bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Optic Disc Ovality Index and Rotation Angle Measurements in Myopic Eyes Using Photography and OCT Based Techniques
Authors: Rezapour Jasmin , Tran Andrew Q. , Bowd Christopher , El-Nimri Nevin W. , Belghith Akram , Christopher Mark , Brye Nicole , Proudfoot James A. , Dohleman Jade , Fazio Massimo A. , Jonas Jost B. , Weinreb Robert N. , Zangwill Linda M. 
Published: June 2022

PurposeTo compare optic nerve head (ONH) ovality index and rotation angle measurements based on semi-automated delineation of the clinical ONH margin derived from photographs and automated BMO configuration derived from optical coherence tomography (OCT) images in healthy and glaucomatous eyes with high-, mild- and no axial myopia.MethodsOne hundred seventy-five healthy and glaucomatous eyes of 146 study participants enrolled in the Diagnostic Innovations in Glaucoma Study (DIGS) with optic disc photographs and Spectralis OCT ONH scans acquired on the same day were stratified by level of axial myopia (non-myopic [n = 56, axial length (AL) &lt;24 mm], mild-myopic [n = 58, AL 24–26 mm] and high-myopic [n = 32, AL &gt;26 mm]. The clinical disc margin of each photograph was manually annotated, and semi-automated measurements were recorded of the ovality index and rotation angle based on a best-fit ellipse generated using ImageJ software. These semi-automated photograph-based measurements were compared to ovality index and rotation angle generated from custom automated BMO-based analysis using segmented OCT ONH volumes. R2 values from linear mixed effects models were used to describe the associations between semi-automated, photograph-based and automated OCT-based measurements.ResultsAverage (95% CI) axial length was 23.3 (23.0, 23.3) mm, 24.8 (24.7, 25.0) mm and 26.8 (26.6, 27.0) mm in non-myopic, mild-myopic and high-myopic eyes, respectively (ANOVA, p ≤ 0.001 for all). The R2 association (95% CI) between semi-automated photograph-based and automated OCT-based assessment of ONH OI for all eyes was [0.26 (0.16, 0.36); p &lt; 0.001]. This association was weakest in non-myopic eyes [0.09 (0.01, 0.26); p = 0.02], followed by mild-myopic eyes [0.13 (0.02, 0.29); p = 0.004] and strongest in high-myopic eyes [0.40 (0.19, 0.60); p &lt; 0.001]. No significant associations were found between photography- and OCT-based assessment of rotation angle with R2 values ranging from 0.00 (0.00, 0.08) in non-myopic eyes to 0.03 (0.00, 0.21) in high-myopic eyes (all associations p ≥ 0.33).ConclusionsAgreement between photograph-based and automated OCT-based ONH morphology measurements is limited, suggesting that these methods cannot be used interchangeably for characterizing myopic changes in the ONH.
Mycobacterium tuberculosis Methyltransferase Rv1515c Can Suppress Host Defense Mechanisms by Modulating Immune Functions Utilizing a Multipronged Mechanism
Authors: Rani Anshu , Alam Anwar , Ahmad Faraz , P. Manjunath , Saurabh Abhinav , Zarin Sheeba , Mitra Dipendra Kumar , Hasnain Seyed E. , Ehtesham Nasreen Z. 
Published: June 2022

