bluuebunny/crossref_metadata_2025_split huggingface dataset:
The highly continuous reference genome of a leaf-chimeric red pineapple (Ananas comosus var. bracteatus f. tricolor) provides insights into elaboration of leaf color
Authors: Feng Lijun , Wang Juntao , Mao Meiqin , Yang Wei , Adje Mark Owusu , Xue Yanbin , Zhou Xuzixin , Zhang Huiling , Luo Jiaheng , Tang Ruimin , Tan Lin , Lin Dongpu , Zhang Xiaopeng , Zang Yaoqiang , He Yehua , Chen Changming , Luan Aiping , Lin Wenqiu , Xu Wentian , Li Xi , Sun Lingxia , Jiang Fuxing , Ma Jun 
Published: January 2022

Abstract
Ananas comosus var. bracteatus f. tricolor (GL1) is a red pineapple accession whose mostly green leaves with chimeric white leaf margins turn red in spring and autumn and during flowering. It is an important ornamental plant and ideal plant research model for anthocyanin metabolism, chimeric leaf development, and photosynthesis. Here, we generated a highly contiguous chromosome-scale genome assembly for GL1 and compared it with other 3 published pineapple assemblies (var. comosus accessions MD2 and F153, and var. bracteatus accession CB5). The GL1 assembly has a total size of ∼461 Mb, with a contig N50 of ∼2.97 Mb and Benchmarking Universal Single-Copy Ortholog score of 97.3%. More than 99% of the contigs are anchored to 25 pseudochromosomes. Compared with the other 3 published pineapple assemblies, the GL1 assembly was confirmed to be more continuous. Our evolutionary analysis showed that the Bromeliaceae and Poaceae diverged from their nearest common ancestor ∼82.36 million years ago (MYA). Population structure analysis showed that while GL1 has not undergone admixture, bracteatus accession CB5 has resulted from admixture of 3 species of Ananas. Through classification of orthogroups, analysis of genes under positive selection, and analysis of presence/absence variants, we identified a series of genes related to anthocyanin metabolism and development of chimeric leaves. The structure and evolution of these genes were compared among the published pineapple assemblies with reveal candidate genes for these traits. The GL1 genome assembly and its comparisons with other 3 pineapple genome assemblies provide a valuable resource for the genetic improvement of pineapple and serve as a model for understanding the genomic basis of important traits in different pineapple varieties and other pan-cereal crops.
The Effect of Race and Dementia Prevalence on a COVID-19 Infection Control Intervention in Massachusetts Nursing Homes
Authors: Dufour Alyssa B , Kosar Cyrus , Mor Vincent , Lipsitz Lewis A 
Published: January 2022

Abstract

Background
Nursing home (NH) residents, especially those who were Black or with dementia, had the highest infection rates during the COVID-19 pandemic. A 9-week COVID-19 infection control intervention in 360 Massachusetts NHs showed adherence to an infection control checklist with proper personal protective equipment (PPE) use and cohorting was associated with declines in weekly infection rates. NHs were offered weekly webinars, answers to infection control questions, resources to acquire PPE, backup staff, and SARS-CoV-2 testing. We asked whether the effect of this intervention differed by racial and dementia composition of the NHs.

Methods
Data were obtained from 4 state audits using infection control checklists, weekly infection rates, and Minimum Data Set variables on race and dementia to determine whether adherence to checklist competencies was associated with decline in average weekly rates of new COVID-19 infections.

Results
Using a mixed-effects hurdle model, adjusted for county COVID-19 prevalence, we found the overall effect of the intervention did not differ by racial composition, but proper cohorting of residents was associated with a greater reduction in infection rates among facilities with ≥20% non-Whites (n = 83). Facilities in the middle (&gt;50%–62%; n = 121) and upper (&gt;62%; n = 115) tertiles of dementia prevalence had the largest reduction in infection rates as checklist scores improved. Cohorting was associated with greater reductions in infection rates among facilities in the middle and upper tertiles of dementia prevalence.

