Test-time Augmentation for Factual Probing

Factual probing is a method that uses prompts to test if a language model "knows" certain world knowledge facts. A problem in factual probing is that small changes to the prompt can lead to large changes in model output. Previous work aimed to alleviate this problem by optimizing prompts via text mining or fine-tuning. However, such approaches are relation-specific and do not generalize to unseen relation types. Here, we propose to use test-time augmentation (TTA) as a relation-agnostic method for reducing sensitivity to prompt variations by automatically augmenting and ensembling prompts at test time. Experiments show improved model calibration, i.e., with TTA, model confidence better reflects prediction accuracy. Improvements in prediction accuracy are observed for some models, but for other models, TTA leads to degradation. Error analysis identifies the difficulty of producing high-quality prompt variations as the main challenge for TTA.Comment: 12 pages, 4 figures, accepted to EMNLP 2023 Findings (short paper

Preparation of BaTiO3 nanotube arrays, CoFe2O4 nanoparticles and their composite

Multiferroic nanocomposites which possess both ferroelectric and ferromagnetic properties are attracting much attention because of their scientific interest and significant technological promise in the novel multifunctional devices. Gas-phase syntheses have been typically used to fabricate multiferroic nanocomposites [1]; however, high production cost has been hindering further expansion of the research field. In this research, the components of multiferroic nanocomposites are fabricated by anodization and hydrothermal treatment which were then used to fabricate multiferroic nanocomposites through electrophoretic deposition (EPD) as cheaper alternatives to the costly gas-phase processes. TiO2 nanotubes arrays were firstly formed on Ti metal foils by anodization in an electrolyte containing ethylene glycol, dimethyl sulfoxide, ammonium fluoride and water. Then, BaTiO3 nanotube arrays were obtained by hydrothermal treatment of TiO2 nanotube arrays using Ba-containing aqueous solution. The morphologies and crystal structure of BaTiO3 nanotube arrays were analyzed by a scanning electron microscope (SEM) and an X-ray diffractometer (XRD). Please click Additional Files below to see the full abstract

Evolution of self-compatibility in Arabidopsis by a mutation in the male specificity gene

Ever since Darwin's pioneering research, the evolution of self-fertilisation (selfing) has been regarded as one of the most prevalent evolutionary transitions in flowering plants. A major mechanism to prevent selfing is the self-incompatibility (SI) recognition system, which consists of male and female specificity genes at the S-locus and SI modifier genes. Under conditions that favour selfing, mutations disabling the male recognition component are predicted to enjoy a relative advantage over those disabling the female component, because male mutations would increase through both pollen and seeds whereas female mutations would increase only through seeds. Despite many studies on the genetic basis of loss of SI in the predominantly selfing plant Arabidopsis thaliana, it remains unknown whether selfing arose through mutations in the female specificity gene (S-receptor kinase, SRK), male specificity gene (S-locus cysteine-rich protein, SCR; also known as S-locus protein 11, SP11) or modifier genes, and whether any of them rose to high frequency across large geographic regions. Here we report that a disruptive 213-base-pair (bp) inversion in the SCR gene (or its derivative haplotypes with deletions encompassing the entire SCR-A and a large portion of SRK-A) is found in 95% of European accessions, which contrasts with the genome-wide pattern of polymorphism in European A. thaliana. Importantly, interspecific crossings using Arabidopsis halleri as a pollen donor reveal that some A. thaliana accessions, including Wei-1, retain the female SI reaction, suggesting that all female components including SRK are still functional. Moreover, when the 213-bp inversion in SCR was inverted and expressed in transgenic Wei-1 plants, the functional SCR restored the SI reaction. The inversion within SCR is the first mutation disrupting SI shown to be nearly fixed in geographically wide samples, and its prevalence is consistent with theoretical predictions regarding the evolutionary advantage of mutations in male components

Cell Type-Specific Transcriptome of Brassicaceae Stigmatic Papilla Cells From a Combination of Laser Microdissection and RNA Sequencing

Pollination is an early and critical step in plant reproduction, leading to successful fertilization. It consists of many sequential processes, including adhesion of pollen grains onto the surface of stigmatic papilla cells, foot formation to strengthen pollen-stigma interaction, pollen hydration and germination, and pollen tube elongation and penetration. We have focused on an examination of the expressed genes in papilla cells, to increase understanding of the molecular systems of pollination. From three representative species of Brassicaceae (Arabidopsis thaliana, A. halleri and Brassica rapa), stigmatic papilla cells were isolated precisely by laser microdissection, and cell type-specific gene expression in papilla cells was determined by RNA sequencing. As a result, 17,240, 19,260 and 21,026 unigenes were defined in papilla cells of A. thaliana, A. halleri and B. rapa, respectively, and, among these, 12,311 genes were common to all three species. Among the17,240 genes predicted in A. thaliana, one-third were papilla specific while approximately half of the genes were detected in all tissues examined. Bioinformatics analysis revealed that genes related to a wide range of reproduction and development functions are expressed in papilla cells, particularly metabolism, transcription and membrane-mediated information exchange. These results reflect the conserved features of general cellular function and also the specific reproductive role of papilla cells, highlighting a complex cellular system regulated by a diverse range of molecules in these cells. This study provides fundamental biological knowledge to dissect the molecular mechanisms of pollination in papilla cells and will shed light on our understanding of plant reproduction mechanism