Mycobacterium tuberculosis (M. tb) gene Rv1515c encodes a conserved hypothetical protein exclusively present within organisms of MTB complex and absent in non-pathogenic mycobacteria. In silico analysis revealed that Rv1515c contain S-adenosylmethionine binding site and methyltransferase domain. The DNA binding and DNA methyltransferase activity of Rv1515c was confirmed in vitro. Knock-in of Rv1515c in a model mycobacteria M. smegmatis (M. s_Rv1515c) resulted in remarkable physiological and morphological changes and conferred the recombinant strain with an ability to adapt to various stress conditions, including resistance to TB drugs. M. s_Rv1515c was phagocytosed at a greater rate and displayed extended intra-macrophage survival in vitro. Recombinant M. s_Rv1515c contributed to enhanced virulence by suppressing the host defense mechanisms including RNS and ROS production, and apoptotic clearance. M. s_Rv1515c, while suppressing the phagolysosomal maturation, modulated pro-inflammatory cytokine production and also inhibited antigen presentation by downregulating the expression of MHC-I/MHC-II and co-stimulatory signals CD80 and CD86. Mice infected with M. s_Rv1515c produced more Treg cells than vector control (M. s_Vc) and exhibited reduced effector T cell responses, along-with reduced expression of macrophage activation markers in the chronic phase of infection. M. s_Rv1515c was able to survive in the major organs of mice up to 7 weeks post-infection. These results indicate a crucial role of Rv1515c in M. tb pathogenesis.
Rich-Club Analysis of Structural Brain Network Alterations in HIV Positive Patients With Fully Suppressed Plasma Viral Loads
Authors: Aili Xire , Wang Wei , Zhang Aidong , Jiao Zengxin , Li Xing , Rao Bo , Li Ruili , Li Hongjun 
Published: June 2022

ObjectiveEven with successful combination antiretroviral therapy (cART), patients with human immunodeficiency virus positive (HIV+) continue to present structural alterations and neuropsychological impairments. The purpose of this study is to investigate structural brain connectivity alterations and identify the hub regions in HIV+ patients with fully suppressed plasma viral loads.MethodsIn this study, we compared the brain structural connectivity in 48 patients with HIV+ treated with a combination of antiretroviral therapy and 48 healthy controls, using diffusion tensor imaging. Further comparisons were made in 24 patients with asymptomatic neurocognitive impairment (ANI) and 24 individuals with non-HIV-associated neurocognitive disorders forming a subset of HIV+ patients. The graph theory model was used to establish the topological metrics. Rich-club analysis was used to identify hub nodes across groups and abnormal rich-club connections. Correlations of connectivity metrics with cognitive performance and clinical variables were investigated as well.ResultsAt the regional level, HIV+ patients demonstrated lower degree centrality (DC), betweenness centrality (BC), and nodal efficiency (NE) at the occipital lobe and the limbic cortex; and increased BC and nodal cluster coefficient (NCC) in the occipital lobe, the frontal lobe, the insula, and the thalamus. The ANI group demonstrated a significant reduction in the DC, NCC, and NE in widespread brain regions encompassing the occipital lobe, the frontal lobe, the temporal pole, and the limbic system. These results did not survive the Bonferroni correction. HIV+ patients and the ANI group had similar hub nodes that were mainly located in the occipital lobe and subcortical regions. The abnormal connections were mainly located in the occipital lobe in the HIV+ group and in the parietal lobe in the ANI group. The BC in the calcarine fissure was positively correlated with complex motor skills. The disease course was negatively correlated with NE in the middle occipital gyrus.ConclusionThe results suggest that the occipital lobe and the subcortical regions may be important in structural connectivity alterations and cognitive impairment. Rich-club analysis may contribute to our understanding of the neuropathology of HIV-associated neurocognitive disorders.
Auditory Phenotype and Histopathologic Findings of a Mutant Nlrp3 Expression Mouse Model
Authors: Kim Yehree , Lee Sang-Yeon , Kim Min Young , Park Kyusun , Han Jin Hee , Kim Jung Ho , Kim Bong Jik , Choi Byung Yoon 
Published: June 2022

