3,145 research outputs found
Stellar spectroscopy: Fermions and holographic Lifshitz criticality
Electron stars are fluids of charged fermions in Anti-de Sitter spacetime.
They are candidate holographic duals for gauge theories at finite charge
density and exhibit emergent Lifshitz scaling at low energies. This paper
computes in detail the field theory Green's function G^R(w,k) of the
gauge-invariant fermionic operators making up the star. The Green's function
contains a large number of closely spaced Fermi surfaces, the volumes of which
add up to the total charge density in accordance with the Luttinger count.
Excitations of the Fermi surfaces are long lived for w <~ k^z. Beyond w ~ k^z
the fermionic quasiparticles dissipate strongly into the critical Lifshitz
sector. Fermions near this critical dispersion relation give interesting
contributions to the optical conductivity.Comment: 38 pages + appendices. 9 figure
Categorical Dimensions of Human Odor Descriptor Space Revealed by Non-Negative Matrix Factorization
In contrast to most other sensory modalities, the basic perceptual dimensions of olfaction remain unclear. Here, we use non-negative matrix factorization (NMF) – a dimensionality reduction technique – to uncover structure in a panel of odor profiles, with each odor defined as a point in multi-dimensional descriptor space. The properties of NMF are favorable for the analysis of such lexical and perceptual data, and lead to a high-dimensional account of odor space. We further provide evidence that odor dimensions apply categorically. That is, odor space is not occupied homogenously, but rather in a discrete and intrinsically clustered manner. We discuss the potential implications of these results for the neural coding of odors, as well as for developing classifiers on larger datasets that may be useful for predicting perceptual qualities from chemical structures
Antimalarial 4(1H)-pyridones bind to the Qisite of cytochromebc1
Cytochrome bc1 is a proven drug target in the prevention and treatment of malaria. The rise in drug-resistant strains of Plasmodium falciparum, the organism responsible for malaria, has generated a global effort in designing new classes of drugs. Much of the design/redesign work on overcoming this resistance has been focused on compounds that are presumed to bind the Qo site (one of two potential binding sites within cytochrome bc1) using the known crystal structure of this large membrane-bound macromolecular complex via in silico modeling. Cocrystallization of the cytochrome bc1 complex with the 4(1H)-pyridone class of inhibitors, GSK932121 and GW844520, that have been shown to be potent antimalarial agents in vivo, revealed that these inhibitors do not bind at the Qo site but bind at the Qi site. The discovery that these compounds bind at the Qi site may provide a molecular explanation for the cardiotoxicity and eventual failure of GSK932121 in phase-1 clinical trial and highlight the need for direct experimental observation of a compound bound to a target site before chemical optimization and development for clinical trials. The binding of the 4(1H)-pyridone class of inhibitors to Qi also explains the ability of this class to overcome parasite Qo-based atovaquone resistance and provides critical structural information for future design of new selective compounds with improved safety profiles
Incremental dimension reduction of tensors with random index
We present an incremental, scalable and efficient dimension reduction
technique for tensors that is based on sparse random linear coding. Data is
stored in a compactified representation with fixed size, which makes memory
requirements low and predictable. Component encoding and decoding are performed
on-line without computationally expensive re-analysis of the data set. The
range of tensor indices can be extended dynamically without modifying the
component representation. This idea originates from a mathematical model of
semantic memory and a method known as random indexing in natural language
processing. We generalize the random-indexing algorithm to tensors and present
signal-to-noise-ratio simulations for representations of vectors and matrices.
We present also a mathematical analysis of the approximate orthogonality of
high-dimensional ternary vectors, which is a property that underpins this and
other similar random-coding approaches to dimension reduction. To further
demonstrate the properties of random indexing we present results of a synonym
identification task. The method presented here has some similarities with
random projection and Tucker decomposition, but it performs well at high
dimensionality only (n>10^3). Random indexing is useful for a range of complex
practical problems, e.g., in natural language processing, data mining, pattern
recognition, event detection, graph searching and search engines. Prototype
software is provided. It supports encoding and decoding of tensors of order >=
1 in a unified framework, i.e., vectors, matrices and higher order tensors.Comment: 36 pages, 9 figure
Holographic Josephson Junctions and Berry holonomy from D-branes
We construct a holographic model for Josephson junctions with a defect system
of a Dp brane intersecting a D(p+2) brane. In addition to providing a
geometrical picture for the holographic dual, this leads us very naturally to
suggest the possibility of non-Abelian Josephson junctions characterized in
terms of the topological properties of the branes. The difference between the
locations of the endpoints of the Dp brane on either side of the defect
translates into the phase difference of the condensate in the Josephson
junction. We also add a magnetic flux on the D(p+2) brane and allow it evolve
adiabatically along a closed curve in the space of the magnetic flux, while
generating a non-trivial Berry holonomy.Comment: 20 pages, 2 figure
Reliability of Eye Tracking and Pupillometry Measures in Individuals with Fragile X Syndrome
Recent insight into the underlying molecular and cellular mechanisms of fragile X syndrome (FXS) has led to the proposal and development of new pharmaceutical treatment strategies, and the initiation of clinical trials aimed at correcting core symptoms of the developmental disorder. Consequently, there is an urgent and critical need for outcome measures that are valid for quantifying specific symptoms of FXS and that are consistent across time. We used eye tracking to evaluate test–retest reliability of gaze and pupillometry measures in individuals with FXS and we demonstrate that these measures are viable options for assessing treatment-specific outcomes related to a core behavioral feature of the disorder
Gauge-theoretic invariants for topological insulators: A bridge between Berry, Wess-Zumino, and Fu-Kane-Mele
We establish a connection between two recently-proposed approaches to the
understanding of the geometric origin of the Fu-Kane-Mele invariant
, arising in the context of 2-dimensional
time-reversal symmetric topological insulators. On the one hand, the
invariant can be formulated in terms of the Berry connection and
the Berry curvature of the Bloch bundle of occupied states over the Brillouin
torus. On the other, using techniques from the theory of bundle gerbes it is
possible to provide an expression for containing the square root
of the Wess-Zumino amplitude for a certain -valued field over the
Brillouin torus.
