bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of an auxin biosynthesis inhibitor, p-phenoxyphenyl boronic acid, on auxin biosynthesis and development in rice
Authors: Watanabe Mayu , Shigihara Masaru , Hirota Yuna , Takato Shin , Sato Akiko , Kakei Yusuke , Kikuchi Rie , Ishii Takahiro , Soeno Kazuo , Nakamura Ayako , Shimada Yukihisa 
Published: January 2021

ABSTRACT
p-Phenoxyphenyl boronic acid (PPBo) is a specific inhibitor of auxin biosynthesis in Arabidopsis. We examined the inhibitory activity of PPBo in rice. The activity of OsYUCCA, a key enzyme for auxin biosynthesis, was inhibited by PPBo in vitro. The endogenous indole-3-acetic acid (IAA) level and the expression levels of auxin-response genes were significantly reduced in PPBo-treated rice seedlings, which showed typical auxin-deficiency phenotypes. Seminal root growth was promoted by 1 µM PPBo, which was reversed by co-treatment of IAA and PPBo. By contrast, the inhibition of root growth by 10 µM PPBo was not recovered by IAA. The root meristem morphology and cell division were restored by IAA at 60 µM, but that concentration may be too high to support root growth. In conclusion, PPBo is an inhibitor of auxin biosynthesis that targets YUCCA in rice.
A sequence-based deep learning approach to predict CTCF-mediated chromatin loop
Authors: Lv Hao , Dao Fu-Ying , Zulfiqar Hasan , Su Wei , Ding Hui , Liu Li , Lin Hao 
Published: January 2021

AbstractThree-dimensional (3D) architecture of the chromosomes is of crucial importance for transcription regulation and DNA replication. Various high-throughput chromosome conformation capture-based methods have revealed that CTCF-mediated chromatin loops are a major component of 3D architecture. However, CTCF-mediated chromatin loops are cell type specific, and most chromatin interaction capture techniques are time-consuming and labor-intensive, which restricts their usage on a very large number of cell types. Genomic sequence-based computational models are sophisticated enough to capture important features of chromatin architecture and help to identify chromatin loops. In this work, we develop Deep-loop, a convolutional neural network model, to integrate k-tuple nucleotide frequency component, nucleotide pair spectrum encoding, position conservation, position scoring function and natural vector features for the prediction of chromatin loops. By a series of examination based on cross-validation, Deep-loop shows excellent performance in the identification of the chromatin loops from different cell types. The source code of Deep-loop is freely available at the repository https://github.com/linDing-group/Deep-loop.
Glucose metabolism characterization during mouse in vitro maturation identifies alterations in cumulus cells†
Authors: Akin Nazli , von Mengden Lucia , Herta Anamaria-Cristina , Billooye Katy , van Leersum Julia , Cava-Cami Berta , Saucedo-Cuevas Laura , Klamt Fabio , Smitz Johan , Anckaert Ellen 
Published: January 2021

AbstractIn vitro maturation (IVM) is an assisted reproduction technique with reduced hormone-related side-effects. Several attempts to implement IVM in routine practice have failed, primarily due to its relatively low efficiency compared with conventional in vitro fertilization (IVF). Recently, capacitation (CAPA)-IVM—a novel two-step IVM method—has improved the embryology outcomes through synchronizing the oocyte nuclear and cytoplasmic maturation. However, the efficiency gap between CAPA-IVM and conventional IVF is still noticeable especially in the numerical production of good quality embryos. Considering the importance of glucose for oocyte competence, its metabolization is studied within both in vivo and CAPA-IVM matured mouse cumulus-oocyte-complexes (COCs) through direct measurements in both cellular compartments, from transcriptional and translational perspectives, to reveal metabolic shortcomings within the CAPA-IVM COCs. These results confirmed that within in vivo COC, cumulus cells (CCs) are highly glycolytic, whereas oocytes, with low glycolytic activity, are deviating their glucose towards pentose phosphate pathway. No significant differences were observed in the CAPA-IVM oocytes compared with their in vivo counterparts. However, their CCs exhibited a precocious increase of glycolytic activity during the pre-maturation culture step and activity was decreased during the IVM step. Here, specific alterations in mouse COC glucose metabolism due to CAPA-IVM culture were characterized using direct measurements for the first time. Present data show that, while CAPA-IVM CCs are able to utilize glucose, their ability to support oocytes during final maturation is impaired. Future CAPA-IVM optimization strategies could focus on adjusting culture media energy substrate concentrations and/or implementing co-culture strategies.
Soil Seed Banks, Alternative Stable State Theory, and Ecosystem Resilience
Authors: Ma Miaojun , Collins Scott L , Ratajczak Zak , Du Guozhen 
Published: January 2021