ObjectiveThe pathogenesis of hearing loss in autoinflammatory disorders due to activation of the inflammasome remains incompletely understood. Previously no animals expressing mutant Nlrp3 (NOD-, LRR- and pyrin domain-containing protein 3) survived to an age when hearing evaluation was possible due to embryonic lethality. We aimed to establish a novel mouse model that manifests quantifiable hearing loss with other syndromic features due to alteration of Nlrp3 and investigate the audiologic and histopathologic phenotype in the cochlea to clarify how the genetic alterations of NLRP3 could induce autoinflammatory hearing loss.MethodsTo induce inner ear expression of the mutant Nlrp3, Nlrp3D301NneoR mice were bred with Gfi1Cre knock-in mice for conditional mutant Nlrp3 activation in the cochlea and hematopoietic cells. Hearing thresholds were measured. Hematoxylin-eosin sections of the cochlea, brain, kidney, and liver were examined under light microscopy. Immunohistochemical analyses using polyclonal anti-NLRP3 antibodies on cochlear whole-mount preparations and frozen sections were performed.ResultsWe, for the first time in the literature, established a mouse model that manifests quantifiable hearing loss due to Nlrp3 alteration. ABR recordings of Nlrp3D301NneoR/+; Gfi1Cre/+ mice, albeit with limited life expectancy, exhibited severe to profound hearing loss at postnatal day 20 (P20). There was overall overexpression of mutant Nlrp3, and mutant Nlrp3 expression was noted in the spiral prominence, the outer sulcus region (Claudius cells and outer sulcus cells), the organ of Corti, the inner sulcus, and the spiral ganglion neurons in the cochlea. The hematoxylin-eosin sections of Nlrp3D301NneoR/+; Gfi1Cre/+ mice cochleae at P12 exhibited a disorganized organ of Corti between the outer hair cells/supporting Deiters' cells and basilar membrane compared with the normal phenotype mice, leading to a collapsed Nuel's space. This morphologic feature gradually returned to normal by P15. Varying degrees of inflammation with lymphocytic infiltrations were observed in the brain, kidney, and liver.ConclusionWe report the first mutant Nlrp3 overexpression mouse model (Nlrp3D301NneoR/+; Gfi1Cre/+) that shows obvious overexpression of Nlrp3 in the cochlea, a transient developmental lag of the cochlea, and severe to profound hearing loss. We expect that this mouse line, which models human autoinflammatory hearing loss, could provide a valuable tool to elucidate the underlying pathogenic mechanism of inflammasome activation-mediated hearing loss.
Elevated Homocysteine Levels Predict Hospital-Acquired Pneumonia and Poor Functional Outcomes in Primary Intracerebral Hemorrhage
Authors: Peng Jun , Zhu Guanghua , Xiao Sheng , Liu Shucheng 
Published: June 2022

BackgroundHomocysteine (Hcy) has been extensively acknowledged to be correlated with inflammation. In this study, the relationship between Hcy and hospital-acquired pneumonia (HAP) in primary intracerebral hemorrhage (pICH) was explored.MethodsWe conducted a hospital-based study on screened eligible patients with primary intracerebral hemorrhage admitted within 24 h after symptom onset from January 2019 to June 2021. The associations between Hcy and HAP and poor outcomes in pICH were investigated using univariate and multivariate logistic regression analyses. The predictive accuracy of Hcy was assessed by the receiver operating characteristic curve and the optimal cutoff value of Hcy was determined by Youden Index. The patterns and magnitudes of associations between Hcy and HAP and poor outcomes were evaluated using a restricted cubic spline (RCS).ResultsA total of 579 patients with pICH were included in the study. Hcy level was significantly higher in patients with HAP and poor outcomes (p &lt; 0.001). The univariate and multivariate logistic regression analyses demonstrated that elevated Hcy was independently associated with both HAP and poor outcomes (p &lt; 0.001). Furthermore, receiver operating characteristic analysis indicated that Hcy exhibited a moderate predictive accuracy for both HAP and poor outcomes after pICH. The RCS model showed that there were linear relationships between Hcy and HAP and poor outcomes.ConclusionsHigher Hcy level was independently associated with HAP and poor outcomes in patients with pICH.
Differential Attention Functioning in Pediatric Chronic Kidney Disease
Authors: Duquette Peter J. , Gipson Debbie S. , Hooper Stephen R. 
Published: June 2022

