bluuebunny/crossref_metadata_2025_split huggingface dataset:
ANTsX neuroimaging-derived structural phenotypes of UK Biobank
Authors: Tustison Nicholas J. , Yassa Michael A. , Rizvi Batool , Cook Philip A. , Holbrook Andrew J. , Sathishkumar Mithra T. , Tustison Mia G. , Gee James C. , Stone James R. , Avants Brian B. 
Published: October 2023

Abstract
UK Biobank is a large-scale epidemiological resource for investigatingprospective correlations between various lifestyle, environmental, and geneticfactors with health and disease progression. In addition to individual subject information obtained through surveys and physical examinations, a comprehensive neuroimaging battery consisting of multiple modalities provides imaging-derived phenotypes (IDPs) that can serve as biomarkers in neuroscience research. In this study, we augment the existing set of UK Biobank neuroimaging structural IDPs,obtained from well-established software libraries such as FSL and FreeSurfer, with related measurements acquired through the Advanced Normalization Tools Ecosystem. This includes previously established cortical and subcortical measurements defined, in part, based on the Desikan-Killiany-Tourville atlas. Also included are morphological measurements from two recent developments: medial temporal lobe parcellation of hippocampal and extra-hippocampal regions in addition to cerebellum parcellation and thickness based on the Shannem ananatomical labeling. Through predictive modeling, we assess the clinical utility of these IDP measurements, individually and in combination, using commonly studied phenotypic correlates including age, fluid intelligence, numeric memory,and several other sociodemographic variables. The predictive accuracy of these IDP-based models, in terms of root-mean-squared-error or area-under-the-curve for continuous and categorical variables, respectively, provides comparative insights between software libraries as well as potential clinical interpretability. Results demonstrate varied performance between package-based IDP sets and their combination, emphasizing the need for careful considerationin their selection and utilization.
A Novel Nomogram for Predicting Mucosal Healing in Crohn's Disease in Children
Authors: Wang Enhui , Han Lina , Guo Jing , Zhang Mingyu , Xu Lingfen 
Published: October 2023

Abstract
Purpose: To analyze the clinical risk factors and establish a non-invasive nomogram clinical prediction model for mucosal healing in children with Crohn's disease.
Methods:The clinical data of patients aged 1–14 years with Crohn's disease were retrospectivelyanalyzed. Patients were divided into the mucosal healing and non-mucosal healing groups. General data, clinical symptoms, and laboratory examination results of the two groups were compared. The risk factors affecting mucosal healing were analyzed statistically, and nomogram models were established.
Results: From January 2011 to June 2023, a total of 74 patients who were continuously diagnosed with Crohn's disease and underwent endoscopy and follow-up after treatment were included in the study. There were 41 patients in the mucosal healing group and 33 in the non-mucosal healing group. Multivariate logistic regression analysis revealed that the erythrocyte sedimentation rate (ESR), platelet-to-lymphocyte ratio (PLR),and C-reactive protein-to-albumin ratio (CAR) were independent risk factors for mucosal healing; thus, they were included in the prediction model. A nomogram was constructed based on the results of the multivariate analysis. The area under the receiver operating characteristic curve of this model was 0.942 (95% confidence interval: 0.842–0.950). The Hosmer–Lemeshow test showed that the decision graph had good calibration (P=0.708).
Conclusion:A nomogram model was established based on three related factors (ESR, PLR, and CAR), which can be used to predict mucosal healing in children with Crohn’s disease after treatment, thus reducing the frequency of endoscopic examination.
Metabolic Basis for the Microbial Oxidation of Atmospheric Methane
Authors: Schmider Tilman , Hestnes Anne Grethe , Brzykcy Julia , Schmidt Hannes , Schintlmeister Arno , Roller Benjamin , Söllinger Andrea , Schmidt Oliver , Polz Martin , Richter Andreas , Svenning Mette , Tveit Alexander 
Published: October 2023

