bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenome-wide association study of the major histocompatibility complex region in the Korean population identifies novel association signals
Authors: Kim Chanwoo , Kim Young Jin , Choi Wanson , Jang Hye-Mi , Hwang Mi Yeong , Jung Sunwoo , Lim Hyunjoon , Hong Sang Bin , Yoon Kyungheon , Kim Bong-Jo , Park Hyun-Young , Han Buhm 
Published: January 2022

AbstractHuman leukocyte antigen (HLA) gene variants in the major histocompatibility complex (MHC) region are associated with numerous complex human diseases and quantitative traits. Previous phenome-wide association studies (PheWAS) for this region demonstrated that HLA association patterns to the phenome have both population-specific and population-shared components. We performed MHC PheWAS in the Korean population by analyzing associations between phenotypes and genetic variants in the MHC region using the Korea Biobank Array project data samples from the Korean Genome and Epidemiology Study cohorts. Using this single-population dataset, we curated and analyzed 82 phenotypes for 125 673 Korean individuals after imputing HLA using CookHLA, a recently developed imputation framework. More than one-third of these phenotypes showed significant associations, confirming 56 known associations and discovering 13 novel association signals that were not reported previously. In addition, we analyzed heritability explained by the variants in the MHC region and genetic correlations among phenotypes based on the MHC variants.
Pear genetics: Recent advances, new prospects, and a roadmap for the future
Authors: Li Jiaming , Zhang Mingyue , Li Xiaolong , Khan Awais , Kumar Satish , Allan Andrew Charles , Lin-Wang Kui , Espley Richard Victor , Wang Caihong , Wang Runze , Xue Cheng , Yao Gaifang , Qin Mengfan , Sun Manyi , Tegtmeier Richard , Liu Hainan , Wei Weilin , Ming Meiling , Zhang Shaoling , Zhao Kejiao , Song Bobo , Ni Jiangping , An Jianping , Korban Schuyler S , Wu Jun 
Published: January 2022

AbstractPear, belonging to the genus Pyrus, is one of the most economically important temperate fruit crops. Pyrus is an important genus of the Rosaceae family, subfamily Maloideae, and has at least 22 different species with over 5000 accessions maintained or identified worldwide. With the release of draft whole-genome sequences for Pyrus, opportunities for pursuing studies on the evolution, domestication, and molecular breeding of pear, as well as for conducting comparative genomics analyses within the Rosaceae family, have been greatly expanded. In this review, we highlight key advances in pear genetics, genomics, and breeding driven by the availability of whole-genome sequences, including whole-genome resequencing efforts, pear domestication, and evolution. We cover updates on new resources for undertaking gene identification and molecular breeding, as well as for pursuing functional validation of genes associated with desirable economic traits. We also explore future directions for “pear-omics”.
The NAC-like transcription factor CsNAC7 positively regulates the caffeine biosynthesis-related gene yhNMT1 in Camellia sinensis
Authors: Ma Wenhui , Kang Xin , Liu Ping , She Kexin , Zhang Yuanyuan , Lin Xiaorong , Li Bin , Chen Zhongzheng 
Published: January 2022

Abstract
Caffeine is an important functional substance and is abundant in tea plant, but little is known about how its biosynthesis is regulated by transcription factors. In this study, the NAC-like transcription factor-encoding gene CsNAC7, which is involved in caffeine synthesis, was isolated from a Yinghong 9 cDNA library using a yeast one-hybrid assay; this gene comprises 1371 bp nucleotides and is predicted to encode 456 amino acids. The expression of CsNAC7 at the transcriptional level in tea shoots shared a similar pattern with that of the caffeine synthase gene yhNMT1 in the spring and summer, and its expressed protein was localized in the nucleus. Assays of gene activity showed that CsNAC7 has self-activation activity in yeast, that the active region is at the N-terminus, and that the transient expression of CsNAC7 could significantly promote the expression of yhNMT1 in tobacco leaves. In addition, overexpression or silencing of CsNAC7 significantly increased or decreased the expression of yhNMT1 and the accumulation of caffeine in transgenic tea calli, respectively. Our data suggest that the isolated transcription factor CsNAC7 positively regulates the caffeine synthase gene yhNMT1 and promotes caffeine accumulation in tea plant.
Chloroplast phylogenomics in Camelina (Brassicaceae) reveals multiple origins of polyploid species and the maternal lineage of C. sativa
Authors: Brock Jordan R , Mandáková Terezie , McKain Michael , Lysak Martin A , Olsen Kenneth M 
Published: January 2022