ObjectiveTo compare specific attention functions for school-age children with chronic kidney disease (CKD) to those of a typically developing control group.MethodsA cross-sectional study examined attention dimensions for children and adolescents with CKD (n = 30) in comparison to a typically developing control group (n = 41). The CKD group consisted of those receiving maintenance dialysis (n = 15) and those with mild/moderate CKD treated conservatively (n = 15). Measures aligning with Mirsky’s conceptual multidimensional model of attention were selected to compare groups across five dimensions of attention: Focus/Execute, Sustain, Stability, Shift, and Encode.ResultsSignificant group differences were revealed, with the CKD group performing worse than controls on the Focus/Execute, Sustain, and Encode dimensions. The CKD group also had a larger proportion of children with scores one standard deviation or more below the mean on the Shift and Encode domains, suggesting an at-risk level of functioning in these dimensions. Secondary analyses showed disease severity to be correlated with worse attention functions for children with CKD.ConclusionChildren with CKD may be vulnerable to subtle, specific deficits in numerous attention dimensions relative to their typically developing peers, particularly for those with more severe disease.
Dose-Response and Substitution Analyzes of Sweet Beverage Consumption and Body Weight in Dutch Adults: The Lifelines Cohort Study
Authors: Buso Marion E. C. , Brouwer-Brolsma Elske M. , Naomi Novita D. , Harrold Joanne A. , Halford Jason C. G. , Raben Anne , Feskens Edith J. M. 
Published: June 2022

Background/MethodsProspective studies investigating sweet beverages and body weight associations show inconsistent results. Within the SWEET project, we examined prospective dose-response associations of sugar-sweetened beverages (SSB), low/no-calorie beverages (LNCB), and fruit juice with body weight-related outcomes among 78,286 Dutch adults followed for ~4 years. Baseline intakes were assessed using a validated food-frequency questionnaire (FFQ) with 150 ml representing a standard serving. Outcome variables were body weight change, waist circumference change, overweight/obesity, and abdominal obesity. Associations were investigated by using linear and non-linear dose-response analysis, as well as substitution models while adjusting for multiple socio-demographic, lifestyle, health, and dietary variables.ResultsParticipants were 46 ± 13 (mean ± SD) years old and 60% were women. Adjusted dose-response analyzes indicated an association between SSB and LNCB, and both body weight (+0.02 kg/year; SE 0.01 and +0.06 kg/year; SE 0.01) and waist circumference changes (+0.04 cm/year; SE: 0.01 and +0.11 cm/year; SE: 0.01). Associations for overweight/obesity and abdominal obesity incidence were +3% (95%CI: 1.00–1.06) and +2% (95%CI: 0.99–1.06) for SSB and +8% (95%CI: 1.06–1.11) and +5% (95%CI: 1.03–1.07) for LNCB, respectively. Substitution of SSB with LNCB was associated with higher weight change (+0.04 kg/year), waist circumference change (+0.09 cm/year), overweight/obesity incidence (+6%), but not abdominal obesity incidence. For fruit juice, we observed beneficial associations for intake levels below ~1 serving/day with weight, waist circumference change, and overweight/obesity incidence, and no association with abdominal obesity. Subsequent substitution analyzes indicated a small beneficial association for the replacement of SSB with fruit juice on weight (−0.04 kg/year) and waist circumference (−0.04 cm/year), but not with other outcomes.ConclusionsOverall, our results suggest that habitual consumption of both SSB and LNCB may adversely affect weight-related outcomes. In contrast, fruit juice consumption &lt;150 ml may be beneficial with respect to weight and waist circumference.
Deep Learning Radiomics Nomogram to Predict Lung Metastasis in Soft-Tissue Sarcoma: A Multi-Center Study
Authors: Liang Hao-yu , Yang Shi-feng , Zou Hong-mei , Hou Feng , Duan Li-sha , Huang Chen-cui , Xu Jing-xu , Liu Shun-li , Hao Da-peng , Wang He-xiang 
Published: June 2022

