bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aging‐dependent temporal regulation of MIR156 epigenetic silencing by CiLDL1 and CiNF‐YB8 in chrysanthemum
Authors: Gao Xuekai , Liu Lei , Wang Tianle , Jiang Chuyan , Xue Yujin , Sun Yahui , Gu Zhaoyu , Xu Yanjie , Jiang Cai‐Zhong , Gao Junping , Hong Bo , Ma Chao 
Published: January 2025

Summary
Temporal decline in microRNA miR156 expression is crucial for the transition to, and maintenance of, the adult phase and flowering competence in flowering plants. However, the molecular mechanisms underlying the temporal regulation of miR156 reduction remain largely unknown.
Here, we investigated the epigenetic mechanism regulating the temporal silencing of cin‐MIR156 in wild chrysanthemum (Chrysanthemum indicum), focusing on the role of the lysine‐specific demethylase CiLDL1 and the nuclear factor Y complex.
CiLDL1 and CiNF‐YB8 interact with the classical histone‐like fold domain (HFD) of CiNF‐YC1 and CiNF‐YA3, which form distinct heterotrimers binding to the ‘CCAAT’ box in the promoter region of cin‐MIR156ab. CiLDL1 and CiNF‐YB8 have opposing effects on cin‐MIR156ab expression, with influencing histone 3 lysine 4 demethylation (H3K4me2) levels at the cin‐MIR156ab locus. During aging, decreased CiNF‐YB8 expression leads to a quantitative switch from the CiNF‐YA3–CiNF‐YC1–CiNF‐YB8 heterotrimer to the CiNF‐YA3–CiNF‐YC1–CiLDL1 heterotrimer, which reduces H3K4me2 levels at the cin‐MIR156ab locus, thus temporal silencing its expression.
Our results thus reveal that the dynamic regulatory shift between CiLDL1 and CiNF‐YB8 ensures proper aging‐dependent flowering in chrysanthemum.
Translational State Power: Managing Interpreters to Make Asylum Seekers Talk in the French Asylum Bureaucracy
Authors: Maréchal Maxime 
Published: January 2025

ABSTRACTThis article highlights the translational state power at work in the adjudication of asylum, to analyse the conditions in which asylum officials hear asylum seekers' narratives thanks to the intervention of subordinated interpreters. The provision of language interpreting is shaped by managerial objectives of bureaucratic efficiency which creates the illusion of a transparent translation, both semantically and politically, to ground the legitimacy of the procedure. By analysing the management of interpreters and their practical margins, this contribution shows that language interpreting is a major stake in the implementation of asylum policies and constitutes a crucial dimension of the power of the state over asylum seekers.
Perceptions of Poverty and Policy Preferences: The Contribution of Q Methodology
Authors: Sinclair Stephen , McHugh Neil , McKendrick John H. , Lightbody Ruth , Robertson Laura , McHardy Fiona 
Published: January 2025

ABSTRACTThe nature, causes and consequences of poverty have been debated for many years and remain controversial. However, some degree of consensus is a pre‐requisite for feasible, sustainable and effective policy responses to poverty. Research methods which can improve understanding of public attitudes towards poverty and identify potential areas of consensus are particularly valuable. Q methodology is a research tool which has the potential to identify points of consensus and contention in relation to poverty. This article introduces the main features of Q and illustrates its potential value by outlining how it was applied to inform the policy recommendations of a Poverty Commission in a city in Britain. The project identified a number of significant points of consensus and controversy in participants’ perceptions of the consequences of poverty and preferences regarding responses to it. These findings are related to ideas about how the poverty discourse can be framed to cultivate a more supportive narrative of how poverty is understood and addressed.
Long‐term no‐tillage increases soil organic matter and cation exchange capacity, but reduces P and K, in irrigated rice
Authors: Carlos Filipe Selau , Marcolin Elio , Kunde Roberta Jeske , Weinert Cristiano , Pasa Ezequiel Helbig , Schaffer Naihana , de Sousa Rogério Oliveira , dos Reis Robson Bosa , Andreazza Robson , de Oliveira Jakeline Rosa , Camargo Flávio Anastácio de Oliveira 
Published: January 2025

