bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uncovering the genomic diversity of the wild forage crop Setaria sphacelata
Authors: Franco Ana Luiza , Azevedo Ana Luisa Sousa , Reis Aryane Campos , Matos Elyabe Monteiro , Fonseca Marina Arantes , Pereira Antônio Vander , Leitch Ilia J. , Leitch Andrew R. , Viccini Lyderson Facio 
Published: September 2024

AbstractGrasses are considered one of the most important angiosperm groups in economic terms. The Setaria sphacelata complex is an intriguing species with considerable variation in genome size (GS). It is currently being explored from a genomic perspective especially because of its great adaptability under winter periods. Repetitive DNA sequences are known to contribute significantly to GS diversity, which in turn can play a role in impacting the ecology and evolution of a species. This study is aimed to characterize the GS and repetitive elements of different germplasm accessions of S. sphacelata. We analyzed 540 plants from 70 accessions collected worldwide. Flow cytometry was used for GS estimation, together with chromosome counting, fluorescent in situ hybridization (FISH), and bioinformatic analysis. Most (i.e., 80%) accessions were tetraploids (2n = 4x = 36) with GS ranging from 3.0 to 3.7 pg/2C. Additionally, a low number of diploids (2n = 2x = 18; ∼1.6 to 2 pg/2C), pentaploids (2n = 5x = 45: ∼4 pg/2C), hexaploids (2n = 6x = 54; ∼4.4 pg/2C), and octoploids (2n = 8x = 72; ∼6 pg/2C,) were detected. The greatest variation was found in accessions from South Africa. RepeatExplorer2 showed that 39% and 43% of the genomes of two diploid accessions comprised repetitive sequences, with Ty3/gypsy retrotransposons being the most abundant repeats. However, variation in the percentage of two Ty3/gypsy sublineages, Athila and Ogre, suggests different process of amplification and deletion of repeats during the evolution of the species complex. In contrast, FISH revealed some satellite repeats with a conserved localized distribution in pericentromeric regions between accessions. Although differences in the distribution of the FISH signals over the chromosomes were observed between the different ploidy levels, the data suggest that increases in the ploidy level were associated with the occurrence of hybridization and DNA loss.
Collision detection and mitigation based on optimization and Kronecker recurrent neural network in WSN
Authors: Khare Akhil , Selvakumar Kannapiran , Dugyala Raman 
Published: September 2024

SummaryNowadays, wireless sensor networks (WSNs) have paid huge attention among researchers due to their wide applications. WSNs possess multiple sensor nodes that transmit data to each other by using constrained energy resources. The sensor nodes are highly affected by collision due to the transmission of packets over the network by one or two nodes at the same time. Collision detection is necessary to increase network security and enhance the lifetime of sensor nodes. In most of the previous research, efficiently implementing collision detection algorithms while minimizing resource usage remains a significant challenge. Thus, a hybrid deep learning model deep Kronecker recurrent neural network (DKRNN) is developed in this research. Here, the cluster head is selected using the chronological skill optimization algorithm (CSOA) algorithmic approach by considering multi‐objective parameters like energy, distance, delay, and trust. The network‐based parameters are then extracted from the network. Later, the collision is detected using the DKRNN approach and the collision is mitigated finally using a packet pre‐scheduling model named Dolphin Ant Lion Optimization (Dolphin ALO). Moreover, the detection performance of CSOA+ DKRNN is validated, and it achieved superior performance with a collision detection rate (CDR) of 0.940, packet delivery ratio (PDR) of 0.660, throughput of 0.850Mbps, and energy consumption of 0.110 J.
Differences in phenology across three trophic levels between two Afrotropical sites separated by four degrees latitude
Authors: Jarrett Crinan , Simon Ojodomo Godday , Tchana Christian N. , Pev Thaddeus Apezan , Meigang Kamkeng Michelle Fany , Wandji Alain Christel , Manu Shiiwua A. , Tchoumbou Mélanie Adèle , Helm Barbara , Powell Luke L. , Nwaogu Chima J. 
Published: September 2024

