bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diverse WGBS profiles of longissimus dorsi muscle in Hainan black goats and hybrid goats
Authors: Ren Yuwei , Chen Xing , Zheng Xinli , Wang Feng , Sun Ruiping , Wei Limin , Zhang Yan , Liu Hailong , Lin Yanning , Hong Lingling , Huang Xiaoxian , Chao Zhe 
Published: December 2023

Abstract
Background
Goat products have played a crucial role in meeting the dietary demands of people since the Neolithic era, giving rise to a multitude of goat breeds globally with varying characteristics and meat qualities. The primary objective of this study is to pinpoint the pivotal genes and their functions responsible for regulating muscle fiber growth in the longissimus dorsi muscle (LDM) through DNA methylation modifications in Hainan black goats and hybrid goats.

Methods
Whole-genome bisulfite sequencing (WGBS) was employed to scrutinize the impact of methylation on LDM growth. This was accomplished by comparing methylation differences, gene expression, and their associations with growth-related traits.

Results
In this study, we identified a total of 3,269 genes from differentially methylated regions (DMR), and detected 189 differentially expressed genes (DEGs) through RNA-seq analysis. Hypo DMR genes were primarily enriched in KEGG terms associated with muscle development, such as MAPK and PI3K-Akt signaling pathways. We selected 11 hub genes from the network that intersected the gene sets within DMR and DEGs, and nine genes exhibited significant correlation with one or more of the three LDM growth traits, namely area, height, and weight of loin eye muscle. Particularly, PRKG1 demonstrated a negative correlation with all three traits. The top five most crucial genes played vital roles in muscle fiber growth: FOXO3 safeguarded the myofiber’s immune environment, FOXO6 was involved in myotube development and differentiation, and PRKG1 facilitated vasodilatation to release more glucose. This, in turn, accelerated the transfer of glucose from blood vessels to myofibers, regulated by ADCY5 and AKT2, ultimately ensuring glycogen storage and energy provision in muscle fibers.

Conclusion
This study delved into the diverse methylation modifications affecting critical genes, which collectively contribute to the maintenance of glycogen storage around myofibers, ultimately supporting muscle fiber growth.
International diet quality index and revised diet quality index relationship with non-alcoholic fatty liver disease: a case-control study
Authors: Najibi Narjes , Jahromi Mitra Kazemi , Teymoori Farshad , Farhadnejad Hossein , Salehi-Sahlabadi Ammar , Mirmiran Parvin 
Published: December 2023

Abstract
Background/objectives
Recent studies show the potential role of dietary quality and quantity in predicting the risk of chronic diseases, such as liver disease, therefore, in the present study, we aimed to assess the association of diet quality index International (DQI-I) and diet quality index revised (DQI-R) and their main components with the odds of non-alcoholic fatty liver disease (NAFLD) in adult populations.

Methods
The current case-control study was conducted on 225 patients with NAFLD and 450 controls. Dietary intake was assessed using a validated 168-item food frequency questionnaire, and DQI-I and DQI-R were calculated in participants. Multi-variable logistic regression was used to examine the association of DQI-I and DQI-R and their components with the odds of NAFLD.

Results
The mean (SD) age and BMI of participants (53% men) were 38.1 (8.8) years and 26.8 (4.3) kg/m2, respectively. In the final model, each one SD increment in the DQI-I score was associated with decreased odds of NAFLD (OR = 0.63; 95%CI = 0.40–0.98) (P = 0.040). Also, of DQI-I components, high adequacy score was related to lower odds of NAFLD (OR = 0.16; 95%CI = 0.06–0.40) (P < 0.001). Also, our findings showed that participants in the highest tertile of DQI-R score had lower odds of NAFLD compared to the lowest tertile of DQI-R (OR = 0.24; 95%CI = 0.10–0.53) (P < 0.001). Furthermore, of DQI-R components, high moderation score are linked to a lower risk of NAFLD (OR = 0.17;95%CI = 0.07–0.43) (P < 0.001).

