bluuebunny/crossref_metadata_2025_split huggingface dataset:
Copper ion (Cu2+) is involved in the transcription of the tyrosinase-encoding melB gene of Aspergillus oryzae in solid-state culture
Authors: Chen Jun , Tonouchi Akio 
Published: November 2023

ABSTRACT
In Aspergillus oryzae, the tyrosinase-encoding gene melB causes undesirable browning of sake and sake lees. This gene is known to be expressed specifically in solid-state culture; however, its expression mechanisms remain unknown. Here, we evaluated the possible factors affecting the transcription of melB and found that the copper ion (Cu2+) significantly enhanced the transcription level of melB in solid-state culture.
RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures
Authors: Xu Xiaoming , Yin Zekun , Yan Lifeng , Yi Huiguang , Wang Hua , Schmidt Bertil , Liu Weiguo 
Published: November 2023

Abstract

Summary
We propose RabbitKSSD, a high-speed genome distance estimation tool. Specifically, we leverage load-balanced task partitioning, fast I/O, efficient intermediate result accesses, and high-performance data structures to improve overall efficiency. Our performance evaluation demonstrates that RabbitKSSD achieves speedups ranging from 5.7× to 19.8× over Kssd for the time-consuming sketch generation and distance computation on commonly used workstations. In addition, it significantly outperforms Mash, BinDash, and Dashing2. Moreover, RabbitKSSD can efficiently perform all-vs-all distance computation for all RefSeq complete bacterial genomes (455 GB in FASTA format) in just 2 min on a 64-core workstation.

Availability and implementation
RabbitKSSD is available at https://github.com/RabbitBio/RabbitKSSD.
Modified RNAs and predictions with the ViennaRNA Package
Authors: Varenyk Yuliia , Spicher Thomas , Hofacker Ivo L , Lorenz Ronny 
Published: November 2023

Abstract

Motivation
In living organisms, many RNA molecules are modified post-transcriptionally. This turns the widely known four-letter RNA alphabet ACGU into a much larger one with currently more than 300 known distinct modified bases. The roles for the majority of modified bases remain uncertain, but many are already well-known for their ability to influence the preferred structures that an RNA may adopt. In fact, tRNAs sometimes require certain modifications to fold into their cloverleaf shaped structure. However, predicting the structure of RNAs with base modifications is still difficult due to the lack of efficient algorithms that can deal with the extended sequence alphabet, as well as missing parameter sets that account for the changes in stability induced by the modified bases.

Results
We present an approach to include sparse energy parameter data for modified bases into the ViennaRNA Package. Our method does not require any changes to the underlying efficient algorithms but instead uses a set of plug-in constraints that adapt the predictions in terms of loop evaluation at runtime. These adaptations are efficient in the sense that they are only performed for loops where additional parameters are actually available for. In addition, our approach also facilitates the inclusion of more modified bases as soon as further parameters become available.

Availability and implementation
Source code and documentation are available at https://www.tbi.univie.ac.at/RNA.
‘Shown love from the brokenness of a system’: Themes from a Poetic Inquiry Reimagining Child Welfare
Authors: Clark Shelby L , Akin Becci A , McCall Sarah , Byers Kaela , Gomez Mariana 
Published: November 2023

Abstract
Child welfare (CW) reforms have called for including family and youth voice. Yet, most initiatives have remained at individual levels, and research has rarely included youth, parent and professional voices simultaneously and equally. This study sought to integrate these perspectives and identify systems-level strategies that could reimagine CW. Using an arts-based method and thematic analysis, researchers investigated recommendations for policy and practice changes needed to transform CW to better support youth. Data were collected from individual and relational poems written by forty-one participants, including youth with foster care (FC) experience and CW professionals. Participants were located in a Midwestern state in the USA. Four themes were generated and several key findings were highlighted. First, results demonstrated relationship-building as central to supporting youth in FC. Secondly, participants described complex, fragmented and fluctuating views about the purpose of CW. Thirdly, strong emotions were commonly demonstrated by both youth and professionals. Fourthly, participants offered prescriptive actions needed to better support youth. Overall, this study indicates that CW should centre relationship-building, youth self-determination and practices that build resilience for youth and professionals. Findings also provide hope for transforming CW towards an accountable, family-centred, well-being system.
Upgrading process of palm empty fruit bunches as alternative solid fuel: a review
Authors: Hardianto Toto , Wenas Ari Akbariyanto , Juangsa Firman Bagja 
Published: November 2023

