bluuebunny/crossref_metadata_2025_split huggingface dataset:
EVMP: enhancing machine learning models for synthetic promoter strength prediction by Extended Vision Mutant Priority framework
Authors: Yang Weiqin , Li Dexin , Huang Ranran 
Published: July 2023

IntroductionIn metabolic engineering and synthetic biology applications, promoters with appropriate strengths are critical. However, it is time-consuming and laborious to annotate promoter strength by experiments. Nowadays, constructing mutation-based synthetic promoter libraries that span multiple orders of magnitude of promoter strength is receiving increasing attention. A number of machine learning (ML) methods are applied to synthetic promoter strength prediction, but existing models are limited by the excessive proximity between synthetic promoters.MethodsIn order to enhance ML models to better predict the synthetic promoter strength, we propose EVMP(Extended Vision Mutant Priority), a universal framework which utilize mutation information more effectively. In EVMP, synthetic promoters are equivalently transformed into base promoter and corresponding k-mer mutations, which are input into BaseEncoder and VarEncoder, respectively. EVMP also provides optional data augmentation, which generates multiple copies of the data by selecting different base promoters for the same synthetic promoter.ResultsIn Trc synthetic promoter library, EVMP was applied to multiple ML models and the model effect was enhanced to varying extents, up to 61.30% (MAE), while the SOTA(state-of-the-art) record was improved by 15.25% (MAE) and 4.03% (R2). Data augmentation based on multiple base promoters further improved the model performance by 17.95% (MAE) and 7.25% (R2) compared with non-EVMP SOTA record.DiscussionIn further study, extended vision (or k-mer) is shown to be essential for EVMP. We also found that EVMP can alleviate the over-smoothing phenomenon, which may contributes to its effectiveness. Our work suggests that EVMP can highlight the mutation information of synthetic promoters and significantly improve the prediction accuracy of strength. The source code is publicly available on GitHub: https://github.com/Tiny-Snow/EVMP.
A bibliometric analysis of the global impact of metaproteomics research
Authors: Ascandari AbdulAziz , Aminu Suleiman , Safdi Nour El Houda , El Allali Achraf , Daoud Rachid 
Published: July 2023

BackgroundMetaproteomics is a subfield in meta-omics that is used to characterize the proteome of a microbial community. Despite its importance and the plethora of publications in different research area, scientists struggle to fully comprehend its functional impact on the study of microbiomes. In this study, bibliometric analyses are used to evaluate the current state of metaproteomic research globally as well as evaluate the specific contribution of Africa to this burgeoning research area. In this study, we use bibliometric analyses to evaluate the current state of metaproteomic research globally, identify research frontiers and hotspots, and further predict future trends in metaproteomics. The specific contribution of Africa to this research area was evaluated.MethodsRelevant documents from 2004 to 2022 were extracted from the Scopus database. The documents were subjected to bibliometric analyses and visualization using VOS viewer and Biblioshiny package in R. Factors such as the trends in publication, country and institutional cooperation networks, leading scientific journals, author’s productivity, and keywords analyses were conducted. The African publications were ranked using Field-Weighted Citation Impact (FWCI) scores.ResultsA total of 1,138 documents were included and the number of publications increased drastically from 2004 to 2022 with more publications (170) reported in 2021. In terms of publishers, Frontiers in Microbiology had the highest number of total publications (62). The United States of America (USA), Germany, China, and Canada, together with other European countries were the most productive. Institution-wise, the Helmholtz Zentrum für Umweltforschung, Germany had more publications while Max Plank Institute had the highest total collaborative link strength. Jehmlich N. was the most productive author whereas Hettich RL had the highest h-index of 63. Regarding Africa, only 2.2% of the overall publications were from the continent with more publication outputs from South Africa. More than half of the publications from the continent had an FWCI score ≥ 1.ConclusionThe scientific outputs of metaproteomics are rapidly evolving with developed countries leading the way. Although Africa showed prospects for future progress, this could only be accelerated by providing funding, increased collaborations, and mentorship programs.
Differences of spinal cord gadolinium enhancement features of neuromyelitis optica spectrum disorder and long-segment degenerative cervical myelopathy
Authors: Sun Xingwen , Zhao Qiang , Zhang Lihua , Yuan Huishu 
Published: July 2023

