bluuebunny/crossref_metadata_2025_split huggingface dataset:
Iron homeostasis in the annual and perennial stem zones of Arabis alpina
Authors: Sergeeva A. , Mai H.‐J. , Bauer P. 
Published: February 2025

Abstract
Plants store nutrients, including the micronutrient iron, in bioavailable forms to support growth in subsequent seasons. The perennial lifestyle is preponderant in nature. Arabis alpina is a perennial model organism with a particular architecture of branches having proximal perennial (PZ) and distal annual (AZ) stem zones with distinct anatomy and physiology. PZ undergoes secondary growth and stores carbon‐rich macromolecules. Here, we investigated iron homeostasis in PZ versus AZ.
We localized iron in stem internodes of PZ and AZ using Perls staining and ferritin immunodetection in the wild‐type Pajares (Paj) and perpetual flowering 1 mutant. We mined transcriptome data of the developing PZ and AZ.
Iron accumulated at various development stages in PZ and AZ. Iron levels in PZ were ca. two‐fold higher than in AZ, irrespective of flowering. Iron was predominantly located within plastid‐bound ferritin. Gene expression patterns supported the significance of ferritin and demonstrated enrichment of transcripts related to iron homeostasis within stems. Distinct patterns of expression among iron homeostasis genes were observed in relation to iron content in PZ and AZ, indicating tissue‐specific regulatory mechanisms governing iron accumulation.
Secondary growth in PZ plays a role in iron storage in the perennial A. alpina, while AZ may transiently store iron for seed production. Future research will address different iron homeostasis signalling pathways in AZ and PZ.
Rice RuBisCO activase promotes the dark‐induced leaf senescence by enhancing the degradation of filamentation temperature‐sensitive H
Authors: Zhang Yanli , Dong Guojun , Wu Xiaoyue , Chen Fei , Ruan Banpu , Jiang Yaohuang , Zhang Ying , Liu Lu , Yuan Yao‐Wu , Wu Limin , Wei Jian , Qian Qian , Yu Yanchun 
Published: February 2025

SUMMARYLeaf senescence is a complex process that is triggered by many developmental and environmental factors. However, the mechanisms regulating leaf senescence remain unclear. Here, we revealed that rice ribulose‐1,5‐bisphosphate carboxylase/oxygenase activase (RCA) promotes the onset of basal dark‐induced senescence. RCA was mainly expressed in the leaves, and its expression level quickly declined under dark conditions. Furthermore, rca mutant plants presented a prolonged leaf longevity phenotype in the dark, whereas overexpression of the large isoform of RCA (RCAL), not small isoform (RCAS), in rice and Arabidopsis accelerated leaf senescence. Filamentation temperature‐sensitive H (OsFtsH1), a zinc metalloprotease, interacts with RCAL and RCAS and presents a higher binding efficiency to RCAL than RCAS in darkness. Furthermore, we found that RCAL promotes 26S proteasome‐mediated degradation of OsFtsH1 protein, which can be inhibited by protease inhibitor MG132. Consequently, OsFtsH1 loss‐of‐function mutants exhibit accelerated leaf senescence, whereas OsFtsH1‐overexpressing plants display delayed senescence. Collectively, our findings highlight the significant role of RCAL isoform in regulating leaf senescence under dark conditions, particularly through enhancing the degradation of OsFtsH1.
Hydrogen sulfide interferes with ethylene biosynthesis and signaling pathway in tomato by the mediation of SlERF.D2 persulfidation
Authors: Sun Ying , Zhang Min , Geng Meihui , Geng Zhikun , Lu Zixu , Liu Nannan , Liu Zhanmin , Zeng Dexin , Yao Gaifang , Hu Kangdi , Zhang Hua 
Published: February 2025

