LiSum: Open Source Software License Summarization with Multi-Task Learning

Open source software (OSS) licenses regulate the conditions under which users can reuse, modify, and distribute the software legally. However, there exist various OSS licenses in the community, written in a formal language, which are typically long and complicated to understand. In this paper, we conducted a 661-participants online survey to investigate the perspectives and practices of developers towards OSS licenses. The user study revealed an indeed need for an automated tool to facilitate license understanding. Motivated by the user study and the fast growth of licenses in the community, we propose the first study towards automated license summarization. Specifically, we released the first high quality text summarization dataset and designed two tasks, i.e., license text summarization (LTS), aiming at generating a relatively short summary for an arbitrary license, and license term classification (LTC), focusing on the attitude inference towards a predefined set of key license terms (e.g., Distribute). Aiming at the two tasks, we present LiSum, a multi-task learning method to help developers overcome the obstacles of understanding OSS licenses. Comprehensive experiments demonstrated that the proposed jointly training objective boosted the performance on both tasks, surpassing state-of-the-art baselines with gains of at least 5 points w.r.t. F1 scores of four summarization metrics and achieving 95.13% micro average F1 score for classification simultaneously. We released all the datasets, the replication package, and the questionnaires for the community

Kinetics, SOA yields, and chemical composition of secondary organic aerosol from β-caryophyllene ozonolysis with and without nitrogen oxides between 213 and 313 K

β-caryophyllene (BCP) is one of the most important sesquiterpenes (SQTs) in the atmosphere, with a large potential contribution to secondary organic aerosol (SOA) formation mainly from reactions with ozone (O$_{3}$) and nitrate radicals (NO$_{3}$). In this work, we study the temperature dependence of the kinetics of BCP ozonolysis, SOA yields, and SOA chemical composition in the dark and in the absence and presence of nitrogen oxides including nitrate radicals (NO$_{3}$. We cover a temperature range of 213–313 K, representative of tropospheric conditions. The oxidized components in both gas and particle phases were characterized on a molecular level by a chemical ionization mass spectrometer equipped with a filter inlet for gases and aerosols using iodide as the reagent ion (FIGAERO-iodide-CIMS). The batch mode experiments were conducted in the 84.5 m$^{3}$ aluminium simulation chamber AIDA at the Karlsruhe Institute of Technology (KIT). In the absence of nitrogen oxides, the temperature-dependent rate coefficient of the endocyclic double bond in BCP reacting with ozone between 243–313 K is negatively correlated with temperature, corresponding to the following Arrhenius equation: k= (1.6 ± 0.4) × 10$^{-15}$ × exp((559 ±  97)/T). The SOA yields increase from 16 ± 5 % to 37 ± 11 %, with temperatures decreasing from 313 to 243 K at a total organic particle mass of 10 µg m$^{-3}$. The variation in the ozonolysis temperature leads to a substantial impact on the abundance of individual organic molecules. In the absence of nitrogen oxides, monomers C$_{14-15}$H$_{22-24}$O$_{3-7}$ (37.4 %), dimers C$_{28-30}$H$_{44-48}$O$_{5-9}$ (53.7 %), and trimers C$_{41-44}$H$_{62-66}$O$_{9-11}$ (8.6 %) are abundant in the particle phase at 213 K. At 313 K, we observed more oxidized monomers (mainly C$_{14-15}$H$_{22-24}$O$_{6-9}$, 67.5 %) and dimers (mainly C$_{27-29}$H$_{42-44}$O$_{9-11}$, 27.6 %), including highly oxidized molecules (HOMs; C$_{14}$H$_{22}$O$_{Zahl}$7,9 C$_{15}$H$_{22}$O$_{7,9}$C$_{15}$H$_{24}$O$_{7,9}$), which can be formed via hydrogen shift mechanisms, but no significant trimers. In the presence of nitrogen oxides, the organonitrate fraction increased from 3 % at 213 K to 12 % and 49 % at 243 and 313 K, respectively. Most of the organonitrates were monomers with C15 skeletons and only one nitrate group. More highly oxygenated organonitrates were observed at higher temperatures, with their signal-weighted O:C atomic ratio increasing from 0.41 to 0.51 from 213 to 313 K. New dimeric and trimeric organic species without nitrogen atoms (C$_{20}$, C$_{35}$) were formed in the presence of nitrogen oxides at 298–313 K, indicating potential new reaction pathways. Overall, our results show that increasing temperatures lead to a relatively small decrease in the rate coefficient of the endocyclic double bond in BCP reacting with ozone but to a strong decrease in SOA yields. In contrast, the formation of HOMs and organonitrates increases significantly with temperature