ObjectivesNeuromyelitis optica spectrum disorder (NMOSD) and long-segment degenerative cervical myelopathy (DCM) may have a similar appearance on MRI. This study aimed to identify the differences in spinal cord gadolinium enhancement features between NMOSD and long-segment DCM.MethodsSpinal cord gadolinium enhancement of 27 NMOSD patients and 30 long-segment DCM patients were retrospectively analyzed. Enhancements were evaluated for their number, length, location on the sagittal images, distribution on the axial images, and form on the sagittal images. The Wilcoxon rank sum test was performed to compare numerical variables. The Pearson chi-squared test was performed to compare categorical variables.ResultsThe median number of enhanced lesions (p &lt; 0.05), the median length of the enhancements (p &lt; 0.05), and the location of enhancement on sagittal images (p &lt; 0.05) of NMOSD patients and long-segment DCM patients showed significant differences. The axial distribution of enhancements did not show a significant difference between NMOSD and long-segment DCM patients (p = 0.115). On the sagittal images, linear and ring-formed enhancements were observed in 10 (27.0%) and 17 (63.0%) NMOSD patients, respectively. The enhancements in long-segment DCM patients had a transverse band or pancake-like appearance in 15 (50%) patients and an irregular flake-like appearance with a longitudinally oriented long axis in 15 patients (50%).ConclusionBy analyzing the number, length, location, and form of the gadolinium enhancements, NMOSD and long-segment DCM could be well-differentiated.
High frequency of cerebrospinal fluid autoantibodies in patients with seizures or epilepsies of unknown etiology
Authors: Schulz Paulina , Lütt Alva , Stöcker Winfried , Teegen Bianca , Holtkamp Martin , Prüss Harald 
Published: July 2023

IntroductionThe increasing identification of specific autoantibodies against brain structures allows further refinement of the group of autoimmune-associated epilepsies and affects diagnostic and therapeutic algorithms. The early etiological allocation of a first seizure is particularly challenging, and the contribution of cerebrospinal fluid (CSF) analysis is not fully understood.MethodsIn this retrospective study with a mean of 7.8 years follow-up involving 39 well-characterized patients with the initial diagnosis of new-onset seizure or epilepsy of unknown etiology and 24 controls, we determined the frequency of autoantibodies to brain proteins in CSF/serum pairs using cell-based assays and unbiased immunofluorescence staining of unfixed murine brain sections.ResultsAutoantibodies were detected in the CSF of 30.8% of patients. Underlying antigens involved glial fibrillary acidic protein (GFAP) and N-methyl-D-aspartate (NMDA) receptors, but also a range of yet undetermined epitopes on neurons, glial and vascular cells. While antibody-positive patients had higher frequencies of cancer, they did not differ from antibody-negative patients with respect to seizure type, electroencephalography (EEG) and cranial magnetic resonance imaging (cMRI) findings, neuropsychiatric comorbidities or pre-existing autoimmune diseases. In 5.1% of patients with seizures or epilepsy of initially presumed unknown etiology, mostly CSF findings resulted in etiological reallocation as autoimmune-associated epilepy.DiscussionThese findings strengthen the potential role for routine CSF analysis. Further studies are needed to understand the autoantibody contribution to etiologically unclear epilepsies, including determining the antigenic targets of underlying autoantibodies.
Train duration and inter-train interval determine the direction and intensity of high-frequency rTMS after-effects
Authors: Jin Jingna , Wang Xin , Wang He , Li Ying , Liu Zhipeng , Yin Tao 
Published: July 2023

