Linear model for fast background subtraction in oligonucleotide microarrays

One important preprocessing step in the analysis of microarray data is background subtraction. In high-density oligonucleotide arrays this is recognized as a crucial step for the global performance of the data analysis from raw intensities to expression values. We propose here an algorithm for background estimation based on a model in which the cost function is quadratic in a set of fitting parameters such that minimization can be performed through linear algebra. The model incorporates two effects: 1) Correlated intensities between neighboring features in the chip and 2) sequence-dependent affinities for non-specific hybridization fitted by an extended nearest-neighbor model. The algorithm has been tested on 360 GeneChips from publicly available data of recent expression experiments. The algorithm is fast and accurate. Strong correlations between the fitted values for different experiments as well as between the free-energy parameters and their counterparts in aqueous solution indicate that the model captures a significant part of the underlying physical chemistry.Comment: 21 pages, 5 figure

Unified Scenario for Composite Right-Handed Neutrinos and Dark Matter

We entertain the possibility that neutrino masses and dark matter (DM) originate from a common composite dark sector. A minimal effective theory can be constructed based on a dark $SU(3)_D$ interaction with three flavors of massless dark quarks; electroweak symmetry breaking gives masses to the dark quarks. By assigning a $\mathbb Z_2$ charge to one flavor, a stable "dark kaon" can provide a good thermal relic DM candidate. We find that "dark neutrons" may be identified as right handed Dirac neutrinos. Some level of "neutron-anti-neutron" oscillation in the dark sector can then result in non-zero Majorana masses for light Standard Model neutrinos. A simple ultraviolet completion is presented, involving additional heavy $SU(3)_D$-charged particles with electroweak and lepton Yukawa couplings. At our benchmark point, there are "dark pions" that are much lighter than the Higgs and we expect spectacular collider signals arising from the UV framework. This includes the decay of the Higgs boson to $\tau \tau \ell \ell^{\prime}$, where $\ell$($\ell'$) can be any lepton, with displaced vertices. We discuss the observational signatures of this UV framework in dark matter searches and primordial gravitational wave experiments; the latter signature is potentially correlated with the $H \to \tau \tau \ell \ell^{\prime}$ decay.Comment: 8 pages, 4 figures, 1 table. Version published on PR

Event Indexing Systems for Efficient Selection and Analysis of HERA Data

The design and implementation of two software systems introduced to improve the efficiency of offline analysis of event data taken with the ZEUS Detector at the HERA electron-proton collider at DESY are presented. Two different approaches were made, one using a set of event directories and the other using a tag database based on a commercial object-oriented database management system. These are described and compared. Both systems provide quick direct access to individual collision events in a sequential data store of several terabytes, and they both considerably improve the event analysis efficiency. In particular the tag database provides a very flexible selection mechanism and can dramatically reduce the computing time needed to extract small subsamples from the total event sample. Gains as large as a factor 20 have been obtained.Comment: Accepted for publication in Computer Physics Communication

Multi-electrode nerve cuff recording - model analysis of the effects of finite cuff length

The effect of finite cuff length on the signals recorded by electrodes at different positions along the nerve was analysed in a model study. Relations were derived using a one-dimensional model. These were evaluated in a more realistic axially symmetric 3D model. This evaluation indicated that the cuff appeared shorter because of edge effects at the beginning and end of the cuff. The method for velocity selective filtering introduced by Donaldson was subsequently analysed. In this method, velocity selective filtering is achieved by summing the signals of subsequent tripoles after applying time shifts tuned to a certain conduction velocity. It was also found that the optimum electrode distance for a given cuff length for maximum summed RMS of symmetrical tripoles in the cuff is larger than when evaluating peak-peak amplitudes of single fibre action potentials. Velocity selective filtering yields better selectivity when using symmetrical tripoles, but may yield larger signal RMS when using the wider asymmetrical tripoles, potentially allowing for shorter cuffs. It is speculated that application of a multi-electrode reference may improve velocity selectivity for asymmetrical tripoles

Automatic diagnostics and prognostics of energy conversion processes via knowledge-based systems

This paper presents a critical and analytical description of an ongoing research program aimed at the implementation of an expert system capable of monitoring, through an Intelligent Health Control procedure, the instantaneous performance of a cogeneration plant. An application has been tested on a real plant, located on the grounds of the ENEA-Casaccia Energy Laboratories. The expert system, denominated PROMISE as the Italian acronym for PROgnostic and Intelligent Monitoring Expert System, generates, in real time and in a form directly useful to the plant manager, information on the existence and severity of faults, forecasts on the future time history of both detected and likely faults, and suggestions on how to control the problem. The expert procedure, working where and if necessary with the support of a process simulator, derives from real-time data a list of selected performance indicators for each plant component. For a set of faults, pre-defined with the help of the plant operator, proper rules are defined in order to establish whether the component is working correctly; in several instances, since one single failure (symptom) can originate from more than one fault (cause), complex sets of rules expressing the combination of multiple indices have been introduced in the knowledge base as well. Creeping faults are detected by analyzing the trend of the variation of an indicator in a pre-assigned interval of time. Whenever the value of this "discrete time derivative" becomes "high" with respect to a specified limit value, a "latent creeping fault" condition is prognosed. The expert system architecture is based on an object-oriented paradigm. The knowledge base (facts and rules) is clustered: the chunks of knowledge pertain to individual components. A graphic user interface (GUI) allows the user to interrogate PROMISE about its rules, procedures, classes and objects, and about its inference path. The paper also presents the results of some tests conducted on the real plant. © 2004 Elsevier Ltd. All rights reserved

Foreword

n/

Supporting Device Discovery and Spontaneous Interaction with Spatial References

The RELATE interaction model is designed to support spontaneous interaction of mobile users with devices and services in their environment. The model is based on spatial references that capture the spatial relationship of a user’s device with other co-located devices. Spatial references are obtained by relative position sensing and integrated in the mobile user interface to spatially visualize the arrangement of discovered devices, and to provide direct access for interaction across devices. In this paper we discuss two prototype systems demonstrating the utility of the model in collaborative and mobile settings, and present a study on usability of spatial list and map representations for device selection

Can QCD axion stars explain Subaru HSC microlensing?

Publisher Copyright: © 2021 authors. Published by the American Physical Society.A non-negligible fraction of the QCD axion dark matter may form gravitationally bound Bose Einstein condensates, which are commonly known as axion stars or axion clumps. Such astrophysical objects have been recently proposed as the cause for the single candidate event reported by Subaru Hyper Suprime-Cam (HSC) microlensing search in the Andromeda galaxy. Depending on the breaking scale of the Peccei-Quinn symmetry and the details of the dark matter scenario, QCD axion clumps may form via gravitational condensation during radiation domination, in the dense core of axion miniclusters, or within axion minihalos around primordial black holes. We analyze all these scenarios and conclude that the microlensing candidate detected by the Subaru HSC survey is likely not caused by QCD axion stars.A non-negligible fraction of the QCD axion dark matter may form gravitationally bound Bose Einstein condensates, which are commonly known as axion stars or axion clumps. Such astrophysical objects have been recently proposed as the cause for the single candidate event reported by Subaru Hyper Suprime-Cam (HSC) microlensing search in the Andromeda galaxy. Depending on the breaking scale of the Peccei-Quinn symmetry and the details of the dark matter scenario, QCD axion clumps may form via gravitational condensation during radiation domination, in the dense core of axion miniclusters, or within axion minihalos around primordial black holes. We analyze all these scenarios and conclude that the microlensing candidate detected by the Subaru HSC survey is likely not caused by QCD axion stars.Peer reviewe