bluuebunny/crossref_metadata_2025_split huggingface dataset:
PiERF1 undergoes ethylene signalling and regulates cold tolerance in Plumbago indica L.
Authors: Zhao Zi-An , Li Yi-Rui , Lei Ting , Liu Cai-Lei , Zeng Qing-Xiao , Liu Xuan , Yang Li-Juan , Li Jia-Ni , Gao Su-Ping 
Published: December 2024

Abstract

Ethylene is an essential regulatory factor in the signalling pathways involved in plant responses to abiotic stress, including cold stress, and plays a regulatory role in the cold response. Recent studies have shown that the exogenous application of 1-aminocyclopropane-1-carboxylate (ACC), an ethylene promoter, affects plant cold tolerance. The cold-responsive specific gene DREB plays a crucial role in enhancing cold tolerance in plants by activating several cold-responsive (COR) genes. However, how the ethylene biosynthesis pathway regulates this gene in the cold response of thermophilic plants has yet to be fully elucidated. In this study, the thermophilic plant Plumbago indica L. was used as an example, and physiological experiments and transcriptomic analyses revealed that cold stress treatment induced the synthesis of endogenous ACC and regulated the ethylene signalling activator PiERF1, while cold signalling also activated PiDREB1A. Spray experiments also revealed that ACC-induced upregulation of the PiERF1 gene reduced the cold tolerance of P. indica, and decreased the expression level of the PiDREB1A gene. These results indicate that ethylene signalling directly regulates the downstream gene PiERF1 and initiates the DREB‒COR cold-responsive signalling pathway to regulate cold tolerance, resulting in the negative regulation of cold tolerance in thermophilic plants.Ethylene is an essential regulatory factor in the signalling pathways involved in plant responses to abiotic stress, including cold stress, and plays a regulatory role in the cold response. Recent studies have shown that the exogenous application of 1-aminocyclopropane-1-carboxylate (ACC), an ethylene promoter, affects plant cold tolerance. The cold-responsive specific gene DREB plays a crucial role in enhancing cold tolerance in plants by activating several cold-responsive (COR) genes. However, how the ethylene biosynthesis pathway regulates this gene in the cold response of thermophilic plants has yet to be fully elucidated. In this study, the thermophilic plant Plumbago indica L. was used as an example, and physiological experiments and transcriptomic analyses revealed that cold stress treatment induced the synthesis of endogenous ACC and regulated the ethylene signalling activator PiERF1, while cold signalling also activated PiDREB1A. Spray experiments also revealed that ACC-induced upregulation of the PiERF1 gene reduced the cold tolerance of P. indica, and decreased the expression level of the PiDREB1A gene. These results indicate that ethylene signalling directly regulates the downstream gene PiERF1 and initiates the DREB‒COR cold-responsive signalling pathway to regulate cold tolerance, resulting in the negative regulation of cold tolerance in thermophilic plants.
Functional differentiation of Human Dental Pulp Stem Cells into neuron-like cells exhibiting electrophysiological activity
Authors: Pardo-Rodríguez Beatriz , Baraibar Andrés Mateo , Manero-Roig Irene , Luzuriaga Jon , Salvador-Moya Jone , Polo Yurena , Basanta-Torres Ruth , Unda Fernando , Mato Susana , Ibarretxe Gaskon , Pineda Jose R. 
Published: December 2024