AbstractBirds time their life cycle events to favourable windows in environmental conditions. In tropical environments, where photoperiod variation is small, birds show high variability in the timing of life cycle stages, yet these species have been severely underrepresented in phenology research. Here, we investigated temporal patterns in bird life cycles and resource availability in two sites in tropical Africa: Weppa (Nigeria, 7° N) and Elat (Cameroon, 3° N). In these sites we captured common bulbuls (Pycnonotus barbatus), a widespread generalist, and recorded breeding and moult over a 12‐month period. Simultaneously, we surveyed fruiting tree and arthropod abundance. Our aim was to quantify seasonal patterns in moult and breeding in bulbuls at both sites, and link them to fluctuations in local fruit and arthropod abundance and precipitation. Moult was more seasonal than breeding in both sites, and seasonality of both life cycle events was stronger in Nigeria than Cameroon. The peak timing for moult was 1.5 months earlier in Nigeria than Cameroon. Seasonal variation in abundance of fruiting trees and arthropods was different between sites, as were the associations with breeding and moulting. In Nigeria, we found a positive association between moult and arthropod abundance, and a negative one with fruiting tree abundance. In contrast, in Cameroon moult was associated with higher precipitation, while breeding occurred at times with higher fruit abundance. Our results provide evidence that, even in similar habitats separated by four degrees in latitude, seasonal patterns across three trophic levels are variable. Understanding links between environmental conditions and life cycle events can reveal potential vulnerabilities of tropical species, and guide conservation efforts.
Niche partitioning and host specialisation in fish‐parasitising isopods: Trait‐dependent patterns from three ecosystems on the east coast of India
Authors: Mohapatra Sandeep Kumar , Swain Anshuman , Ray Dipanjan , Behera Rajesh Kumar , Tripathy Basudev , Seth Jaya Kishor , Mohapatra Anil 
Published: September 2024

AbstractDue to their large size and obligate nature, Cymothoid isopods inflict a high degree of tissue damage to fish. Still, they are understudied at an ecosystem level despite their global presence and ecological role. In this work, we collected fish host‐isopod parasite data, along with their life history and ecological traits, from the northern part of the east coast of India and investigated patterns in host specialisation and preference of isopod parasites using a trait‐based network perspective. We observed that the region of attachment of the parasite (buccal cavity, branchial cavity, and skin) and host fish ecology (schooling behaviour and habitat characteristics) influenced host specialisation and preference. We found that branchial cavity‐attaching parasites preferred schooling, pelagic fishes, whereas buccal cavity‐attaching parasites preferred mostly non‐schooling, demersal fishes. Skin‐attaching parasites were found to be generalists and had no preference based on our examined host traits.
Epigenotoxicity: Decoding the epigenetic imprints of genotoxic agents and their implications for regulatory genetic toxicology
Authors: Godschalk Roger , Faulk Christopher , LaRocca Jessica , van Benthem Jan , Marchetti Francesco 
Published: September 2024

AbstractRegulatory genetic toxicology focuses on DNA damage and subsequent gene mutations. However, genotoxic agents can also affect epigenetic marks, and incorporation of epigenetic data into the regulatory framework may thus enhance the accuracy of risk assessment. Additionally, epigenetic alterations may identify non‐genotoxic carcinogens that are not captured with the current battery of tests. Epigenetic alterations could also explain long‐term consequences and potential transgenerational effects in the absence of DNA mutations. Therefore, at the 2022 International Workshops on Genotoxicity Testing (IWGT) in Ottawa (Ontario, Canada), an expert workgroup explored whether including epigenetic endpoints would improve regulatory genetic toxicology. Here we summarize the presentations and the discussions on technical advancements in assessing epigenetics, how the assessment of epigenetics can enhance strategies for detecting genotoxic and non‐genotoxic carcinogens and the correlation between epigenetic alterations with other relevant apical endpoints.
Design and implementation of tilting‐plate drainage equipment for paddy field
Authors: Duan Zhenhua , Xiang Chun , Shi Gaoping , Wang Jinhao 
Published: September 2024