Abstract
A total of 37.5 million tons of palm empty fruit bunches (EFBs) produced in Indonesia in 2018 have the potential to be used as an alternative eco-friendly solid fuel. However, a pretreatment process is necessary to increase the heating value and reduce the potassium content of EFBs. Several methods can be employed to improve the characteristics of EFBs as a solid fuel, such as drying and torrefaction to increase the heating value and the leaching process for reducing the potassium content of EFBs. The main concept of increasing the heating value is to increase the fuel content, which is carbon. Through drying, the carbon ratio can be increased by reducing the moisture content and, through torrefaction, the carbon ratio could be increased due to the decomposition of lignocellulose. A simple way to reduce the potassium content of EFBs is the leaching process. Two types of leaching treatment have been studied before: soaking and stirring treatment. This study reviews those methods to make EFBs more suitable as a solid fuel with a high heating value and less potassium content. Increasing the carbon content in EFBs is crucial for enhancing their heating value as a fuel. Drying and torrefaction decrease the moisture content and modify the chemical structure, resulting in higher carbon ratios. The leaching process effectively reduces the potassium content of EFBs and stirring treatment is more effective than immersion treatment. Torrefaction positively affects leaching by decreasing the potassium content, while hydrophobicity may hinder leaching by repelling water. The high moisture content of leached EFBs requires additional energy for evaporation during torrefaction, resulting in a lower energy density yield compared with raw EFBs. Adjustments may also be required to account for the decreased mineral content, which functions as a torrefaction catalyst in EFBs that have not been leached.
Beta-blocker and calcium-channel blocker toxicity: current evidence on evaluation and management
Authors: Goldfine Charlotte E , Troger Andrew , Erickson Timothy B , Chai Peter R 
Published: November 2023

Abstract
Beta-blocker and calcium-channel blocker overdoses are associated with severe morbidity and mortality; therefore, it is important to recognize and appropriately treat individuals with toxicity. The most common clinical findings in toxicity are bradycardia and hypotension. In addition to supportive care and cardiac monitoring, specific treatment includes administration of calcium salts, vasopressors, and high-dose insulin euglycaemia treatment. Other advanced treatments (e.g. ECMO) may be indicated depending on the severity of toxicity and specific agents involved.
Assessing heterogeneity on cardiovascular magnetic resonance imaging: a novel approach to diagnosis and risk stratification in cardiac diseases
Authors: Hesse Kerrick , Khanji Mohammed Y , Aung Nay , Dabbagh Ghaith Sharaf , Petersen Steffen E , Chahal C Anwar A 
Published: November 2023