Conclusion
Our findings suggested that greater adherence to diet with a higher score of DQI-I and DQI-R may be associated with lower odds of NAFLD.
Radiomic texture analysis based on neurite orientation dispersion and density imaging to differentiate glioblastoma from solitary brain metastasis
Authors: Bai Jie , He Mengyang , Gao Eryuan , Yang Guang , Yang Hongxi , Dong Jie , Ma Xiaoyue , Gao Yufei , Zhang Huiting , Yan Xu , Zhang Yong , Cheng Jingliang , Zhao Guohua 
Published: December 2023

Abstract
Background
We created discriminative models of different regions of interest (ROIs) using radiomic texture features of neurite orientation dispersion and density imaging (NODDI) and evaluated the feasibility of each model in differentiating glioblastoma multiforme (GBM) from solitary brain metastasis (SBM).

Methods
We conducted a retrospective study of 204 patients with GBM (n = 146) or SBM (n = 58). Radiomic texture features were extracted from five ROIs based on three metric maps (intracellular volume fraction, orientation dispersion index, and isotropic volume fraction of NODDI), including necrosis, solid tumors, peritumoral edema, tumor bulk volume (TBV), and abnormal bulk volume. Four feature selection methods and eight classifiers were used for the radiomic texture feature selection and model construction. Receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic performance of the models. Routine magnetic resonance imaging (MRI) radiomic texture feature models generated in the same manner were used for the horizontal comparison.

Results
NODDI-radiomic texture analysis based on TBV subregions exhibited the highest accuracy (although nonsignificant) in differentiating GBM from SBM, with area under the ROC curve (AUC) values of 0.918 and 0.882 in the training and test datasets, respectively, compared to necrosis (AUCtraining:0.845, AUCtest:0.714), solid tumor (AUCtraining:0.852, AUCtest:0.821), peritumoral edema (AUCtraining:0.817, AUCtest:0.762), and ABV (AUCtraining:0.834, AUCtest:0.779). The performance of the five ROI radiomic texture models in routine MRI was inferior to that of the NODDI-radiomic texture model.

Conclusion
Preoperative NODDI-radiomic texture analysis based on TBV subregions shows great potential for distinguishing GBM from SBM.
Two novel mutations within FREM1 gene in patients with bifid nose
Authors: Chen Xiaoxue , Yu Baofu , Wang Zi , Li Qingfeng , Dai Chuanchang , Wei Jiao 
Published: December 2023

Abstract
Background
Bifid nose is a rare congenital deformity and the etiology is unknown. The purpose of this study was to report genetic variation in family of patients with bifid nose.

Methods
Twenty-three consecutive patients who were diagnosed with mild bifid nose were operated with z-plasty from 2009 to 2021. Three underage patients (a pair of twins and a girl) from two family lines, who came to our hospital for surgical treatment, were enrolled. Whole exome sequencing and Sanger sequencing were conducted. Z-shaped flaps were created and the cartilago alaris major were re-stitched. Photographs and CT scan before and after surgery were obtained. Clinical outcomes, complications and patients’ satisfaction were evaluated and analyzed. The follow-up time ranges from 2 to 3 years (2.4 ± 1.2 years).

Results
Most patients were satisfied with the outcome (96.2%). The nasal deformities were corrected successfully with z-plasty technique in one-stage. FREM1 c.870_876del and c.2 T > C were detected with Whole exome sequencing, which have not been reported before. The results of Sanger sequencing were consistent with those of Whole exome sequencing.

Conclusions
The newly detected mutations of FREM1 have a certain heritability, and are helpful to make an accurate diagnosis and provide a better understanding of bifid nose mechanism. Z-plasty technique can be an effective technical approach for correcting mild bifid nose deformity.
Do the New Rural Pension Scheme promote the health status of chronic patients in old age? —Evidence from CHARLS 2018 in China
Authors: Liang Qihong , Chen Yuxuan , Zhang Zheng , An Shengli 
Published: December 2023

Abstract
Background
Many researchers have examined the impact of social insurance on health in elderly. However, in most cases, they have only demonstrated correlational results and have not been able to determine causal effects, possibly because confounding biases have not been fully addressed. In this study, we investigated the health effects of the New Rural Pension Scheme (NRPS) on the elderly (age≥60 years old) with chronic diseases in rural areas, and to explore the causal relationship and effects of NRPS and health status.

