bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Cancer-Specific Qualitative Method for Estimating the Proportion of Tumor-Infiltrating Immune Cells
Authors: Xiao Huiting , Zhang Jiashuai , Wang Kai , Song Kai , Zheng Hailong , Yang Jing , Li Keru , Yuan Rongqiang , Zhao Wenyuan , Hui Yang 
Published: May 2021

Tumor-infiltrating immune cells are important components in the tumor microenvironment (TME) and different types of these cells exert different effects on tumor development and progression; these effects depend upon the type of cancer involved. Several methods have been developed for estimating the proportion of immune cells using bulk transcriptome data. However, there is a distinct lack of methods that are capable of predicting the immune contexture in specific types of cancer. Furthermore, the existing methods are based on absolute gene expression and are susceptible to experimental batch effects, thus resulting in incomparability across different datasets. In this study, we considered two common neoplasms as examples (colorectal cancer [CRC] and melanoma) and introduced the Tumor-infiltrating Immune Cell Proportion Estimator (TICPE), a cancer-specific qualitative method for estimating the proportion of tumor-infiltrating immune cells. The TICPE was based on the relative expression orderings (REOs) of gene pairs within a sample and is notably insensitive to batch effects. Performance evaluation using public expression data with mRNA mixtures, single-cell RNA-Seq (scRNA-Seq) data, immunohistochemistry data, and simulated bulk RNA-seq samples, indicated that the TICPE can estimate the proportion of immune cells with levels of accuracy that are clearly superior to other methods. Furthermore, we showed that the TICPE could effectively detect prognostic signals in patients with tumors and changes in the fractions of immune cells during immunotherapy in melanoma. In conclusion, our work presented a unique novel method, TICPE, to estimate the proportion of immune cells in specific cancer types and explore the effect of the infiltration of immune cells on the efficacy of immunotherapy and the prognosis of cancer. The source code for TICPE is available at https://github.com/huitingxiao/TICPE.
The Association Between the Baseline and the Change in Neutrophil-to-Lymphocyte Ratio and Short-Term Mortality in Patients With Acute Respiratory Distress Syndrome
Authors: Zhang Wei , Wang Yadan , Li Weijie , Wang Guizuo 
Published: May 2021

Background: Two previous studies have shown that increased neutrophil to lymphocyte ratio (NLR) is associated with short-term prognosis in patients with acute respiratory distress syndrome (ARDS), but it is usually assessed as a single threshold value at baseline. We investigated the relationship between the baseline and the early change in NLR and 30-day mortality in patients with ARDS to evaluate the prognostic value of NLR baseline and NLR changes during the first 7 days after ICU admission.Methods: This is a retrospective cohort study, with all ARDS patients diagnosed according to the Berlin definition from the Medical Information Mart for Intensive Care III (MIMIC-III) database. We calculated the NLR by dividing the neutrophil count by the lymphocyte count. The multivariable logistic regression analysis was used to investigate the relationship between the baseline NLR and short-term mortality. Then the generalized additive mixed model was used to compare trends in NLR over time among survivors and non-survivors after adjusting for potential confounders.Results: A total of 1164 patients were enrolled in our study. Multivariable logistic regression analysis showed that after adjusting for confounders, elevated baseline NLR was a significant risk factor predicting 30-day mortality (OR 1.02, 95%CI 1.01, 1.03, P = 0.0046) and hospital mortality (OR 1.02, 95%CI 1.01, 1.03, P = 0.0003). The result of the generalized additive mixed model showed that the NLR decreased in the survival group and increased in the non-survival group gradually within 7 days after ICU admission. The difference between the two groups showed a trend of increase gradually and the difference increased by an average of 0.67 daily after adjusting for confounders.Conclusions: We confirmed that there was a positive correlation between baseline NLR and short-term mortality, and we found significant differences in NLR changes over time between the non-survival group and the survival group. The early increase in NLR was associated with short-term mortality in ARDS patients.
Mortality Rate and Characteristics of Deaths Following COVID-19 Vaccination
Authors: Lv Gang , Yuan Jing , Xiong Xiaomo , Li Minghui 
Published: May 2021

