bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benchmarking framework for machine learning classification from fNIRS data
Authors: Benerradi Johann , Clos Jeremie , Landowska Aleksandra , Valstar Michel F. , Wilson Max L. 
Published: March 2023

BackgroundWhile efforts to establish best practices with functional near infrared spectroscopy (fNIRS) signal processing have been published, there are still no community standards for applying machine learning to fNIRS data. Moreover, the lack of open source benchmarks and standard expectations for reporting means that published works often claim high generalisation capabilities, but with poor practices or missing details in the paper. These issues make it hard to evaluate the performance of models when it comes to choosing them for brain-computer interfaces.MethodsWe present an open-source benchmarking framework, BenchNIRS, to establish a best practice machine learning methodology to evaluate models applied to fNIRS data, using five open access datasets for brain-computer interface (BCI) applications. The BenchNIRS framework, using a robust methodology with nested cross-validation, enables researchers to optimise models and evaluate them without bias. The framework also enables us to produce useful metrics and figures to detail the performance of new models for comparison. To demonstrate the utility of the framework, we present a benchmarking of six baseline models [linear discriminant analysis (LDA), support-vector machine (SVM), k-nearest neighbours (kNN), artificial neural network (ANN), convolutional neural network (CNN), and long short-term memory (LSTM)] on the five datasets and investigate the influence of different factors on the classification performance, including: number of training examples and size of the time window of each fNIRS sample used for classification. We also present results with a sliding window as opposed to simple classification of epochs, and with a personalised approach (within subject data classification) as opposed to a generalised approach (unseen subject data classification).Results and discussionResults show that the performance is typically lower than the scores often reported in literature, and without great differences between models, highlighting that predicting unseen data remains a difficult task. Our benchmarking framework provides future authors, who are achieving significant high classification scores, with a tool to demonstrate the advances in a comparable way. To complement our framework, we contribute a set of recommendations for methodology decisions and writing papers, when applying machine learning to fNIRS data.
Associations of the Healthy Eating Index-2010 with risk of all-cause and heart disease mortality among adults with hypertension: Results from the National Health and Nutrition Examination Survey 2007–2014
Authors: Zhang Yuhui , Li Duanbin , Zhang Haizhu 
Published: March 2023

BackgroundStudies regarding the impact of the Healthy Eating Index-2010 (HEI-2010) on the mortality of adults with hypertension are lacking.ObjectivesThis study aimed to prospectively explore the relationships between HEI-2010 and mortality from heart disease and all causes in adults with hypertension based on the National Health and Nutrition Examination Survey (NHANES), 2007–2014.MethodsThis is a prospective cohort study including 6,690 adults with hypertension from NHANES (2007–2014). National Death Index data up to 31 December 2019 were used to determine the number of deaths due to heart disease and all other causes. We evaluated hazard ratios (HRs) and 95% confidence intervals (CIs) using the Cox proportional hazards model.ResultsA total of 1,259 deaths from all causes, including 338 due to heart disease, were documented over an average follow-up duration of 8.4 years. In comparison with the lowest quartile of HEI-2010 scores, multivariable-adjusted HRs (95% CIs) for all-cause mortality were 0.82 (0.70, 0.97), 0.78 (0.64, 0.95), and 0.68 (0.54, 0.85) for the second, third, and fourth quartiles of the HEI-2010 scores (P-trend &lt; 0.001) and for heart disease mortality were 0.60 (0.44, 0.81), 0.59 (0.40, 0.89), and 0.53 (0.35, 0.80) (P-trend = 0.010). Each increment in natural-log-transformed HEI-2010 scores was linked to a 43% reduction in the risk of all-cause mortality (P &lt; 0.001) and a 55% reduction in the risk of heart disease mortality (P = 0.003). Among the 12 components of HEI-2010, adherence to a higher intake of greens and beans, vegetables, total protein foods, seafood and plant proteins, and unsaturated fatty acids, as well as moderate consumption of empty calories, were related to a 21–29% lower risk of all-cause mortality.ConclusionIn the current study, there was a statistically significant inverse relationship between HEI-2010 and mortality from heart disease and all causes among adults with hypertension. Based on the findings, it may help guide the dietary intake for adults with hypertension.
Prognostic value of nectin-4 in human cancers: A meta-analysis
Authors: Liu Rongqiang , Zhao Kailiang , Wang Kunpeng , Zhang Lilong , Ma Wangbin , Qiu Zhengdong , Wang Weixing 
Published: March 2023

