bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel evolution and cryptic diversification in a common and widespread Amazonian tree, Protium subserratum
Authors: Misiewicz Tracy M. , Simmons Tracey , Carter Benjamin E. , Fine Paul V. A. , Moore Abigail J. 
Published: February 2023

AbstractThe lowland Amazon rainforest houses some of the greatest tree diversity on Earth. While the vast majority of these species are rare, a small number are common and widespread and thus considered to play a disproportionate role in many of the global ecosystem services provided by the Amazon. However, the extent to which dominant Amazonian tree species actually include multiple clades, each on their own unique evolutionary trajectory, is unknown. Here we investigate the extent to which lineage divergence may be occurring within Protium subserratum (Burseraceae), a common and widespread tree species that is monophyletic with populations exhibiting genotypic and phenotypic differences associated with soil and geography. Utilizing a combination of phylogenomic and population genomic methods with sampling from across the range, we found that P. subserratum contains at least eight distinct clades. Specialization onto white‐sand soils has evolved independently at least twice within the species; however, phenotype is not correlated with soil type. Finally, cryptic diversity at the base of the Andes is associated with elevational shifts. Together these results lend support to the hypothesis that common and widespread Amazon tree species may not represent evolutionary cohesive units. Instead, these dominant species may more commonly represent species complexes, undergoing evolutionary transitions on a trajectory to become multiple range‐restricted, specialist species.
vsiRNA18 derived from tobacco curly shoot virus can regulate virus infection in Nicotiana benthamiana
Authors: Wu Rui , Wu Gentu , Huang Yongjie , Zhang Haolan , Tang Jiaxin , Li Mingjun , Qing Ling 
Published: February 2023

AbstractVirus‐derived small interfering RNAs (vsiRNAs) play important roles in regulating host endogenous gene expression to promote virus infection and induce RNA silencing to suppress virus infection. However, to date, how vsiRNAs affect geminivirus infection in host plants has been less studied. In this study, we found that tobacco curly shoot virus (TbCSV)‐derived vsiRNA18 (TvsiRNA18) can regulate TbCSV infection in Nicotiana benthamiana plants. The virus‐mediated small RNA expression system and stable transformation technique were used to clarify the molecular role of TvsiRNA18 in TbCSV infection. The results indicate that TvsiRNA18 can aggravate disease symptoms in these plants and enhance viral DNA accumulation. ATP‐dependent RNA helicase (ATP‐dRH) was proven to be a target of TvsiRNA18, and down‐regulation of ATP‐dRH in plants was shown to induce virus‐like leaf curling symptoms and increase TbCSV infection. These results suggest that TvsiRNA18 is an important regulator of TbCSV infection by suppressing ATP‐dRH expression. This is the first report to demonstrate that TbCSV‐derived vsiRNA can target host endogenous genes to affect symptom development, which helps to reveal the molecular mechanism of symptom occurrence after the virus infects the host.
Insights into cryptochrome modulation of ABA signaling to mediate dormancy regulation in Marchantia polymorpha
Authors: Liao Jiakai , Deng Ban , Yang Qixin , Li Yu , Zhang Yuxiang , Cong Jiajing , Wang Xiaqin , Kohnen Markus V. , Liu Zhong‐Jian , Lu Meng‐Zhu , Lin Deshu , Gu Lianfeng , Liu Bobin 
Published: February 2023

Summary

The acquisition of dormancy capabilities has enabled plants to survive in adverse terrestrial environmental conditions. Dormancy accumulation and release is coupled with light signaling, which is well studied in Arabidopsis, but it is unclear in the distant nonvascular relative. We study the characteristics and function on dormancy regulation of a blue light receptor cryptochrome in Marchantia polymorpha (MpCRY).

Here, we identified MpCRY via bioinformatics and mutant complement analysis. The biochemical characteristics were assessed by multiple protein‐binding assays. The function of MpCRY in gemma dormancy was clarified by overexpression and mutation of MpCRY, and its mechanism was analyzed via RNA sequencing and quantitative PCR analyses associated with hormone treatment.

