bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic improvement of low‐lignin poplars: a new strategy based on molecular recognition, chemical reactions and empirical breeding
Authors: Duan Huaichuan , Li Siyao , Wang Xin , Ge Yutong , Song Yuting , Hu Dongling , Liu Wei , Hu Jianping , Shi Hubing 
Published: December 2024

AbstractAs an important source of pollution in the papermaking process, the presence of lignin in poplar can seriously affect the quality and process of pulping. During lignin synthesis, Caffeoyl‐CoA‐O methyltransferase (CCoAOMT), as a specialized catalytic transferase, can effectively regulate the methylation of caffeoyl‐coenzyme A (CCoA) to feruloyl‐coenzyme A. Targeting CCoAOMT, this study investigated the substrate recognition mechanism and the possible reaction mechanism, the key residues of lignin binding were mutated and the lignin content was validated by deep convolutional neural‐network model based on genome‐wide prediction (DCNGP). The molecular mechanics results indicate that the binding of S‐adenosyl methionine (SAM) and CCoA is sequential, with SAM first binding and inducing inward constriction of the CCoAOMT; then CCoA binds to the pocket, and this process closes the outer channel, preventing contamination by impurities and ensuring that the reaction proceeds. Next, the key residues in the recognition process of SAM (F69 and D91) and CCoA (I40, N170, Y188 and D218) were analyzed, and we identified that K146 as a base catalyst is important for inducing the methylation reaction. Immediately after that, the possible methylation reaction mechanism was deduced by the combination of Restrained Electrostatic Potential (RESP) and Independent Gradient Model (IGM) analysis, focusing on the catalytic center electron cloud density and RESP charge distribution. Finally, the DCNGP results verified that the designed mutant groups were all able to effectively reduce the lignin content and increase the S‐lignin content/ G‐lignin content ratio, which was beneficial for the subsequent lignin removal. Multifaceted consideration of factors that reduce lignin content and combined deep learning to screen for favorable mutations in target traits provides new ideas for targeted breeding of low‐lignin poplars.
L‐DOPA promotes cadmium tolerance and modulates iron deficiency genes in Arabidopsis thaliana
Authors: Chang Ching‐Yuan , Hsieh En‐Jung , Wang Shan‐Li , Grillet Louis 
Published: December 2024

AbstractCadmium (Cd) is a toxic element and a widespread health hazard. Preventing its entry into crops is an outstanding issue. 3,4‐Dihydroxy‐L‐phenylalanine (L‐DOPA) is a non‐proteinogenic amino acid that is secreted by a few legume plants and affects neighboring plants. Exogenous L‐DOPA triggers iron (Fe) uptake by roots of Arabidopsis thaliana Columbia‐0 ecotype through transcriptional activation of Fe deficiency genes, including IRONMANs (IMAs), which encode peptides regulating Fe homeostasis. Ectopic expression of IRONMAN1 was reported to enhance Cd tolerance in Arabidopsis. We therefore hypothesized that L‐DOPA could also enhance Cd tolerance by stimulating the expression of IMAs. In the present study, the elemental profile and the expression of key genes of plants exposed to a combination of Cd and L‐DOPA were studied. The results show that exogenous L‐DOPA considerably enhances the Cd tolerance of Arabidopsis thaliana, abolishing the Cd‐induced chlorosis and necrosis, and reducing Cd accumulation. This increased tolerance is not due to an enhanced Fe uptake and is not mediated by IMAs. Instead, L‐DOPA triggered a peculiar transcriptional program that led to an increased expression of a branch of the Fe deficiency pathway comprising the transcription factor bHLH39 but, surprisingly, not its target genes FRO2 and IRT1. The NICOTIANAMINE SYNTHASE 4 (NAS4) gene, which mediates Cd tolerance, was highly and specifically upregulated by the application of L‐DOPA and Cd combined. These results suggest that Fe homeostasis is controlled by small molecules through currently unknown mechanisms that could be leveraged to manipulate Fe and Cd accumulation in plants.
Resilient gas dependency–based planning of electricity distribution systems considering energy storage systems
Authors: Ghasemi Mostafa , Gilani Mohammad Amin , Amirioun Mohammad Hassan 
Published: December 2024

