bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mutational analysis of the RB1 gene in patients with unilateral retinoblastoma
Authors: Yousef Yacoub A. , Mohammad Mona , Baqain Laith , Al-Hussaini Maysa , Shanap Mayada Abu , Halalsheh Hadeel , Khzouz Jakub , Jaradat Imad , Mehyar Mustafa , Sultan Iyad , AlNawaiseh Ibrahim , Shawagfeh Munir 
Published: August 2024

PurposeRetinoblastoma, a childhood cancer originating in the retina, is primarily attributed to pathogenic RB1 mutations The aim of this study is to conduct a mutational analysis of the RB1 gene in cases of unilateral Retinoblastoma among individuals within the Jordanian population.MethodsIn this study, the peripheral blood of 50 unilateral Rb patients was collected, genomic DNA was extracted, and mutations were identified using Next Generation Sequencing (NGS) analysis.ResultsIn this cohort of 50 unrelated patients with unilateral Rb, the median age at diagnosis was eight months (mean, 12 months; range; 2 weeks to 54 months). Twenty-eight (56%) were males, 29 (58%) had the disease in the right eye, 3 (6%) had a positive family history of Rb, and 20 (40%) were diagnosed within the first year of life. RB1 gene pathogenic mutations were detected in 14 out of 50 (28%) patients, indicating germline disease. Among unilateral non-familial cases, 11 out of 47 (23%) were found to have germline RB1 mutations. Overall, five (36%) of the germline cases had the same mutation detected in one of the parents consistent with an inherited disease (four (80%) were of paternal origin); 3 (60%) of these had affected carrier parent, two (40%) had an unaffected carrier parent. Nine (64%) patients had the nonsense mutation, and six (43%) had the mosaic mutation. The significant prognostic factors for positive genetic testing were positive family history (p = 0.018) and age at diagnosis less than 12 months (p = 0.03). At a median of 54 months follow-up, two (4%) patients were dead from distant metastasis. The overall eye salvage rate was 44% (n = 22/50) eyes; 100% for groups A, B, and C, 60% for group D, and none for group E eyes. There was no correlation between the presence of germline mutation and outcome in terms of eye salvage, metastasis, and survival.ConclusionIn this study, 28% of patients with unilateral Rb had germline RB1 mutations, of which 43% were inherited, and one-third presented beyond their first year of life. Therefore, molecular screening is critical for genetic counseling regarding the risk for inherited Rb in unilateral cases, including those with no family history, regardless of the age at diagnosis. However, germline mutations did not appear to significantly predict patient outcomes regarding eye salvage, metastasis, and survival.
The association between the aggregate index of systemic inflammation and risk of rheumatoid arthritis: retrospective analysis of NHANES 1999–2018
Authors: Yin Xiaoshuang , Zou Jinmei , Yang Jing 
Published: August 2024

ObjectiveThe investigation purpose was to examine the correlation between the aggregate index of systemic inflammation (AISI) and rheumatoid arthritis (RA) by utilizing the NHANES database from the years 1999 to 2018.MethodsThe NHANES database was utilized to extract data spanning from 1999 to 2018. AISI, comprising neutrophils (NEU), monocytes (MONO), platelets (PLT), and lymphocytes (LYM), was computed based on counts. The identification of RA patients was accomplished through questionnaire data. To investigate the connection between AISI and RA, a weighted multivariate regression and subgroup analysis were conducted. In addition, restricted cubic splines (RCS) were employed for examining non-linear associations.ResultsThe study encompassed a total of 41,986 patients, among whom 2,642 (6.29%) were diagnosed with RA. Upon controlling for all covariates, the outcomes of the multivariate logistic regression assay demonstrated a statistically significant association between higher Ln(AISI) levels and elevated odds of RA (odds ratio [OR]: 1.097; 95% confidence interval [CI]: 1.096–1.099, p &lt; 0.001). The interaction test findings indicate that there is no statistically significant impact within this particular association. The results of the RCS regression model revealed a non-linear pattern in the correlation between Ln(AISI) and RA. The threshold level of AISI for RA was determined as 298.9. The risk of RA rises steeply when AISI surpasses the threshold value.ConclusionOverall, a positive association has been observed between AISI and RA. This study highlights the potential of AISI as an innovative, vital, and appropriate inflammatory biomarker for predicting the risk of developing rheumatoid arthritis in older individuals residing in the United States.
Colorectal cancer-specific microbiome in peripheral circulation and cancer tissues
Authors: Yan Shushan , Liu Tie , Zhao Haobin , Zhao Chunbo , Zhu Yuxin , Dai Wenqing , Sun Wenchang , Wang Honggang , Sun Junxi , Zhao Lu , Xu Donghua 
Published: August 2024

