bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversity and breed-informative SNPs identification in domestic pig populations using coding SNPs
Authors: Hayah Ichrak , Talbi Chouhra , Chafai Narjice , Houaga Isidore , Botti Sara , Badaoui Bouabid 
Published: November 2023

Background: The use of breed-informative genetic markers, specifically coding Single Nucleotide Polymorphisms (SNPs), is crucial for breed traceability, authentication of meat and dairy products, and the preservation and improvement of pig breeds. By identifying breed informative markers, we aimed to gain insights into the genetic mechanisms that influence production traits, enabling informed decisions in animal management and promoting sustainable pig production to meet the growing demand for animal products.Methods: Our dataset consists of 300 coding SNPs genotyped from three Italian commercial pig populations: Landrace, Yorkshire, and Duroc. Firstly, we analyzed the genetic diversity among the populations. Then, we applied a discriminant analysis of principal components to identify the most informative SNPs for discriminating between these populations. Lastly, we conducted a functional enrichment analysis to identify the most enriched pathways related to the genetic variation observed in the pig populations.Results: The alpha diversity indexes revealed a high genetic diversity within the three breeds. The higher proportion of observed heterozygosity than expected revealed an excess of heterozygotes in the populations that was supported by negative values of the fixation index (FIS) and deviations from the Hardy-Weinberg equilibrium. The Euclidean distance, the pairwise FST, and the pairwise Nei’s GST genetic distances revealed that Yorkshire and Landrace breeds are genetically the closest, with distance values of 2.242, 0.029, and 0.033, respectively. Conversely, Landrace and Duroc breeds showed the highest genetic divergence, with distance values of 2.815, 0.048, and 0.052, respectively. We identified 28 significant SNPs that are related to phenotypic traits and these SNPs were able to differentiate between the pig breeds with high accuracy. The Functional Enrichment Analysis of the informative SNPs highlighted biological functions related to DNA packaging, chromatin integrity, and the preparation of DNA into higher-order structures.Conclusion: Our study sheds light on the genetic underpinnings of phenotypic variation among three Italian pig breeds, offering potential insights into the mechanisms driving breed differentiation. By prioritizing breed-specific coding SNPs, our approach enables a more focused analysis of specific genomic regions relevant to the research question compared to analyzing the entire genome.
Prognostic value of fatty acid metabolism-related genes in colorectal cancer and their potential implications for immunotherapy
Authors: Huang Xi , Sun Yiwen , Song Jia , Huang Yusong , Shi Huizhong , Qian Aihua , Cao Yuncan , Zhou Youci , Wang Qijun 
Published: November 2023

IntroductionColorectal cancer is one of the most common gastrointestinal cancers and the second leading cause of cancer-related death. Although colonoscopy screening has greatly improved the early diagnosis of colorectal cancer, its recurrence and metastasis are still significant problems. Tumour cells usually have the hallmark of metabolic reprogramming, while fatty acids play important roles in energy storage, cell membrane synthesis, and signal transduction. Many pathways of fatty acid metabolism (FAM) are involved in the occurrence and development of colon cancer, and the complex molecular interaction network contains a variety of genes encoding key enzymes and related products.MethodsClinical information and RNA sequencing data were collected from TCGA and GEO databases. The prognosis model of colon cancer was constructed by LASSO-Cox regression analysis among the selected fatty acid metabolism genes with differential expression. Nomogram for the prognosis model was also constructed in order to analyze its value in evaluating the survival and clinical stage of the colon cancer patients. The differential expression of the selected genes was verified by qPCR and immunohistochemistry. GSEA and GSVA were used to analyze the enrichment pathways for high- and low-risk groups. CIBERSORT was used to analyze the immune microenvironment of colon cancer and to compare the infiltration of immune cells in the high- and low-risk groups. The “circlize” package was used to explore the correlation between the risk score signature and immunotherapy for colon cancer.ResultsWe analysed the differential expression of 704 FAM-related genes between colon tumour and normal tissue and screened 10 genes with prognostic value. Subsequently, we constructed a prognostic model for colon cancer based on eight optimal FAM genes through LASSO Cox regression analysis in the TCGA-COAD dataset, and its practicality was validated in the GSE39582 dataset. Moreover, the risk score calculated based on the prognostic model was validated as an independent prognostic factor for colon cancer patients. We further constructed a nomogram composed of the risk score signature, age and American Joint Committee on Cancer (AJCC) stage for clinical application. The colon cancer cohort was divided into high- and low-risk groups according to the optimal cut-off value, and different enrichment pathways and immune microenvironments were depicted in the groups.DiscussionSince the risk score signature was significantly correlated with the expression of immune checkpoint molecules, the prognostic model might be able to predict the immunotherapy response of colon cancer patients. In summary, our findings expand the prognostic value of FAM-related genes in colon cancer and provide evidence for their application in guiding immunotherapy.
Comparison of 1064-nm Nd:YAG picosecond laser using fractional micro-lens array vs. ablative fractional 2940-nm Er:YAG laser for the treatment of atrophic acne scar in Asians: a 20-week prospective, randomized, split-face, controlled pilot study
Authors: Dai Ru , Cao Yiyu , Su Yiping , Cai Suiqing 
Published: November 2023

