Identity Avoidance and Rendaku

One important observation that is made in the past phonological research is that constraints on output structures can both block and trigger phonological processes (i.e., conspiracy: Kisseberth 1970). This paper reports an experiment which shows that an Identity Avoidance constraint (a.k.a. the OCP) both blocks and triggers one phonological process in the same language, namely rendaku in Japanese. Our wug- experiment shows that rendaku is more likely to apply when the two CV moras across a morpheme boundary are identical; i.e. an Identity Avoidance constraint triggers rendaku. The experiment also shows that rendaku is less likely to apply when it would result in two adjacent identical CV moras across a morpheme boundary; i.e. the Identity Avoidance constraint blocks rendaku. These blocking and triggering effects of the general Identity Avoidance constraint on rendaku are a new discovery in Japanese phonology, despite the fact that rendaku has been studied extensively in the previous literature, suggesting the importance of experimentation in phonological research. Moreover, our case study offers experimental confirmation of the OCP conspiracy in natural languages

Testing Rosen\u27s Rule and Strong Lyman\u27s Law

慶應義塾大学岡山県立大学Keio UniversityOkayama Prefectural University本研究では,実験によりローゼンの法則と強いライマンの法則についてその心理的実在を検証した。ローゼンの法則に従えば,複合語前部要素が2モーラよりも3モーラの方が連濁が起こりやすくなる。また,強いライマンの法則に従えば,複合語前部要素に濁音が含まれている場合,連濁が起こりにくくなる。しかしながら,無意味語を用いた実験の結果,両法則の影響は確認されなかった。統計的に有意でない結果から負の証明は不可能であるものの,他の実験結果と比較しても,両法則の影響は本質的なものではなく,現在の日本語話者の知識においては機能していないと思われる。The current experiment investigates the psychological reality of Rosen\u27s Rule and Strong Lyman\u27s Law. Rosen\u27s Rule predicts, in part, that rendaku is more likely to occur when N1 has three moras than when it has two moras. Strong Lyman\u27s Law predicts that rendaku is less likely when N1 contains a voiced obstruent. Our wug-test shows neither of these predictions to be borne out. Although the null results must be interpreted with caution, by comparing the current results with those from previous experimental studies on rendaku, we conclude that the effects of these two factors are not substantial, and that they are not synchronically active in the minds of Japanese speakers, at least not for the Japanese community as a whole

日本語の二重目的語構文の基本語順について

National Institute for Japanese Language and LinguisticsMonash UniversityKeio University会議名: 言語資源活用ワークショップ2018, 開催地: 国立国語研究所, 会期: 2018年9月4日-5日, 主催: 国立国語研究所 コーパス開発センター本稿では日本語の二重目的語構文の基本語順について予測する統計モデルについて議論する。『現代日本語書き言葉均衡コーパス』コアデータに係り受け構造・述語項構造・共参照情報を悉皆付与したデータから、二重目的語構文を抽出し、格要素と述語要素に分類語彙表番号を付与したうえで、ベイジアン線形混合モデルにより分析を行った。結果、名詞句の情報構造の効果として知られている旧情報が新情報よりも先行する現象と、モーラ数が多いものが少ないものに先行する現象が確認された。分類語彙表番号による効果は、今回の分析では確認されなかった

Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome.

The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Optimization of the Verbal Inflectional Paradigm by the Cyclic Application of Morphophonological Processes: Evidence from Potential Forms in Japanese

In Japanese, a series of morphophonological changes that reorganizes the verbal inflectional paradigms is currently underway. The changes in potential forms involve two innovative processes: ar-Deletion and re-Insertion. This paper analyzes these morphophonological changes in the Japanese potential forms, and models the mechanism that governs the sequential changes, using the Corpus of Spontaneous Japanese. By positing a chronological order between the changes, I argue that the initial change in consonant-final verbs is motivated by semantic disambiguation, and the subsequent change in vowel-final verbs is triggered by analogical leveling for the optimization of the conjugation paradigm. This analogical leveling reorganizes the paradigm in order to counter the increased discrepancy between potential forms of consonant-final verbs and vowel-final verbs caused by the previous change. I propose that positing this two-step process is crucial to understanding the diachronic changes at issue