bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hydrostatic pressure induces transformations in the organic matter and microbial community composition of marine snow particles
Authors: Stief Peter , Schauberger Clemens , Becker Kevin W. , Elvert Marcus , Balmonte John Paul , Franco-Cisterna Belén , Middelboe Mathias , Glud Ronnie N. 
Published: October 2023

AbstractIn the hadal zone of the ocean (6–11 km), the characteristics of sinking marine snow particles and their attached microbial communities remain elusive, despite their potential importance for benthic life thriving at extreme pressures (60–110 MPa). Here, we used simulation experiments to explore how increasing pressure levels modify the microbial degradation, organic matter composition, and microbiome of sinking diatom aggregates. Individual aggregates were incubated in rotating tanks in which pressure was incrementally increased to simulate a descent from surface to hadal depth within 20 days. Incubations at atmospheric pressure served as controls. With increasing pressure, microbial respiration and diatom degradation decreased gradually and ceased completely at 60 MPa. Dissolved organic carbon leaked substantially from the aggregates at ≥40 MPa, while diatom lipid and pigment contents decreased moderately. Bacterial abundance remained stable at >40 MPa, but bacterial community composition changed significantly at 60–100 MPa. Thus, pressure exposure reduces microbial degradation and transforms both organic matter composition and microbiomes of sinking particles, which may seed hadal sediments with relatively fresh particulate organic matter and putative pressure-tolerant microbes.
Widespread occurrence of chitinase-encoding genes suggests the Endozoicomonadaceae family as a key player in chitin processing in the marine benthos
Authors: da Silva Daniela M G , Pedrosa Filipa R , Ângela Taipa M , Costa Rodrigo , Keller-Costa Tina 
Published: October 2023

Abstract
Chitin is the most abundant natural polymer in the oceans, where it is primarily recycled by chitin-degrading microorganisms. Endozoicomonadaceae (Oceanospirillales) bacteria are prominent symbionts of sessile marine animals, particularly corals, and presumably contribute to nutrient cycling in their hosts. To reveal the chitinolytic potential of this iconic, animal-dwelling bacterial family, we examined 42 publicly available genomes of cultured and uncultured Endozoicomonadaceae strains for the presence of chitinase-encoding genes. Thirty-two of 42 Endozoicomonadaceae genomes harbored endo-chitinase- (EC 3.2.1.14), 25 had exo-chitinase- (EC 3.2.1.52) and 23 polysaccharide deacetylase-encoding genes. Chitinases were present in cultured and uncultured Endozoicomonadaceae lineages associated with diverse marine animals, including the three formally described genera Endozoicomonas, Paraendozoicomonas and Kistimonas, the new genus Candidatus Gorgonimonas, and other, yet unclassified, groups of the family. Most endo-chitinases belonged to the glycoside hydrolase family GH18 but five GH19 endo-chitinases were also present. Many endo-chitinases harbored an active site and a signal peptide domain, indicating the enzymes are likely functional and exported to the extracellular environment where endo-chitinases usually act. Phylogenetic analysis revealed clade-specific diversification of endo-chitinases across the family. The presence of multiple, distinct endo-chitinases on the genomes of several Endozoicomonadaceae species hints at functional variation to secure effective chitin processing in diverse micro-niches and changing environmental conditions. We demonstrate that endo-chitinases and other genes involved in chitin degradation are widespread in the Endozoicomonadaceae family and posit that these symbionts play important roles in chitin turnover in filter- and suspension-feeding animals and in benthic, marine ecosystems at large.
An intelligent age of information based self‐energized UAV‐assisted wireless communication system
Authors: Jeganathan Anandpushparaj , Dhayabaran Balaji , Jayakody Dushantha Nalin K. , Don Sanjaya Arunapriya Ranchagodage , Muthuchidambaranathan P. 
Published: October 2023

