bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of spinal fusion on joint space narrowing of the hip: comparison among non-fusion, short fusion, and middle or long fusion
Authors: Ukai Taku , Katoh Hiroyuki , Yokoyama Katsuya , Sato Masato , Watanabe Masahiko 
Published: January 2023

Abstract
Background
Lumbar fusion corrects spinal deformities and improves spinal complications. Hip osteoarthritis (OA) is strongly correlated with spinal mobility, and joint space narrowing of the hip after spinal fusion has gained attention. This study aimed to elucidate the effect of spinal fusion on hip joint space narrowing.

Materials and methods
We retrospectively examined 530 hips of 270 patients who underwent spinal surgery. All the patients underwent whole-spine radiography before and at the final follow-up. Patients were divided into three groups (N group: non-spinal fusion, S group: up to three interbody fusions, and L group: more than four interbody fusions). The rates of joint space narrowing, spinal parameters (sagittal vertical axis, thoracic kyphosis, lumbar lordosis, sacral slope, pelvic tilt, and pelvic incidence), and limb length discrepancy at the final follow-up were compared. A multilinear regression analysis was performed to identify the risk factors for the rate of joint space narrowing.

Results
The rate of joint space narrowing was significantly higher in the L group than in the N and S groups (P < 0.001). No significant difference in the rate of joint space narrowing was observed between the N and S groups. Multiple linear regression analysis revealed that the number of fusion levels (p < 0.05) and follow-up period (p < 0.001) were independent risk factors for joint space narrowing. Spinal parameters at the final follow-up were not independent risk factors.

Conclusions
Long spinal fusion (more than four levels) led to significantly greater joint space narrowing of the hip than short (up to three levels) or no fusion. Spinal alignment did not affect joint space narrowing of the hip. Surgeons should be aware that more than four interbody fusions may result in worse joint space narrowing of the hip.

Level of evidence
IV, retrospective study
Role of the endocannabinoid system in fragile X syndrome: potential mechanisms for benefit from cannabidiol treatment
Authors: Palumbo Joseph M. , Thomas Brian F. , Budimirovic Dejan , Siegel Steven , Tassone Flora , Hagerman Randi , Faulk Christopher , O’Quinn Stephen , Sebree Terri 
Published: January 2023

AbstractMultiple lines of evidence suggest a central role for the endocannabinoid system (ECS) in the neuronal development and cognitive function and in the pathogenesis of fragile X syndrome (FXS). This review describes the ECS, its role in the central nervous system, how it is dysregulated in FXS, and the potential role of cannabidiol as a treatment for FXS. FXS is caused by deficiency or absence of the fragile X messenger ribonucleoprotein 1 (FMR1) protein, FMRP, typically due to the presence of >200 cytosine, guanine, guanine sequence repeats leading to methylation of the FMR1 gene promoter. The absence of FMRP, following FMR1 gene-silencing, disrupts ECS signaling, which has been implicated in FXS pathogenesis. The ECS facilitates synaptic homeostasis and plasticity through the cannabinoid receptor 1, CB1, on presynaptic terminals, resulting in feedback inhibition of neuronal signaling. ECS-mediated feedback inhibition and synaptic plasticity are thought to be disrupted in FXS, leading to overstimulation, desensitization, and internalization of presynaptic CB1 receptors. Cannabidiol may help restore synaptic homeostasis by acting as a negative allosteric modulator of CB1, thereby attenuating the receptor overstimulation, desensitization, and internalization. Moreover, cannabidiol affects DNA methylation, serotonin 5HT1A signal transduction, gamma-aminobutyric acid receptor signaling, and dopamine D2 and D3 receptor signaling, which may contribute to beneficial effects in patients with FXS. Consistent with these proposed mechanisms of action of cannabidiol in FXS, in the CONNECT-FX trial the transdermal cannabidiol gel, ZYN002, was associated with improvements in measures of social avoidance, irritability, and social interaction, particularly in patients who are most affected, showing ≥90% methylation of the FMR1 gene.
Rice Defense Responses Orchestrated by Oral Bacteria of the Rice Striped Stem Borer, Chilo suppressalis
Authors: Xue Rongrong , Li Qing , Guo Ruiqing , Yan Hui , Ju Xueyang , Liao Lu , Zeng Rensen , Song Yuanyuan , Wang Jie 
Published: January 2023

