IsoTV: processing and visualizing functional features of translated transcript isoforms

Despite the continuous discovery of new transcript isoforms, fueled by the recent increase in accessibility and accuracy of long-read RNA sequencing data, functional differences between isoforms originating from the same gene often remain obscure. To address this issue and enable researchers to assess potential functional consequences of transcript isoform variation on the proteome, we developed IsoTV. IsoTV is a versatile pipeline to process, predict and visualize the functional features of translated transcript isoforms. Attributes such as gene and isoform expression, transcript composition and functional features are summarized in an easy-to-interpret visualization. IsoTV is able to analyze a variety of data types from all eukaryotic organisms, including short- and long-read RNA-seq data. Using Oxford Nanopore long read data, we demonstrate that IsoTV facilitates the understanding of potential protein isoform function in different cancer cell types

Alpha Cygnids: a possible July minor meteor shower

We present a comprehensive study of a possible $\alpha$-Cygnid meteor shower. Based on visual and telescopic observations made by Polish observers we estimate basic parameters of the stream. Activity of $\alpha$-Cygnids lasts from around June 30 to July 31 with clear maximum near July 16-17 (solar longitude $\lambda_\odot=116.5^\circ$). Maximal Zenithal Hourly Rates (ZHRs) are equal to $3.6\pm1.2$. The structure of the radiant analyzed by {\sc radiant} software is most compact for geocentric velocity of the events equal to 41 km/s, and for the drift of the radiant (in units $^\circ$/day) equal to of maximum is $\alpha=302.5^\circ$ $\delta=+46.3^\circ$.We derive population index $r$ equal to $2.55\pm0.14$ from magnitude distribution of 738 possible members of the stream. Comparing the veloctity distributions of 754 possible tests we conclude that both distributions are different with probability very close to 1.0. Telescopic observations strictly confirm the results obtained from visual observations. The smallest values of $\chi^2$ parameter we obtained for the geocentric velocity equal to 40 km/s and for the drift of the radiant (in units $^\circ$/day) equal to $\Delta\alpha=+0.6$ $\Delta\delta=+0.2$. The center of the radiant for moment of maximum is $\alpha=304.9^\circ$ $\delta=+46.2^\circ$. In spite of making many photographic exposures we still have no photographic or video confirmation of the existence of this stream

Kaon physics with the KLOE detector

In this paper we discuss the recent finalized analyses by the KLOE experiment at DA$\Phi$NE: the CPT and Lorentz invariance test with entangled $K^0 \bar{K}^0$ pairs, and the precision measurement of the branching fraction of the decay ${ K^+} \rightarrow \pi^+\pi^-\pi^+(\gamma)$. We also present the status of an ongoing analysis aiming to precisely measure the $K^{\pm}$ mass

Conserved DNA sequence features underlie pervasive RNA polymerase pausing

Pausing of transcribing RNA polymerase is regulated and creates opportunities to control gene expression. Research in metazoans has so far mainly focused on RNA polymerase II (Pol II) promoter-proximal pausing leaving the pervasive nature of pausing and its regulatory potential in mammalian cells unclear. Here, we developed a pause detecting algorithm (PDA) for nucleotide-resolution occupancy data and a new native elongating transcript sequencing approach, termed nested NET-seq, that strongly reduces artifactual peaks commonly misinterpreted as pausing sites. Leveraging PDA and nested NET-seq reveal widespread genome-wide Pol II pausing at single-nucleotide resolution in human cells. Notably, the majority of Pol II pauses occur outside of promoter-proximal gene regions primarily along the gene-body of transcribed genes. Sequence analysis combined with machine learning modeling reveals DNA sequence properties underlying widespread transcriptional pausing including a new pause motif. Interestingly, key sequence determinants of RNA polymerase pausing are conserved between human cells and bacteria. These studies indicate pervasive sequence-induced transcriptional pausing in human cells and the knowledge of exact pause locations implies potential functional roles in gene expression

Towards graphical user interface redefinition without source code access: System design and evaluation