Abstract
The genus Camelina (Brassicaceae) comprises 7–8 diploid, tetraploid, and hexaploid species. Of particular agricultural interest is the biofuel crop, C. sativa (gold-of-pleasure or false flax), an allohexaploid domesticated from the widespread weed, C. microcarpa. Recent cytogenetics and genomics work has uncovered the identity of the parental diploid species involved in ancient polyploidization events in Camelina. However, little is known about the maternal subgenome ancestry of contemporary polyploid species. To determine the diploid maternal contributors of polyploid Camelina lineages, we sequenced and assembled 84 Camelina chloroplast genomes for phylogenetic analysis. Divergence time estimation was used to infer the timing of polyploidization events. Chromosome counts were also determined for 82 individuals to assess ploidy and cytotypic variation. Chloroplast genomes showed minimal divergence across the genus, with no observed gene-loss or structural variation. Phylogenetic analyses revealed C. hispida as a maternal diploid parent to the allotetraploid Camelina rumelica, and C. neglecta as the closest extant diploid contributor to the allohexaploids C. microcarpa and C. sativa. The tetraploid C. rumelica appears to have evolved through multiple independent hybridization events. Divergence times for polyploid lineages closely related to C. sativa were all inferred to be very recent, at only ~65 thousand years ago. Chromosome counts confirm that there are two distinct cytotypes within C. microcarpa (2n = 38 and 2n = 40). Based on these findings and other recent research, we propose a model of Camelina subgenome relationships representing our current understanding of the hybridization and polyploidization history of this recently-diverged genus.
Complex and reticulate origin of edible roses (Rosa, Rosaceae) in China
Authors: Cui Wei-Hua , Du Xin-Yu , Zhong Mi-Cai , Fang Wei , Suo Zhi-Quan , Wang Dan , Dong Xue , Jiang Xiao-Dong , Hu Jin-Yong 
Published: January 2022

Abstract
While roses are today among the most popular ornamental plants, the petals and fruits of some cultivars have flavored foods for millennia. The genetic origins of these edible cultivars remain poorly investigated. We collected the major varieties of edible roses available in China, assembled their plastome sequences, and phased the haplotypes for internal transcribed spacers (ITS1/ITS2) of the 18S-5.8S-26S nuclear ribosomal cistron. Our phylogenetic reconstruction using 88 plastid genomes, of primarily maternal origin, uncovered well-supported genetic relationships within Rosa, including all sections and all subgenera. We phased the ITS sequences to identify potential donor species ancestral to the development of known edible cultivars. The tri-parental Middle-Eastern origin of R. × damascena, the species most widely used in perfume products and food additives, was confirmed as a descendent of past hybridizations among R. moschata, R. gallica, and R. majalis/R. fedtschenkoana/R. davurica. In contrast, R. chinensis, R. rugosa, and R. gallica, in association with six other wild species, were the main donors for fifteen varieties of edible roses. The domesticated R. rugosa ‘Plena’ was shown to be a hybrid between R. rugosa and R. davurica, sharing a common origin with R. ‘Fenghua’. Only R. ‘Jinbian’ and R. ‘Crimson Glory’ featured continuous flowering. All remaining cultivars of edible roses bloomed only once a year. Our study provides important resources for clarifying the origin of edible roses and suggests a future for breeding new cultivars with unique traits, such as continuous flowering.
Genome sequencing and population resequencing provide insights into the genetic basis of domestication and diversity of vegetable soybean
Authors: Liu Na , Niu Yongchao , Zhang Guwen , Feng Zhijuan , Bo Yuanpeng , Lian Jinmin , Wang Bin , Gong Yaming 
Published: January 2022

