Author Correction: Analysis of the Human Protein Atlas Image Classification competition.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Publisher Correction: Analysis of the Human Protein Atlas Image Classification competition.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Analysis of the Human Protein Atlas Image Classification competition.

Pinpointing subcellular protein localizations from microscopy images is easy to the trained eye, but challenging to automate. Based on the Human Protein Atlas image collection, we held a competition to identify deep learning solutions to solve this task. Challenges included training on highly imbalanced classes and predicting multiple labels per image. Over 3 months, 2,172 teams participated. Despite convergence on popular networks and training techniques, there was considerable variety among the solutions. Participants applied strategies for modifying neural networks and loss functions, augmenting data and using pretrained networks. The winning models far outperformed our previous effort at multi-label classification of protein localization patterns by ~20%. These models can be used as classifiers to annotate new images, feature extractors to measure pattern similarity or pretrained networks for a wide range of biological applications.

Random Search in Fluid Flow Aided by Chemotaxis.

In this paper, we consider the dynamics of a 2D target-searching agent performing Brownian motion under the influence of fluid shear flow and chemical attraction. The analysis is motivated by numerous situations in biology where these effects are present, such as broadcast spawning of marine animals and other reproduction processes or workings of the immune systems. We rigorously characterize the limit of the expected hit time in the large flow amplitude limit as corresponding to the effective one-dimensional problem. We also perform numerical computations to characterize the finer properties of the expected duration of the search. The numerical experiments show many interesting features of the process and in particular existence of the optimal value of the shear flow that minimizes the expected target hit time and outperforms the large flow limit.

Characterization of the stray light in a space borne atmospheric AOTF spectrometer.

Acousto-optic tunable filter (AOTF) spectrometers are being criticized for spectral leakage, distant side lobes of their spectral response function (SRF), or the stray light. SPICAM-IR is the AOTF spectrometer in the range of 1000-1700 nm with a resolving power of 1800-2200 operating on the Mars Express interplanetary probe. It is primarily dedicated to measurements of water vapor in the Martian atmosphere. SPICAM H(2)O retrievals are generally lower than simultaneous measurements with other instruments, the stray light suggested as a likely explanation. We report the results of laboratory measurements of water vapor in quantity characteristic for the Mars atmosphere (2-15 precipitable microns) with the Flight Spare model of SPICAM-IR. We simulated the measured spectra with HITRAN-based synthetic model, varying the water abundance, and the level of the stray light, and compared the results to the known amount of water in the cell. The retrieved level of the stray light, assumed uniformly spread over the spectral range, is below 1-1.3·10(-4). The stray may be responsible for the underestimation of water abundance of up to 8%, or 0.6 pr. µm. The account for the stray light removes the bias completely; the overall accuracy to measure water vapor is ~0.2 pr. µm. We demonstrate that the AOTF spectrometer dependably measures the water abundance and can be employed as an atmospheric spectrometer.

Compact echelle spectrometer for occultation sounding of the Martian atmosphere: design and performance.

The echelle spectrometer TIMM-2 is the instrument developed for the unsuccessful Russian mission Phobos-Grunt. The instrument was dedicated to solar occultation studies of the Martian atmosphere by measuring the amount of methane, by sensitive measuring of other minor constituents, and by profiling the D/H ratio and the aerosol structure. The spectral range of the instrument is 2300-4100 nm, the spectral resolving power λ/Δλ exceeds 25,000, and the field of view is 1.5×21 arc min. The spectra are measured in narrow spectral intervals, corresponding to discreet diffraction orders. One measurement cycle includes several spectral intervals. To study the vertical profiles of aerosol, the instrument incorporates four photometers in the UV to near-IR spectral range. The mass of the instrument is 2800 g, and its power consumption is 12 W. One complete flight model remains available after the Phobos-Grunt launch. We discuss the science objectives of the occultation experiment for the case of Mars, the implementation of the instrument, and the results of ground calibrations.

A simple reaction-diffusion system as a possible model for the origin of chemotaxis.

Chemotaxis is a directed cell movement in response to external chemical stimuli. In this paper, we propose a simple model for the origin of chemotaxis - namely how a directed movement in response to an external chemical signal may occur based on purely reaction-diffusion equations reflecting inner working of the cells. The model is inspired by the well-studied role of the rho-GTPase Cdc42 regulator of cell polarity, in particular in yeast cells. We analyse several versions of the model to better understand its analytic properties and prove global regularity in one and two dimensions. Using computer simulations, we demonstrate that in the framework of this model, at least in certain parameter regimes, the speed of the directed movement appears to be proportional to the size of the gradient of signalling chemical. This coincides with the form of the chemical drift in the most studied mean field model of chemotaxis, the Keller-Segel equation.

Confirmation of the random tiling hypothesis for a decagonal quasicrystal.

Mechanisms that stabilize quasicrystals are much discussed but not finally resolved. We confirm the random tiling hypothesis and its predictions in a fully atomistic decagonal quasicrystal model by calculating the free energy and the phason elastic constants over a wide range of temperatures. The Frenkel-Ladd method is applied for the phonon part, and an approach of uncorrelated phason flips is applied for the configurational part. When lowering the temperature, a phase transition to an approximant occurs. Close to the transition temperature, one of the phason elastic constants becomes soft.