bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-modal characteristics of lncRNAs-derived subtypes in colorectal cancer
Authors: Xiong Minghao , Li Jie , Li Xue , Zhao Jiaojiao , Liu Qin , Tu Mengjie , Zeng Fanxin 
Published: April 2024

Abstract
Background: The growing knowledge of long non-coding RNA (lncRNA) has suggested the role and predictive potential of lncRNA in cancer, but has not been translated into effective practical tools. The morbidity of colorectal cancer (CRC) has been declining because of effective screening tools. However, the mechanism of the disease is not well understood.
Methods: The LncRNAs that extracted using univariable cox analysis were explored for the potential functions and applied for classification of lncRNAs-derived subtypes of CRC. Multi-modal data involving microscope to macroscope levels were applied to evaluate the molecular, cell, and medical image characteristics of lncRNAs-derived subtypes. Radiomic signature calculated by LASSO regression analysis was utilized for distinguishing the CRC subtypes. The performance of lncRNA and radiomic signature were assessed with respect to its calibration, discrimination, and clinical usefulness.
Results: The lncRNA signature which composed of 8 lncRNAs that significantly associated with prognosis, metabolism and organismal system showed good performance in patients prognosis assessment (AUC, 0.717; time-depended ROC > 0.71). And patients separated into two subtypes (HRG vs LRG) based on the lncRNA signature displayed notably prognostic differences (Kaplan-Meier, p < .001). Multi-modal analysis indicated obvious heterogeneity between HRG and LRG subgroups, mainly focused on the abnormal enrichment of glycerophospholipid metabolism pathway, different cellular differentiation, and density level characteristics in tumor region. In addition, the radiomic signature showed good accuracy (AUC, 0.919), discrimination (p < .05) and generalization ability (external independent test cohort, p < .05) for lncRNA-derived subgroups assessment.
Conclusion: This study described multi-modal characteristics landscape of lncRNAs-derived subtypes in CRC and strengthened the connection form microscope to macroscope levels.
Comprehensive prediction and analysis of human protein essentiality based on a pre-trained protein large language model
Authors: Kang Boming , Fan Rui , Cui Chunmei , Cui Qinghua 
Published: April 2024

Abstract

Human essential genes and their protein products are indispensable for the viability and development of the individuals. Thus, it is quite important to decipher the essential proteins and up to now numerous computational methods have been developed for the above purpose. However, the current methods failed to comprehensively measure human protein essentiality at levels of humans, human cell lines, and mice orthologues. For doing so, here we developed Protein Importance Calculator (PIC), a sequence-based deep learning model, which was built by fine-tuning a pre-trained protein language model. As a result, PIC outperformed existing methods by increasing 5.13%-12.10% AUROC for predicting essential proteins at human cell-line level. In addition, it improved an average of 9.64% AUROC on 323 human cell lines compared to the only existing cell line-specific method, DeepCellEss. Moreover, we defined Protein Essential Score (PES) to quantify protein essentiality based on PIC and confirmed its power of measuring human protein essentiality and functional divergence across the above three levels. Finally, we successfully used PES to identify prognostic biomarkers of breast cancer and at the first time to quantify the essentiality of 617462 human microproteins.
Exploring the Role of Artificial Intelligence in Gauging Pain Severity caused by Local Dental Anesthetic Injections in Children: a cross-sectional study
Authors: Alkhouli Muaaz , Al-Nerabieah Zuhair , Al-Issa Sami , Dashash Mayssoon 
Published: April 2024

Abstract

Pain assessment in children is essential for effective management, particularly during dental procedures. This study aimed to validate an AI software that utilizes facial expression analysis for pain assessment in children undergoing dental injections. A total of 300 children aged 6–9 years were included in the study. Pain assessment was conducted using both the AI software and the widely used FLACC scale. The AI software used a CNN algorithm to detected the action units (AUs) associated with pain. Statistical analysis, including correlation and regression, was performed to evaluate the performance of the AI software and the agreement between the FLACC scores and AI scores. The results showed a high sensitivity and specificity of the AI software in pain assessment, with an almost perfect agreement observed between the AI scores and the FLACC scores (r = 0.921). The AI model accurately detected pain levels in children, with comparable results for boys and girls. The findings of this study support the validity and reliability of the AI software for pain assessment in children undergoing dental injections. The AI software demonstrated high sensitivity and specificity in detecting pain.
No Genetic Causal Association between Periodontitis and Autoimmune Thyroiditis: A Bidirectional Two-Sample Mendelian Randomization Analysis
Authors: Zhang Bitong , Mi Zhongqian , Shang Huiyu , Qiu Xinjie , Zhao Miaomiao , Yan Xuedan , Cheng Rui , Gao Jinhua , Ren Xiuyun 
Published: April 2024