AbstractPlant defenses in response to chewing insects are generally regulated by jasmonic acid (JA) signaling pathway, whereas salicylic acid (SA) signaling is mainly involved in plant defense against biotrophic pathogens and piercing-sucking insects. Previous studies showed that both JA- and SA-related defenses in rice plants were triggered by the infestation of the rice striped stem borer (SSB, Chilo suppressalis), a destructive pest causing severe damage to rice production. Herbivore-associated microbes play an important role in modulating plant–insect interaction, and thus we speculate that the SSB symbiotic microbes acting as a hidden player may cause this anomalous result. The antibiotics (AB) treatment significantly depressed the performance of field-collected SSB larvae on rice plants, and reduced the quantities of bacteria around the wounds of rice stems compared to non-AB treatment. In response to mechanical wounding and oral secretions (OS) collected from non-AB treated larvae, rice plants exhibited lower levels of JA-regulated defenses, but higher levels of SA-regulated defenses compared to the treatment of OS from AB-treated larvae determined by using a combination of biochemical and molecular methods. Among seven culturable bacteria isolated from the OS of SSB larvae, Enterobacter and Acinetobacter contributed to the suppression of JA signaling-related defenses in rice plants, and axenic larvae reinoculated with these two strains displayed better performance on rice plants. Our findings demonstrate that SSB larvae exploit oral secreted bacteria to interfere with plant anti-herbivore defense and avoid fully activating the JA-regulated antiherbivore defenses of rice plants.
Negation detection in Dutch clinical texts: an evaluation of rule-based and machine learning methods
Authors: van Es Bram , Reteig Leon C. , Tan Sander C. , Schraagen Marijn , Hemker Myrthe M. , Arends Sebastiaan R. S. , Rios Miguel A. R. , Haitjema Saskia 
Published: January 2023

AbstractWhen developing models for clinical information retrieval and decision support systems, the discrete outcomes required for training are often missing. These labels need to be extracted from free text in electronic health records. For this extraction process one of the most important contextual properties in clinical text is negation, which indicates the absence of findings. We aimed to improve large scale extraction of labels by comparing three methods for negation detection in Dutch clinical notes. We used the Erasmus Medical Center Dutch Clinical Corpus to compare a rule-based method based on ContextD, a biLSTM model using MedCAT and (finetuned) RoBERTa-based models. We found that both the biLSTM and RoBERTa models consistently outperform the rule-based model in terms of F1 score, precision and recall. In addition, we systematically categorized the classification errors for each model, which can be used to further improve model performance in particular applications. Combining the three models naively was not beneficial in terms of performance. We conclude that the biLSTM and RoBERTa-based models in particular are highly accurate accurate in detecting clinical negations, but that ultimately all three approaches can be viable depending on the use case at hand.
Ensemble feature selection with data-driven thresholding for Alzheimer's disease biomarker discovery
Authors: Spooner Annette , Mohammadi Gelareh , Sachdev Perminder S. , Brodaty Henry , Sowmya Arcot ,   for the Sydney Memory and Ageing Study and the Alzheimer’s Disease Neuroimaging Initiative
Published: January 2023

AbstractBackgroundFeature selection is often used to identify the important features in a dataset but can produce unstable results when applied to high-dimensional data. The stability of feature selection can be improved with the use of feature selection ensembles, which aggregate the results of multiple base feature selectors. However, a threshold must be applied to the final aggregated feature set to separate the relevant features from the redundant ones. A fixed threshold, which is typically used, offers no guarantee that the final set of selected features contains only relevant features. This work examines a selection of data-driven thresholds to automatically identify the relevant features in an ensemble feature selector and evaluates their predictive accuracy and stability. Ensemble feature selection with data-driven thresholding is applied to two real-world studies of Alzheimer's disease. Alzheimer's disease is a progressive neurodegenerative disease with no known cure, that begins at least 2–3 decades before overt symptoms appear, presenting an opportunity for researchers to identify early biomarkers that might identify patients at risk of developing Alzheimer's disease.ResultsThe ensemble feature selectors, combined with data-driven thresholds, produced more stable results, on the whole, than the equivalent individual feature selectors, showing an improvement in stability of up to 34%. The most successful data-driven thresholds were the robust rank aggregation threshold and the threshold algorithm threshold from the field of information retrieval. The features identified by applying these methods to datasets from Alzheimer's disease studies reflect current findings in the AD literature.ConclusionsData-driven thresholds applied to ensemble feature selectors provide more stable, and therefore more reproducible, selections of features than individual feature selectors, without loss of performance. The use of a data-driven threshold eliminates the need to choose a fixed threshold a-priori and can select a more meaningful set of features. A reliable and compact set of features can produce more interpretable models by identifying the factors that are important in understanding a disease.
Comparative analysis of codon usage patterns in chloroplast genomes of ten Epimedium species
Authors: Wang Yingzhe , Jiang Dacheng , Guo Kun , Zhao Lei , Meng Fangfang , Xiao Jinglei , Niu Yuan , Sun Yunlong 
Published: January 2023

