The age of data-driven proteomics : how machine learning enables novel workflows

A lot of energy in the field of proteomics is dedicated to the application of challenging experimental workflows, which include metaproteomics, proteogenomics, data independent acquisition (DIA), non-specific proteolysis, immunopeptidomics, and open modification searches. These workflows are all challenging because of ambiguity in the identification stage; they either expand the search space and thus increase the ambiguity of identifications, or, in the case of DIA, they generate data that is inherently more ambiguous. In this context, machine learning-based predictive models are now generating considerable excitement in the field of proteomics because these predictive models hold great potential to drastically reduce the ambiguity in the identification process of the above-mentioned workflows. Indeed, the field has already produced classical machine learning and deep learning models to predict almost every aspect of a liquid chromatography-mass spectrometry (LC-MS) experiment. Yet despite all the excitement, thorough integration of predictive models in these challenging LC-MS workflows is still limited, and further improvements to the modeling and validation procedures can still be made. In this viewpoint we therefore point out highly promising recent machine learning developments in proteomics, alongside some of the remaining challenges

Super-massive binary black holes and emission lines in active galactic nuclei

The broad emission spectral lines emitted from AGNs are our main probe of the geometry and physics of the broad line region (BLR) close to the SMBH. There is a group of AGNs that emits very broad and complex line profiles, showing two displaced peaks, one blueshifted and one redshifted from the systemic velocity defined by the narrow lines, or a single such peak. It has been proposed that such line shapes could indicate a supermassive binary black hole (SMB) system. We discuss here how the presence of an SMB will affect the BLRs of AGNs and what the observational consequences might be. We review previous claims of SMBs based on broad line profiles and find that they may have non-SMB explanations as a consequence of a complex BLR structure. Because of these effects it is very hard to put limits on the number of SMBs from broad line profiles. It is still possible, however, that unusual broad line profiles in combination with other observational effects (line ratios, quasi-periodical oscillations, spectropolarimetry, etc.) could be used for SMBs detection. Some narrow lines (e.g., [O\,III]) in some AGNs show a double-peaked profile. Such profiles can be caused by streams in the Narrow Line Region (NLR), but may also indicate the presence of a kilo-parsec scale mergers. A few objects indicated as double-peaked narrow line emitters are confirmed as kpc-scale margers, but double-peaked narrow line profiles are mostly caused by the complex NLR geometry. We briefly discuss the expected line profile of broad Fe K$\alpha$ that probably originated in the accretion disk(s) around SMBs. Finally we consider rare configurations where a SMB system might be gravitationally lensed by a foreground galaxy, and discuss the expected line profiles in these systems.Comment: The work was presented as an invited talk at special workshop "Spectral lines and super-massive black holes" held on June 10, 2011 as a part of activity within the frame of COST action 0905 "Black holes in a violent universe" and as a part of the 8th Serbian Conference on Spectral Line Shapes in Astrophysics.Sent to New Astronomy Review as a review pape

The Outer Disks of Early-Type Galaxies. I. Surface-Brightness Profiles of Barred Galaxies

We present a study of 66 barred, early-type (S0-Sb) disk galaxies, focused on the disk surface brightness profile outside the bar region and the nature of Freeman Type I and II profiles, their origins, and their possible relation to disk truncations. This paper discusses the data and their reduction, outlines our classification system, and presents $R$-band profiles and classifications for all galaxies in the sample. The profiles are derived from a variety of different sources, including the Sloan Digital Sky Survey (Data Release 5). For about half of the galaxies, we have profiles derived from more than one telescope; this allows us to check the stability and repeatability of our profile extraction and classification. The vast majority of the profiles are reliable down to levels of mu_R ~ 27 mag arcsec^-2; in exceptional cases, we can trace profiles down to mu_R > 28. We can typically follow disk profiles out to at least 1.5 times the traditional optical radius R_25; for some galaxies, we find light extending to ~ 3 R_25. We classify the profiles into three main groups: Type I (single-exponential), Type II (down-bending), and Type III (up-bending). The frequencies of these types are approximately 27%, 42%, and 24%, respectively, plus another 6% which are combinations of Types II and III. We further classify Type II profiles by where the break falls in relation to the bar length, and in terms of the postulated mechanisms for breaks at large radii ("classical trunction" of star formation versus the influence of the Outer Lindblad Resonance of the bar). We also classify the Type III profiles by the probable morphology of the outer light (disk or spheroid). Illustrations are given for all cases. (Abridged)Comment: 41 pages, 26 PDF figures. To appear in the Astronomical Journal. Version with full-resolution figures available at http://www.mpe.mpg.de/~erwin/research

