bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sub‐Milankovitch Signals in the Northern Polar Layered Deposits of Mars
Authors: Sotzen J. P. , Lewis K. W. 
Published: October 2024

AbstractOur understanding of the paleoclimate of Mars and the dominant forcing functions that drive large‐scale changes largely remains a mystery. However, the Martian Polar Layered Deposits (PLD) offer a promising avenue for unraveling the planet's recent paleoclimate history. Despite recent progress to detect a climate signal in the PLD, definitive evidence of a correlation between the stratigraphic record and Mars' recent orbital history remains elusive. We utilized new and updated techniques, including high‐resolution stratigraphic reconstruction from High Resolution Imagine Science Experiment stereo imagery and digital terrain models, combined with a technique of variable dip correction to account for three dimensional bedding orientations. Signal processing methods, such as wavelet and Fourier analysis, were applied to perform detailed time‐series analysis. These analyses revealed a quasi‐periodic signal indicative of fine bedding at a scale of approximately 2 m. Based on previously proposed deposition rates, these fine layers appear to correspond to timescales centering around 4,000 years. This suggests that the meter‐scale layers may not be the result of orbital forcing and hint at an unknown sub‐Milankovitch climate forcing mechanism. We discuss potential exogenic causal mechanisms, such as cyclic variations in solar activity, and endogenic factors, including large‐scale changes in dust distribution. Understanding the formation processes of these fine layers may significantly enhance our knowledge of Martian climate history and its driving forces.
Genetic analysis of a Yayoi individual from the Doigahama site provides insights into the origins of immigrants to the Japanese Archipelago
Authors: Kim Jonghyun , Mizuno Fuzuki , Matsushita Takayuki , Matsushita Masami , Aoto Saki , Ishiya Koji , Kamio Mami , Naka Izumi , Hayashi Michiko , Kurosaki Kunihiko , Ueda Shintaroh , Ohashi Jun 
Published: October 2024

AbstractMainland Japanese have been recognized as having dual ancestry, originating from indigenous Jomon people and immigrants from continental East Eurasia. Although migration from the continent to the Japanese Archipelago continued from the Yayoi to the Kofun period, our understanding of these immigrants, particularly their origins, remains insufficient due to the lack of high-quality genome samples from the Yayoi period, complicating predictions about the admixture process. To address this, we sequenced the whole nuclear genome of a Yayoi individual from the Doigahama site in Yamaguchi prefecture, Japan. A comprehensive population genetic analysis of the Doigahama Yayoi individual, along with ancient and modern populations in East Asia and Northeastern Eurasia, revealed that the Doigahama Yayoi individual, similar to Kofun individuals and modern Mainland Japanese, had three distinct genetic ancestries: Jomon-related, East Asian-related, and Northeastern Siberian-related. Among non-Japanese populations, the Korean population, possessing both East Asian-related and Northeastern Siberian-related ancestries, exhibited the highest degree of genetic similarity to the Doigahama Yayoi individual. The analysis of admixture modeling for Yayoi individuals, Kofun individuals, and modern Japanese respectively supported a two-way admixture model assuming Jomon-related and Korean-related ancestries. These results suggest that between the Yayoi and Kofun periods, the majority of immigrants to the Japanese Archipelago originated primarily from the Korean Peninsula.
Novel homozygous ESAM variants in two families with perinatal strokes showing variable neuroradiologic and clinical findings
Authors: Abdel-Salam Ghada M. H. , Esmail Asmaa , Nagy Dina , Abdel-Ghafar Sherif F. , Abdel-Hamid Mohamed S. 
Published: October 2024