Abstract
Background
The Phenomenon of codon usage bias exists in the genomes of prokaryotes and eukaryotes. The codon usage pattern is affected by environmental factors, base mutation, gene flow and gene expression level, among which natural selection and mutation pressure are the main factors. The study of codon preference is an effective method to analyze the source of evolutionary driving forces in organisms. Epimedium species are perennial herbs with ornamental and medicinal value distributed worldwide. The chloroplast genome is self-replicating and maternally inherited which is usually used to study species evolution, gene expression and genetic transformation.

Results
The results suggested that chloroplast genomes of Epimedium species preferred to use codons ending with A/U. 17 common high-frequency codons and 2–6 optimal codons were found in the chloroplast genomes of Epimedium species, respectively. According to the ENc-plot, PR2-plot and neutrality-plot, the formation of codon preference in Epimedium was affected by multiple factors, and natural selection was the dominant factor. By comparing the codon usage frequency with 4 common model organisms, it was found that Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae were suitable exogenous expression receptors.

Conclusion
The evolutionary driving force in the chloroplast genomes of 10 Epimedium species probably comes from mutation pressure. Our results provide an important theoretical basis for evolutionary analysis and transgenic research of chloroplast genes.
Silencing of GhORP_A02 enhances drought tolerance in Gossypium hirsutum
Authors: Tajo Sani Muhammad , Pan Zhaoe , Jia Yinhua , He Shoupu , Chen Baojun , Sadau Salisu Bello , KM Yusuf , Ajadi Aboleri Adijat , Nazir Mian Faisal , Auta Umar , Geng Xiaoli , Du Xiongming 
Published: January 2023

Abstract
Background
ORP (Oxysterol-binding protein-related proteins) genes play a role in lipid metabolism, vesicular transferring and signaling, and non-vesicular sterol transport. However, no systematic identification and analysis of ORP genes have been reported in cotton.

Result
In this study, we identified 14, 14, 7, and 7 ORP genes in G. hirsutum, G. barbadense, G. arboreum, and G. raimondii, respectively. Phylogenetic analysis showed that all ORP genes could be classified into four groups. Gene structure and conserved motif analysis suggest that the function of this gene family was conserved. The Ka/Ks analysis showed that this gene family was exposed to purifying selection during evolution. Transcriptome data showed that four ORP genes, especially GhORP_A02, were induced by abiotic stress treatment. The cis-acting elements in the ORP promoters were responsive to phytohormones and various abiotic stresses. The silenced plants of GhORP_A02 were more sensitive to drought stress when compared to control.

Conclusion
The major finding of this study shed light on the potential role of ORP genes in abiotic stress and provided a fundamental resource for further analysis in cotton.
Comparative proteomic analysis of seminal plasma exosomes in buffalo with high and low sperm motility
Authors: Yu Kai , Xiao Kai , Sun Qin-qiang , Liu Run-feng , Huang Liang-feng , Zhang Peng-fei , Xu Hui-yan , Lu Yang-qing , Fu Qiang 
Published: January 2023

