bluuebunny/crossref_metadata_2025_split huggingface dataset:
LcProt: Proteomics‐based identification of plasma biomarkers for lung cancer multievent, a multicentre study
Authors: Liang Hengrui , Wang Runchen , Cheng Ran , Ye Zhiming , Zhao Na , Zhao Xiaohong , Huang Ying , Jiang Zhanpeng , Li Wangzhong , Zheng Jianqi , Deng Hongsheng , Jiang Yu , Lin Yuechun , Yan Yun , Song Lei , Li Jie , Xu Xin , Liang Wenhua , Liu Jun , He Jianxing 
Published: January 2025

ABSTRACTBackgroundPlasma protein has gained prominence in the non‐invasive predicting of lung cancer. We utilised Zeolite Zotero NaY‐based plasma proteomics to investigate its potential for multiple event predicting, including lung cancer diagnosis (task #1), lymph node metastasis detection (task #2) and tumour‒node‒metastasis (TNM) staging (task #3).MethodsA total of 4703 plasma proteins were quantified from 241 participants based on a prospective cohort of 2757 participants. An additional 46 participants from external prospective cohort of 735 participants were used for validation. Feature selection was performed using differential expressed protein analysis, area under curve (AUC) evaluation and least absolute shrinkage and selection operator (LASSO) regression. Random forest was used for multitask model construction based on the key proteins. Feature importance was interpreted using Shapley additive explanations (SHAP) algorithm.ResultsFor task #1, 10 proteins panel showed an AUC of .87 (.77‒.97) in the external validation. After integrating clinical factors, a significant increase diagnostic accuracy was observed with AUC of .91 (.85‒.98). For task #2, nine proteins panel achieved an AUC of .88 (.80‒.96), integration model showed an increase diagnostic accuracy with AUC of .90 (.85‒.97). For task #3, 10 proteins panel showed an AUC of .88 (.74‒.96) for stage I, .92 (.84‒.97) for stage II, .88 (.76‒.96) for stage III and .99 (.98‒.99) for stage IV in the integration model.ConclusionsThis study comprehensively profiled the NaY‐based plasma proteome biomarker, laying the foundation for a high‐performance blood test for predicting multiple events in lung cancer.Key points
Our study developed an innovative nanomaterial, Zeolite NaY, which addressed the masking effect and improved the depth of the proteome.
The performance of NaY‐based plasma proteomics as a preclinical diagnostic tool was validated through both internal and external cohort.
Furthermore, we explored the different patterns of plasma protein changes during the progression of lung cancer and used the explanations method to elucidate the roles of proteins in the multitask predictive model.
Immunoregulatory programs in anti‐N‐methyl‐D‐aspartate receptor encephalitis identified by single‐cell multi‐omics analysis
Authors: Li Xinhui , Xu Yicong , Zhang Weixing , Chen Zihao , Peng Dongjie , Ren Wenxu , Tang Zhongjie , Li Huilu , Xu Jin , Shu Yaqing 
Published: January 2025