Abstract
Biallelic loss of function variants in ESAM (endothelial cell adhesion molecule) have recently been reported in 14 individuals (9 families) presenting with prenatal intracranial hemorrhage. Here, we describe four patients from two unrelated families in whom three of them presented with variable onset encephalopathy and seizures while one only displayed profound delay without seizures. Brain MRI showed variable onset intracranial hemorrhage that evolved to hydrocephalus in 3 patients, whereas hemosiderin deposits, white matter volume loss, and porencephalic cysts were noted in one patient. Unlike the majority of described cases, the youngest brother of the first family did not show microcephaly and failure to thrive. Exome sequencing identified two novel homozygous ESAM variants. A splice variant (c.731-2A>G) was identified in one family which was confirmed by investigating the patient’s mRNA to result in exon skipping and early protein truncation. In addition, a missense variant (c.561G>C; p.Trp187Cys) was identified in the other family, which is the first disease causing missense variant to be described in patients with ESAM deficient phenotype. In addition, a maternally inherited pathogenic MC4R variant (c.811T>C; p.Cys271 Arg) was also identified in the youngest brother of the first family. Variants in the MC4R gene are associated with a non-syndromic form of obesity that could explain the unusual macrocephaly and obesity. Our work establishes ESAM as a tight junction gene that can present with variable neuroradiological and clinical phenotypes when mutated. Moreover, it refines the phenotype of this ultrarare syndrome and extends the number and type of variants described to date.
Periodontitis impacts on thrombotic diseases: from clinical aspect to future therapeutic approaches
Authors: Ge Jinting , Zhu Xuanzhi , Weng Chengxin , Yuan Ding , Zhao Jichun , Zhao Lei , Wang Tiehao , Wu Yafei 
Published: October 2024

AbstractPeriodontitis is a chronic inflammatory disease initiated by biofilm microorganisms and mediated by host immune imbalance. Uncontrolled periodontal infections are the leading cause of tooth loss in adults. Thrombotic diseases can lead to partial or complete obstruction of blood flow in the circulatory system, manifesting as organ or tissue ischemia and necrosis in patients with arterial thrombosis, and local edema, pain and circulatory instability in patients with venous thrombosis, which may lead to mortality or fatality in severe case. Recent studies found that periodontitis might enhance thrombosis through bacterial transmission or systemic inflammation by affecting platelet-immune cell interactions, as well as the coagulation, and periodontal therapy could have a prophylactic effect on patients with thrombotic diseases. In this review, we summarized clinical findings on the association between periodontitis and thrombotic diseases and discussed several novel prothrombotic periodontitis-related agents, and presented a perspective to emphasize the necessity of oral health management for people at high risk of thrombosis.
Population-wide DNA methylation polymorphisms at single-nucleotide resolution in 207 cotton accessions reveal epigenomic contributions to complex traits
Authors: Zhao Ting , Guan Xueying , Hu Yan , Zhang Ziqian , Yang Han , Shi Xiaowen , Han Jin , Mei Huan , Wang Luyao , Shao Lei , Wu Hongyu , Chen Qianqian , Zhao Yongyan , Pan Jiaying , Hao Yupeng , Dong Zeyu , Long Xuan , Deng Qian , Zhao Shengjun , Zhang Mengke , Zhu Yumeng , Ma Xiaowei , Chen Zequan , Deng Yayuan , Si Zhanfeng , Li Xin , Zhang Tianzhen , Gu Fei , Gu Xiaofeng , Fang Lei 
Published: October 2024

AbstractDNA methylation plays multiple regulatory roles in crop development. However, the relationships of methylation polymorphisms with genetic polymorphisms, gene expression, and phenotypic variation in natural crop populations remain largely unknown. Here, we surveyed high-quality methylomes, transcriptomes, and genomes obtained from the 20-days-post-anthesis (DPA) cotton fibers of 207 accessions and extended the classical framework of population genetics to epigenetics. Over 287 million single methylation polymorphisms (SMPs) were identified, 100 times more than the number of single nucleotide polymorphisms (SNPs). These SMPs were significantly enriched in intragenic regions while depleted in transposable elements. Association analysis further identified a total of 5,426,782 cis-methylation quantitative trait loci (cis-meQTLs), 5078 cis-expression quantitative trait methylation (cis-eQTMs), and 9157 expression quantitative trait loci (eQTLs). Notably, 36.39% of cis-eQTM genes were not associated with genetic variation, indicating that a large number of SMPs associated with gene expression variation are independent of SNPs. In addition, out of the 1715 epigenetic loci associated with yield and fiber quality traits, only 36 (2.10%) were shared with genome-wide association study (GWAS) loci. The construction of multi-omics regulatory networks revealed 43 cis-eQTM genes potentially involved in fiber development, which cannot be identified by GWAS alone. Among these genes, the role of one encoding CBL-interacting protein kinase 10 in fiber length regulation was successfully validated through gene editing. Taken together, our findings prove that DNA methylation data can serve as an additional resource for breeding purposes and can offer opportunities to enhance and expedite the crop improvement process.
The potential of gene drives in malaria vector species to control malaria in African environments
Authors: Hancock Penelope A. , North Ace , Leach Adrian W. , Winskill Peter , Ghani Azra C. , Godfray H. Charles J. , Burt Austin , Mumford John D. 
Published: October 2024