IntroductionAccumulating evidence has supported that gut microbiota and metabolite profiles play indispensable roles in the pathogenesis of colorectal cancer (CRC), which ranks as the third most common cancer and the second leading cause of cancer-related deaths worldwide. However, alterations in tumoral or circulating microbiomes in CRC remain incompletely understood. It has been well-documented that tissue or serum microbiomes with low microbial biomass could be screened by use of 2bRAD sequencing for microbiome (2bRAD-M) at the species resolution.MethodsIn order to validate the microbial biomarkers distinguishing CRC and the variations in microorganisms present in serum and tumors, we performed 2bRAD-M to characterize the microbiomes in serum and cancer tissues of CRC patients with and without lymph node or liver metastasis.ResultsThe composition of dominated microbiota in serum was different from that of tissue samples, while the microbial community composition of tumors was similar to that of the tumor-adjacent tissues. The analysis of α-diversity and β-diversity has revealed notable variations in serum microbiota diversities in CRC patients, particularly those with liver metastasis. Multiple CRC-specific microbial species, such as Moraxella A cinereus, Flavobacterium sp001800905, and Acinetobacter albensis, were identified in serum. Complicated functions and KEGG pathways were also confirmed in CRC according to the metastasis status.DiscussionThis study has found significant alterations in the microbial compositions and diversities in CRC and CRC-specific microbial species in both circulation and cancer tissues, which may serve as promising biomarkers for the screening, diagnosis and prognosis prediction of CRC. In particular, CRC-specific bacterial taxa are promising markers, holding transformative potentials in establishing personalized screening and risk stratification, refining much earlier non-invasive diagnostic approaches, and enhancing diagnostic sensitivity.
Rapid and sensitive detection of methicillin-resistant Staphylococcus aureus through the RPA-PfAgo system
Authors: Chen Weizhong , Zhang Jiexiu , Wei Huagui , Su Jie , Lin Jie , Liang Xueyan , Chen Jiangtao , Zhou Rong , Li Lin , Lu Zefang , Sun Guangyu 
Published: August 2024

IntroductionBoth the incidence and mortality rates associated with methicillin-resistant Staphylococcus aureus (MRSA) have progressively increased worldwide. A nucleic acid testing system was developed in response, enabling swift and precise detection of Staphylococcus aureus (S. aureus) and its MRSA infection status. This facilitates improved prevention and control of MRSA infections.MethodsIn this work, we introduce a novel assay platform developed by integrating Pyrococcus furiosus Argonaute (PfAgo) with recombinase polymerase amplification (RPA), which was designed for the simultaneous detection of the nuc and mecA genes in MRSA.ResultsThis innovative approach enables visual MRSA detection within 55 mins, boasting a detection limit of 102 copies/μL. Characterized by its high specificity, the platform accurately identifies MRSA infections without cross-reactivity to other clinical pathogens, highlighting its unique capability for S. aureus infection diagnostics amidst bacterial diversity. Validation of this method was performed on 40 clinical isolates, demonstrating a 95.0% accuracy rate in comparison to the established Vitek2-COMPACT system.DiscussionThe RPA-PfAgo platform has emerged as a superior diagnostic tool, offering enhanced sensitivity, specificity, and identification efficacy for MRSA detection. Our findings underscore the potential of this platform to significantly improve the diagnosis and management of MRSA infection.
The signatures and crosstalk of gut microbiome, mycobiome, and metabolites in decompensated cirrhotic patients
Authors: Li Yangjie , Liu Danping , He Yanglan , Zhang Zeming , Zeng Ajuan , Fan Chunlei , Lyu Lingna , He Zilong , Ding Huiguo 
Published: August 2024