Background: The emergency use authorization for coronavirus disease 2019 (COVID-19) vaccines brought both hopes and concerns to the Americans and others. We aimed to estimate the mortality rate of COVID-19 vaccination and presented characteristics of deaths following COVID-19 vaccination.Methods: Data on deaths following COVID-19 vaccination were obtained from the Vaccine Adverse Event Reporting System (VAERS) from December 11, 2020 through January 8, 2021. The Centers for Disease Control and Prevention (CDC) COVID Data Tracker was used to identify the total number of people receiving COVID-19 vaccines during the same period to estimate the mortality rate. Stratified analysis was conducted by the location of vaccination.Results: As of January 8, 2021, 55 deaths were reported, and the mortality rate of COVID-19 vaccination was 8.2 per million population. A total of 37 deaths were reported among long-term care facility residents, and the mortality rate was 53.4 per million population. Top reported comorbidities associated with deaths included hypertension, dementia, chronic obstructive pulmonary disease (COPD), diabetes, and heart failure. In addition, dementia was more likely to be associated with deaths vaccinated at long-term care facilities than at other locations.Conclusion: The benefits of COVID-19 vaccines outweigh the potential risks in older frail populations, and our findings do not support actions to exclude older adults from being vaccinated. However, continued monitoring of COVID-19 vaccination is still warranted.
Metabolomics Reveals Differences in Aqueous Humor Composition in Patients With and Without Pseudoexfoliation Syndrome
Authors: Dmuchowska Diana Anna , Pietrowska Karolina , Krasnicki Pawel , Kowalczyk Tomasz , Misiura Magdalena , Grochowski Emil Tomasz , Mariak Zofia , Kretowski Adam , Ciborowski Michal 
Published: May 2021

Pseudoexfoliation syndrome (XFS) is stress- or inflammation-induced elastosis accompanied by excessive production of microfibrils and their deposition in the anterior segment of the eye. Approximately 60–70 million people are affected by XFS worldwide. It is a component of a systemic disorder, considered a major risk factor for accelerated cataract formation, cataract surgery complications and development of glaucoma, which untreated or inadequately treated may lead to blindness. Moreover, XFS has been associated with cardiovascular and cerebrovascular morbidity, dementia, sensorineural hearing loss and pelvic organ prolapse. The pathogenesis of XFS has not been fully elucidated yet. Aqueous humor (AH) is a transparent fluid filling the anterior and posterior chambers of the eye. Determination of AH metabolites that are characteristic for XFS may provide valuable information about the molecular background of this ocular disorder. The aim of this study was to compare the composition of AH in XFS and non-XFS patients undergoing cataract surgery. The AH samples from 34 patients (15 with XFS and 19 without) were analyzed using liquid chromatography coupled to a Quadrupole Time-of-Flight mass spectrometer (LC-QTOF-MS). The obtained metabolic fingerprints were analyzed using multivariate statistics. Eleven statistically significant metabolites were identified. Compared with the non-XFS group, the AH of patients with XFS contained significantly lower levels of amino acids and their derivatives, for example, arginine (−31%, VIP = 2.38) and homo-arginine (−19%, VIP = 1.38). Also, a decrease in the levels of two acylcarnitines, hydroxybutyrylcarnitine (−29%, VIP = 1.24) and decatrienoylcarnitine (−46%, VIP = 1.89), was observed. However, the level of indoleacetaldehyde in XFS patients was significantly higher (+96%, VIP = 2.64). Other significant metabolites were two well-recognized antioxidants, ascorbic acid (−33%, VIP = 2.11) and hydroxyanthranilic acid (−33%, VIP = 2.25), as well as S-adenosylmethionine, a compound with anti-inflammatory properties (−29%, VIP = 1.93). Metabolic pathway analysis demonstrated that the identified metabolites belonged to eight metabolic pathways, with cysteine and methionine metabolism as well as arginine and proline metabolism being the most frequently represented. XFS can be associated with enhanced oxidative stress and inflammation, as well as with the disturbances of cellular respiration and mitochondrial energy production. Implementation of non-targeted metabolomics provided a better insight into the still not fully understood pathogenesis of XFS.
Acupuncture for Mild Cognitive Impairment and Dementia: An Overview of Systematic Reviews
Authors: He Wenbo , Li Meixuan , Han Xuemei , Zhang Wei 
Published: May 2021