AbstractBackgroundAnti‐N‐methyl‐D‐aspartate receptor encephalitis (anti‐NMDARE) is a prevalent type of autoimmune encephalitis caused by antibodies targeting the NMDAR's GluN1 subunit. While significant progress has been made in elucidating the pathophysiology of autoimmune diseases, the immunological mechanisms underlying anti‐NMDARE remain elusive. This study aimed to characterize immune cell interactions and dysregulation in anti‐NMDARE by leveraging single‐cell multi‐omics sequencing technologies.MethodsPeripheral blood mononuclear cells (PBMCs) from patients in the acute phase of anti‐NMDARE and healthy controls were sequenced using single‐cell joint profiling of transcriptome and chromatin accessibility. Differential gene expression analysis, transcription factor activity profiling, and cell‐cell communication modeling were performed to elucidate the immune mechanisms underlying the disease. In parallel, single‐cell B cell receptor sequencing (scBCR‐seq) and repertoire analysis were conducted to assess antigen‐driven clonal expansion within the B cell population.ResultsThe study revealed a significant clonal expansion of B cells, particularly plasma cells, in anti‐NMDARE patients. The novel finding of type I interferon (IFN‐I) pathway activation suggests a regulatory mechanism that may drive this expansion and enhance antibody secretion. Additionally, activation of Toll‐like receptor 2 (TLR2) in myeloid cells was noted, which may connect to tumor necrosis factor‐alpha (TNF‐α) secretion. This cytokine may contribute to the activation of B and T cells, thereby perpetuating immune dysregulation.ConclusionsThis study presents a comprehensive single‐cell multi‐omics characterization of immune dysregulation in anti‐NMDARE, highlighting the expansion of B cell and the activation of the IFN‐I and TLR2 pathways. These findings provide deeper insights into the molecular mechanism driving the pathogenesis of anti‐NMDARE and offer promising targets for future therapeutic intervention.Key points
Significant B cell clonal expansion, particularly in plasma cells, driven by antigen recognition.
IFN‐I pathway activation in plasma cells boosts their antibody production and potentially exacerbates immune dysregulation.
TLR2 pathway activation in myeloid cells contributes to TNF‐α secretion and could influence adaptive immune responses.
Transmit Antenna Selection for Full‐Duplex Relay Millimeter‐Wave Communications Employing Rate‐Splitting Multiple Access
Authors: Hung Dinh Cong , Nghia Pham Xuan , Thi Thanh Huyen Le , Tan Tran Dinh , Cao Nguyen Ba 
Published: January 2025

ABSTRACTThis article suggests using rate‐splitting multiple access (RSMA) and transmit antenna selection (TAS) within a full‐duplex relay (FDR) system that operates at high millimeter‐wave (MW) frequencies. We perform a mathematical analysis to derive closed‐form formulas for the outage probabilities (OPs) and throughputs for two users in the proposed RSMA‐MW system with TAS, taking into account the effects of residual self‐interference (RSI) at the FDR. Additionally, we consider practical system and channel parameters in our analysis. The numerical results indicate that the OPs in the RSMA‐MW system are significantly lower than those in a conventional nonorthogonal multiple access (NOMA)‐MW system. Importantly, high MW frequencies have a considerable impact on the OPs and throughputs of the RSMA‐MW system. In this context, using multiple antennas at the base station with TAS can greatly enhance the performance of the RSMA‐MW system. Furthermore, we thoroughly assess the effects of RSI caused by FDR, the distances between transmitters and receivers, transmit power, common and private rates, power allocation coefficients, and frequencies. Based on the observed behaviors of the RSMA‐MW system, several strategies are proposed to reduce OPs and increase throughputs. Finally, Monte Carlo simulations are performed to validate the derived formulas.
Sparse Code Multiple Access With Time Spreading and Repetitive Transmissions
Authors: Ülgen Oğuz , Kagan Tufekci Tolga , Sadi Yalcin , Erkucuk Serhat , Anpalagan Alagan , Baykaş Tunçer 
Published: January 2025

ABSTRACTFor the next‐generation communication systems, to improve spectral efficiency and increase the data rate, new multiple access techniques have been investigated. Orthogonal multiple access techniques are widely used in traditional communication systems while nonorthogonal multiple access (NOMA), proposed in 5G, has been a promising technology for satisfying the demand for future wireless communication networks. Sparse code multiple access (SCMA) is a code‐domain NOMA method that provides diversity gain with signal constellation coding. However, to increase the performance of SCMA, there are only limited works provided in the literature in terms of codebook design and receiver design. In this paper, a new multiple‐access model is proposed by applying various diversity techniques for downlink SCMA. The performance of the proposed model is evaluated with both computer simulations and theoretical analysis. Results show that the proposed model provides a 1.6 dB gain in terms of the bit error rate (BER) under the Rayleigh fading channel.
Serous Cystadenoma of the Pancreas: An Easily Missed Cytological Diagnosis and Clues to Diagnosis
Authors: Cuber Alicia , Chopra Shefali 
Published: January 2025