BackgroundNumerous studies have confirmed that gut microbiota plays a crucial role in the progression of cirrhosis. However, the contribution of gut fungi in cirrhosis is often overlooked due to the relatively low abundance.MethodsWe employed 16S ribosomal RNA sequencing, internal transcribed spacer sequencing, and untargeted metabolomics techniques to investigate the composition and interaction of gut bacteria, fungi, and metabolites in cirrhotic patients.ResultsCirrhotic patients exhibited significant differences in the diversity and composition of gut microbiota and their metabolites in cirrhotic patients compared to healthy individuals. Increase in pathogenic microbial genera and a decrease in beneficial microbial genera including bacteria and fungi were observed. Various clinical indexes were closely connected with these increased metabolites, bacteria, fungi. Additionally, endoscopic treatment was found to impact the gut microbiota and metabolites in cirrhotic patients, although it did not significantly alter the gut ecology. Finally, we constructed a cirrhosis diagnostic model based on different features (bacteria, fungi, metabolites, clinical indexes) with an AUC of 0.938.ConclusionOur findings revealed the characteristics of gut microbial composition and their intricate internal crosstalk in cirrhotic patients, providing cutting-edge explorations of potential roles of gut microbes in cirrhosis.
Serum biomarker-based risk model construction for primary Sjögren’s syndrome with interstitial lung disease
Authors: Liu Xiaoli , Zhang Xia , Shi Juan , Li Shiqing , Zhang Xiuzhi , Wang Huiling 
Published: August 2024

BackgroundCytokine network disturbances in primary Sjögren’s syndrome (pSS) have been reported in many studies. However, their functions in patients with primary Sjögren’s syndrome and interstitial lung disease (pSS-ILD) is controversial. In this study, we aim to investigate the associations of immunological characteristics and cytokine profiles with pSS-ILD pathogenesis and explore their predictive values for pSS progression.MethodsA total of 256 patients initially diagnosed with pSS at Henan Provincial People’s Hospital were enrolled. After excluding the patients previously diagnosed with various serious acute and chronic respiratory system diseases and cases with other connective tissue diseases or congenital heart diseases, 94 pSS patients were included for further analysis, including 40 patients with ILD (pSS-ILD) and 54 patients without ILD (pSS-N-ILD). For comparison, 41 age- and sex-matched healthy individuals were included as normal controls. Their clinical symptoms and serological data including cyclic citrullinated peptide (CCP) antibody (anti-CCP), antinuclear antibody (ANA), anti-Ro52, anti-SSA, anti-SSB, C-reactive protein, IgG, IgM, IgA, C3, C4, and 10 cytokines and chemokines were obtained. Wilcoxon test, chi-square test, Spearman correlation analysis, and logistics regression analysis were performed.ResultsHigher positive rates of anti-SSB and higher incidence of dry cough, dyspnea, and arthrosis symptoms were shown in pSS-ILD patients than in the pSS-N-ILD cases. Anti-CCP antibodies and cytokines (IL-1β, TNFα, IL-6, IL-5, IL-12p70, and IL-17) were higher, while C3 was lower in pSS-ILD patients than in pSS-N-ILD cases. Significant negative correlations of IgG with C3 and C4 and positive correlations of IL-12p70 and IL-17 with IL-6 were only shown in pSS-ILD patients. The anti-CCP antibody was positively correlated with IL-5 in pSS-ILD patients, but not in pSS-N-ILD cases. Multi-variable logistics regression analysis revealed the combination of anti-CCP, IL-17, IL-12p70, and IL-5 was effective in predicting the status of pSS-ILD in the pSS cases.ConclusionThere were significant differences in serum marker levels between pSS-ILD and pSS-N-ILD cases. The combination of anti-CCP, IL-17, IL-12p70, and IL-5 might be a potential risk predictor for pSS-ILD occurrence. The cytokines might be involved in the development and progression of pSS-ILD. These results would provide new therapeutic targets for pSS-ILD treatment.
Incidence and etiology of traumatic spinal cord injury in Rwanda: a prospective population-based study
Authors: Kanyoni Maurice , Wikmar Lena Nilsson , Philips Joliana , Joseph Conran , Tumusiime David K. 
Published: August 2024