Conclusions
Adherence to proper infection control procedures, particularly cohorting of residents, can reduce COVID-19 infections, even in facilities with high percentages of high-risk residents (non-White and dementia).
Alternative transcription and feedback regulation suggest that SlIDI1 is involved in tomato carotenoid synthesis in a complex way.
Authors: Zhou Ming , Deng Lei , Guo Shaogui , Yuan Guoliang , Li Chuanyou , Li Changbao 
Published: January 2022

Abstract
Carotenoid pigments confer photoprotection and visual attraction and serve as precursors for many important signaling molecules. Herein, the orange-fruited phenotype of a tomato elite inbred line resulting from sharply reduced carotenoid levels and an increased β-carotene-to-lycopene ratio in fruit was shown to be controlled by a single recessive gene, oft3. BSA-Seq combined with fine mapping delimited the oft3 gene to a 71.23 kb interval on chromosome 4, including eight genes. Finally, the oft3 candidate gene SlIDI1, harboring a 116 bp deletion mutation, was identified by genome sequence analysis. Further functional complementation and CRISPR–Cas9 knockout experiments confirmed that SlIDI1 was the gene underlying the oft3 locus. qRT–PCR analysis revealed that the expression of SlIDI1 was highest in flowers and fruit and increased with fruit ripening or flower maturation. SlIDI1 simultaneously produced long and short transcripts by alternative transcription initiation and alternative splicing. Green fluorescent protein fusion expression revealed that the long isoform was mainly localized in plastids and that an N-terminal 59-amino acid extension sequence was responsible for plastid targeting. Short transcripts were identified in leaves and fruit by 5’ RACE and in fruit by 3’ RACE, which produced corresponding proteins lacking transit peptides and/or putative peroxisome targeting sequences, respectively. In SlIDI1 mutant fruit, SlBCH1 transcription involved in β-carotenoid catabolism was obviously suppressed, which may be responsible for the higher β-carotene-to-lycopene ratio and suggested potential feedback regulatory mechanisms involved in carotenoid pathway flux.
Ideology, socialization and hegemony in Disciplinary International Relations
Authors: Persaud Randolph B 
Published: January 2022

Abstract
This article argues that Disciplinary International Relations (DIR) does not only explain international affairs, but it also socializes and hegemonizes publics and professionals into an ideological worldview consistent with the interest of states that underwrite the world economic and security order based on hegemonic liberalism. Considerable emphasis is placed on tracing the continuities between the early theorization of IR in the United Kingdom and the United States, and the contemporary academic/foreign policy/security ‘complex’ dedicated to the maintenance of a hegemonic world order. The article demonstrates that the call for a greater theory–policy nexus in international affairs is redundant because leading American scholars double up as policy-makers, either directly or through other avenues such as consultancies. Some of the most prominent IR scholars, such as Michael Doyle, John Lewis Gaddis, Samuel Huntington, G. John Ikenberry, Stephen Krasner, Theodore H. Moran, Joseph Nye and Anne-Marie Slaughter, among others, have served in high-level positions in the United States foreign policy and security apparatus. The article also shows the ways in which in the early days of IR theorizing in the UK, scholars such as Lionel Curtis, Alfred Zimmern and Norman Angell doubled as staunch defenders of the British Empire, albeit in the language of liberal internationalism.
The colonial roots of counter-insurgencies in international politics
Authors: Sen Somdeep 
Published: January 2022

Abstract
There is a state-centrism in the way insurgencies are conceived in international politics. Herein, policy and practice targeting insurgencies draw on the long-established scholarly perception that war-making is the vocation of the state and that the violence of non-state insurgent factions is a source of insecurity. However, this state-centrism also has a colonial legacy and is an outgrowth of the colonial hostility towards anti-colonial factions. In this article, I establish the colonial roots of the current standing of insurgencies in international politics. Empirically, I focus on the European Union's (EU) peacebuilding efforts in the occupied Palestinian territories (oPt). These efforts are largely premised on the notion that state-building is synonymous with peacebuilding and are focused on furbishing the state-like institutions of the Palestinian Authority (PA). But, in doing so, this manner of peacebuilding also replicates the scholarly antagonism towards non-state armed factions and, with it, the logic of colonial counterinsurgencies, as it de-legitimizes the varied forms of insurgent politics that occur outside the institutional limits of the PA. In the end, it is not entirely surprising that this mode of engagement has not secured peace—especially since it is premised on a certain antagonism towards insurgent politics. Therefore, I conclude, a substantial understanding (and incorporation) of the political grievances that drive insurgent politics, and their appeal, is essential for effective peacebuilding.
Colonial policy studies in Japan: racial visions of Nan'yo, or the early creation of a global South
Authors: Baji Tomohito 
Published: January 2022