ABSTRACTSerous cystadenoma (SCA) of the pancreas is a benign nonmucinous cystic pancreatic neoplasm and the second most common type of pancreatic cystic neoplasm. Conservative management is advocated in asymptomatic cases as they have indolent clinical behavior and risk for postoperative morbidity, making an exact diagnosis essential. Morphologically, serous cystadenoma has a prominent subepithelial capillary meshwork causing the aspirate to be paucicellular and nondiagnostic. Therefore, cytologic diagnosis can be challenging, resulting in repeat aspirations or even unnecessary surgical resections. Since this is a diagnosis that is often overlooked, herein we offer a concise review of SCA along with characteristic radiology findings, diagnostic criteria including ancillary studies and possible differential considerations.
Advances in precise cell manipulation
Authors: Ma Yuan , Liang Zhenwei , Chen Yiqing , Wang Jiadao 
Published: January 2025

AbstractResearch on cells and organ‐like tissues is critical in the fields of molecular biology, genetic analysis, proteomics analysis, tissue engineering, and others. In recent years, advancements in precise cell manipulation technologies have made precise positioning and batch processing of cells feasible. Various methods are used for cell recognition, positioning, manipulation, and assembly, often introducing external fields such as electric, magnetic, acoustic, or optical fields into the liquid environment to interact with cells, applying forces to induce cell movement and rearrangement. Alternatively, three‐dimensional (3D) bioprinting technology is employed for precise cell positioning and assembly. This review will comprehensively assess the status, principles, advantages, disadvantages, and prospects of these precise cell manipulation technologies, covering single‐cell manipulation, multicellular assembly, and biological 3D printing techniques.
Linking Functional Traits To Trophic Roles In Scavenger Assemblages
Authors: Marie Montenegro Violeta , Mateo‐Tomás Patricia , Schneider Jessica , Dent Daisy H. , Crowther Tom , Bello Carolina 
Published: January 2025

ABSTRACTScavenging is a widespread feeding strategy involving a diversity of taxa from different trophic levels, from apex predators to obligate scavengers. Scavenger species play a crucial role in ecosystem functioning by removing carcasses, recycling nutrients and preventing disease spread. Understanding the trophic roles of scavenger species can help identify specialized species with unique roles and species that may be more vulnerable to ecological changes. To identify species with specialized roles, we studied three scavenger networks (one in north temperate Spain and two in central‐south Mediterranean Spain) that comprised 25 scavenger species (65% birds and 35% mammals), consuming carcasses of four wild ungulate species. We characterized the trophic role of a species by combining four species‐level network metrics (normalized degree, specialization, closeness, and betweenness centrality) into a single centrality metric, quantifying how scavenger species interact with carcass species within their ecological network. Higher centrality indicates the species feeds on a greater variety of carcasses and may contribute more to carrion consumption than species with lower centrality, which have more peripheral and specialized roles. The griffon vulture (Gyps fulvus) and the azure‐winged magpie (Cyanopica cyanus) had the highest centrality. In contrast, the red kite (Milvus milvus) in the northern site had the lowest centrality, and the Egyptian vulture (Neophron percnopterus) was among the most peripheral species for all three networks. In general, scavengers with large home ranges and nocturnal or crepuscular activity patterns tended to have more central roles, whereas species that forage silently tended to have more peripheral roles. Changes in species' centrality between sites and the high centrality of species with large home ranges suggest that management strategies in one location can have implications that extend beyond, highlighting the need to implement coordinated transboundary protection efforts to ensure the resilience and functionality of scavenger networks and derived ecosystem services.
Uncovering Diversity within the Glomeromycota: Novel Clades, Family Distributions, and Land Use Sensitivity
Authors: Delavaux Camille S. , Aellen Alexis , Stürmer Sidney L. , Primieri Silmar , Schütte Ursel M. E. , Drown Devin M. , Ramos Robert J. , Crowther Thomas W. , Bever James D. 
Published: January 2025