Abstract

Atmospheric methane oxidizing bacteria (atmMOB) constitute the sole biological sink for atmospheric methane and have been discovered worldwide over the past decades. Still, insufficient knowledge about the metabolic basis of atmMOB, caused by the lack of pure cultures, limits our ability to manage, study, and exploit the atmospheric methane sink and thus to fight the 21st century methane surge. Here we combine filter cultivation, trace gas oxidation, 15N2-incorporation experiments, and comparative proteomics, to assess the potential of seven methanotrophic species to grow on atmospheric methane. Four species, three of which are outside the canonical atmMOB group USCα, enduringly oxidized atmospheric methane, hydrogen, and carbon monoxide with distinct substrate preferences over a 12-month growth period "on air". Despite this mixotrophy and high specific affinities for methane, the estimated energy yields of the atmMOB were substantially lower than previously assumed necessary for cellular maintenance, contradicting the basic energy premise for atmMOB. Comparative proteomics indicate major physiological adjustments to grow “on air” as the atmMOB allocated their proteomes to decrease energy intensive processes, including biosynthesis, and increase investments into trace gases oxidation. Our work outlines the metabolic basis of atmMOB, microorganisms that exploit the atmosphere as energy and carbon source while mitigating the potent greenhouse gas methane.
Consciousness transitions during epilepsy seizures through the lens of Integrated Information Theory
Authors: Baglivo Fabricio H. , Campora Nuria , Mininni Camilo J. , Kochen Silvia , Lew Sergio E. 
Published: October 2023

Abstract
Consciousness is one of the most complex aspects of human experience. Studying the mechanisms involved in transitions and in different levels of consciousness is one of the greatest challenges of neuroscience. In this study we use a measure based on computing the integrated information using an autoregressive system (ΦAR) to evaluate dynamic changes during consciousness transitions. This index is applied to an intracranial electroencephalography (iEEG) dataset collected from 6 patients that suffer from refractory epilepsy. These records were obtained during resting state and during the crisis. Networks outside epileptogenic regions were created in order to study the ΦAR index evolution when a crisis is detected. By using the Consciousness Seizure Scale (CCS) we show that changes on ΦAR are significantly correlated with changes in the reported states of consciousness.
Prediction of Machine Tool Spindle Assembly Quality Variation Based on the Stacking Ensemble Model
Authors: Liu Min-Sin , Kuo Ping-Huan , Chen Shyh-Leh 
Published: October 2023

Abstract

This paper presents a stacking ensemble model to predict the assembly quality variation of machine tool spindles. The model uses data from 925 single-spindle inspections and extracts evaluation metrics from multiple domains to extract valuable information. Feature selection is performed using a correlation model to identify important features, and various lightweight supervised learning algorithms are applied to analyze the data. To further enhance the model's performance, a stacking ensemble approach is proposed, which combines algorithms. The proposed ensemble model achieves an accuracy rate of 85.47%, a precision rate of 86.44%, a recall rate of 85.64%, and an F1 value of 86.04%. The results demonstrate that the proposed stacking ensemble model is an effective approach for predicting the assembly quality variation of machine tool spindles, using the data available.
Psychometric properties of the environmental determinants of health questionnaire: development and validation of the English version in Nigeria
Authors: Sabo Abdulwali , Kuan Garry , Abdullah Sarimah , Kuay Hue San , Kueh Yee Cheng 
Published: October 2023