Background and objectiveIt has been proved that repetitive transcranial magnetic stimulation (rTMS) triggers the modulation of homeostatic metaplasticity, which causes the effect of rTMS to disappear or even reverse, and a certain length of interval between rTMS trains might break the modulation of homeostatic metaplasticity. However, it remains unknown whether the effects of high-frequency rTMS can be modulated by homeostatic metaplasticity by lengthening the train duration and whether homeostatic metaplasticity can be broken by prolonging the inter-train interval.MethodsIn this study, 15 subjects participated in two experiments including different rTMS protocols targeting the motor cortex. In the first experiment, high-frequency rTMS protocols with different train durations (2 s and 5 s) and an inter-train interval of 25 s were adopted. In the second experiment, high-frequency rTMS protocols with a train duration of 5 s and different inter-train intervals (50 s and 100 s) were adopted. A sham protocol was also included. Changes of motor evoked potential amplitude acquired from electromyography, power spectral density, and intra-region and inter-region functional connectivity acquired from electroencephalography in the resting state before and after each rTMS protocol were evaluated.ResultsHigh-frequency rTMS with 2 s train duration and 25 s inter-train interval increased cortex excitability and the power spectral density of bilateral central regions in the alpha frequency band and enhanced the functional connectivity between central regions and other brain regions. When the train duration was prolonged to 5 s, the after-effects of high-frequency rTMS disappeared. The after-effects of rTMS with 5 s train duration and 100 s inter-train interval were the same as those of rTMS with 2 s train duration and 25 s inter-train interval.ConclusionOur results indicated that train duration and inter-train interval could induce the homeostatic metaplasticiy and determine the direction of intensity of rTMS after-effects, and should certainly be taken into account when performing rTMS in both research and clinical practice.
Risk factors for agitation in home-cared older adults with dementia: evidence from 640 elders in East China
Authors: Liu Jiaxin , Lin Taoyu , Liu Guanjun , Dong Xiaoxin , Min Rui 
Published: July 2023

BackgroundAgitation is common among older adults with dementia, negatively affecting their quality of life and their caregivers’. Since home care remains the dominant approach for older adults, this study investigates the risk factors for agitation in older adults with dementia in China.MethodsWe perform a cross-sectional study of home-cared older adults with dementia in Ningbo, China, using 2020 data. We use a self-made questionnaire to investigate the risks of agitated behavior and its related factors. We perform descriptive, univariate, and regression analyses.FindingsWe address 640 older Chinese adults; 42.8% of the sample exhibits one or more agitated behaviors. We find that basic health issues, such as activities of daily living (ADL), family support issues, such as Zarit Burden Interview (ZBI) scale and Family APGAR Questionnaire (APGAR), and behavioral awareness issues, such as fall and scald, significantly influence the occurrence of agitation behaviors (p &lt; 0.05). Older adults with severe ADL disorder (b = 6.835, β = 0.196, p &lt; 0.001), ZBI score of 67.00–88.0 (b = 10.212, β = 0.248, p = 0.005), severe APGAR disorder (b = 3.699, β = 0.100, p = 0.012) and a history of fall (b = 9.311, β = 0.199, P = &lt;0.001) or scald (b = 9.288, β = 0.125, p = 0.002) are more likely to exhibit agitated behaviors.InterpretationAgitated behavior in home-cared older adults with dementia are diverse and related to mental state, family support, and behavioral awareness issues. Caregivers, often family members, should be attentive to the needs of dementia patients and take active and effective measures to improve their quality of life. They should be aware of the causes and triggers of agitated behavior and take steps to reduce its occurrence.
Profiling of miRNAs and their interfering targets in peripheral blood mononuclear cells from patients with chronic myeloid leukaemia
Authors: Wu Sheng-Cheng , Lai Shiue-Wei , Lu Xin-Jie , Lai Hsing-Fan , Chen Yu-Guang , Chen Po-Huang , Ho Ching-Liang , Wu Yi-Ying , Chiu Yi-Lin 
Published: July 2023

