bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preoperative MRI-based radiomic nomogram for distinguishing solitary fibrous tumor from angiomatous meningioma: a multicenter study
Authors: Li Mengjie , Fu Shengli , Du Jingjing , Han Xiaoyu , Duan Chongfeng , Ren Yande , Qiao Yaqian , Tang Yueshan 
Published: September 2024

PurposeThis study evaluates the efficacy of radiomics-based machine learning methodologies in differentiating solitary fibrous tumor (SFT) from angiomatous meningioma (AM).Materials and methodsA retrospective analysis was conducted on 171 pathologically confirmed cases (94 SFT and 77 AM) spanning from January 2009 to September 2020 across four institutions. The study comprised a training set (n=137) and a validation set (n=34). All patients underwent contrast-enhanced T1-weighted (CE-T1WI) and T2-weighted(T2WI) MRI scans, from which 1166 radiomics features were extracted. Subsequently, seventeen features were selected through minimum redundancy maximum relevance (mRMR) and the least absolute shrinkage and selection operator (LASSO). Multivariate logistic regression analysis was employed to assess the independence of these features as predictors. A clinical model, established via both univariate and multivariate logistic regression based on MRI morphological features, was integrated with the optimal radiomics model to formulate a radiomics nomogram. The performance of the models was assessed utilizing the area under the receiver operating characteristic curve (AUC), accuracy (ACC), sensitivity (SEN), specificity (SPE), positive predictive value (PPV), and negative predictive value (NPV).ResultsThe radiomics nomogram demonstrated exceptional discriminative performance in the validation set, achieving an AUC of 0.989. This outperformance was evident when compared to both the radiomics algorithm (AUC= 0.968) and the clinical model (AUC = 0.911) in the same validation sets. Notably, the radiomics nomogram exhibited impressive values for ACC, SEN, and SPE at 97.1%, 93.3%, and 100%, respectively, in the validation set.ConclusionsThe machine learning-based radiomic nomogram proves to be highly effective in distinguishing between SFT and AM.
Validation of a novel medical device (Chloe SED®) for the administration of analgesia during manual vacuum aspiration: a randomized controlled non-inferiority pilot study
Authors: Ramanathan Aparna , Samenjo Karlheinz Tondo , Bailey Robert C. , Imbamba Javan , Odenyo Stella , Koksal Erin , Diehl Jan Carel , Omoto Jackton , Gwer Stephen 
Published: September 2024

IntroductionMillions of women worldwide annually undergo manual vacuum aspiration (MVA) with no pain medication, which is a violation of their basic human dignity. We designed a novel device (Chloe SED®) to administer paracervical block (PCB) during MVA in countries where pain medication is not typically given due to the high cost of the necessary tools.MethodsWe conducted a single-blinded, randomized controlled non-inferiority trial including 61 patients at two hospitals in Kisumu, Kenya, to validate Chloe SED® for administration of PCB during MVA. PCB administered with Chloe SED® was compared to PCB administered with a standard spinal needle. Patients requiring MVA were block randomized in blocks of six, each provider completing six PCBs—three with the Chloe SED® and three with the standard spinal needle. The trial was registered with the Kenya Pharmacy and Poisons Board, ECCT/19/03/01 (https://ctr.pharmacyboardkenya.org/applications/index/protocol_no:RUNDVC8xOS8wMy8wMQ__/filter:/investigator:/sites:/pages:5/start_date:/end_date:/disease_condition:/users:/ercs:/stages). An intention-to-treat analysis was completed. The primary outcome was the non-inferiority of the pain score during uterine evacuation with a non-inferiority margin of 2 points on an 11-point numerical rating scale. Secondary outcomes included the non-inferiority of the pain score at four other time points and patient satisfaction.ResultsChloe SED® showed non-inferiority of the primary outcome with a mean pain score during evacuation of 3.8 [90% confidence interval (CI): 3.1–4.6] compared with the spinal needle at 4.1 (90% CI: 3.5–4.7). Non-inferiority of the pain score was shown at all time points. Most patients expressed a desire for the continued use of the device to administer PCB for MVA. No adverse events were noted.ConclusionIn summary, the Chloe SED® appears non-inferior to the spinal needle and desirable for the administration of PCB during MVA.
Quantitative and functional changes in platelets and fibrinogen following cardiopulmonary by-pass in children
Authors: Plebani Margherita , Longchamp David , Lauwers Pauline , Di Bernardo Stefano , Perez Maria-Helena 
Published: September 2024