Kinetics, SOA yields, and chemical composition of seconaary organic aerosol from beta-caryophyllene ozonolysis with and without nitrogen oxides between 213 and 313 K

beta-caryophyllene (BCP) is one of the most important sesquiterpenes (SQTs) in the atmosphere, with a large potential contribution to secondary organic aerosol (SOA) formation mainly from reactions with ozone (O-3) and nitrate radicals (NO3). In this work, we study the temperature dependence of the kinetics of BCP ozonolysis, SOA yields, and SOA chemical composition in the dark and in the absence and presence of nitrogen oxides including nitrate radicals (NO3). We cover a temperature range of 213-313 K, representative of tropospheric conditions. The oxidized components in both gas and particle phases were characterized on a molecular level by a chemical ionization mass spectrometer equipped with a filter inlet for gases and aerosols using iodide as the reagent ion (FIGAERO-iodide-CIMS). The batch mode experiments were conducted in the 84.5 m(3) aluminium simulation chamber AIDA at the Karlsruhe Institute of Technology (KIT). In the absence of nitrogen oxides, the temperature-dependent rate coefficient of the endocyclic double bond in BCP reacting with ozone between 243-313 K is negatively correlated with temperature, corresponding to the following Arrhenius equation: k = (1.6 +/- 0.4) x 10(-15) x exp((559 +/- 97)/ T). The SOA yields increase from 16 +/- 5 % to 37 +/- 11 %, with temperatures decreasing from 313 to 243 K at a total organic particle mass of 10 mu g m(-3). The variation in the ozonolysis temperature leads to a substantial impact on the abundance of individual organic molecules. In the absence of nitrogen oxides, monomers C14-15H22-24O3-7 (37.4 %), dimers C28-30H44-48O5-9 (53.7 %), and timers C41_44H62_6609_11 (8.6 %) are abundant in the particle phase at 213 K. At 313 K, we observed more oxidized monomers (mainly C14-15H22-24O6-9, 67.5 %) and dimers (mainly C27-29H42-44O9-11, 27.6 %), including highly oxidized molecules (HOMs; C14H22O7,9C15H22O7,9C15H24O7,9), which can be formed via hydrogen shift mechanisms, but no significant timers. In the presence of nitrogen oxides, the organonitrate fraction increased from 3 % at 213 K to 12 % and 49 % at 243 and 313 K, respectively. Most of the organonitrates were monomers with Cis skeletons and only one nitrate group. More highly oxygenated organonitrates were observed at higher temperatures, with their signal-weighted O : C atomic ratio increasing from 0.41 to 0.51 from 213 to 313 K. New dimeric and timeric organic species without nitrogen atoms (C-20, C-35) were formed in the presence of nitrogen oxides at 298-313 K, indicating potential new reaction pathways. Overall, our results show that increasing temperatures lead to a relatively small decrease in the rate coefficient of the endocyclic double bond in BCP reacting with ozone but to a strong decrease in SOA yields. In contrast, the formation of HOMs and organonitrates increases significantly with temperature.Peer reviewe

LED-based solar simulator to study photochemistry over a wide temperature range in the large simulation chamber AIDA

