Miracle-dz/UniFAR-FTUs huggingface dataset:
A Multi-Modal Transformer-based Code Summarization Approach for Smart Contracts

Code comment has been an important part of computer programs, greatly facilitating the understanding and maintenance of source code. However, high-quality code comments are often unavailable in smart contracts, the increasingly popular programs that run on the blockchain. In this paper, we propose a Multi-Modal Transformer-based (MMTrans) code summarization approach for smart contracts. Specifically, the MMTrans learns the representation of source code from the two heterogeneous modalities of the Abstract Syntax Tree (AST), i.e., Structure-based Traversal (SBT) sequences and graphs. The SBT sequence provides the global semantic information of AST, while the graph convolution focuses on the local details. The MMTrans uses two encoders to extract both global and local semantic information from the two modalities respectively, and then uses a joint decoder to generate code comments. Both the encoders and the decoder employ the multi-head attention structure of the Transformer to enhance the ability to capture the long-range dependencies between code tokens. We build a dataset with over 300K pairs of smart contracts, and evaluate the MMTrans on it. The experimental results demonstrate that the MMTrans outperforms the state-of-the-art baselines in terms of four evaluation metrics by a substantial margin, and can generate higher quality comments.
Measuring Voice UX Quantitatively: A Rapid Review

Computer voice is experiencing a renaissance through the growing popularity of voice-based interfaces, agents, and environments. Yet, how to measure the user experience (UX) of voice-based systems remains an open and urgent question, especially given that their form factors and interaction styles tend to be non-visual, intangible, and often considered disembodied or “body-less. ” As a first step, we surveyed the ACM and IEEE literatures to determine which quantitative measures and measurements have been deemed important for voice UX. Our findings show that there is little consensus, even with similar situations and systems, as well as an overreliance on lab work and unvalidated scales. In response, we offer two high-level descriptive frameworks for guiding future research, developing standardized instruments, and informing ongoing review work. Our work highlights the current strengths and weaknesses of voice UX research and charts a path towards measuring voice UX in a more comprehensive way.
Effect of Annealing on Improved Hydrophobicity of Vapor Phase Deposited Self-Assembled Monolayers

The hydrolytic stability and the effect of annealing on the improved aging properties of self-assembled monolayer (SAM) hydrophobic coatings have been investigated. Surfaces coated with hydrophobic SAM coatings give higher flow rate and are of wide interest to researchers in the area of microfluidics. Hydrophobic SAM of fluorooctyltrichlorosilane (FOTS) was deposited on silicon by using a vapor phase technique. The aging of the hydrophobic property was examined by using contact angle measurements. It has been found that while such a monolayer suffers from a loss of hydrophobicity with time, annealing can partially recover the hydrophobicity. The mechanism of aging was investigated through Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS), which revealed very little chemical change in annealed monolayers. Surface roughness and morphological changes due to hydrolytic attack was studied by atomic force microscopy (AFM). A spontaneous formation of silane mounds on the s.
Reviewing the impacts of community energy initiatives in New Zealand

ABSTRACT The New Zealand government has earmarked community energy as an investment mechanism that could assist the country in reaching its climate change goals, as well as lead to local benefits for its citizens. The objective of this paper is to identify what community energy initiatives are occurring in New Zealand, and the respective impacts that have arisen. A desk survey was undertaken, through an academic database and internet search to collect relevant resources and data. The country has a history of community energy initiatives; however, data on the impacts of community energy initiatives are scarce, at both a local and national level. The study also found diversity in the communities that are, or possibly could, benefit from community energy projects, each with differing motivations for participation. A national understanding of the successful impacts of community energy initiatives is needed, as well as more monitoring and analysis on the impacts of current projects. Ascertaining the true value of community energy is a complex task, but vital should development of these projects be pursued.
The differential effect of apoferritin-PbS nanocomposites on cell cycle progression in normal and cancerous cells

