HCPC: Human centric program comprehension by grouping static execution scenarios

New members of a software team can struggle to locate user requirements if proper software engineering principles are not practiced. Reading through code, finding relevant methods, classes and files take a significant portion of software development time. Many times developers have to fix issues in code written by others. Having a good tool support for this code browsing activity can reduce human effort and increase overall developers' productivity. To help program comprehension activities, building an abstract code summary of a software system from the call graph is an active research area. A call graph is a visual representation of caller-callee relationships between different methods of a software project. Call graphs can be difficult to comprehend for a larger code-base. The motivation is to extract the essence from the call graph by finding execution scenarios from a call graph and then cluster them together by concentrating the information in the code-base. Later, different techniques are applied to label nodes in the abstract code summary tree. In this thesis, we focus on static call graphs for creating an abstract code summary tree as it clusters all possible program scenarios and groups similar scenarios together. Previous work on static call graph clusters execution paths and uses only one information retrieval technique without any feedback from developers. First, to advance existing work, we introduced new information retrieval techniques alongside human-involved evaluation. We found that developers prefer node labels generated by terms in method names with TFIDF (term frequency-inverse document frequency). Second, from our observation, we introduced two new types of information (text description using comments and execution patterns) for abstraction nodes to provide better overview. Finally, we introduced an interactive software tool which can be used to browse the code-base in a guided way by targeting specific units of the source code. In the user study, we found developers can use our tool to overview a project alongside finding help for doing particular jobs such as locating relevant files and understanding relevant domain knowledge

Light-cone spreading of perturbations and the butterfly effect in a classical spin chain

We find that localised perturbations in a chaotic classical many-body system-- the classical Heisenberg We find that the effects of a localised perturbation in a chaotic classical many-body system--the classical Heisenberg chain at infinite temperature--spread ballistically with a finite speed even when the local spin dynamics is diffusive. We study two complementary aspects of this butterfly effect: the rapid growth of the perturbation, and its simultaneous ballistic (light-cone) spread, as characterised by the Lyapunov exponents and the butterfly speed respectively. We connect this to recent studies of the out-of-time-ordered commutators (OTOC), which have been proposed as an indicator of chaos in a quantum system. We provide a straightforward identification of the OTOC with a natural correlator in our system and demonstrate that many of its interesting qualitative features are present in the classical system. Finally, by analysing the scaling forms, we relate the growth, spread and propagation of the perturbation with the growth of one-dimensional interfaces described by the Kardar-Parisi-Zhang (KPZ) equation.Comment: 6 pages, 6 figures. Journal Ref. added: Physical Review Letters 121, 024101 (2018

CENCPP* - Beyond-birthday-secure Encryption from Public Permutations

Public permutations have been established as important primitives for the purpose of designing cryptographic schemes. While many such schemes for authentication and encryption have been proposed in the past decade, the birthday bound in terms of the primitive\u27s block length $n$ has been mostly accepted as the standard security goal. Thus, remarkably little research has been conducted yet on permutation-based modes with higher security guarantees. At CRYPTO\u2719, Chen et al. showed two constructions with higher security based on the sum of two public permutations. Their work has sparked increased interest in this direction by the community. However, since their proposals were domain-preserving, the question of encryption schemes with beyond-birthday-bound security was left open. This work tries to address this gap by proposing $\textsf{CENCPP}^*$, a nonce-based encryption scheme from public permutations. Our proposal is a variant of Iwata\u27s block-cipher-based mode \textsf{CENC} that we adapt for public permutations, thereby generalizing Chen et al.\u27s Sum-of-Even-Mansour construction to a mode with variable output lengths. Like \textsf{CENC}, our proposal enjoys a comfortable rate-security trade-off that needs $w + 1$ calls to the primitive for $w$ primitive outputs. We show a tight security level for up to $O(2^{2n/3}/w^2)$ primitive calls. While the term of $w \geq 1$ can be arbitrary, two independent keys suffice. Beyond our proposal of $\textsf{CENCPP}^*$ in a generic setting with $w + 1$ independent permutations, we show that only $\log_2(w + 1)$ bits of the input for domain separation suffice to obtain a single-permutation variant with a security level of up to $O(2^{2n/3}/w^4)$ queries

