Automatically Extracting Instances of Code Change Patterns with AST Analysis

A code change pattern represents a kind of recurrent modification in software. For instance, a known code change pattern consists of the change of the conditional expression of an if statement. Previous work has identified different change patterns. Complementary to the identification and definition of change patterns, the automatic extraction of pattern instances is essential to measure their empirical importance. For example, it enables one to count and compare the number of conditional expression changes in the history of different projects. In this paper we present a novel approach for search patterns instances from software history. Our technique is based on the analysis of Abstract Syntax Trees (AST) files within a given commit. We validate our approach by counting instances of 18 change patterns in 6 open-source Java projects.Comment: ICSM - 29th IEEE International Conference on Software Maintenance (2013

Conditional expression in corticothalamic efferents reveals a developmental role for nicotinic acetylcholine receptors in modulation of passive avoidance behavior

Prenatal nicotine exposure has been linked to attention deficit hyperactivity disorder and cognitive impairment, but the sites of action for these effects of nicotine are still under investigation. High-affinity nicotinic acetylcholine receptors (nAChRs) contain the .2 subunit and modulate passive avoidance (PA) learning in mice. Using an inducible, tetracycline-regulated transgenic system, we generated lines of mice with expression of high-affinity nicotinic receptors restored in specific neuronal populations. One line of mice shows functional .2 subunit-containing nAChRs localized exclusively in corticothalamic efferents. Functional, presynaptic nAChRs are present in the thalamus of these mice as detected by nicotine-elicited rubidium efflux assays from synaptosomes. Knock-out mice lacking high-affinity nAChRs show elevated baseline PA learning, whereas normal baseline PA behavior is restored in mice with corticothalamic expression of these nAChRs. In contrast, nicotine can enhance PA learning in adult wild-type animals but not in corticothalamic-expressing transgenic mice. When these transgenic mice are treated with doxycycline in adulthood to switch off nAChR expression, baseline PA is maintained even after transgene expression is abolished. These data suggest that high-affinity nAChRs expressed on corticothalamic neurons during development are critical for baseline PA performance and provide a potential neuroanatomical substrate for changes induced by prenatal nicotine exposure leading to long-term behavioral and cognitive deficits

A Low-Overhead Script Language for Tiny Networked Embedded Systems

With sensor networks starting to get mainstream acceptance, programmability is of increasing importance. Customers and field engineers will need to reprogram existing deployments and software developers will need to test and debug software in network testbeds. Script languages, which are a popular mechanism for reprogramming in general-purpose computing, have not been considered for wireless sensor networks because of the perceived overhead of interpreting a script language on tiny sensor nodes. In this paper we show that a structured script language is both feasible and efficient for programming tiny sensor nodes. We present a structured script language, SCript, and develop an interpreter for the language. To reduce program distribution energy the SCript interpreter stores a tokenized representation of the scripts which is distributed through the wireless network. The ROM and RAM footprint of the interpreter is similar to that of existing virtual machines for sensor networks. We show that the interpretation overhead of our language is on par with that of existing virtual machines. Thus script languages, previously considered as too expensive for tiny sensor nodes, are a viable alternative to virtual machines

A quantitative image analysis pipeline for the characterization of filamentous fungal morphologies as a tool to uncover targets for morphology engineering: a case study using aplD in Aspergillus niger