IntroductionCardiopulmonary bypass (CPB) causes coagulopathy, increasing the risk of postoperative bleeding and mortality. The underlying causes of post-CPB coagulopathy and the factors associated with its occurrence are not yet fully understood. This study assesses platelet and fibrinogen concentration and function following CPB in children with congenital heart diseases (CHD).MethodsWe analyzed prospective data from 104 patients aged 0–16 years who underwent CPB surgery for CHD. Blood samples were collected before surgery and within 30 min of CPB completion. In addition to usual coagulation tests, functional analyses were performed using point of care systems with thromboelastometry and impedance aggregometry.ResultsPlatelet count, fibrinogen concentration, and platelet and fibrinogen activities significantly decreased after CPB. The duration of CPB was directly associated with a reduction in platelet count and fibrinogen level (r = −0.38, p &lt; 0.001; r = −0.21, p = 0.03, respectively), but not with their measured activity. Postoperative percentages of baseline values for platelet count (58.36% [43.34–74.44] vs. 37.44% [29.81–54.17], p &lt; 0.001) and fibrinogen concentration (73.68% [66.67–82.35] vs. 65.22% [57.89–70.83], p &lt; 0.001) were significantly higher in patients who did not experience hypothermia during surgery. Age was inversely associated with the decrease in platelet count (r = 0.63, p &lt; 0.001), TRAPTEM AUC (r = 0.43, p &lt; 0.001), fibrinogen concentration (r = 0.44, p &lt; 0.001) and FIBTEM MCF (r = 0.57, p &lt; 0.001).ConclusionPost-CPB coagulopathy is multifactorial and not solely attributed to hemodilution. It also involves functional changes in coagulation cascade components, which can be demonstrated by thromboelastometry and impedance aggregometry. Young children, patients requiring prolonged CPB surgery, or those experiencing hypothermia are particularly affected.
Lentivirus-mediated RNA interference targeting HMGB1 modulates AQP1 to reduce pain induced by chronic compression of the dorsal root ganglia
Authors: Li Jinlu , Yang Kaihong , Yao Fuchao , Wei Hui 
Published: September 2024

BackgroundsNeuropathic pain (NP) is a kind of chronic pain that has attracted much attention in clinical practice, characterized by high morbidity, complex mechanisms, and difficulties in clinical treatment, with which the activation of High mobility group box 1 (HMGB1) is closely related. The aim of this study was to investigate the effects of lentivirus-mediated RNA interference gene therapy targeting HMGB1 on neuropathic pain in rats with chronic dorsal root ganglion compression (CCD) and its specific mechanisms, so as to explore new pharmacological targets.MethodsAdult male Wistar rats were surgically subjected to chronic compression of the dorsal root ganglia (CCD). Behavioral tests were performed by calculating the paw withdrawal mechanical threshold (PWMT) and the thermal paw withdrawal latency (TPWL). Co-immunoprecipitation (CO-IP) was used to clarify protein interactions. Gene silencing was induced by injecting lentivirus expressing HMGB1 short hairpin RNA (shRNA) into rats. An LPS-inflammation-stimulated rat astrocyte model was established to validate the animal experiment results further. Western blot analysis and real-time quantitative PCR were used to detect pathway protein expression.ResultsAfter first establishing the rat CCD model, both PWMT and PTWL were significantly reduced in rats, indicating that the model construction was successful. After lentiviral silencing of HMGB1 expression, NP was significantly alleviated in CCD rats. CO-IP experiments showed a link between HMGB1 and AQP1; After silencing HMGB1 expression, the expression of AQP1 was significantly reduced, and HMGB1 was able to modulate the effect of AQP1 on NP. Further use of an inhibitor of the HMGB1 receptor showed that after inhibition of RAGE, AQP1 was significantly reduced; HMGB1 may regulate AQP1 through its receptor RAGE to affect NP. Silencing of HMGB1 resulted in a significant decrease in NF-κB, and HMGB1 affects the inflammatory pathways it mediates. After silencing AQP1, NF-κB also decreased significantly, indicating that AQP1 is an upstream regulator of NF-κB.ConclusionLentivirus-mediated RNA interference (RNAi) silencing targeting HMGB1 may play a key role in the development of neuropathic pain in rats by regulating AQP1 expression via RAGE and ultimately activating NF-κB.
Genetic dissection of stem and leaf rachis prickles in diploid rose using a pedigree-based QTL analysis
Authors: Rawandoozi Zena J. , Barocco Andrew , Rawandoozi Maad Y. , Klein Patricia E. , Byrne David H. , Riera-Lizarazu Oscar 
Published: September 2024