AbstractInternet‐of‐things is an enabling technology in the fourth‐generation industrial revolution. The freshness of the data sent by a sensor node (SN) is an important parameter in the Internet‐of‐things, unlike the throughput in cellular communications. A relatively new performance metric named age of information (AoI) is used in this paper to quantify the freshness of the data. The SN, located in the transport infrastructure, harvests energy from radio frequency signals transmitted by the FD‐UAV. This is used to transmit real‐time sensor observations to the data sink via FD‐UAV. The SN generates an update after replenishing the battery and transmits it by using the harvested energy. A closed‐form expression for average AoI is derived as a function of time allocated for energy harvesting. The optimal time allocation for energy harvesting that maximizes the freshness of data update is identified. A deep learning technique namely long‐short term memory is used to predict the average AoI. Simulation results demonstrate the usefulness of the performance bounds in terms of the freshness of data updates.
Optimal frequency fault‐tolerant control of virtual synchronous generator based on adaptive dynamic programming with fuzzy critic estimator
Authors: Pan Yanjiang , Wang Tianbiao , Jiang Yixin , Liu Zhen , Hu Xuguang 
Published: October 2023

AbstractWith the popularity of renewable energy sources, fault‐tolerant frequency stability of distributed generation systems has become a major challenge. This paper proposes an optimal frequency fault‐tolerant control method in the distributed generation system, utilizing adaptive dynamic programming combined with fuzzy critic estimation. First, based on the operational state of the system, a non‐linear dynamic model for the virtual synchronous generator is established. Then, considering the occurrence of actuator faults, the fault‐tolerant control problem is formulated as an optimal control problem, where a fault observer is designed to estimate the fault signals. Furthermore, the proposed adaptive dynamic programming method based on fuzzy critic estimation is employed to effectively solve the highly coupled nonlinear Hamilton–Jacobi–Bellman equation and ensure the state convergence of the system with uniform ultimate boundedness. The optimal fault‐tolerant control law ensures a bounded frequency error for the virtual synchronous generator system in the event of faults. Finally, the effectiveness of the optimal control method is verified by two sets of simulations.
Extended‐state‐observer‐based adaptive robust control of a single‐axis hydraulic shaking table
Authors: Wen Jiabao , Zhao Chengcheng , Wang Yong , Shi Zhiguo 
Published: October 2023

AbstractThe shaking table test has been widely recognized as one of the most reliable methods for assessing the dynamic response of structures and systems when exposed to a range of vibrations. Replicating these vibrations, recorded as acceleration signals, necessitates precise controller designs. However, traditional controller designs primarily rely on linear system assumptions, leading to complications in incorporating parametric uncertainty and uncertain non‐linearity. This paper presents a novel approach to the acceleration trajectory control problem of single‐axis hydraulic shaking table systems from a non‐linear perspective. This strategy employs a controller combined with an extended state observer (ESO) and adaptive control, offering a design that more closely reflects real‐world scenarios and requires less parameter adjustment. The ESO estimates the uncertain non‐linearity using the displacement signal, while the parametric uncertainty is tackled through adaptive control. The proposed controller's effectiveness is validated through theoretical proof using Lyapunov analysis. The analysis demonstrates that asymptotic tracking performance is guaranteed when the uncertain non‐linearity is time‐invariant. Moreover, with time‐variant uncertain non‐linearity, the controller can also ensure both prescribed transient tracking performance and final tracking accuracy. Comparative experiment results underscore the superior performance of the proposed controller.
Adaptive RBFNN‐based predictive control for the nanopositioning of an electrostatic MEMS actuator
Authors: Rezvani Nava , Keymasi‐Khalaji Ali 
Published: October 2023

AbstractElectrostatic micro electro mechanical system (MEMS) as an actuator is one of the most widely used actuators in micro dimension systems. Due to the high nonlinear characteristics in the micro actuator's model, nanopositioning has been a challenging problem for researchers. In addition, the system is subject to uncertainties associated with the system's unknown parameters and un‐modelled dynamics. Thus, to overcome these problems and achieve precise positioning a robust non‐linear control method is required. In this research, an optimal voltage control algorithm is initially designed utilizing the nonlinear predictive control approach. The Taylor expansion sequence is used to estimate the final position of the parallel plate actuator. To approximate unknown disturbances, a radial basis function neural network (RBFNN) has been designed. The estimations made were used in updating the control input in the previous step, and the obtained results showed an increase in the robustness of the designed controller. The stability of the closed‐loop system is also analyzed. Finally, a comparison is accomplished between the potential of the proposed controller and that of the feedback linearization and sliding mode controllers. The obtained results indicate better performance and robustness of the suggested controller.
Optimization of iron and steel manufacturing plant considering electricity price tariff and electric arc furnace control
Authors: Lee Seok‐Young , Lee Gyu‐Sub , Moon Seung‐Il , Yoon Yong‐Tae 
Published: October 2023