AbstractDrainage equipment is an important part of paddy field drainage and irrigation system, and its performance research and application are conducive to the promotion and implementation of high‐standard farmland construction. Aiming at the different water demand of rice in different growing stages, low water level control precision, large manual operation and extensive management of existing drainage machinery, a tilting‐plate drainage equipment using upper overflow mode was proposed in this paper. Based on the Geneva mechanism principle, a unique linkage mechanism is designed, which can realize water retaining operation and silt discharge operation through a single motor drive, and the relationship between the motor angle and the water retaining height is established. Through mechanical analysis and dynamic simulation of the mechanism, the motion characteristics of the water baffle, silt plate and the change of the motor torque are studied. A remote control system based on a 4G module is designed to control the drainage equipment easily through the user layer. The performance test of the prototype shows that the precision error of the optimized water retaining height control is less than 3.75%. The maximum height of water retaining operation is 180 mm, and the maximum load of silt discharge operation is 10 kg, which can meet the actual operation requirements. The design is beneficial to improve the precision and intelligence level of paddy field drainage management, and the research process can provide some help for the development and application of this kind of equipment.
Development of the critical zone environment in the highly dynamic landscape of the Forni Glacier forefield: Winds, tree vegetation, pedogenesis and surface waters after glacier retreat
Authors: Leonelli Giovanni , Masseroli Anna , Trombino Luca , Golzio Alessio , Bonetti Adalberto , Maggi Valter , Pelfini Manuela 
Published: September 2024

AbstractThe expansion of glacier‐free forelands after glacier retreat is emerging as a typical climate change‐dependent feature that is widely studied for assessing biogeomorphic feedbacks and analysing the vertical processes and changes occurring in the critical zone (CZ). However, the horizontal processes occurring in the CZ environment are still poorly understood. Here, we comprehensively analyse the development of the CZ environment over time in the Forni Glacier forefield, Italian Alps, since the end of the Little Ice Age (LIA) by considering different sectors (air, forest, water and soil) in two portions of the glacier forefield: the lower portion, which occurs below the glacier‐forefield treeline (GFT), where a fully functioning CZ environment has developed, and the upper portion, which occurs above the GFT, in the proglacial area (PA), where only an incipient CZ exists. The early stages of CZ development in the PA are highly influenced by katabatic winds, which impact the colonisation patterns of saplings and young trees, and characterised by high‐energy geomorphic processes that cause sediment reworking and initial stages of soil development. Below the GFT, the minimum tree ecesis interval after glacier retreat reaches a median value of 38 years (n = 8), and the fully developed CZ environment (with trees reaching at least 2 m in height after 20 years) formed after ~60 years following glacier retreat and is characterised by forest cover, soils organised in a chronosequence and contrasting isotopic signatures of surface and running waters. The correlation with the isotopic signatures of tree rings allowed us to estimate a groundwater flow period of approximately 2 months from the slopes into the CZ of the valley floor. By analysing the horizontal processes driving the geomorphic and biotic evolution patterns of a glacier forefield, this work introduces a novel approach for assessing the development of the CZ environment over time.
The oral ferroportin inhibitor vamifeport prevents liver iron overload in a mouse model of hemochromatosis
Authors: Nyffenegger Naja , Flace Anna , Varol Ahmet , Altermatt Patrick , Doucerain Cédric , Sundstrom Hanna , Dürrenberger Franz , Manolova Vania 
Published: September 2024

AbstractHemochromatosis is an inherited iron overload condition caused by mutations that reduce the levels of the iron‐regulatory hormone hepcidin or its binding to ferroportin. The hepcidin–ferroportin axis is pivotal to iron homeostasis, providing opportunities for therapeutic intervention in iron overload disorders like hemochromatosis. The aim of this study was to evaluate the efficacy of the oral ferroportin inhibitor vamifeport in the Hfe C282Y mouse model, which carries the most common mutation found in patients with hemochromatosis. A single oral dose of vamifeport lowered serum iron levels in Hfe C282Y mice, with delayed onset and shorter duration than observed in wild‐type mice. Vamifeport induced transient hypoferremia by inhibiting ferroportin and resulted in a feedback regulation of liver Hamp in wild‐type mice, which was absent in Hfe C282Y mice, reflecting the dysregulated systemic iron sensing in this hemochromatosis model. Chronic dosing with vamifeport led to sustained serum and liver iron reductions in Hfe C282Y mice, as well as markedly reducing liver Hamp expression in Hfe C282Y mice, suggesting distinct regulation of liver Hamp expression following acute or continuous iron restriction via vamifeport. At the tested dose, vamifeport retained its activity when combined with phlebotomy and did not significantly interfere with liver iron removal by phlebotomy in Hfe C282Y mice. These data demonstrate that chronic vamifeport treatment significantly reduces serum iron levels and prevents liver iron loading in the Hfe C282Y mouse model of hemochromatosis, thus providing preclinical proof of concept for the efficacy of vamifeport in hemochromatosis with or without phlebotomy.
Improving the natural convection of the heat sink inside an enclosure by fin perforation for electronic applications
Authors: Abdulsahib Ahmed Dhafer , Alkhafaji Dhirgham , Albayati Ibrahim M. 
Published: September 2024