Methods
This paper used data from the 2018 China Health and Retirement Longitudinal Study (CHARLS) and applied Bayesian networks and fuzzy regression discontinuity design to conduct causal analysis. Bayesian networks were used to explore the causal directed acyclic graphs of factors related to NRPS and health status. Based on the results of Bayesian network, a fuzzy regression discontinuity design was employed to estimate the causal effect of NRPS on health status.

Results
Among rural elderly with chronic diseases, Bayesian network mapping of causal relationships among NRPS, health status and covariates showed that age was a common cause of NRPS receipt and satisfaction with health. The results of the fuzzy regression discontinuity analysis showed that the effect of receiving NRPS on the health status was positive, but there was no statistically significant difference concerning the interval estimates. The results of the subgroup analysis with chronic obstructive pulmonary disease (COPD) and asthma indicated that the effect of NRPS receipt on the health status of elderly people with COPD was positive. There was a statistically significant effect of receiving NRPS on self-rated health description ($${\beta }_{1}=3.653,P=0.032$$

β
1

=
3.653
,
P
=
0.032

) and health satisfaction ($${\beta }_{1}=4.204,P=0.033$$

β
1

=
4.204
,
P
=
0.033

) in COPD population and a statistically significant effect of receiving NRPS on health satisfaction in asthma population ($${\beta }_{1}=9.844,P=0.008$$

β
1

=
9.844
,
P
=
0.008

).

Conclusion
This paper has confirmed the contribution and positive causal effect of NRPS on health status in a subgroup of older adults with COPD and asthma, using the CHARLS database as evidence. Thus, Chinese government should increase the take-up rate of the NRPS to enhance their positive impact on health status of elderly people with chronic diseases in rural areas.
Biomechanical behaviour of a novel bone cement screw in the minimally invasive treatment of Kummell's disease: a finite element study
Authors: Xu Hanpeng , Feng Qing , Ma Xiang , Lan Jie , Ji Jingtao , Zhang Zepei , Miao Jun 
Published: December 2023

Abstract
Objective
To investigate and evaluate the biomechanical behaviour of a novel bone cement screw in the minimally invasive treatment of Kummell's disease (KD) by finite element (FE) analysis.

Methods
A validated finite element model of healthy adult thoracolumbar vertebrae T12-L2 was given the osteoporotic material properties and the part of the middle bone tissue of the L1 vertebral body was removed to make it wedge-shaped. Based on these, FE model of KD was established. The FE model of KD was repaired and treated with three options: pure percutaneous vertebroplasty (Model A), novel unilateral cement screw placement (Model B), novel bilateral cement screw placement (Model C). Range of motion (ROM), maximum Von-Mises stress of T12 inferior endplate and bone cement, relative displacement of bone cement, and stress distribution of bone cement screws of three postoperative models and intact model in flexion and extension, as well as lateral bending and rotation were analyzed and compared.

Results
The relative displacements of bone cement of Model B and C were similar in all actions studied, and both were smaller than that of Model A. The minimum value of relative displacement of bone cement is 0.0733 mm in the right axial rotation of Model B. The maximum Von-Mises stress in T12 lower endplate and bone cement was in Model C. The maximum Von-Mises stress of bone cement screws in Model C was less than that in Model B, and it was the most substantial in right axial rotation, which is 34%. There was no substantial difference in ROM of the three models.

Conclusion
The novel bone cement screw can effectively reduce the relative displacement of bone cement by improving the stability of local cement. Among them, novel unilateral cement screw placement can obtain better fixation effect, and the impact on the biomechanical environment of vertebral body is less than that of novel bilateral cement screw placement, which provides a reference for minimally invasive treatment of KD in clinical practice.
Effectiveness of Salvadora persica toothbrush and Salvadora persica chewing stick in plaque and gingivitis control: a randomized control trial
Authors: Azizan Nurul Fatin , Mohd Nurulhuda , Nik Azis Nik Madihah , Baharin Badiah 
Published: December 2023

Abstract
Background
The values of plant-based products have taken on an expanding relevance in dentistry. Salvadora persica chewing stick (miswak) has been practiced for centuries and is recommended by the World Health Organization as a customary oral hygiene tool. The therapeutic effects of S. persica chewing stick are contributed by its mechanical cleansing action, active chemicals released, or the combination of these two actions. However, the S. persica chewing stick in its natural form can be difficult to maneuver in certain parts of the mouth. This concern has inspired the innovation of the S. persica toothbrush that is designed to merge the ease of use of a toothbrush with the beneficial natural properties of S. persica preserved in its bristle. The present study aimed to compare the clinical effectiveness between S. persica toothbrush, S. persica chewing stick and the standard toothbrush in plaque and gingivitis control.