BackgroundMany reports have described that abnormal nectin-4 expression may be used as a prognostic marker in many tumors. However, these studies failed to reach a consensus. Here, we performed a meta-analysis to comprehensively evaluate the prognostic value of nectin-4 in cancers.MethodsRelevant studies were identified through a comprehensive search of PubMed, EMBASE and Web of science until August 31, 2022. Pooled hazard ratios (HRs) with 95% confidence intervals (CIs) were used to evaluate the relationship between nectin-4 expression and overall survival (OS) and disease-free survival/progression-free survival/relapse-free survival (DFS/PFS/RFS). Odds ratios (ORs) with 95% CIs were applied to assess the relationship between nectin-4 expression and clinicopathologic features. Subgroup analysis was performed to explore the sources of heterogeneity. Sensitivity analysis and funnel plot were used to test the reliability of the results. All data analyses were performed using STATA version 12.0 software.ResultsFifteen articles involving 2245 patients were included in the meta-analysis. The pooled analysis showed that high nectin-4 expression was significantly associated with poor OS (HR: 1.75, 95% CI: 1.35–2.28). There was no relationship between high nectin-4 expression and DFS/PFS/RFS (HR: 178, 95% CI: 0.78–4.08).Subgroup analyses revealed that that high nectin-4 expression mainly presented adverse OS in esophageal cancer (EC) (HR: 1.78, 95% CI: 1.30–2.44) and gastric cancer (GC) (HR: 1.92, 95% CI: 1.43–2.58). We also found that high nectin-4 expression was associated with tumor diameter (big vs small) (OR: 1.96, 95% CI: 1.02–3.75), tumor stage (III-IV vs I-II) (OR: 2.04, 95% CI: 1.01–4.12) and invasion depth (T3+T4 vs T2+T1) (OR: 3.95, 95% CI: 2.06–7.57).ConclusionsNectin-4 can be used as an effective prognostic indicator for specific cancers.
ImmuneScore of eight-gene signature predicts prognosis and survival in patients with endometrial cancer
Authors: Gu Jiahui , Wang Zihao , Wang B. O. , Ma Xiaoxin 
Published: March 2023

BackgroundEndometrial cancer (EC) is a common gynecological cancer worldwide and the sixth most common female malignant tumor. A large number of studies conducted through database mining have identified many biomarkers that may be related to survival and prognosis. However, the predictive ability of single-gene biomarkers is not sufficiently accurate. In recent years, tumors have been shown to interact closely with their microenvironment, and tumor-infiltrating immune cells in the tumor microenvironment were associated with therapeutic effects. Furthermore, sequencing technology has evolved and allowed the identification of genetic signatures that may improve prediction results. The purpose of this research was to discover the Cancer Genome Atlas (TCGA) data to evaluate new genetic features that can predict the prognosis of EC.MethodsmRNA expression profiling was analyzed in patients with EC identified in the TCGA database (n = 530). Differentially expressed genes at different stages of EC were screened using the immune cell enrichment score (ImmuneScore). Univariate and multivariate Cox regression analyses was applied to evaluate genes significantly related to overall survival and establish the prognostic risk parameter formula. Kaplan–Meier survival curves and the logarithmic rank method were applied to verify the importance of risk parameters for the prognostic forecast. The accuracy of survival prediction was confirmed using the nomogram and Receiver Operating Characteristic (ROC) curve analysis. The mRNA expression of eight genes were measured by qRT-PCR. According to COX and HR values, NBAT1, a representative gene among 8 genes, was selected for CCK-8 assay, colony formation assay and transwell invasion assay to verify the effect on survival.ResultsEight related genes (NBAT1, GFRA4, PTPRT, DLX4, RANBP3L, UNQ6494, KLRB1, and PRAC1) were discovered to be significantly associated with the overall survival rate. According to these eight-gene signatures, 530 patients with EC were assigned to high- and low-risk subgroups. The prognostic capability of the eight-gene signature was not influenced by other elements.ConclusionsEight related gene markers were identified using ImmuneScore, which could predict prognosis and survival in patients with EC. These findings provide a basis for understanding the application of biological information in tumors and identifying the poor prognosis of EC.
Cancer care in times of conflict: Treatment of patients from Afghanistan, in Pakistan
Authors: Mahmood Shahid , Khawaja Shehryar Nasir , Yusuf Muhammed Aasim 
Published: March 2023

