Mining code change patterns to aid software development

Mining Software Repositories (MSR) has become a complete and mature research field, also due to the increasing number of open source projects publicly available. Repository hosting services such as GitHub provide unprecedented access to millions of events generated during development activities (e.g., code commits, pull requests), that can be mined and analyzed to extract new pieces of knowledge. By analyzing the source code of a large corpus of software systems, recent work showed that most software is natural, meaning that it is likely to be repetitive and predictable. In other words, development and maintenance activities are likely the results of unexposed code change patterns that, if properly exploited, can be used to support code-related activities (e.g., implementing a new feature). Starting from these observations, we formulate our thesis statement: Mining code change patterns from open source repositories enables researchers to gather large-scale, historical infor- mation about development and maintenance activities performed by developers. The collected empirical knowledge, once converted into actionable items, can support software developers on code-related tasks. We investigated the possibility of acquiring new empirical knowledge from mining three specific types of code change patterns in open source repositories: (i) the introduction and fix of code- comment inconsistencies, (ii) omitted code changes in developers' commits and (iii) implementation patterns followed by developers when implementing a new feature. We leveraged the knowledge acquired from the last type of patterns, to design and build FeaRS, an approach and a tool that, given the methods developers already wrote in the IDE, is able to suggest the complete code of the next method they are likely to implement. Our results show that mining unexposed code change patterns from open source repositories can help in better understanding development activities and potentially support developers during software development

The post-PAM interaction of RNA-guided spCas9 with DNA dictates its target binding and dissociation

International audienc

Visualization and Inhibition of Mitochondria-Nuclear Translocation of Apoptosis Inducing Factor by a Graphene Oxide-DNA Nanosensor

High concentrations of oxidized low density lipoprotein (oxLDL) induce aberrant apoptosis of vascular smooth muscle cells (VSMCs) in atherosclerotic plaques. This apoptosis cannot be blocked completely by the inhibition of caspase, and it eventually potentiates plaque disruption and risk for cardiovascular disease. Given the important role of apoptosis inducing factor (AIF) in caspase-independent apoptosis, here we develop an AIF-targeting nanosensor by the assembly of graphene oxide (GO) nanosheets and dye-labeled DNA hybrid structures. This nanosensor selectively localizes in the cytosol of VSMCs, where it exhibits a “turn-off” fluorescence signal. Under oxLDL stimuli, the release of AIF from mitochondria into cytosol liberates the DNA hybrid structures from the surface of GO and results in a “turn-on” fluorescence signal. This nanosensor is shown to possess rapid response, high sensitivity, and selectivity for AIF that enables real-time imaging of AIF translocation in VSMCs. Using this novel nanosensor, a better assessment of the apoptotic level of VSMCs and a more accurate evaluation of the extent of atherosclerotic lesions can be obtained. More importantly, the abundant binding between DNA hybrid structures and AIF inhibits the translocation of AIF into the nucleus and subsequent apoptosis in VSMCs. This inhibition may help stabilize plaque and reduce the risk of heart attack and stroke

Dynamics of Staphylococcus aureus

International audienceStaphylococcus aureus Cas9 (SaCas9) is an RNA-guided endonuclease that targets complementary DNA adjacent to a protospacer adjacent motif (PAM) for cleavage. Its small size facilitates in vivo delivery for genome editing in various organisms. Herein, using single-molecule and ensemble approaches, we systemically study the mechanism of SaCas9 underlying its interplay with DNA. We find that the DNA binding and cleavage of SaCas9 require complementarities of 6and 18-bp of PAM-proximal DNA with guide RNA, respectively. These activities are mediated by two steady interactions among the ternary complex, one of which is located approximately 6 bp from the PAM and beyond the apparent footprint of SaCas9 on DNA. Notably, the other interaction within the protospacer is significantly strong and thus poses DNA-bound SaCas9 a persistent block to DNA-tracking motors. Intriguingly, after cleavage, SaCas9 autonomously releases the PAM-distal DNA while retaining binding to the PAM. This partial DNA release immediately abolishes its strong interaction with the protospacer DNA and consequently promotes its subsequent dissociation from the PAM. Overall, these data provide a dynamic understanding of SaCas9 and instruct its effective applications

Determination of the number of ψ(3686)\psi(3686) events at BESIII

The numbers of ψ(3686) events accumulated by the BESIII detector for the data taken during 2009 and 2012 are determined to be and , respectively, by counting inclusive hadronic events, where the uncertainties are systematic and the statistical uncertainties are negligible. The number of events for the sample taken in 2009 is consistent with that of the previous measurement. The total number of ψ(3686) events for the two data taking periods is