AbstractBackgroundExosomes are nanosized membranous vesicles secreted by various types of cells, which facilitate intercellular communication by transporting bioactive compounds. Exosomes are abundant in biological fluids including semen, and their protein composition and the potential of seminal plasma exosomes (SPEs) as fertility biomarkers were elucidated in humans, however, little information is available regarding buffalo (Bubalus bubalis). Here, we examined protein correlation between spermatozoa, seminal plasma (SP), and SPEs, and we compared and analyzed protein differences between high-motility (H-motility) and low-motility (L-motility) SPEs in buffalo.ResultsSPEs were concentrated and purified by ultracentrifugation combined with sucrose density gradient centrifugation, followed by verification using western blotting, nanoparticle tracking analysis, and transmission electron microscopy. Protein composition in spermatozoa, SP and SPEs, and protein difference in H- and L-motility SPEs were identified by LC-MS/MS proteomic analysis and were functionally analyzed through comprehensive bioinformatics. Many SPEs proteins originated from spermatozoa and SP, and nearly one third were also present in spermatozoa and SP. A series of proteins associated with reproductive processes including sperm capacitation, spermatid differentiation, fertilization, sperm-egg recognition, membrane fusion, and acrosome reaction were integrated in a functional network. Comparative proteomic analyses showed 119 down-regulated and 41 up-regulated proteins in L-motility SPEs, compared with H-motility SPEs. Gene Ontology (GO) enrichment of differentially expressed proteins (DEPs) showed that most differential proteins were located in sperm and vesicles, with activities of hydrolase and metalloproteinase, and were involved in sperm-egg recognition, fertilization, single fertilization, and sperm-zona pellucida binding processes, etc. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that differential proteins were mainly involved in the PPRP signaling pathway, calcium signaling pathway, and cAMP signaling pathway, among others. Furthermore, 6 proteins associated with reproduction were validated by parallel reaction monitoring analysis.ConclusionThis study provides a comprehensive description of the seminal plasma exosome proteome and may be of use for further screening of biomarkers associated with male infertility.
Prevalence and molecular characterization of Mycobacterium tuberculosis complex in cattle and humans, Maiduguri, Borno state, Nigeria: a cross-sectional study
Authors: Kwaghe Ayi Vandi , Ameh James Agbo , Kudi Caleb Ayuba , Ambali Abdul-Ganiyu , Adesokan Hezekiah Kehinde , Akinseye Victor Oluwatoyin , Adelakun Olubukola Deborah , Usman Joy Gararawa , Cadmus Simeon Idowu 
Published: January 2023

AbstractIntroductionGlobally, the highest burden of bovine and human tuberculosis resides in Africa and Asia. Tuberculosis (TB) is the second leading single infectious killer after severe acute respiratory syndrome corona virus-2 (SARSCOV-2). Bovine TB remains a treat to wild and domesticated animals, humans and hinders international trade in endemic countries like Nigeria. We aimed at determining the prevalence of bovine and human tuberculosis, and the spoligotypes ofMycobacterium tuberculosiscomplex in cattle and humans in Maiduguri.MethodsWe conducted a cross sectional study on bovine and human tuberculosis in Maiduguri, Borno state. We calculated sample size using the method of Thrusfield. Lesions suggestive of TB from 160 slaughtered cattle were obtained from Maiduguri Central Abattoir. Sputum samples from humans; 82 abattoir workers and 147 suspected TB patients from hospitals/clinics were obtained. Lesions and sputum samples were cultured for the isolation ofMycobacteriumspp. Positive cultures were subjected genus typing, deletion analysis and selected isolates were spoligotyped. Data was analysed using SPSS VERSION 16.0.ResultsPrevalence of 32.5% (52/160) was obtained in cattle. Damboa local government area (LGA), where majority of the infected animals were obtained from had 35.5% bTB prevalence. All categories analysed (breed, age, sex, body conformation and score) hadP-values that were not significant (P > 0.05). Sputum culture revealed a prevalence of 3.7% (3/82) from abattoir workers and 12.2% from hospitals/clinics. A significantP-value (0.03) was obtained when positive culture from abattoir and that of hospitals/clinics were compared. Out of the 52 culture positive isolates obtained from cattle, 26 (50%) belonged toM. tuberculosiscomplex (MTC) and 17/26 (65.4%) were characterized asM. bovis. In humans, 7/12 (58.3%) MTC obtained were characterized asM. tuberculosis. Spoligotyping revealed SB0944 and SB1025 in cattle, while SIT838, SIT61 of LAM10_CAM and SIT1054, SIT46 of Haarlem (H) families were obtained from humans.ConclusionsCattle in Damboa LGA need to be screened for bTB as majority of the infected animals were brought from there. Our findings revealed the presence of SB0944 and SB1025 spoligotypes from cattle in Borno state. We isolatedM. tuberculosisstrain of the H family mainly domiciled in Europe from humans.
How general practitioners perceive the aging trajectory of oldest-old - A qualitative study
Authors: Escourrou Emile , Joyeux Thomas , Guilhem Matthieu , Oustric Stéphane , Gardette Virginie 
Published: January 2023

Abstract
Background
A new population of older people is growing: the oldest-old. The care of the oldest-old (individuals aged 90 and over) is a new challenge in primary care. This study aimed to analyze the perception of General Practitioners (GP) on (1) the aging process of their patients up to a very advanced age, (2) how to adapt their practice to the care of these patients.