AbstractGene drives are a promising means of malaria control with the potential to cause sustained reductions in transmission. In real environments, however, their impacts will depend on local ecological and epidemiological factors. We develop a data-driven model to investigate the impacts of gene drives that causes vector population suppression. We simulate gene drive releases in sixteen ~ 12,000 km2 areas of west Africa that span variation in vector ecology and malaria prevalence, and estimate reductions in vector abundance, malaria prevalence and clinical cases. Average reductions in vector abundance ranged from 71.6–98.4% across areas, while impacts on malaria depended strongly on which vector species were targeted. When other new interventions including RTS,S vaccination and pyrethroid-PBO bednets were in place, at least 60% more clinical cases were averted when gene drives were added, demonstrating the benefits of integrated interventions. Our results show that different strategies for gene drive implementation may be required across different African settings.
Antisolvent controls the shape and size of anisotropic lead halide perovskite nanocrystals
Authors: Frank Kilian , Henke Nina A. , Lampe Carola , Lorenzen Tizian , März Benjamin , Sun Xiao , Haas Sylvio , Gutowski Olof , Dippel Ann-Christin , Mayer Veronika , Müller-Caspary Knut , Urban Alexander S. , Nickel Bert 
Published: October 2024

AbstractColloidal lead halide perovskite nanocrystals have potential for lighting applications due to their optical properties. Precise control of the nanocrystal dimensions and composition is a prerequisite for establishing practical applications. However, the rapid nature of their synthesis precludes a detailed understanding of the synthetic pathways, thereby limiting the optimisation. Here, we deduce the formation mechanisms of anisotropic lead halide perovskite nanocrystals, 1D nanorods and 2D nanoplatelets, by combining in situ X-ray scattering and photoluminescence spectroscopy. In both cases, emissive prolate nanoclusters form when the two precursor solutions are mixed. The ensuing antisolvent addition induces the divergent anisotropy: The intermediate nanoclusters are driven into a dense hexagonal mesophase, fusing to form nanorods. Contrastingly, nanoplatelets grow freely dispersed from dissolving nanoclusters, stacking subsequently in lamellar superstructures. Shape and size control of the nanocrystals are determined primarily by the antisolvent’s dipole moment and Hansen hydrogen bonding parameter. Exploiting the interplay of antisolvent and organic ligands could enable more complex nanocrystal geometries in the future.
Inorganic nitrogen inhibits symbiotic nitrogen fixation through blocking NRAMP2-mediated iron delivery in soybean nodules
Authors: Zhou Min , Li Yuan , Yao Xiao-Lei , Zhang Jing , Liu Sheng , Cao Hong-Rui , Bai Shuang , Chen Chun-Qu , Zhang Dan-Xun , Xu Ao , Lei Jia-Ning , Mao Qian-Zhuo , Zhou Yu , Duanmu De-Qiang , Guan Yue-Feng , Chen Zhi-Chang 
Published: October 2024

AbstractSymbiotic nitrogen fixation (SNF) in legume-rhizobia serves as a sustainable source of nitrogen (N) in agriculture. However, the addition of inorganic N fertilizers significantly inhibits SNF, and the underlying mechanisms remain not-well understood. Here, we report that inorganic N disrupts iron (Fe) homeostasis in soybean nodules, leading to a decrease in SNF efficiency. This disruption is attributed to the inhibition of the Fe transporter genes Natural Resistance-Associated Macrophage Protein 2a and 2b (GmNRAMP2a&2b) by inorganic N. GmNRAMP2a&2b are predominantly localized at the tonoplast of uninfected nodule tissues, affecting Fe transfer to infected cells and consequently, modulating SNF efficiency. In addition, we identified a pair of N-signal regulators, nitrogen-regulated GARP-type transcription factors 1a and 1b (GmNIGT1a&1b), that negatively regulate the expression of GmNRAMP2a&2b, which establishes a link between N signaling and Fe homeostasis in nodules. Our findings reveal a plausible mechanism by which soybean adjusts SNF efficiency through Fe allocation in response to fluctuating inorganic N conditions, offering valuable insights for optimizing N and Fe management in legume-based agricultural systems.
Body orientation change of neighbors leads to scale-free correlation in collective motion
Authors: Zheng Zhicheng , Tao Yuan , Xiang Yalun , Lei Xiaokang , Peng Xingguang 
Published: October 2024