Abstract
Cardiac disease affects the heart non-uniformly. Examples include focal septal or apical hypertrophy with reduced strain in hypertrophic cardiomyopathy, replacement fibrosis with akinesia in an infarct-related coronary artery territory, and a pattern of scarring in dilated cardiomyopathy. The detail and versatility of cardiovascular magnetic resonance (CMR) imaging mean it contains a wealth of information imperceptible to the naked eye and not captured by standard global measures. CMR-derived heterogeneity biomarkers could facilitate early diagnosis, better risk stratification, and a more comprehensive prediction of treatment response. Small cohort and case–control studies demonstrate the feasibility of proof-of-concept structural and functional heterogeneity measures. Detailed radiomic analyses of different CMR sequences using open-source software delineate unique voxel patterns as hallmarks of histopathological changes. Meanwhile, measures of dispersion applied to emerging CMR strain sequences describe variable longitudinal, circumferential, and radial function across the myocardium. Two of the most promising heterogeneity measures are the mean absolute deviation of regional standard deviations on native T1 and T2 and the standard deviation of time to maximum regional radial wall motion, termed the tissue synchronization index in a 16-segment left ventricle model. Real-world limitations include the non-standardization of CMR imaging protocols across different centres and the testing of large numbers of radiomic features in small, inadequately powered patient samples. We, therefore, propose a three-step roadmap to benchmark novel heterogeneity biomarkers, including defining normal reference ranges, statistical modelling against diagnosis and outcomes in large epidemiological studies, and finally, comprehensive internal and external validations.
The impact of air pollution on hospitalization for COPD patients in China
Authors: Chen Chen , Wang Yi , Song Jinglin , Yan Juanjuan 
Published: November 2023

Abstract

Background
With the rapid development of the global economy and the acceleration of urbanization, air pollution has become a major environmental problem threatening human health. There is limited evidence on the acute effects of air pollution on chronic obstructive pulmonary disease (COPD).

Methods
From 2014 to 2019, we collected data on daily admissions for COPD patients from a city in China. We used the generalized additive model together with distributed lag models to fit the associations of air pollutants with hospital admissions.

Results
We observed significant increments in the number of daily admissions (0.086–0.109%) for COPD for a unit range increase in air quality index, PM2.5 and PM10 over four lag days. The impact of air pollution on the number of daily admissions was mainly reflected in the COPD patients who were hospitalized through outpatient departments and tertiary hospitals.

Discussion
Short-term exposure to outdoor air pollution may induce the occurrence or exacerbation of COPD patients; therefore, government departments should strengthen the management of air pollution, improve supervision and control mechanisms, pay attention to the quality of medical services, and reduce the adverse effects of air pollution on patients' health.
Does fear-of-failure mediate the relationship between educational expectations and stress-related complaints among Swedish adolescents? A structural equation modelling approach
Authors: Cashman Matthew R , Strandh Mattias , Högberg Björn 
Published: November 2023

Abstract

Background
This study investigated the possible mediating role of fear-of-failure between educational expectations and adolescent stress-related complaints with a specific focus on gender differences among Swedish adolescents, and related these findings more broadly to school-related demands and stress-related complaints.

Methods
A total of N = 5504 Swedish adolescents (Mage = 15 years, SD = 0.0 years, 50.2% girls) were drawn from the 2018 Swedish Programme for International Student Assessment study for our investigation. We used structural equation models to explore if fear-of-failure mediates the relationship between educational expectations and negative affect, with a specific focus on gender differences. Educational expectations were utilized in the measurement model. Fear-of-failure was constructed as a latent mediating variable. Negative affect was constructed as a latent variable and utilized as an outcome variable. We subsequently undertook bootstrapping tests of indirect effects and non-linear comparisons of indirect effects to assess the reliability of the results.

Results
Fear-of-failure partially mediated the association between educational expectations and negative affect (39%). Our gender-specific structural equation model demonstrated that this relationship was more pronounced for girls, suggesting girls are more vulnerable to negative affect as a result of experiencing higher levels of fear of failing.