AbstractThis article presents a planning framework to improve the weather‐related resilience of natural gas–dependent electricity distribution systems. The problem is formulated as a two‐stage stochastic mixed integer linear programing model. In the first stage, the measures for distribution line hardening, gas‐fired distributed generation (DG) placement, electrical energy storage resource allocation, and tie‐switch placement are determined. The second stage minimizes the electricity distribution system load shedding in realized hurricanes to achieve a compromise between operational benefits and investment costs when the dependence of electricity distribution system on the natural gas exists. The proposed stochastic model considers random failures of electricity distribution system lines and random errors in forecasting the load demand. The Monte Carlo simulation is employed to generate multiple scenarios for defining the uncertainties of electricity distribution system. For the sake of simplicity, weather‐related outages of natural gas pipelines are considered deterministic. The nonlinear natural gas constraints are linearized and incorporated into the stochastic optimization model. The proposed framework was successfully implemented on an interconnected energy system composed of a 33‐bus electricity distribution system and a 14‐node natural gas distribution network. Numerical results of the defined case studies and a devised comparative study validate the effectiveness of the proposed framework as well.
Correlation analysis of the impact of
Clonorchis sinensis
juvenile on gut microbiota and transcriptome in mice
Authors: Deng Xueling , Li Shitao , Wu Yuhong , Yao Jiali , Hou Wei , Zheng Jiangyao , Liang Boying , Liang Xiaole , Hu Qiping , Wu Zhanshuai , Tang Zeli 
Published: December 2024

ABSTRACT

Clonorchiasis
remains a non-negligible global zoonosis, imposing serious socio-economic burdens in endemic regions. The interplay between gut microbiota and the host transcriptome is crucial for maintaining health; however, the impact of
Clonorchiasis sinensis
juvenile infection on these factors is still poorly understood. This study aimed to investigate their relationship and potential pathogenic mechanisms. The BALB/c mouse model of early infection with
C. sinensis
juvenile was constructed. Pathological analyses revealed that
C. sinensis
juvenile triggered liver inflammation, promoted intestinal villi growth, and augmented goblet cell numbers in the ileum. Additionally, the infection altered the diversity and structure of gut microbiota, particularly affecting beneficial bacteria that produce short-chain fatty acids, such as
Lactobacillus
and
Muribaculaceae
, and disrupted the Firmicutes/Bacteroidetes ratio. Gut transcriptome analysis demonstrated an increase in the number of differentially expressed genes (DEGs) as infection progressed. Enriched Gene Ontology items highlighted immune and detoxification-related processes, including immunoglobulin production and xenobiotic metabolic processes. Kyoto Encyclopedia of Genes and Genomes pathway analysis further indicated involvement in circadian rhythm, as well as various detoxification and metabolic-related pathways (e.g., glutathione metabolism and glycolysis/gluconeogenesis). Prominent DEGs associated with these pathways included Igkv12-41, Mcpt2, Arntl, Npas2, Cry1, and Gsta1. Correlation analysis additionally identified
Bacteroides_sartorii
as a potential key regulator in the interaction between gut microbiota and transcriptome. This study sheds light on the alterations in gut microbiota and transcriptome in mice following
C. sinensis
juvenile infection, as well as their correlation, laying a foundation for a better understanding of their interaction during infection.

IMPORTANCE

This study highlighted the impact of
C. sinensis
juvenile infection on the gut microbiota and transcriptome of BALB/c mice. It induced liver inflammation, promoted intestinal villi growth, and altered goblet cell numbers. The infection also disrupted the diversity and structure of gut microbiota, particularly affecting beneficial bacteria. Transcriptome analysis revealed increased expression of genes related to immune response and detoxification processes. Important pathways affected included circadian rhythm, glutathione metabolism, and glycolysis/gluconeogenesis. Notable genes implicated included Igkv12-41, Mcpt2, Arntl, Npas2, Cry1, and Gsta1.
Bacteroides_sartorii
emerged as a potential key regulator in this interaction.
Transendothelial migration of the Lyme disease spirochete involves spirochete internalization as an intermediate step through a transcellular pathway that involves Cdc42 and Rac1
Authors: Alvarez-Olmedo Daiana , Kamaliddin Claire , Verhey Theodore B. , Ho May , De Vinney Rebekah , Chaconas George 
Published: December 2024

