197 research outputs found
Analytical approximation for the structure of differentially rotating barotropes
Approximate analytical formula for density distribution in differentially
rotating stars is derived. Any barotropic EOS and conservative rotation law can
be handled with use of this method for wide range of differential rotation
strength. Results are in good qualitative agreement with comparison to the
other methods. Some applications are suggested and possible improvements of the
formula are discussed.Comment: 10 pages, 13 figures, accepted for publication in Monthly Notice
BlinkML: Efficient Maximum Likelihood Estimation with Probabilistic Guarantees
The rising volume of datasets has made training machine learning (ML) models
a major computational cost in the enterprise. Given the iterative nature of
model and parameter tuning, many analysts use a small sample of their entire
data during their initial stage of analysis to make quick decisions (e.g., what
features or hyperparameters to use) and use the entire dataset only in later
stages (i.e., when they have converged to a specific model). This sampling,
however, is performed in an ad-hoc fashion. Most practitioners cannot precisely
capture the effect of sampling on the quality of their model, and eventually on
their decision-making process during the tuning phase. Moreover, without
systematic support for sampling operators, many optimizations and reuse
opportunities are lost.
In this paper, we introduce BlinkML, a system for fast, quality-guaranteed ML
training. BlinkML allows users to make error-computation tradeoffs: instead of
training a model on their full data (i.e., full model), BlinkML can quickly
train an approximate model with quality guarantees using a sample. The quality
guarantees ensure that, with high probability, the approximate model makes the
same predictions as the full model. BlinkML currently supports any ML model
that relies on maximum likelihood estimation (MLE), which includes Generalized
Linear Models (e.g., linear regression, logistic regression, max entropy
classifier, Poisson regression) as well as PPCA (Probabilistic Principal
Component Analysis). Our experiments show that BlinkML can speed up the
training of large-scale ML tasks by 6.26x-629x while guaranteeing the same
predictions, with 95% probability, as the full model.Comment: 22 pages, SIGMOD 201
APAF1 is a key transcriptional target for p53 in the regulation of neuronal cell death
p53 is a transcriptional activator which has been implicated as a key regulator of neuronal cell death after acute injury. We have shown previously that p53-mediated neuronal cell death involves a Bax-dependent activation of caspase 3; however, the transcriptional targets involved in the regulation of this process have not been identified. In the present study, we demonstrate that p53 directly upregulates Apaf1 transcription as a critical step in the induction of neuronal cell death. Using DNA microarray analysis of total RNA isolated from neurons undergoing p53-induced apoptosis a 5â6-fold upregulation of Apaf1 mRNA was detected. Induction of neuronal cell death by camptothecin, a DNA-damaging agent that functions through a p53-dependent mechanism, resulted in increased Apaf1 mRNA in p53-positive, but not p53-deficient neurons. In both in vitro and in vivo neuronal cell death processes of p53-induced cell death, Apaf1 protein levels were increased. We addressed whether p53 directly regulates Apaf1 transcription via the two p53 consensus binding sites in the Apaf1 promoter. Electrophoretic mobility shift assays demonstrated p53âDNA binding activity at both p53 consensus binding sequences in extracts obtained from neurons undergoing p53-induced cell death, but not in healthy control cultures or when p53 or the p53 binding sites were inactivated by mutation. In transient transfections in a neuronal cell line with p53 and Apaf1 promoterâluciferase constructs, p53 directly activated the Apaf1 promoter via both p53 sites. The importance of Apaf1 as a p53 target gene in neuronal cell death was evaluated by examining p53-induced apoptotic pathways in primary cultures of Apaf1-deficient neurons. Neurons treated with camptothecin were significantly protected in the absence of Apaf1 relative to those derived from wild-type littermates. Together, these results demonstrate that Apaf1 is a key transcriptional target for p53 that plays a pivotal role in the regulation of apoptosis after neuronal injury
On the alleged simplicity of impure proof
Roughly, a proof of a theorem, is âpureâ if it draws only on what is âcloseâ or âintrinsicâ to that theorem. Mathematicians employ a variety of terms to identify pure proofs, saying that a pure proof is one that avoids what is âextrinsic,â âextraneous,â âdistant,â âremote,â âalien,â or âforeignâ to the problem or theorem under investigation. In the background of these attributions is the view that there is a distance measure (or a variety of such measures) between mathematical statements and proofs. Mathematicians have paid little attention to specifying such distance measures precisely because in practice certain methods of proof have seemed self- evidently impure by design: think for instance of analytic geometry and analytic number theory. By contrast, mathematicians have paid considerable attention to whether such impurities are a good thing or to be avoided, and some have claimed that they are valuable because generally impure proofs are simpler than pure proofs. This article is an investigation of this claim, formulated more precisely by proof- theoretic means. After assembling evidence from proof theory that may be thought to support this claim, we will argue that on the contrary this evidence does not support the claim