Background Fungal fermentation is used to produce a diverse repertoire of enzymes, chemicals, and drugs for various industries. During submerged cultivation, filamentous fungi form a range of macromorphologies, including dispersed mycelia, clumped aggregates, or pellets, which have critical implications for rheological aspects during fermentation, gas/nutrient transfer, and, thus, product titres. An important component of strain engineering efforts is the ability to quantitatively assess fungal growth phenotypes, which will drive novel leads for morphologically optimized production strains. Results In this study, we developed an automated image analysis pipeline to quantify the morphology of pelleted and dispersed growth (MPD) which rapidly and reproducibly measures dispersed and pelleted macromorphologies from any submerged fungal culture. It (i) enables capture and analysis of several hundred images per user/day, (ii) is designed to quantitatively assess heterogeneous cultures consisting of dispersed and pelleted forms, (iii) gives a quantitative measurement of culture heterogeneity, (iv) automatically generates key Euclidian parameters for individual fungal structures including particle diameter, aspect ratio, area, and solidity, which are also assembled into a previously described dimensionless morphology number MN, (v) has an in-built quality control check which enables end-users to easily confirm the accuracy of the automated calls, and (vi) is easily adaptable to user-specified magnifications and macromorphological definitions. To concomitantly provide proof of principle for the utility of this image analysis pipeline, and provide new leads for morphologically optimized fungal strains, we generated a morphological mutant in the cell factory Aspergillus niger based on CRISPR-Cas technology. First, we interrogated a previously published co-expression networks for A. niger to identify a putative gamma-adaptin encoding gene (aplD) that was predicted to play a role in endosome cargo trafficking. Gene editing was used to generate a conditional aplD expression mutant under control of the titratable Tet-on system. Reduced aplD expression caused a hyperbranched growth phenotype and diverse defects in pellet formation with a putative increase in protein secretion. This possible protein hypersecretion phenotype could be correlated with increased dispersed mycelia, and both decreased pellet diameter and MN. Conclusion The MPD image analysis pipeline is a simple, rapid, and flexible approach to quantify diverse fungal morphologies. As an exemplar, we have demonstrated that the putative endosomal transport gene aplD plays a crucial role in A. niger filamentous growth and pellet formation during submerged culture. This suggests that endocytic components are underexplored targets for engineering fungal cell factories.DFG, 414044773, Open Access Publizieren 2019 - 2020 / Technische Universität Berli

Functional exploration of co-expression networks identifies a nexus for modulating protein and citric acid titres in Aspergillus niger submerged culture

Background: Filamentous fungal cell factories are used to produce numerous proteins, enzymes, and organic acids. Protein secretion and filamentous growth are tightly coupled at the hyphal tip. Additionally, both these processes require ATP and amino acid precursors derived from the citric acid cycle. Despite this interconnection of organic acid production and protein secretion/filamentous growth, few studies in fungi have identified genes which may concomitantly impact all three processes. Results: We applied a novel screen of a global co-expression network in the cell factory Aspergillus niger to identify candidate genes which may concomitantly impact macromorphology, and protein/organic acid fermentation. This identified genes predicted to encode the Golgi localized ArfA GTPase activating protein (GAP, AgeB), and ArfA guanine nucleotide exchange factors (GEFs SecG and GeaB) to be co-expressed with citric acid cycle genes. Consequently, we used CRISPR-based genome editing to place the titratable Tet-on expression system upstream of ageB, secG, and geaB in A. niger. Functional analysis revealed that ageB and geaB are essential whereas secG was dispensable for early filamentous growth. Next, gene expression was titrated during submerged cultivations under conditions for either protein or organic acid production. ArfA regulators played varied and culture-dependent roles on pellet formation. Notably, ageB or geaB expression levels had major impacts on protein secretion, whereas secG was dispensable. In contrast, reduced expression of each predicted ArfA regulator resulted in an absence of citric acid in growth media. Finally, titrated expression of either GEFs resulted in an increase in oxaloacetic acid concentrations in supernatants. Conclusion: Our data suggest that the Golgi may play an underappreciated role in modulating organic acid titres during industrial applications, and that this is SecG, GeaB and AgeB dependent in A. niger. These data may lead to novel avenues for strain optimization in filamentous fungi for improved protein and organic acid titres.TU Berlin, Open-Access-Mittel - 201

A construct with fluorescent indicators for conditional expression of miRNA

<p>Abstract</p> <p>Background</p> <p>Transgenic RNAi holds promise as a simple, low-cost, and fast method for reverse genetics in mammals. It may be particularly useful for producing animal models for hypomorphic gene function. Inducible RNAi that permits spatially and temporally controllable gene silencing in vivo will enhance the power of transgenic RNAi approach. Furthermore, because microRNA (miRNA) targeting specific genes can be expressed simultaneously with protein coding genes, incorporation of fluorescent marker proteins can simplify the screening and analysis of transgenic RNAi animals.</p> <p>Results</p> <p>We sought to optimally express a miRNA simultaneously with a fluorescent marker. We compared two construct designs. One expressed a red fluorescent protein (RFP) and a miRNA placed in its 3' untranslated region (UTR). The other expressed the same RFP and miRNA, but the precursor miRNA (pre-miRNA) coding sequence was placed in an intron that was inserted into the 3'-UTR. We found that the two constructs expressed comparable levels of miRNA. However, the intron-containing construct expressed a significantly higher level of RFP than the intron-less construct. Further experiments indicate that the 3'-UTR intron enhances RFP expression by its intrinsic gene-expression-enhancing activity and by eliminating the inhibitory effect of the pre-miRNA on the expression of RFP. Based on these findings, we incorporated the intron-embedded pre-miRNA design into a conditional expression construct that employed the Cre-loxP system. This construct initially expressed EGFP gene, which was flanked by loxP sites. After exposure to Cre recombinase, the transgene stopped EGFP expression and began expression of RFP and a miRNA, which silenced the expression of specific cellular genes.</p> <p>Conclusion</p> <p>We have designed and tested a conditional miRNA-expression construct and showed that this construct expresses both the marker genes strongly and can silence the target gene efficiently upon Cre-mediated induction of the miRNA expression. This construct can be used to increase the efficiency of making cell lines or transgenic animals that stably express miRNA targeting specific genes.</p