Abstract

Background Recent studies have reported associations between periodontitis and autoimmune disorders; however, it remains unclear whether the association between periodontitis and autoimmune thyroiditis (AIT) is causal. The purpose of this study was to investigate the causal association between periodontitis and AIT. Methods We conducted a two-sample bidirectional Mendelian randomization (MR) analysis using publicly available genome-wide association study (GWAS) statistics. The single-nucleotide polymorphisms (SNPs) for AIT were derived from 244 patients and 187,684 controls. The pooled periodontitis association data included up to 17,353 individuals. The inverse-variance weighted (IVW) method was used for the primary analysis. We applied two complementary methods, the weighted median and MR-Egger. Then, these causal estimates were expressed as dominance ratios [odds ratios (ORs)]. Results Genetically determined AIT did not have a causal effect on probing depth (PD) (IVW OR = 0.998, 95% confidence interval (CI) = 0.948 ~ 1.051, p = 0.952). Furthermore, we did not find a significant causal effect of PD on AIT in the reverse MR analysis (IVW OR = 1.044, 95% confidence interval (CI) = 0.789 ~ 1.382, p = 0.759). The MR-Egger regression and weighted median results were consistent with those of the IVW method. Horizontal pleiotropy was unlikely to distort the causal estimates according to the sensitivity analysis. Conclusion Within the limits of MR studies, the outcomes neither supported periodontitis affecting autoimmune thyroiditis nor autoimmune thyroiditis affecting periodontitis.
Virulence variation of Israeli populations of Puccinia graminis f. sp. tritici during the period 2009 – 2019
Authors: Kosman Evsey G. , Anikster Yehoshua , Ben-Yehuda Pnina , Manisterski Jacob , Sela Hanan 
Published: April 2024

Abstract

This paper is dedicated to the memory of the APS Fellow Prof. Yehoshua Anikster (1934 -2023).
A total of 336 urediniospore isolates of Pucciniagraminis f. sp. tritici (Pgt) were derived from samples collected in Israel from 2009 to 2019 and analyzed for virulence with the standard set of 20 differentials. Seventy-two virulence phenotypes were identified during the survey. Two Pgt phenotypes (TKTTF, TTTTF) were found in nine annual populations while 49 appeared in only one year. The yearly pathogen collections of 2009 – 2014 differed from the collections of 2015-2018, and the 2019 collection diverged from all others. No virulence to Sr24 and Sr31 indicators of UG99 was detected. Comparing the 2009 – 2014 and 2015 – 2018 periods, virulence frequencies declined on Sr17, 30, and 38 genes from 0.853 - 0.973 to 0.308 – 0.587, whereas the frequency on Sr36 rose (0.418 vs. 0.865). The average relative virulence complexity of the Pgt phenotypes decreased from 0.833 (2009 - 2014) and 0.786 (2015 – 2018) to 0.671 in 2019. Variability within the annual populations gradually increased over time. The Pgt collections of isolates in 2009 – 2014 and 2015 – 2018 were significantly different (p = 0.01). The effective number of different annual populations in 2009 – 2018 was 2.04 (β-variation = 0.116). Since Pgt does not over-summer in Israel, the northern source of inoculum from Turkey and Russia seems the most probable.
Nephrology Providers’ Perspective and Use of Mortality Prognostic Tools in Dialysis Patients
Authors: Bergeron Jennifer , Cheung Katharine L. , Marchese Christina , Jensen Colton , Meagher Sean , Kennedy Amanda G. , Tompkins Bradley 
Published: April 2024