BackgroundThe 1064-nm Nd:YAG picosecond lasers using fractional micro-lens array (P-MLA) was a promising therapy for skin resurfacing. However, no studies have compared P-MLA with ablative fractional 2940-nm Er:YAG lasers (AF-Er) in the treatment of atrophic acne scars.ObjectivesTo evaluate the efficacy and safety of P-MLA and AF-Er for the treatment of atrophic acne scars.MethodsWe performed a prospective, randomized, split-face, controlled pilot study. Thirty-one Asian patients with mild to moderate atrophic acne scars underwent four consecutive sessions of randomized split-face treatment with P-MLA and AF-Fr at 4-week intervals. The efficacy of the two devices were evaluated by Echelle d’Evaluation Clinique des Cicatrices d’acne (ECCA) grading scale, Investigator’s Global Assessment (IGA) score and patient’s satisfaction. VISIA analysis was also performed to evaluate the pore and skin texture. Adverse events were recorded at each follow-up.ResultsThe P-MLA afforded comparable clinical responses in scar appearance as AF-Er based on the investigator’s assessments (ECCA percent reduction: 39.11% vs. 43.73%; IGA score: 2.97 ± 0.65 vs. 3.16 ± 0.68; P &gt; 0.05 for both). However, the result of patient satisfaction indicated the AF-Er-treated side achieved a slightly greater improvement in scar appearance (3.97 ± 0.78 vs. 3.55 ± 0.71; P &lt; 0.05). Overall, the two devices did not differ largely in terms of efficacy. VISIA analysis revealed similar changing patterns of the pore and skin texture between two devices. For safety profiles, no serious side effects were reported on both sides. The P-MLA showed lower pain level, shortened duration of crust shed and edema, and less occurrence of PIH (P &lt; 0.05 for all).ConclusionCompared with AF-Er, P-MLA afforded comparable effect and more safety profiles in treating atrophic acne scars in Asian patients.Clinical trial registrationClinicalTrials.gov, identifier NCT 05686603.
A scoping review of music-based interventions for swallowing difficulties: implications for treating older adults with presbyphagia
Authors: Kim Soo Ji , Yeo Myung Sun , Kim So Yeon , Kang Seo Yeon 
Published: November 2023