Background: Dementia is a gradual decline in cognitive ability and is becoming more common in our elderly population. Mild cognitive impairment (MCI) is defined as a slight clinical deterioration of memory capacity, below the level of normal aging, but does not constitute a clinical diagnosis of dementia. To date, no interventions have been proven to cure MCI and dementia fully.Purpose: To evaluate the potential effectiveness and safety of acupuncture for mild cognitive impairment (MCI) and dementia and evaluate the methodological quality of systematic reviews (SRs).Methods: We conducted a literature search for SRs with meta-analyses in seven Chinese and international databases through October 1, 2020. The basic characteristics of the included SRs/meta-analyses and the basic information of the original included randomized controlled trials were extracted by three reviewers independently. A meta-analysis of the original randomized controlled trials from the included SRs/meta-analyses was performed using Stata 12.0 software. The Assessing the Methodological Quality of Systematic Reviews 2 was used to assess the methodological quality of the included SRs/meta-analyses, and the Grading of Recommendations, Assessment, Development, and Evaluation was used to rate the quality of evidence.Results: A total of 35 SRs/meta-analyses were included, and the majority showed that acupuncture was more effective than western medicine or conventional therapy for MCI and dementia [odds ratio =1.39; 95% confidence interval (CI): 1.24, 1.56]. There was a statistically significant difference in the Mini-Mental State Examination score (weighted mean difference = 1.23; 95% CI: 0.78, 1.68; p &lt; 0.00001), and there was no significant improvement in the activities of daily living score (weighted mean difference = 1.58; 95% CI: −0.02, 3.18; p = 0.053). The assessment results of Assessing the Methodological Quality of Systematic Reviews 2 showed that the methodological quality of most included SRs/meta-analyses was critically low; the lowest scores were items 2, 7, and 10. For Grading of Recommendations, Assessment, Development, and Evaluation, of the 73 outcomes, 50 (68.5%) outcomes were low or very low quality, and 23 (31.5%) outcomes were moderate quality.Conclusions: Acupuncture can be considered as an alternative for the treatment of MCI and dementia when western medicine or other therapies are contraindicated. More high-quality evidence is needed to determine further the effectiveness of acupuncture.
Validation of Predictive Models for Autoimmune Encephalitis-Related Antibodies to Cell-Surface Proteins Expressed in Neurons: A Retrospective Study Based in a Hospital
Authors: Ding Siqi , Gong Jiaoni , Lin Jiahe , Wang Yi , Hua Yingjie , Li Xueying , Du Yanru , Xia Niange , Zhu Zhenguo , Wang Xinshi , Zheng Rongyuan , Xu Huiqin 
Published: May 2021

Objective: Autoimmune encephalitis (AE) is a severe but treatable autoimmune disorder that is diagnosed by antibody (Ab) testing. However, it is unrealistic to obtain an early diagnosis in some areas since the Ab status cannot be immediately determined due to time and technology restrictions. In our study, we aimed to validate the Antibody Prevalence in Epilepsy and Encephalopathy (APE2) score among patients diagnosed with possible AE as a predictive model to screen AE patients with antibodies to cell-surface proteins expressed in neurons.Methods: A total of 180 inpatients were recruited, and antibodies were detected through serological and/or cerebrospinal fluid (CSF) evaluations. The APE2 score was used to validate the predictive models of AE with autoantibodies.Results: The mean APE2 score in the Ab-positive cases was 7.25, whereas the mean APE2 score in the Ab-negative cases was 3.18 (P &lt; 0.001). The APE2 score had a receiver operating characteristic (ROC) area under the curve of 0.924 [P &lt; 0.0001, 95% confidence interval (CI) = 0.875–0.973]. With a cutoff score of 5, the APE2 score had the best psychometric properties, with a sensitivity of 0.875 and a specificity of 0.791.Conclusion: The APE2 score is a predictive model for AE with autoantibodies to cell-surface proteins expressed in neurons and was validated and shown to have high sensitivity and specificity in our study. We suggest that such a model should be used in patients with a suspected diagnosis of AE, which could increase the detection rate of Abs, reduce testing costs, and help patients to benefit from treatment quickly.
Pre-operative MRI Radiomics for the Prediction of Progression and Recurrence in Meningiomas
Authors: Ko Ching-Chung , Zhang Yang , Chen Jeon-Hor , Chang Kai-Ting , Chen Tai-Yuan , Lim Sher-Wei , Wu Te-Chang , Su Min-Ying 
Published: May 2021