A light source has been built at the AIDA (Aerosol Interactions and Dynamics in the Atmosphere) simulation chamber at the Karlsruhe Institute of Technology, simulating solar radiation at ground level. Instead of full spectra light sources, it uses a combination of LEDs with a narrow emission spectrum, resulting in a combined spectrum similar to the solar spectrum between 300 and 530 nm. The use of LEDs leads to an energy-efficient, robust and versatile illumination concept. The light source can be used over a wide temperature range down to −90 ∘C and is adjustable in intensity and spectral width as well as easily adjustable to new technological developments or scientific needs. Characterization of the illumination conditions shows a vertical intensity gradient in the chamber. The integral intensity corresponds to a NO₂ photolysis frequency j(NO₂) of ($1.58 \pm 0.21(1σ)) x 10^{-3} s^{−1}$ for temperatures between 213 and 295 K. At constant temperature, the light intensity is stable within ±1 %. While the emissions of the different LEDs change with temperature, they can be adjusted, and thus it is possible to adapt the spectrum for different temperatures. Although the illumination of the simulation chamber leads to an increase of 0.7 K $h^{−1}$ of the mean gas temperature, it is possible to perform experiments with aqueous droplets at relative humidities up to ≤95 % and also above water or ice saturation with corresponding clouds. Additionally, temperature- and wavelength-dependent photolysis experiments with 2,3-pentanedione have been conducted. The photolysis of 2,3-pentanedione occurs mainly between 400 and 460 nm, resulting in a mean photolysis frequency of $(1.03 \pm 0.15) x 10^{-4} s^{−1}$ independent of temperature in the range 213–298 K with a quantum yield of 0.36±0.04. In contrast, the yield of the two main photolysis products, acetaldehyde and formaldehyde, decreases with temperature. Furthermore, the light source was applied to study the photochemistry of aerosol particles. For the atmospheric brown carbon proxy compound 3,5-diacetyl-2,4,6-trimethyl-1,4-dihydropyridine, photochemical reaction products were identified. In aerosol particles containing iron oxalate as a photosensitizer, the photosensitized degradation of organic acids (pinic and pinonic acid) was studied. Although the light source only generates about one-third of the maximum solar irradiation at ground level at Karlsruhe (49.007∘ N, 8.404∘ E; 12:00 UTC+2) on a clear summer day with a substantial intensity gradient throughout the simulation chamber, it could be shown that this type of light source allows reproducible experiments over a wide range of simulated atmospheric conditions and with a large flexibility and control of the irradiation spectrum

Chromophores and chemical composition of brown carbon characterized at an urban kerbside by excitation–emission spectroscopy and mass spectrometry

The optical properties, chemical composition, and potential chromophores of brown carbon (BrC) aerosol particles were studied during typical summertime and wintertime at a kerbside in downtown Karlsruhe, a city in central Europe. The average absorption coefficient and mass absorption efficiency at 365 nm (Abs365 and MAE365) of methanol-soluble BrC (MS-BrC) were lower in the summer period (1.6 ± 0.5 Mm−1, 0.5 ± 0.2 m2 g−1) than in the winter period (2.8 ± 1.9 Mm−1, 1.1 ± 0.3 m2 g−1). Using a parallel factor (PARAFAC) analysis to identify chromophores, two different groups of highly oxygenated humic-like substances (HO-HULIS) dominated in summer and contributed 96 ± 6 % of the total fluorescence intensity. In contrast, less-oxygenated HULIS (LO-HULIS) dominated the total fluorescence intensity in winter with 57 ± 12 %, followed by HO-HULIS with 31 ± 18 %. Positive matrix factorization (PMF) analysis of organic compounds detected in real time by an online aerosol mass spectrometer (AMS) led to five characteristic organic compound classes. The statistical analysis of PARAFAC components and PMF factors showed that LO-HULIS chromophores were most likely emitted from biomass burning in winter. HO-HULIS chromophores could be low-volatility oxygenated organic aerosol from regional transport and oxidation of biogenic volatile organic compounds (VOCs) in summer. Five nitro-aromatic compounds (NACs) were identified by a chemical ionization mass spectrometer (C7H7O3N, C7H7O4N, C6H5O5N, C6H5O4N, and C6H5O3N), which contributed 0.03 ± 0.01 % to the total organic mass but can explain 0.3 ± 0.1 % of the total absorption of MS-BrC at 365 nm in winter. Furthermore, we identified 316 potential brown carbon molecules which accounted for 2.5 ± 0.6 % of the organic aerosol mass. Using an average mass absorption efficiency (MAE365) of 9.5 m2g−1 for these compounds, we can estimate their mean light absorption to be 1.2 ± 0.2 Mm−1, accounting for 32 ± 15 % of the total absorption of MS-BrC at 365 nm. This indicates that a small fraction of brown carbon molecules dominates the overall absorption. The potential BrC molecules assigned to the LO-HULIS component had a higher average molecular weight (265 ± 2 Da) and more nitrogen-containing molecules (62 ± 1 %) than the molecules assigned to the HO-HULIS components. Our analysis shows that the LO-HULIS, with a high contribution of nitrogen-containing molecules originating from biomass burning, dominates aerosol fluorescence in winter, and HO-HULIS, with fewer nitrogen-containing molecules as low-volatility oxygenated organic aerosol from regional transport and oxidation of biogenic volatile organic compounds (VOC), dominates in summer