AbstractCollective motion, such as milling, flocking, and collective turning, is a common and captivating phenomenon in nature, which arises in a group of many self-propelled individuals using local interaction mechanisms. Recently, vision-based mechanisms, which establish the relationship between visual inputs and motion decisions, have been applied to model and better understand the emergence of collective motion. However, previous studies often characterize the visual input as a transient Boolean-like sensory stream, which makes it challenging to capture the salient movements of neighbors. This further hinders the onset of the collective response in vision-based mechanisms and increases demands on visual sensing devices in robotic swarms. An explicit and context-related visual cue serving as the sensory input for decision-making in vision-based mechanisms is still lacking. Here, we hypothesize that body orientation change (BOC) is a significant visual cue characterizing the motion salience of neighbors, facilitating the emergence of the collective response. To test our hypothesis, we reveal the significant role of BOC during collective U-turn behaviors in fish schools by reconstructing scenes from the view of individual fish. We find that an individual with the larger BOC often takes on the leading role during U-turns. To further explore this empirical finding, we build a pairwise interaction mechanism on the basis of the BOC. Then, we conduct experiments of collective spin and collective turn with a real-time physics simulator to investigate the dynamics of information transfer in BOC-based interaction and further validate its effectiveness on 50 real miniature swarm robots. The experimental results show that BOC-based interaction not only facilitates the directional information transfer within the group but also leads to scale-free correlation within the swarm. Our study highlights the practicability of interaction governed by the neighbor’s body orientation change in swarm robotics and the effect of scale-free correlation in enhancing collective response.
Paenilamicins are context-specific translocation inhibitors of protein synthesis
Authors: Koller Timm O. , Berger Max J. , Morici Martino , Paternoga Helge , Bulatov Timur , Di Stasi Adriana , Dang Tam , Mainz Andi , Raulf Karoline , Crowe-McAuliffe Caillan , Scocchi Marco , Mardirossian Mario , Beckert Bertrand , Vázquez-Laslop Nora , Mankin Alexander S. , Süssmuth Roderich D. , Wilson Daniel N. 
Published: October 2024

AbstractThe paenilamicins are a group of hybrid nonribosomal peptide–polyketide compounds produced by the honey bee pathogen Paenibacillus larvae that display activity against Gram-positive pathogens, such as Staphylococcus aureus. While paenilamicins have been shown to inhibit protein synthesis, their mechanism of action has remained unclear. Here we determine structures of paenilamicin PamB2-stalled ribosomes, revealing a unique binding site on the small 30S subunit located between the A- and P-site transfer RNAs (tRNAs). In addition to providing a precise description of interactions of PamB2 with the ribosome, the structures also rationalize the resistance mechanisms used by P. larvae. We further demonstrate that PamB2 interferes with the translocation of messenger RNA and tRNAs through the ribosome during translation elongation, and that this inhibitory activity is influenced by the presence of modifications at position 37 of the A-site tRNA. Collectively, our study defines the paenilamicins as a class of context-specific translocation inhibitors.
Enhanced ANN-based ensemble method for bridge damage characterization using limited dataset
Authors: Izonin Ivan , Nesterenko Illia , Kazantzi Athanasia K. , Tkachenko Roman , Muzyka Roman , Mitoulis Stergios Aristoteles 
Published: October 2024