Abstract
This article examines Japanese colonial policy studies (shokumin seisaku gaku) with a particular focus on its relationship with the distinct region of ‘Nan'yo’ (the South Seas). Specifically analysing the works of Takekoshi Yosaburo (1865–1950), Nitobe Inazo (1862–1933) and Yanaihara Tadao (1893–1961), it seeks to uncover the ways in which the exponents of this study area accounted for Nan'yo based on their conceptions of race. It also shows how they inflicted envisaged racial hierarchies on the southern Pacific and how such attempts were related to colonial policy debates behind the practice of Japanese imperialism. Part of the findings point out that Takekoshi's and Nitobe's comparable projections of strict racial hierarchies on the Malays served to justify the southward colonization of the Japanese. Yanaihara's depiction of Nan'yo islanders as radically underdeveloped was tailored to championing Japan's sustained espousal of the League Mandate. The article argues that their accounts of Nan'yo formed part of a transnational knowledge chain about colonial and racial victimization. Like their western counterparts including Gustav Le Bon, Paul Leroy-Beaulieu, Paul S. Reinsch and J. A. Hobson, they built purported racial pyramids with the tropical areas at their bottom, the bulk of which correspond to today's global South. They have been accomplices in this colonial present.
The impact of colonialism on policy and knowledge production in International Relations
Authors: Gani Jasmine K , Marshall Jenna 
Published: January 2022

Abstract
Is there an academic–policy divide, and does that gap need to be bridged? For decades, International Relations (IR) scholars have reflected on their roles and responsibilities towards the ‘real world’, while policy-makers have often critiqued the detachment of academic research. In response, there have been increased calls for academics to descend from their ‘ivory tower’. However, the articles in this 100th anniversary special issue of International Affairs interrogate this so-called theory–policy divide and problematize the exchange of knowledge between academics and practitioners, highlighting the colonial underpinnings of their historical entanglements. In this introductory article we bring together the core arguments of the special issue contributions to delineate three prominent dynamics in the academic–practitioner nexus: the role of academia as a supplier of knowledge for colonial policies; the influence of imperial practice and policy-makers in shaping IR and academic knowledge production; and the contestation from academics and/or practitioners against racial hierarchies in knowledge production and policy-making. Confronting the exclusions, amnesias and denials of colonialism in the theory and practice of International Relations is the necessary first step in any process of repair towards a more just and viable politics.
Effects of Motivational Downshifts on Specific Pavlovian-Instrumental Transfer in Rats
Authors: Sommer Susanne , Münster Alexandra , Fehrentz Jean-Alain , Hauber Wolfgang 
Published: January 2022

Abstract

Background
Pavlovian stimuli predictive of appetitive outcomes can exert a powerful influence on the selection and initiation of action, a phenomenon termed outcome-selective Pavlovian-instrumental transfer (sPIT). Rodent studies suggest that sPIT is insensitive to motivational downshift induced by outcome devaluation, an effect that is, however, relatively underexplored.

Methods
Here we examined in detail the effects of distinct shifts in motivation from hunger to a state of relative satiety on sPIT in rats.

Results
A motivational downshift by outcome-specific devaluation immediately prior to testing markedly reduced overall lever responding and magazine entries but left intact the sPIT effect. A motivational downshift prior testing by (1) giving ad libitum rather than restricted access to maintenance diet in the home cage for 24 hours or by (2) a systemic blockade of hormone secretagogue receptor subtype 1A receptors to inhibit orexigenic actions of ghrelin both reduced overall lever responding and magazine entries. Moreover, these latter motivational downshifts reduced the sPIT effect; however, the sizes of the sPIT effects were still large.