Variations of PM2.5 sources in the context of meteorology and seasonality at an urban street canyon in Southwest Germany

In order to assess the factors controlling urban air pollution, we characterized fine particulate matter (PM$_{2.5}$) at an urban street canyon in southwest Germany, in summer 2019 and winter 2020. The average mass concentration of PM$_{2.5}$ was higher in dry and hot summer (7.0 ± 3.5 μg m$^{−3}$) than in cold and humid winter (5.8 ± 2.8 μg m$^{−3}$) with frequent wet scavenging. The non-refractory PM$_{2.5}$ (NR-PM$_{2.5}$) measured with an aerosol mass spectrometer (AMS) plus black carbon (BC) mostly consists of organic aerosol (OA) with 60% in summer and 44% in winter. The contributions of sulfate to NR-PM$_{2.5}$ plus BC was higher in summer (18%) than in winter (13%), while that of nitrate was lower in summer (6%) than in winter (22%). During the entire measurement periods in both seasons, relatively flat diurnal variations of sulfate were found, suggesting that it was associated with regional transport. However, occasionally rapid increase of sulfate can be caused by the transport of upwind industrial sources and enhanced vertical mixing processes. Nitrate showed a peak at morning rush hours related to traffic emissions, and then subsequently decreased by evaporation processes during daytime with higher temperature. Positive matrix factorization analysis revealed that the total OA was dominated by secondary organic aerosol (SOA) over the primary traffic emissions with ~82% in summer and ~48% in winter. A detailed analysis of two pollution episodes clearly demonstrated the impact of meteorological conditions on secondary aerosol formation and accumulation. A summertime heatwave episode showed high contributions of SOA to PM$_{2.5}$ mass, which formed locally through daytime photochemical oxidation as well as nighttime chemistry of biogenic precursors. A wintertime transitional episode occurred with significant shift from relatively warm and humid to cold and dry conditions. The fast formation of sulfate, nitrate, ammonium and SOA were found under the warm and humid period after receiving a local industrial emission plume. The cold and dry period was influenced by various sources including long-range transport of Saharan dust and anthropogenic emissions in central Europe. This study highlights the variations of urban PM$_{2.5}$ sources under certain meteorological conditions such as summer heatwave and humid winter, which are expected high occurrence in future. Our results provide the implication on actual needs of mitigation actions to these pollution episodes in less-polluted western Europe cities

Volatility of Secondary Organic Aerosol from β-Caryophyllene Ozonolysis over a Wide Tropospheric Temperature Range