IntroductionAfghanistan has been in a near-continuous armed conflict, which has degraded the country’s health infrastructure. Due to this, Afghans have opted to seek cancer treatment in Pakistan. This manuscript aims to understand the complex cancer journey of patients from Afghanistan seeking care in the largest tertiary care cancer institutions in Pakistan.MethodsThis retrospective study explores the demographics, epidemiology and outcomes of Afghan cancer patients treated at the Shaukat Khanum Memorial Cancer Hospital and Research Centres (SKMCH&amp;RC) in Lahore and Peshawar, Pakistan, over the period from 1995 to June 2022.ResultsA total of 6,370 patients from Afghanistan have undergone cancer care since 1995. The mean age at presentation was 40.7 years, 57% were male, and 87% were adults &gt;19 years. Close to 30% of these patients came from Kabul and Nangarhar districts. 56% of all patients presented with stage III or IV disease. 34% of adult patients achieved a complete response to treatment, but more than half of all patients have since been lost to follow-up. Children generally had better outcomes, with 43% showing a complete response to treatment.DiscussionThe cancer journey for these patients remains long and difficult and the inability to ensure follow-up in so many remains frustrating for both patients and providers. The lack of a cancer infrastructure in Afghanistan after decades of conflict, means that policymakers need to develop and support alternative systems and structures to provide post-conflict domestic and cross-border cancer care.
Association between anlotinib trough plasma concentration and treatment outcomes in advanced non-small-cell lung cancer
Authors: Chen Ling , Jiang Hong , Rao Jun-jie , Wang Liu-sheng , Yan Wei , Ye Jian , Lou Jiang 
Published: March 2023

BackgroundEfficacy and toxicities of anlotinib (ANL) show large inter-patient variation, which may partly be explained by differences in ANL exposure. Exposure-response/toxicities relationship have not been investigated for ANL. Therefore, the aim of the present study was to explore the association between the trough plasma concentration (Ctrough) of ANL and treatment outcomes in Chinese patients with advanced non-small cell lung cancer (NSCLC).MethodsPatients with advanced NSCLC who started third-line or further ANL alone therapy between January 2021 and October 2022. This study examined the ANL Ctrough and clinical response evaluation at day 43 after initiation of ANL treatment. We evaluated the association between the ANL Ctrough and clinical efficacy and toxicities. Additionally, this study defined patients with complete response (CR), partial response (PR) and stable disease (SD) as responder. The receiver-operating characteristic (ROC) curve combined with Youden index was identify the potential threshold value of ANL Ctrough for the responder.Results52 patients were evaluated for analyses. The median ANL Ctrough was 11.45ng/ml (range, 3.69-26.36 ng/ml). The ANL Ctrough values in the PR group (n=6, 15.51 ng/ml (range, 8.19-17.37 ng/ml)) was significantly higher than in the PD group (n=8, 7.44 ng/ml (range, 5.41-14.69 ng/ml), p=0.001). The area under the ROC curve (AUCROC) was 0.76 (95% confidence interval (CI), 0.58-0.93; p=0.022) and threshold value of ANL Ctrough predicting responder was 10.29 ng/ml (sensitivity 65.9% and specificity 87.5%, the best Youden index was 0.53). The disease control rate (DCR) was 84.6%, and DCR was significantly higher in the high-exposure group (≥10.29ng/ml) than low-exposure group (&lt;10.29ng/ml) (96.67% vs 68.18%, p=0.005). Although there was no significant difference in ANL Ctrough between grade ≥ 3 and grade ≤2 toxicities, the incidence of any grade hand-foot syndrome (70.0% vs 36.36%, p=0.016) and thyroid-stimulating hormone elevation (53.33% vs 22.73%, p =0.026) was significantly higher in the high-exposure group compared with the low-exposure group.ConclusionsConsidering these results, we propose that maintaining ANL Ctrough ≥ 10.29ng/ml was important for achieving the response in advanced NSCLC patients treated with ANL.
Association between endotypes of prematurity and pharmacological closure of patent ductus arteriosus: A systematic review and meta-analysis
Authors: Gonzalez-Luis Gema E , Borges-Lujan Moreyba , Villamor Eduardo 
Published: March 2023