AbstractThe iron and steel industry, which is a highly energy‐intensive sector, seeks to increase energy efficiency and reduce operating costs by optimizing the distributions of byproduct gases, steam, and electricity throughout the production process. The operating costs of an iron and steel plant typically include the purchase cost of liquefied natural gas fuel, electricity, and penalties for byproduct gas holders. Electricity tariffs have a significant impact on energy costs through two factors: the energy charge, which is related to energy consumption varying with time, and the demand charge, which is proportional to the peak power. In this study, the characteristics of electricity tariffs and multi‐energy systems, specifically for iron and steel plants, are considered. In the proposed method, electric arc furnaces are employed as controllable units to flexibly manage the power load. The optimization model utilized in the plant adopts a mixed‐integer linear programming approach to minimize the overall operating costs. Several case studies were conducted to verify the effectiveness of the proposed methods, and the total costs associated with different cases were compared.
Validation of the AC[La]+EPOCfast Method in
Sprinters and Middle-distance Runners
Authors: Hatauta Shuya , Oki Shota , Nabekura Yoshiharu 
Published: October 2023

AbstractThe anaerobic capacity (AC[La]+EPOCfast) method is of interest
as it can differentiate between the contributions of phosphocreatine (PCr) and
glycolytic energy, assess the anaerobic metabolism during a single effort, and
evaluate various exercise modalities. However, no previous studies have
investigated whether the superiority of the PCr and glycolytic systems can be
assessed in athletes with high anaerobic capacity. This study aimed to compare
the AC[La]+EPOCfast method in seven sprinters (SP) and seven
middle-distance runners (MD). The participants underwent a graded exercise test
and constant-load exercise at 115% ˙VO2max until
exhaustion using a bicycle ergometer. AC[La]+EPOCfast was
calculated as the sum of oxygen equivalents from the phosphagen
(EPCr) and glycolytic (ELa) pathways. This study reveals
that there was no significant difference in AC[La]+EPOCfast
or maximal accumulated oxygen deficit (MAOD) between the two groups. Although
EPCr was not significantly different between groups,
ELa was significantly higher in the SP group than in the MD
group. In conclusion, the AC[La]+EPOCfast method can be used
to evaluate high and low anaerobic capacities. However, further studies on
athletes with high aerobic capacity are required.
Black box problem and African views of trust
Authors: Ewuoso Cornelius 
Published: October 2023

AbstractThis article draws on the thinking about trust in African scholarship to describe the problems black box clinical artificial intelligence (AI) generates in health professional-patient relationships. Notably, under the assumption of a black box problem, the view of trust as inherently relational implies that health professionals cannot explain whether and how a clinical AI incorporates a patient’s values or leverages the same (in its outputs) to honour fiduciary relations. Additionally, the African view of trust as experience-based and accepting responsibility implies that health professionals can neither be held accountable for black box clinical AI outputs that they can hardly understand nor provide material information (concerning what the clinical AI does and why). Finally, given the understanding of trust as a normative concept, health professionals cannot accept patients’ vulnerabilities, and patients cannot give the same. Given that trust will play a vital role in the global acceptance of clinical AI, future studies should research—from other positionalities—how the black box problem will challenge the relationship of trust in the medical context.
Kuratsuki bacteria and sake making
Authors: Nishida Hiromi 
Published: October 2023