AbstractBridges are vital assets of transport infrastructure, systems, and communities. Damage characterization is critical in ensuring safety and planning adaptation measures. Nondestructive methods offer an efficient means towards assessing the condition of bridges, without causing harm or disruption to transport services, and these can deploy measurable evidence of bridge deterioration, e.g., deflections due to tendon loss. This paper presents an enhanced input-doubling technique and the Artificial Neural Network (ANN)-based cascade ensemble method for bridge damage state identification and is exclusively relying on small datasets, that are common in structural assessments. A new data augmentation scheme rooted in the principles of linearizing response surfaces is introduced, which significantly boosts the efficiency of intelligent data analysis when faced with limited volumes of data. Furthermore, improvements to a two-step ANN-based ensemble method, designed for solving the stated task, are presented. By adding the improved input-doubling methods as simple predictors in the first part of the cascade ensemble and optimizing it, we significantly boost accuracy (7%, 0.5%, and 8% based on R2 in predicting tendon losses for three critical zones that were defined across the deck of a real deteriorated prestressed balanced cantilever bridge). This improvement is strong evidence of the accuracy of the proposed method for the task at hand that is proven to be more accurate than other methods available in the international literature.
Optimal circuit breaker allocation strategy in DC transmission-connected systems
Authors: Kim Beopsoo , Kim Insu 
Published: October 2024

AbstractThe purpose of this study is to provide data for the best possible circuit breaker allocation in power grids with HVDC transmission while taking circuit breaker failure into account. The lack of a suitable selection of HVDC circuit breakers is one of the primary obstacles to establishing an appropriate protection system for HVDC transmission. This research focuses on finding the optimal circuit breaker allocation strategy with respect to the transient response of the system, especially when the grid operator is using existing circuit breakers, rather than on the necessary steps to improve the technology of circuit breakers. Case studies are simulated using PSCAD/EMTDC in order to verify the transient response of the transmission system corresponding to the allocation of circuit breakers and the circumstance of circuit breaker failure. It is crucial to remember that there isn’t a strategy that is always the best. Consequently, a detailed analysis of the suggested approach is required, taking into account the benefits and drawbacks from the standpoints of fault clearing, power system planning, and operational factors. In the context of HVDC transmission, the authors hope that their research will spark and start conversations about circuit breaker allocation strategies.
A lumped parameter modelling study of cerebral autoregulation in normal pressure hydrocephalus suggests the brain chooses to be ischemic
Authors: Bateman Grant Alexander , Bateman Alexander Robert 
Published: October 2024

AbstractNormal pressure hydrocephalus (NPH) is associated with a reduction in cerebral blood flow and an ischemic metabolic state. Ischemia should exhaust the available autoregulation in an attempt to correct the metabolic imbalance. There is evidence of some retained autoregulation reserve in NPH. The aim of this study is to model the cerebral autoregulation in NPH to discover a solution to this apparent paradox. A lumped parameter model was developed utilizing the known limits of autoregulation in man. The model was tested by predicting the cerebral blood volume changes which would be brought about by changes in resistance. NPH and the post shunt state were then modeled using the known constraints provided from the literature. The model successfully predicted the cerebral blood volume changes brought about by altering the cerebral perfusion pressure to the limit of autoregulation. The model suggests that NPH is associated with a balanced increase in resistance within the arterial and venous outflow segments. The arterial resistance decreased after modelling shunt insertion. The model suggests that the cerebral blood flow is actively limited in NPH by arteriolar constriction. This may occur to minimize the rise in ICP by reducing the apparent CSF formation rate.
Low concentration cell painting images enable the identification of highly potent compounds
Authors: Ha Son V. , Jaensch Steffen , Freitas Lorena G. A. , Herman Dorota , Czodrowski Paul , Ceulemans Hugo 
Published: October 2024

AbstractImage-based models that use features extracted from cell microscopy images can estimate the activity of small molecules in various biological assays. Typically, models are trained on images stained by an optimized protocol (e.g. Cell Painting) after exposure to a fairly high small molecule concentration (referred to as ’image concentration’) of $$10\; \upmu {\text{M}}$$

10

μ
M

or higher. Low concentration images (e.g. $$0.16$$

0.16

μM, $$0.8$$

0.8

μM, $$4$$

4

μM) tend to yield models with worse performance. In this work, we nevertheless report a practical use for low image concentration data. We propose the combination of well-performing models trained at higher image concentrations, with lower image concentration for inference to identify more potent compounds. We show that this approach improves on the conventional method (directly training a high-potency model) in 65$$\%$$
%
of assays investigated in terms of AUC-ROC, and 75$$\%$$
%
of assays in terms of RIPtoP-corrected AUC-PR.