IntroductionEndotypes leading to very and extremely preterm birth are clustered into two groups: infection/inflammation and dysfunctional placentation. We conducted a systematic review of observational studies exploring the association between these two endotypes and the pharmacological closure of patent ductus arteriosus (PDA) induced by cyclooxygenase (COX) inhibitors. Chorioamnionitis represented the infectious-inflammatory endotype, while dysfunctional placentation proxies were hypertensive disorders of pregnancy (HDP) and small for gestational age (SGA) or intrauterine growth restriction.MethodsPubMed/Medline and Embase databases were searched. The random-effects odds ratio (OR) and 95% confidence interval (CI) were calculated for each association. We included 30 studies (12,639 infants).ResultsMeta-analysis showed a significant association between exposure to HDP and increased rate of pharmacological closure of PDA (17 studies, OR 1.41, 95% CI 1.10–1.81, p = 0.006). In contrast, neither chorioamnionitis (13 studies, OR 0.75, 95% CI 0.47–1.18, p = 0.211) nor SGA (17 studies, OR 1.20, 95% CI 0.96–1.50, p = 0.115) were significantly associated with the response to therapy. Subgroup analyses showed that the higher response to COX inhibitors in the HDP group was significant for indomethacin (OR 1.568, 95% CI 1.147–2.141, p = 0.005) but not for ibuprofen (OR 1.107, 95% CI 0.248–4.392, p = 0.894) or for the studies using both drugs (OR 1.280, 95% CI 0.935–1.751, p = 0.124). However, meta-regression showed that this difference between the drugs was not statistically significant (p = 0.404).Discussion/ConclusionOur data suggest that the pathologic condition that triggers prematurity may alter the response to pharmacological treatment of PDA. The DA of infants exposed to HDP appears to be more responsive to COX inhibitors.
Body mass index percentiles versus body composition assessments: Challenges for disease risk classifications in children
Authors: Clasey Jody L. , Easley Elizabeth A. , Murphy Margaret O. , Kiessling Stefan G. , Stromberg Arnold , Schadler Aric , Huang Hong , Bauer John A. 
Published: March 2023

BackgroundIdentifying at-risk children with optimal specificity and sensitivity to allow for the appropriate intervention strategies to be implemented is crucial to improving the health and well-being of children. We determined relationships of body mass indexes for age and sex percentile (BMI%) classifications to actual body composition using validated and convenient methodologies and compared fat and non-fat mass estimates to normative cut-off reference values to determine guideline reliability. We hypothesized that we would achieve an improved ability to identify at-risk children using simple, non-invasive body composition and index measures.MethodsCross-sectional study of a volunteer convenience sample of 1,064 (537 boys) young children comparing Body Fat Percentage (BF%), Fat Mass Index (FMI), Fat-Free Mass Index (FFMI), determined via rapid bioimpedance methods vs. BMI% in children. Comparisons determined among weight classifications and boys vs. girls.ResultsAmongst all subjects BMI% was generally correlated to body composition measures and indexes but nearly one quarter of children in the low-risk classifications (healthy weight or overweight BMI%) had higher BF% and/or lower FFMI than recommended standards. Substantial evidence of higher than expected fatness and or sarcopenia was found relative to risk status. Inaccuracies were more common in girls than boys and girls were found to have consistently higher BF% at any BMI%.ConclusionsThe population studied raises concerns regarding actual risks for children of healthy or overweight categorized BMI% since many had higher than expected BF% and potential sarcopenia. When body composition and FMI and FFMI are used in conjunction with BMI% improved sensitivity, and accuracy of identifying children who may benefit from appropriate interventions results. These additional measures could help guide clinical decision making in settings of disease-risks stratifications and interventions.
Titanium elastic nails vs locking plate in pediatric subtrochanteric femur fractures: A systematic review and meta-analysis
Authors: Zhang Yaqiang , Xue Yun , Zhao Maosheng , Chen Xianxia , Gao Qiuming 
Published: March 2023