Abstract
Background
The environmental determinants of health (EDH) have a significant impact on people's physical, mental, and social wellbeing. Everyone needs access to environmental resources of all types, including food, materials, and energy, to survive. However, there is no valid and reliable instrument available that can be used to evaluate individuals' perceived levels of EDH. Hence, the purpose of this study was to create a short, self-reported measure for evaluating perceived EDH.
Method
A cross-sectional survey was conducted among university undergraduate students in Nigeria. The respondents were selected using a convenience sampling method to evaluate their perceptions regarding EDH. To determine the psychometric properties of the newly created EDH scale, the Content Validity Index (CVI), Face Validity Index (FVI), Exploratory Factor Analysis (EFA), Confirmatory Factor Analysis (CFA), Composite Reliability (CR), Average Variance Extracted (AVE), Cronbach's alpha, and Intraclass Correlation Coefficient (ICC) were all computed.
Results
The study involved 300 respondents in the EFA (males 55.7%, females 44.3%) and 430 respondents in the CFA (males 54.0%, females 46.0%). In the EFA, two constructs were identified (the natural environment and the built environment). The EFA model was able to explain 63.57% of the total cumulative variance, and the factor correlation was 0.671. The Cronbach's alpha values of the two constructs were 0.918 (natural environment) and 0.935 (built environment). In the CFA, some modifications were done on the measurement model. The final re-specified measurement model showed that the EDH scale, which has two constructs and 18 items, has adequate construct validity (CFI = 0.948, TLI = 0.938, SRMR = 0.046, RMSEA = 0.052, and RMSEA p-value = 0.344). The CRs were 0.845 (natural environment) and 0.854 (built environment). The ICCs were 0.976 (natural environment) and 0.970 (built environment).
Conclusion
The results show that the newly created EDH has sufficient construct validity and may be utilized to assess participants' perceptions of their level of EDH. It is strongly encouraged that this instrument be examined in populations with different age ranges and other demographic characteristics.
Exploring the impact of PEGylation on pharmacokinetics: a size-dependent effect of polyethylene glycol on prostate specific membrane antigen inhibitors
Authors: Liu Yang , Xia Li , Li Haiyang , Cai Ping , Tang Sufan , Feng Yue , Liu Guangfu , Chen Yue , Liu Nan , zhou Zhijun 
Published: October 2023

Abstract
Background.
Prostate cancer (PCa) is the second most frequent cancer and the fifth leading cause of cancer-related deaths in men. Prostate-specific membrane antigen (PSMA) as a target has gained increasing attention. This research aims to investigate and understand how altering size of PEG impacts the in vitro and in vivo behavior and performance of PSMA inhibitors, with a specific focus on their pharmacokinetic characteristics and targeting properties.
Results.
Two 68Ga-labeled PSMA-targeted radiotracers were developed, namely [68Ga]Ga-PP4-WD and [68Ga]Ga-PP8-WD, with varying sizes of polyethylene glycol (PEG). [68Ga]Ga-PP4-WD and [68Ga]Ga-PP8-WD had excellent affinity for PSMA with IC50 being 8.06 ± 0.91, 6.13 ± 0.79 nM, respectively. Both tracers enabled clear visualization of LNCaP tumors in PET images with excellent tumor-to-background contrast. They also revealed highly efficient uptake and internalization into LNCaP cells, increasing over time. The biodistribution studies demonstrated that both radioligands exhibited significant and specific uptake into LNCaP tumors. Furthermore, they were rapidly cleared through the renal pathway, as evidenced by [68Ga]Ga-PP4-WD and [68Ga]Ga-PP8-WD showing a 10-fold and a 5-fold less in renal uptake, respectively, compared to [68Ga]Ga-Flu-1 in 30 min. Both in vitro and in vivo experiments demonstrated that PEG size significantly impacted tumor-targeting and pharmacokinetic properties.
Conclusions.
These radiotracers have demonstrated their effectiveness in significantly reducing kidney uptake while maintaining the absorbed dose in tumors. Both radiotracers exhibited strong binding and internalization characteristics in vitro, displayed high specificity and affinity for PSMA in vivo.
Beware of Leigh Syndrome Pedigrees with MT-ATP6 Mutation Whose Primary Diagnosis is Retinitis Pigmentosa
Authors: Li Yike , Liu Yang , Du Ziyu , Zhou Kaijin , Mao Bin , Zhang Lu , Yu AYong 
Published: October 2023