IntroductionPrickles are often deemed undesirable traits in many crops, including roses (Rosa sp.), and there is demand for rose cultivars with no or very few prickles. This study aims to identify new and/or validate reported quantitative trait loci (QTLs) associated with stem and leaf rachis prickle density, characterize the effects of functional haplotypes for major QTLs, and identify the sources of QTL-alleles associated with increased/decreased prickle density in roses.MethodsQTL mapping using pedigree-based analysis (PBA), and haplotype analysis were conducted on two multi-parental diploid rose populations (TX2WOB and TX2WSE).Results and discussionTwelve QTLs were identified on linkage groups (LGs) 2, 3, 4, and 6. The major QTLs for the stem prickle density were located between 42.25 and 45.66 Mbp on chromosome 3 of the Rosa chinensis genome assembly, with individual QTLs explaining 18 to 49% of phenotypic variance (PVE). The remaining mapped QTLs were minor. As for the rachis prickle density, several QTLs were detected on LG3, 4, and 6 with PVE 8 to 17%. Also, this study identified that ancestors R. wichurana ‘Basye’s Thornless’, ‘Old Blush’, and the pollen parent of M4-4 were common sources of favorable alleles (q) associated with decreased prickle density, whereas ’Little Chief’ and ‘Srche Europy’ were the source of unfavorable alleles (Q) in the TX2WOB and TX2WSE populations, respectively. The outcomes of this work complement other studies to locate factors that affect prickle density. These results can also be utilized to develop high-throughput DNA tests and apply parental selection to develop prickle-free rose cultivars.
Experimental evidence of inbreeding depression for competitive ability and its population-level consequences in a mixed-mating plant
Authors: Walker Mark J. , Spigler Rachel B. 
Published: September 2024

Inbreeding depression is a key factor regulating the evolution of self-fertilization in plants. Despite predictions that inbreeding depression should evolve with selfing rates as deleterious alleles are increasingly exposed and removed by selection, evidence of purging the genetic load in wild populations is equivocal at best. This discordance could be explained, in part, if the load underlying inbreeding depression is subject to soft selection, i.e., the fitness of selfed individuals depends on the frequency and density of selfed vs. outcrossed individuals in the population. Somewhat counterintuitively, this means that populations with contrasting mutation load can have similar fitness. Soft selection against selfed individuals may be expected when there is inbreeding depression for competitive ability in density-regulated populations. We tested population-level predictions of inbreeding depression in competitive ability by creating a density series of potted plants consisting of either purely outcrossed, purely selfed, or mixed (50% outcrossed, 50% selfed) seed of the mixed-mating biennial Sabatia angularis (Gentianaceae) representing ecological neighborhoods. Focusing on the growth and survival of juveniles, we show that mean plant size is independent of neighborhood composition when resources are limiting, but greatest in outcrossed neighborhoods at low densities. Across a range of densities, this manifests as stronger density-dependence in outcrossed populations compared to selfed or mixed ones. We also found significantly greater size inequalities among individuals in mixed neighborhoods, even at high densities where mean juvenile size converged, a key signature of asymmetric competition between outcrossed and selfed individuals. Our work illustrates how soft selection could shelter the genetic load underlying inbreeding depression and its demographic consequences.
Endophytic bacteria with allelopathic potential regulate gene expression and metabolite production in host Casuarina equisetifolia
Authors: Wang Ying , Chen Pan , Lin Qi , Zuo Linzhi , Li Lei 
Published: September 2024