We report the effects induced by near-infrared apoferritin-PbS (AFt-PbS) nanocomposites on cell cycle progression in non-tumorigenic and cancerous human cells. By using flow cytometry and Annexin V assay, we show that the cell cycle of non-tumorigenic cells is not altered by exposure to AFt-PbS nanoparticles at concentrations up to 1 mg mL−1. In contrast, exposure of human-derived breast cancer cell lines to AFt-PbS at concentrations > 0.2 mg mL−1 triggers apoptotic cell death. The selective death of cancerous cells and the near-infrared fluorescence properties of AFt-PbS could be exploited in both nanomedicine and in vivo imaging studies.
Application of recurrent neural network for prediction of the time-varying storm surge

ABSTRACT This study investigates the overall performance of non-linear regression models based either on DNN or on RNN for the fast predictions of time-varying storm surge heights. We selected Tokyo-Bay as a case study site and conducted numerical simulations of storm surges induced by 151 recorded typhoons that passed around Japan from 1951 to 2017. Obtained time-series data of the storm surge heights at selected 10 target points were used as outcome variables of the non-linear regression model. The corresponding predictor variables are obtained from the time series of typhoon data and the recent time history of the storm surges height at the same target point. This study then performed a parametric study to explore the optimum model setups of: (i) types of optimizer; (ii) the number of hidden layers (iii) the number of nodes of each hidden layer; and (iv) the duration time and the lead time of the time-series data of the typhoon and the recent storm surge height. Besides the optimum conditions of the present regression model, it was found that RNN showed clearly better predictive skills than DNN, and the recent history of the storm surge did not significantly improve the predictive performance of the present regression model.
Monographs on invasive plants in Europe N° 4: Arundo donax L.

ABSTRACT Arundo donax L. (Poaceae) is considered to be one of the worst invasive plants in the world, and here, we present a synthesis of all aspects of its biology, ecology and management that are relevant to understanding its invasive behaviour. This report presents information on the taxonomy, morphology, distribution, history of introduction and spread, ecology, responses to abiotic and biotic factors, biology, negative impacts, management and uses within the framework of a series of Botany Letters on Monographs on invasive plants in Europe. Arundo donax (giant reed) originated in subtropical Asia and is invasive in other warm regions worldwide, especially in degraded riparian areas. Introduced for use in agriculture, erosion control and construction in the Mediterranean European region since ancient times, it has become naturalized in several freshwater habitats and in disturbed areas. In its introduced range, A. donax shows strong genetic uniformity and no seed production. This situation is reversed in Asia, where this taxon is fertile and morphologically and genetically polymorphic. This perennial grass combines rhizomatous clonal growth with a tolerance to a wide variety of ecological conditions, such as high salinity levels and long droughts. This tall reed can increase the risk of fire, alter the natural drainage of channels and invade very sensitive habitats, posing a serious threat to riparian habitats and freshwater ecosystems. Effective methods to control A. donax are tarps on a cleared giant reed field to completely cover the affected zone, rhizome removal using a modified backhoe bucket adapted to separate soil from the rhizomes, and herbicide application on leaves. The combined technique of herbicide treatment plus stem-cutting can be included in management programmes, and this technique needs to be monitored over the long term to assess its success and to ensure native species colonization and ecosystem recovery. Regarding biological control, A. donax is host to different insect species that have been released to control it in parts of its non-native range (North America) with some success. However, these different methods of control should continue to be studied, evaluating the risks posed to the environment and the control level achieved. In this context, scientific, political and administrative efforts as well as environmental education are effective assets to address the management of this invasive species.
Resolution and uncertainties in estimates of earthquake stress drop and energy release

Our models and understanding of the dynamics of earthquake rupture are based largely on estimates of earthquake source parameters, such as stress drop and radiated seismic energy. Unfortunately, the measurements, especially those of small and moderate-sized earthquakes (magnitude less than about 5 or 6), are not well resolved, containing significant random and potentially systematic uncertainties. The aim of this review is to provide a context in which to understand the challenges involved in estimating these measurements, and to assess the quality and reliability of reported measurements of earthquake source parameters. I also discuss some of the ways progress is being made towards more reliable parameter measurements. At present, whether the earthquake source is entirely self-similar, or not, and which factors and processes control the physics of the rupture remains, at least in the author's opinion, largely unconstrained. Detailed analysis of the best recorded earthquakes, using the increasing quantity and quality of data available, and methods less dependent on simplistic source models is one approach that may help provide better constraints. This article is part of the theme issue ‘Fracture dynamics of solid materials: from particles to the globe’.
Ruthenium mononitro and mononitroso terpyridine complexes incorporating azoimine based ancillary ligands. Synthesis, crystal structure, spectroelectrochemical properties and kinetic aspects