Abstract

purpose:Maternally Inherited Leigh Syndrome (MILS) is a group of systemic diseases caused by defects in mitochondrial oxidative phosphorylation (OXPHOS). We aim to investigate the clinical and genetic characteristics of MILSpedigree with MT-ATP6 mutation who were first diagnosed with RP.Methods:This study included a family pedigree consisting of a proband with visual blurring symptoms, his mother with similar symptoms, and a father who was asymptomatic. The medical history was asked, and the best corrected visual acuity (BCVA), intraocular pressure, slit-lamp, wide-field fundus photography, optical coherence tomography (OCT), visual evoked potential (VEP) and whole exome sequencing were performed. In addition, brain Magnetic Resonance Imaging (MRI) and physical examination were performed for the mother and child.Results:Whole exon sequencing showed that the proband carried mitochondrial MT-ATP6 gene mutation. The proband's mother carried an 8993T>G heterozygous mutation, with a heterozygous mutation load of 86%, which was inherited from the proband's mother (heterozygous mutation load of 62%). This gene is the primary pathogenic gene of MILS. The patient was diagnosed with MILS after a complete physical examination and imaging examination.Conclusions:This study suggests that RP can be the cause of the first visit of MILS patients. Therefore, ophthalmologists should be alert to MILS when they find patients with clinical symptoms of the nervous system in the face of RP patients. MT-ATP6 mutation is one of the causes of RP, and its pathogenic mechanism has not been clearly explained. In the future, the research and intervention of MT-ATP6 mutation may provide a new direction for the diagnosis and treatment of MILS-related RP.
The genome of Citrus australasica reveals disease resistance and other species specific genes
Authors: Nakandala Upuli , Furtado Agnelo , Masouleh Ardashir Kharabian , Smith Malcolm W. , Williams Darren C. , Henry Robert J. 
Published: October 2023

Abstract
Background
The finger lime (Citrus australasica), one of six Australian endemic citrus species shows a high natural phenotypic diversity and novel characteristics. The wide variation and unique horticultural features have made this lime an attractive candidate for domestication. Here we present a high quality, haplotype-resolved reference genome for this species using PacBio HiFi and Hi-C sequencing.
Results
Hifiasm assembly and SALSA scaffolding resulted in a collapsed genome size of 344.2 Mb and 321.1 Mb and 323.2 Mb size for the two haplotypes. The nine pseudochromosomes of the collapsed genome had an N50 of 35.2 Mb, 99.1% genome assembly completeness and 98.9% gene annotation completeness (BUSCO). A total of 41,304 genes were predicted in the nuclear genome. Comparison with C. australis revealed that 13,661 genes in pseudochromosomes were unique in C. australasica. These were mainly involved in plant-pathogen interactions, stress response, cellular metabolic and developmental processes, and signal transduction. The two genomes showed a syntenic arrangement at the chromosome level with large structural rearrangements in some chromosomes. Genetic variation among five C. australasica cultivars was analysed. Genes related to defense, synthesis of volatile compounds and red/yellow coloration were identified in the genome. A major expansion of genes encoding thylakoid curvature proteins was found in the C. australasica genome.
Conclusions
This high quality, haplotype resolved genome contributes to our understanding of citrus evolution and reveals disease resistance and quality related genes with potential to accelerate the genetic improvement of citrus.
Transcriptome variations in hybrids of wild emmer wheat (Triticum turgidum ssp. dicoccoides)
Authors: Ziv Alon , kashkush Khalil 
Published: October 2023

Abstract

Background
Wild emmer wheat is a great candidate to revitalize domesticated wheat genetic diversity. Recent years have seen intensive investigation into the evolution and domestication of wild emmer wheat, including whole-genome DNA and transcriptome sequencing. However, the impact of intraspecific hybridization on the transcriptome of wild emmer wheat has been poorly studied. In this study, we assessed changes in methylation patterns and transcriptomic variations in two accessions of wild emmer wheat collected from two marginal populations, Mt. Hermon and Mt. Amasa, and in their stable F4 hybrid.
Results
Methylation-Sensitive Amplified Polymorphism (MSAP) detected significant cytosine demethylation in F4 hybrids vs. parental lines, suggesting potential transcriptome variation. After a detailed analysis, we examined nine RNA-Seq samples, which included three biological replicates from the F4 hybrid and its parental lines. RNA-Seq databases contained approximately 200 million reads, with each library consisting of 15 to 25 million reads. There are a total of 62,490 well-annotated genes in these databases, with 6,602 genes showing differential expression between F4 hybrid and parental lines Mt. Hermon and Mt. Amasa. The differentially expressed genes were classified into four main categories based on their expression patterns. Gene ontology (GO) analysis revealed that differentially expressed genes are associated with DNA/RNA metabolism, photosynthesis, defense response, and phosphorylation.
Conclusion
This study highlights the significant transcriptomic changes resulting from intraspecific hybridization within natural plant populations, which might aid the nascent hybrid in adapting to various environmental conditions.
Complex PTSD symptom clusters and executive function in UK Armed Forces veterans: a cross-sectional study
Authors: Biscoe Natasha , New Emma , Murphy Dominic 
Published: October 2023