AbstractBrazil is one of the main countries in the adoption of no tillage (NT) in highlands, however, in lowlands, under irrigated rice cultivation, the adoption of this important soil management is incipient (<5%). Thus, the objective of this work was to evaluate the dynamics of soil chemical attributes under long‐term NT and rice cultivation. Throughout the field trial, irrigated rice monoculture prevailed continuously in succession with ryegrass prevailed for 23 years, under the adoption of different management systems, conventional tillage (CT), pre‐germinated (PG) and NT in an soil Albaqualf (soil under hydromorphic condition) under a randomized block design with three replications. Active acidity, potential acidity, soil organic matter, cation exchange capacity (CEC), phosphorus, potassium, calcium and magnesium were evaluated in the stratified profile at depths: superficial (0–10 cm), intermediate (10–20 cm) and deep (20–40 cm). An increase in the potential acidity of the soil in the NT was observed in the surface layer, an increase in organic matter and in the exchangeable forms of calcium and magnesium. However, there was a reduction in the availability of phosphorus by 20% and potassium by 32% in the topsoil in the NT compared with PG and NT. NT is a soil conservation system that increases organic matter and CEC levels. However, strategies aimed at improving the availability of phosphorus and potassium under NT in paddy fields must be used not to reduce the productive potential of rice grains.
Mapping
C. difficile
TcdB interactions with host cell-surface and intracellular factors using proximity-dependent biotinylation labeling
Authors: Ward Jennifer S. , Schreiber Karl J. , Tam John , Youn Ji-Young , Melnyk Roman A. 
Published: January 2025

ABSTRACT

Many bacterial toxins exert their cytotoxic effects by enzymatically inactivating one or more cytosolic targets in host cells. To reach their intracellular targets, these toxins possess functional domains or subdomains that interact with and exploit various host factors and biological processes. Despite great progress in identifying many of the key host factors involved in the uptake of toxins, significant knowledge gaps remain as to how partially characterized and newly discovered microbial toxins exploit host factors or processes to intoxicate target cells. Proximity-dependent biotinylation (e.g., BioID) is a powerful method to identify nearby host factors in living cells, offering the potential to identify host targets of microbial toxins. Here, we used BioID to interrogate proximal interactors of the multi-domain
Clostridioides difficile
TcdB toxin. Expressed fusions of TurboID to different fragments of TcdB identified several high-confidence proteins in the cytosol, including members of the Rho GTPase signaling network and the actin cytoskeletal network. Additionally, we developed an extracellular proximity labeling method using recombinant TurboID-toxin chimeras, which uncovered a limited number of cell-surface targets including LRP1, which was previously identified as a cell-surface receptor of TcdB. Our work reveals surface receptors and intracellular components exploited by bacterial toxins, highlighting key vulnerabilities in host cells.

IMPORTANCE
Bacterial toxins are the causative agents of many human diseases. Further characterizing the intoxication mechanisms of these proteins is important for the development of vaccines and treatments for toxin-mediated disease. Proximity-dependent biotinylation approaches offer an orthogonal approach to complement genetic screens. Here, we evaluate the potential of this method to identify host-toxin interactions on the cell surface and in the cytosol, where the toxin modifies essential host targets. Critically, we have highlighted several limitations of this method as applied to protein toxins, which are important for researchers to weigh when considering this technique for exotoxin studies.
Different Composite Veneer Surface Preparations for Metal Orthodontic Bracket Bonding: An In Vitro Study
Authors: Omidkhoda Maryam , Hosseini Rivandi Maryam , Mohammadipour Hamideh Sadat , Dehghani Mahboobe 
Published: January 2025