Abstract
In restoration ecology, the transition from desired to degraded state is based solely on the composition of the aboveground plant community, whereas belowground propagules are often neglected. We developed a conceptual framework integrating seed bank dynamics into alternative stable state theory, highlighting the important relationship between aboveground and belowground composition. This integration emphasizes the role of resilience in systems that appear to have shifted to an “undesirable” state. Belowground propagules, especially soil seed and bud banks, provide buffering capacity and may serve as valuable indicators of potential resistance to state transition based on the degree of similarity between belowground and aboveground vegetation composition. Ecosystem states may have multiple components that differ in their rate of change, as well as in their capacity to promote resilience. We recommend that the application of alternative stable state theory from a management perspective should incorporate components of both above- and belowground vegetation.
Factors associated with delays in revascularization in patients with chronic limb-threatening ischaemia: population-based cohort study
Authors: Birmpili P , Johal A , Li Q , Waton S , Chetter I , Boyle J R , Cromwell D 
Published: January 2021

Abstract

Background
Prompt revascularization in patients with chronic limb-threatening ischaemia (CLTI) is important, and recent guidance has suggested that patients should undergo revascularization within 5 days of an emergency admission to hospital. The aim of this cohort study was to identify factors associated with the ability of UK vascular services to meet this standard of care.

Methods
Data on all patients admitted non-electively with CLTI who underwent open or endovascular revascularization between 2016 and 2019 were extracted from the National Vascular Registry. The primary outcome was interval between admission and procedure, analysed as a binary variable (5 days or less, over 5 days). Multivariable Poisson regression was used to examine the relationship between time to revascularization and patient and admission characteristics.

Results
The study analysed information on 11 398 patients (5973 open, 5425 endovascular), 50.6 per of whom underwent revascularization within 5 days. The median interval between admission and intervention was 5 (i.q.r. 2–9) days. Patient factors associated with increased risk of delayed revascularization were older age, greater burden of co-morbidity, non-smoking status, presentation with infection and tissue loss, and a Fontaine score of IV. Patients admitted later in the week were less likely undergo revascularization within 5 days than those admitted on Sundays and Mondays (P &lt; 0.001). Delays were slightly worse among patients having open compared with endovascular procedures (P = 0.005) and in hospitals with lower procedure volumes (P &lt; 0.001).

Conclusion
Several factors were associated with delays in time to revascularization for patients with CLTI in the UK, most notably the weekday of admission, which reflects how services are organized. The results support arguments for vascular units providing revascularization to have the resources for a 7-day service.
Skipping the Dry Diagonal: spatio-temporal evolution ofCrotonsectionCleodora(Euphorbiaceae) in the Neotropics
Authors: Masa-Iranzo Irene , Sanmartín Isabel , Caruzo Maria Beatriz R , Riina Ricarda 
Published: January 2021

AbstractCroton is one of the largest angiosperm genera, with &gt; 1200 species in the tropics worldwide. The arborescent Croton section Cleodora stands out for its disjunct geographical distribution with two main centres of diversity in the Amazonian and Atlantic Forest regions, separated by the Caatinga, Cerrado and Chaco biomes (the ‘Dry Diagonal’). This disjunction is found in other Neotropical lineages and attributed to Neogene geological and climatic events. We inferred a nearly complete phylogenetic reconstruction of Croton section Cleodora based on DNA sequences of nuclear ITS and five plastid regions (rps16, trnH-psbA, trnL-F, trnT-L and ycf1). We further estimated divergence times and reconstructed ancestral ranges using Bayesian methods. Our results show that Croton section Cleodora is monophyletic with two main clades; we also confirm the phylogenetic adscription of eight Croton spp. recently described or assigned to section Cleodora based on morphology. Divergence of section Cleodora from its sister clade occurred c. 25 Mya, and diversification within this group started 20 Mya. Biogeographic analyses suggest the section originated in the Amazonian region, from where it dispersed to other forested Neotropical regions, including the Atlantic Forest. Divergence between Amazonian and Atlantic Forest taxa appears to have been triggered by the formation of the South American Dry Diagonal.
Longitudinal deterioration of white-matter integrity: heterogeneity in the ageing population
Authors: Poulakis Konstantinos , Reid Robert I , Przybelski Scott A , Knopman David S , Graff-Radford Jonathan , Lowe Val J , Mielke Michelle M , Machulda Mary M , Jack Clifford R , Petersen Ronald C , Westman Eric , Vemuri Prashanthi 
Published: January 2021