An Exploratory Study to Find Motives Behind Cross-platform Forks from Software Heritage Dataset

The fork-based development mechanism provides the flexibility and the unified processes for software teams to collaborate easily in a distributed setting without too much coordination overhead.Currently, multiple social coding platforms support fork-based development, such as GitHub, GitLab, and Bitbucket. Although these different platforms virtually share the same features, they have different emphasis. As GitHub is the most popular platform and the corresponding data is publicly available, most of the current studies are focusing on GitHub hosted projects. However, we observed anecdote evidences that people are confused about choosing among these platforms, and some projects are migrating from one platform to another, and the reasons behind these activities remain unknown.With the advances of Software Heritage Graph Dataset (SWHGD),we have the opportunity to investigate the forking activities across platforms. In this paper, we conduct an exploratory study on 10popular open-source projects to identify cross-platform forks and investigate the motivation behind. Preliminary result shows that cross-platform forks do exist. For the 10 subject systems in this study, we found 81,357 forks in total among which 179 forks are on GitLab. Based on our qualitative analysis, we found that most of the cross-platform forks that we identified are mirrors of the repositories on another platform, but we still find cases that were created due to preference of using certain functionalities (e.g. Continuous Integration (CI)) supported by different platforms. This study lays the foundation of future research directions, such as understanding the differences between platforms and supporting cross-platform collaboration.Comment: Accepted at 17th International Conference on Mining Software Repositories, October 5--6, 2020, Seoul, Republic of Kore

A simple ethanol wash of the tissue homogenates recovers high-quality genomic DNA from Corchorus species characterized by highly acidic and proteinaceous mucilages

A simple miniprep based on early elimination of highly acidic and proteinaceous mucilages through ethanol washing of the tissue homogenates has been developed for the extraction of genomic DNA from mature leaves and seeds of Corchorus spp. As compared to high cetyltrimethylammonium bromide (CTAB)-NaCl DNA extraction followed by ethanol-based removal of remnant mucilages from the DNA pellet, this simple miniprep consistently and reproducibly recovers high amounts of DNA with good spectral qualities at A260/A280 and A260/A230. The purified DNA is efficiently digested by restriction endonucleases, and is suitable for PCR amplification of nuclear microsatellites with expected allele sizes

Berberine Chloride Mediates Its Anti-Leishmanial Activity via Differential Regulation of the Mitogen Activated Protein Kinase Pathway in Macrophages

BACKGROUND: A complex interplay between Leishmania and macrophages influences parasite survival and necessitates disruption of signaling molecules, eventually resulting in impairment of macrophage function. In this study, we demonstrate the immunomodulatory activity of Berberine chloride in Leishmania infected macrophages. PRINCIPAL FINDINGS: The IC(50) of Berberine chloride, a quaternary isoquinoline alkaloid was tested in an amastigote macrophage model and its safety index measured by a cell viability assay. It eliminated intracellular amastigotes, the IC(50) being 2.8 fold lower than its IC(50) in promastigotes (7.10 µM vs. 2.54 µM) and showed a safety index >16. Levels of intracellular and extracellular nitric oxide (NO) as measured by flow cytometry and Griess assay respectively showed that Berberine chloride in Leishmania infected macrophages increased production of NO. Measurement of the mRNA expression of iNOS, IL-12 and IL-10 by RT-PCR along with levels of IL-12p40 and IL-10 by ELISA showed that in infected macrophages, Berberine chloride enhanced expression of iNOS and IL-12p40, concomitant with a downregulation of IL-10. The phosphorylation status of extracellular signal related kinase (ERK1/2) and p38 mitogen activated protein kinase (p38 MAPK) was studied by western blotting. In infected macrophages, Berberine chloride caused a time dependent activation of p38 MAPK along with deactivation of ERK1/2; addition of a p38 MAPK inhibitor SB203580 inhibited the increased generation of NO and IL-12p40 by Berberine chloride as also prevented its decrease of IL-10. CONCLUSIONS: Berberine chloride modulated macrophage effector responses via the mitogen activated protein kinase (MAPK) pathway, highlighting the importance of MAPKs as an antiparasite target