BackgroundTraumatic spinal cord injury (TSCI) is not only a life-threatening but also life changing event that happens suddenly, the effects extends beyond the TSCI survivors to include their families. In Rwanda to the best knowledge of authors, there is no published information on the epidemiology of TSCI. The aim of this study was therefore to determine the incidence rate, etiology and injury characteristics of TSCI.MethodsAll survivors of acute TSCI who met the inclusion criteria were prospectively recruited for a one-year period. The International Spinal Cord Injury Core Data Set was used to collect the minimum set of variables to facilitate worldwide comparison of epidemiological data, while the International Standards for the Neurological Classification was used to categorize TSCI according to the American Spinal Injury Association Impairment Scale (AIS). Data were collected by trained physiotherapists.Study designA prospective, open-ended, cohort study design.SettingAll referral hospitals within the Republic of Rwanda.ResultsOverall, 122 adult individuals sustained a TSCI between 10th October 2019 until 9th October 2020 and all consented to take part in the study. The male-to-female ratio was 3.9:1, and the mean age was 42.5 (SD = ±14.8) years. The crude incidence rate of TSCI was 22.2 per million people (95% CI, 18.4–26.5) with significant differences in sex-adjusted rates for all age groups while men 46 years of age and older presented with the highest incidence. The leading causes of TSCI were falls (73.8%), followed by road traffic accidents (18.9%). Moreover, SCI lesions of the cervical region (n = 69) were the most common, followed by the lumbosacral region (n = 27). Fifty-one (41.8%) participants were diagnosed as complete injury, i.e., AIS A, while incomplete injury category C constituted 35 (28.7%).ConclusionThe incidence and etiology of TSCI in Rwanda are comparable to worldwide estimates and figures. Largely, the etiology of TSCI are preventable as it is caused due to falls and road traffic accidents. There is a need to consider preventive strategies and policies on activities that predispose people to falls. Policies should focus largely on occupational health and safety in both formal and informal sectors of work.
Association of higher triglyceride–glucose index and triglyceride-to-high-density lipoprotein cholesterol ratio with early neurological deterioration after thrombolysis in acute ischemic stroke patients
Authors: Deng Mingzhu , Song Kangping , Xu Wei , He Guohua , Hu Jue , Xiao Hui , Zhou Nina , Chen Sufen , Xu Guilan , Tong Yangping , Zhang Dan , Wang Zhen , Li Fangyi 
Published: August 2024

BackgroundInsulin resistance (IR) can predict the prognosis of patients suffering from cerebrovascular disorders. The triglyceride–glucose (TyG) index and triglyceride-to-high-density lipoprotein cholesterol (TG/HDL-C) ratio have been confirmed to be easy and reliable indicators of IR. However, the relationships between the TyG index or TG/HDL-C ratio and early neurological deterioration (END) after thrombolysis in patients with acute ischemic stroke (AIS) are uncertain.MethodsA retrospective analysis of 1,187 patients diagnosed with AIS who underwent intravenous thrombolysis between January 2018 and February 2024 was performed. Post-thrombolysis END was defined as an increase in the National Institutes of Health Stroke Scale (NIHSS) score of ≥4 within 24 h after thrombolysis. Logistic regression analysis was performed to explore the relationships of the TyG index and TG/HDL-C ratio with post-thrombolysis END. Receiver operating characteristic (ROC) analysis was used to assess the ability of the TyG index and TG/HDL-C ratio to discriminate post-thrombolysis END.ResultsAmong the 1,187 recruited patients, 179 (15.08%) were diagnosed with post-thrombolysis END, and 1,008 (84.92%) were diagnosed with non-END. A binary logistic regression model indicated that the TyG index (odds ratio [OR], 2.015; 95% confidence interval [CI] 1.964–2.414, p = 0.015) and TG/HDL-C ratio (OR, 1.542; 95% CI, 1.160–2.049, p = 0.004) were independent factors for post-thrombolysis END. The area under the curve (AUC) values for the TyG index, TG/HDL-C ratio, and TyG index combined with the TG/HDL-C ratio for post-thrombolysis END were 0.704, 0.674, and 0.755, respectively.ConclusionThis study indicates that the TyG index and TG/HDL-C ratio can be used as prognostic factors to predict post-thrombolysis END.
Proteomic characterization of head and neck paraganglioma and its molecular classification
Authors: Wang Xi , Sun Jiameng , Feng Guodong , Tian Xu , Zhao Yang , Gao Zhiqiang , Sun Wei 
Published: August 2024