IntroductionMicroRNAs may be implicated in the acquisition of drug resistance in chronic myeloid leukemia as they regulate the expression of not only BCR-ABL1 but also genes associated with the activation of drug transfer proteins or essential signaling pathways.MethodsTo understand the impact of specifically expressed miRNAs in chronic myeloid leukemia and their target genes, we collected peripheral blood mononuclear cells (PBMC) from patients diagnosed with chronic myeloid leukemia (CML) and healthy donors to determine whole miRNA expression by small RNA sequencing and screened out 31 differentially expressed microRNAs (DE-miRNAs) with high expression. With the utilization of miRNA set enrichment analysis tools, we present here a comprehensive analysis of the relevance of DE-miRNAs to disease and biological function. Furthermore, the literature-based miRNA-target gene database was used to analyze the overall target genes of the DE-miRNAs and to define their associated biological responses. We further integrated DE-miRNA target genes to identify CML miRNA targeted gene signature singscore (CMTGSS) and used gene-set enrichment analysis (GSEA) to analyze the correlation between CMTGSS and Hallmark gene-sets in PBMC samples from clinical CML patients. Finally, the association of CMTGSS stratification with multiple CML cell lineage gene sets was validated in PBMC samples from CML patients using GSEA.ResultsAlthough individual miRNAs have been reported to have varying degrees of impact on CML, overall, our results show that abnormally upregulated miRNAs are associated with apoptosis and aberrantly downregulated miRNAs are associated with cell cycle. The clinical database shows that our defined DE-miRNAs are associated with the prognosis of CML patients. CMTGSS-based stratification analysis presented a tendency for miRNAs to affect cell differentiation in the blood microenvironment.ConclusionCollectively, this study defined differentially expressed miRNAs by miRNA sequencing from clinical samples and comprehensively analyzed the biological functions of the differential miRNAs in association with the target genes. The analysis of the enrichment of specific myeloid differentiated cells and immune cells also suggests the magnitude and potential targets of differentially expressed miRNAs in the clinical setting. It helps us to make links between the different results obtained from the multi-faceted studies to provide more potential research directions.
Spinal cord stimulation for refractory pericarditis: a case report and a review of the mechanism of action
Authors: Elsliger Simon , Saucier Jacob , Schneider Andre , El Helou Antonios 
Published: July 2023

Background and objectivesIn recent years, spinal cord stimulation (SCS) has emerged as a promising management option for chronic pain of multiple etiologies. While its effectiveness has been strongly suggested in many patients, the exact mechanism of action of SCS is incompletely understood. This article reviews the leading mechanisms underlying the analgesic and cardiovascular effects of SCS and reports its novel benefits in a case of recurrent pericarditis.Literature reviewThroughout history, the analgesic properties of SCS were thought to arise via stimulation of the spinothalamic tract. Although this mechanism has been thoroughly reported, new research and patient outcomes from SCS have revealed various additional properties that cannot be fully explained by this mechanism alone. Evidence suggests that SCS enhances calcitonin gene-related peptide release and modulates inflammatory cytokine secretion, sympathetic tone, and inhibitory neurotransmitter secretion. These distinct mechanisms likely collectively contribute to the therapeutic effects of SCS on the cardiovascular system and pain management.Case reportWe report the case of a 48-year-old male patient with recurrent pericarditis, characterized by refractory angina-like pain and reduced left ventricular ejection fraction (LVEF). After 1 year of having a spinal cord stimulator implanted, the patient is free from pain and narcotics, with a reduction of 428 mg equivalent dose of morphine. The patient's LVEF increased from 40% to 45% without changes to his previous medical treatment. This is the first reported case of refractory pericarditis managed with spinal cord stimulation.ConclusionRecognizing the improved pain management, reduced narcotic usage, and improved LVEF in our patient following SCS is critical to paving the way toward a complete understanding of the mechanism of action of SCS. This case reveals the therapeutic potential of SCS for cardiovascular pathologies other than refractory angina pectoris.
Identification of five novel variants of ADAR1 in dyschromatosis symmetrica hereditaria by next-generation sequencing
Authors: Ma Qian , Che Lingyi , Chen Yibing , Gu Zhuoyu 
Published: July 2023

BackgroundDyschromatosis symmetrica hereditaria (DSH) is a rare autosomal dominant inherited pigmentary dermatosis characterized by a mixture of hyperpigmented and hypopigmented freckles on the dorsal aspect of the distal extremities. To date, pathogenic mutations causing DSH have been identified in the adenosine deaminase acting on RNA1 gene (ADAR1), which is mapped to chromosome 1q21.ObjectiveThe present study aimed to investigate the underlying pathological mechanism in 14 patients with DSH from five unrelated Chinese families. Next-generation sequencing (NGS) and direct sequencing were performed on a proband with DSH to identify causative mutations. All coding, adjacent intronic, and 5′- and 3′-untranslated regions ofADAR1were screened, and variants were identified.ResultThese mutations consisted of three missense mutations (NM_001025107: c.716G&gt;A, NM_001111.5: c.3384G&gt;C, and NM_001111.5: c.3385T&gt;G), one nonsense mutation (NM_001111.5:c.511G&gt;T), and one splice-site mutation (NM_001111.5: c.2080-1G&gt;T) located in exon 2, exon 14, and the adjacent intronic region according to recommended Human Genome Variation Society (HGVS) nomenclature. Moreover, using polymerase chain reaction and Sanger sequencing, we identified five novelADAR1variants, which can be predicted to be pathogenic by in silico genome sequence analysis. Among the mutations, the missense mutations had no significant effect on the spatial structure of the protein, while the stop codon introduced by the nonsense mutation truncated the protein.ConclusionOur results highlighted that the advent of NGS has facilitated high-throughput screening for the identification of disease-causing mutations with high accuracy, stability, and specificity. Five novel genetic mutations were found in five unrelated families, thereby extending the pathogenic mutational spectrum ofADAR1in DSH and providing new insights into this complex genetic disorder.
The relationship between sleep disturbance and obsessive– compulsive symptoms: the mediation of repetitive negative thinking and the moderation of experiential avoidance
Authors: Zhao Xudong , Shen Liao , Pei Yufei , Wu Xiaojun , Zhou Ningning 
Published: July 2023