ABSTRACTArbuscular mycorrhizal fungi (AMF, phylum Glomeromycota) are essential to plant community diversity and ecosystem functioning. However, increasing human land use represents a major threat to native AMF globally. Characterizing the loss of AMF diversity remains challenging because many taxa are undescribed, resulting in poor documentation of their biogeography and family‐level disturbance sensitivity. We survey sites representing native and human‐altered ecosystems across the American continents—in Alaska, Kansas, and Brazil—to shed light on these gaps. Using a recently developed pipeline for phylogenetic placement of eDNA, we find evidence for three putative novel clades within the Glomeromycota, sister to Entrophosporaceae, Glomeraceae, and Archaeosporaceae, with evidence for geographic structuring. We further find that taxa in the Diversisporaceae, Glomeraceae, and Entrophosporaceae relatively high families are overrepresented and more diverse in temperate samples. By contrast, the diversity of taxa that cannot be placed into a family is higher in tropical samples, suggesting that tropical sites harbor relatively high undescribed AMF diversity. Moreover, we find evidence that Entrophosporaceae is more tolerant, while Glomeraceae is more sensitive to disturbance. These results underscore the vast undescribed diversity of AMF while highlighting a way forward to systematically improve our understanding of AMF biogeography and response to human disturbance.
How Does Landscape Structure Affect Dung Beetle Assemblages in Amazon Cities?
Authors: Mesquita Vanessa Pontes , Bernardino Glenda Vanessa dos Santos , Bobrowiec Paulo Estefano Dineli , Salomão Renato Portela , Cornelius Cintia 
Published: January 2025

ABSTRACTThe growth of cities is one of the main direct and indirect factors responsible for the loss of native vegetation cover. Urbanization directly affects the biological communities inhabiting forest remnants inserted in cities, compromising the maintenance of urban and natural ecosystems. By understanding the effects of landscape transformation due to urbanization, we can have insights regarding the distribution of land uses that allow a proper maintenance of the urban ecosystems. This work assessed the effects of landscape structure variables (forest cover, agricultural area, edge density, and number of forest patches) on dung beetle assemblages and functional groups (i.e., diet and resource removal strategy) sampled in 38 sites located along an urban–rural gradient of six cities belonging to the metropolitan area of Manaus in Central Amazonia. Losses of forest cover were the most determining factor, negatively affecting species richness, abundance, and body size. The increases in agriculture cover negatively affected dung beetle abundance, while edge density positively affected their abundance. The number of forest patches positively affected dung beetle abundances—except for dweller species—and negatively affected the body size of diet‐generalist species. These results demonstrate that changes in ecological diversity caused by urbanization are driven mostly by forest cover loss, although forest configuration is important for dung beetle abundance. This study contributes to the understanding of how changes in the amount and distribution of forest cover in tropical cities affect the taxonomic diversity of dung beetle assemblages.
Gyrfalcon Prey Abundance and Their Habitat Associations in a Changing Arctic
Authors: Gustafson Michaela , McCabe Jennifer D. , Rolek Brian W. , Booms Travis L. , Henderson Michael T. , Dunn Leah , Anderson David L. , Cruz Jennyffer 
Published: January 2025

ABSTRACTArctic habitats are changing rapidly and altering trophic webs and ecosystem functioning. Understanding how species' abundances and distributions differ among Arctic habitats is important in predicting future species shifts and trophic‐web consequences. We aimed to determine the habitat–abundance relationships for three small herbivores on the Seward Peninsula of Alaska, USA by fitting data from 983 point counts (collected during 2019, 2021, and 2022) with N‐mixture models that account for imperfect detection. These herbivore species, Willow Ptarmigan (Lagopus lagopus), Rock Ptarmigan (L. muta), and Arctic ground squirrels (Urocitellus parryii), are fundamental to tundra food webs, and primary prey for Arctic raptors including Gyrfalcons (Falco rusticolus). Second, we aimed to map herbivore densities within Gyrfalcon breeding territories. Third, we aimed to evaluate whether Gyrfalcons were more likely to occupy territories with higher prey densities using a multi‐season occupancy model coupled with occupancy observations from helicopter surveys conducted during 2016–2022 at 97 Gyrfalcon territories. We found that male Willow Ptarmigan were more abundant in areas with greater cover of tundra, tall shrubs, and tussock tundra. Conversely, male Rock Ptarmigan were more abundant in areas with greater cover of sparse vegetation and tundra. Arctic ground squirrels were more abundant at higher elevations with greater cover of sparse vegetation and low shrubs. Willow Ptarmigan were widespread within Gyrfalcon breeding territories, whereas Rock Ptarmigan and Arctic ground squirrels had patchier distributions with few areas of high abundance. Lastly, Gyrfalcons were more likely to occupy territories with higher densities of Willow Ptarmigan and Arctic ground squirrels. As the Artic continues to warm, Rock Ptarmigan and Arctic ground squirrels may be vulnerable to ongoing shrub encroachment, whereas Willow Ptarmigan may benefit. By tying abundances of three prey to Gyrfalcon occupancy, our results contribute to understanding potential impacts on higher levels of this Arctic trophic web.
Development of SNP for Sebastes Species Identification With Special Focus on the Cryptic Species Complex of Sebastes norvegicus
Authors: Johansen Torild , Hanebrekke Tanja , Besnier Francois , Westgaard Jon Ivar , Bruvold Ingrid Marie , Dahle Geir , Unneland Laila , Torp Christensen Helle , Saha Atal 
Published: January 2025

