bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Robust Seven-Gene Signature Associated With Tumor Microenvironment to Predict Survival Outcomes of Patients With Stage III–IV Lung Adenocarcinoma
Authors: Zhao Hao , Zhang Xuening , Guo Lan , Shi Songhe , Lu Ciyong 
Published: September 2021

BackgroundDue to the relatively insidious early symptoms of lung adenocarcinoma (LUAD), most LUAD patients are at an advanced stage at the time of diagnosis and lose the best chance of surgical resection. Mounting evidence suggested that the tumor microenvironment (TME) was highly correlated with tumor occurrence, progress, and prognosis. However, TME in advanced LUAD remained to be studied and reliable prognostic signatures based on TME in advanced LUAD also had not been well-established. This study aimed to understand the cell composition and function of TME and construct a gene signature associated with TME in advanced LUAD.MethodsThe immune, stromal, and ESTIMATE scores of each sample from The Cancer Genome Atlas (TCGA) database were, respectively, calculated using an ESTIMATE algorithm. The LASSO and Cox regression model were applied to select prognostic genes and to construct a gene signature associated with TME. Two independent datasets from the Gene Expression Omnibus (GEO) were used for external validation. Twenty-two subsets of tumor-infiltrating immune cells (Tiics) were analyzed using the CIBERSORT algorithm.ResultsFavorable overall survival (OS) and progression-free survival (PFS) were found in patients with high immune score (p = 0.048 and p = 0.028; respectively) and stromal score (p = 0.024 and p = 0.025; respectively). Based on the immune and stromal scores, 453 differentially expressed genes (DEGs) were identified. Using the LASSO and Cox regression model, a seven-gene signature containing AFAP1L2, CAMK1D, LOXL2, PIK3CG, PLEKHG1, RARRES2, and SPP1 was identified to construct a risk stratification model. The OS and PFS of the high-risk group were significantly worse than that of the low-risk group (p &lt; 0.001 and p &lt; 0.001; respectively). The receiver operating characteristic (ROC) curve analysis confirmed the good potency of the seven-gene signature. Similar findings were validated in two independent cohorts. In addition, the proportion of macrophages M2 and Tregs was higher in high-risk patients (p = 0.041 and p = 0.022, respectively).ConclusionOur study established and validated a seven-gene signature associated with TME, which might serve as a prognosis stratification tool to predict survival outcomes of advanced LUAD patients. In addition, macrophages M2 polarization may lead to worse prognosis in patients with advanced LUAD.
Establishment of an Endocytosis-Related Prognostic Signature for Patients With Low-Grade Glioma
Authors: Wang Dawei , Liu Shiguang , Wang Guangxin 
Published: September 2021

BackgroundLow-grade glioma (LGG) is a heterogeneous tumor that might develop into high-grade malignant glioma, which markedly reduces patient survival time. Endocytosis is a cellular process responsible for the internalization of cell surface proteins or external materials into the cytosol. Dysregulated endocytic pathways have been linked to all steps of oncogenesis, from initial transformation to late invasion and metastasis. However, endocytosis-related gene (ERG) signatures have not been used to study the correlations between endocytosis and prognosis in cancer. Therefore, it is essential to develop a prognostic model for LGG based on the expression profiles of ERGs.MethodsThe Cancer Genome Atlas and the Genotype-Tissue Expression database were used to identify differentially expressed ERGs in LGG patients. Gene ontology, Kyoto Encyclopedia of Genes and Genomes, and Gene set enrichment analysis methodologies were adopted for functional analysis. A protein-protein interaction (PPI) network was constructed and hub genes were identified based on the Search Tool for the Retrieval of Interacting Proteins database. Univariate and multivariate Cox regression analyses were used to develop an ERG signature to predict the overall survival (OS) of LGG patients. Finally, the association between the ERG signature and gene mutation status was further analyzed.ResultsSixty-two ERGs showed distinct mRNA expression patterns between normal brain tissues and LGG tissues. Functional analysis indicated that these ERGs were strikingly enriched in endosomal trafficking pathways. The PPI network indicated that EGFR was the most central protein. We then built a 29-gene signature, dividing patients into high-risk and low-risk groups with significantly different OS times. The prognostic performance of the 29-gene signature was validated in another LGG cohort. Additionally, we found that the mutation scores calculated based on the TTN, PIK3CA, NF1, and IDH1 mutation status were significantly correlated with the endocytosis-related prognostic signature. Finally, a clinical nomogram with a concordance index of 0.881 predicted the survival probability of LGG patients by integrating clinicopathologic features and ERG signatures.ConclusionOur ERG-based prediction models could serve as an independent prognostic tool to accurately predict the outcomes of LGG.
Establishment and Validation of a Genetic Label Associated With M2 Macrophage Infiltration to Predict Survival in Patients With Colon Cancer and to Assist in Immunotherapy
Authors: Xu Boyang , Peng Ziqi , Yan Guanyu , Wang Ningning , Chen Moye , Yao Xue , Sun Mingjun , An Yue 
Published: September 2021