ABSTRACT

Despite its importance in pathogenesis, the hematogenous dissemination pathway of
Borrelia burgdorferi
is still largely uncharacterized. To probe the molecular details of transendothelial migration more easily, we studied this process using cultured primary or telomerase-immortalized human microvascular endothelial cells in a medium that maintains both the human cells and the spirochetes. In
B. burgdorferi
-infected monolayers, we observed ~55% of wild-type spirochetes crossing the monolayer. Microscopic characterization revealed entrance points across the cellular surface rather than at cellular junctions, supporting a transcellular route. In support of this pathway, locking the endothelial junctions using a vascular endothelial protein tyrosine phosphatase (VE-PTP) inhibitor did not reduce transendothelial migration. We also used inhibitors to block the most common endocytic pathways to elucidate effectors that might be involved in
B. burgdorferi
uptake and/or transmigration. Directly inhibiting Cdc42 reduced spirochete transmigration by impeding internalization. However, blocking Rac1 alone dramatically reduced transmigration by ~84% and resulted in a concomitant doubling in spirochete accumulation in the cell. Our combined results support that
B. burgdorferi
internalization is an intermediate step in the transendothelial migration process, which requires both Cdc42 and Rac1; Cdc42 is needed for spirochete internalization, while Rac1 is required for cellular egress. These are the first two host proteins implicated in
B. burgdorferi
transmigration across endothelial cells.

IMPORTANCE

Lyme borreliosis is caused by
Borrelia burgdorferi
and related bacteria. It is the most common tick-transmitted illness in the Northern Hemisphere. The ability of this pathogen to spread to a wide variety of locations results in a diverse set of clinical manifestations, yet little is known regarding vascular escape of the spirochete, an important pathway for dissemination. Our current work has studied the traversal of
B. burgdorferi
across a monolayer of microvascular endothelial cells grown using a new culture system. We show that this occurs by passage of the spirochetes directly through cells rather than at cellular junctions and that internalization of
B. burgdorferi
is an intermediate step in transmigration. We also identify the first two host proteins, Cdc42 and Rac1, that are used by the spirochetes to promote traversal of the cellular monolayer. Our new experimental system also provides a new avenue for further studies of this important process.
Improving outcomes for very preterm babies in England: does place of birth matter? Findings from OPTI-PREM, a national cohort study
Authors: Pillay Thillagavathie , Seaton Sarah E , Yang Miaoqing , Bountziouka Vasiliki , Banda Victor , Campbell Helen , Dawson Kelvin , Manktelow Bradley N , Draper Elizabeth S , Modi Neena , Boyle Elaine M , Rivero-Arias Oliver 
Published: December 2024

ObjectiveBabies born between 27+0and 31+6weeks of gestation contribute substantially towards infant mortality and morbidity. In England, their care is delivered in maternity services colocated with highly specialised neonatal intensive care units (NICU) or less specialised local neonatal units (LNU). We investigated whether birth setting offered survival and/or morbidity advantages to inform National Health Service delivery.DesignRetrospective national cohort study.SettingLNU, NICU, England.PatientsUK National Neonatal Research Database whole population data for births between 27+0and 31+6weeks of gestation, discharged from/died within neonatal units between 1 January 2014 and 31 December 2018. We linked baby-level data to mortality information from the Office for National Statistics.Outcome measuresDeath during neonatal care, up to 1 year (infant mortality), surgically treated necrotising enterocolitis, retinopathy of prematurity, severe brain injury (SBI), bronchopulmonary dysplasia.InterventionBirth in NICU versus LNU setting. We used an instrumental variable (maternal excess travel time between the nearest NICU and LNU) estimation approach to determine treatment effect.ResultsOf 18 847 babies (NICU: 10 379; LNU: 8468), 574 died in NICU/LNU care, and 121 postdischarge (infant mortality 3.7%). We found no effect of birth setting on neonatal or infant mortality. Significantly more babies born into LNU settings experienced SBI (mean difference −1.1% (99% CI −2.2% to −0.1%)). This was attenuated after excluding births at 27 weeks, and early postnatal transfers.ConclusionsIn England, LNU teams should use clinical judgement, risk assessing benefits of transfer versus risk of SBI for preterm births at 27 weeks of gestation. 28 weeks of gestation is a safe threshold for preterm birth in either NICU/LNU settings.Trial registration numberNCT02994849/ISRCTN74230187.
Mitigating unintentional injury deaths in sport and recreation: insights from 14 years of coroner recommendations in Québec, Canada
Authors: Richard Philippe , Gagné Mathieu , Sylvain-Morneau Jérémie , Perron Paul-André , Charbonneau Maxime 
Published: December 2024