BackgroundStudies have found that sleep disturbance is associated with obsessive–compulsive symptoms. This study aimed to elaborate on the mediating and moderating mechanisms between these two variables. We hypothesized that repetitive negative thinking plays a mediating role in the relationship between sleep disturbance and obsessive–compulsive symptoms, and experiential avoidance plays a moderating role.MethodThis study included 639 Chinese adults. A questionnaire survey was used to assess sleep quality, obsessive–compulsive symptoms, experiential avoidance, repetitive negative thinking, and depression symptoms. A moderated mediation model was established.ResultsAfter controlling for depressive symptoms, repetitive negative thinking partially mediated the positive correlation between sleep disturbance and obsessive–compulsive symptoms. This indirect relationship was significant in individuals with lower experiential avoidance levels. Particularly, the relationship between sleep disturbance and repetitive negative thinking was significant among individuals with lower experiential avoidance levels, but not among individuals with higher experiential avoidance levels.ConclusionThis study demonstrated that repetitive negative thinking partially mediated the impact of sleep disturbance on obsessive–compulsive symptoms. The findings suggest that when providing support to individuals with sleep disturbance and obsessive–compulsive symptoms, assessing their level of experiential avoidance is necessary for performing targeted interventions. Individuals with low experiential avoidance may benefit from a clinical intervention targeting repetitive negative thinking to improve sleep quality and obsessive–compulsive symptoms.
Psychometric validation of the 15-item Questionnaire about the Process of Recovery in Spain (QPR-15-SP)
Authors: Goodman-Casanova Jessica Marian , Cuesta-Lozano Daniel , Alupoaei Catalina , Grasa Bello Eva María , Herrera-Imbroda Jesús , Mayoral-Cleries Fermin , Guzman-Parra Jose 
Published: July 2023

IntroductionReliable and valid instruments are needed to measure the impact of mental health services and programs on the journeys of recovery of service users. The aim of this study was to explore the psychometric properties of the cross-culturally adapted 15-item Questionnaire about the Process of Recovery in Spain (QPR-15-SP).MethodsOne hundred and ten participants from three locations in Spain (Málaga, Barcelona and Madrid), who were users of primary and specialized mental health services, were interviewed from October 2021 to June 2022.ResultsThe internal consistency obtained was excellent: ω  =.93 and α =.92. Temporal reliability using intraclass correlation coefficients was moderate (ICC=.684, p &lt;.000). Regarding convergent validity, the QPR-15-SP had a moderate correlation with the Clinical Outcomes in Routine Evaluation-Outcome Measure (CORE-OM) (ρ =-.500, p &lt;.000), a Visual Numeric Recovery Scale (VNRS) (ρ =.591, p &lt;.000), and the Stages of Recovery Instrument (STORI) (r =.566, p &lt;.000). Correlations between advanced stages of recovery and higher QPR-15-SP scores were found (Moratorium: ρ  =-.579, p &lt;.000; Awareness: ρ =-.130, p =.189; Preparation: r =-.043, P=.665; Rebuilding: r =.460, p &lt;.000; Growth: ρ  =.697, p &lt;.000). In terms of divergent validity, the QPR-15-SP had low correlation with the DUKE-UNC Functional Social Support Scale (ρ =.273, p &lt;.005). The confirmatory factor analysis of the 1-factor structure obtained reasonable goodness of fit indexes.DiscussionThe QPR-15-SP has acceptable psychometric properties, providing support for measuring recovery in Spain and allowing international comparison research.