Conclusions
Collectively, our rodent findings indicate that major effects of various motivational downshifts are overall inhibition of lever pressing and magazine approach, possibly reflecting reduced general motivation. The observed effects of motivational downshifts on sPIT have implications with regard to the role of general motivating effects in sPIT and to the contribution of Pavlovian-instrumental interactions to excessive food seeking as well as obesity in humans.
The Farrell–Jones Conjecture for Hyperbolic-by-Cyclic Groups
Authors: Bestvina Mladen , Fujiwara Koji , Wigglesworth Derrick 
Published: January 2022

Abstract
We prove the Farrell–Jones conjecture (FJC) for mapping tori of automorphisms of virtually torsion-free hyperbolic groups. The proof uses recently developed geometric methods for establishing the FJC by Bartels–Lück–Reich, as well as the structure theory of mapping tori by Dahmani–Krishna.
DIY Cruelty: The Global Political Micro-Practices of Hateful Memes
Authors: Marlin-Bennett Renée , Jackson Susan T 
Published: January 2022

AbstractCruel memes spread messages of hate via social media. The Internet itself extends the memes’ geographical reach, and many such cruel memes circulate across borders. This article examines the activities of cruel memeing—practices of creating, commenting on, reinforcing (“liking”), sharing, remixing, and otherwise endorsing cruel memes—as microscale hostile engagements in global politics. This is a politics of the everyday that is accessible to people in their ordinary lives and that is designed to be entertaining as well as cruel. The research draws on a large dataset of memes, comment threads, and related information from two opposed Reddit communities, r/TheLeftCantMeme and r/TheRightCantMeme. The power-flow theoretical framework structures an interpretive analysis of how cruel memes circulate within the social media space. We examine content (including narrative, degree of cruelty, and other components), and velocity of information flow, as well as access to the flow. Focusing on racism, antisemitism, and disdain for political opponents, we draw on interpretive methods to analyze the flow of information that spreads hate. We find: (1) normalization of divisiveness, derisiveness, and bigotry; (2) justifications of violence; and (3) emergence of agents despite pseudonymity. Cruel memeing activities combine with the structure of the online communities to spread hatred far beyond social media platforms.
Clinical Performance of a Lateral Flow SARS-CoV-2 Total Antibody Assay
Authors: Cobb Beth L , Lloyd Matthew , Hock Karl G , Farnsworth Christopher W 
Published: January 2022

Abstract

Background
Serological assays for SARS-CoV-2 are important tools for diagnosis in patients with negative RT-PCR testing, pediatric patients with multisystem inflammatory syndrome, and serosurveillance studies. However, lateral flow-based serological assays have previously demonstrated poor analytical and clinical performance, limiting their utility.

Methods
We assessed the ADEXUSDx COVID-19 lateral flow assay for agreement with diagnostic RT-PCR testing using 120 specimens from RT-PCR–positive patients, 77 specimens from symptomatic RT-PCR–negative patients, and 47 specimens obtained prepandemic. Specimens collected &lt;14 days from symptom onset in RT-PCR–positive patients were compared relative to the Abbott SARS-CoV-2 IgG assay.

Results
The ADEXUSDx COVID-19 Test yielded an overall positive percent agreement (PPA) of 92.5% (95%CI 85.8 to 96.3) and negative percent agreement of 99.2% (95% CI 94.9–100.0) relative to RT-PCR and in prepandemic specimens. Relative to days from symptom onset, the PPA after 13 days was 100% (95% CI 94.2–100); from 7 to 13 days, 89.7 (95% CI 71.5–97.2); and from 0 to 7 days, 53.8 (95% CI 26.1–79.6). The overall agreement between the Abbott and ADEXUSDx assays was 80.9%. Twenty-five specimens were positive by both assays, 9 specimens were negative by both assays, and 8 specimens were positive by only the ADEXUSDx assay.

Conclusions
We demonstrate high PPA and negative percent agreement of the ADEXUSDx COVID-19 assay and diagnostic testing by RT-PCR, with PPA approximately 90% by 7 days following symptom onset. The use of waived testing for antibodies to SARS-CoV-2 with high sensitivity and specificity provide a further tool for combatting the COVID-19 pandemic.
Capturing Difference: The Wurstelprater Photobook in Turn-of-the-Century Vienna
Authors: Samols Steven 
Published: January 2022