Ruthenium mononitro and mononitroso terpyridine complexes incorporating strong π-acidic azopyridine ligands of the types [RuII(trpy)(L)(NO2)]ClO46–10 and [RuII(trpy)(L)(NO)][ClO4]311–15 [trpy = 2,2′∶6′,2″-terpyridine; L = NC5H4NNC6H4(R), R = H, m-Me/Cl or p-Me/Cl] respectively have been synthesized starting from [RuII(trpy)L(H2O)]2+1–5. The single crystal X-ray structure of the nitro complex 7 has been determined. In acetonitrile solvent the nitro complexes exhibit strong MLCT transitions near 500 nm and the same MLCT bands are observed to be blue shifted near 370 nm in the case of the nitroso derivatives. The nitrosyl complexes exhibit νNO in the range 1960–1950 cm−1. The nitro (6–10) and nitroso (11–15) complexes exhibit ruthenium(II)–ruthenium(III) oxidation in the ranges 1.33–1.47 V and 1.62–1.72 V versus SCE respectively. The nitroso complexes exhibit two successive one-electron reductions near 0.7 and 0.0 V due to reductions of coordinated NO+ → NO and NO → NO− respectively. All the complexes (6–15) systematically display three ligand based (trpy and L) reductions to negative potentials of the SCE. The nitro complexes (6–10) display weak emissions near 700 nm (Φ = 0.83 × 10−2–2.98 × 10−2). The electrochemically generated 6+++++–10+++++ show LMCT transitions near 490 nm and rhombic EPR spectra in acetonitrile at 77 K. The pseudo first order rate constants (k) and the thermodynamic parameters (ΔH‡, ΔS ‡ and K) for formation of the nitro complexes, [RuII(trpy)(L)(H2O)]2+ → [RuII(trpy)(L)(NO2)]+, and the conversion [RuII(trpy)(L)(NO)]3+ → [RuII(trpy)(L)(NO2)]+ have been determined.
Simple Correlations for Estimating the Energy Production of Turkey

Industrialization and population increases make the availability of potential energy in most areas a problem of great importance. Energy is considered to be a prime agent in the generation of wealth and also a significant factor in economic development. Most of the locations in Turkey have abundant energy resources, and energy utilization technologies can be profitably applied to these regions. In this study, we analyze the current status of Turkey's energy resources in terms of energy production and present simple corrections with high correlation coefficients for future projections. It is expected that this study will he helpful in developing highly applicable and productive planning for energy policies.
Diversification, spread, and admixture of octoploid strawberry in the Western Hemisphere

Premise of the study Octoploid strawberry (Fragaria sp.) has a complex evolutionary history that has until recently been intractable due to limitations of available genomic resources. While recent work has further uncovered the evolutionary history of the octoploid strawberry, there are still open questions. Much is still unknown about the evolutionary relationship of the wild octoploid species, Fragaria virginiana and Fragaria chiloensis, and gene flow within and among species after the original formation of the octoploid genome. Methods We leveraged a diversity collection of wild octoploid eco-types of strawberry representing the recognized subspecies and ranging from Alaska to Southern Chile, and a high density SNP array to investigate wild octoploid strawberry evolution. Evolutionary relationships are interrogated with phylogenetic analysis and genetic clustering algorithms. Additionally, admixture among and within species is assessed with model-based and tree-based approaches. Key Results Phylogenetic analysis revealed that the two octoploid strawberry species are monophyletic sister lineages. The genetic clustering results show substructure between North Americana and South American F. chiloensis populations. Additionally, model-based and tree-based methods support gene flow within and among the two octoploid species, including newly identified admixture in the Hawaiian F. chiloensis subsp. sandwicensis population that appears to be from an ancestral F. chiloensis population. Conclusion F. virginiana and F. chiloensis are supported as monophyletic and sister lineages. All but one of the subspecies recognized within both octoploid species show extensive paraphyly. Furthermore, the phylogenetic relationship among F. chiloensis populations supports a single population range expansion southward from North America. The inter- and intraspecific relationships of octoploid strawberry are complex and suggest substantial and deep gene flow between sympatric populations among and within species.
Cost-effective long-read assembly of a hybrid Formica aquilonia × Formica polyctena wood ant genome from a single haploid individual

