pinecone/core-2020-05-10-deduplication huggingface dataset:
A Principle to Determine the Number (3 + 1) of Large Spacetime
  Dimensions

We assume that our universe originated from highly excited and interacting
strings with coupling constant g_s = {\cal O} (1). Fluctuations of spacetime
geometry are large in such strings and the physics dictating the emergence of a
final spacetime configuration is not known. We propose that, nevertheless, it
is determined by an entropic principle that the final spacetime configuration
must have maximum entropy for a given amount of energy. This principle implies,
under some assumptions, that the spacetime configuration that emerges finally
is a (3 + 1) -- dimensional FRW universe filled with w = 1 perfect fluid and
with 6 -- dimensional compact space of size l_s; in particular, the number of
large spacetime dimensions is d = 3 + 1. Such an universe may evolve
subsequently into our universe, perhaps as in Banks -- Fischler scenario.Comment: 11 pages. Latex file. Version 2: References adde
The problem of completeness for Gromov-Hausdorff metrics on C*-algebras

It is proved that the family of equivalence classes of Lip-normed C*-algebras
introduced by M. Rieffel, up to isomorphisms preserving the Lip-seminorm, is
not complete w.r.t. the matricial quantum Gromov-Hausdorff distance introduced
by D. Kerr. This is shown by exhibiting a Cauchy sequence whose limit, which
always exists as an operator system, is not completely order isomorphic to any
C*-algebra.
  Conditions ensuring the existence of a C*-structure on the limit are
considered, making use of the notion of ultraproduct. More precisely, a
necessary and sufficient condition is given for the existence, on the limiting
operator system, of a C*-product structure inherited from the approximating
C*-algebra. Such condition can be considered as a generalisation of the
f-Leibniz conditions introduced by Kerr and Li. Furthermore, it is shown that
our condition is not necessary for the existence of a C*-structure tout court,
namely there are cases in which the limit is a C*-algebra, but the C*-structure
is not inherited.Comment: 31 pages. Accepted for publication in Journal of Functional Analysi
A C*-algebra of geometric operators on self-similar CW-complexes.
  Novikov-Shubin and L^2-Betti numbers

A class of CW-complexes, called self-similar complexes, is introduced,
together with C*-algebras A_j of operators, endowed with a finite trace, acting
on square-summable cellular j-chains. Since the Laplacian Delta_j belongs to
A_j, L^2-Betti numbers and Novikov-Shubin numbers are defined for such
complexes in terms of the trace. In particular a relation involving the
Euler-Poincare' characteristic is proved. L^2-Betti and Novikov-Shubin numbers
are computed for some self-similar complexes arising from self-similar
fractals.Comment: 30 pages, 7 figure
Scattering of positronium by H, He, Ne, and Ar

The low-energy scattering of ortho positronium (Ps) by H, He, Ne, and Ar
atoms has been investigated in the coupled-channel framework by using a
recently proposed time-reversal-symmetric nonlocal electron-exchange model
potential with a single parameter $C$. For H and He we use a three-Ps-state
coupled-channel model and for Ar and Ne we use a static-exchange model. The
sensitivity of the results is studied with respect to the parameter $C$.
Present low-energy cross sections for He, Ne and Ar are in good agreement with
experiment.Comment: 8 pages Latex with 4 postscript figure
Invariants for 1-dimensional cohomology classes arising from TQFT

Let $(V,Z)$ be a Topological Quantum Field Theory over a field $f$ defined on
a cobordism category whose morphisms are oriented $n+1$-manifolds perhaps with
extra structure. Let $(M,\chi)$ be a closed oriented $n+1$-manifold $M$ with
this extra structure together with $\chi \in H^1(M).$ Let $M_{\infty}$ denote
the infinite cyclic cover of $M$ given by $\chi.$ Consider a fundamental domain
$E$ for the action of the integers on $M_{\infty}$ bounded by lifts of a
surface $\Sigma$ dual to $\chi,$ and in general position. $E$ can be viewed as
a cobordism from $\Sigma$ to itself. We give Turaev and Viro's proof of their
theorem that the similarity class of the non-nilpotent part of $Z(E)$ is an
invariant. We give a method to calculate this invariant for the $(V_p,Z_p)$
theories of Blanchet,Habegger, Masbaum and Vogel when $M$ is zero framed
surgery to $S^3$ along a knot K. We give a formula for this invariant when $K$
is a twisted double of another knot. We obtain formulas for the quantum
invariants of branched covers of knots, and unbranched covers of 0-surgery to
$S^3$ along knots.Comment: 38 pages, in AmS-TeX- Version 2.1 , needs epsf.tex, decode figures.uu
  file to get fig1.eps through fig10.eps. This version corrects and improves
  the discussion of when p is ordinary with respect to n (on page 15), updates
  references, and includes other minor change
The Physical Implementation of Quantum Computation