ObjectivesPresbyphagia refers to age-related changes in the swallowing mechanism (e.g., reduced skeletal muscle strength that decreases bolus control). If left untreated, these changes can lead to dysphagia, which refers to impaired swallowing (e.g., coughing or choking when eating). Given that swallowing difficulties are common among older adults that they make up the fastest growing age group globally, the need for interventions to address presbyphagia is gaining urgency. To begin to address this need, we conducted a scoping review to analyze music therapy research aimed at enhancing swallowing function. The objective was to identify key intervention characteristics and propose clinical implications for treating presbyphagia using music therapy.MethodsThis review followed the methodological frameworks outlined by Arksey and O’Malley and Levac et al. and used the Preferred Reporting Items for Systematic Reviews and Meta-Analysis for Scoping Reviews for analysis and reporting. Four electronic databases (i.e., ProQuest, PubMed, RISS, Web of Science) were searched for quantitative and qualitative studies in English or Korean that used music-based interventions to address swallowing function in older adults. Content analysis was conducted to identify and compare the main features of music interventions for swallowing difficulties among older adults.ResultsTen articles were identified and analyzed. It was found that three core components–respiration, vocalization, and singing–were employed to enhance swallowing function in populations with neurological impairments, dementia, or head and neck cancer. Notably, actions closely linked to swallowing function, such as laryngeal elevation and oral movements, were utilized therapeutically to speak or sing. Based on these characteristics, clinical implications are proposed to address presbyphagia.ConclusionSinging entails a systematic and focused incorporation of stepwise activities that can be used to address swallowing disorders. In this context, critical clinical implications that music therapists should consider when treating individuals with presbyphagia include warmup breathing, vocalizing targeting laryngeal control, and singing targeting oral motor control. This review can contribute to the expansion of music therapy with older adults and the advancement of music therapy techniques.
The impact of electroacupuncture on anxiety-like behavior and gut microbiome in a mouse model of chronic restraint stress
Authors: Bai Jie , Wei Jia-Quan , Tian Qian , Xue Fen , Zhang Wen , He Hong 
Published: November 2023

IntroductionElectroacupuncture (EA) is a beneficial physiotherapy approach for addressing neuropsychiatric disorders. Nevertheless, the impact of EA on the gut microbiome in relation to anxiety disorders remains poorly understood.MethodsTo address this gap, we conducted a study using a chronic restraint stress (CRS) mouse model to investigate the anti-anxiety outcome of EA and its influence on gut microbiota. Our research involved behavioral tests and comprehensive sequencing of full-length 16S rRNA microbiomes.ResultsOur findings revealed that CRS led to significant anxiety-like behaviors and an imbalance in the gut microbiota. Specifically, we identified 13 species that exhibited changes associated with anxiety-like behaviors. Furthermore, EA partially alleviated both behaviors related to anxiety and the dysbiosis induced by CRS.DiscussionIn summary, this study sheds light on the alterations in gut microbiota species resulting from CRS treatment and brings new light into the connection between EA’s anti-anxiety effects and the gut microbiota.
Disentangling the neurological basis of chronic ocular pain using clinical, self-report, and brain imaging data: use of K-means clustering to explore patient phenotypes
Authors: Holmes Scott , Reyes Nicholas , Huang Jaxon J. , Galor Anat , Pattany Pradip M. , Felix Elizabeth R. , Moulton Eric A. 
Published: November 2023

IntroductionThe factors that mediate the expression of ocular pain and the mechanisms that promote chronic ocular pain symptoms are poorly understood. Central nervous system involvement has been postulated based on observations of pain out of proportion to nociceptive stimuli in some individuals. This investigation focused on understanding functional connectivity between brain regions implicated in chronic pain in persons reporting ocular pain symptoms.MethodsWe recruited a total of 53 persons divided into two cohorts: persons who reported no ocular pain, and persons who reported chronic ocular pain, irrespective of ocular surface findings. We performed a resting state fMRI investigation that was focused on subcortical brain structures including the trigeminal nucleus and performed a brief battery of ophthalmological examinations.ResultsPersons in the pain cohort reported higher levels of pain symptoms relating to neuropathic pain and ocular surface disease, as well as more abnormal tear metrics (stability and tear production). Functional connectivity analysis between groups evinced multiple connections exemplifying both increases and decreases in connectivity including regions such as the trigeminal nucleus, amygdala, and sub-regions of the thalamus. Exploratory analysis of the pain cohort integrating clinical and brain function metrics highlighted subpopulations that showed unique phenotypes providing insight into pain mechanisms.DiscussionStudy findings support centralized involvement in those reporting ocular-based pain and allude to mechanisms through which pain treatment services may be directed in future research.
MiR-324-5p inhibition after intrahippocampal kainic acid-induced status epilepticus does not prevent epileptogenesis in mice
Authors: McGann Amanda M. , Westerkamp Grace C. , Chalasani Alisha , Danzer Cole S. K. , Parkins Emma V. , Rajathi Valerine , Horn Paul S. , Pedapati Ernest V. , Tiwari Durgesh , Danzer Steve C. , Gross Christina 
Published: November 2023