Abstract
Deterioration in white-matter health plays a role in cognitive ageing. Our goal was to discern heterogeneity of white-matter tract vulnerability in ageing using longitudinal imaging data (two to five imaging and cognitive assessments per participant) from a population-based sample of 553 elderly participants (age ≥60 years). We found that different clusters (healthy white matter, fast white-matter decliners and intermediate white-matter group) were heterogeneous in the spatial distribution of white-matter integrity, systemic health and cognitive trajectories. White-matter health of specific tracts (genu of corpus callosum, posterior corona radiata and anterior internal capsule) informed about cluster assignments. Not surprisingly, brain amyloidosis was not significantly different between clusters. Clusters had differential white-matter tract vulnerability to ageing (commissural fibres &gt; association/brainstem fibres). Identification of vulnerable white-matter tracts is a valuable approach to assessing risk for cognitive decline.
Hepatic Steatosis Associated With Exposure to Elvitegravir and Raltegravir
Authors: Kirkegaard-Klitbo Ditte Marie , Thomsen Magda Teresa , Gelpi Marco , Bendtsen Flemming , Nielsen Susanne Dam , Benfield Thomas 
Published: January 2021

Abstract
Moderate-to-severe hepatic steatosis in people living with human immunodeficiency virus (HIV) without viral hepatitis or excessive alcohol intake was associated with cumulative exposure to stavudine, elvitegravir, and raltegravir. Prospective trials are required to establish a causal association.
Clinical Trials Registration. NCT02382822.
Evaluation of Vaccine Safety After the First Public Sector Introduction of Typhoid Conjugate Vaccine—Navi Mumbai, India, 2018
Authors: Longley Ashley T , Date Kashmira , Luby Stephen P , Bhatnagar Pankaj , Bentsi-Enchill Adwoa D , Goyal Vineet , Shimpi Rahul , Katkar Arun , Yewale Vijay , Jayaprasad Niniya , Horng Lily , Kunwar Abhishek , Harvey Pauline , Haldar Pradeep , Dutta Shanta , Gidudu Jane F 
Published: January 2021

Abstract

Background
In December 2017, the World Health Organization (WHO) prequalified the first typhoid conjugate vaccine (TCV; Typbar-TCV). While no safety concerns were identified in pre- and postlicensure studies, WHO’s Global Advisory Committee on Vaccine Safety recommended robust safety evaluation with large-scale TCV introductions. During July–August 2018, the Navi Mumbai Municipal Corporation (NMMC) launched the world’s first public sector TCV introduction. Per administrative reports, 113 420 children 9 months–14 years old received TCV.

Methods
We evaluated adverse events following immunization (AEFIs) using passive and active surveillance via (1) reports from the passive NMMC AEFI surveillance system, (2) telephone interviews with 5% of caregivers of vaccine recipients 48 hours and 7 days postvaccination, and (3) chart abstraction for adverse events of special interest (AESIs) among patients admitted to 5 hospitals using the Brighton Collaboration criteria followed by ascertainment of vaccination status.

Results
We identified 222/113 420 (0.2%) vaccine recipients with AEFIs through the NMMC AEFI surveillance system: 211 (0.19%) experienced minor AEFIs, 2 (0.002%) severe, and 9 serious (0.008%). At 48 hours postvaccination, 1852/5605 (33%) caregivers reported ≥1 AEFI, including injection site pain (n = 1452, 26%), swelling (n = 419, 7.5%), and fever (n = 416, 7.4%). Of the 4728 interviews completed at 7 days postvaccination, the most reported AEFIs included fever (n = 200, 4%), pain (n = 52, 1%), and headache (n = 42, 1%). Among 525 hospitalized children diagnosed with an AESI, 60 were vaccinated; no AESIs were causally associated with TCV.