Macrophage depletion disrupts immune balance and energy homeostasis.

Increased macrophage infiltration in tissues including white adipose tissue and skeletal muscle has been recognized as a pro-inflammatory factor that impairs insulin sensitivity in obesity. However, the relationship between tissue macrophages and energy metabolism under non-obese physiological conditions is not clear. To study a homeostatic role of macrophages in energy homeostasis, we depleted tissue macrophages in adult mice through conditional expression of diphtheria toxin (DT) receptor and DT-induced apoptosis. Macrophage depletion robustly reduced body fat mass due to reduced energy intake. These phenotypes were reversed after macrophage recovery. As a potential mechanism, severe hypothalamic and systemic inflammation was induced by neutrophil (NE) infiltration in the absence of macrophages. In addition, macrophage depletion dramatically increased circulating granulocyte colony-stimulating factor (G-CSF) which is indispensable for NE production and tissue infiltration. Our in vitro study further revealed that macrophages directly suppress G-CSF gene expression. Therefore, our study indicates that macrophages may play a critical role in integrating immune balance and energy homeostasis under physiological conditions

Dissection of a Bug Dataset: Anatomy of 395 Patches from Defects4J

Well-designed and publicly available datasets of bugs are an invaluable asset to advance research fields such as fault localization and program repair as they allow directly and fairly comparison between competing techniques and also the replication of experiments. These datasets need to be deeply understood by researchers: the answer for questions like "which bugs can my technique handle?" and "for which bugs is my technique effective?" depends on the comprehension of properties related to bugs and their patches. However, such properties are usually not included in the datasets, and there is still no widely adopted methodology for characterizing bugs and patches. In this work, we deeply study 395 patches of the Defects4J dataset. Quantitative properties (patch size and spreading) were automatically extracted, whereas qualitative ones (repair actions and patterns) were manually extracted using a thematic analysis-based approach. We found that 1) the median size of Defects4J patches is four lines, and almost 30% of the patches contain only addition of lines; 2) 92% of the patches change only one file, and 38% has no spreading at all; 3) the top-3 most applied repair actions are addition of method calls, conditionals, and assignments, occurring in 77% of the patches; and 4) nine repair patterns were found for 95% of the patches, where the most prevalent, appearing in 43% of the patches, is on conditional blocks. These results are useful for researchers to perform advanced analysis on their techniques' results based on Defects4J. Moreover, our set of properties can be used to characterize and compare different bug datasets.Comment: Accepted for SANER'18 (25th edition of IEEE International Conference on Software Analysis, Evolution and Reengineering), Campobasso, Ital

Encoding many-valued logic in {\lambda}-calculus

We extend the well-known Church encoding of two-valued Boolean Logic in $\lambda$-calculus to encodings of $n$-valued propositional logic (for $3\leq n\leq 5$) in well-chosen infinitary extensions in $\lambda$-calculus. In case of three-valued logic we use the infinitary extension of the finite $\lambda$-calculus in which all terms have their B\"ohm tree as their unique normal form. We refine this construction for $n\in\{4,5\}$. These $n$-valued logics are all variants of McCarthy's left-sequential, three-valued propositional calculus. The four- and five-valued logic have been given complete axiomatisations by Bergstra and Van de Pol. The encodings of these $n$-valued logics are of interest because they can be used to calculate the truth values of infinitary propositions. With a novel application of McCarthy's three-valued logic we can now resolve Russell's paradox. Since B\"ohm trees are always finite in Church's original $\lambda{\mathbf I}$-calculus, we believe their construction to be within the technical means of Church. Arguably he could have found this encoding of three-valued logic and used it to resolve Russell's paradox.Comment: 15 page