KGTorrent: A dataset of python jupyter notebooks from kaggle

Computational notebooks have become the tool of choice for many data scientists and practitioners for performing analyses and disseminating results. Despite their increasing popularity, the research community cannot yet count on a large, curated dataset of computational notebooks. In this paper, we fill this gap by introducing KGTorrent, a dataset of Python Jupyter notebooks with rich metadata retrieved from Kaggle, a platform hosting data science competitions for learners and practitioners with any levels of expertise. We describe how we built KGTorrent, and provide instructions on how to use it and refresh the collection to keep it up to date. Our vision is that the research community will use KGTorrent to study how data scientists, especially practitioners, use Jupyter Notebook in the wild and identify potential shortcomings to inform the design of its future extensions

Towards productizing AI/ML Models: An industry perspective from data scientists

The transition from AI/ML models to production-ready AI-based systems is a challenge for both data scientists and software engineers. In this paper, we report the results of a workshop conducted in a consulting company to understand how this transition is perceived by practitioners. Starting from the need for making AI experiments reproducible, the main themes that emerged are related to the use of the Jupyter Notebook as the primary prototyping tool, and the lack of support for software engineering best practices as well as data science specific functionalities

Engaging End-Users in the Collaborative Development of Domain-Speci c Modelling Languages

International audienceDomain-Speci c Modelling Languages (DSMLs) are high-level languages specially designed to perform tasks in a particular domain. When developing DSMLs, the participation of end-users is normally limited to providing domain knowledge and testing the resulting language prototypes. Language developers, which are perhaps not domain experts, are therefore in control of the language development and evolution. This may cause misinterpretations which hamper the development process and the quality of the DSML. Thus, it would be bene cial to promote a more active participation of end-users in the development process of DSMLs. While current DSML workbenches are mono-user and designed for technical experts, we present a process and tool support for the example-driven, collaborative construction of DSMLs in order to engage end-users in the creation of their own languages

FUNCTIONAL STUDY OF LIPOXYGENASE-MEDIATED RESISTANCE AGAINST ASPERGILLUS FLAVUS AND FUSARIUM VERTICILLIOIDES INFECTION IN MAIZE

Mycotoxin contamination of maize kernels by fungal pathogens Aspergillus flavus (Af) and Fusarium verticillioides (Fv) is a chronic global challenge impacting food security, health and trade. Current disease management practices are proven inadequate and strategies gearing towards hostmediated resistance can be an effective and sustainable approach to strengthen efforts to control the pathogens. Lipid modification into a diverse array of compounds, oxylipins, are recognized in response of plants to fungal pathogens. Lipoxygenase genes (LOXs) play a crucial role in the enzymatic oxidation of polyunsaturated fatty acids (PUFAs) into 9(S)- and 13(S)-hydroperoxides that are further metabolized into different oxylipins including jasmonates, oxo- and keto-fatty acids and volatiles. The involvement of maize LOXs (ZmLOXs) in this respect has been a subject of studies and their genetic manipulation resulted in the alteration of resistance or susceptibility to fungal pathogens in maize. However, the maize genome encodes six 9-LOX and seven 13-LOX isoforms and the specific role of each isoform remains elusive. The current study investigated the role of ZmLOXs in host resistance against the fungi Af and Fv using in silico and in planta approaches. The phylogenetic relationship, sequence similarity, protein domain structures, and transcript level structural variations were explored by comparing publicly available maize pan-genomes. Furthermore, the role of ZmLOXs against Af and Fv infection was investigated through their expression analysis along with further key genes involved in oxylipin biosynthesis, mycotoxin accumulation and lipid profiles in a ZmLOX4 mutant line (UFMulox4) together with W22, Mo17 and Tzi18 inbred lines at 3- and 7-days post-inoculation (dpi). ZmLOX proteins showed considerable variations in their sequences, functional domain structure and transcript structural variations among the pan-genome members. Among the studied lines, Tzi18 showed the highest resistance to the pathogens coupled with the lowest mycotoxin accumulation, while the mutant, UFMulox4, was highly susceptible to both pathogens with the most elevated content of mycotoxins. Fv inoculation determined a stronger induction of ZmLOXs and maize allene oxide synthase genes as compared to Af . Higher constitutive levels of 9-LOXs genes, ZmLOX1 and ZmLOX2 and an induction of ZmLOX4 were recorded in Tzi18, while the upregulation of ZmLOX1 and ZmLOX4 observed in Mo17 might have larger active role in resistance against Fv. Liquid chromatography-mass spectrometry further revealed an increased accumulation of the linoleic (18:2) derived 9-cyclopentenone, 10- oxo-11-phytoenoic acid (10-OPEA), in Fv inoculated kernels of Tzi18 and Mo17, which was previously identified to inhibit fungal growth in vitro. Hence, the results confirm the pivotal role of ZmLOXs in controlling the resistance mechanisms against these two pathogens