BackgroundUnintentional injury deaths in sport and recreation represent a significant public health concern. This study analysed coronial recommendations related to such deaths, focusing on case specifics and recurring themes from January 2006 to December 2019.MethodsThis mixed-methods study used data from the Bureau du coroner du Québec. Reports with recommendations were analysed by sex, age group, context, mechanism and activity. A four-phase thematic analysis was conducted to emphasise the developed themes and connect them with the existing literature.ResultsOf 1937 coronial reports reviewed, 13.3% (n=258) contained at least one recommendation, totalling 609 recommendations (31 per 100 activity-related deaths). Reports were more likely to contain at least one recommendation for women (20.3%, p=0.0004), paediatric populations (≤5 years: 30.3%, p<0.0001; 6–11 years: 29.3%, p=0.0003; 12–17 years: 27.6%, p<0.0001), and organised events (55.0%, p<0.0001), despite most deaths occurring among men, adults and during unstructured events. All-terrain vehicle and snowmobile activities showed significantly lower rates of reports with recommendations (8.1%, p=0.0008 and 8.6%, p=0.0044, respectively). Most frequently addressed themes wereDevelopment, inspection and modification of bicycle infrastructurefor cycling andLake and river safety measuresfor swimming.Conflict with other types of userswas the top theme for land motorsports, whilePersonal flotation device usewas the most common for navigation activities.ConclusionsPatterns from reports with recommendations will be shared with the Bureau du Coroner du Québec to improve coronial practices. Integrating recurrent themes and recommendations with activity-specific risk factors will help identify critical patterns and inform preventive measures holistically.
Ternary chalcogenides NbInX2 (X = S, Se): A comprehensive investigation of mechanical, electronic, vibrational, optical and thermophysical properties
Authors: Mia M. H. , Parvin F. , Islam A. K. M. A. , Khatun Mst. A. 
Published: December 2024

A comprehensive investigation of the unexplored mechanical, electronic, Mulliken bond population, vibrational, optical and thermophysical properties of the synthesized compounds NbIn[Formula: see text] (X = S, Se) have been made for the first time using the density functional theory. The chemical, mechanical and dynamical stabilities of the compounds are established in our calculations. Both compounds are soft, machinable and brittle. The anisotropic nature of the studied compounds is shown by 3D representations of elastic moduli. The density of states and electronic band structure demonstrate that the compounds are metallic. Fermi surfaces of both compounds are almost similar and contain both hole- and electron-like topologies. The characteristics of chemical bonding among different atoms of the compounds are studied via a charge density distribution map and bond population analysis. Both the compounds possess optical anisotropy. Reflectivity is high (above 44%) in the IR–visible–UV region indicating that the phases may be effective in reducing solar heat. Minimum thermal conductivity, [Formula: see text] (used to select appropriate material for thermal barrier coating) and its anisotropy are calculated for the first time. The results show that both compounds have [Formula: see text] much smaller than the reference value of 1.25[Formula: see text]W[Formula: see text]m[Formula: see text][Formula: see text]K[Formula: see text].
Investigation of Structural, Dielectric, Electrical, Optical, and Magnetic Properties of Sr(Mn0.45Fe0.05)Nb0.5O3 for Electronic Device Applications
Authors: Mohanty Raj Mohan , Behera Srikant , Mishra Raj Kishore , Parida Sabyasachi , Anwar Muhammad Shahid , Nayak Priyabrata , Tripathy B. S. 
Published: December 2024

