Macromolecular crowding explains overflow metabolism in cells

Overflow metabolism is a metabolic phenotype of cells characterized by mixed oxidative phosphorylation (OxPhos) and fermentative glycolysis in the presence of oxygen. Recently, it was proposed that a combination of a protein allocation constraint and a higher proteome fraction cost of energy generation by OxPhos relative to fermentation form the basis of overflow metabolism in the bacterium, Escherichia coli. However, we argue that the existence of a maximum or optimal macromolecular density is another essential requirement. Here we re-evaluate our previous theory of overflow metabolism based on molecular crowding following the proteomic fractions formulation. We show that molecular crowding is a key factor in explaining the switch from OxPhos to overflow metabolism

Stack Overflow: A Code Laundering Platform?

Developers use Question and Answer (Q&A) websites to exchange knowledge and expertise. Stack Overflow is a popular Q&A website where developers discuss coding problems and share code examples. Although all Stack Overflow posts are free to access, code examples on Stack Overflow are governed by the Creative Commons Attribute-ShareAlike 3.0 Unported license that developers should obey when reusing code from Stack Overflow or posting code to Stack Overflow. In this paper, we conduct a case study with 399 Android apps, to investigate whether developers respect license terms when reusing code from Stack Overflow posts (and the other way around). We found 232 code snippets in 62 Android apps from our dataset that were potentially reused from Stack Overflow, and 1,226 Stack Overflow posts containing code examples that are clones of code released in 68 Android apps, suggesting that developers may have copied the code of these apps to answer Stack Overflow questions. We investigated the licenses of these pieces of code and observed 1,279 cases of potential license violations (related to code posting to Stack overflow or code reuse from Stack overflow). This paper aims to raise the awareness of the software engineering community about potential unethical code reuse activities taking place on Q&A websites like Stack Overflow.Comment: In proceedings of the 24th IEEE International Conference on Software Analysis, Evolution, and Reengineering (SANER

Analysis of a Splitting Estimator for Rare Event Probabilities in Jackson Networks

We consider a standard splitting algorithm for the rare-event simulation of overflow probabilities in any subset of stations in a Jackson network at level n, starting at a fixed initial position. It was shown in DeanDup09 that a subsolution to the Isaacs equation guarantees that a subexponential number of function evaluations (in n) suffice to estimate such overflow probabilities within a given relative accuracy. Our analysis here shows that in fact O(n^{2{\beta}+1}) function evaluations suffice to achieve a given relative precision, where {\beta} is the number of bottleneck stations in the network. This is the first rigorous analysis that allows to favorably compare splitting against directly computing the overflow probability of interest, which can be evaluated by solving a linear system of equations with O(n^{d}) variables.Comment: 23 page

Is Stack Overflow Overflowing With Questions and Tags

Programming question and answer (Q & A) websites, such as Quora, Stack Overflow, and Yahoo! Answer etc. helps us to understand the programming concepts easily and quickly in a way that has been tested and applied by many software developers. Stack Overflow is one of the most frequently used programming Q\&A website where the questions and answers posted are presently analyzed manually, which requires a huge amount of time and resource. To save the effort, we present a topic modeling based technique to analyze the words of the original texts to discover the themes that run through them. We also propose a method to automate the process of reviewing the quality of questions on Stack Overflow dataset in order to avoid ballooning the stack overflow with insignificant questions. The proposed method also recommends the appropriate tags for the new post, which averts the creation of unnecessary tags on Stack Overflow.Comment: 11 pages, 7 figures, 3 tables Presented at Third International Symposium on Women in Computing and Informatics (WCI-2015

Cholinergic modulation of dopamine overflow in the rat neostriatum: A fast cyclic voltammetric study in vitro

Stimulus-evoked dopamine overflow in rat neostriatal slices was determined using fast cyclic voltammetry. The dopamine efflux induced by intrastriatal stimulation increased with stimulus intensity and was found to be enhanced by more than 100% upon application of the dopamine uptake inhibitor nomifensine. The acetylcholine esterase inhibitor eserine concentration-dependently and reversibly depressed stimulus-induced dopamine overflow. This effect was mediated by both, muscarinic and nicotinic cholinergic receptors: the action of eserine was mimicked by cholinergic agonists (muscarine and nicotine) and the effects of these agonists were blocked by muscarinic and nicotinic antagonists (atropine and dihydro-β-erythroidine). These experiments suggest that endogenous acetylcholine exerts an inhibitory control on stimulus-evoked (i.e. phasic) dopamine overflow in vitro by affecting striatal dopaminergic nerve terminals

From Query to Usable Code: An Analysis of Stack Overflow Code Snippets

Enriched by natural language texts, Stack Overflow code snippets are an invaluable code-centric knowledge base of small units of source code. Besides being useful for software developers, these annotated snippets can potentially serve as the basis for automated tools that provide working code solutions to specific natural language queries. With the goal of developing automated tools with the Stack Overflow snippets and surrounding text, this paper investigates the following questions: (1) How usable are the Stack Overflow code snippets? and (2) When using text search engines for matching on the natural language questions and answers around the snippets, what percentage of the top results contain usable code snippets? A total of 3M code snippets are analyzed across four languages: C\#, Java, JavaScript, and Python. Python and JavaScript proved to be the languages for which the most code snippets are usable. Conversely, Java and C\# proved to be the languages with the lowest usability rate. Further qualitative analysis on usable Python snippets shows the characteristics of the answers that solve the original question. Finally, we use Google search to investigate the alignment of usability and the natural language annotations around code snippets, and explore how to make snippets in Stack Overflow an adequate base for future automatic program generation.Comment: 13th IEEE/ACM International Conference on Mining Software Repositories, 11 page