Learning to Fix Build Errors with Graph2Diff Neural Networks

Professional software developers spend a significant amount of time fixing builds, but this has received little attention as a problem in automatic program repair. We present a new deep learning architecture, called Graph2Diff, for automatically localizing and fixing build errors. We represent source code, build configuration files, and compiler diagnostic messages as a graph, and then use a Graph Neural Network model to predict a diff. A diff specifies how to modify the code’s abstract syntax tree, represented in the neural network as a sequence of tokens and of pointers to code locations. Our network is an instance of a more general abstraction which we call Graph2Tocopo, which is potentially useful in any development tool for predicting source code changes. We evaluate the model on a dataset of over 500k real build errors and their resolutions from professional developers. Compared to the approach of DeepDelta [23], our approach tackles the harder task of predicting a more precise diff but still achieves over double the accuracy

Learning to Fix Build Errors with Graph2Diff Neural Networks

Professional software developers spend a significant amount of time fixing builds, but this has received little attention as a problem in automatic program repair. We present a new deep learning architecture, called Graph2Diff, for automatically localizing and fixing build errors. We represent source code, build configuration files, and compiler diagnostic messages as a graph, and then use a Graph Neural Network model to predict a diff. A diff specifies how to modify the code’s abstract syntax tree, represented in the neural network as a sequence of tokens and of pointers to code locations. Our network is an instance of a more general abstraction which we call Graph2Tocopo, which is potentially useful in any development tool for predicting source code changes. We evaluate the model on a dataset of over 500k real build errors and their resolutions from professional developers. Compared to the approach of DeepDelta [23], our approach tackles the harder task of predicting a more precise diff but still achieves over double the accuracy

Spectra of supernovae in the nebular phase

When supernovae enter the nebular phase after a few months, they reveal spectral fingerprints of their deep interiors, glowing by radioactivity produced in the explosion. We are given a unique opportunity to see what an exploded star looks like inside. The line profiles and luminosities encode information about physical conditions, explosive and hydrostatic nucleosynthesis, and ejecta morphology, which link to the progenitor properties and the explosion mechanism. Here, the fundamental properties of spectral formation of supernovae in the nebular phase are reviewed. The formalism between ejecta morphology and line profile shapes is derived, including effects of scattering and absorption. Line luminosity expressions are derived in various physical limits, with examples of applications from the literature. The physical processes at work in the supernova ejecta, including gamma-ray deposition, non-thermal electron degradation, ionization and excitation, and radiative transfer are described and linked to the computation and application of advanced spectral models. Some of the results derived so far from nebular-phase supernova analysis are discussed.Comment: Book chapter for 'Handbook of Supernovae,' edited by Alsabti and Murdin, Springer. 51 pages, 14 figure

A bacterial formula with native strains as alternative to chemical fertiliser for tomato crop

Global tomato productivity is threatened by biotic and abiotic stressors. To support and guarantee an adequate yield of tomato crops, agricultural practices have been based on the intensive use of fertilisers with negative impacts on the environment. This study presents a simple and effective strategy of functional bioaugmentation, suitable for different varieties, to replace chemical fertilisation. A tailored microbial formula composed by eight indigenous strains (including the genera Delftia, Pseudomonas, Paenarthrobacter, Phyllobacterium, Bacillus, and Acinetobacter) was developed as biofertilizer. Strains were selected from native soil for their plant growth-promoting (PGP) functions, and combined respecting the taxonomic composition of the original PGP heterotrophic community structure. The effect of the bio-fertilisation vs chemical fertilisation was tested in three successive field trials in the company greenhouse, with different tomato varieties (Camone, Oblungo, Cherry). When bio-fertilisation was applied only twice during the Camone's life cycle, tomato yield was significantly reduced (0.8 vs 2.1 kg per plant, p = 0.0003). However, monthly inoculation during plant growth led to a fruit yield comparable to that obtained with chemical fertilisers (about 1.5 kg per plant for Oblungo, and about 2 kg per plant for Cherry variety, p = 0.9999). Bio-fertilization did not significantly affect plant height; only during the last growing period of the Cherry variety, a significantly higher average plant height (p < 0.0001) was observed with chemical fertiliser. The results indicate that a knowledge-based bacterial formula and monthly inoculation during the plant growth can be a successful bio-fertilisation strategy. These findings may pave the way towards more sustainable tomato production, since farming practices are becoming increasingly crucial, in accordance with Agenda 2030 and the UE "Farm to Fork" strategy.[GRAPHICS]

Errors in chromosome segregation during oogenesis and early embryogenesis

Errors in chromosome segregation occurring during human oogenesis and early embryogenesis are very common. Meiotic chromosome development during oogenesis is subdivided into three distinct phases. The crucial events, including meiotic chromosome pairing and recombination, take place from around 11 weeks until birth. Oogenesis is then arrested until ovulation, when the first meiotic division takes place, with the second meiotic division not completed until after fertilization. It is generally accepted that most aneuploid fetal conditions, such as trisomy 21 Down syndrome, are due to maternal chromosome segregation errors. The underlying reasons are not yet fully understood. It is also clear that superimposed on the maternal meiotic chromosome segregation errors, there are a large number of mitotic errors taking place post-zygotically during the first few cell divisions in the embryo. In this chapter, we summarise current knowledge of errors in chromosome segregation during oogenesis and early embryogenesis, with special reference to the clinical implications for successful assisted reproduction