Objectives: A subset of meningiomas may show progression/recurrence (P/R) after surgical resection. This study applied pre-operative MR radiomics based on support vector machine (SVM) to predict P/R in meningiomas.Methods: From January 2007 to January 2018, 128 patients with pathologically confirmed WHO grade I meningiomas were included. Only patients who had undergone pre-operative MRIs and post-operative follow-up MRIs for more than 1 year were studied. Pre-operative T2WI and contrast-enhanced T1WI were analyzed. On each set of images, 32 first-order features and 75 textural features were extracted. The SVM classifier was utilized to evaluate the significance of extracted features, and the most significant four features were selected to calculate SVM score for each patient.Results: Gross total resection (Simpson grades I–III) was performed in 93 (93/128, 72.7%) patients, and 19 (19/128, 14.8%) patients had P/R after surgery. Subtotal tumor resection, bone invasion, low apparent diffusion coefficient (ADC) value, and high SVM score were more frequently encountered in the P/R group (p &lt; 0.05). In multivariate Cox hazards analysis, bone invasion, ADC value, and SVM score were high-risk factors for P/R (p &lt; 0.05) with hazard ratios of 7.31, 4.67, and 8.13, respectively. Using the SVM score, an AUC of 0.80 with optimal cutoff value of 0.224 was obtained for predicting P/R. Patients with higher SVM scores were associated with shorter progression-free survival (p = 0.003).Conclusions: Our preliminary results showed that pre-operative MR radiomic features may have the potential to offer valuable information in treatment planning for meningiomas.
Pre-surgical fMRI Localization of the Hand Motor Cortex in Brain Tumors: Comparison Between Finger Tapping Task and a New Visual-Triggered Finger Movement Task
Authors: Ciavarro Marco , Grande Eleonora , Pavone Luigi , Bevacqua Giuseppina , De Angelis Michelangelo , di Russo Paolo , Morace Roberta , Committeri Giorgia , Grillea Giovanni , Bartolo Marcello , Paolini Sergio , Esposito Vincenzo 
Published: May 2021

Introduction:Pre-surgical mapping is clinically essential in the surgical management of brain tumors to preserve functions. A common technique to localize eloquent areas is functional magnetic resonance imaging (fMRI). In tumors involving the peri-rolandic regions, the finger tapping task (FTT) is typically administered to delineate the functional activation of hand-knob area. However, its selectivity may be limited. Thus, here, a novel cue-induced fMRI task was tested, the visual-triggered finger movement task (VFMT), aimed at eliciting a more accurate functional cortical mapping of the hand region as compared with FTT.Method:Twenty patients with glioma in the peri-rolandic regions underwent pre-operative mapping performing both FTT and VFMT. The fMRI data were analyzed for surgical procedures. When the craniotomy allowed to expose the motor cortex, the correspondence with intraoperative direct electrical stimulation (DES) was evaluated through sensitivity and specificity (mean sites = 11) calculated as percentage of true-positive and true-negative rates, respectively.Results:Both at group level and at single-subject level, differences among the tasks emerged in the functional representation of the hand-knob. Compared with FTT, VFMT showed a well-localized activation within the hand motor area and a less widespread activation in associative regions. Intraoperative DES confirmed the greater specificity (97%) and sensitivity (100%) of the VFMT in determining motor eloquent areas.Conclusion:The study provides a novel, external-triggered fMRI task for pre-surgical motor mapping. Compared with the traditional FTT, the new VFMT may have potential implications in clinical fMRI and surgical management due to its focal identification of the hand-knob region and good correspondence to intraoperative DES.
Comparison of Age-Related Pigmentary Changes in the Auditory and Vestibular Systems Within Mouse and Human Temporal Bones
Authors: Andresen Nicholas S. , Coreas Sarah , Villavisanis Dillan F. , Lauer Amanda M. 
Published: May 2021