Abstract
Background: Less is known about complex posttraumatic stress disorder (PTSD) than PTSD in military veterans, yet this population may be at greater risk of the former diagnosis. Executive function impairment has been linked to PTSD treatment outcomes. The current study therefore aimed to explore possible associations between each complex PTSD symptom cluster and executive function to understand if similar treatment trajectories might be observed with the disorder.
Methods: A total of 428 veterans from a national charity responded to a self-report questionnaire which measured complex PTSD symptom clusters using the International Trauma Questionnaire, and executive function using the Adult Executive Function Inventory. Single and multiple linear regression models were used to analyse the relationship between complex PTSD symptom clusters and executive function, including working memory and inhibition.
Results: Each complex PTSD symptom cluster was significantly associated with higher executive function impairment, even after controlling for possible mental health confounding variables. Emotion dysregulation was the complex PTSD symptom cluster most strongly associated with executive function impairment.
Conclusions: This is the first study to explore the relationship between executive function and complex PTSD symptom clusters. The study builds on previous findings and suggests that executive function could be relevant to complex PTSD treatment trajectories, as is the case with PTSD alone. Future research should further explore such clinical implications.
Detection of bacteria carried by ticks from the mountain areas of Guizhou, Southwestern China
Authors: Zhan Lin , Wu Shengchun , He Xian Hai , Zhou Xiao Quan , Meng Jiao , Zhou Cao Min , Yang Bin , Huang JianSheng , Yang Guanghong , Jiang Jia Fu , Xiao Zheng , Sun Yi , Wu Jia Hong , Cao Wu Chun , Yu Fu xun 
Published: October 2023

Abstract
Background: Emerging tick-borne bacterial pathogens pose a threat to public health. The bacterial community and diversity in ticks have been reported with high-throughput sequencing methods that have been widely used in microorganism identification. Tick-borne bacterial pathogens such as Rickettsia, Ehrlichia, Coxiella, and Bartonella amplified by PCR methods have been reported in Guizhou. Little information has been reported on the diversity of the bacterial community in ticks in the areas. The aim of this study was to explore the diversity of the bacterial community in ticks from Guizhou Province, southwestern China.
Methods: Ticks were collected in the mountainous areas of three counties in Guizhou Province from 2019-2022. Tick species were identified by morphology and molecular biology. DNA was extracted from tick samples, followed by high-throughput sequencing of the full-length 16S rRNA gene to analyze the diversity of the bacterial community of ticks.
Results: A total of 554 ticks were captured, including 453 Rhipicephalus microplus and 101 Haemaphysalis longicornis, from cattle and sheep in Ziyun, Shibing, and Luodian Counties. In total, 823 operational taxonomic units (OTUs) were identified with 13 phyla, 22 classes, 55 orders, 121 families, and 253 genera of bacteria. The dominant bacterial genera were Staphylococcus, Pseudomonas, and Stenotrophomonas. We noticed that Rickettsia and Coxiella were abundant in the samples collected from Luodian County. Other tick-borne pathogens, such as Bartonella, Yersinia, Brucella, Anaplasma, and Francisella,were distinguished in the ticks.
Conclusions: These results helped us to understand the diversity of the bacterial community in ticks in Guizhou mountain areas. Further studies are needed to uncover the pathogenicity of these tick-carried bacteria and their potential public health threats.