ISAI: Investigating Solar Axion by Iron-57

The existence of the axion is a unique solution for the strong CP problem, and the axion is one of the most promising candidates of the dark matter. Investigating Solar Axion by Iron-57 (ISAI) is being prepared as a complemented table-top experiment to confirm the solar axion scenario. Probing an X-ray emission from the nuclear transitions associated with the axion-nucleon coupling is a leading approach. ISAI searches for the monochromatic 14.4 keV X-ray from the first excited state of 57Fe using a state-of-the-art pixelized silicon detector, dubbed XRPIX, under an extremely low-background environment. We highlight scientific objectives, experimental design and the latest status of ISAI

Crowdsourcing genomic analyses of ash and ash dieback – power to the people

Ash dieback is a devastating fungal disease of ash trees that has swept across Europe and recently reached the UK. This emergent pathogen has received little study in the past and its effect threatens to overwhelm the ash population. In response to this we have produced some initial genomics datasets and taken the unusual step of releasing them to the scientific community for analysis without first performing our own. In this manner we hope to ‘crowdsource’ analyses and bring the expertise of the community to bear on this problem as quickly as possible. Our data has been released through our website at oadb.tsl.ac.uk and a public GitHub repository

Transcriptional Characteristics and Differences in Arabidopsis Stigmatic Papilla Cells Pre- and Post-Pollination

Pollination is an important early step in sexual plant reproduction. In Arabidopsis thaliana, sequential pollination events, from pollen adhesion onto the stigma surface to pollen tube germination and elongation, occur on the stigmatic papilla cells. Following successful completion of these events, the pollen tube penetrates the stigma and finally fertilizes a female gametophyte. The pollination events are thought to be initiated and regulated by interactions between papilla cells and pollen. Here, we report the characterization of gene expression profiles of unpollinated (UP), compatible pollinated (CP) and incompatible pollinated (IP) papilla cells in A. thaliana. Based on cell type-specific transcriptome analysis from a combination of laser microdissection and RNA sequencing, 15,475, 17,360 and 16,918 genes were identified as expressed in UP, CP and IP papilla cells, respectively, and, of these, 14,392 genes were present in all three data sets. Differentially expressed gene (DEG) analyses identified 147 and 71 genes up-regulated in CP and IP papilla cells, respectively, and 115 and 46 genes down-regulated. Gene Ontology and metabolic pathway analyses revealed that papilla cells play an active role as the female reproductive component in pollination, particularly in information exchange, signal transduction, internal physiological changes and external morphological modification. This study provides fundamental information on the molecular mechanisms involved in pollination in papilla cells, furthering our understanding of the reproductive role of papilla cell

Significant contribution of subseafloor microparticles to the global manganese budget

Ferromanganese minerals are widely distributed in subseafloor sediments and on the seafloor in oceanic abyssal plains. Assessing their input, formation and preservation is important for understanding the global marine manganese cycle and associated trace elements. However, the extent of ferromanganese minerals buried in subseafloor sediments remains unclear. Here we show that abundant (108–109 particles cm−3) micrometer-scale ferromanganese mineral particles (Mn-microparticles) are found in the oxic pelagic clays of the South Pacific Gyre (SPG) from the seafloor to the ~100 million-year-old sediments above the basement. Three-dimensional micro-texture, and major and trace element compositional analyses revealed that these Mn-microparticles consist of poorly crystalline ferromanganese oxides precipitating from bottom water. Based on our findings, we extrapolate that 1.5–8.8 × 1028 Mn-microparticles, accounting for 1.28–7.62 Tt of manganese, are globally present in oxic subseafloor sediments. This estimate is at least two orders of magnitude larger than the manganese budget for nodules and crusts on the seafloor. Subseafloor Mn-microparticles thus contribute significantly to the global manganese budget.This study was supported in part by the Japan Society for the Promotion of Science (JSPS) Strategic Fund for Strengthening Leading-Edge Research and Development (to JAMSTEC and F.I.), the JSPS Funding Program for Next Generation World-Leading Researchers (GR102 to F.I.), JSPS Grant-in-Aid for Scientific Research (24687004 and 15H05608 to Y.M., 25871219 to G.-I.U., 15H02810 to R.W., 18H04134, 17H06458 and 17H04582 to Y.T., and 26251041 to F.I.), JSPS Grant-in-Aid for JSPS Fellows (14J00199 to G.-I.U.), and Ministry of Education, Culture, Sports, Science, and Technology (MEXT) Fund Leading Initiative for Excellent Young Researchers (to Kochi University and G.-I.U.)