Methods
We conducted a qualitative study using focus group (face to face) and individual (video call) interviews of GPs in southwest France. The sampling was purposive. We analyzed the interviews using an inductive approach based on the phases of thematic analysis. We used researchers’ triangulation during the process. Collection was concluded when saturation was reached.

Results
Three focus groups and one individual interview were conducted with a total of seventeen general practitioners. GP perception concerning aging and very advanced age were based on their personal experience and their daily clinical practice. Aging was perceived as an individual, unconscious, unpredictable and irreversible phenomenon. The shift towards “very old age” appeared inevitable. It could be a physical or psychological shift, or patients neglecting themselves or lacking a project. The care of the oldest-old became more specific and individual, adapted to the wishes of the patient. Those adaptations involve medical disengagement to focus on the most essential outcomes. The objectives of health care needed to be less strict with limited invasive practices. Prevention needed to focus mainly on prevention of falls and limitation of functional decline.

Conclusion
GPs identified an inevitable and unpredictable shift from old age to very old age. The adaption of the theory of disengagement allowed us to identify a medical disengagement of the GPs in the care of their oldest patients.
A prospective patient registry to monitor safety, effectiveness, and utilisation of bedaquiline in patients with multidrug-resistant tuberculosis in South Korea
Authors: Shim Tae Sun , Pai Helen , Mok JeongHa , Lee Seung Heon , Kwon Yong-Soo , Choi Jae Chol , Park JaeSeok , Birmingham Eileen , Mao Gary , Alquier Lori , Davis Kourtney , Thoret-Bauchet Florence , Kim Ji Hyun , Kim Hyeongyeong , Bakare Nyasha 
Published: January 2023

Abstract
Background
Multidrug-resistant tuberculosis (MDR-TB) represents a major public health concern, with an ongoing need for new effective treatments. Bedaquiline is an oral diarylquinoline that has shown encouraging treatment success and culture conversion rates in MDR-TB.

Methods
A South Korean patient registry was set up across 19 centres between 2016 and 2018 for the prospective collection of data from patients with MDR-TB who received either a bedaquiline-containing or a non-bedaquiline-containing regimen. Treatment was at the physician’s discretion (bedaquiline use requiring approval by special committee) and was based on patient characteristics, disease status, and local treatment guidelines.

Results
The safety population included 172 patients (88 bedaquiline and 84 non-bedaquiline). The mean (standard deviation, SD) duration of follow-up was 24.3 (9.5) months. Mean (SD) durations of treatment were 5.4 (1.8) months in bedaquiline-treated patients and 15.7 (6.7) months in the non-bedaquiline group. Treatment success (cured and treatment completed according to WHO 2013 treatment outcome definitions) was achieved by 56.3% of bedaquiline-treated and 45.2% of non-bedaquiline-treated patients. Sputum culture conversion rates were 90.4% and 83.7% with and without bedaquiline, respectively. Diarrhoea and nausea were the most frequently reported treatment-emergent adverse events (TEAEs) in the bedaquiline group (27.3% [24/88] and 22.7% [20/88], respectively). The most frequent bedaquiline-related TEAEs were prolonged QT interval (10.2%; 9/88), and diarrhoea and nausea (9.1% each; 8/88). QT interval prolongation was reported in 19.3% (17/88) of bedaquiline-treated and 2.4% (2/84) of non-bedaquiline-treated patients, but bedaquiline was not discontinued for any patient for this reason. There were 13 (14.7%) and three (3.6%) deaths in the bedaquiline-treated and non-bedaquiline groups, respectively. Review of fatal cases revealed no unexpected safety findings, and no deaths were bedaquiline-related. The most common cause of death was worsening cancer (three patients). Patients in the bedaquiline group tended to have poorer baseline risk profiles than non-bedaquiline patients and were more likely to have relapsed or already failed second-line treatment. Interpretation of mortality data was complicated by high rates of loss to follow-up in both groups.

Conclusions
The South Korean registry findings support previous risk/benefit observations and the continued use of bedaquiline as part of combination therapy in patients with MDR-TB.