All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins
All-optical electrophysiologyâspatially resolved simultaneous optical perturbation and measurement of membrane voltageâwould open new vistas in neuroscience research. We evolved two archaerhodopsin-based voltage indicators, QuasAr1 and QuasAr2, which show improved brightness and voltage sensitivity, have microsecond response times and produce no photocurrent. We engineered a channelrhodopsin actuator, CheRiff, which shows high light sensitivity and rapid kinetics and is spectrally orthogonal to the QuasArs. A coexpression vector, Optopatch, enabled cross-talkâfree genetically targeted all-optical electrophysiology. In cultured rat neurons, we combined Optopatch with patterned optical excitation to probe back-propagating action potentials (APs) in dendritic spines, synaptic transmission, subcellular microsecond-timescale details of AP propagation, and simultaneous firing of many neurons in a network. Optopatch measurements revealed homeostatic tuning of intrinsic excitability in human stem cellâderived neurons. In rat brain slices, Optopatch induced and reported APs and subthreshold events with high signal-to-noise ratios. The Optopatch platform enables high-throughput, spatially resolved electrophysiology without the use of conventional electrodes
Shannon Information Theory and Molecular Biology
The role and the contribution of Shannon Information Theory to the development of Molecular Biology has been the object of stimulating debates during the last thirty years. This seems to be connected with some semantic charms associated with the use of the word \u201cinformation\u201d in the biological context. Furthermore information itself, if viewed in a broader perspective, is far from being completely defined in a fashion that overcomes the technical level at which the classical Information Theory has been conceived. This review aims at building on the acknowledged contribution of Shannon Information Theory to Molecular Biology, so as to discover if it is only a technical tool to analyze DNA and proteinic sequences, or if it can rise, at least in perspective, to a higher role that exerts an influence on the construction of a suitable model for handling the genetic information in Molecular Biology
Integrating ecology and evolutionary theory. A game changer for biodiversity conservation?
Currently, one of the central arguments in favour of biodiversity conservation is that it is essential for the maintenance of ecosystem services, that is, the benefits that people receive from ecosystems. However, the relationship between ecosystem services and biodiversity is contested and needs clarification. The goal of this chapter is to spell out the interaction and reciprocal influences between conservation science, evolutionary biology, and ecology, in order to understand whether a stronger integration of evolutionary and ecological studies might help clarify the interaction between biodiversity and ecosystem functioning as well as influence biodiversity conservation practices. To this end, the eco-evolutionary feedback theory proposed by David Post and Eric Palkovacs is analysed, arguing that it helps operationalise niche construction theory and develop a more sophisticated understanding of the relationship between ecosystem functioning and biodiversity. Finally, it is proposed that by deepening the integration of ecological and evolutionary factors in our understanding of ecosystem functioning, the eco-evolutionary feedback theory is supportive of an âevolutionary-enlightened managementâ of biodiversity within the ecosystem services approach.info:eu-repo/semantics/publishedVersio
Micromechanical Properties of Injection-Molded StarchâWood Particle Composites
The micromechanical properties of injection molded starchâwood particle composites were investigated as a function of particle content and humidity conditions.
The composite materials were characterized by scanning electron microscopy and X-ray diffraction methods. The microhardness
of the composites was shown to increase notably with the concentration of the wood particles. In addition,creep behavior under the indenter and temperature dependence
were evaluated in terms of the independent contribution of the starch matrix and the wood microparticles to the hardness value. The influence of drying time on the density
and weight uptake of the injection-molded composites was highlighted. The results revealed the role of the mechanism of water evaporation, showing that the dependence of water uptake and temperature was greater for the starchâwood composites than for the pure starch sample. Experiments performed during the drying process at 70°C indicated that
the wood in the starch composites did not prevent water loss from the samples.Peer reviewe
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