Inverse scope and unaccusativity alternation

In this paper, I first review evidence for the claim that there is an inverse correlation between Japanese scrambling and QR: that is, Japanese is scope rigid because it allows scrambling as a syntactic option (Szabolcsi 1997, Bobaljik and Wurmbrand 2012). According to Bobaljik and Wurmbrand's approach, QR is blocked in Japanese because Japanese has scrambling. There are, however, cases in which apparent inverse scope is easily available in Japanese (Oku 2010), which is problematic to Bobaljik and Wurmbrand and to any theoretical attempt to account for Szabolcsi's inverse correlation. To explain this conflicting situation, I will propose that verbs involved in such apparent counterexamples are actually unaccusatives so that the surface subject is the underlying complement of the verb: the apparent inverse scope is read off at the underlying structure where the surface subject is c-commanded by the PP. As independent evidence for the unaccusasivity of the verbs in question, I will show that the floating quantifier fact (Miyagawa 1989) confirms what I propose. Further, the unaccusativity alternation in Japanese (reported by Yamada 1998) is endorsed by the inverse scope facts explored in this paper

Genomic characterization of biliary tract cancers identifies driver genes and predisposing mutations

Background & Aims Biliary tract cancers (BTCs) are clinically and pathologically heterogeneous and respond poorly to treatment. Genomic profiling can offer a clearer understanding of their carcinogenesis, classification and treatment strategy. We performed large-scale genome sequencing analyses on BTCs to investigate their somatic and germline driver events and characterize their genomic landscape. Methods We analyzed 412 BTC samples from Japanese and Italian populations, 107 by whole-exome sequencing (WES), 39 by whole-genome sequencing (WGS), and a further 266 samples by targeted sequencing. The subtypes were 136 intrahepatic cholangiocarcinomas (ICCs), 101 distal cholangiocarcinomas (DCCs), 109 peri-hilar type cholangiocarcinomas (PHCs), and 66 gallbladder or cystic duct cancers (GBCs/CDCs). We identified somatic alterations and searched for driver genes in BTCs, finding pathogenic germline variants of cancer-predisposing genes. We predicted cell-of-origin for BTCs by combining somatic mutation patterns and epigenetic features. Results We identified 32 significantly and commonly mutated genes including TP53 , KRAS , SMAD4 , NF1 , ARID1A , PBRM1 , and ATR , some of which negatively affected patient prognosis. A novel deletion of MUC17 at 7q22.1 affected patient prognosis. Cell-of-origin predictions using WGS and epigenetic features suggest hepatocyte-origin of hepatitis-related ICCs. Deleterious germline mutations of cancer-predisposing genes such as BRCA1 , BRCA2 , RAD51D , MLH1 , or MSH2 were detected in 11% (16/146) of BTC patients. Conclusions BTCs have distinct genetic features including somatic events and germline predisposition. These findings could be useful to establish treatment and diagnostic strategies for BTCs based on genetic information. Lay summary We here analyzed genomic features of 412 BTC samples from Japanese and Italian populations. A total of 32 significantly and commonly mutated genes were identified, some of which negatively affected patient prognosis, including a novel deletion of MUC17 at 7q22.1 . Cell-of-origin predictions using WGS and epigenetic features suggest hepatocyte-origin of hepatitis-related ICCs. Deleterious germline mutations of cancer-predisposing genes were detected in 11% of patients with BTC. BTCs have distinct genetic features including somatic events and germline predisposition

Impact of Gender on In-hospital Mortality in Patients with Acute Myocardial Infarction in Nagasaki

Acute myocardial infarction (AMI) is one of the leading causes of death in Japan. Immediate reperfusion therapy, includingcoronary intervention, improves patient prognosis. Despite this, females are said to be more prone to poor prognosis. A regional AMI registry in Nagasaki prefecture has been instituted recently that will evaluate whether female gender might predict short-term in-hospital death. Seventeen regional AMI centers enrolled all AMI patients from September 2014 through March 2016. A propensity score (PS) was derived using logistic regression to model the probability of females as a total function of the potential confounding covariates. Two types of PS techniques were used: PS matching and PS stratification. The consistency of in-hospital death was determined between PS matched patients of both genders. Based on PS, patients were ranked and stratified into five groups for the PS stratification. Out of 996 patients, 67 (6.7%) died during hospitalization: 31 (10.4%) out of 298 females and 36 (5.2%) out of 698 males (p < 0.0025). The proportion of cardiac and non-cardiac related death was almost same between genders (25 and 6 in female, 29 and 7 in male, respectively). Among 196 PS matched patients, there was a consistency between genders regarding in-hospital deaths (McNemar test, p = 0.6698). The 717 propensity scored patients had no significant differences between genders among propensity quintiles (Cochran-Mantel-Heanszel test, p = 0.7117). We found that gender alone is not an indicator of short-term in-hospital death in acute myocardial infarction patients

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

A Theory of Selection and Reconstruction in the Minimalist Perspective

This study extends two ideas of the minimalist program in linguistic theory (Chomsky 1992, 1994, 1995a) (LF feature decomposition and elimination of D-structure), and explores various consequences of this extension. First, Chomsky (1995a) proposes the Move F(eature) hypothesis which implies that feature decomposition of a lexical item (or a syntactic object consisting of lexical items) is possible in covert syntax (LF). Assuming that LF Copy is a syntactic operation to construct a phonologically missing element in ellipsis structures, I propose the subset copy principle to the effect that a (proper) subset of the . antecedent features can construct the contents of a phonologically missing element under LF Copy; the feature composition of a copy can be less than the feature composition of the original. I argue that the subset copy principle plays a significant role in LF construction and interpretation of both verbal morphology (Chapter 2) and nominal expressions (Chapter4) in the elliptic site. A certain asymmetry in verbal morphology construction in VP-ellipsis receives a natural account under the subset copy principle, and a new theory of interpretation of nominal expressions in VP-ellipsis is developed, which gives an account of possible interpretation of VP-ellipsis when a full copy of the original cannot provide an appropriate LF representation. The second part of this work discusses the nature of Selection in the minimalist program. Selection has been stated as a D-structure property (e.g., Chomsky 1965, (981) but it cannot be stated in such a way in the minimalist framework. since one of the characteristics of the minimalist program is its attempt to eliminate D-structure (and S-structure). Extending Boskovic and Takahashi's (1998) theory of LF Lowering movement into a θ-position, I propose that selectional properties of a head are syntactic features to be checked during the derivation, and that some selectional features are weak in the sense that they can be checked in covert syntax. Some properties of Japanese null arguments receive an account based on exactly the same theory of Japanese predicates as the one proposed in Boskovic and Takahashi. Consequences of the selection theory on English VP-ellipsis/VP-fronting are also explored