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

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

Advanced Conducting Project

El Grillo by Josquin Desprez If Ye Love Me by Thomas Tallis Jauchzet dem Herren by Heinrich Schütz Jesu, Joy of Man\u27s Desiring by J.S. Bach Sanctus by Wolfgang Amadeus Mozart When Jesus Wept by William Billings He Watching Over Israel by Felix Mendelssohn How Lovely is Thy Dwelling Place by Johannes Brahms The Best of Rooms by Randall Thompson If Music be the Food of Love by David Dickau Amor de mi Alma by Z. Randall Stroope There Will Be Rest by Frank Ticheli

The blind men and the elephant: Integrated offline/online optimization under uncertainty

open3noOptimization problems under uncertainty are traditionally solved either via offline or online methods. Offline approaches can obtain high-quality robust solutions, but have a considerable computational cost. Online algorithms can react to unexpected events once they are observed, but often run under strict time constraints, preventing the computation of optimal solutions. Many real world problems, however, have both offline and online elements: a substantial amount of time and information is frequently available (offline) before an online problem is solved (e.g. energy production forecasts, or historical travel times in routing problems); in other cases both offline (i.e. strategic) and online (i.e. operational) decisions need to be made. Surprisingly, the interplay of these offline and online phases has received little attention: like in the blind men and the elephant tale, we risk missing the whole picture, and the benefits that could come from integrated offline/online optimization. In this survey we highlight the potential shortcomings of pure methods when applied to mixed offline/online problems, we review the strategies that have been designed to take advantage of this integration, and we suggest directions for future research.openDe Filippo A.; Lombardi M.; Milano M.De Filippo A.; Lombardi M.; Milano M

"Die Natur und Kunst zu betrachten": Carlo Farina's Capriccio stravagante (1627) and the Cultures of Collecting at the Court of Saxony

Discusses the Capriccio stravagante by the Italian violin virtuoso Carlo Farina, as court Konzertmeister at the court of Saxony in Dresden. Suggests that the model for the Capriccio may be found in the many collections at the Dresden court and in the early modern strategies of learning, knowing and experiencing the world through the act of collecting. Shows that the Capriccio was not without precedent; other works of music and music theory may also be related to the practices of courtly collecting, and so offer a context for understanding Farina's work. (Quotes from original text

Advanced Conducting Project

Contents include: El Grillo by Josquin Desprez If Ye Love Me by Thomas Tallis Jauchzet dem Herren by Heinrich Schütz Jesu, Joy of Man\u27s Desiring by J.S. Bach Sanctus by Wolfgang Amadeus Mozart When Jesus Wept by William Billings He Watching Over Israel by Felix Mendelssohn How Lovely is Thy Dwelling Place by Johannes Brahms The Best of Rooms by Randall Thompson If Music be the Food of Love by David Dickau Amor de mi Alma by Z. Randall Stroope There Will Be Rest by Frank Ticheli

The Notification Oriented Paradigm Language to Digital Hardware as an Intuitive High-level Synthesis Tool

The parallelism allowed by FPGAs has attracted attention for knowing applications that need processing power. However, the need for specific and very technical development language has not stimulate its broad use. As an alternative, there are High-level Synthesis Languages (HSL), which allow less complicated FPGA use. However, they do not tend to take full advantage of the FPGA technology. Therefore, another alternative was developed, based on the Notification Oriented Paradigm (NOP), called NOP for Digital Hardware (NOP-DH). NOP allows development in high level with its rule-oriented language called NOPL. Its entity decoupling, parallelism, and redundancy avoidance are useful for best performance. In turn, the NOP-DH brings NOP for the FPGA context with the benefits observed in software but enhanced by hardware nature. This paper reviews the NOPL for NOP-DH (NOPL-DH) that aims high level programming for FPGA. The paper proposes the NOPL-DH test by independent developers, by developing a monitoring device for a box transporting bidirectional conveyer. As a result, NOPL-DH allowed high-level development under the NOP-DH structure in an FPGA, without the need for technical knowledge and, still, maintaining and exploring the NOP properties in FPG

Modern Valence-Bond Description of Homoaromaticity

Spin-coupled (SC) theory is used to obtain modern valence-bond descriptions of the electronic structures of local minimum and transition-state geometries of three species that have been considered to exhibit homoconjugation and homoaromaticity: the homotropenylium ion, C8H9+, the cycloheptatriene neutral ring, C7H8, and the 1,3-bishomotropenylium ion, C9H11+. The resulting compact SC wave functions are of comparable quality to complete-active-space self-consistent field constructions that are based on the same “N electrons in M orbitals” active spaces, but they are much easier to interpret directly. Analysis of the forms of the SC orbitals and of the overlaps between them, as well as an examination of the compositions of the associated resonance patterns, strongly suggest that both of the homotropenylium and 1,3-bishomotropenylium ions are homoaromatic at their local minimum geometries, with all of the other cases that were considered being nonaromatic. The SC results also show that the differences between “no-bond” and “bond” homoconjugated systems are very likely to be much smaller than previously thought