AbstractThe present study aims to enhance the natural convection in the heat sink inside an enclosure by perforating fins for power electronic applications. The enclosure is a cube that is manufactured in such a way that the upper and lower surfaces, as well as the front and back surfaces, are thermally insulated. The right surface is hot, while the left surface is cold at a temperature difference ∆T of (4°C, 8°C, 10°C). The heat sink used consists of five fins that are attached to the heated surface. The heat sink fins are perforated with perforation number NP (4, 8, 12, and 16) and perforation diameter DP (0.5 and 1 cm). Temperatures are measured using 13 thermocouples placed within the enclosure and the temperature distribution is determined using a FLIR E30BX IR thermal camera, while velocity contours are obtained using numerical software. The main results showed improvement in heat transfer with an increase in the number of perforations and (DP = 1 cm) was found to be more efficient than (DP = .5 cm), for instance, when (∆T = 10°C) for (NP = 16) and (DP = .5 cm). There is a 2.9% improvement in temperature reduction on the fins' tip, while at =(DP = 1 cm), the percentage of improvement was 3.5% and showed a greater expansion of the velocity lines between the fins at (∆T = 10°C), where the rate of increase in the velocity contours from (∆T = 4 and 8°C) reaches 20% and 7% respectively. In addition, heat sinks with perforated fins are both lighter and more cost‐effective in terms of metal usage during the manufacturing process.
The balance between helper T 17 and regulatory T cells in osteoimmunology and relevant research progress on bone tissue engineering
Authors: Zhu Shuyu , Zhou Jing , Xie Zhigang 
Published: September 2024

AbstractBackgroundBone regeneration is a well‐regulated dynamic process, of which the prominent role of the immune system on bone homeostasis is more and more revealed by recent research. Before fully activation of the bone remodeling cells, the immune system needs to clean up the microenvironment in facilitating the bone repair initiation. Furthermore, this microenvironment must be maintained properly by various mechanisms over the entire bone regeneration process.ObjectiveThis review aims to summarize the role of the T‐helper 17/Regulatory T cell (Th17/Treg) balance in bone cell remodeling and discuss the relevant progress in bone tissue engineering.ResultsThe role of the immune response in the early stages of bone regeneration is crucial, especially the impact of the Th17/Treg balance on osteoclasts, mesenchymal stem cells (MSCs), and osteoblasts activity. By virtue of these knowledge advancements, innovative approaches in bone tissue engineering, such as nano‐structures, hydrogel, and exosomes, are designed to influence the Th17/Treg balance and thereby augment bone repair and regeneration.ConclusionTargeting the Th17/Treg balance is a promising innovative strategy for developing new treatments to enhance bone regeneration, thus offering potential breakthroughs in bone injury clinics.
ImageGP 2 for enhanced data visualization and reproducible analysis in biomedical research
Authors: Chen Tong , Liu Yong‐Xin , Chen Tao , Yang Mei , Fan Siqing , Shi Minglei , Wei Buqing , Lv Huijiao , Cao Wandi , Wang Chongming , Cui Jianzhou , Zhao Jiwen , Han Yilai , Xi Jiao , Zheng Ziqiang , Huang Luqi 
Published: September 2024