Conclusions
No unexpected safety signals were identified with TCV introduction. This provides further reassurance for the large-scale use of Typbar-TCV among children 9 months–14 years old.
Digging Into the Channels of Bunching: Evidence from the Uruguayan Income Tax
Authors: Bergolo Marcelo , Burdin Gabriel , De Rosa Mauricio , Giaccobasso Matias , Leites Martin 
Published: January 2021

Abstract
Based on detailed administrative tax records, we implement a bunching design to explore how individual taxpayers respond to personal income taxation in Uruguay. We estimate a very modest elasticity of taxable income at the first kink point (0.06) driven by a combination of gross labour income and deduction responses. Taxpayers use personal deductions more intensively close to the kink point and underreport income to the tax authority. Our results suggest that the efficiency costs of taxation are not necessarily large in contexts characterised by limited deduction opportunities. Policy efforts should be directed at broadening the tax base and improving enforcement capacity.
Summary: international consensus statement on nomenclature and classification of the congenital bicuspid aortic valve and its aortopathy, for clinical, surgical, interventional and research purposes
Authors: Michelena Hector I , Della Corte Alessandro , Evangelista Arturo , Maleszewski Joseph J , Edwards William D , Roman Mary J , Devereux Richard B , Fernández Borja , Asch Federico M , Barker Alex J , Sierra-Galan Lilia M , De Kerchove Laurent , Fernandes Susan M , Fedak Paul W M , Girdauskas Evaldas , Delgado Victoria , Abbara Suhny , Lansac Emmanuel , Prakash Siddharth K , Bissell Malenka M , Popescu Bogdan A , Hope Michael D , Sitges Marta , Thourani Vinod H , Pibarot Phillippe , Chandrasekaran Krishnaswamy , Lancellotti Patrizio , Borger Michael A , Forrest John K , Webb John , Milewicz Dianna M , Makkar Raj , Leon Martin B , Sanders Stephen P , Markl Michael , Ferrari Victor A , Roberts William C , Song Jae-Kwan , Blanke Philipp , White Charles S , Siu Samuel , Svensson Lars G , Braverman Alan C , Bavaria Joseph , Sundt Thoralf M , Khoury Gebrine El , De Paulis Ruggero , Enriquez-Sarano Maurice , Bax Jeroen J , Otto Catherine M , Schäfers Hans-Joachim 
Published: January 2021

AbstractThis International evidence-based nomenclature and classification consensus on the congenital bicuspid aortic valve and its aortopathy recognizes 3 types of bicuspid aortic valve: 1. Fused type, with 3 phenotypes: right-left cusp fusion, right-non cusp fusion and left-non cusp fusion; 2. 2-sinus type with 2 phenotypes: Latero-lateral and antero-posterior; and 3. Partial-fusion or forme fruste. This consensus recognizes 3 bicuspid-aortopathy types: 1. Ascending phenotype; root phenotype; and 3. extended phenotypes.
Validation of risk scores for ischaemic stroke in atrial fibrillation across the spectrum of kidney function
Authors: de Jong Ype , Fu Edouard L , van Diepen Merel , Trevisan Marco , Szummer Karolina , Dekker Friedo W , Carrero Juan J , Ocak Gurbey 
Published: January 2021

Abstract

Aims
The increasing prevalence of ischaemic stroke (IS) can partly be explained by the likewise growing number of patients with chronic kidney disease (CKD). Risk scores have been developed to identify high-risk patients, allowing for personalized anticoagulation therapy. However, predictive performance in CKD is unclear. The aim of this study is to validate six commonly used risk scores for IS in atrial fibrillation (AF) patients across the spectrum of kidney function.

Methods and results
Overall, 36 004 subjects with newly diagnosed AF from SCREAM (Stockholm CREAtinine Measurements), a healthcare utilization cohort of Stockholm residents, were included. Predictive performance of the AFI, CHADS2, Modified CHADS2, CHA2DS2-VASc, ATRIA, and GARFIELD-AF risk scores was evaluated across three strata of kidney function: normal kidney function [estimated glomerular filtration rate (eGFR) &gt;60 mL/min/1.73 m2], mild CKD (eGFR 30–60 mL/min/1.73 m2), and advanced CKD (eGFR &lt;30 mL/min/1.73 m2). Predictive performance was assessed by discrimination and calibration. During 1.9 years, 3069 (8.5%) patients suffered an IS. Discrimination was dependent on eGFR: the median c-statistic in normal eGFR was 0.75 (range 0.68–0.78), but decreased to 0.68 (0.58–0.73) and 0.68 (0.55–0.74) for mild and advanced CKD, respectively. Calibration was reasonable and largely independent of eGFR. The Modified CHADS2 score showed good performance across kidney function strata, both for discrimination [c-statistic: 0.78 (95% confidence interval 0.77–0.79), 0.73 (0.71–0.74) and 0.74 (0.69–0.79), respectively] and calibration.