IntroductionCasuarina equisetifolia is a common protective forest in coastal areas. However, artificial C. equisetifolia forests cannot self-renew, mainly due to the accumulation of allelochemicals. Endophytic bacteria may alleviate the root growth inhibition caused by allelochemicals in C. equisetifolia seedlings. B. amyloliquefaciens and B. aryabhattai were endophytic bacteria with strong allelopathy in C. equisetifolia root. The allelopathy mechanism of these two endophytes and their interaction with C. equisetifolia remains to be studied.MethodsWhole-genome sequencing of B. amyloliquefaciens and B. aryabhattai isolated from the roots of allelochemical-accumulating C. equisetifolia was performed using Illumina Hiseq and PacBio single-molecule sequencing platforms. Sterile seedlings of C. equisetifolia were treated with either individual or mixed bacterial cultures through root drenching. Transcriptional and metabolomics analyses were conducted after 3 days of infection.Results and discussionWhole-genome sequencing of Bacillus aryabhattai and Bacillus amyloliquefaciens showed that the two strains contained various horizontal gene transfer elements such as insertion sequence, prophage and transposon. In addition, these two strains also contain numerous genes related to the synthesis and catabolism of allelochemicals. After these two strains of bacteria were individually or mixed infected with C. equisetifolia, metabolomics and transcriptomic analysis of C. equisetifolia showed the 11 important secondary metabolite biosynthesis among them alkaloids biosynthesis, phenylpropanoid and terpenes biosynthesis and related genes were putatively regulated. Correlation analysis revealed that 48 differentially expressed genes had strong positive correlations with 42 differential metabolites, and 48 differentially expressed genes had strong negative correlations with 36 differential metabolites. For example, CMBL gene showed positive correlations with the allelochemical (-)-Catechin gallate, while Bp10 gene showed negative correlations with (-)-Catechin gallate.ConclusionThe intergenerational accumulation of allelochemicals may induce horizontal gene transfer in endogenic bacteria of Casuarina equisetifolia root. Endophytic Bacillus plays an allelopathic role by assisting the host in regulating gene expression and the production and/or variety of allelochemicals. This comprehensive study sheds light on the intricate genetic and metabolic interactions between Bacillus endophytes and C. equisetifolia. These findings provide insights into endophyte-mediated allelopathy and its potential uses in plant biology and forest sustainability.
Organic waste recycling application increases N availability and mitigates N2O emission without crop yield penalty in the North China Plain
Authors: Chen Lin , Du Hailun , Liu Qing , Gao Wangsheng , Cui Jixiao , Chen Yuanquan 
Published: September 2024