Conclusions
The findings suggest that fear-of-failure partially explains the association between educational expectations and negative affect and that this association is more pronounced for girls. This study provides insights into better understanding adolescent stress-related complaints, and the differential role fear of failing has in regards to gender.
Intrinsic apoptosis is evolutionarily divergent among metazoans
Authors: Krasovec Gabriel , Horkan Helen R , Quéinnec Éric , Chambon Jean-Philippe 
Published: November 2023

Abstract
Apoptosis is regulated cell death that depends on caspases. A specific initiator caspase is involved upstream of each apoptotic signaling pathway. Characterized in nematode, fly, and mammals, intrinsic apoptosis is considered to be ancestral, conserved among animals, and depends on shared initiators: caspase-9, Apaf-1 and Bcl-2. However, the biochemical role of mitochondria, the pivotal function of cytochrome c and the modality of caspase activation remain highly heterogeneous and hide profound molecular divergence among apoptotic pathways in animals. Uncovering the phylogenetic history of apoptotic actors, especially caspases, is crucial to shed light on the evolutionary history of intrinsic apoptosis. Here, we demonstrate with phylogenetic analyses that caspase-9, the fundamental key of intrinsic apoptosis, is deuterostome-specific, while caspase-2 is ancestral to bilaterians. Our analysis of Bcl-2 and Apaf-1 confirms heterogeneity in functional organization of apoptotic pathways in animals. Our results support emergence of distinct intrinsic apoptotic pathways during metazoan evolution.
Community-level exposomics: a population-centered approach to address public health concerns
Authors: Stingone Jeanette A , Geller Andrew M , Hood Darryl B , Makris Konstantinos C , Mouton Charles P , States J Christopher , Sumner Susan J , Wu K Lily , Rajasekar Arcot K 
Published: November 2023

Abstract
Environmental factors affecting health and vulnerability far outweigh genetics in accounting for disparities in health status and longevity in US communities. The concept of the exposome, the totality of exposure from conception onwards, provides a paradigm for researchers to investigate the complex role of the environment on the health of individuals. We propose a complementary framework, community-level exposomics, for population-level exposome assessment. The goal is to bring the exposome paradigm to research and practice on the health of populations, defined by various axes including geographic, social, and occupational. This framework includes the integration of community-level measures of the built, natural and social environments, environmental pollution-derived from conventional and community science approaches, internal markers of exposure that can be measured at the population-level and early responses associated with health status that can be tracked using population-based monitoring. Primary challenges to the implementation of the proposed framework include needed advancements in population-level measurement, lack of existing models with the capability to produce interpretable and actionable evidence and the ethical considerations of labeling geographically-bound populations by exposomic profiles. To address these challenges, we propose a set of recommendations that begin with greater engagement with and empowerment of affected communities and targeted investment in community-based solutions. Applications to urban settings and disaster epidemiology are discussed as examples for implementation.
Determinants and effectiveness of annual wellness visits among Medicare beneficiaries in 2020
Authors: Park Sungchul , Nguyen Ann M 
Published: November 2023

Abstract

Background
Annual wellness visits (AWVs) have the potential to improve general health and well-being, but little is known about the role of AWVs during the COVID-19 pandemic.

Objective
We examined the determinants and effectiveness of having an AWV among Medicare beneficiaries in 2020.

Methods
We employed a cross-sectional study design using data from the 2020 Medicare Current Beneficiary Survey. Our outcomes included AWV utilization, preventive care utilization, health status, and care satisfaction. To examine the determinants for having an AWV, we performed a linear regression model and explored the associations with other individual-level variables (demographic, socioeconomic, and health characteristics). To examine the effectiveness of having an AWV, we performed a linear regression model on each outcome measure while adjusting for individual-level variables.

Results
We found that there were several determinants of having an AWV. The four most notable determinants were having a usual source of care, enrolling in Medicare Advantage, being non-Hispanic Black, and being Hispanic. We also found that having an AWV was associated with increases in preventive care use (COVID vaccine, flu shot, pneumonia shot, and blood pressure measurement), but was limited in improving health status and care satisfaction.