ABSTRACT
Kuratsuki bacteria enter during the sake-making process and interact with sake yeast until their growth is attenuated by the ethanol produced by sake yeast. Due to the interaction between kuratsuki bacteria and sake yeast, the metabolism of sake yeast changes, affecting the composition of esters and organic acids and subsequently the flavor and taste of sake. We cultivated kuratsuki bacteria and sake yeast, and performed test making at sake breweries to clarify the interaction among microorganisms in the sake-making process. We aim to propose a sake-making process that controls the flavor and taste of sake by utilizing the functions of kuratsuki bacteria.
SGAE: single-cell gene association entropy for revealing critical states of cell transitions during embryonic development
Authors: Zhong Jiayuan , Han Chongyin , Chen Pei , Liu Rui 
Published: October 2023

Abstract
The critical point or pivotal threshold of cell transition occurs in early embryonic development when cell differentiation culminates in its transition to specific cell fates, at which the cell population undergoes an abrupt and qualitative shift. Revealing such critical points of cell transitions can track cellular heterogeneity and shed light on the molecular mechanisms of cell differentiation. However, precise detection of critical state transitions proves challenging when relying on single-cell RNA sequencing data due to their inherent sparsity, noise, and heterogeneity. In this study, diverging from conventional methods like differential gene analysis or static techniques that emphasize classification of cell types, an innovative computational approach, single-cell gene association entropy (SGAE), is designed for the analysis of single-cell RNA-seq data and utilizes gene association information to reveal critical states of cell transitions. More specifically, through the translation of gene expression data into local SGAE scores, the proposed SGAE can serve as an index to quantitatively assess the resilience and critical properties of genetic regulatory networks, consequently detecting the signal of cell transitions. Analyses of five single-cell datasets for embryonic development demonstrate that the SGAE method achieves better performance in facilitating the characterization of a critical phase transition compared with other existing methods. Moreover, the SGAE value can effectively discriminate cellular heterogeneity over time and performs well in the temporal clustering of cells. Besides, biological functional analysis also indicates the effectiveness of the proposed approach.
Molecular phylogenetics of Oxalis subg. Thamnoxys (Oxalidaceae) reveals artificial arrangements of traditional sections
Authors: Cabral Fernando S , Lima Duane F , Vaio Magdalena , Fiaschi Pedro 
Published: October 2023

Abstract
Oxalis subg. Thamnoxys is a mostly South American group of Oxalis encompassing almost 80 species from tropical habitats that are currently separated into nine sections based on morphology and geographic distributions. In this study, we investigated whether Oxalis subg. Thamnoxys and its sections are monophyletic. DNA sequences of the nrITS, trnL-trnL-trnF, and petA-psbJ from 92 specimens of Oxalis (55 from O. subg. Thamnoxys, 37 from O. subg. Oxalis, and five outgroup taxa) were used to investigate phylogenetic relationships among its nine sections. Nuclear and plastid molecular markers were subjected to maximum likelihood and Bayesian inference analyses individually and in a combined data matrix. Our phylogenetic trees recovered O. subg. Thamnoxys as monophyletic only if O. praetexta, previously included in O. sect. Robustae, is transferred to O. subg. Oxalis. The remaining samples of the subgenus emerged in a clade with full bootstrap and posterior probability support. Within it, O. sect. Holophyllum was the only section that was recovered as monophyletic, whereas the remaining sections were not, either because of sampling a single species of each (O. sect. Foliosae, Hedysaroideae, and Phyllodoxys), to the unexpected placement of O. goyazensis (O. sect. Robustae) in O. sect. Psoraleoideae, or to the sister relationship between O. densifolia (O. sect. Foliosae) with O. pyrenea var. macrochaeta (O. sect. Thamnoxys), suggesting the need of revaluating some specific affinities and updating sectional circumscriptions. This phylogenetic study with an improved sampling of O. subg. Thamnoxys is the first step towards an updated classification of the subgenus and for interpreting both its morphological diversification and biogeographic history in South America.
Verifying and refining early statuses in Alzheimer’s disease progression: a possibility from deep feature comparison
Authors: Liu Mianxin , Cui Liang , Zhao Zixiao , Ren Shuhua , Huang Lin , Guan Yihui , Guo Qihao , Xie Fang , Huang Qi , Shen Dinggang 
Published: October 2023