Abstract
Published in 1911 Vienna, the Wurstelprater photobook offered a very different image of the city from the one people were used to finding in postcards. The book toured readers through the Wurstelprater, the amusement section of the larger Prater park, focusing on its eclectic attractions and diverse crowds. Wurstelprater combined text written by future Bambi author Felix Salten with 75 pictures by photographer Emil Mayer. Those words and images had appeared earlier in separate forms, but the photobook brought them together for the first time. While many saw the Prater as a space of blight, Salten and Mayer cherished its distinctiveness from the rest of the city. The Prater had a special significance for Vienna’s Jews. It was not only a place of entertainment, but also a space where rigid Viennese social hierarchies could be suspended.
Scholars have detailed Jewish involvement in the production of spaces, performances, and literatures in ‘Vienna 1900’. The emergence of the photobook as a medium of Jewish difference has, however, remained underexplored. This article analyses how Wurstelprater fused two Jewish genres, the feuilleton and street photography, making the experience of a disappearing Prater durable and portable. Assembling words and images in an unprecedented format, Wurstelprater constructed a sense of movement, nostalgia, and outsiderness. It presaged what most associate with interwar photojournalism and photo essays. Wurstelprater also became a tool of history. In the 1960s, those who rediscovered Wurstelprater treated it as evidence of what the late Habsburg empire had been. Originally conceived by outsiders, the photobook came to be a mainstream historical record.
A Thermodynamic Atlas of Proteomes Reveals Energetic Innovation across the Tree of Life
Authors: Chin Alexander F , Wrabl James O , Hilser Vincent J 
Published: January 2022

Abstract
Protein stability is a fundamental molecular property enabling organisms to adapt to their biological niches. How this is facilitated and whether there are kingdom specific or more general universal strategies are unknown. A principal obstacle to addressing this issue is that the vast majority of proteins lack annotation, specifically thermodynamic annotation, beyond the amino acid and chromosome information derived from genome sequencing. To address this gap and facilitate future investigation into large-scale patterns of protein stability and dynamics within and between organisms, we applied a unique ensemble-based thermodynamic characterization of protein folds to a substantial portion of extant sequenced genomes. Using this approach, we compiled a database resource focused on the position-specific variation in protein stability. Interrogation of the database reveals: 1) domains of life exhibit distinguishing thermodynamic features, with eukaryotes particularly different from both archaea and bacteria; 2) the optimal growth temperature of an organism is proportional to the average apolar enthalpy of its proteome; 3) intrinsic disorder content is also proportional to the apolar enthalpy (but unexpectedly not the predicted stability at 25 °C); and 4) secondary structure and global stability information of individual proteins is extractable. We hypothesize that wider access to residue-specific thermodynamic information of proteomes will result in deeper understanding of mechanisms driving functional adaptation and protein evolution. Our database is free for download at https://afc-science.github.io/thermo-env-atlas/ (last accessed January 18, 2022).
MethReg: estimating the regulatory potential of DNA methylation in gene transcription
Authors: Silva Tiago C , Young Juan I , Martin Eden R , Chen X Steven , Wang Lily 
Published: January 2022

AbstractEpigenome-wide association studies often detect many differentially methylated sites, and many are located in distal regulatory regions. To further prioritize these significant sites, there is a critical need to better understand the functional impact of CpG methylation. Recent studies demonstrated that CpG methylation-dependent transcriptional regulation is a widespread phenomenon. Here, we present MethReg, an R/Bioconductor package that analyzes matched DNA methylation and gene expression data, along with external transcription factor (TF) binding information, to evaluate, prioritize and annotate CpG sites with high regulatory potential. At these CpG sites, TF–target gene associations are often only present in a subset of samples with high (or low) methylation levels, so they can be missed by analyses that use all samples. Using colorectal cancer and Alzheimer’s disease datasets, we show MethReg significantly enhances our understanding of the regulatory roles of DNA methylation in complex diseases.
Moneyness, Underlying Asset Volatility, and the Cross-Section of Option Returns
Authors: Aretz Kevin , Lin Ming-Tsung , Poon Ser-Huang 
Published: January 2022

Abstract
We study the effect of an asset’s volatility on the expected returns of European options on the asset. Deriving predictions from a stochastic discount factor model, we show that the effect depends on whether variations in the asset’s volatility are driven by systematic or idiosyncratic volatility. While idiosyncratic-volatility-induced variations only affect the option elasticity, systematic-volatility-induced variations also oppositely affect the expected return of the asset. Since the expected asset return (elasticity) effect dominates for options with more linear (non-linear) payoffs, systematic volatility prices sufficiently in-the-money (out-of-the-money) options with the opposite (same) sign as idiosyncratic volatility. Using single-stock calls as test assets, double-sorted portfolios and Fama–MacBeth (1973) regressions broadly support the model’s predictions.