Abstract

Background: Mortality prognostic tools exist to aid in shared decision making with kidney failure patients but are underutilized. This study aimed to elucidate nephrology providers’ practice patterns and understand barriers to prognostic tool use.
Methods: Nephrology providers (8 physicians and 2 nurse practitioners) at an academic medical center underwent semi-structured interviews regarding their experience and perspective on the utility of mortality prognostic tools. Common themes were identified independently by 2 reviewers using grounded theory. Three six-month mortality prognostic tools were applied to the 279 prevalent dialysis patients that the interviewed providers care for. The C statistic was calculated for each tool based on via logistic regression and subsequent ROC analysis. Nephrology providers reviewed the performance of the prognostication tools in their own patient population. A post interview reassessed perspectives and any change in attitudes regarding the tools.
Results: Nephrology providers did not use these mortality prognostic tools in their practice. Key barriers identified were provider concern that the tools were not generalizable to their patients, providers’ trust in their own clinical judgement over that of a prognostic tool, time constraints, and lack of knowledge about the data behind these tools. When re-interviewed with the results of the three prognostic tools in their patients, providers thought the tools performed as expected, but still did not intend to use the tools in their practice. They reported that these tools are good for populations, but not individual patients. The providers preferred to use clinical gestalt for prognostication.
Conclusion: Although several well validated prognostic tools are available for predicting mortality, the nephrology providers studied do not use them in routine practice, even after an educational intervention. Other approaches should be explored to help incorporate prognostication in shared-decision-making for patients receiving dialysis.
The impact of qualitative 18F-FDG PET/CT in Predicting Clinical Outcomes of Post-surgical Differentiated Thyroid Cancer Patients with Elevated Thyroglobulin and Negative Radioiodine Whole-Body Scan
Authors: Ha Le Ngoc , Phuong Nguyen Thi , Son Mai Hong 
Published: April 2024

Abstract

Background
18F-FDG PET/CT (FDG PET/CT) has been widely used as a diagnostic tool in detection and localization of recurrent non-avid radioiodine lesions in post-operative differentiated thyroid cancer (DTC) patients with elevated serum thyroglobulin but negative radioiodine whole-body scan (TENIS) syndrome. The aim of our study was to evaluate the role of FDG PET/CT in prediction on outcomes of these DTC patients.
Methods
Post-operative DTC patients with TENIS syndrome were collected in the department of nuclear medicine, Hospital 108 from 2019 to 2023. Patients underwent FDG PET/CT with standard protocol following EANM guideline for tumor imaging version 2.0. The qualitative FDG PET/CT imaging characteristics were classified into three categories: (i) negative FDG PET/CT, (ii) minimal FDG PET/CT volume of lesions, (iii) extensive FDG PET/CT volume of lesions. Progression-free survival (PFS) and overall survival (OS) were the end point of the study. The prognosis of qualitative FDG PET/CT in predicting PFS and OS was illustrated by Kaplan-Meier survival analysis. The independent factors predicting PFS and OS were determined by univariate and multivariate analysis using logistic regression.
Results
There were 164 consecutive patients, 51.2% female and 48.8% female. The most common histopathology type was papillary accounting for 87.8%. The median time of follow-up was 33.3 months, (range 6.57–82.5). There was 70 (36.6%) progressions and 12 (7.35%) deaths. Negative FDG PET/CT uptake patients had median PFS with median 57.1 months which was higher than that of minimal category (46.2 months), and extensive category (37.6 months) (p < 0,001). 1-year OS and 5-year OS in extensive PET/CT category was 97.8% and 86.2% respectively which were significantly lower than that of negative and minimal categories (p = 0.053). In multivariate analysis, pulmonary, bone metastases and extensive FDG PET/CT volume of lesions were the independent factor predicting PFS. Bone metastasis was only the factor could predict OS in multivariate analysis.
Conclusions
The minimal and negative FDG PET/CT categories had better prognosis than extensive category in PFS and OS. Extensive FDG PET/CT category was an independent factor for predicting PFS. Bone metastasis was only the independent factor that could predict both PFS and OS.
CD147 and PCSK9 as Predictors of Cancer in Patients with Type 2 Diabetes: A Comparative Study with Healthy Individuals
Authors: Tsao Lien-Cheng , Lin Chi-Chien , Kuo Chen-Ling , Cheng Yu-Shan , Huang Ching-Shan , Liu Chin-San , Su Shih-Li 
Published: April 2024