Methods
In this single-blinded and parallel randomized controlled trial, 78 participants were randomly divided into three groups to either use (i) S. persica toothbrush (MTB); (ii) S. persica chewing stick (MCS); or (iii) standard toothbrush (STB) in a standardized manner for three weeks. Plaque Index (PI) and Periodontal Inflamed Surface Area (PISA) values, measuring plaque levels and severity of gingivitis, respectively, were evaluated at baseline, one- and three-week post-interventions.

Results
The MCS group showed a significant improvement in the mean PISA values of the anterior teeth compared to the MTB and STB groups (MCS: from 16.35 ± 10.03 to 3.41 ± 1.14; MTB: from 25.20 ± 14.01 to 3.57 ± 1.19; STB: from 26.54 ± 8.64 to 6.17 ± 0.86; p < .050). All three groups reported significant improvements (p < .001) in the plaque levels and the severity of gingivitis from baseline to three weeks after the intervention.

Conclusions
Following correct techniques, S. persica toothbrush and chewing sticks are as effective as the standard toothbrush in plaque control and gingival health, which represent the reputed anti-plaque and anti-gingivitis properties of S. persica.

Trial registration
This clinical trial was prospectively registered in ClinicalTrials.gov with registration NCT04650685 (25/11/2020).
Computer-aided autism diagnosis using visual attention models and eye-tracking: replication and improvement proposal
Authors: Franco Felipe O. , Oliveira Jessica S. , Portolese Joana , Sumiya Fernando M. , Silva Andréia F. , Machado-Lima Ariane , Nunes Fatima L.S. , Brentani Helena 
Published: December 2023

Abstract
Background
Autism Spectrum Disorder (ASD) diagnosis can be aided by approaches based on eye-tracking signals. Recently, the feasibility of building Visual Attention Models (VAMs) from features extracted from visual stimuli and their use for classifying cases and controls has been demonstrated using Neural Networks and Support Vector Machines. The present work has three aims: 1) to evaluate whether the trained classifier from the previous study was generalist enough to classify new samples with a new stimulus; 2) to replicate the previously approach to train a new classifier with a new dataset; 3) to evaluate the performance of classifiers obtained by a new classification algorithm (Random Forest) using the previous and the current datasets.

Methods
The previously approach was replicated with a new stimulus and new sample, 44 from the Typical Development group and 33 from the ASD group. After the replication, Random Forest classifier was tested to substitute Neural Networks algorithm.

Results
The test with the trained classifier reached an AUC of 0.56, suggesting that the trained classifier requires retraining of the VAMs when changing the stimulus. The replication results reached an AUC of 0.71, indicating the potential of generalization of the approach for aiding ASD diagnosis, as long as the stimulus is similar to the originally proposed. The results achieved with Random Forest were superior to those achieved with the original approach, with an average AUC of 0.95 for the previous dataset and 0.74 for the new dataset.

Conclusion
In summary, the results of the replication experiment were satisfactory, which suggests the robustness of the approach and the VAM-based approaches feasibility to aid in ASD diagnosis. The proposed method change improved the classification performance. Some limitations are discussed and additional studies are encouraged to test other conditions and scenarios.
An FGFR2 mutation as the potential cause of a new phenotype including early-onset osteoporosis and bone fractures: a case report
Authors: Dantsev Ilya S , Parfenenko Mariia A , Radzhabova Gulnara M , Nikolaeva Ekaterina A 
Published: December 2023

