2012
Nernst effect of iron pnictide and cuprate superconductors: signatures
  of spin density wave and stripe order

The Nernst effect has recently proven a sensitive probe for detecting unusual
normal state properties of unconventional superconductors. In particular, it
may sensitively detect Fermi surface reconstructions which are connected to a
charge or spin density wave (SDW) ordered state, and even fluctuating forms of
such a state. Here we summarize recent results for the Nernst effect of the
iron pnictide superconductor $\rm LaO_{1-x}F_xFeAs$, whose ground state evolves
upon doping from an itinerant SDW to a superconducting state, and the cuprate
superconductor $\rm La_{1.8-x}Eu_{0.2}Sr_xCuO_4$ which exhibits static stripe
order as a ground state competing with the superconductivity. In $\rm
LaO_{1-x}F_xFeAs$, the SDW order leads to a huge Nernst response, which allows
to detect even fluctuating SDW precursors at superconducting doping levels
where long range SDW order is suppressed. This is in contrast to the impact of
stripe order on the normal state Nernst effect in $\rm
La_{1.8-x}Eu_{0.2}Sr_xCuO_4$. Here, though signatures of the stripe order are
detectable in the temperature dependence of the Nernst coefficient, its overall
temperature dependence is very similar to that of $\rm La_{2-x}Sr_xCuO_4$,
where stripe order is absent. The anomalies which are induced by the stripe
order are very subtle and the enhancement of the Nernst response due to static
stripe order in $\rm La_{1.8-x}Eu_{0.2}Sr_xCuO_4$ as compared to that of the
pseudogap phase in $\rm La_{2-x}Sr_xCuO_4$, if any, is very small.Comment: To appear in: 'Properties and applications of thermoelectric
  materials - II', V. Zlatic and A. Hewson, editors, Proceedings of NATO
  Advanced Research Workshop, Hvar, Croatia, September 19 -25, 2011, NATO
  Science for Peace and Security Series B: Physics and Biophysics, (Springer
  Science+Business Media B.V. 2012
The Out-of-Equilibrium Time-Dependent Gutzwiller Approximation

We review the recently proposed extension of the Gutzwiller approximation, M.
Schiro' and M. Fabrizio, Phys. Rev. Lett. 105, 076401 (2010), designed to
describe the out-of-equilibrium time-evolution of a Gutzwiller-type variational
wave function for correlated electrons. The method, which is strictly
variational in the limit of infinite lattice-coordination, is quite general and
flexible, and it is applicable to generic non-equilibrium conditions, even far
beyond the linear response regime. As an application, we discuss the quench
dynamics of a single-band Hubbard model at half-filling, where the method
predicts a dynamical phase transition above a critical quench that resembles
the sharp crossover observed by time-dependent dynamical mean field theory. We
next show that one can actually define in some cases a multi-configurational
wave function combination of a whole set of mutually orthogonal Gutzwiller wave
functions. The Hamiltonian projected in that subspace can be exactly evaluated
and is equivalent to a model of auxiliary spins coupled to non-interacting
electrons, closely related to the slave-spin theories for correlated electron
models. The Gutzwiller approximation turns out to be nothing but the mean-field
approximation applied to that spin-fermion model, which displays, for any
number of bands and integer fillings, a spontaneous $Z_2$ symmetry breaking
that can be identified as the Mott insulator-to-metal transition.Comment: 25 pages. Proceedings of the Hvar 2011 Workshop on 'New materials for
  thermoelectric applications: theory and experiment