After a brief introduction to the principles and promise of quantum
information processing, the requirements for the physical implementation of
quantum computation are discussed. These five requirements, plus two relating
to the communication of quantum information, are extensively explored and
related to the many schemes in atomic physics, quantum optics, nuclear and
electron magnetic resonance spectroscopy, superconducting electronics, and
quantum-dot physics, for achieving quantum computing.Comment: Prepared for Fortschritte der Physik special issue, Experimental
  Proposals for Quantum Computation. Version 2: many small corrections. Version
  3: more small corrections & references adde
Discrimination between nonorthogonal two-photon polarization states

It is shown that generalized measurements, required for optimally
discriminating between nonorthogonal joint polarization states of two
indistinguishable photons, can be realized with the help of
polarization-dependent two-photon absorption and by means of sum-frequency
generation. Optimization schemes are investigated with respect to minimizing
the error probability in inferring the states, as well as with respect to
maximizing the probability of success for unambiguous discrimination. Moreover,
an implementation of error-minimizing discrimination between N symmetric
single-photon states is studied. The latter can be used to extract information
from the inconclusive results occurring in unambiguous discrimination between
three symmetric two-photon polarization states.Comment: 7 pages, submitted for the Proceedings of the 8th Central-European
  Workshop on Quantum Optics, April 27 - 30, 200
Quantum mechanics from a Heisenberg-type equality

The usual Heisenberg uncertainty relation for position and momentum may be
replaced by an exact equality, for suitably chosen measures of position and
momentum uncertainty. This "exact" uncertainty relation is valid for_all_ pure
states, and is sufficiently strong to provide an axiomatic basis for moving
from classical mechanics to quantum mechanics. In particular, the assumption of
a nonclassical momentum fluctuation, having a strength which scales inversely
with uncertainty in position, leads from the classical equations of motion to
the Schroedinger equation.Comment: Latex, 6 pages, contribution to the symposium "100 Years of Werner
  Heisenberg - Works and Impact" in Bamberg, to appear in Fortschritte der
  Physi
Mapping differential interactomes by affinity purification coupled with data independent mass spectrometry acquisition

Characterizing changes in protein-protein interactions associated with sequence variants (e.g. disease-associated mutations or splice forms) or following exposure to drugs, growth factors or hormones is critical to understanding how protein complexes are built, localized and regulated. Affinity purification (AP) coupled with mass spectrometry permits the analysis of protein interactions under near-physiological conditions, yet monitoring interaction changes requires the development of a robust and sensitive quantitative approach, especially for large-scale studies where cost and time are major considerations. To this end, we have coupled AP to data-independent mass spectrometric acquisition (SWATH), and implemented an automated data extraction and statistical analysis pipeline to score modulated interactions. Here, we use AP-SWATH to characterize changes in protein-protein interactions imparted by the HSP90 inhibitor NVP-AUY922 or melanoma-associated mutations in the human kinase CDK4. We show that AP-SWATH is a robust label-free approach to characterize such changes, and propose a scalable pipeline for systems biology studies
Discovery of non-directional and directional pioneer transcription factors by modeling DNase profile magnitude and shape

Here we describe Protein Interaction Quantitation (PIQ), a computational method that models the magnitude and shape of genome-wide DNase profiles to facilitate the identification of transcription factor (TF) binding sites. Through the use of machine learning techniques, PIQ identified binding sites for >700 TFs from one DNase-seq experiment with accuracy comparable to ChIP-seq for motif-associated TFs (median AUC=0.93 across 303 TFs). We applied PIQ to analyze DNase-seq data from mouse embryonic stem cells differentiating into pre-pancreatic and intestinal endoderm. We identified (n=120) and experimentally validated eight ‘pioneer’ TF families that dynamically open chromatin, enabling other TFs to bind to adjacent DNA. Four pioneer TF families only open chromatin in one direction from their motifs. Furthermore, we identified a class of ‘settler’ TFs whose genomic binding is principally governed by proximity to open chromatin. Our results support a model of hierarchical TF binding in which directional and non-directional pioneer activity shapes the chromatin landscape for population by settler TFs
Relationships, Expertise, Incentives, and Governance: Supporting Care Home Residents' Access to Health Care :
                    An interview study from England