Abstract

Diabetes has a higher cancer prevalence and a poorer prognosis than nondiabetes. Traditional parameters of blood pressure, sugar, and lipids unmet cancer prognosis. Novel biomarkers that predict the possibility of cancer development and mortality are still desirable in the clinic. 141 patients with type 2 diabetes and 172 healthy individuals with observation are enrolled. The differentiation cluster 147 (CD147), oxidized low-density lipoprotein (oxLDL), antibody (oxLDL-Ab), proprotein convertase subtilisin/kexin type 9 (PCSK9), and cyclophilin A (CyP A) were examined. Cancer morbidity and all-cause mortality were compared between the diabetic and control group. Body mass index (BMI) ≥ 27 kg/m2 (37.6% vs. 10.6%, p < 0.001), 10-year mortality rate (35% vs. 2.3%, p < 0.001), and cancer morbidity (16% vs. 5.23%, p < 0.001) were higher in the diabetic group. Obese diabetes had high oxLDL, soluble intercellular adhesion molecule-1-1 (sICAM-1), PCSK9, CyP A, and CD147. Deceased diabetes had a higher cancer rate and a low CD147 level. CD147 and PCSK9 levels show predictive efficacy in cancer and diabetes without obesity (area under the curve [AUC], 0.665) and diabetes and obesity (AUC, 0.726), respectively. CD147 and PCSK9 levels were better predictors of cancer in diabetes, regardless of whether they were obese or not.
Late Onset Hearing Loss in Very Low Birth Weight Infants
Authors: Iwamoto Lynn , Liu Chloe Anne 
Published: April 2024

Abstract

Objective: To determine the incidence of late onset hearing loss and associated risk factors in very low birth weight (VLBW) infants.
Study Design: Retrospective study (2003-2015) of post-discharge hearing outcomes and risk factors in the VLBW infant population, before and after the institution of a standardized follow-up program.
Results: Late onset hearing loss increased from 2.9 per 100 VLBW infants to 7.8 per 100 after instituting a monitoring protocol. The follow-up compliance rate nearly doubled. Both infants with late-onset sensorineural hearing loss and those with a conductive component were identified. The rate of conductive loss detection increased seven-fold.
Conclusion: The institution of a standardized hearing follow-up program significantly increased the detection of late onset hearing loss in VLBW infants. A significant proportion of those with late onset hearing loss had a conductive component. Without identification and treatment, even conductive losses may negatively impact speech and language development.
High Body Mass Index with the Risk of Allergic Conjunctivitis in Children: A Case-Control Study in Southwest China
Authors: Tang Xiao-Jiao , He Jia-Tong , Liu Qing , Chen Lin 
Published: April 2024

Abstract

Purpose
To assess the correlation of body mass index (BMI), diet and lifestyle with allergic conjunctivitis (AC) in children.
Methods
This prospective case-control study included 105 children with AC and 105 age- and sex-matched children. Clinical data were collected, including BMI, dietary habits, physical activity, and sleep time. Multivariate regression analysis was used to analyze the risk factors for AC.
Results
Dietary habits including vitamin A supplement use (χ2 = 0.00; P = 1.00), the consumption of sweet food (χ2 = 6.70; P = 0.08), fast food (χ2 = 3.74; P = 0.29), beverages (χ2 = 1.17; P = 0.76), and seafood and fish (χ2 = 6.15; P = 0.10) and snacking before sleep (χ2 = 2.23; P = 0.53), were not associated with AC. There were significant differences in physical activity (χ2 = 12.64; P < 0.01) between the children with AC and healthy children, but there were no differences in sleep duration (χ2 = 5.39; P = 0.07). Multivariate regression analysis revealed that a high BMI (overweight and obesity) (OR = 3.05; 95% CI: 1.30–7.20; P = 0.01) was a significant risk factor for AC. The consumption of fish oil supplements (OR = 0.38; 95% CI: 0.17–0.81; P = 0.01) and having been breastfed (OR = 0.34; 95% CI: 0.16–0.72; p = 0.005) were protective factors against AC.
Conclusion
A high BMI (overweight and obesity) can increase the incidence of AC. Breastfeeding and dietary supplementation with fish oil are recommended for children susceptible to AC.
Applying the scene reappearance-based learning (SRBL) method in medical humanities training in the context of anesthesiology residency
Authors: Yi Tingting , Wu You , Lv Zhiquan , Luo Hongxia , Ma Linyu , Wang Shouyong 
Published: April 2024