SUMMARYHydrogen sulfide (H2S), as a signaling molecule, is found to delay fruit ripening and senescence by antagonizing the biosynthesis and signaling of ethylene, whereas the mechanism remains unclear. In the current work, exogenous H2S fumigation could alleviate tomato fruit ripening and an ethylene response factor SlERF.D2 was found to be persulfidated at Cys35 by mass spectrometry analysis. Meanwhile, ethylene biosynthesis related genes SlACS1 and SlACO3 were significantly downregulated at gene expression level in H2S‐treated fruit. By CRISPR/Cas9 and gene overexpression, we showed that overexpression of SlERF.D2 promoted fruit ripening by accelerating chlorophyll degradation and carotenoid accumulation and upregulating the expression of ripening related genes SlPAO, SlPPH, SlSGR1, SlACS1, SlACS2, SlACS4, SlEIN2, SlACO1, and SlACO3, while the mutation of slerf.d2 delayed fruit ripening. Additionally, slerf.d2 mutant showed delayed ethylene production during tomato fruit ripening. Moreover, SlERF.D2 was found to interact with the kinase SlMAPK4 and was phosphorylated at Ser42 by yeast two‐hybrid screening, pull down and LC–MS/MS. By cis‐element analysis, electrophoretic mobility shift assay and dual‐luciferase assay, SlERF.D2 could activate the transcription of the ethylene pathway‐associated gene SlACO3 and SlEIN2. Besides, we provided evidence that SlERF.D2 persulfidation weakened the transcriptional activity of SlERF.D2 on the target gene SlACO3 and SlEIN2. In contrast, SlMAPK4‐mediated phosphorylation enhanced SlERF.D2's transcriptional activation activity on SlACO3 and SlEIN2. Therefore, the present research provides insights into the mechanism of H2S in antagonizing the biosynthesis and signaling transduction of ethylene and reveals the importance of SlERF.D2 persulfidation and phosphorylation in dynamically regulating tomato fruit ripening.
Nitrate activates an MKK3‐dependent MAPK module via NLP transcription factors in Arabidopsis
Authors: Schenk Sebastian T. , Brehaut Virginie , Chardin Camille , Boudsocq Marie , Marmagne Anne , Colcombet Jean , Krapp Anne 
Published: February 2025

SUMMARYPlant responses to nutrient availability are critical for plant development and yield. Nitrate, the major form of nitrogen in most soils, serves as both a nutrient and signaling molecule. Nitrate itself triggers rapid, major changes in gene expression, especially via nodule inception (NIN)‐like protein (NLP) transcription factors, and stimulates protein phosphorylation. Mitogen‐activated protein kinase (MAPK)‐related genes are among the early nitrate‐responsive genes; however, little is known about their roles in nitrate signaling pathways. Here, we show that nitrate resupply to nitrogen‐depleted Arabidopsis (Arabidopsis thaliana) plants triggers, within minutes, an MAPK cascade that requires NLP‐dependent transcriptional induction of mitogen‐activated protein kinase kinase kinase 13 (MAP3K13) and MAP3K14 and that the MAPK cascade is composed of MKK3 and likely C‐clade MAPKs (MPK1/2/7/14). Importantly, nitrate reductase‐deficient mutants exhibited nitrate‐induced MPK7 activities comparable to those observed in wild‐type plants, indicating that nitrate itself is the signal that stimulates the cascade. We show that the modified expression of MAP3K13 and MAP3K14 affects nitrate‐stimulated BT2 expression and modulates plant responses to nitrogen availability, such as nitrate uptake and senescence. Our finding that an MAPK cascade involving MAP3K13 and MAP3K14 functions in the complex regulatory network governing responses to nitrate availability will guide future strategies to optimize plant responses to nitrogen fertilization and nitrogen use efficiency.
Chromosome engineering points to the cis‐acting mechanism of chromosome arm‐specific telomere length setting and robustness of plant phenotype, chromatin structure and gene expression
Authors: Helia Ondřej , Matúšová Barbora , Havlová Kateřina , Hýsková Anna , Lyčka Martin , Beying Natalja , Puchta Holger , Fajkus Jiří , Fojtová Miloslava 
Published: February 2025

SUMMARYThe study investigates the impact of targeted chromosome engineering on telomere dynamics, chromatin structure, gene expression, and phenotypic stability in Arabidopsis thaliana. Using precise CRISPR/Cas‐based engineering, reciprocal translocations of chromosome arms were introduced between non‐homologous chromosomes. The subsequent homozygous generations of plants were assessed for phenotype, transcriptomic changes and chromatin modifications near translocation breakpoints, and telomere length maintenance. Phenotypically, translocated lines were indistinguishable from wild‐type plants, as confirmed through morphological assessments and principal component analysis. Gene expression profiling detected minimal differential expression, with affected genes dispersed across the genome, indicating negligible transcriptional impact. Similarly, ChIPseq analysis showed no substantial alterations in the enrichment of key histone marks (H3K27me3, H3K4me1, H3K56ac) near junction sites or across the genome. Finally, bulk and arm‐specific telomere lengths remained stable across multiple generations, except for minor variations in one translocation line. These findings highlight the remarkable genomic and phenotypic robustness of A. thaliana despite large‐scale chromosomal rearrangements. The study offers insights into the cis‐acting mechanisms underlying chromosome arm‐specific telomere length setting and establishes the feasibility of chromosome engineering for studies of plant genome evolution and crop improvement strategies.
Hybrid Physics-Infused 1 Dimensional-Convolutional Neural Network (1D-CNN) based Ensemble Learning Framework for Diesel Engine Fault Diagnostics
Authors: Singh Shubhendu Kumar , Khawale Raj Pradip , Hazarika Subhashis , Rai Rahul 
Published: February 2025