Nowadays several interactive computing systems (ICSs) still have Graphical User Interfaces (GUIs) that are inadequate in terms of usability and user experience. Numerous improvements were made in the development of better GUIs however, little has been done to improve existing ones. This might be explained by the fact that most ICSs do not provide source code access. In most cases, this means that only persons with source code access can (easily) enhance the respective GUI. This paper presents a tool using computer vision (CV) algorithms to semi-automatically redefine existing GUIs without accessing their source code. The evaluation of a new GUI obtained from the redefinition of an existing GUI using the tool is described. Results show statistically significant improvements in usability (reduction of interaction mistakes), improved task completion success rate and improved user satisfaction.info:eu-repo/semantics/acceptedVersio

Compressive Sensing of Signals Generated in Plastic Scintillators in a Novel J-PET Instrument

The J-PET scanner, which allows for single bed imaging of the whole human body, is currently under development at the Jagiellonian University. The dis- cussed detector offers improvement of the Time of Flight (TOF) resolution due to the use of fast plastic scintillators and dedicated electronics allowing for sam- pling in the voltage domain of signals with durations of few nanoseconds. In this paper we show that recovery of the whole signal, based on only a few samples, is possible. In order to do that, we incorporate the training signals into the Tikhonov regularization framework and we perform the Principal Component Analysis decomposition, which is well known for its compaction properties. The method yields a simple closed form analytical solution that does not require iter- ative processing. Moreover, from the Bayes theory the properties of regularized solution, especially its covariance matrix, may be easily derived. This is the key to introduce and prove the formula for calculations of the signal recovery error. In this paper we show that an average recovery error is approximately inversely proportional to the number of acquired samples

Studies of unicellular micro-organisms Saccharomyces cerevisiae by means of Positron Annihilation Lifetime Spectroscopy

Results of Positron Annihilation Lifetime Spectroscopy (PALS) and microscopic studies on simple microorganisms: brewing yeasts are presented. Lifetime of ortho - positronium (o-Ps) were found to change from 2.4 to 2.9 ns (longer lived component) for lyophilised and aqueous yeasts, respectively. Also hygroscopicity of yeasts in time was examined, allowing to check how water - the main component of the cell - affects PALS parameters, thus lifetime of o-Ps were found to change from 1.2 to 1.4 ns (shorter lived component) for the dried yeasts. The time sufficient to hydrate the cells was found below 10 hours. In the presence of liquid water an indication of reorganization of yeast in the molecular scale was observed. Microscopic images of the lyophilised, dried and wet yeasts with best possible resolution were obtained using Inverted Microscopy (IM) and Environmental Scanning Electron Microscopy (ESEM) methods. As a result visible changes to the surface of the cell membrane were observed in ESEM images.Comment: Nukleonika (2015

Searches for discrete symmetries violation in ortho-positronium decay using the J-PET detector

In this paper we present prospects for using the J-PET detector to search for discrete symmetries violations in a purely leptonic system of the positronium atom. We discuss tests of CP and CPT symmetries by means of ortho-positronium decays into three photons. No zero expectation values for chosen correlations between ortho-positronium spin and momentum vectors of photons would imply the existence of physics phenomena beyond the Standard Model. Previous measurements resulted in violation amplitude parameters for CP and CPT symmetries consistent with zero, with an uncertainty of about 10-3. The J-PET detector allows to determine those values with better precision thanks to a unique time and angular esolution combined with a high geometrical acceptance. Achieving the aforementioned is possible due to application of polymer scintillators instead of crystals as detectors of annihilation quanta.Comment: in Nukleonika 201

Beam profile investigation of the new collimator system for the J-PET detector

Jagiellonian Positron Emission Tomograph (J-PET) is a multi-purpose detector which will be used for search for discrete symmetries violations in the decays of positronium atoms and for investigations with positronium atoms in life-sciences and medical diagnostics. In this article we present three methods for determination of the beam profile of collimated annihilation gamma quanta. Precise monitoring of this profile is essential for time and energy calibration of the J-PET detector and for the determination of the library of model signals used in the hit-time and hit-position reconstruction. We have we have shown that usage of two lead bricks with dimensions of 5x10x20 cm^3 enables to form a beam of annihilation quanta with Gaussian profile characterized by 1 mm FWHM. Determination of this characteristic is essential for designing and construction the collimator system for the 24-module J-PET prototype. Simulations of the beam profile for different collimator dimensions were performed. This allowed us to choose optimal collimation system in terms of the beam profile parameters, dimensions and weight of the collimator taking into account the design of the 24 module J-PET detector.Comment: 14 pages, 9 figure