Empirical Research Plan: Effects of Sketching on Program Comprehension

Sketching is an important means of communication in software engineering practice. Yet, there is little research investigating the use of sketches. We want to contribute a better understanding of sketching, in particular its use during program comprehension. We propose a controlled experiment to investigate the effectiveness and efficiency of program comprehension with the support of sketches as well as what sketches are used in what way.Comment: 5 pages, 0 figures, Proc. International Conference on Agile Software Development (XP'16). Volume 251 of the book series Lecture Notes in Business Information Processing (LNBIP). Springer, 201

Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals

We investigated human alternative protein isoforms of >2600 genes based on full-length cDNA clones and SwissProt. We classified the isoforms and examined their co-occurrence for each gene. Further, we investigated potential relationships between these changes and differential subcellular localization. The two most abundant patterns were the one with different C-terminal regions and the one with an internal insertion, which together account for 43% of the total. Although changes of the N-terminal region are less common than those of the C-terminal region, extension of the C-terminal region is much less common than that of the N-terminal region, probably because of the difficulty of removing stop codons in one isoform. We also found that there are some frequently used combinations of co-occurrence in alternative isoforms. We interpret this as evidence that there is some structural relationship which produces a repertoire of isoformal patterns. Finally, many terminal changes are predicted to cause differential subcellular localization, especially in targeting either peroxisomes or mitochondria. Our study sheds new light on the enrichment of the human proteome through alternative splicing and related events. Our database of alternative protein isoforms is available through the internet

TMBETA-NET: discrimination and prediction of membrane spanning β-strands in outer membrane proteins

We have developed a web-server, TMBETA-NET for discriminating outer membrane proteins and predicting their membrane spanning β-strand segments. The amino acid compositions of globular and outer membrane proteins have been systematically analyzed and a statistical method has been proposed for discriminating outer membrane proteins. The prediction of membrane spanning segments is mainly based on feed forward neural network and refined with β-strand length. Our program takes the amino acid sequence as input and displays the type of the protein along with membrane-spanning β-strand segments as a stretch of highlighted amino acid residues. Further, the probability of residues to be in transmembrane β-strand has been provided with a coloring scheme. We observed that outer membrane proteins were discriminated with an accuracy of 89% and their membrane spanning β-strand segments at an accuracy of 73% just from amino acid sequence information. The prediction server is available at

Properties of holographic dark energy at the Hubble length

We consider holographic cosmological models of dark energy in which the infrared cutoff is set by the Hubble's radius. We show that any interacting dark energy model, regardless of its detailed form, can be recast as a non interacting model in which the holographic parameter $c^{2}$ evolves slowly with time. Two specific cases are analyzed. We constrain the parameters of both models with observational data, and show that they can be told apart at the perturbative level.Comment: 4 pages, 6 figures. Contribution to the Proceedings ERE201

TMBETA-GENOME: database for annotated β-barrel membrane proteins in genomic sequences

We have developed the database, TMBETA-GENOME, for annotated β-barrel membrane proteins in genomic sequences using statistical methods and machine learning algorithms. The statistical methods are based on amino acid composition, reside pair preference and motifs. In machine learning techniques, the combination of amino acid and dipeptide compositions has been used as main attributes. In addition, annotations have been made using the criterion based on the identification of β-barrel membrane proteins and exclusion of globular and transmembrane helical proteins. A web interface has been developed for identifying the annotated β-barrel membrane proteins in all known genomes. The users have the feasibility of selecting the genome from the three kingdoms of life, archaea, bacteria and eukaryote, and five different methods. Further, the statistics for all genomes have been provided along with the links to different algorithms and related databases. It is freely available at

High Prevalence of False Chordae Tendinae in Patients Without Left Ventricular Tachycardia

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74774/1/j.1540-8159.2007.00628.x.pd

Interacting Ricci Dark Energy and its Statefinder Description

In this paper we have considered an interacting Ricci dark energy in flat FRW universe. We have reconstructed the Hubble's parameter under this interaction. Also, we have investigated the statefinder diagnostics. It has been revealed that the equation of state parameter behaves like quintessence in this interaction and from the statefinder diagnostics it has been concluded that the interacting Ricci dark energy interpolates between dust and $\Lambda$CDM stages of the universe.Comment: 9 pages, 3 figure

Do food scares explain supplier concentration? An analysis of EU agri-food imports

We investigate how rising sanitary risk of agri-food products affects the geographical concentration of European Union (EU) imports at the product level. We first estimate a product-specific measure of sanitary risk based on the count of food alerts at EU borders. Then we regress the evolution of geographical concentration indices on our measure of product risk and year. We find that product sanitary risk indeed affected the EU import pattern. Overall, the EU diversified its import sources, but with diversification at the extensive margin and concentration at the intensive margin. This pattern is stronger for risky products, leading to a two-tier system

Inferring Core-Collapse Supernova Physics with Gravitational Waves

Stellar collapse and the subsequent development of a core-collapse supernova explosion emit bursts of gravitational waves (GWs) that might be detected by the advanced generation of laser interferometer gravitational-wave observatories such as Advanced LIGO, Advanced Virgo, and LCGT. GW bursts from core-collapse supernovae encode information on the intricate multi-dimensional dynamics at work at the core of a dying massive star and may provide direct evidence for the yet uncertain mechanism driving supernovae in massive stars. Recent multi-dimensional simulations of core-collapse supernovae exploding via the neutrino, magnetorotational, and acoustic explosion mechanisms have predicted GW signals which have distinct structure in both the time and frequency domains. Motivated by this, we describe a promising method for determining the most likely explosion mechanism underlying a hypothetical GW signal, based on Principal Component Analysis and Bayesian model selection. Using simulated Advanced LIGO noise and assuming a single detector and linear waveform polarization for simplicity, we demonstrate that our method can distinguish magnetorotational explosions throughout the Milky Way (D <~ 10kpc) and explosions driven by the neutrino and acoustic mechanisms to D <~ 2kpc. Furthermore, we show that we can differentiate between models for rotating accretion-induced collapse of massive white dwarfs and models of rotating iron core collapse with high reliability out to several kpc.Comment: 22 pages, 9 figure