Abstract

Background and Aim:
Human dental pulp stem cells (hDPSCs) constitute a promising alternative for central nervous system (CNS) cell therapy. Unlike other human stem cells, hDPSCs can be differentiated, without genetic modification, to neural cells that secrete neuroprotective factors. However, a better understanding of their real capacity to give rise to functional neurons and integrate into synaptic networks is still needed. For that, ex vivo differentiation protocols must be refined, especially to avoid the use of fetal animal serum. The aim of our study is to improve existing differentiation protocols of hDPSCs into neuron-like cells.
Methods
We compared the effects of the 1) absence or presence of fetal serum during the initial expansion phase as a step prior to switching cultures to neurodifferentiation media. We 2) improved hDPSC neurodifferentiation by adding retinoic acid (RA) and potassium chloride (KCl) pulses for 21 or 60 days and characterized the results by immunofluorescence, digital morphometric analysis, RT-qPCR and electrophysiology.
Results
We found that neural markers like Nestin, GFAP, S100β and p75NTR were expressed differently in neurodifferentiated hDPSC cultures depending on the presence or absence of serum during the initial cell expansion phase. In addition, hDPSCs previously grown as spheroids in serum-free medium exhibited in vitro expression of neuronal markers such as doublecortin (DCX), neuronal nuclear antigen (NeuN), Ankyrin-G and MAP2 after neurodifferentiation. Presynaptic vGLUT2, Synapsin-I, and excitatory glutamatergic and inhibitory GABAergic postsynaptic scaffold proteins and receptor subunits were also present in these neurodifferentiated hDPSCs. Treatment with KCl and RA increased the amount of both voltage-gated Na+ and K+ channel subunits in neurodifferentiated hDPSCs at the transcript level. Consistently, these cells displayed voltage-dependent K+ and TTX-sensitive Na+ currents as well as spontaneous electrophysiological activity and repetitive neuronal action potentials with a full baseline potential recovery.
Conclusion
Our study demonstrates that hDPSCs can be differentiated to neuronal-like cells that display functional excitability and thus evidence the potential of these easily accessible human stem cells for nerve tissue engineering. These results highlight the importance of choosing an appropriate culture protocol to successfully neurodifferentiate hDPSCs.
Optimizing Nitrogen Fertilizer and Planting Density to Improve Yield and Nitrogen Use Efficiency of Direct Seeded Shaga Rice in Ethiopia
Authors: Tafere christian , Assega Habtamu , Tadesse Zelalem 
Published: December 2024

Abstract

Achieving high yield and quality rice with low environmental impact costs is the main driver of modern rice production systems. However, limited recommendations on optimal nitrogen (N) fertilizer and planting density for site-specific locations in Ethiopia are a challenge for achieving increased rice yield and nitrogen use efficiency (NUE). The purpose of this study was to optimize N fertilizer and planting density to improve the NUE, yield and yield attributes of Shaga rice. A factorial combination of N rates (N 184 , N 276 & N 368 kgha− 1) and planting density (D 60 , D 80 & D 100 kgha− 1 was presented as a randomized complete block design with three replications in the field experiments carried out between the 2020–2021 and 2021–2022 cropping seasons. The findings showed that the partial factor productivity of nitrogen (PFPn), NUE, grain yield, leaf area indices, number of filled spikelets, spikletes per panicle, and biomass accumulation of shaga rice were all significantly affected by the interaction between N rates and D. Grain yield and NUE increased by 49.2% and 0.342%, respectively, with optimized N184 kgha-1. Increasing N application rate by N 368 kgha− 1 resulted in low PFPn (8.4%). N 184 kgha− 1 application along with D 100 kgha− 1 significantly increased grain yield (6.7tha− 1) for Fogera and N 276 with D 60 kgha− 1 combination attained better grain yield (6.2tha− 1) for North Achefer. Low temperature stress (14.40C) reduced the number of fertile spikelets. Days to 50% heading significantly delayed (102 days) by combination of D 100 and with N 368 kgha− 1 application rate. The application of a high N dose (N 368 kgha− 1) delayed physiological maturity (157 days) by promoting vegetative growth and leaf photosynthesis. NUE, PFPn, and quality of high yielding Shaga rice with application of high N rate (N 368 kgha− 1), was low and improved by reducing the N rate and increasing D. Low PFPn, 19.2% with application of N 276 kgha− 1 shows attention should be given to the application of slow – release N fertilizer, to the application of slow-release N fertilizer, split application, and time of application to minimize loss of N. The economic analysis revealed that the combination of N 184 and D 100 kgha− 1, and N 276 and D 60 kgha− 1 yielded the highest net income return of 2,722.43 and 2,460.91 US$ ha− 1 respectively, in Fogera as the optimal recommendation for achieving high profit with rice production in North Achefer.
Research on an Ultrafine Water Mist Partition Multistage Dust Suppression System in Underground Excavation Tunnel
Authors: Jing Deji , Kan Qisheng , Dai Mingying , Ma Jichuang , Bao Chunhua , Du Pengyu , Chang Ping 
Published: December 2024