ObjectivesTo build and evaluate a deep learning radiomics nomogram (DLRN) for preoperative prediction of lung metastasis (LM) status in patients with soft tissue sarcoma (STS).MethodsIn total, 242 patients with STS (training set, n=116; external validation set, n=126) who underwent magnetic resonance imaging were retrospectively enrolled in this study. We identified independent predictors for LM-status and evaluated their performance. The minimum redundancy maximum relevance (mRMR) method and least absolute shrinkage and selection operator (LASSO) algorithm were adopted to screen radiomics features. Logistic regression, decision tree, random forest, support vector machine (SVM), and adaptive boosting classifiers were compared for their ability to predict LM. To overcome the imbalanced distribution of the LM data, we retrained each machine-learning classifier using the synthetic minority over-sampling technique (SMOTE). A DLRN combining the independent clinical predictors with the best performing radiomics prediction signature (mRMR+LASSO+SVM+SMOTE) was established. Area under the receiver operating characteristics curve (AUC), calibration curves, and decision curve analysis (DCA) were used to assess the performance and clinical applicability of the models.ResultComparisons of the AUC values applied to the external validation set revealed that the DLRN model (AUC=0.833) showed better prediction performance than the clinical model (AUC=0.664) and radiomics model (AUC=0.799). The calibration curves indicated good calibration efficiency and the DCA showed the DLRN model to have greater clinical applicability than the other two models.ConclusionThe DLRN was shown to be an accurate and efficient tool for LM-status prediction in STS.
Systemic Immun e–Inflammation Index as a Predictor for Head and Neck Cancer Prognosis: A Meta-Analysis
Authors: Wang Yun-Ting , Kuo Liang-Tseng , Weng Hsu-Huei , Hsu Cheng-Ming , Tsai Ming-Shao , Chang Geng-He , Lee Yi-Chan , Huang Ethan I. , Tsai Yao-Te 
Published: June 2022

BackgroundStudies have reported inconsistent results regarding the prognostic value of the systemic immune–inflammation index (SII) in head and neck cancer (HNC). Thus, the present meta-analysis assessed the literature on the prognostic value of SII in those with HNC.MethodsThe Cochrane Library, EMBASE, and PubMed databases were searched, and study methodological quality was assessed using the Newcastle–Ottawa quality assessment scale. To determine the association of the SII with survival outcomes, pooled hazard ratios (HRs) as well as the associated 95% confidence intervals (CIs) were used. To assess the associations of the SII with clinicopathological features, the odds ratios (ORs) and corresponding 95% CIs were considered. Begg’s funnel plot and Egger’s linear regression test were used to assess publication bias.ResultsA total of 12 studies that together enrolled 4369 patients with HNC were analyzed. In the pooled results, a high pretreatment SII was correlated with poorer overall survival (HR = 2.09, 95% CI = 1.62–2.70,p&lt; 0.001), disease-free survival (HR = 2.79, 95% CI = 1.99−3.89,p&lt; 0.001), and progression-free survival (HR = 1.80, 95% CI = 1.30−2.48,p&lt; 0.001). A stratified analysis indicated that SII for overall survival was applicable regardless of tumor site, treatment modality, overall stage, sample size, SII cutoff, and method for determining the SII cutoff. Furthermore, a high SII was correlated with a more advanced T classification (OR = 1.14, 95% CI = 1.09–1.18,p&lt; 0.001) and nodal metastasis (OR = 1.55, 95% CI = 1.18–2.05,p= 0.002) in patients with HNC.ConclusionsAn elevated pretreatment SII predicts more advanced tumor and nodal status and poorer survival outcomes in cases of HNC. Because the measurement of SII is convenient and its use is cost-effective, we suggest that it can be applied by clinicians in the management of HNC.
Intra- and Peritumoral Radiomics Model Based on Early DCE-MRI for Preoperative Prediction of Molecular Subtypes in Invasive Ductal Breast Carcinoma: A Multitask Machine Learning Study
Authors: Zhang Shuhai , Wang Xiaolei , Yang Zhao , Zhu Yun , Zhao Nannan , Li Yang , He Jie , Sun Haitao , Xie Zongyu 
Published: June 2022