Conclusion
In the most clinically relevant stages of CKD, predictive performance of the majority of risk scores was poor, increasing the risk of misclassification and thus of over- or undertreatment. The Modified CHADS2 score performed good and consistently across all kidney function strata, and should therefore be preferred for risk estimation in AF patients.
Can centre-based childcare buffer against the negative effects of family adversity on child socio-emotional wellbeing?
Authors: Parkes Alison , Green Michael , Pearce Anna 
Published: January 2021

AbstractBackgroundDifferent configurations of family adversity affect children’s socio-emotional development differently; however, we lack knowledge of moderators amenable to policy intervention. This study explored whether early childhood centre-based childcare moderated the impact of family adversity configurations on socio-emotional development.MethodsData were from the Growing Up in Scotland first birth cohort, born 2004–05. Latent class analysis of 19 early childhood family adversity indicators identified four classes: ‘Low Risk’ (68%), ‘Poor Maternal Health’ (16.5%), ‘Economic Hardship’ (10.0%) and ‘Multiple Adversities’ (5.5%). Latent growth models of externalizing and internalizing symptom trajectories (age 46–152 months, n = 3561) by family adversity controlled for confounding. Moderation by centre-based childcare use was examined through stratification.ResultsCompared to ‘Low Risk’, high-risk classes had more externalizing and internalizing symptoms and internalizing symptoms increased at a faster rate, with ‘Multiple Adversities’ faring worst. The effects of ‘Economic Hardship’ on change in externalizing symptoms over time varied by childcare (P = 0.035): relative to the Low Risk group, symptoms increased (+0.04 points/year) among those not using childcare, and decreased (–0.09 points/year) among those who did. The effect of ‘Multiple Adversities’ on internalizing symptoms also varied (P = 0.034): +0.12 without centre-based childcare; +0.33 with centre-based childcare (patterns were similar for externalizing symptoms but with wide confidence intervals). No moderation was found by ‘Poor Maternal Health’.ConclusionsCentre-based childcare may alleviate disadvantages in socio-emotional wellbeing for children experiencing mainly economic hardship, but may exacerbate them for those experiencing multiple adversities. A better understanding of how early years’ services can support families with complex needs is required.
Air Power, NGOs, and Collateral Killings
Authors: Allen Susan H , Bell Sam R , Martinez Machain Carla 
Published: January 2021

Abstract
Air strikes have become an essential tool in major powers’ military arsenals. Yet, despite the precise technology that air power represents, its use can also result in unintended killings. In this paper, we explore how air strikes affect civilian killings as collateral damage by third party interveners. In particular, we argue that this effect is conditioned by the presence of non-governmental civil society actors on the ground. We thus explore how air strikes affect civilian killings by government actors involved in conflicts and how civil society can diminish harm against civilian actors during aerial bombing campaigns. Our results suggest that air strikes may cause deaths through collateral killings. Yet, when air strikes occur in countries where human rights organizations are active, these civilian deaths may be mitigated.
Robust modeling of additive and nonadditive variation with intuitive inclusion of expert knowledge
Authors: Hem Ingeborg Gullikstad , Selle Maria Lie , Gorjanc Gregor , Fuglstad Geir-Arne , Riebler Andrea 
Published: January 2021

AbstractWe propose a novel Bayesian approach that robustifies genomic modeling by leveraging expert knowledge (EK) through prior distributions. The central component is the hierarchical decomposition of phenotypic variation into additive and nonadditive genetic variation, which leads to an intuitive model parameterization that can be visualized as a tree. The edges of the tree represent ratios of variances, for example broad-sense heritability, which are quantities for which EK is natural to exist. Penalized complexity priors are defined for all edges of the tree in a bottom-up procedure that respects the model structure and incorporates EK through all levels. We investigate models with different sources of variation and compare the performance of different priors implementing varying amounts of EK in the context of plant breeding. A simulation study shows that the proposed priors implementing EK improve the robustness of genomic modeling and the selection of the genetically best individuals in a breeding program. We observe this improvement in both variety selection on genetic values and parent selection on additive values; the variety selection benefited the most. In a real case study, EK increases phenotype prediction accuracy for cases in which the standard maximum likelihood approach did not find optimal estimates for the variance components. Finally, we discuss the importance of EK priors for genomic modeling and breeding, and point to future research areas of easy-to-use and parsimonious priors in genomic modeling.