Abstract

A large amount of coal dust is produced in coal mine excavation, which has a serious impact on the working environment and health of underground workers. To address this problem, the spatial and temporal evolution process of coal dust in the excavation tunnel is analyzed via numerical simulation, and an ultrafine water mist partition multistage dust suppression system is developed. The results show that in the original ventilation mode, the air velocity within 5 m from the workface varies greatly, up to 17 m/s. When the airflow impacts the workface, it shifts to the return air side and gradually stabilizes below 2 m/s. Driven by airflow, coal dust gathers around the tunneling machine and diffuses to the rear of the tunnel, the speed increases first and then decreases, and the whole tunnel is filled in 40 s. Within 10 s, the water mist particles cover the whole tunnel at a high speed, capture and settle the coal dust particles, and prevent the further spread of coal dust. After application to the I030409 excavation workface in the Qipanjing Coal Mine, the average reduction efficiency for total dust and respirable dust in the tunnel reached 91.74% and 93.4%, respectively. Therefore, the system successfully achieves partitioning multilevel dust reduction.
DTX1 Modulates Microglial M1 Polarization and Exacerbates Neuroinflammation in Traumatic Brain Injury model rats through NF - κB/IRF5
Authors: Zhang Yonghui , Li Rongwei , Zou Zongxing , Fu Xiaochuan , Li Ganyu , Wang Lu , Zhang Yan , Chen Yuyu , Chen Zuzhi , Yang Dongfang , Jiao Yan , Zhang Weiguang , Mei Tieniu , Tan Liang , Cao Ying , Yin Changlin 
Published: December 2024

Abstract

Neuroinflammation significantly contributes to the progression of traumatic brain injury (TBI), in which microglial activation playing a crucial role. This study explores the impact of Deltex E3 ubiquitin ligase 1 (DTX1) on microglial polarization and neuroinflammation post-TBI. We investigated DTX1 expression in a rat TBI model. Through gain- and loss-of-function approaches, we elucidated DTX1’s role in modulating inflammatory cytokine production and microglial polarization by reverse transcription PCR, Western blot, and enzyme-linked immunosorbent assay (ELISA). DTX1 expression was significantly up-regulated in LPS-stimulated microglia and post-TBI rat brains. Overexpression of DTX1 promoted the production of proinflammatory cytokines and induced an M1 microglial phenotype, marked by elevated inducible nitric oxide synthase (iNOS) and reduced Arginase-1 (Arg1). Conversely, DTX1 silencing exhibited anti-inflammatory effects. In the TBI rat model, DTX1 overexpression exacerbated neuroinflammation and cognitive impairments, while its knockdown ameliorated these effects. Our findings suggested that DTX1 is a key regulator of microglial polarization and neuroinflammation, herald a promising therapeutic target for TBI treatment.
scLong: A Billion-Parameter Foundation Model for Capturing Long-Range Gene Context in Single-Cell Transcriptomics
Authors: Xie Pengtao , Bai Ding , Mo Shentong , Zhang Ruiyi , Luo Yingtao , Gao Jiahao , Yang Jeremy , Wu Qiuyang , Singh Digvijay , Rahmani Hamidreza , Amariuta Tiffany , Grotjahn Danielle , Zhong Sheng , Lewis Nathan , Wang Wei , Ideker Trey , Xing Eric 
Published: December 2024

Abstract

Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of cellular heterogeneity by providing gene expression data at single-cell resolution, uncovering insights into rare cell populations, cell-cell interactions, and gene regulation. Foundation models pretrained on large-scale scRNA-seq datasets have shown great promise in analyzing such data, but existing approaches are often limited to modeling a small subset of highly expressed genes and lack the integration of external gene-specific knowledge. To address these limitations, we present scLong, a billion-parameter foundation model pretrained on 48 million cells. scLong performs self-attention across the entire set of 28,000 genes in the human genome. This enables the model to capture long-range dependencies between all genes, including lowly expressed ones, which often play critical roles in cellular processes but are typically excluded by existing foundation models. Additionally, scLong integrates gene knowledge from the Gene Ontology using a graph convolutional network, enriching its contextual understanding of gene functions and relationships. In extensive evaluations, scLong surpasses both state-of-the-art scRNA-seq foundation models and task-specific models across diverse tasks, including predicting transcriptional responses to genetic and chemical perturbations, forecasting cancer drug responses, and inferring gene regulatory networks.
Surrogate model and machine learning approaches for thermal field reconstruction from weld pool contour: application to GTA welding
Authors: Boutaleb Zaid , Bendaoud Issam , Rouquette Sébastien , Soulié Fabien 
Published: December 2024