We link the two formulas by showing directly the equality between the above
mentioned Wess-Zumino amplitude and the Berry phase, as well as between their
square roots. An essential tool of independent interest is an equivariant
version of the adjoint Polyakov-Wiegmann formula for fields , of which we provide a proof employing only basic homotopy theory and
circumventing the language of bundle gerbes.Comment: 23 pages, 1 figure. To appear in Letters in Mathematical Physic
Caspase-2 is upregulated after sciatic nerve transection and its inhibition protects dorsal root ganglion neurons from Apoptosis after serum withdrawal
Sciatic nerve (SN) transection-induced apoptosis of dorsal root ganglion neurons (DRGN) is one factor determining the efficacy of peripheral axonal regeneration and the return of sensation. Here, we tested the hypothesis that caspase-2(CASP2) orchestrates apoptosis of axotomised DRGN both in vivo and in vitro by disrupting the local neurotrophic supply to DRGN. We observed significantly elevated levels of cleaved CASP2 (C-CASP2), compared to cleaved caspase-3 (C-CASP3), within TUNEL+DRGN and DRG glia (satellite and Schwann cells) after SN transection. A serum withdrawal cell culture model, which induced 40% apoptotic death in DRGN and 60% in glia, was used to model DRGN loss after neurotrophic factor withdrawal. Elevated C-CASP2 and TUNEL were observed in both DRGN and DRG glia, with C-CASP2 localisation shifting from the cytosol to the nucleus, a required step for induction of direct CASP2-mediated apoptosis. Furthermore, siRNAmediated downregulation of CASP2 protected 50% of DRGN from apoptosis after serum withdrawal, while downregulation of CASP3 had no effect on DRGN or DRG glia survival. We conclude that CASP2 orchestrates the death of SN-axotomised DRGN directly and also indirectly through loss of DRG glia and their local neurotrophic factor support. Accordingly, inhibiting CASP2 expression is a potential therapy for improving both the SN regeneration response and peripheral sensory recovery
Protecting Clinical Trial Participants and Protecting Data Integrity: Are We Meeting the Challenges?
Susan Ellenberg discusses alternative approaches towards evaluating data as it accumulates in clinical trials, and to protecting the integrity and preventing undue risks to participants, as the trial continues
Interferon regulatory factor 8-deficiency determines massive neutrophil recruitment but T cell defect in fast growing granulomas during tuberculosis
Following Mycobacterium tuberculosis (Mtb) infection, immune cell recruitment in lungs is pivotal in establishing protective immunity through granuloma formation and neogenesis of lymphoid structures (LS). Interferon regulatory factor-8 (IRF-8) plays an important role in host defense against Mtb, although the mechanisms driving anti-mycobacterial immunity remain unclear. In this study, IRF-8 deficient mice (IRF-8−/−) were aerogenously infected with a low-dose Mtb Erdman virulent strain and the course of infection was compared with that induced in wild-type (WT-B6) counterparts. Tuberculosis (TB) progression was examined in both groups using pathological, microbiological and immunological parameters. Following Mtb exposure, the bacterial load in lungs and spleens progressed comparably in the two groups for two weeks, after which IRF-8−/− mice developed a fatal acute TB whereas in WT-B6 the disease reached a chronic stage. In lungs of IRF-8−/−, uncontrolled growth of pulmonary granulomas and impaired development of LS were observed, associated with unbalanced homeostatic chemokines, progressive loss of infiltrating T lymphocytes and massive prevalence of neutrophils at late infection stages. Our data define IRF-8 as an essential factor for the maintenance of proper immune cell recruitment in granulomas and LS required to restrain Mtb infection. Moreover, IRF-8−/− mice, relying on a common human and mouse genetic mutation linked to susceptibility/severity of mycobacterial diseases, represent a valuable model of acute TB for comparative studies with chronically-infected congenic WT-B6 for dissecting protective and pathological immune reactions
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