Objective: This research aimed to assess the shear bond strength (SBS) of metal brackets bonded to composite veneers using different surface preparations.Methods: One‐hundred composite disks were divided into 10 different groups whereby each group combines a surface preparation (roughening or no roughening), etching agent (37% phosphoric or 9.5% hydrofluoric acid), adhesive protocol (self‐etch or total‐etch), and bonding agent (with or without G‐Premio Bond). Orthodontic metal brackets were bonded to prepared composite surfaces by Transbond XT resin and light‐cured. The prepared samples were incubated at 37˚C for 24 h and underwent thermocycling. A universal testing machine was loaded until the failure moment to assess SBS. Adhesive remnant index (ARI) was used to classify the failure sites between the composite surface and bracket base. Tukey, Fisher’s exact, and chi‐square tests were used for statistical analyses. Statistical significance level was 0.05.Results: Surface roughening and the type of material used for surface preparation significantly affected bond strength (p  < 0.0001). There was no significant difference in bond strength between phosphoric acid and hydrofluoric acid (p  > 0.05). The highest bond strength was observed in the group with roughening + total‐etch with phosphoric acid + G‐Premio Bond (10.24 ± 2.99 MPa). The lowest bond strength was found in the group without roughening, etched with phosphoric acid (1.47 ± 1.06 MPa). In the groups without roughening, ARI scores of 0 and 1 were found, while in the groups with roughening, ARI scores of 0, 1, and 4 were observed.Conclusions: The SBS with G‐Premio Bond is high with ARI score 4 which may pose a risk of damage to the veneers during debonding. Therefore, surface preparation of the veneers that result in lesser bond strength should be used unless in patients with frequent bracket breakages.
The Cost of Randomness in Evolutionary Algorithms: Crossover Can Save Random Bits
Authors: Kneissl Carlo , Sudholt Dirk 
Published: January 2025

Abstract
Evolutionary algorithms make countless random decisions during selection, mutation and crossover operations. These random decisions require a steady stream of random numbers. We analyze the expected number of random bits used throughout a run of an evolutionary algorithm and refer to this as the cost of randomness. We give general bounds on the cost of randomness for mutation-based evolutionary algorithms using 1-bit flips or standard mutations using either a naive or a common, more efficient implementation that uses Θ(logn) random bits per mutation.
Uniform crossover is a potentially wasteful operator as the number of random bits used equals the Hamming distance of the two parents, which can be up to n. However, we show for a (2+1) Genetic Algorithm that is known to optimize the test function ONEMAX in roughly (e/2)nlnn expected evaluations, twice as fast as the fastest mutation-based evolutionary algorithms, that the total cost of randomness during all crossover operations on ONEMAX is only Θ(n). A more pronounced effect is shown for the common test function JUMPk, where there is an asymptotic decrease both in the number of evaluations and in the cost of randomness. Consequently, the use of crossover can reduce the cost of randomness below that of the fastest evolutionary algorithms that only use standard mutations.
Implications of the Revised Draft EU Accession Agreement for the echr
Authors: Lock Tobias 
Published: January 2025

Abstract
This article explores the implications of the EU’s accession to the echr from the echr perspective based on the revised Draft Accession Agreement (daa 2023). The article analyses key procedural innovations in the daa 2023, notably how the co-respondent mechanism, the prior involvement of the cjeu, and the daa’s solutions for advisory opinion requests and for dealing with the EU law concept of mutual trust would work. It exposes the EU’s new role as a gatekeeper in relation to certain procedural questions. The article further contrasts the position of EU member states and non-EU member states post-accession by pointing out potential inconsistencies and assesses proposed solutions in light of their effectiveness and workability. The article suggests that, despite the considerable concessions made to the EU, EU accession to the echr would nonetheless result in a strengthening of the echr system and is thus worth the effort and compromises.
Using a mobile app comprising neurofeedback-based meditation and binaural beat music to treat PTSD symptoms: A qualitative analysis
Authors: Choi Yun-Jung , Lee Na-Rae 
Published: January 2025

Background There is a significant need for an effective and convenient symptom management and healing program for people experiencing post-traumatic stress disorder (PTSD) symptoms; however, research on this topic is lacking. Objective This study explored the experiences of individuals with PTSD who used a mobile traumatic stress management app with neurofeedback-based meditation and binaural beat music to promote their psychological recovery. Methods This study used a qualitative research method to explore the experiences of neurofeedback-based meditation and binaural beat music using a mobile traumatic stress management app to promote the psychological recovery of people experiencing chronic traumatic stress. The research question was “What is the experience of neurofeedback-based meditation and binaural beat music using the mobile traumatic stress management app?” Results The thematic content analysis of in-depth interviews held with nine participants derived 26 codes, eight sub-categories, three categories, and one theme (“Holding hope for healing from agony of mind and body”). Conclusion Neurofeedback-based meditation and binaural beat music using a mobile app helped people with PTSD symptoms to truly understand the symptoms caused by traumatic stress. Continued use of this program provides the participants with physical and psychological stability; it instills them with faith and hope.
Knowledge Driven Machine Learning Towards Interpretable Intelligent Prognostics and Health Management: Review and Case Study
Authors: Yan Ruqiang , Zhou Zheng , Shang Zuogang , Wang Zhiying , Hu Chenye , Li Yasong , Yang Yuangui , Chen Xuefeng , Gao Robert X. 
Published: January 2025