Formica red wood ants are a keystone species of boreal forest ecosystems and an emerging model system in the study of speciation and hybridization. Here we performed a standard DNA extraction from a single, field-collected Formica aquilonia × Formica polyctena haploid male and assembled its genome using ∼60× of PacBio long reads. After polishing and contaminant removal, the final assembly was 272 Mb (4,687 contigs, N50 = 1.16 Mb). Our reference genome contains 98.5% of the core Hymenoptera BUSCOs and was scaffolded using the pseudo-chromosomal assembly of a related species, F. selysi (28 scaffolds, N50 = 8.49 Mb). Around one third of the genome consists of repeats, and 17,426 gene models were annotated using both protein and RNAseq data (97.4% BUSCO completeness). This resource is of comparable quality to the few other single individual insect genomes assembled to date and paves the way to genomic studies of admixture in natural populations and comparative genomic approaches in Formica wood ants.
Trio-binned genomes of the woodrats Neotoma bryanti and N. lepida reveal novel gene islands and rapid copy number evolution of xenobiotic metabolizing cytochrome p450 genes

The genomic architecture underlying the origins and maintenance of biodiversity is an increasingly accessible feature of species, due in large part to third-generation sequencing and novel analytical toolsets. Woodrats of the genus Neotoma provide a unique opportunity to study how vertebrate herbivores respond to climate change, as two sister species (N. bryanti and N. lepida) independently achieved a major dietary feat – switching to the novel and toxic food source creosote bush (Larrea tridentata) – in the aftermath of a natural warming event. To better understand the genetic mechanisms underlying this ability, we employed a trio binning sequencing approach with a N. bryanti × N. lepida F1 hybrid, resulting in phased, chromosome-level, highly complete, haploid genome assemblies for each species from one individual. Using these new assemblies, we explored the genomic architecture of three cytochrome p450 subfamilies (2A, 2B, and 3A) that play key roles in the metabolism of naturally occurring toxic dietary compounds. We found that woodrats show expansions of all three p450 gene families, including the evolution of multiple novel gene islands within the 2B and 3A subfamilies. Our assemblies demonstrate that trio binning from an F1 hybrid rodent effectively recovers parental genomes from species that diverged more than a million years ago. Turnover and novelty in detoxification gene islands in herbivores is widespread within distinct p450 subfamilies, and may have provided the crucial substrate for dietary adaptation during environmental change.
Harnessing Mesenchymal Stromal Cells for the Engineering of Human Hematopoietic Niches

Tissue engineering opens multiple opportunities in regenerative medicine, drug testing, and modeling of the hematopoiesis in health and disease. Recapitulating the organization of physiological microenvironments supporting leukocyte development is essential to model faithfully the development of immune cells. Hematopoietic organs are shaped by spatially organized niches defined by multiple cellular contributions. A shared feature of immune niches is the presence of mesenchymal stromal cells endowed with unique roles in organizing niche development, maintenance, and function. Here, we review challenges and opportunities in harnessing stromal cells for the engineering of artificial immune niches and hematopoietic organoids recapitulating leukocyte ontogeny both in vitro and in vivo.
Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts

The bioprospecting of secondary metabolites from endophytic fungi received great attention in the 1990s and 2000s, when the controversy around taxol production from Taxus spp. endophytes was at its height. Since then, hundreds of reports have described the isolation and characterization of putative secondary metabolites from endophytic fungi. However, only very few studies also report the genetic basis for these phenotypic observations. With low sequencing cost and fast sample turnaround, genetics- and genomics-based approaches have risen to become comprehensive approaches to study natural products from a wide-range of organisms, especially to elucidate underlying biosynthetic pathways. However, in the field of fungal endophyte biology, elucidation of biosynthetic pathways is still a major challenge. As a relatively poorly investigated group of microorganisms, even in the light of recent efforts to sequence more fungal genomes, such as the 1000 Fungal Genomes Project at the Joint Genome Institute (JGI), the basis for bioprospecting of enzymes and pathways from endophytic fungi is still rather slim. In this review we want to discuss the current approaches and tools used to associate phenotype and genotype to elucidate biosynthetic pathways of secondary metabolites in endophytic fungi through the lens of bioprospecting. This review will point out the reported successes and shortcomings, and discuss future directions in sampling, and genetics and genomics of endophytic fungi. Identifying responsible biosynthetic genes for the numerous secondary metabolites isolated from endophytic fungi opens the opportunity to explore the genetic potential of producer strains to discover novel secondary metabolites and enhance secondary metabolite production by metabolic engineering resulting in novel and more affordable medicines and food additives.
Homozygous of MRP4 Gene rs1751034 C Allele Is Related to Increased Risk of Intravenous Immunoglobulin Resistance in Kawasaki Disease

Background: Kawasaki disease (KD) is a systemic vasculitis in childhood, which mainly causes damage to coronary arteries, and intravenous immunoglobulin (IVIG) is the initial therapy. IVIG resistance increased risk of coronary complication in KD. And genetic background is involved in the occurrence of IVIG resistance. Our previous study indicated the susceptibility of Multi-drug resistance protein 4 (MRP4) SNPs to KD. This study was to clarify the relationship between MRP4 polymorphisms and IVIG resistance. Methods: We genotyped the six polymorphisms of MRP4 gene in 760 cases of KD using Taqman methods. Results: Among the six polymorphisms, only the rs1751034 polymorphism was significantly associated with IVIG resistance in KD [CC vs. TT: adjusted odds ratio (OR) = 2.54, 95% confidence interval (CI) = 1.21–5.34; CC vs. TT/TC: adjusted OR = 2.33, 95% CI = 1.12–4.83, p = 0.023]. Combined analysis of three polymorphisms indicated that patients with 3–6 risk genotypes exhibited significantly elevated risk of IVIG resistance, when compared with those with 0–2 risk genotypes (adjusted OR = 1.52, 95% CI = 1.04–2.22, p = 0.0295). Stratified analysis revealed that in term of age and gender, rs1751034 CC carriers were associated with increased risk of IVIG resistance in those aged ≤ 60 months (adjusted OR = 2.65, 95% CI = 1.23–5.71, p = 0.0133). The presence of three or more risk genotypes was significantly associated with risk of IVIG resistance in children younger than 5 years of age and males. Conclusion: Our results suggest that MRP4 rs1751034 CC is associated with increased risk of IVIG resistance in KD.
Improved Yield of Recombinant Protein via Flagella Regulator Deletion in Escherichia coli

Protein production requires a significant amount of intracellular energy. Eliminating the flagella has been proposed to help Escherichia coli improve protein production by reducing energy consumption. In this study, the gene encoding a subunit of FlhC, a master regulator of flagella assembly, was deleted to reduce the expression of flagella-related genes. FlhC knockout in the ptsG-deleted strain triggered significant growth retardation with increased ATP levels and a higher NADPH/NADP+ ratio. Metabolic flux analysis using a 13C-labeled carbon substrate showed increased fluxes toward the pentose phosphate and tricarboxylic acid cycle pathways in the flhC- and ptsG-deleted strains. Introduction of a high copy number plasmid or overexpression of the recombinant protein in this strain restored growth rate without increasing glucose consumption. These results suggest that the metabolic burden caused by flhC deletion was resolved by recombinant protein production. The recombinant enhanced green fluorescent protein yield per glucose consumption increased 1.81-fold in the flhC mutant strain. Thus, our study demonstrates that high-yield production of the recombinant protein was achieved with reduced flagella formation.