Abstract
Due to their high thermal efficiency and long functional life, diesel engines have become ubiquitous in automobiles. Diesel engines are vulnerable to component failure and sensor faults. New cognitive fault diagnosis algorithms are crucial for the safe operation of equipment. Conventional model-based approaches are limited in their capabilities owing to the approximations made during the development of these models. In comparison, the efficacy of most of the data-driven approaches depends on the quantity of data. Additionally, the existing data-driven algorithms do not consider the system's physics and are susceptible to overfitting issues. To address the aforementioned issues, we propose an end-to-end autonomous hybrid physics-infused 1D CNN-based ensemble learning framework combining a low-fidelity physics-based engine model, Auto Encoder (AE), 1D CNNs (Convolutional Neural Networks), and a Multi-Layer Perceptron (MLP) for fault diagnosis. The system used to demonstrate the capabilities of the devised model is a 7.6 L, 6-cylinder, 4-stroke diesel engine. The physics model guarantees that the estimations produced by the framework conform to the engine's actual behavior, and the ensemble deep learning module overcomes the overfitting issue. Empirical results show that the framework is efficient and reliable against data from a real engine setup under various operating conditions, such as changing injection duration, varying injection pressure, and engine speed. Besides, the framework is tested against noisy data, reaffirming the model's robustness when subjected to actual working conditions where acquired noise is a norm.
FORECASTING THE RANGE OF POSSIBLE HUMAN HAND MOVEMENT IN CONSUMER ELECTRONICS DISASSEMBLY USING MACHINE LEARNING
Authors: Liao Hao-yu , Chen Yuhao , Hu Boyi , Liang Xiao , Behdad Sara 
Published: February 2025

Abstract
Robotic technology can benefit disassembly operations by reducing human operators' workload and assisting them with handling hazardous materials. Safety consideration and prediction of human movement are priorities in close collaboration between humans and robots. The point-by-point forecasting of human hand motion, which forecasts one point at each time, does not provide enough information on human movement due to errors between the actual movement and predicted value. This study provides a range of possible hand movements to increase safety. It applies three machine learning techniques, including Long Short-Term Memory (LSTM), Gated Recurrent Unit (GRU), and Bayesian Neural Network (BNN) combined with Bagging and Monte Carlo Dropout (MCD), namely LSTM-Bagging, GRU-Bagging, and BNN-MCD to predict the possible movement range. The study uses an Inertial Measurement Units (IMU) dataset collected from the disassembly of desktop computers by several participants to show the application of the proposed method.
Establishment and characterization of persistent
Pseudomonas aeruginosa
infections in air–liquid interface cultures of human airway epithelial cells
Authors: Bouheraoua Safaa , Cleeves Sven , Preusse Matthias , Müsken Mathias , Braubach Peter , Fuchs Maximilian , Falk Christine , Sewald Katherina , Häussler Susanne 
Published: February 2025

ABSTRACT

Bacteria exhibit distinct behaviors in laboratory settings compared to infection environments. The presence of host cells induces changes in bacterial activity, while pathogens trigger immune responses that shape the microenvironment. Studying infection dynamics by microscopy, cytokine screening, and dual RNA sequencing in an air–liquid interface model, we found that prolonged
Pseudomonas aeruginosa
colonization of airway epithelium led to a pro-inflammatory response, consistent across
P. aeruginosa
strains, despite differences in the dynamics of this response. Concurrently,
P. aeruginosa
formed non-attached aggregates on the apical side of the cell layer and upregulated genes involved in biofilm formation and virulence. Notably, there was remarkable resemblance between the
P. aeruginosa
transcriptional profile in our model and that previously reported upon host cell contact. Developing a platform that replicates host microenvironments is vital not only for gaining deeper insights into the interplay between host and pathogen but also for evaluating therapeutic strategies in conditions that closely mirror clinical environments.
Gene regulatory network resource aids in predicting trans-acting regulators of biosynthetic gene clusters in
Aspergillus fumigatus
Authors: Seo Hye-won , Bok Jin Woo , Keller Nancy P. 
Published: February 2025