Abstract
Despite significant progress in the Prognostics and Health Management (PHM) domain using pattern learning systems from data, machine learning (ML) still faces challenges related to limited generalization and weak interpretability. A promising approach to overcoming these challenges is to embed domain knowledge into the ML pipeline, enhancing the model with additional pattern information. In this paper, we review the latest developments in PHM, encapsulated under the concept of Knowledge Driven Machine Learning (KDML). We propose a hierarchical framework to define KDML in PHM, which includes scientific paradigms, knowledge sources, knowledge representations, and knowledge embedding methods. Using this framework, we examine current research to demonstrate how various forms of knowledge can be integrated into the ML pipeline and provide roadmap to specific usage. Furthermore, we present several case studies that illustrate specific implementations of KDML in the PHM domain, including inductive experience, physical model, and signal processing. We analyze the improvements in generalization capability and interpretability that KDML can achieve. Finally, we discuss the challenges, potential applications, and usage recommendations of KDML in PHM, with a particular focus on the critical need for interpretability to ensure trustworthy deployment of artificial intelligence in PHM.
Myoelectric pattern recognition with virtual reality and serious gaming improves upper limb function in chronic stroke: a single case experimental design study
Authors: Munoz-Novoa Maria , Kristoffersen Morten B. , Sunnerhagen Katharina S. , Naber Autumn , Ortiz-Catalan Max , Alt Murphy Margit 
Published: January 2025

Abstract

Background
Myoelectric pattern recognition (MPR) combines multiple surface electromyography channels with a machine learning algorithm to decode motor intention with an aim to enhance upper limb function after stroke. This study aims to determine the feasibility and preliminary effectiveness of a novel intervention combining MPR, virtual reality (VR), and serious gaming to improve upper limb function in people with chronic stroke.

Methods
In this single case experimental A-B-A design study, six individuals with chronic stroke and moderate to severe upper limb impairment completed 18, 2 h sessions, 3 times a week. Repeated assessments were performed using the Fugl-Meyer Assessment of Upper Extremity (FMA-UE), Action Research Arm Test (ARAT), grip strength, and kinematics of the drinking task at baseline, during, and post intervention. The results were analyzed by using visual analysis and Tau-U statistics.

Results
All participants improved upper limb function assessed by FMA-UE (Tau-U 0.72–1.0), and five out of six improved beyond the minimal clinical important difference (MCID). Four participants improved ARAT and grip strength scores (Tau-U 0.84–1.0), with one reaching the MCID for ARAT. Three out of four participants in the kinematic analysis achieved improvements beyond the MCID in movement time and smoothness, two with a Tau-U > 0.90, and two participants improved trunk displacement beyond the MCID (Tau-U 0.68). Most participants showed some deterioration in the follow-up phase.

Conclusions
MPR combined with VR and serious gaming is a feasible and promising intervention for improving upper limb function in people with chronic stroke.

Trial Registration: ClinicalTrials.gov, reference number NCT04154371.
Impact of dumpsite compost on heavy metal accumulation in some cultivated plants
Authors: Abd-Elhalim Basma T. , Gideon Mathew , Anton Kuzmin , Boyi Mercy O. 
Published: January 2025

Abstract
The study examines the concentrations of heavy metals in agricultural soil, compost from landfills, maize plants, and spinach crops. The results show that compost from landfills had levels exceeding EU requirements for Cd, Cu, Ni, Pb, and Zn. However, agricultural soil contained trace amounts of heavy metals. The order of metal absorption by plants was Cd > Pb > Cu > Ni > Cr > Zn > Fe > Mn. This highlights potential health risks associated with consuming crops grown in compost or soil tainted with heavy metals.
Sperm-borne small non-coding RNAs: potential functions and mechanisms as epigenetic carriers
Authors: Naveed Muhammad , Shen Zhaokang , Bao Jianqiang 
Published: January 2025