BackgroundAcquired epilepsies are caused by an initial brain insult that is followed by epileptogenesis and finally the development of spontaneous recurrent seizures. The mechanisms underlying epileptogenesis are not fully understood. MicroRNAs regulate mRNA translation and stability and are frequently implicated in epilepsy. For example, antagonism of a specific microRNA, miR-324-5p, before brain insult and in a model of chronic epilepsy decreases seizure susceptibility and frequency, respectively. Here, we tested whether antagonism of miR-324-5p during epileptogenesis inhibits the development of epilepsy.MethodsWe used the intrahippocampal kainic acid (IHpKa) model to initiate epileptogenesis in male wild type C57BL/6 J mice aged 6–8 weeks. Twenty-four hours after IHpKa, we administered a miR-324-5p or scrambled control antagomir intracerebroventricularly and implanted cortical surface electrodes for EEG monitoring. EEG data was collected for 28 days and analyzed for seizure frequency and duration, interictal spike activity, and EEG power. Brains were collected for histological analysis.ResultsHistological analysis of brain tissue showed that IHpKa caused characteristic hippocampal damage in most mice regardless of treatment. Antagomir treatment did not affect latency to, frequency, or duration of spontaneous recurrent seizures or interictal spike activity but did alter the temporal development of frequency band-specific EEG power.ConclusionThese results suggest that miR-324-5p inhibition during epileptogenesis induced by status epilepticus does not convey anti-epileptogenic effects despite having subtle effects on EEG frequency bands. Our results highlight the importance of timing of intervention across epilepsy development and suggest that miR-324-5p may act primarily as a proconvulsant rather than a pro-epileptogenic regulator.
The impact of sMICA/sMICB on immunochemotherapy outcomes in newly diagnosed diffuse large B-cell lymphoma
Authors: Yoon Sang Eun , Park Sujin , Cho Junhun , Ryu Kyung Ju , Yandava Booma , Lee Sewon , Kim Seok Jin , Kim Won Seog 
Published: November 2023

IntroductionSoluble MHC class I-related chain A (sMICA) and B (sMICB) play a critical role tumor evolution and poor prognosis through an immune evasion mechanism. Thus, this study determines the interaction between sMICA/sMICB and the tumor immune environment in newly diagnosed diffuse large B-cell lymphoma (ND-DLBCL).MethodsWe analyzed sMICA/sMICB, cytokine in serum, and macrophage polarization analysis in tissue samples before the first chemotherapy administration. This research was performed to investigate the correlation between sMICA/sMICB expression and treatment outcomes as well as their influence on the immune system within ND-DLBCL.ResultsOf the 262 patients, 47.3% (n = 124) presented stage III or IV at diagnosis and 50.8% (n = 133) had a high International Prognostic Index (IPI ≥ 3). The patients with high (p = 0.034 and 0.004), elevated lactate dehydrogenase (p = 0.002 and 0.030), advanced stage (p = 0.003 and 0.012), and higher IPI risk (p = 0.009, and 0.032) correlated with the detection of sMICA or sMICB. The median progression-free survival (PFS) of patients with sMICA (p = 0.006) or sMICB (p =0.032) was inferior. Among the patients with advanced-stage or high IPI, those with sMICA or sMICB presented an inferior PFS and OS compared to those without. TNF-a, a pro-inflammatory cytokine, showed statistical significance with detected sMICA (p = 0.035) or sMICB (p = 0.044). Among anti-inflammatory cytokines, IL-1RA (P-value = 0.013) and IL-10 (p = 0.005) were associated with detecting sMICB, but not sMICA. In tissue samples, sMICA or sMICB detection did not correlate with the CD68/CD163 ratio.DiscussionConclusively, the identification of sMICA/sMICB presented unfavorable immunochemotherapy outcomes, and it was assumed that sMICA or sMICB and various cytokines interact, but the relationship with macrophage differentiation is unclear. Therefore, further research is needed to determine the relationship between sMICA/sMICB and tumor microenvironment in DLBCL.
Long non-coding RNA PRR7-AS1 promotes osteosarcoma progression via binding RNF2 to transcriptionally suppress MTUS1
Authors: Chen-Xi Gu , Jin-Fu Xu , An-Quan Huang , Xiao Yu , Ying-Hui Wu , Suo-Yuan Li , Cong Shen , Tian-Ming Zou , Jun Shen 
Published: November 2023