BackgroundMelanin pigmentation is present within the auditory and vestibular systems of the mammalian inner ear and may play a role in maintaining auditory and vestibular function. Melanocytes within the stria vascularis (SV) are necessary for the generation of the endocochlear potential (EP) and decreased EP has been linked to age-related hearing loss. Melanocytes and pigment-containing “dark cells” are present within the vestibular system, but have a less well-defined role. African–American individuals have increased pigmentation within the SV and vestibular system, which is hypothesized to be related to lower rates of age-related hearing loss and vestibular dysfunction. It remains unclear if increased pigmentation confers lifelong protection against hearing loss and vestibular dysfunction.MethodsMouse temporal bones were collected from juvenile (3–4 week) and aged (20–32 months) CBA/CaJ mice. Pediatric and adult human temporal bones from Caucasian or African–American individuals were examined from the Johns Hopkins Temporal Bone Collection. Information regarding Fitzpatrick skin type were unavailable, and self-identified race/ethnicity was used as a proxy. Images were taken using light microscopy at 20× magnification. ImageJ software (v1.53) was used to measure pigment within the SV and vestibular system.ResultsIn mouse temporal bones pigmentation within the SV increased with age, but pigmentation within the vestibular system did not increase with age. In human temporal bones pigmentation within the SV increased with age and pigmentation within the vestibular system increased within the wall of the utricle, but not other regions of the vestibular system. African–American individuals had higher amounts of pigment within the SV and vestibular system, among both pediatric and adult populations.ConclusionStria vascularis pigmentation increases with age in mouse and human temporal bones. Pigmentation within the vestibular system did not increase with age in mouse specimens and only increased within the utricular wall with age in human specimens. Individuals who identified as African–American had higher pigment content within the SV and vestibular system, both as children and as adults. These results highlight how similar age-related pigmentary changes occur in the auditory and vestibular systems across species and underscore the importance of racial/ethnic diversity in human temporal bone studies.
Food Sources Contributing to Intake of Choline and Individual Choline Forms in a Norwegian Cohort of Patients With Stable Angina Pectoris
Authors: Van Parys Anthea , Karlsson Therese , Vinknes Kathrine J. , Olsen Thomas , Øyen Jannike , Dierkes Jutta , Nygård Ottar , Lysne Vegard 
Published: May 2021

Background: Choline is an essential nutrient involved in a wide range of physiological functions. It occurs in water- and lipid-soluble forms in the body and diet. Foods with a known high choline content are eggs, beef, chicken, milk, fish, and selected plant foods. An adequate intake has been set in the US and Europe, however, not yet in the Nordic countries. A higher intake of lipid-soluble choline forms has been associated with increased risk of acute myocardial infarction, highlighting the need for knowledge about food sources of the individual choline forms. In general, little is known about the habitual intake and food sources of choline, and individual choline forms.Objective: Investigate foods contributing to the intake of total choline and individual choline forms.Design: The study population consisted of 1,929 patients with stable angina pectoris from the Western Norway B Vitamin Intervention Trial. Dietary intake data was obtained through a 169-item food frequency questionnaire. Intake of total choline and individual choline forms was quantified using the USDA database, release 2.Results: The geometric mean (95% prediction interval) total choline intake was 287 (182, 437) mg/d. Phosphatidylcholine accounted for 42.5% of total choline intake, followed by free choline (25.8%) and glycerophosphocholine (21.2%). Phosphocholine and sphingomyelin contributed 4.2 and 4.5%, respectively. The main dietary choline sources were eggs, milk, fresh vegetables, lean fish, and bread. In general, animal food sources were the most important contributors to choline intake.Conclusion: This study is, to the best of our knowledge, the first to assess the intake of all choline forms and their dietary sources in a European population. Most choline was consumed in the form of phosphatidylcholine and animal food sources contributed most to choline intake. There is a need for accurate estimates of the dietary intake of this essential nutrient to issue appropriate dietary recommendations.