Buckling Instabilities of a Confined Colloid Crystal Layer

A model predicting the structure of repulsive, spherically symmetric, monodisperse particles confined between two walls is presented. We study the buckling transition of a single flat layer as the double layer state develops. Experimental realizations of this model are suspensions of stabilized colloidal particles squeezed between glass plates. By expanding the thermodynamic potential about a flat state of $N$ confined colloidal particles, we derive a free energy as a functional of in-plane and out-of-plane displacements. The wavevectors of these first buckling instabilities correspond to three different ordered structures. Landau theory predicts that the symmetry of these phases allows for second order phase transitions. This possibility exists even in the presence of gravity or plate asymmetry. These transitions lead to critical behavior and phases with the symmetry of the three-state and four-state Potts models, the X-Y model with 6-fold anisotropy, and the Heisenberg model with cubic interactions. Experimental detection of these structures is discussed.Comment: 24 pages, 8 figures on request. EF508

ISO spectroscopy of gas and dust: from molecular clouds to protoplanetary disks

Observations of interstellar gas-phase and solid-state species in the 2.4-200 micron range obtained with the spectrometers on board the Infrared Space Observatory are reviewed. Lines and bands due to ices, polycyclic aromatic hydrocarbons, silicates and gas-phase atoms and molecules (in particular H2, CO, H2O, OH and CO2) are summarized and their diagnostic capabilities illustrated. The results are discussed in the context of the physical and chemical evolution of star-forming regions, including photon-dominated regions, shocks, protostellar envelopes and disks around young stars.Comment: 56 pages, 17 figures. To appear in Ann. Rev. Astron. Astrophys. 2004. Higher resolution version posted at http://www.strw.leidenuniv.nl/~ewine/araa04.pd

High Levels of Heavy Metal(loid)s Related to Biliary Hyperplasia in Hedgehogs (Erinaceus europaeus)

Simple Summary Heavy metal(loid)s are hazardous substances for humans, animals and ecosystems. The liver is one of the most affected organs, presenting lesions after being acutely or chronically exposed to these substances. In this study, hepatic metal(loid)s' concentrations were associated with biliary hyperplasia, which was the most common hepatic lesion found in a group of western-European hedgehogs from rescue centres in Portugal. With exception of arsenic (As), all metal(loid)s were present in higher concentrations in animals with biliary hyperplasia. Further research is necessary to support these results and clarify the molecular mechanisms that lead to hepatic lesions provoked by these compounds. Heavy metal(loid) pollution of ecosystems is a current One Health problem. The liver is one of the most affected organs in cases of acute or chronic exposure to abnormal amounts of these substances, inducing histopathologic lesions. In order to assess the influence of heavy metal(loids), forty-five European hedgehogs (Erinaceus europaeus) were submitted to necropsy, and liver samples were collected for a routine histopathology exam and metal(loid)s determination (As, Cd, Co, Cr, Cu and Pb) by ICP-MS. Age was estimated during the necropsy exam. Biliary hyperplasia was the most frequent lesion observed (16/45; 35.56%). No statistically significant associations were found between biliary hyperplasia and age or sex. Metal(loid)s' concentrations were higher in animals with biliary hyperplasia (except for As). There was a statistically significant difference for both Cd and Co. For As, Cd and Co, cubs and juveniles animals showed significantly lower concentrations than elder individuals. Only for Pb were significant differences found between females and males. As described in the literature, exposure to metal(loid)s may be a cause of biliary hyperplasia, although further research (including the use of biochemical methods) is needed to support these results. To the authors' knowledge, this is the first report of this association in hedgehogs.This work was supported by National Funds by the Portuguese Foundation for Science and Technology (FCT). The authors of the research unit CITAB (CJB and PAO) received funding from FCT-reference of the project: UIDB/04033/2020. The author of the research unit CECAV (FS) received funding from FCT-reference of the project: UIDB/CVT/00772/2020. CJB was supported by FCT due to the phD scholarship 2021.04520.BD. TLM was supported by UIDB/CVT/00772/2020 and LA/P/0059/2020 funded by FCT

Multimodal Treatment Eliminates Cancer Stem Cells and Leads to Long-Term Survival in Primary Human Pancreatic Cancer Tissue Xenografts.

Copyright: 2013 Hermann et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.PURPOSE: In spite of intense research efforts, pancreatic ductal adenocarcinoma remains one of the most deadly malignancies in the world. We and others have previously identified a subpopulation of pancreatic cancer stem cells within the tumor as a critical therapeutic target and additionally shown that the tumor stroma represents not only a restrictive barrier for successful drug delivery, but also serves as a paracrine niche for cancer stem cells. Therefore, we embarked on a large-scale investigation on the effects of combining chemotherapy, hedgehog pathway inhibition, and mTOR inhibition in a preclinical mouse model of pancreatic cancer. EXPERIMENTAL DESIGN: Prospective and randomized testing in a set of almost 200 subcutaneous and orthotopic implanted whole-tissue primary human tumor xenografts. RESULTS: The combined targeting of highly chemoresistant cancer stem cells as well as their more differentiated progenies, together with abrogation of the tumor microenvironment by targeting the stroma and enhancing tissue penetration of the chemotherapeutic agent translated into significantly prolonged survival in preclinical models of human pancreatic cancer. Most pronounced therapeutic effects were observed in gemcitabine-resistant patient-derived tumors. Intriguingly, the proposed triple therapy approach could be further enhanced by using a PEGylated formulation of gemcitabine, which significantly increased its bioavailability and tissue penetration, resulting in a further improved overall outcome. CONCLUSIONS: This multimodal therapeutic strategy should be further explored in the clinical setting as its success may eventually improve the poor prognosis of patients with pancreatic ductal adenocarcinoma