We investigated secondary organic aerosol (SOA) from β-caryophyllene oxidation generated over a wide tropospheric temperature range (213–313 K) from ozonolysis. Positive matrix factorization (PMF) was used to deconvolute the desorption data (thermograms) of SOA products detected by a chemical ionization mass spectrometer (FIGAERO-CIMS). A nonmonotonic dependence of particle volatility (saturation concentration at 298 K, C298K*) on formation temperature (213–313 K) was observed, primarily due to temperature-dependent formation pathways of β-caryophyllene oxidation products. The PMF analysis grouped detected ions into 11 compound groups (factors) with characteristic volatility. These compound groups act as indicators for the underlying SOA formation mechanisms. Their different temperature responses revealed that the relevant chemical pathways (e.g., autoxidation, oligomer formation, and isomer formation) had distinct optimal temperatures between 213 and 313 K, significantly beyond the effect of temperature-dependent partitioning. Furthermore, PMF-resolved volatility groups were compared with volatility basis set (VBS) distributions based on different vapor pressure estimation methods. The variation of the volatilities predicted by different methods is affected by highly oxygenated molecules, isomers, and thermal decomposition of oligomers with long carbon chains. This work distinguishes multiple isomers and identifies compound groups of varying volatilities, providing new insights into the temperature-dependent formation mechanisms of β-caryophyllene-derived SOA particles

Generation of Genetically Modified Mice by Oocyte Injection of Androgenetic Haploid Embryonic Stem Cells

SummaryHaploid cells are amenable for genetic analysis. Recent success in the derivation of mouse haploid embryonic stem cells (haESCs) via parthenogenesis has enabled genetic screening in mammalian cells. However, successful generation of live animals from these haESCs, which is needed to extend the genetic analysis to the organism level, has not been achieved. Here, we report the derivation of haESCs from androgenetic blastocysts. These cells, designated as AG-haESCs, partially maintain paternal imprints, express classical ESC pluripotency markers, and contribute to various tissues, including the germline, upon injection into diploid blastocysts. Strikingly, live mice can be obtained upon injection of AG-haESCs into MII oocytes, and these mice bear haESC-carried genetic traits and develop into fertile adults. Furthermore, gene targeting via homologous recombination is feasible in the AG-haESCs. Our results demonstrate that AG-haESCs can be used as a genetically tractable fertilization agent for the production of live animals via injection into oocytes.PaperCli

Loci-specific phase separation of FET fusion oncoproteins promotes gene transcription

Abnormally formed FUS/EWS/TAF15 (FET) fusion oncoproteins are essential oncogenic drivers in many human cancers. Interestingly, at the molecular level, they also form biomolecular condensates at specific loci. However, how these condensates lead to gene transcription and how features encoded in the DNA element regulate condensate formation remain unclear. Here, we develop an in vitro single-molecule assay to visualize phase separation on DNA. Using this technique, we observe that FET fusion proteins undergo phase separation at target binding loci and the phase separated condensates recruit RNA polymerase II and enhance gene transcription. Furthermore, we determine a threshold number of fusion-binding DNA elements that can enhance the formation of FET fusion protein condensates. These findings suggest that FET fusion oncoprotein promotes aberrant gene transcription through loci-specific phase separation, which may contribute to their oncogenic transformation ability in relevant cancers, such as sarcomas and leukemia

Variation in chemical composition and volatility of oxygenated organic aerosol in different rural, urban, and mountain environments

The apparent volatility of atmospheric organic aerosol (OA) particles is determined by their chemical composition and environmental conditions (e.g., ambient temperature). A quantitative, experimental assessment of volatility and the respective importance of these two factors remains challenging, especially in ambient measurements. We present molecular composition and volatility of oxygenated OA (OOA) particles in different rural, urban, and mountain environments (including Chacaltaya, Bolivia; Alabama, US; Hyytiälä, Finland; Stuttgart and Karlsruhe, Germany; and Delhi, India) based on deployments of a filter inlet for gases and aerosols coupled to a high-resolution time-of-flight chemical ionization mass spectrometer (FIGAERO-CIMS). We find on average larger carbon numbers (nC) and lower oxygen-to-carbon (O : C) ratios at the urban sites (nC: 9.8 ± 0.7; O : C: 0.76 ± 0.03; average ±1 standard deviation) compared to the rural (nC: 8.8 ± 0.6; O : C: 0.80 ± 0.05) and mountain stations (nC: 8.1 ± 0.8; O : C: 0.91 ± 0.07), indicative of different emission sources and chemistry