Abstract
Vegetable soybean is one of the most important vegetables in China, and the demand for this vegetable has markedly increased worldwide over the past two decades. Here, we present a high-quality de novo genome assembly of the vegetable soybean cultivar Zhenong 6 (ZN6), which is one of the most popular cultivars in China. The 20 pseudochromosomes cover 94.57% of the total 1.01 Gb assembly size, with contig N50 of 3.84 Mb and scaffold N50 of 48.41 Mb. A total of 55 517 protein-coding genes were annotated. Approximately 54.85% of the assembled genome was annotated as repetitive sequences, with the most abundant long terminal repeat transposable elements. Comparative genomic and phylogenetic analyses with grain soybean Williams 82, six other Fabaceae species and Arabidopsis thaliana genomes highlight the difference of ZN6 with other species. Furthermore, we resequenced 60 vegetable soybean accessions. Alongside 103 previously resequenced wild soybean and 155 previously resequenced grain soybean accessions, we performed analyses of population structure and selective sweep of vegetable, grain, and wild soybean. They were clearly divided into three clades. We found 1112 and 1047 genes under selection in the vegetable soybean and grain soybean populations compared with the wild soybean population, respectively. Among them, we identified 134 selected genes shared between vegetable soybean and grain soybean populations. Additionally, we report four sucrose synthase genes, one sucrose-phosphate synthase gene, and four sugar transport genes as candidate genes related to important traits such as seed sweetness and seed size in vegetable soybean. This study provides essential genomic resources to promote evolutionary and functional genomics studies and genomically informed breeding for vegetable soybean.
Warriors, pacifists and empires: race and racism in international thought before 1914
Authors: Ashworth Lucian M 
Published: January 2022

Abstract
Before 1914 scholars of international thought frequently relied on racist arguments, yet the ways that race was used varied widely from author to author. This article charts the way that race was used by two groups of Anglophone writers. The warriors used biological arguments to construct views of international affairs that relied on racist analysis. Pacifists might have used racist language that relied more on cultural prejudices, and would often base their more progressive views of international affairs on the idea of a civilizing mission. Using A. T. Mahan and Brooks Adams as exemplars of the warrior approach, and Norman Angell and H. N. Brailsford for the pacifists, I argue that race and racism play an important part in international thought before the First World War. This racism was directed at the colonized in the global South, Indigenous peoples in settler colonial states, and Jews in the global North. This use of race and racism in pre-First World War international thought has implications for how we view the development of International Relations today. It is not just statues and stately homes that require a thorough reassessment of attitudes to race, but also our understanding of the progression of ideas in international thought.
Exploring mechanisms of whiteness: how counterterrorism practitioners disrupt anti-racist expertise
Authors: Abu-Bakare Amal 
Published: January 2022

Abstract
This article situates the subject of the academic–practitioner (AP) exchange within an International Relations-orientated critique of the imperial dynamics of counterterrorism practices and racial subjugation. It uses an analytical framework that upholds the significance of racial hierarchy to knowledge production. A key contribution of this article is to situate the AP nexus within the circumstances of liberal democratic counterterrorism regimes, to demonstrate how race becomes meaningful to the knowledge that is produced about Islamophobia. The main argument of this article is that in present policy debates concerning the existence of systemic racism, one of the mechanisms enabling counterterrorism practitioners to regulate the AP exchange is that of institutionalized whiteness. Exploring two scenarios of AP exchanges in the United Kingdom and Canada, where counterterrorism practitioners were challenged to reconcile with academic explanations of Islamophobia as a systemic issue, this article uses colour-line inspired critiques of white logic to identify instances where anti-racist knowledge was subjugated in the name of imperialism. The article finds that in each scenario discussed, practitioners demonstrate trajectories of white logic by contesting the suitability of anti-racist knowledge put forward by academics, on the basis of racial hierarchy and self-aggrandizement. It concludes by discussing how a lack of practitioner–academic consensus continues to affect the dissemination of knowledge concerning systemic racism, thus prompting considerations of what this means for an anti-racist future.
Elite–mass agreement in British foreign policy
Authors: Vucetic Srdjan 
Published: January 2022