BackgroundColon cancer is a malignant tumor with high morbidity and mortality. Researchers have tried to interpret it from different perspectives and divided it into different subtypes to facilitate individualized treatment. With the rise in the use of immunotherapy, its value in the field of tumor has begun to emerge. From the perspective of immune infiltration, this study classified colon cancer according to the infiltration of M2 macrophages in patients with colon cancer and further explored the same.MethodsCibersort algorithm was used to analyze the level of immune cell infiltration in patients with colon cancer in The Cancer Genome Atlas (TCGA) database. Weighted gene co-expression network analysis (WGCNA), Consensus Clustering analysis, Lasso analysis, and univariate Kaplan–Meier analysis were used to screen and verify the hub genes associated with M2 macrophages. Principal component analysis (PCA) was used to establish the M2 macrophage-related score (M2I Score). The correlation between M2I Score and somatic cell variation and microsatellite instability (MSI) were analyzed. Furthermore, the correlation between M2 macrophage score and differences in immunotherapy sensitivity was also explored.ResultsM2 macrophage infiltration was associated with poor prognosis. Four hub genes (ANKS4B, CTSD, TIMP1, and ZNF703) were identified as the progression-related genes associated with M2 macrophages. A stable and accurate M2I Score for M2 macrophages used in colon adenocarcinoma was determined based on four hub genes. The M2I Score was positively correlated with the tumor mutation load (TMB). The M2I Score of the group with high instability of microsatellites was higher than that of the group with low instability of microsatellites and microsatellite-stable group. Combined with the Cancer Immunome Atlas database, we concluded that patients with high M2I Scores were more sensitive to programmed cell death protein 1 (PD-1) inhibitors and PD-1 inhibitors combined with cytotoxic T-lymphocyte–associated antigen 4 (CTLA-4) inhibitors. The low-rating group may have better efficacy without immune checkpoint inhibitors or with CTLA4 inhibitors alone.ConclusionFour prognostic hub genes associated with M2 macrophages were screened to establish the M2I Score. Patients were divided into two subgroups: high M2I Score group and low M2I Score group. TMB, MSI, and sensitivity to immunotherapy were higher in the high-rated group. PD-1 inhibitors or PD-1 combined with CTLA-4 inhibitors are preferred for patients in the high-rated group who are more sensitive to immunotherapy.
Infants Younger Than 90 Days Admitted for Late-Onset Sepsis Display a Reduced Abundance of Regulatory T Cells
Authors: Fortmann Ingmar , Dammann Marie-Theres , Siller Bastian , Humberg Alexander , Demmert Martin , Tüshaus Ludger , Lindert Judith , van Zandbergen Vera , Pagel Julia , Rupp Jan , Herting Egbert , Härtel Christoph 
Published: September 2021