Abstract
Over the past two decades, the study of sperm-borne small non-coding RNAs (sncRNAs) has garnered substantial growth. Once considered mere byproducts during germ cell maturation, these sncRNAs have now been recognized as crucial carriers of epigenetic information, playing a significant role in transmitting acquired traits from paternal to offspring, particularly under environmental influences. A growing body of evidence highlights the pivotal role of these sncRNAs in facilitating epigenetic inheritance across generations. However, the exact mechanisms through which these paternally supplied epigenetic carriers operate remain unclear and are under hot debate. This concise review presents the most extensive evidence to date on environmentally-responsive sperm-borne sncRNAs, encompassing brief summary of their origin, dynamics, compartmentalization, characteristics, as well as in-depth elaboration of their functional roles in epigenetic and transgenerational inheritance. Additionally, the review delves into the potential mechanisms by which sperm-delivered sncRNAs may acquire and transmit paternally acquired traits to offspring, modulating zygotic gene expression and influencing early embryonic development.
Biomarkers of sepsis-induced coagulopathy: diagnostic insights and potential therapeutic implications
Authors: Curtiaud Anaïs , Iba Toshiaki , Angles-Cano Eduardo , Meziani Ferhat , Helms Julie 
Published: January 2025

Abstract
Diagnosing coagulopathy in septic patients remains challenging in intensive care. Disseminated intravascular coagulation (DIC) indeed presents with complex pathophysiology, complicating timely diagnosis. Epidemiological data indicate a significant prevalence of DIC in septic patients, with mortality rates up to 60%. Despite advances, current biomarker-based diagnostic tools often fail to provide early and accurate detection. This review evaluates the utility and limitations of traditional and emerging biomarkers for diagnosing sepsis-induced coagulopathy (SIC) and DIC. We also assess the effectiveness of anticoagulant therapy guided by biomarker-based diagnostic criteria.
Actionable Gene Alterations Identified in Patients With Malignant Melanoma by Targeted Sequencing in Japan
Authors: Noguchi Takuro , Ariga Shin , Moku Rika , Kikuchi Junko , Amano Toraji , Maeda Takuya , Ishikawa Kosuke , Maeda Taku , Shiiya Akihiko , Goda Tomohiro , Ohhara Yoshihito , Hagio Kanako , Saito Yusuke , Hatanaka Kanako C. , Hatanaka Yutaka , Taguchi Jun , Takeuchi Satoshi , Shimizu Yasushi , Kinoshita Ichiro 
Published: January 2025

PURPOSE
Precision medicine plays an important role in the treatment of patients with advanced melanoma. Despite its high incidence in White patients, advanced melanoma is rare in Asian countries, hampering prospective clinical trials targeting the Asian population. This retrospective study aimed to elucidate the real-world molecular diagnoses and outcomes of Japanese patients with melanoma using comprehensive genome profiling (CGP).

MATERIALS AND METHODS
Patients with melanoma who completed standard anticancer medical treatments (including those expected to complete the treatments) underwent CGP, which is covered by the National Health Insurance. We analyzed the results and clinical annotations of 569 patients registered before August 2023 in a national database.

RESULTS

Skin, mucosal, and uveal melanomas accounted for 64%, 28%, and 7% of cases, respectively. Patients with
BRAF
,
NRAS
,
NF1
, and
KIT
variants represented 25%, 20%, 17%, and 17%, respectively. Eighty-two percent of
BRAF
, 97% of
NRAS
, 69% of
NF1
, and 54% of
KIT
were actionable alterations (ie,
BRAF
classes I, II, and III,
NRAS
Q61, G12, G13,
NF1
loss-of-function,
KIT
gain-of-function variants).
BRAF
V600E/K variants occurred in 22% of skin and 2% of mucosal melanomas, but not in uveal melanomas. The mean tumor mutation burden in cutaneous melanomas was 4.2 variants/Mb. Patients previously treated with BRAF-targeted therapy harbored amplifications of
BRAF
and cell cycle genes more frequently than therapy-naive patients. Thirty-six patients (6.3%) were treated following the molecular tumor board (MTB) recommendations.

CONCLUSION

Actionable gene alterations in
BRAF
,
NRAS
,
NF1
, and
KIT
are common in Japanese patients with melanoma. However, few patients were treated according to the MTB recommendations, suggesting that there is an unmet need to increase accessibility to gene-matched clinical trials in Japan.