ABSTRACT

The field of secondary metabolism has greatly benefitted from computational advances in recent years. This has been particularly true for fungal natural product studies. Strides in genome mining have led to the identification of an extraordinary number of secondary metabolite biosynthetic gene clusters (BGCs) across the fungal Kingdom and metabologenomic platforms can group BGCs into gene cluster families and link them to initial chemical structures. Missing are computational applications focused on identifying BGC regulatory networks. Here, we applied the new online gene regulatory network resource, GRAsp (
G
ene
R
egulation of

Asp
ergillus fumigatus

), to identify unknown and unpredictable BGC trans-acting transcriptional/metabolite production modules. GRAsp correctly predicted a two-component regulatory module composed of the transcription factors (TFs), RogA (
r
egulation
o
f
g
liotoxin) and HsfA, which negatively regulate the gliotoxin BGC and are also involved in gliotoxin self-protection. RogA functions through the repression of
gliZ,
the pathway-specific gliotoxin TF, and HsfA functions by activating
rogA
expression. Furthermore, GRAsp identified TFs that regulate the production of two BGCs lacking pathway-specific TFs, the helvolic acid and fumitremorgin BGCs, respectively. Finally, the known TF, NsdD, was predicted and found to regulate the hexadehydroastechrome BGC. These advances highlight the power of inference algorithms to uncover unpredictable networks in specialized metabolite synthesis.

IMPORTANCE

Toxic secondary metabolites are virulence factors of the opportunistic fungal pathogen
Aspergillus fumigatus,
yet the transcriptional networks regulating secondary metabolite production remain elusive. Uncovering novel regulators without any prior information is challenging. Computational programs have gained prominence in the field of secondary metabolite research due to their accuracy and ability to handle vast amounts of data, including DNA, RNA, and protein data. In this study, a newly developed online computer platform, Gene Regulation of
A. fumigatus
, was used to identify five regulators involved in the production of several
A. fumigatus
toxins, including gliotoxin, helvolic acid, fumitremorgin, and hexadehydroastechrome. This work illustrates the potential for discovering new trans-acting regulators and mechanisms of secondary metabolite regulation through the examination of computational gene regulatory networks.
Rapid and sensitive isolation of
Campylobacter jejuni
using immunomagnetic separation from patient specimens exposed to oxygen
Authors: Kim So Yeon , Yun Young-Sun , Lee Kwang-Jun , Kim Jonghyun 
Published: February 2025

ABSTRACT

This study describes a method for detecting
Campylobacter jejuni
in patient stools with subsequent isolation using antibody–magnetic beads in conjunction with selective culture and PCR. Monoclonal antibodies specific for the flagellin A and major outer membrane protein of
C. jejuni
were generated; two clones (1C7 and 4B2) were used to coat magnetic beads for immunomagnetic separation (IMS).
C. jejuni
strain NCTC11168 was recovered from human stool samples spiked with varying concentrations (10
1
–10
5
CFU/mL) by
Campylobacter
(Campy)-IMS or a conventional culture-based method and plated on modified charcoal–cefoperazone–deoxycholate agar; the number of colonies was enumerated. The detection limits of Campy-IMS and conventional culture-based method with spiked stool samples were 10
2
and 10
4
CFU/mL, respectively. The sensitivity of IMS-PCR was 10–10,000-fold higher than that of direct PCR. The recovery rate of
C. jejuni
from spiked stools stored for 12 to 72 h decreased from 72.3 to 5.9% with Campy-IMS and from 48.5 to 0.1% with the conventional culture-based method. Importantly, of 20 PCR (+)/bacterial culture (−) samples that were diagnosed as probable cases according to general criteria, 95% (19/20) were confirmed positive by Campy-IMS. Thus, this study suggests a solution to overcome the problems caused by the inconsistency between probable and confirmed cases of
Campylobacter
infection.