ABSTRACTThe genus Sebastes in the North Atlantic comprises of long lived deep‐waters species that have been extensively fished upon, and many stocks are severely depleted across the Atlantic. This is particularly evident for the species Sebastes norvegicus. In recent papers, cryptic species have been indicated within this genus and molecular markers are therefore needed to provide identification for the Sebastes species, including the cryptic species as a basis for advice regarding management and rebuilding of the stocks. A suite of 2800 Single Nucleotide Polymorphism (SNP) markers were identified from ddRAD sequencing data, of which 56 SNPs were organized in two multiplex reactions and tested on 191 Sebastes spp. from different sampling locations from Norway and Greenland. Good‐quality amplification products were successfully obtained from 49 SNP markers for Sebastes species ID, and 3 TaqMan probes were designed to successfully assign S. mentella, S. viviparus, and the two cryptic species S. norvegicus types A and B. A total 47 SNPs were biallelic, with averaged HE per locus ranging between 0.053 and 0.50. This SNP‐based method establishes a foundation for genetically identifying the Northeast Atlantic Sebastes species. The findings presented should be followed by an effort to look for morphological characters to recognize the S. norvegicus cryptic species on site. In general, the SNP markers are a proper tool for monitoring the distribution of the species from a management perspective.
A Double‐Blind Comparative Study of burstDR Versus Tonic Epidural Motor Cortex Stimulation for the Treatment of Intractable Neuropathic Pain
Authors: Seznec Yann , Thomas Joy , Jean Baptiste Pelletier , Buhot Benjamin , Convers Philippe , Peyron Roland , Vassal François 
Published: January 2025

ABSTRACTBackgroundPreliminary studies on epidural motor cortex stimulation (eMCS) for the treatment of drug‐resistant neuropathic pain have supported the extension to novel stimulation waveforms, in particular burstDR. However, only a low level of evidence is available. The aim of this retrospective observational study was to compare the analgesic efficacy of burstDR versus tonic eMCS.MethodsPatients suffering from unilateral, drug‐resistant neuropathic pain were selected for eMCS. During the trial phase, burstDR and tonic waveforms were successively applied for three consecutive months in a double‐blinded fashion and in a random order. The primary outcome criterion was the percentage of pain relief (%PR) at 3 and 6 months. The secondary outcome criterion was the proportion of patients reporting a superior %PR with the burstDR waveform.ResultsThirteen patients were included. The averaged %PR was 75.4% ± 18.6% after burstDR eMCS and 61.1% ± 28.6% after tonic eMCS (p = 0.21). Nine patients preferred the burstDR waveform for chronic eMCS (p = 0.16), and six of them were able to decrease or withdraw their analgesic drug intake. No adverse side effect was encountered in relation to burstDR eMCS.ConclusionsBurstDR eMCS seems at least as effective as tonic eMCS for the treatment of drug‐resistant neuropathic pain and shows a similar safety profile. Although the precise mechanisms of action remain to be fully elucidated, adequate matching between the oscillatory rhythm in the motor cortex and that of the burstDR waveform may increase synaptic efficacy, thus enhancing the functional connectivity of the motor cortex with remote brain networks involved in pain modulation.Significance StatementIn the present paper, we provide for the first time a double‐blinded study comparing burstDR versus tonic eMCS for the treatment of intractable, drug‐resistant neuropathic pain. Our results show that burstDR eMCS is a promising option in a population of patients especially difficult to treat, and support the ongoing move toward new stimulation waveforms able to more efficiently activate the brain networks involved in pain modulation.