Conclusion
Our finding raises critical concerns about inequitable access to health care services for disease prevention and health promotion during the pandemic. Furthermore, the effectiveness of AWVs was mostly in increased preventive care use, suggesting a limited role in meeting the wellness needs of a diverse population of older adults.
Intraspecific Variation of Transposable Elements Reveals Differences in the Evolutionary History of Fungal Phytopathogen Pathotypes
Authors: Nakamoto Anne A , Joubert Pierre M , Krasileva Ksenia V 
Published: November 2023

Abstract
Transposable elements (TEs) contribute to intraspecific variation and play important roles in the evolution of fungal genomes. However, our understanding of the processes that shape TE landscapes is limited, as is our understanding of the relationship between TE content, population structure, and evolutionary history of fungal species. Fungal plant pathogens, which often have host-specific populations, are useful systems in which to study intraspecific TE content diversity. Here, we describe TE dynamics in five lineages of Magnaporthe oryzae, the fungus that causes blast disease of rice, wheat, and many other grasses. We identified differences in TE content across these lineages and showed that recent lineage-specific expansions of certain TEs have contributed to overall greater TE content in rice-infecting and Setaria-infecting lineages. We reconstructed the evolutionary histories of long terminal repeat-retrotransposon expansions and found that in some cases they were caused by complex proliferation dynamics of one element and in others by multiple elements from an older population of TEs multiplying in parallel. Additionally, we found evidence suggesting the recent transfer of a DNA transposon between rice- and wheat-infecting M. oryzae lineages and a region showing evidence of homologous recombination between those lineages, which could have facilitated such a transfer. By investigating intraspecific TE content variation, we uncovered key differences in the proliferation dynamics of TEs in various pathotypes of a fungal plant pathogen, giving us a better understanding of the evolutionary history of the pathogen itself.
Light quality regulates plant biomass and fruit quality through a photoreceptor-dependent HY5-LHC/CYCB module in tomato
Authors: Yan Jiarong , Liu Juan , Yang Shengdie , Jiang Chenghao , Liu Yanan , Zhang Nan , Sun Xin , Zhang Ying , Zhu Kangyou , Peng Yinxia , Bu Xin , Wang Xiujie , Ahammed Golam Jalal , Meng Sida , Tan Changhua , Liu Yufeng , Sun Zhouping , Qi Mingfang , Wang Feng , Li Tianlai 
Published: November 2023

Abstract
Increasing photosynthesis and light capture offers possibilities for improving crop yield and provides a sustainable way to meet the increasing global demand for food. However, the poor light transmittance of transparent plastic films and shade avoidance at high planting density seriously reduce photosynthesis and alter fruit quality in vegetable crops, and therefore it is important to investigate the mechanisms of light signaling regulation of photosynthesis and metabolism in tomato (Solanum lycopersicum). Here, a combination of red, blue, and white (R1W1B0.5) light promoted the accumulation of chlorophyll, carotenoid, and anthocyanin, and enhanced photosynthesis and electron transport rates by increasing the density of active reaction centers and the expression of the genes LIGHT-HARVESTING COMPLEX B (SlLHCB) and A (SlLHCA), resulting in increased plant biomass. In addition, R1W1B0.5 light induced carotenoid accumulation and fruit ripening by decreasing the expression of LYCOPENE β-CYCLASE (SlCYCB). Disruption of SlCYCB largely induced fruit lycopene accumulation, and reduced chlorophyll content and photosynthesis in leaves under red, blue, and white light. Molecular studies showed that ELONGATED HYPOCOTYL 5 (SlHY5) directly activated SlCYCB, SlLHCB, and SlLHCA expression to enhance chlorophyll accumulation and photosynthesis. Furthermore, R1W1B0.5 light-induced chlorophyll accumulation, photosynthesis, and SlHY5 expression were largely decreased in the slphyb1cry1 mutant. Collectively, R1W1B0.5 light noticeably promoted photosynthesis, biomass, and fruit quality through the photoreceptor (SlPHYB1 and SlCRY1)-SlHY5-SlLHCA/B/SlCYCB module in tomato. Thus, the manipulation of light environments in protected agriculture is a crucial tool to regulate the two vital agronomic traits related to crop production efficiency and fruit nutritional quality in tomato.