PurposeThe aim of this study is to investigate radiomics features extracted from the optimal peritumoral region and the intratumoral area on the early phase of dynamic contrast-enhanced MRI (DCE-MRI) for predicting molecular subtypes of invasive ductal breast carcinoma (IDBC).MethodsA total of 422 IDBC patients with immunohistochemical and fluorescence in situ hybridization results from two hospitals (Center 1: 327 cases, Center 2: 95 cases) who underwent preoperative DCE-MRI were retrospectively enrolled. After image preprocessing, radiomic features were extracted from the intratumoral area and four peritumoral regions on DCE-MRI from two centers, and selected the optimal peritumoral region. Based on the intratumoral, peritumoral radiomics features, and clinical–radiological characteristics, five radiomics models were constructed through support vector machine (SVM) in multiple classification tasks related to molecular subtypes and visualized by nomogram. The performance of radiomics models was evaluated by receiver operating characteristic curves, confusion matrix, calibration curves, and decision curve analysis.ResultsA 6-mm peritumoral size was defined the optimal peritumoral region in classification tasks of hormone receptor (HR)-positive vs others, triple-negative breast cancer (TNBC) vs others, and HR-positive vs human epidermal growth factor receptor 2 (HER2)-enriched vs TNBC, and 8 mm was applied in HER2-enriched vs others. The combined clinical–radiological and radiomics models in three binary classification tasks (HR-positive vs others, HER2-enriched vs others, TNBC vs others) obtained optimal performance with AUCs of 0.838, 0.848, and 0.930 in the training cohort, respectively; 0.827, 0.813, and 0.879 in the internal test cohort, respectively; and 0.791, 0.707, and 0.852 in the external test cohort, respectively.ConclusionRadiomics features in the intratumoral and peritumoral regions of IDBC on DCE-MRI had a potential to predict the HR-positive, HER2-enriched, and TNBC molecular subtypes preoperatively.
A Novel Matrisomal-Related LncRNA Signature Associated With Survival Outcome and Immune Evasion in Patients With Gastric Cancer
Authors: Yang Yuan , Shi Li , Zhang Jun , Zheng Ya , Wu Guozhi , Sun Jie , Liu Min , Chen Zhaofeng , Wang Yuping , Ji Rui , Guo Qinghong , Zhou Yongning 
Published: June 2022

BackgroundDifferent matrisomal patterns are shared across carcinomas. However, little is known about whether there exists a unique tumor matrisome that modulates GC progression and immune regulation.MethodsWe conducted a genome-wide analysis based on matrisomal-related lncRNAs (MRLs) in 375 patients with GC from the Cancer Genome Atlas (TCGA) database. Patients were split into the training set and validation set at a ratio of 1:1 using the R package cart. Pearson correlation analysis (PCA) was performed to identify lncRNAs that correlated with matrisome based on differential expression genes. Subsequently, we performed univariate Cox regression analyses and lasso Cox analysis on these lncRNAs to construct a risk model. Considering the primary effect of GRASLND on the GC prognosis, we chose it for further validation in an experimental setting.ResultsWe identified a 15-MRL signature to predict overall survival and immune cell infiltration of patients with GC. The AUC values to predict 5-year outcome in three sets were 0.89, 0.65, and 0.78, respectively. Further analyses suggested that the high-risk group showed more obvious immune cell infiltration, and demonstrated an immunologically “cold” profile. In vitro, knockdown of GRASLND could inhibit the invasion capability of GC cells, and downregulate the protein expression of crucial matrisomal-related gene MMP9.ConclusionsThe 15-MRL gene signature might serve as a relatively good predictive tool to manage patients with GC.