ObjectiveTitanium elastic nails (TENs) and locking plates (LPs) are currently the main internal fixation for treating pediatric subtrochanteric femur fractures, and the optimal choice of internal fixation is controversial. This study aimed to systematically evaluate the effectiveness and safety of TENs and LPs in treating subtrochanteric fractures in children to provide a theoretical basis and reference for clinical treatment.MethodsThe literature related to TENs and LPs for treating subtrochanteric fractures in children was searched using the CNKI, PubMed, Cochrane, Embase, and Web of Science, and the search time frame was from the establishment of the database to October 2022. Two evaluators screened the literature according to the inclusion and exclusion criteria and extracted relevant data. Meta-analysis was performed using Stata14.0 software.ResultsA total of 9 studies with 407 patients with subtrochanteric femur fractures were included in the final screening, including 210 cases with TENs and 197 cases with LPs. Meta-analysis results showed that compared with the locking plate, TEN had a shorter operative time [WMD = −1.3, 95%CI(−1.94,-0.66),p &lt; 0.01], less intraoperative bleeding [WMD = −84.45, 95%CI(−111.09, −57.82),p &lt; 0.01], shorter fracture healing time [WMD = −1.3, 95%CI(−1.94,−0.66),P &lt; 0.01], shorter hospital stays [WMD = −2.80, 95% CI(−4.63,−0.98),p &lt; 0.01], and earlier full weight bearing [SMD = −0.48, 95% CI(−0.91,−0.04),p &lt; 0.05] but more intraoperative fluoroscopy [WMD = 28.23, 95% CI(15.22,41.25),p &lt; 0.05]. The overall complication rate was high [OR = 3.52, 95% CI(1.96,6.34),p &lt; 0.05], and the postoperative period was prone to angulation, rotation, and inversion deformity [OR = 3.68, 95% CI(1.40, 9.68),p &lt; 0.05]. No significant difference in the incidence of lower limb inequality between the two types of internal fixation [OR = 0.83, 95% CI(0.38, 1.85),p &gt; 0.05] and no significant difference in the Harris score of the hip at the last follow-up between the two types of internal fixation [WMD = −0.67, 95% CI(−2.01,0.67),p &gt; 0.05] were found.ConclusionIn comparison to LPs, TENs have a shorter operation time, less intraoperative bleeding, and a shorter fracture healing time, and the child can be fully weight-bearing earlier. Locking plates can reduce the operator's x-ray exposure, and the incidence rate of postoperative angulation, rotation, and inversion deformity is low. Therefore, TENs and LPs are the best internal fixation methods for treating subtrochanteric fractures in children.
Non-thyroidal illness syndrome and its relationship with mortality risk in critically ill children
Authors: Carreras Laura , Riaño Isolina , Vivanco Ana , Avello Noelia , Iglesias Tania , Rey Corsino 
Published: March 2023

IntroductionNon-thyroidal illness syndrome (NTIS) is considered to be associated with adverse outcomes in critically ill children.The hypothesis that thyroid hormones and inflammatory markers are associated with increased prediction of mortality risk scores is tested in this paper.MethodsA prospective observational study was set up in a pediatric intensive care unit (PICU). One hundred and three patients were included. NTIS was defined as a low free triiodothyronine (FT3) value for the patient's age. Thyroid hormones levels and inflammatory markers were determined at admission: FT3, FT4 (free thyroxine), TSH (thyroid-stimulating hormone), rT3 (reverse triiodothyronine), CRP (C-reactive protein) and PCT (Procalcitonin). They were compared between children with a pediatric risk of mortality score PRISM-III &gt;75th percentile (group A, n= 25) and the rest (group B, n = 78).ResultsA FT4 value lower than 16.6 pmol/L showed an area under the curve (AUC) of 0.655 (0.56–0.78, p = 0.02), with 76% sensitivity and 61.5% specificity to detect a high risk of mortality. A multiple regression analysis revealed that a FT4 lower than 16.6 pmol/L [OR: 4.92 (1.60–18.19), p = 0.009] and having NTIS [OR: 6.04 (1.45–27.93), p = 0.016] could predict a high risk of mortality.ConclusionsIn unselected critically ill children, FT4 and FT3 values at admission could be used as a good predictor of a high mortality risk. We have not achieved a predictive model that combines hormones with inflammatory markers.