IntroductionAgricultural organic waste recycling can supply nutrients for crop production and partially replace chemical nitrogen fertilizers, which is beneficial for waste management and environmental protection. Nevertheless, comprehensive evaluation of the effects of different organic materials applications on crop yield and the environment is limited.MethodsTherefore, in this study, a comprehensive investigation of the synergistic effects of straw, pig manure, and biogas residue recycling on the wheat (Triticum aestivum L.) and maize (Zea mays L.) systems was carried out in the North China Plain. Field experiments were conducted from 2019 to 2021, comprising five treatments: straw (ST), pig manure (PM), and biogas residue (BR) partially replacing chemical nitrogen fertilizer, sole application of chemical nitrogen fertilizer (CF), and a control with no nitrogen application (WN).Results and discussionThe results showed that organic materials significantly increased soil total nitrogen (3.04%–9.10%) and N recovery efficiency (REN; 42.21%–44.99%), but pig manure was more beneficial in increasing crop yields (3.50%), especially wheat yields (8.72%), and REN was significantly higher than that of the other treatments. Organic materials performed differently in wheat and maize seasons, and wheat yield could be improved by organic materials return. Organic materials stimulated N2O emission in wheat season (4.28%–32.20%), while biogas residue inhibited the N2O emission in maize season (47.47%). The negative effect of straw and biogas residue on yield decreased with increasing years of return, and pig manure continued to contribute to yield. In conclusion, pig manure is the optimal alternative that can increase crop yield, soil N content, and REN without stimulating N2O emissions.
The effect of chess on cognition: a graph theory study on cognitive data
Authors: Gonzalez-Burgos Lissett , Lozano-Rodriguez Candida , Molina Yaiza , Garcia-Cabello Eloy , Aciego Ramón , Barroso José , Ferreira Daniel 
Published: September 2024

ObjectivesWe aimed to advance our understanding of the effect of chess on cognition by expanding previous univariate studies with the use of graph theory on cognitive data. Specifically, we investigated the cognitive connectome of adult chess players.MethodWe included 19 chess players and 19 controls with ages between 39 and 69 years. Univariate analysis and graph theory included 27 cognitive measures representing multiple cognitive domains and subdomains. Graph analysis included global and nodal measures of integration, segregation, and centrality. We also performed an analysis of community structures to gain an additional understanding of the cognitive architecture of chess players.ResultsThe analysis of global graph measures showed that chess players had a higher local efficiency than controls at the cost of a lower global efficiency, which did not permeate segregation aspects of their connectome. The nodal graph measures showed that executive/attention/processing speed and visuoconstructive nodes had a central role in the connectome of chess players. The analysis of communities showed that chess players had a slightly reorganized cognitive architecture into three modules. These graph theory findings were in the context of better cognitive performance in chess players than controls in visuospatial abilities.ConclusionWe conclude that the cognitive architecture of chess players is slightly reorganized into functionally and anatomically coherent modules reflecting a distinction between visual, verbal, and executive/attention/processing speed-related functions, perhaps reminiscent of right hemisphere and left hemisphere subnetworks orchestrated by the frontal lobe and its white matter connections.
Analyses of single-cell and bulk RNA sequencing combined with machine learning reveal the expression patterns of disrupted mitophagy in schizophrenia
Authors: Yang Wei , Lian Kun , Ye Jing , Cheng Yuqi , Xu Xiufeng 
Published: September 2024

BackgroundMitochondrial dysfunction is an important factor in the pathogenesis of schizophrenia. However, the relationship between mitophagy and schizophrenia remains to be elucidated.MethodsSingle-cell RNA sequencing datasets of peripheral blood and brain organoids from SCZ patients and healthy controls were retrieved. Mitophagy-related genes that were differentially expressed between the two groups were screened. The diagnostic model based on key mitophagy genes was constructed using two machine learning methods, and the relationship between mitophagy and immune cells was analyzed. Single-cell RNA sequencing data of brain organoids was used to calculate the mitophagy score (Mitoscore).ResultsWe found 7 key mitophagy genes to construct a diagnostic model. The mitophagy genes were related to the infiltration of neutrophils, activated dendritic cells, resting NK cells, regulatory T cells, resting memory T cells, and CD8 T cells. In addition, we identified 12 cell clusters based on the Mitoscore, and the most abundant neurons were further divided into three subgroups. Results at the single-cell level showed that Mitohigh_Neuron established a novel interaction with endothelial cells via SPP1 signaling pathway, suggesting their distinct roles in SCZ pathogenesis.ConclusionWe identified a mitophagy signature for schizophrenia that provides new insights into disease pathogenesis and new possibilities for its diagnosis and treatment.