We found that the unique MpCRY protein in M. polymorpha undergoes both blue light‐promoted interaction with itself (self‐interaction) and blue light‐dependent phosphorylation. MpCRY has the specific characteristics of blue light‐induced nuclear localization and degradation. We further demonstrated that MpCRY transcriptionally represses abscisic acid (ABA) signaling‐related gene expression to suppress gemma dormancy, which is dependent on blue light signaling.

Our findings indicate that MpCRY possesses specific biochemical and molecular characteristics, and modulates ABA signaling under blue light conditions to regulate gemma dormancy in M. polymorpha.
Impact of carotid atherosclerosis on arrhythmia recurrence following atrial fibrillation catheter ablation
Authors: Luo Fangyuan , Sun Liping , Li Jiaju , Chen Jiawei , Zhang Yuekun , Wang Zhe , Chen Xiaojie , Chen Yingwei , Dong Jianzeng 
Published: February 2023

AbstractBackgroundIt remains unclear whether carotid atherosclerosis (CAS) increases the atrial fibrillation (AF) recurrence rate after ablation. The aim was to assess the association between CAS, defined as carotid intima‐media thickness (CIMT) ≥1 mm and or presence of carotid plaques, and AF recurrence rate after ablation.MethodsWe retrospectively collected patients who underwent carotid ultrasonography and AF ablation at the First Affiliated Hospital of Zhengzhou University. The AF recurrence was defined as documented atrial arrhythmias over 30 s on ECG or 24‐h Holter monitoring after the first three months blanking period. Cox regression models were used to analyze the risk of AF recurrence.ResultsOverall, 385 patients were analyzed (mean age, 60.58±10.98 years old; female, 41.30%; persistent AF, 47.27%). After a follow‐up of 1 year, 138 (35.84%) patients experienced recurrence, Kaplan–Meier analysis showed that patients with the presence of carotid plaques, CIMT ≥1 mm, and CAS had a higher risk of recurrence compared with the absence (all log‐rank p < .05). In multivariate Cox regression analysis, CAS (HR 2.159, ±95% CI 1.320‐3.532, p = .002), carotid plaque (HR 1.815, ±95%CI 1.160‐2.841, p = .009), and CIMT ≥1 mm (HR 1.696, ±95%CI 1.192‐2.413, p = .003) were independently associated with a higher risk of recurrence. In subgroup analysis, the association of CAS, carotid plaque, and AF recurrence rate was weaker in men than women.ConclusionCarotid atherosclerosis, CIMT ≥1 mm, and carotid plaque were significantly associated with a higher AF recurrence rate after radiofrequency catheter ablation. They were all risk factors for the recurrence of AF.
Diet‐associated vertically transferred metabolites and risk of asthma, allergy, eczema, and infections in early childhood
Authors: Brustad Nicklas , Olarini Alessandra , Kim Min , Chen Liang , Ali Mina , Wang Tingting , Cohen Arieh S. , Ernst Madeleine , Hougaard David , Schoos Ann‐Marie , Stokholm Jakob , Bønnelykke Klaus , Lasky‐Su Jessica , Rasmussen Morten A. , Chawes Bo 
Published: February 2023