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)Objectives: To explore what commissioners of care, regulators, providers and care home residents in England identify as the key mechanisms or components of different service delivery models that support the provision of NHS services to independent care homes. Methods: Qualitative, semi-structured interviews with a purposive sample of people with direct experience of commissioning, providing and regulating health care provision in care homes and care home residents. Data from interviews were augmented by a secondary analysis of previous interviews with care home residents on their personal experience of and priorities for access to health care. Analysis was framed by the assumptions of realist evaluation and drew on the constant comparative method to identify key themes about what is required to achieve quality health care provision to care homes and resident health. Results: Participants identified three overlapping approaches to the provision of National Health Services (NHS) that they believed supported access to health care for older people in care homes. These were: 1. Investment in relational working that fostered continuity and shared learning between visiting NHS staff and care home staff; 2. The provision of age appropriate clinical services and; 3. Governance arrangements that used contractual and financial incentives to specify a minimum service that care homes should receive. Conclusion: The three approaches, and how they were typified as working, provide a rich picture of the stakeholder perspectives and the underlying assumptions about how service delivery models should work with care homes. The findings inform how evidence on effective working in care homes will be interrogated to identify how different approaches, or specifically key elements of those approaches, achieve different health-related outcomes in different situations for residents and associated health and social care organisation
Evolutionary connectionism: algorithmic principles underlying the evolution of biological organisation in evo-devo, evo-eco and evolutionary transitions

The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term “evolutionary connectionism” to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary systems and modify the adaptive capabilities of natural selection over time. We review the evidence supporting the functional equivalences between the domains of learning and of evolution, and discuss the potential for this to resolve conceptual problems in our understanding of the evolution of developmental, ecological and reproductive organisations and, in particular, the major evolutionary transitions
Menopause as a predictor of new-onset asthma

<p>Background: There is limited and conflicting evidence on the effect of menopause on asthma.</p> <p>Objectives: We sought to study whether the incidence of asthma and respiratory symptoms differ by menopausal status in a longitudinal population-based study with an average follow-up of 12 years.</p> <p>Methods: The Respiratory Health in Northern Europe study provided questionnaire data pertaining to respiratory and reproductive health at baseline (1999-2001) and follow-up (2010-2012). The study cohort included women aged 45 to 65 years at follow-up, without asthma at baseline, and not using exogenous hormones (n 5 2322). Menopausal status was defined as nonmenopausal, transitional, early postmenopausal, and late postmenopausal. Associations with asthma (defined by the use of asthma medication, having asthma attacks, or both) and respiratory symptoms scores were analyzed by using logistic (asthma) and negative binomial (respiratory symptoms) regressions, adjusting for age, body mass index, physical activity, smoking, education, and study center.</p> <p>Results: The odds of new-onset asthma were increased in women who were transitional (odds ratio, 2.40; 95% CI, 1.09-5.30), early postmenopausal (odds ratio, 2.11; 95% CI,1.06-4.20), and late postmenopausal (odds ratio, 3.44; 95% CI, 1.31-9.05) at follow-up compared with nonmenopausal women. The risk of respiratory symptoms increased in early postmenopausal (coefficient, 0.40; 95% CI, 0.06-0.75) and late postmenopausal (coefficient, 0.69; 95% CI, 0.15-1.23) women. These findings were consistent irrespective of smoking status and across study centers.</p> <p>Conclusions: New-onset asthma and respiratory symptoms increased in women becoming postmenopausal in a longitudinal population-based study. Clinicians should be aware that respiratory health might deteriorate in women during reproductive aging. (J Allergy Clin Immunol 2016;137:50-7.)</p
Suppression of charged particle production at large transverse momentum in central Pb–Pb collisions at √sNN = 2.76 TeV

Inclusive transverse momentum spectra of primary charged particles in Pb–Pb collisions at √sNN = 2.76 TeV have been measured by the ALICE Collaboration at the LHC. The data are presented for central and peripheral collisions, corresponding to 0–5% and 70–80% of the hadronic Pb–Pb cross section. The measured charged particle spectra in |η| &lt; 0.8 and 0.3 &lt; pT &lt; 20 GeV/c are compared to the expectation in pp collisions at the same √sNN, scaled by the number of underlying nucleon–nucleon collisions. The comparison is expressed in terms of the nuclear modification factor RAA. The result indicates only weak medium effects (RAA ≈ 0.7) in peripheral collisions. In central collisions, RAA reaches a minimum of about 0.14 at pT = 6–7 GeV/c and increases significantly at larger pT . The measured suppression of high-pT particles is stronger than that observed at lower collision energies, indicating that a very dense medium is formed in central Pb–Pb collisions at the LHC
From d logs to dilogs; the super Yang-Mills MHV amplitude revisited