Abstract

Thermal cycles in arc welding are crucial as they determine the metallurgy, residual stresses and distortions of welded parts. Experimentally measuring the temperature everywhere in the welded parts is not possible. This can be achieved with a thermal simulation but finite element analysis requires long computational times especially for large parts. This study aimed to predict the thermal field using a data-driven approach using numerical and experimental data. First, thermal modeling is defined and arc heating is described with an equivalent heat source. The numerical design of experiments was conducted by varying the heat source parameters. Weld pool contour is extracted from each simulations for building a numerical dataset. The numerical dataset is used for training a surrogate model. The surrogate model is used for estimating the heat source parameters from the weld pool contour using an optimization technique. Then a K-Nearest Neighbors algorithm is used to predict the thermal field from the estimated heat source parameters. A significant reduction in computational time is obtained for predicting the thermal field from experimental weld pool contour. Numerical analysis showed that the predicted thermal field is fairly good in the solid than in the weld pool.
Landslide Susceptibility Zonation Based on Slope Units and Grid Units Using the Weight of Evidence and Frequency Ratio Methods in the Kulon Progo Mountains, Indonesia
Authors: Erzagian Egy , Fathani Teuku Faisal , Wilopo Wahyu 
Published: December 2024

Abstract

The Kulon Progo Mountains in the south of Java Island have complex geological conditions and are highly susceptible to landslides, resulting in significant material losses and threats to human safety. In recent years, the frequency of landslides in Kulon Progo has increased markedly, from 208 events in 2020 to 622 in 2022, with estimated material losses reaching 450 million USD in 2022. To reduce these risks, it is essential to identify landslide susceptibility zones. This study uses grid and slope units to perform landslide susceptibility zonation. The weight of evidence (WoE) and frequency ratio (FR) methods were applied to compare model accuracy. Nine landslide-controlling factors, including slope, aspect, elevation, slope material, lineament density, Normalized Difference Vegetation Index (NDVI), distance to rivers, distance to roads, and rainfall, were analyzed using spatial methods and landslide event data. The results show that slopes steeper than 40° and high lineament density (> 1.61 km/km²) are the most significant factors influencing landslide susceptibility in both units. Validation using the Area Under Curve (AUC) indicates that the slope unit-based WoE method provides better accuracy, with AUC values of 0.812 for the success rate and 0.827 for the prediction rate. The study produced four landslide susceptibility zonation maps, classifying areas from very low to high susceptibility. High susceptibility zones are concentrated in the northern part of the study area, especially on steep slopes, with some areas in the southern part.
The Heparinized Wet-Suction Technique Enhances Aspiration Quality and Quantity of EUS-FNA for Solid Pancreatic Lesions: A Retrospective Study
Authors: Shang Rumin , Han Xiangming , Zhu Meng , Xu Bo , Rong Fang , Lv Fei , Wu Changwei , Ding Xiangwu 
Published: December 2024

Abstract

Background
The optimal suction method for performing endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) on solid pancreatic lesions (SPLs) remains unclear. This study aims to compare the heparinized wet-suction technique (HWST) with the conventional dry-suction technique(DST) for EUS-FNA in SPLs.
Methods
We conducted a retrospective study on EUS-FNA procedures at a single medical center in China. A total of 105 patients were enrolled who received 3 passes of EUS-FNA with 19-G needles. Sample quantity (including specimen adequacy, maximum intact specimen (MIS) length, and macroscopic visible core (MVC) length), sample quality (including cytology and histology blood contamination), diagnostic accuracy, and adverse events were compared between DST and HWST.
Results
From January 2021 to April 2024, a total of 105 patients (DST group: n = 50; HWST group: n = 55) were analyzed in this study. The specimen adequacy score was significantly higher with HWST compared to DST in the first pass (P = 0.006), the second pass (P = 0.032), and the combined total of three passes (P = 0.010). HWST produced longer MIS and MVC lengths than DST in the first pass (MIS: P = 0.001; MVC: P < 0.001), the second pass (MIS: P = 0.001; MVC: P = 0.022), and the combined total of three passes (MIS: P = 0.001; MVC: P < 0.001). Compared with DST, HWST yielded a lower blood contamination score in the first pass (cytology: P = 0.002; histology: P = 0.005), the second pass (histology: P = 0.035), and the combined total of three passes (cytology: P = 0.035; histology: P = 0.036). In terms of diagnostic yield, HWST demonstrated a significantly superior histological accuracy in the first pass compared with DST (P = 0.036).
Conclusions
EUS-FNA with HWST led to significantly higher specimen quantity and quality, improved first-pass histological diagnostic accuracy, and comparable safety to DST. HWST may have a wide range of applications in clinical practice.
Coordination of flux-related leaf and root traits impacts forest community assembly
Authors: Ma Zeqing , Duan Mengcheng , Sack Lawren , Ma Chengen , Li Le , McCormack M , Lu Mingzhen , Guo Dali 
Published: December 2024