AbstractBackgroundEvidence suggests maternal pregnancy dietary intake and nutrition in the early postnatal period to be of importance for the newborn child's health. However, studies investigating diet‐related metabolites transferred from mother to child on disease risk in childhood are lacking. We sought to investigate the influence of vertically transferred metabolites on risk of atopic diseases and infections during preschool age.MethodsIn the Danish population‐based COPSAC2010 mother–child cohort, information on 10 diet‐related vertically transferred metabolites from metabolomics profiles of dried blood spots (DBS) at age 2–3 days was analyzed in relation to the risk of childhood asthma, allergy, eczema, and infections using principal component and single metabolite analyses.ResultsIn 678 children with DBS measurements, a coffee‐related metabolite profile reflected by principal component 1 was inversely associated with risk of asthma (odds ratio (95% CI) 0.78 (0.64; 0.95), p = .014) and eczema at age 6 years (0.79 (0.65; 0.97), p = .022). Furthermore, increasing stachydrine (fruit‐related), 3‐carboxy‐4‐methyl‐5‐propyl‐2‐furanpropanoate (fish‐related), and ergothioneine (fruit‐, green vegetables‐, and fish‐related) levels were all significantly associated with reduced risks of infections at age 0–3 years (p < .05).ConclusionThis study demonstrates associations between pregnancy diet‐related vertically transferred metabolites measured in children in early life and risk of atopic diseases and infections in childhood. The specific metabolites associated with a reduced disease risk in children may contribute to the characterization of a healthy nutritional profile in pregnancy using a metabolomics‐based unbiased tool for predicting childhood health.
Modulation of haematopoiesis by protozoal and helminth parasites
Authors: Cunningham Kyle T. , Mills Kingston H. G. 
Published: February 2023

AbstractDuring inflammation, haematopoietic stem cells (HSCs) in the bone marrow (BM) and periphery rapidly expand and preferentially differentiate into myeloid cells that mediate innate immune responses. HSCs can be directed into quiescence or differentiation by sensing alterations to the haematopoietic niche, including cytokines, chemokines, and pathogen‐derived products. Most studies attempting to identify the mechanisms of haematopoiesis have focused on bacterial and viral infections. From intracellular protozoan infections to large multicellular worms, parasites are a global health burden and represent major immunological challenges that remain poorly defined in the context of haematopoiesis. Immune responses to parasites vary drastically, and parasites have developed sophisticated immunomodulatory mechanisms that allow development of chronic infections. Recent advances in imaging, genomic sequencing, and mouse models have shed new light on how parasites induce unique forms of emergency haematopoiesis. In addition, parasites can modify the haematopoiesis in the BM and periphery to improve their survival in the host. Parasites can also induce long‐lasting modifications to HSCs, altering future immune responses to infection, inflammation or transplantation, a term sometimes referred to as central trained immunity. In this review, we highlight the current understanding of parasite‐induced haematopoiesis and how parasites target this process to promote chronic infections.
Going green or making green? The effects of partisanship and inflation on environmental executive orders, 1945−2020
Authors: Fitz Erin B. 
Published: February 2023

AbstractWhile a growing body of scholarship examines US presidential unilateralism, there remains less focus on policy‐specific areas of unilateral action. Given environmental politics is a particularly constrained and contentious issue area, understanding the conditions that affect the frequency of presidents' environment‐related unilateral activity requires a more nuanced examination. As such, this study draws upon existing theories of unilateralism to explore the relationship between environmental executive orders, Congress, the economy, and environmental disasters in the United States between 1945 and 2020. A broad examination of environmental executive orders provides evidence to suggest that while Democratic presidents are more likely to issue environmental executive orders compared to Republican presidents, presidents are generally more likely to issue environmental executive orders in response to higher inflation. A second analysis using a subset of these data further indicates Democratic presidents are more likely to issue environmental executive orders following technological disasters and that the frequency of these orders increases when their partisanship changes from that of the previous president. Collectively, these findings serve to broaden our current understanding of US presidential unilateralism by providing important linkages between executive power, the environment, and the economy.
A systematic review of fish adulteration and contamination in Bangladesh: A way forward to food safety
Authors: Khan Md. Akhtaruzzaman , Hossain Md. Emran , Islam Md. Sayemul , Rahman Mohammad Saidur , Sudhakaran Pratheesh Omana , Dey Madan Mohan 
Published: February 2023