Recently, loop integrands for certain Yang-Mills scattering amplitudes and correlation functions have been shown to be systematically expressible in d log form, raising the possibility that these loop integrals can be performed directly without Feynman parameters. We do so here to give a new description of the planar 1-loop MHV amplitude in $ \mathcal{N} $ = 4 super Yang-Mills theory. We explicitly incorporate the standard Feynman iϵ prescription into the integrands. We find that the generic MHV diagram contributing to the 1-loop MHV amplitude, known as Kermit, is dual conformal invariant up to the choice of reference twistor explicit in our axial gauge (the generic MHV diagram was already known to be finite). The new formulae for the amplitude are nontrivially related to previous ones in the literature. The divergent diagrams are evaluated using mass regularization. Our techniques extend directly to higher loop diagrams, and we illustrate this by sketching the evaluation of a non-trivial 2-loop example. We expect this to lead to a simple and efficient method for computing amplitudes and correlation functions with less supersymmetry and without the assumption of planarity
AdS 3 / CFT 2 , finite-gap equations and massless modes

It is known that string theory on AdS 3 × M 7 backgrounds, where M 7 = S 3 × S 3 × S 1 or S 3 × T 4 , is classically integrable. This integrability has been previously used to write down a set of integral equations, known as the finite-gap equations. These equations can be solved for the closed string spectrum of the theory. However, it has been known for some time that the finite-gap equations on these AdS 3 × M 7 backgrounds do not capture the dynamics of the massless modes of the closed string theory. In this paper we re-examine the derivation of the AdS 3 × M 7 finite-gap system. We find that the conditions that had previously been imposed on these integral equations in order to implement the Virasoro constraints are too strict, and are in fact not required. We identify the correct implementation of the Virasoro constraints on finite-gap equations and show that this new, less restrictive condition captures the complete closed string spectrum on AdS 3 × M 7
DYRK1A binds to an evolutionarily conserved WD40-repeat protein WDR68 and induces its nuclear translocation.

DYRK1A is encoded in the Down's syndrome critical region on human chromosome 21, and plays an important role in the functional and developmental regulation of many types of cells, including neuronal cells. Here we have identified WDR68, an evolutionarily conserved protein with WD40-repeat domains, as a cellular binding partner of DYRK1A. WDR68 was originally identified in petunia as AN11 that controls the pigmentation of flowers by stimulating the transcription of anthocyanin biosynthetic genes. Experiments with RNA interference showed that WDR68 was indispensable for the optimal proliferation and survival of mammalian cultured cell, and WDR68 depletion induced cell apoptosis. DYRK1A and DYRK1B, but not DYRK2, DYRK3, or DYRK4, bound to endogenous and expressed WDR68. The N-terminal domain, but not the catalytic kinase domain or the C-terminal domain of DYRK1A, was responsible for the WDR68 binding. Deletions in the N-terminal or C-terminal region outside of the central WD40-repeats of WDR68 abolished its binding to DYRK1A, suggesting that WD40 repeats are not sufficient for the association with DYRK1A. Immunofluorescent staining revealed that WDR68 was distributed throughout the cell. Importantly, nuclear accumulation of WDR68 was observed upon co-expression of the wild type and a kinase-dead mutant of DYRK1A. Taken together, these results suggest that DYRK1A binds specifically to WDR68 in cells, and that the binding, but not the phosphorylation event, induces the nuclear translocation of WDR68
Sal-like 4 (SALL4) suppresses CDH1 expression and maintains cell dispersion in basal-like breast cancer.

In cell cultures, the dispersed phenotype is indicative of the migratory ability. Here we characterized Sal-like 4 (SALL4) as a dispersion factor in basal-like breast cancer. Our shRNA-mediated SALL4 knockdown system and SALL4 overexpression system revealed that SALL4 suppresses the expression of adhesion gene CDH1, and positively regulates the CDH1 suppressor ZEB1. Cell behavior analyses showed that SALL4 suppresses intercellular adhesion and maintains cell motility after cell-cell interaction and cell division, which results in the dispersed phenotype. Our findings indicate that SALL4 functions to suppress CDH1 expression and to maintain cell dispersion in basal-like breast cancer