IntroductionOsteosarcoma is a common bone malignant tumor in adolescents with high mortality and poor prognosis. At present, the progress of osteosarcoma and effective treatment strategies are not clear. This study provides a new potential target for the progression and treatment of osteosarcoma.MethodsThe relationship between lncRNA PRR7-AS1 and osteosarcoma was analyzed using the osteosarcoma databases and clinical sample testing. Cell function assays and tumor lung metastasis were employed to study the effects of PRR7-AS1 on tumorigenesis in vivo and in vitro. Potential downstream RNF2 of PRR7-AS1 was identified and explored using RNA pulldown and RIP. The GTRD and KnockTF database were used to predict the downstream target gene, MTUS1, and ChIP-qPCR experiments were used to verify the working mechanismy. Rescue experiments were utilized to confirm the role of MTUS1 in the pathway.ResultsDeep mining of osteosarcoma databases combined with clinical sample testing revealed a positive correlation between lncRNA PRR7-AS1 and osteosarcoma progression. Knockdown of PRR7-AS1 inhibited osteosarcoma cell proliferation and metastasis in vitro and in vivo. Mechanistically, RNA pulldown and RIP revealed that PRR7-AS1 may bind RNF2 to play a cancer-promoting role. ChIP-qPCR experiments were utilized to validate the working mechanism of the downstream target gene MTUS1. RNF2 inhibited the transcription of MTUS1 through histone H2A lysine 119 monoubiquitin. Rescue experiments confirmed MTUS1 as a downstream direct target of PRR7-AS1 and RNF2.DiscussionWe identified lncRNA PRR7-AS1 as an important oncogene in osteosarcoma progression, indicating that it may be a potential target for diagnosis and prognosis of osteosarcoma.
Application and evaluation of hydrodissection in microwave ablation of liver tumours in difficult locations
Authors: Song Yuan , Wu Meng , Zhou Ruhai , Zhao Ping , Mao Dan 
Published: November 2023

ObjectiveTo investigate the safety and mid-term outcomes of hydrodissection-assisted microwave ablation (MWA) of hepatocellular carcinoma (HCC) in various difficult locations.MethodsA total of 131 HCC patients who underwent ultrasound-guided MWA from March 2017 to March 2019 were included. Following ultrasound examination, patients with tumors at difficult locations were treated with hydrodissection-assisted MWA (hydrodissection group), while those with tumors at conventional locations received MWA (control group). Both groups were compared concerning baseline characteristics, ablation parameters, complete ablation rates, and complication rates. Kaplan-Meier curves analyzed local tumor progression and overall survival, with stratified analysis for different difficult locations (adjacent to gastrointestinal tract, diaphragm, and subcapsular tumors). Additionally, Cox regression analyses were conducted to assess the impact of different difficult locations on these outcomes.ResultsComplete ablation rates were similar between the hydrodissection and control groups (91.4% vs. 95.2%, P&gt;0.05). Postoperative complications occurred in three patients, including liver abscess and biliary injury. No significant differences in major or minor complication rates were found between the groups (P&gt;0.05). Local tumor progression was detected in 11 patients (8.4%) at the end of the follow-up period. Neither cumulative local tumor progression rate (P=0.757) nor overall survival rate (P=0.468) differed significantly between the groups. Stratified analysis showed no effect of tumor location difficulty on cumulative local tumor progression or overall survival. Tumor number and size served as independent predictors for overall survival, while minimal ablation margin ≤ 5mm independently predicted local tumor progression. In contrast, the tumor location was not statistically significant. Sensitivity analyses corroborated the robustness of the models.ConclusionHydrodissection-assisted MWA for HCC in various difficult locations demonstrated safe and effective, with complete ablation and mid-term outcomes comparable to those for tumors in conventional locations.