Abstract
Defining the early status of Alzheimer’s disease is challenging. Theoretically, the statuses in the Alzheimer’s disease continuum are expected to share common features. Here, we explore to verify and refine candidature early statuses of Alzheimer’s disease with features learned from deep learning. We train models on brain functional networks to accurately classify between amnestic and non-amnestic mild cognitive impairments and between healthy controls and mild cognitive impairments. The trained models are applied to Alzheimer’s disease and subjective cognitive decline groups to suggest feature similarities among the statuses and identify informative subpopulations. The amnestic mild cognitive impairment vs non-amnestic mild cognitive impairments classifier believes that 71.8% of Alzheimer’s disease are amnestic mild cognitive impairment. And 73.5% of subjective cognitive declines are labeled as mild cognitive impairments, 88.8% of which are further suggested as “amnestic mild cognitive impairment.” Further multimodal analyses suggest that the amnestic mild cognitive impairment-like Alzheimer’s disease, mild cognitive impairment-like subjective cognitive decline, and amnestic mild cognitive impairment-like subjective cognitive decline exhibit more Alzheimer’s disease -related pathological changes (elaborated β-amyloid depositions, reduced glucose metabolism, and gray matter atrophy) than non-amnestic mild cognitive impairments -like Alzheimer’s disease, healthy control-like subjective cognitive decline, and non-amnestic mild cognitive impairments -like subjective cognitive decline. The test–retest reliability of the subpopulation identification is fair to good in general. The study indicates overall similarity among subjective cognitive decline, amnestic mild cognitive impairment, and Alzheimer’s disease and implies their progression relationships. The results support “deep feature comparison” as a potential beneficial framework to verify and refine early Alzheimer’s disease status.
Mechanisms of pathogenicity and the quest for genetic modifiers of kidney disease in branchiootorenal syndrome
Authors: Sewerin Sebastian , Aurnhammer Charlotte , Skubic Cene , Blagotinšek Cokan Kaja , Jeruc Jera , Rozman Damjana , Pfister Frederick , Dittrich Katalin , Mayer Brigitte , Schönauer Ria , Petzold Friederike , Halbritter Jan 
Published: October 2023

ABSTRACT

Backgound
Branchiootorenal (BOR) syndrome is an autosomal dominant disorder caused by pathogenic EYA1 variants and clinically characterized by auricular malformations with hearing loss, branchial arch anomalies, and congenital anomalies of the kidney and urinary tract. BOR phenotypes are highly variable and heterogenous. While random monoallelic expression is assumed to explain this phenotypic heterogeneity, the potential role of modifier genes has not yet been explored.

Methods
Through thorough phenotyping and exome sequencing, we studied one family with disease presentation in at least four generations in both clinical and genetic terms. Functional investigation of the single associated EYA1 variant c.1698+1G&gt;A included splice site analysis and assessment of EYA1 distribution in patient-derived fibroblasts. The candidate modifier gene CYP51A1 was evaluated by histopathological analysis of murine Cyp51+/− and Cyp51−/− kidneys. As the gene encodes the enzyme lanosterol 14α-demethylase, we assessed sterol intermediates in patient blood samples as well.

Results
The EYA1 variant c.1698+1G&gt;A resulted in functional deletion of the EYA domain by exon skipping. The EYA domain mediates protein-protein interactions between EYA1 and co-regulators of transcription. EYA1 abundance was reduced in the nuclear compartment of patient-derived fibroblasts, suggesting impaired nuclear translocation of these protein complexes. Within the affected family, renal phenotypes spanned from normal kidney function in adulthood to chronic kidney failure in infancy. By analyzing exome sequencing data for variants that potentially play roles as genetic modifiers, we identified a canonical splice site alteration in CYP51A1 as the strongest candidate variant.

Conclusion
In this study, we demonstrate pathogenicity of EYA1 c.1698+1G&gt;A, propose a mechanism for dysfunction of mutant EYA1, and conjecture CYP51A1 as a potential genetic modifier of renal involvement in BOR syndrome.