BackgroundHead and neck paragangliomas (HNPGLs) are rare neuroendocrine tumors that pose significant challenges in both diagnosis and treatment. The pathogenic mechanism remains unclear, and there is no proteomic analysis-based molecular classification. Therefore, gaining a deeper understanding of this disease from the protein level is crucial because proteins play a fundamental role in the occurrence and development of tumors.MethodsWe collected 44 tumor samples from patients diagnosed with HNPGL. The adrenal paraganglioma tissue (N = 46) was used as the disease control group and the chorda tympani nerves (N = 18) were used as the control group. High-pH reversed-phase liquid chromatography and liquid chromatography with tandem mass spectrometry analyses were used to build an integrated protein database of tumor samples. We then obtained two sets of differentially expressed proteins between the tumor group and the control group to identify the unique proteomic signatures of HNPGLs. Ingenuity pathway analysis annotations were used to perform the functional analysis. Subsequently, we developed a clinically relevant molecular classification for HNPGLs that connected the clinical characteristics with meaningful proteins and pathways to explain the varied clinical manifestations.ResultsWe identified 6,640 proteins in the HNPGL group, and 314 differentially expressed proteins unique to HNPGL were discovered via inter-group comparison. We identified two HNPGL subgroups that significantly differed in clinical manifestation and proteomic characteristics. On the basis of the proteomic results, we proposed a pathogenic mechanism underlying HNPGL.ConclusionWe conducted a comprehensive analysis of the molecular mechanisms of HNPGL to build, for the first time, a clinically relevant molecular classification. By focusing on differential proteomic analyses between different types of paragangliomas, we were able to obtain a comprehensive description of the proteomic characteristics of HNPGL, which will be valuable for the search for significant biomarkers as a new treatment method for HNPGL.
A novel x-Ray and γ-Ray combination strategy for radiotherapy after breast-conserving surgery in patients with right breast cancer
Authors: Zhang Kunpeng , He Ruixin , Tang Fenwen , Zhou Luping , Zhang Xiaozhi , Li Jinsheng , Wei Zhiwei , Li Yi 
Published: August 2024

Background and purposeRadiotherapy is a primary therapeutic approach for breast cancer following breast-conserving surgery. The TaiChiB dual-modality radiotherapy system combining X-ray and focused γ-ray, offers a new approach to reduce the radiation dose of organs at risk (OARs) and has the potential to mitigate the adverse effects of radiotherapy. Currently, there are few studies on the dosimetric characteristics of the TaiChiB dual-modality system for actual treatment plans for specific diseases. The purpose of this work is to study the dosimetric advantages of dual-modal systems for right breast patients after breast-conserving surgery.Material and methodsTreatment plans for 20 patients with right breast cancer were generated for a linear accelerator (LINAC) based system and the TaiChiB dual-modality system, respectively. Volumetric modulated arc therapy plans with simultaneous integrated boost (VMAT-SIB) were made for the LINAC. Focused γ-ray was used to deliver the boost dose with the dual-modality system. The dosimetric parameters of the target and OARs were evaluated and compared between the treatment plans generated for the two systems.ResultsThe TaiChiB dual-modality plans exhibit a higher conformal index (CI) and lower gradient index (GI) for the PGTV and PTV compared with the LINAC-based VMAT-SIB plans. Compared to VMAT-SIB plans, the PTV Dmax, PTV Dmean, PTV V110, PGTV Dmax, and PGTV Dmean of the TaiChiB dual-modality plans are significantly lower. Meanwhile, the dose to OARs, such as the Dmean of the heart, the V5 of liver, the Dmean of ipsilateral lung, the V30 of ipsilateral lung, the V20 of ipsilateral lung, the V5 of ipsilateral lung, the Dmean of contralateral lung, Dmax of contralateral breast and the Dmean of contralateral breast are significantly reduced.ConclusionsOur study demonstrates the dosimetric advantages of the novel TaiChiB dual-modality radiotherapy system for the treatment of right-sided breast cancer. Overall, for the TaiChiB dual-modality radiotherapy system, the radiation dose outside the target region decreases rapidly, thereby minimizing radiation exposure to neighboring organs and ensuring the conformity of the target area. Our research confirms the potential of the TaiChiB dual-modality system for future radiotherapy.