IMPORTANCE

The isolation, cultivation, and maintenance of
Campylobacter
spp. are difficult because of the microaerophilic conditions and specific medium needed. Although selective media are useful for the initial isolation of
Campylobacter
, subsequent exposure of the sample to oxygen has a detrimental effect on the positive culture rate of
Campylobacter
, significantly lowering the isolation rate from patient samples. In this study, the detection limit was improved by combining immunomagnetic separation and PCR methods to quickly detect
Campylobacter jejuni
in clinical patient stool samples using antibody
–
magnetic beads. Therefore, this study is expected to improve confirmation of
C. jejuni
infection where diagnosis would previously fail with patient samples because of oxygen exposure, inappropriate diagnostic methods, and interference from other bacteria in the sample.
Risk Factors Associated with Collapse of Distal Radius Fractures after Volar Locking Plate Fixation in Older Adults
Authors: LEE Sanglim , JEON Suk Ha 
Published: February 2025

Background: This study aimed to identify the risk factors associated with re-displacement or collapse of distal radius fractures treated using volar locking plates in older adults. Methods: We conducted a retrospective analysis of 131 patients aged ≥65 years with distal radius fractures who underwent volar locking plate fixation. The collapse was classified into three categories: ‘radial collapse’ was determined as the top decile of patients with the greatest decrease in radial inclination; ‘dorsal collapse’ was defined by volar tilt angle on lateral or 25° tilted lateral views and ‘height collapse’ by radial height. To identify the factors related to these three types of collapses, we compared the clinical and radiological parameters between the wrists with each type of collapsed and non-collapsed wrists. Results: Dorsal collapse had no significant associated factors and radial collapse had osteoporosis as a significant different factor. The height collapse group was associated with older age, had a higher prevalence of high-energy injury mechanisms and a limited range of flexion–extension at final follow-up and larger distance between the articular surface and distal screws. Conclusions: The volar locking plate may effectively prevent three types of collapses. Height collapse group included patients with increased age, high-energy injury mechanisms and limited range of flexion–extension at the time of final follow-up. To prevent collapse, the longest possible distal screws must be inserted just beneath the subchondral bone. Level of Evidence: Level IV (Therapeutic)
Sensory Nerve Transfer for Intractable Neuropathic Pain in a Case of C8-T1 Root Avulsion in Brachial Plexus Injury
Authors: MAURYA Sanjay , BENIWAL Shivam , SINGH Onkar 
Published: February 2025

Neuropathic pain in root avulsion brachial plexus injury (BPI) is severe and unrelenting. Routine analgesics and other described methods often provide inadequate pain relief. We report a patient with neuropathic pain following C8T1 root avulsion injury, which was successfully managed with end-to-side ulnar sensory branch transfer to the median nerve. Postoperatively, there was a marked reduction in pain score as determined by visual analogue score (VAS) and a marked improvement in the daily sleep interference scale (DSIS). This option may be considered in patients with severe neuropathic pain in lower root avulsion injury in BPI. Level of Evidence: Level V (Therapeutic)
Pan-cancer analysis of oncogenic MET fusions reveals distinct pathogenomic subsets with differential sensitivity to MET-targeted therapy
Authors: Febres-Aldana Christopher A. , Vojnic Morana , Odintsov Igor , Zhang Tom , Cheng Ryan , Beach Catherine Z. , Lu Daniel , Mattar Marissa S. , Gazzo Andrea M. , Gili Leo , Harshan Manju , Ameri Ali , Machnicki Stephen , Xiao Xiuying , Lockwood William W. , Zhou Xiao-yan , Yao Qianlan , Drilon Alexander , Rekhtman Natasha , Shah Nameeta , Li Anqi , Liu Zebing , Yang Soo-Ryum , Davare Monika A. , Ladanyi Marc , Somwar Romel 
Published: February 2025

Abstract
MET fusions (MET-Fs) are oncogenic drivers that remain poorly characterized. Analysis of 56 MET-F-positive tumors from an institutional cohort of 91,119 patients (79,864 DNA-seq plus 11,255 RNA-seq) uncovered two forms of MET-F pathobiology. The first group featured 5’ partners with homodimerization domains fused in-frame with MET-tyrosine kinase domain (TKD), primarily originated from translocations, frequently excluded MET exon 14, mediated oncogenesis through cytoplasmic aggregation and constitutive activation, and were markedly sensitive to MET tyrosine kinase inhibitors (TKI) in pre-clinical models and patients with lung cancer. The second group lacked partner homodimerization motifs and retained MET transmembrane and extracellular domains. Their pathogenesis involved intrachromosomal rearrangements, resulting in partner selection for promoter hijacking and fusion allele amplification. Membrane-bound fusions were enriched in gliomas with RTK co-alterations. We provide a framework to comprehend the heterogeneous landscape of MET-Fs, supporting that fusion oncogenicity and MET-TKI sensitivity are determined by structural topology and pathogenomic context.