Abstract
Thirty years ago, William Wallace likened British foreign policy to a musical tug-of-war between the ‘Anglo-Saxons’ and ‘Europeans’, attributing ‘all the best tunes’ to the former. This article revisits Wallace's thesis and its main concept: national identity. It finds that Wallace was right to draw attention to the power of the ruling elite to shape Englishness and Britishness. However, the article also finds that ‘global’ foreign policy ideas were never the exclusive province of a segment of the British elite. Rather, they circulated in English and more broadly British society writ large, reflecting and reinforcing deep-seated, even unselfconscious, agreements between both ‘Anglo-Saxon’ and ‘European’ elites on the one hand, and much of the mass consumer public on the other. It follows that the constraints posed on possibilities of foreign policy change were always greater than Wallace had suggested; that a ‘lesser’ British foreign policy that was, and still is, so hard to imagine for the British is significant for analysis of dynamics of ‘western’ knowledge production that come under critique in this special issue. But rather than focusing exclusively on elites, critical analyses of knowledge exchange should be attuned to popular common sense, too.
Reallocation and productivity during the Great Recession: evidence from French manufacturing firms
Authors: Domini Giacomo , Moschella Daniele 
Published: January 2022

Abstract
According to the ‘cleansing hypothesis’, recessions are periods in which productivity-enhancing reallocation intensifies, shifting resources away from less efficient to more efficient firms at a faster pace. Does the Great Recession of 2008–2010 fit this view? We address this question, studying the case of the French manufacturing sector. Based on a panel of firms, built by matching several data sources, we analyze the dynamics of the relation between productivity and reallocation over the period 2002–2013. Our results show that, during the Great Recession, more productive firms decreased their advantage with respect to less productive firms, in terms of both employment growth and probability to survive, in disagreement with the cleansing hypothesis. This attenuation of productivity-enhancing reallocation was significantly driven by the trade collapse and credit crunch that were associated with the crisis, while it does not emerge to depend on labor-market regulations and anti-crisis policies.
Fighting a pandemic: sociodemographic disparities and coronavirus disease-2019 vaccination gaps—a population study
Authors: Benderly Michal , Huppert Amit , Novikov Ilya , Ziv Arnona , Kalter-Leibovici Ofra 
Published: January 2022

Abstract

Background
Data suggest lower coronavirus disease-2019 (COVID-19) vaccination coverage among minority and disadvantaged groups. We aimed to identify interactions between sociodemographic factors associated with vaccination gaps.

Methods
This population study used Israeli National COVID-19 data (extracted: 10 May 2021). The analysis comprised 6 478 999 individuals age ≥15 years with aggregated area-level data on sex and age distribution and no COVID-19 history. We estimated vaccination hazard and cumulative incidence using the Fine and Gray competing risk model.

Results
Older age and higher socioeconomic status (SES) were associated, with stepwise higher cumulative vaccination rates (age 20–24: 67%, age ≥ 75: 96%; SES 1–3: 61%, 4–5: 74.2%, 6–7: 82%, 8–10: 87%). We found the lowest vaccination rates in Arab (65%) and Ultra-Orthodox Jewish (54%) areas. SES modified the association in Arab neighbourhoods, with higher coverage than in the non-Orthodox Jewish reference group in SES 1–3 [adjusted hazard ratio (HR) = 1.06; 95% confidence interval (CI): 1.02–1.11], and gradually lower coverage in higher SES classes (SES 6–7: HR = 0.83; 95% CI: 0.79–0.87). Vaccination rates were also higher among younger Arabs (≤45 years) compared with age counterparts in the reference population group (age 25–34: HR = 1.18; 95% CI: 1.12–1.28) and lower than the reference group among Arabs age ≥45 years. Among Ultra-Orthodox Jews, vaccination HRs remained below one across age and SES classes.