This study explores the structural, dielectric, impedance, and optical characteristics of the perovskite compound Sr(Mn[Formula: see text]Fe[Formula: see text]Nb[Formula: see text]O3. The compound was prepared by the solid-state mixed-oxide method. X-ray diffraction analysis confirmed a single-phase tetragonal crystal structure ([Formula: see text] Å, [Formula: see text] Å, [Formula: see text] Å, space group I4/mcm). Morphological analysis revealed an almost uniform grain distribution with minimal spacing. The Maxwell–Wagner phenomenon was observed in the frequency-dependent dielectric properties by considering various polarization mechanisms. A dielectric anomaly indicating a ferroelectric to paraelectric phase transition was observed around 260∘C during the temperature-dependent dielectric study. Impedance analysis demonstrated the NTCR behavior of the material. According to Jonscher’s power law, conduction is governed by nonoverlapping small polaron tunneling, explaining the relationship between conductivity with frequency. The activation energies for relaxation and conduction suggest electron hopping. Estimated band gap of 1.91[Formula: see text]eV is applicable for optoelectronic devices. The temperature-dependent resistance analysis indicates potential applications in N-type thermistors. The M–H hysteresis loop’s nonlinearity curve suggests weak ferromagnetism at low temperatures.
The Book Review Column
Authors: Tran Nicholas 
Published: December 2024

Foundation Mathematics for Computer Science: A Visual Approach, 4th edition (Springer, 2023) by John Vince (Bournemouth University, UK) is a comprehensive collection of discrete and continuous mathematical topics that are covered in most undergraduate programs in computer science. The subtitle refers to the author's use of colored graphs and tables to illustrate the concepts.
Online Algorithms (Cambridge University Press, 2023) by Rahul Vaze (Tata Institute of Fundamental Research, India) is an accessible but rigorous introduction to the area aimed at advanced undergraduates and beginning graduate students. The book covers the basic as well as applied online problems with a preference of elegant analysis over performance.
Privacy-preserving Computing for Big Data Analytics and AI (Cambridge University Press, 2023) by Kai Chen and Qiang Yang (Hong Kong University of Science and Technology) is a systematic examination of the history, theories, techniques, applications, and future of the field.
Prize-winning neuroscientist Terrence Sejnowski (University of California at San Diego) explains the technology and mathematics behind large language models such as ChatGPT and explores the debate on their so-called comprehension of language in ChatGPT and the Future of AI: The Deep Language Revolution (The MIT Press, 2024).
Distributed Computing Column 88
An Invitation to Local Algorithms
Authors: Alistarh Dan 
Published: December 2024

Overview. In this quarter's column, we have a contribution from Dr. Václav Rozhon, who provides us with a new perspective on the impressive recent progress happening in the area of local algorithms.
Specifically, his column builds up introductory material in terms of definitions and simple examples, but in sufficient depth to understand complex recent results. This chapter is one of three parts of a larger survey written by the author, which I invite you to read if you would like to go deeper into this area. I would like to thank Dr. Rozhon for this tremendous effort in putting together this survey!
Estimating Surfzone Currents with Near-Field Optical Remote Sensing
Authors: Dooley Ciara , Elgar Steve , Raubenheimer Britt , Gorrell Levi 
Published: December 2024

Abstract
Currents transport sediment, larvae, pollutants, and people across and along the surfzone, creating a dynamic interface between the coastal ocean and shore. Previous field studies of nearshore flows primarily have relied on relatively low spatial resolution deployments of in situ sensors, but the development of remote sensing techniques using optical imagery and naturally occurring foam as a flow tracer has allowed for high spatial resolution observations (on the order of a few meters) across the surfzone. Here, algorithms optical current meter (OCM) and particle image velocimetry (PIV) are extended from previous surfzone applications and used to estimate both cross-shore and alongshore 2-, 10-, and 60-min mean surface currents in the nearshore using imagery from both oblique and nadir viewing angles. Results are compared with in situ current meters throughout the surfzone for a wide range of incident wave heights, directions, and directional spreads. Differences between remotely sensed flows and in situ current meters are smallest for nadir viewing angles, where georectification is simplified. Comparisons of 10-min mean flow estimates from a nadir viewing angle with in situ estimates of alongshore and cross-shore currents had correlations r2 = 0.94 and 0.51 with root-mean-square differences (RMSDs) = 0.07 and 0.16 m s−1 for PIV and r2 = 0.88 and 0.44 with RMSDs = 0.08 and 0.22 m s−1 for OCM. Differences between remotely sensed and in situ cross-shore current estimates are at least partially owing to the difference between onshore-directed mass flux on the surface and offshore-directed undertow in the mid–water column.