AbstractOsteoporosis is a systemic, multifactorial disorder of bone mineralization. Many factors contributing to the development of osteoporosis have been identified so far, including gender, age, nutrition, lifestyle, exercise, drug use, as well as a range of comorbidities. In addition to environmental and lifestyle factors, molecular genetic factors account for 50–85% of osteoporosis cases. For example, the vitamin D receptor (VDR), collagen type I (COL1), estrogen receptor (ER), apolypoprotein Е (ApoE), bone morphogenetic protein (BMP), and Low-density lipoprotein receptor-related protein 5 (LRP5) are all involved in the pathogenesis of osteoporosis. Among the candidate genes, the pathogenic variants in which are involved in the pathogenesis of osteoporosis is FGFR2. Additionally, FGFs/FGFRs-dependent signaling has been shown to regulate skeletal development and has been linked to a plethora of heritable disorders of the musculoskeletal system. In this study we present the clinical, biochemical and radiological findings, as well as results of molecular genetic testing of a 13-year-old male proband with heritable osteoporosis, arthralgia and multiple fractures and a family history of abnormal bone mineralization and fractures. Whole exome sequencing found a heterozygous previously undescribed variant in the FGFR2 gene (NM_000141.5) (GRCh37.p13 ENSG00000066468.16: g.123298133dup; ENST00000358487.5:c.722dup; ENSP00000351276.5:p.Asn241LysfsTer43). The same variant was found in two affected relatives. These data lead us to believe that the variant in FGFR2 found in our proband and his relatives could be related to their phenotype. Therefore, modern methods of molecular genetic testing can allow us to differentiate between osteogenesis imperfecta and other bone mineralization disorders.
Structural characterization of SLYM—a 4th meningeal membrane
Authors: Plá Virginia , Bitsika Styliani , Giannetto Michael J , Ladron-de-Guevara Antonio , Gahn-Martinez Daniel , Mori Yuki , Nedergaard Maiken , Møllgård Kjeld 
Published: December 2023

AbstractTraditionally, the meninges are described as 3 distinct layers, dura, arachnoid and pia. Yet, the classification of the connective meningeal membranes surrounding the brain is based on postmortem macroscopic examination. Ultrastructural and single cell transcriptome analyses have documented that the 3 meningeal layers can be subdivided into several distinct layers based on cellular characteristics. We here re-examined the existence of a 4th meningeal membrane, Subarachnoid Lymphatic-like Membrane or SLYM in Prox1-eGFP reporter mice. Imaging of freshly resected whole brains showed that SLYM covers the entire brain and brain stem and forms a roof shielding the subarachnoid cerebrospinal fluid (CSF)-filled cisterns and the pia-adjacent vasculature. Thus, SLYM is strategically positioned to facilitate periarterial influx of freshly produced CSF and thereby support unidirectional glymphatic CSF transport. Histological analysis showed that, in spinal cord and parts of dorsal cortex, SLYM fused with the arachnoid barrier layer, while in the basal brain stem typically formed a 1–3 cell layered membrane subdividing the subarachnoid space into two compartments. However, great care should be taken when interpreting the organization of the delicate leptomeningeal membranes in tissue sections. We show that hyperosmotic fixatives dehydrate the tissue with the risk of shrinkage and dislocation of these fragile membranes in postmortem preparations.
Study of the curative effect of Zhang’s Xibi formula and its underlying mechanism involving inhibition of inflammatory responses and delay of knee osteoarthritis
Authors: Sun Qi , Jin Hongting , Li Wuyin , Tong Peijian , Yuan Wenhua 
Published: December 2023

Abstract
Objective
To verify the clinical efficacy of Zhang’s Xibi formula (ZSXBF) and explain the mechanism underlying its therapeutic effect.

Methods
Preliminary elucidation of the clinical efficacy of ZSXBF in treating KOA in self-control studies, exploration of its mechanism of action with network pharmacology methods, and validation in animal experiments.

Results
In clinical studies, ZSXBF administration effectively improved patient quality of life and reduce pain. Network pharmacology was used to explore the possible mechanisms underlying its treatment effect, and after verification in clinical experience and animal experiments, it was found that ZSXBF regulated the expression of immune-related proteins such as IL-17, ERK1, and TP53 in mouse knee joints.

Conclusion
ZSXBF, which is a traditional Chinese medicine compound that is used to clear heat and detoxify, can effectively improve the clinical symptoms of KOA patients, and its underlying mechanism includes the regulation of human immune-related proteins.