Conclusions
Age and SES modified the association between population group and vaccination coverage. Identifying the interplay between sociodemographic characteristics and the underlying explanations may improve targeted efforts, aimed at closing vaccination coverage gaps and mitigating COVID-19.
‘Treatment Accorded to Aliens Generally’: Article 7(1) of the 1951 Refugee Convention as a Basis for Visa-Free Access to States Parties’ Territory? An Examination of the Prohibition of Nationality Discrimination in the Refugee Convention
Authors: Grundler Maja 
Published: January 2022

Abstract
Visa requirements, coupled with other extraterritorial border controls like carrier sanctions, prevent refugees from accessing the territory of States in the global North and the protection these States offer under the 1951 Refugee Convention. Visa requirements are imposed largely on the basis of an individual’s nationality, and distinctions made between different non-citizens in this context are considered to be legitimate in international law, based on States’ right to control their borders. In light of the 70th anniversary of the Refugee Convention, this article examines whether this instrument can respond to the externalization of border controls, specifically the imposition of visa requirements, and to the impact of these developments on refugees’ access to protection, by relying on the Convention’s non-discrimination clause. The article makes the case for an interpretation of the Refugee Convention that allows for access to States parties’ territory under article 7(1) – by approaching visa requirements as a ‘treatment accorded to aliens generally’ – combined with article 3 – the non-discrimination provision of the Convention, which prohibits discrimination among refugees on grounds of their nationality. It will be suggested that coupled with the declaratory nature of refugee status, these provisions may be read as precluding imposing visa requirements on refugees originating from country A, as long as refugees originating from country B can reach a State’s border visa-free. The article highlights the Refugee Convention’s continued relevance, showing that some of its core principles, such as the non-discrimination provision, offer solutions where States parties attempt to limit their protection obligations towards refugees.
Oral Human Papillomavirus Associated With Differences in Oral Microbiota Beta Diversity and Microbiota Abundance
Authors: Zhang Yuehan , D’Souza Gypsyamber , Fakhry Carole , Bigelow Elaine O , Usyk Mykhaylo , Burk Robert D , Zhao Ni 
Published: January 2022

AbstractBackgroundAlthough cervicovaginal microbiome has been associated with cervical human papillomavirus (HPV) infection, little is known regarding the association of oral microbiome with oral HPV, a cause of oropharyngeal cancer.MethodsA cross-sectional analysis of 495 participants from the Men and Women Offering Understanding of Throat HPV study was conducted. 16S rRNA gene amplicon sequencing was performed on saliva samples. HPV DNA in oral rinse samples was tested. Associations of oral microbiome diversity, taxon abundance, and predicted functional pathways with oral HPV were assessed, adjusting for age, race/ethnicity, education, human immunodeficiency virus, current smoking, and sequencing batch.ResultsParticipants with oral HPV (n = 68) compared with those without HPV had similar oral microbiome alpha-diversity yet different beta-diversity (Bray-Curtis distance for bacterial taxa, P = .009; functional pathways, P = .02). Participants with oral HPV had higher abundance of Actinomycetaceae, Prevotellaceae, Veillonellaceae, Campylobacteraceae, Bacteroidetes, and lower abundance of Gemellaceae (false discovery rate &lt;0.10). We also found differential functional potential of oral microbiome by oral HPV status: xenobiotic biodegradation-related pathways were less abundant among participants with oral HPV, suggesting potential xenobiotic-induced toxic effects with implications for HPV susceptibility.ConclusionsOur findings suggest a shift in oral microbiome community structure, composition, and functional potential between individuals with and without oral HPV.