PAE\textsf{PAE}: Towards More Efficient and BBB-secure AE From a Single Public Permutation

Four recent trends have emerged in the evolution of authenticated encryption schemes: (1) Regarding simplicity, the adoption of public permutations as primitives allows for sparing a key schedule and the need for storing round keys; (2) using the sums of permutation outputs, inputs, or outputs has been a well-studied means to achieve higher security beyond the birthday bound; (3) concerning robustness, schemes should provide graceful security degradation if a limited amount of nonces repeats during the lifetime of a key, and (4) Andreeva et al.\u27s ForkCipher approach can increase the efficiency of a scheme since they can use fewer rounds per output branch compared to full-round primitives. In this work, we improve on the state of the art by combining those aspects for efficient authenticated encryption. We propose $\textsf{PAE}$, an efficient nonce-based AE scheme that employs a public permutation and one call to an XOR-universal hash function. $\textsf{PAE}$ provides $O(2n/3)$-bit security and high throughput by combining forked public-permutation-based variants of $\textsf{nEHtM}$ and an Encrypted Davies-Meyer. Thus, it can use a single, in part round-reduced, public permutation for most operations, spare a key schedule, and guarantee security beyond the birthday bound even under limited nonce reuse

A simple ethanol wash of the tissue homogenates recovers high-quality genomic DNA from Corchorus species characterized by highly acidic and proteinaceous mucilages

A simple miniprep based on early elimination of highly acidic and proteinaceous mucilages through ethanol washing of the tissue homogenates has been developed for the extraction of genomic DNA from mature leaves and seeds of Corchorus spp. As compared to high cetyltrimethylammonium bromide (CTAB)-NaCl DNA extraction followed by ethanol-based removal of remnant mucilages from the DNA pellet, this simple miniprep consistently and reproducibly recovers high amounts of DNA with good spectral qualities at A260/A280 and A260/A230. The purified DNA is efficiently digested by restriction endonucleases, and is suitable for PCR amplification of nuclear microsatellites with expected allele sizes

Comparison between intrathecal isobaric ropivacaine-fentanyl and bupivacaine-fentanyl in elective infraumbilical orthopedic surgery: A randomized controlled study

Background and Aims: We aimed to evaluate and compare the block characteristics and duration of analgesia of intrathecal isobaric ropivacaine-fentanyl and bupivacaine-fentanyl combination in adult patients undergoing lower limb orthopedic surgery. Material and Methods: Seventy-four American Society of Anesthesiologists′ I and II adult patients undergoing lower limb orthopedic surgery under subarachnoid block were randomized to receive either 3 ml 0.5% isobaric ropivacaine and 25 mcg fentanyl (Group R) or 3 ml 0.5% isobaric bupivacaine and 25 mcg fentanyl (Group B). The hemodynamic profiles, maximum upper level of sensory block height, time to reach peak block height, two dermatome regression time, and duration of motor block were recorded. Results: There was no statistically significant difference regarding the hemodynamic parameters between the groups. The median (range) peak sensory block height was T7 (T4-T9) in Group R and T7 (T4-T10) in Group B. Time to reach peak block height (13.2 ± 2.3 min in Group R vs. 13.7 ± 2.2 min in Group B; P = 0.385) was similar between the groups. Two dermatome regression time in sensory block (median 120 min vs. 85 min; P < 0.001) and duration of motor block (median 245 min vs. 150 min; P < 0.001) was significantly higher in Group B. The duration of analgesia (median 360 min vs. 245 min; P < 0.001) was significantly higher in the bupivacaine group. Conclusion: Intrathecal isobaric bupivacaine-fentanyl combination produces a significantly longer duration of analgesia, sensory block and motor block than isobaric ropivacaine-fentanyl combination. As ropivacaine has a shorter duration of sensory and motor block, it may be preferred in day care surgery