Abstract

Background
To propose the novel scene reappearance-based learning method (SRBL) method for education in the medical humanities and to investigate whether this method can be used to curb the negative medical humanistic behavior of anesthesia residents effectively in the context of the assessment of block levels during spinal-epidural anesthesia.
Methods
Based on video recordings, we retrospectively found that anesthesia residents employed the negative humanistic behavior of nipping patients' skin with their fingers to assess block levels during spinal-epidural anesthesia. We further investigated the incidence of such negative behavior among residents, reconstructed the scene for all residents using video recordings, and guided the residents in a discussion of what behavior is appropriate in the context of the medical humanities in this scenario using simulation and roleplaying exercises.
Results
Among the 25 residents included in this training base, 18 used the same method of nipping the patient’s skin to assess block levels during spinal-epidural anesthesia. Through discussion, these 25 students reached consensus regarding ways of respecting patients’ humanistic feelings when assessing block levels during spinal-epidural anesthesia. Once these measures were implemented, the negative humanistic behavior of nipping the patient’s skin was eliminated in the training base within 3 months.
Conclusions
This paper proposes a method of medical humanities education for anesthesia residents that we call SRBL, which is administered during the assessment of block levels during spinal-epidural anesthesia and can quickly curb the negative medical humanistic behavior exhibited by anesthesia residents.
ZnO Q-Dots Nanoparticles: Intensifying ROS Stress to Improve Anticancer Drug Efficacy
Authors: Esmaeili Shadi , Salahi-Niri Aryan 
Published: April 2024

Abstract
Zinc oxide quantum dot Nanoparticles (ZnO Q-Dots NPs) are a conducive and versatile nano-platform with extraordinary biological applications. Despite a legion of studies, ZnO's biological and pharmacological activities have yet to be utilized in therapeutic applications. Recently, arsenic trioxide (ATO), an anti-cancer missile with multiple warheads, has shown harbinger therapeutic potential for acute promyelocytic leukemia (APL) by selectively instigating reactive oxygen species (ROS) stress in cancer cells. However, determining how best to lessen the toxic effects of ATO while increasing its therapeutic efficacy is a severe subject. In this study, we report that ZnO can synergize with ATO and escalate the ROS stress in NB4 cells, thereby greatly enhancing the apoptotic cell death and not only up-regulated the effect the ATO on the expression of anti-apoptotic target genes but also significantly elevating the expression of pro-apoptotic molecules in NB4 cells, as compared to either agent alone. We found that when ATO combined with ZnO, even the lower concentrations could induce flagrantly inhibitory effects on the survival of NB4 through retreating the cells to replicate DNA in the S phase of cell cycle. Moreover, our study indicated for the first time that the anti-leukemic effect of dual therapy combination of ZnO and ATO was coupled with the up-regulation of p21 and, thereby, G2/M cell cycle arrest. Our data suggest that incorporating ZnO with ATO can potentially ameliorate anti-leukemic effect in NB4 cells, thereby providing a synergistic strategy in the development of theranostic nanomedicine in APL patients.
Solid pseudopapillary neoplasms of the pancreas (SPNs): Diagnostic accuracy of CT and CT imaging features
Authors: Zhao Ming , Wang Jie , Lai Jiejuan , Liu Fenghao , Zhang Yujun , Cao Li , Liu Li , Ma Kuansheng , Li Jianwei , Deng Qingsong 
Published: April 2024

Abstract

Purpose: To summarize the abdominal computed tomography (CT) imaging and clinicopathological data of patients with SPNs of the pancreas and analyze the accuracy of preoperative CT diagnosis and features.
Materials and Methods: Between June 2006 and June 2023, CT images of 120 histopathologically proven SPNs in the pancreas were retrospectively reviewed. The 15 features of age, sex, and CT-determined features were included in multiple stepwise regression analysis. The correlation between features and SPNs was evaluated, including odds ratio (OR) and 95% confidence interval (CI).
Results: Of the 120 patients, the diagnostic accuracy of CT was 43.3%. The baseline CT results of patients with a correct diagnosis and misdiagnosis showed that there were significant differences in sex (P=0.043), age (P=0.004), boundary (P=0.037) and encapsulation (P=0.002) between the two groups. The preoperative imaging diagnostic accuracy was significantly greater in females than in males (47.9% vs. 25.0%, P=0.043). There was no significant difference in immunohistochemical indices between the two groups. The results of univariate analysis revealed significant differences in sex (P=0.048), age (P=0.014), tumor length (P=0.023), tumor boundaries (P=0.039) and capsule type (P=0.003). The results of multivariate analysis showed that encapsulation was closely related to the diagnostic accuracy of CT (P=0.04).
Conclusions: The accuracy of CT in the diagnosis of SPNs is low, but the length‒diameter ratio of the tumor approaching 1.0, encapsulation and clear boundary are important CT-determined features. The capsule is an independent CT predictor in the diagnosis of SPNs.