AbstractImageGP is an extensively utilized, open‐access platform for online data visualization and analysis. Over the past 7 years, it has catered to more than 700,000 usages globally, garnering substantial user feedback. The updated version, ImageGP 2 (available at https://www.bic.ac.cn/BIC), introduces a redesigned interface leveraging cutting‐edge web technologies to enhance functionality and user interaction. Key enhancements include the following: (i) Addition of modules for data format transformation, facilitating operations such as matrix merging, subsetting, and transformation between long and wide formats. (ii) Streamlined workflows with features like preparameter selection data validation and grouping of parameters with similar attributes. (iii) Expanded repertoire of visualization functions and analysis tools, including Weighted Gene Co‐Expression Network Analysis, differential gene expression analysis, and FASTA sequence processing. (iv) Personalized user space for uploading large data sets, tracking analysis history, and sharing reproducible analysis data, scripts, and results. (v) Enhanced user support through a simplified error debugging feature accessible with a single click. (vi) Introduction of an R package, ImageGP, enabling local data visualization and analysis. These updates position ImageGP 2 as a versatile tool serving both wet‐lab and dry‐lab researchers with expanded capabilities.
Greater TIMP‐1 protein levels and neointimal formation represent sex‐dependent cellular events limiting aortic vessel expansion in female rats
Authors: Al‐Katat Aya , Boudreau Laurie , Gagnon Emmanuelle , Assous Ines , Villeneuve Louis , Leblanc Charles Alexandre , Bergeron Alexandre , Sirois Martin , El‐Hamamsy Ismael , Calderone Angelino 
Published: September 2024

AbstractFragmentation/loss of the structural protein elastin represents the precipitating event translating to aortic expansion and subsequent aneurysm formation. The present study tested the hypothesis that greater protein expression of tissue inhibitor of matrix metalloproteinase‐1 (TIMP‐1) and neointimal growth secondary to a reduction of medial elastin content represent sex‐dependent events limiting aortic vessel expansion in females. TIMP‐1 protein levels were higher in the ascending aorta of female versus male patients diagnosed with a bicuspid aortic valve (BAV). The latter paradigm was recapitulated in the aorta of adult male and female rats complemented by greater TIMP‐2 expression in females. CaCl2 (0.5 M) treatment of the infrarenal aorta of adult male and female rats increased the in situ vessel diameter and expansion was significantly smaller in females despite a comparable reduction of medial elastin content. The preferential appearance of a neointimal region of the CaCl2‐treated infrarenal aorta of female rats may explain in part the smaller in situ expansion and neointimal growth correlated positively with the % change of the in situ diameter. Neointimal formation was secondary to a significant increase in the density of medial/neointimal vascular smooth muscle cells (VSMCs) that re‐entered the G2‐M phase whereas VSMC cell cycle re‐entry was attenuated in the CaCl2‐treated infrarenal aorta of male rats. Thus, greater TIMP‐1 expression in the aorta of female BAV patients may prevent excessive elastin fragmentation and preferential neointimal growth following CaCl2‐treatment of the infrarenal aorta of female rats represents a sex‐dependent biological event limiting vessel expansion secondary to a significant loss of the structural protein.
GAD1 ameliorates glioma progression through regulating cuproptosis via RAS/MAPK pathway
Authors: Gao Zhiqiang , Yang Jing 
Published: September 2024

AbstractGlioma represents a primary malignant tumor occurring in the central nervous system. Glutamate decarboxylase (GAD1) plays a significant role in tumor development; however, its function of GAD1 and underlying mechanisms in glioma progression remain unclear. Differentially expressed genes (DEGs) obtained from the GSE12657 and GSE15209 datasets that intersected with cuproptosis‐related genes and pivot genes were identified using comprehensive bioinformatics methods. The elesclomol (ES) treatment was used to induce cuproptosis in U251 cells, which was validated by detecting intracellular copper levels and cuproptosis marker expression. Lentivirus‐mediated gene overexpression was performed to explore the effects of GAD1 using functional assays in vitro and in a mouse xenograft model. The RAS agonist ML098 was used to verify the effect of GAD1 on the RAS/MAPK pathway in glioma cells. A total of 87 cuproptosis‐related DEGs and seven hub genes were obtained, with five genes upregulated and two were downregulated in gliomas. Overexpression of GAD1 inhibited proliferation, invasion, and migration, promoted apoptosis of glioma cells, and suppressed tumorigenesis in vivo. In addition, GAD1 overexpression enhanced the sensitivity of glioma cells to cuproptosis. Additionally, ML098 treatment attenuated the inhibitory effect of GAD1 overexpression on the malignant phenotype of ES‐treated cells. GAD1 plays an anti‐oncogenic role in glioma by regulating apoptosis via inhibition of the RAS/MAPK pathway.