AbstractFor decades, the world has been plagued by widespread food adulteration, and Bangladesh is no exception. Dishonest business people and fish farmers unlawfully utilize various preservatives to avoid rotting and extend the shelf life of fish. Although previous research has examined the level of formalin use in fish bodies, no studies focusing on all aspects of fish adulteration and contamination in Bangladesh have been carried out. In this context, the aim of this review is to explore the extent and magnitude of illegal fish adulteration and contamination in Bangladesh. Among the 37 reviewed studies, 11 of them highlighted formalin adulteration in fish samples and fish feed. The extent of formalin use varied between local and imported fish, and between large and small fish. Imported and large fish were substantially more formalin‐contaminated. Several investigations have discovered that antibiotic levels in farm water and fish feed exceed the permitted level. Farmers have used growth promoters incautiously. This study also identifies that certain metal substances, such as chromium, lead, arsenic, cadmium, iron, mercury and cobalt, have been frequently found in fish bodies and feed samples. Furthermore, a distinct type of fish adulteration caused by aromatic compounds has emerged recently. The findings and their ramifications are extremely concerning for human lives. However, since each study employed a different testing kit, the results were quite distinct. Thus, the adoption of a precise and sensitive kit is strongly recommended. The government should make it a top priority to solve the problem of fish adulteration by implementing appropriate food safety laws and policies.
Engineering the plant metabolic system by exploiting metabolic regulation
Authors: Selma Sara , Ntelkis Nikolaos , Nguyen Trang Hieu , Goossens Alain 
Published: February 2023

SUMMARYPlants are the most sophisticated biofactories and sources of food and biofuels present in nature. By engineering plant metabolism, the production of desired compounds can be increased and the nutritional or commercial value of the plant species can be improved. However, this can be challenging because of the complexity of the regulation of multiple genes and the involvement of different protein interactions. To improve metabolic engineering (ME) capabilities, different tools and strategies for rerouting the metabolic pathways have been developed, including genome editing and transcriptional regulation approaches. In addition, cutting‐edge technologies have provided new methods for understanding uncharacterized biosynthetic pathways, protein degradation mechanisms, protein–protein interactions, or allosteric feedback, enabling the design of novel ME approaches.
Re‐arranging the urban: Forms, rhythms, politics
Authors:   The Urban Re‐Arrangements Collective, Abdullah Adam , Cardoso Ricardo , Dasgupta Shreyashi , Pati Sushmita , Plueckhahn Rebekah , Shafique Tanzil , Simone AbdouMaliq , Teo Shaun S. K. , Ye Junjia , Zhao Yimin 
Published: February 2023

AbstractThis intervention is by a collective of scholars working on various facets of urbanisation in Asia. Focusing on the notion of arrangements/re‐arrangements, it seeks to extend the consideration of urban politics as a matter of surges, a provisional consolidation of intensities, inhabitants and their practices, affiliations and orientations that give rise to continuously mutating forms of sense, care, and collective action. Whereas the work and effects of institutions, with their genealogies, remits, and competencies, are to a large extent specifiable according to their operating norms and the various regulatory frameworks that govern their operations, the dispositions of arrangements – what they do, what they actually bring about – are not readily definable or clear, enacting a form of performative ambiguity. Involving workarounds, collaborations, exchanges, and agreements that exceed the familiar protocols of interaction among households, local authorities, markets, civil institutions, brokers, and service providers, arrangements entail the enactment of caring, provisioning, regulating, mapping, and steering as the purview of more provisional, incessantly mutating forms that fold in bits and pieces of discernible institutions. In this heuristic intervention we seek to further the ‘urbanisation’ of urban geography itself, in the sense of complexifying both the terrain and the methodological practices brought to bear. It attempts to open a way of speaking about urbanisation processes that exceed binary formulations, countervailing scales, or structural absences to encompass a broader range of processes at work in shaping dispositions that are materialised or simply potentiated. It proceeds from a process of collective composition whose objective is to diversify the working tools of urban analysis rather than simply offering new conceptual formulations.
Optimal Design and Sensitivity Analysis of the Dynamic Vibration Absorber With Amplifying Mechanism
Authors: Liu Yifan , Cai Jiazhi , Li Haiyuan , Gao Qingbin 
Published: February 2023