Triangulation of gravitational wave sources with a network of detectors

There is significant benefit to be gained by pursuing multi-messenger astronomy with gravitational wave and electromagnetic observations. In order to undertake electromagnetic follow-ups of gravitational wave signals, it will be necessary to accurately localize them in the sky. Since gravitational wave detectors are not inherently pointing instruments, localization will occur primarily through triangulation with a network of detectors. We investigate the expected timing accuracy for observed signals and the consequences for localization. In addition, we discuss the effect of systematic uncertainties in the waveform and calibration of the instruments on the localization of sources. We provide illustrative results of timing and localization accuracy as well as systematic effects for coalescing binary waveforms.Comment: 20 pages, 5 figure

Molecular Beams

Contains research objectives and reports on six research projects

Field Blue Stragglers and Related Mass Transfer Issues

This chapter contains my impressions and perspectives about the current state of knowledge about field blue stragglers (FBS) stars, drawn from an extensive literature that I searched. I conclude my review of issues that attend FBS and mass transfer, by a brief enumeration of a few mildly disquieting observational facts.Comment: Chapter 4, in Ecology of Blue Straggler Stars, H.M.J. Boffin, G. Carraro & G. Beccari (Eds), Astrophysics and Space Science Library, Springe

Knowledge, science and death: the theory of brain-sign

In today’s paradigmatic climate, the possibility of knowledge, and therefore science, still depends upon our being conscious. However, no scientifically accepted account of consciousness exists. In recent years I have developed the theory of brain-sign which replaces consciousness as a wholly physical neural condition. The first tenet is that the brain is a causal organ, not a knowledge organ. The second is that brain-sign, used in inter-neural communication for uncertain or imprecise collective action, derives at each moment from the causal orientation of the brain. Signs are ubiquitous bio-physical entities. Thus there is no problematic dualism, consciousness and world. We now have two accounts of the brain phenomenon. The first (consciousness) is an inexplicable physical anomaly. The second (brain-sign) belongs in the physical universe, and fulfils a crucial neurobiological function. With brain-sign theory we even ‘discover’ that we do not know we are alive or will die

Theories of Reference: What Was the Question?

The new theory of reference has won popularity. However, a number of noted philosophers have also attempted to reply to the critical arguments of Kripke and others, and aimed to vindicate the description theory of reference. Such responses are often based on ingenious novel kinds of descriptions, such as rigidified descriptions, causal descriptions, and metalinguistic descriptions. This prolonged debate raises the doubt whether different parties really have any shared understanding of what the central question of the philosophical theory of reference is: what is the main question to which descriptivism and the causal-historical theory have presented competing answers. One aim of the paper is to clarify this issue. The most influential objections to the new theory of reference are critically reviewed. Special attention is also paid to certain important later advances in the new theory of reference, due to Devitt and others

Anisotropic Colossal Magnetoresistance Effects in Fe_{1-x}Cu_xCr_2S_4

A detailed study of the electronic transport and magnetic properties of Fe$_{1-x}$Cu$_x$Cr$_2$S$_4$ ($x \leq 0.5$) on single crystals is presented. The resistivity is investigated for $2 \leq T \leq 300$ K in magnetic fields up to 14 Tesla and under hydrostatic pressure up to 16 kbar. In addition magnetization and ferromagnetic resonance (FMR) measurements were performed. FMR and magnetization data reveal a pronounced magnetic anisotropy, which develops below the Curie temperature, $T_{\mathrm{C}}$, and increases strongly towards lower temperatures. Increasing the Cu concentration reduces this effect. At temperatures below 35 K the magnetoresistance, $MR = \frac{\rho(0) - \rho(H)}{\rho(0)}$, exhibits a strong dependence on the direction of the magnetic field, probably due to an enhanced anisotropy. Applying the field along the hard axis leads to a change of sign and a strong increase of the absolute value of the magnetoresistance. On the other hand the magnetoresistance remains positive down to lower temperatures, exhibiting a smeared out maximum with the magnetic field applied along the easy axis. The results are discussed in the ionic picture using a triple-exchange model for electron hopping as well as a half-metal utilizing a band picture.Comment: some typos correcte