Enabling the Collaborative Definition of DSMLs

International audienceSoftware development processes are collaborative in nature. Neglecting the key role of end-users leads to software that does not satisfy their needs. This collaboration becomes specially important when creating Domain-Specific Modeling Languages (DSMLs), which are (modeling) languages specifically designed to carry out the tasks of a particular domain. While end-users are actually the experts of the domain for which a DSML is developed, their participation in the DSML specification process is still rather limited nowadays. In this paper we propose a more community-aware language development process by enabling the active participation of all community members (both developers and end-users of the DSML) from the very beginning. Our proposal is based on a DSML itself, called Collaboro, which allows representing change proposals on the DSML design and discussing (and tracing back) possible solutions, comments and decisions arisen during the collaboration

Functional Study of Lipoxygenase-Mediated Resistance against Fusarium verticillioides and Aspergillus flavus Infection in Maize

Mycotoxin contamination of maize kernels by fungal pathogens like Fusarium verticillioides and Aspergillus flavus is a chronic global challenge impacting food and feed security, health, and trade. Maize lipoxygenase genes (ZmLOXs) synthetize oxylipins that play defense roles and govern host-fungal interactions. The current study investigated the involvement of ZmLOXs in maize resistance against these two fungi. A considerable intraspecific genetic and transcript variability of the ZmLOX family was highlighted by in silico analysis comparing publicly available maize pan-genomes and pan-transcriptomes, respectively. Then, phenotyping and expression analysis of ZmLOX genes along with key genes involved in oxylipin biosynthesis were carried out in a maize mutant carrying a Mu transposon insertion in the ZmLOX4 gene (named UFMulox4) together with Tzi18, Mo17, and W22 inbred lines at 3- and 7-days post-inoculation with F. verticillioides and A. flavus. Tzi18 showed the highest resistance to the pathogens coupled with the lowest mycotoxin accumulation, while UFMulox4 was highly susceptible to both pathogens with the most elevated mycotoxin content. F. verticillioides inoculation determined a stronger induction of ZmLOXs and maize allene oxide synthase genes as compared to A. flavus. Additionally, oxylipin analysis revealed prevalent linoleic (18:2) peroxidation by 9-LOXs, the accumulation of 10-oxo-11-phytoenoic acid (10-OPEA), and triglyceride peroxidation only in F. verticillioides inoculated kernels of resistant genotypes

CHARACTERIZATION AND VALORIZATION OF MAIZE LANDRACES FROM VALLE D'AOSTA

During 1949-1950 in Italy begun a formal investigation to characterize maize (Zea mays L.) cultivation. In 1954, started a project for the sampling of all Italian maize landraces; this work ended with the collection of 562 different accessions collected in all regions with the exception of Valle d’Aosta, even if historical cultivation of maize in this Region is well documented. In Italy maize landraces have been extensively grown until the mid of the XX century when the cultivation of hybrid took place due to their significant agronomic performances. Despite that, being Valle d’Aosta a mountain region where intensive maize cultivation never started, it was possible to preserve the presence of some landraces. These local materials, which are still cultivated, mainly at domestic level, have high importance from a genetic and historical point of view. Recently, 5 maize landraces from Valle d’Aosta and 2 landraces from the adjacent Canavese (Piedmont) have been collected and subjected to historic, morphologic and genetic characterization. These landraces were named after the sampling location as it follows: Arnad, Arnad-Crest, Chatillon, Entrebin, Perloz, Bianco Canavese, and Rostrato Canavese. Firstly, on these 6 varieties the historic characterization has been carried out. Information and photographs have been searched in local archives and this was crucial to prove their long presence in all the sampling sites under study. From this historic reconstruction, the variety Entrebin resulted as the one that is better historically characterized. To study the variability and differentiation of landraces from Valle d’Aosta, the genetic characterization was performed by the means of 10 SSR markers tested on 20 samples from each landrace. This study highlighted a significant genetic variability among the landraces and, especially, a good level of differentiation between the accessions under investigation. This last result may be explained by the long reproductive isolation experienced by these materials. Complete morphological characterization is actually ongoing. Preliminary morphological observations revealed that these landraces have, generally, flint kernels with the exception of Bianco Canavese (dent) whose color is variable from white (Bianco Canavese) to dark red (Chatillon). Arnad landrace showed 8 kernel rows, probably being an Eight-rowed Flint while the others presented more rows, like many Derived Races. Interestingly, Perloz and Rostrato Canavese showed kernels with an apical beak which was more pronounced in the latter. This suggest that these two landraces belong to the “Rostrata” group, which is common in mountain areas. The present work confirms the importance of mountain areas in conserving biodiversity and increases the rich Italian maize germplasm with materials well adapted to marginal areas. Such new genetic variability may be used to breed new materials for a more resilient agriculture