Abstract
This work optimizes a dynamic vibration absorber (DVA) model equipped with an additional amplifying mechanism using the H∞ optimization criterion, which aims to minimize the maximum frequency response amplitude of the primary structure. This optimization problem is widely investigated using the fixed-point method, which, however, works only when the primary structure is undamped and gives approximate solutions at best. Instead, we seek the exact solutions, and a resultant-based optimization scheme is accordingly proposed, which allows handling purely univariate polynomial equations in the solving procedure to guarantee the convergence and global optimum conditions. Consequently, exactly numerical and closed-form optimal DVA parameters are obtained when the primary structure is damped and undamped, respectively. Furthermore, we are also interested in the effect of the amplifying mechanism on vibration suppression, showing that it functions as a convenient equivalent mass ratio regulator to benefit the DVA performance. Finally, the presented sensitivity analysis reveals the effect of the small variations of the DVA stiffness and damping on the vibration suppression performance and the role of the amplifying mechanism in balancing such two components’ uncertainties. This work generalizes the existing exact H∞ optimization methods and provides a guideline for the enhanced DVA design using the amplifying mechanism.
Optical Metrology of Critical Dimensions in Large-Area Nanostructure Arrays With Complex Patterns
Authors: Sabbagh Ramin , Stothert Alec , Sreenivasan S. V. , Djurdjanovic Dragan 
Published: February 2023

Abstract
It was recently demonstrated that scatterometry-based metrology has the capability to perform high-throughput metrology on large-area nanopatterned surfaces. However, the way this approach is currently pursued requires an a priori generated library of reflectance spectra to be simulated for an exhaustive set of possible underlying critical dimensions (CDs) characterizing the measured nanopatterns. Generating this library is time consuming and can be infeasible for complex patterns characterized by a large number of CDs. This article addresses the aforementioned drawback of optical inspection of CDs of nanopatterned surfaces through the use of an inverse problem-based optimization methodology coupled with a recently introduced approach for efficient organization of the library of previously simulated reflectance spectra. Specifically, for each physically measured reflectance spectrum, the best matching simulated spectrum is sought in the initial incomplete library in order to serve as the initial guess for the inverse problem optimization process. Through that optimization process, further refinements of the best matching simulated spectra are conducted to obtain sufficiently accurate estimates of the CDs characterizing the inspected nanopattern geometries. Capabilities of the newly proposed approach are evaluated through inspection of semiconductor wafer samples with hourglass patterns characterized by eight CDs. It was observed that one can obtain significantly faster measurements of CDs compared to inspection times associated with scanning electron microscopy, while at the same time not deteriorating the corresponding Gage Repeatability and Reproducibility. In conclusion, this method enables real-time, accurate, and repeatable metrology of CDs of large-area nanostructured surfaces with complex nanopatterns.
Automated Subtractive Timber Manufacturing—Joinery Machines Versus Industrial Robots
Authors: Pantscharowitsch Marc , Kromoser Benjamin 
Published: February 2023

AbstractA high degree of automation, especially through the use of robots, is state of the art in the automotive and electronics industries. Even though the construction sector is currently lagging behind, an increase in automation and the use of robots can be observed. To assess the potential in industrial timber construction with a focus set on subtractive machining, this paper presents the state of the art in terms of the use of industrial robots and joinery machines, compact joinery machines, and gantry-type joinery machines in regard to milling processes. The capabilities of different types of joinery machines are evaluated and compared with vertical articulated industrial robots equipped with machining spindles. An overview of the history and an assessment of various parameters in the categories: Quality, System, Machining and Economy, is given. Publications, manufacturer information, and industry findings are reviewed to answer pressing questions on automation in timber construction. Limitations such as robotic stability or the limited working space of joinery machines and the affordability of robotic systems are elaborated and CAD/CAM (computer-aided design/computer-aided manufacturing) processes are scrutinized. After the evaluation and comparison of four different systems, an approach for future research is proposed. The main findings are a very low degree of robotization and data availability within the timber industry, lower acquisition costs for industrial robots while increasing the flexibility of the workspace, and task-specific advantages of the respective systems, including machining power, potential for improvement in automation (especially CAD/CAM), and machining quality.