Abstract

Understanding the functions and coordination of plant traits is critical for predicting how diverse species respond to climate change. According to hydraulic and economic theories, leaves and roots—key organs for resource acquisition—are expected to function in coordination, such that species with faster resource utilization would possess leaf and root traits that facilitate rapid carbon, nutrient, and water uptake and fluxes. However, there has been limited evidence supporting leaf-root trait coordination and a role for that coordination on community structure. Here, we measured 13 leaf and root functional traits for 101 woody species from six tropical and subtropical forests, and assessed coordination and its association with community dominance. Hydraulic traits, such as leaf vein density and root vessel density, were coordinated between organs and showed compensation trade-offs between traits within organs, such as, leaf vein density and diameter. Economic traits relating to composition, such as nitrogen concentration, were coordinated between organs, whereas economic structural traits were decoupled, such as leaf mass per area and specific root length. Overall, hydraulic traits and economics traits were partially independent. The coordination of flux-related leaf and root traits was associated with ectomycorrhizal symbiosis and with dominance within the community. These findings indicate how trait organization within and across organs contributes to optimal whole plant function, with implications for performance in natural communities.
Anatomical and Functional Factors Influencing Recovery in Idiopathic Epiretinal Membrane after Surgery
Authors: Shih En-Jie , Peng Kai-Ling , Kung Ya-Hsin , Wu Tsung-Tien 
Published: December 2024

Abstract

Purpose
We aimed to explore the anatomical and functional factors influencing recovery outcomes in patients with idiopathic epiretinal membranes (iERM) after surgical intervention.
Methods
Participants diagnosed with iERM underwent pars plana vitrectomy with ERM and internal limiting membrane (ILM) peeling. ERM staging, preoperative and postoperative findings of retinal microstructures, and thickness changes using optic coherence tomography, and inner and outer retinal layer thickness changes preoperatively and postoperatively were analyzed.
Results
The study analyzed 85 eyes from 65 patients (mean age, 65.64 ± 6.19 years) with idiopathic ERM who underwent PPV and both ERM and ILM peeling without recurrence within one year. Male accounted for 44.71% (38/85). The mean preoperative vision was 0.47 [Snellen equivalent (SE), 68/200] ± 0.29 logMAR, and the mean final vision was 0.32 (SE, 96/200) ± 0.30 logMAR. Visual improvements were significant (p < 0.001, paired t-test). Preoperative lens status, preoperative vision, preoperative inner and outer segment junction (IS/OS) distortion, final lens status, and follow-up duration significantly correlated with final vision. Central foveal thickness, inner and outer retinal layer thickness decreased continuously until 12 months postoperatively in the pseudophakia group, whereas for those in the phakia group, the outer retinal layer thickness decreased only in the first 6 months.
Conclusions
Phakia, poor initial vision, IS/OS distortion, and short follow-up do worsen the final visual outcomes. The postoperative central foveal thickness, inner and outer retinal layers thickness showed the longest statistical improvement in pseudophakic eyes over 12 months.
Versatile, tunable method for NaNO2/HX (Cl or Br)–mediated radical dihalogenation or nitration of olefins
Authors: Wang Yaxin 
Published: December 2024

Abstract

We have developed a versatile, tunable method for NaNO2/HX (Cl or Br)–mediated radical nitration or vicinal dihalogenation of olefins. The method allowed us to synthesize high-added-value vicinal dihalides by using inexpensive, low-molecular-weight HCl or HBr as a chloride or bromide source and commercially available NaNO2 under irradiation with blue LEDs without the need for a photocatalyst or metal catalyst. In the absence of light, reactions of the olefins with NaNO2 and HCl gave nitration products in a controllable fashion. This regio- and chemoselective method was compatible with a diverse array of olefin substrates, showed good functional group tolerance, and was successfully used for late-stage dihalogenation and nitration of dozens of derivatives of natural products and active pharmaceutical ingredients. Mechanistic studies showed that in the dihalogenation reactions, a nitrosyl halide (X–N=O) generated in situ by reaction of NaNO2 and aqueous HX not only delivered a halogen radical upon photoirradiation to initiate olefin dihalogenation but also underwent halogen-atom transfer (XAT) process with a carbon radical intermediate to form the vicinal dihalogenation product. In the nitration reactions, a nitric oxide (NO or NO2) that was formed in situ from NaNO2 and the same equivalent of HCl selectively triggered olefin nitration.