ObjectiveTo provide epidemiological data of infants &lt; 90 days of age with suspected late-onset sepsis (LOS) and evaluate distinct immunological specificities. We hypothesized that previously healthy infants &lt; 3 months of age with sepsis have a yet undefined immunological predisposition; e.g. differences in lymphocyte subsets including regulatory T cells.MethodsWe performed an exploratory, single center study between January 1st, 2019 and June 1st, 2021. Routine diagnostics included conventional culture (blood, cerebrospinal fluid, urine), PCR and inflammatory markers in infants &lt; 90 days of age with suspected sepsis. We additionally analyzed lymphocyte subsets and CD4+ CD25+ forkhead box protein (FoxP3)+ Tregs at admission for sepsis workup as compared to age-matched controls.ResultsA convenience sample cohort of n= 51 infants with sepsis workup was enrolled. Invasive bacterial infection (IBI) was diagnosed in 25 (49.0%) patients including two infants with a rhinovirus co-infection and viral infection in 14 (27.5%) neonates. No infectious cause was found in 12 cases. Infants with suspected LOS displayed a decreased abundance of CD4+ FoxP3+ T cells as compared to controls, which was most pronounced in the subgroup of infants with IBI. We also noticed elevated HLA-DR-positive CD3+ cells in infants with LOS and a higher CD4/CD8-ratio in infants with viral infection as compared to healthy controls. Infants with viral infections had a higher number of natural killer cells as compared to infants with IBI.ConclusionOur exploratory data support the concept of a potential immaturity state and failed immune tolerance development for young infants with LOS. Future large-scale studies are needed to elucidate pre-sepsis conditions and to target the microbiome-immunity interplay as a potential risk pattern.
Non-uniform Segmental Range of Motion of the Thoracic Spine During Maximal Inspiration and Exhalation in Healthy Subjects
Authors: Burgos Jesús , Barrios Carlos , Mariscal Gonzalo , Lorente Alejandro , Lorente Rafael 
Published: September 2021

Background and Objective:To analyse the range of motion of the thoracic spine by radiographically measuring changes in the sagittal profile of different thoracic segments during maximal inspiration and exhalation. The starting hypothesis was that forced deep breathing requires an active, but non-uniform widening of the lordotic–kyphotic range of motion of the different thoracic segments.Methods:Cross-sectional study. Participants were 40 healthy volunteers aged 21–60. Conventional anteroposterior and functional sagittal chest radiographs were performed during maximal inspiration and exhalation. The range of motion of each spinal thoracic functional segment, global T1–T12 motion, and the sagittal displacement of the thoracic column during breathing were measured. Considering the different type of ribs and their attachment the spine and sternum, thoracic segments were grouped in T1–T7, T7–T10, and T10–T12. The displacement of the thoracic spine with respect to the sternum and manubrium was also recorded.Results:The mean difference from inspiration to exhalation in the T1–T12 physiologic kyphosis was 15.9° ± 4.6°, reflecting the flexibility of the thoracic spine during deep breathing (30.2%). The range of motion was wider in the caudal hemicurve than in the cranial hemicurve, indicating more flexibility of the caudal component of the thoracic kyphosis. A wide range of motion from inspiration to exhalation was found at T7–T10, responsible for 73% of T1–T12 sagittal movement. When the sample was stratified according to age ranges (20–30, 30–45, and 45–60 yr.), none of the measurements for inspiration or exhalation showed statistically significant differences.Only changes at this level showed a positive correlation with changes in the global thoracic kyphosis (r= 0.794,p&lt;0.001).Conclusion:The range of motion of the thoracic spine plays a relevant role in respiration dynamics. Maximal inspiration appears to be highly dependent on the angular movements of the T7–T10 segment.
Real-Life Experience With First-Line Therapy Bortezomib Plus Melphalan and Prednisone in Elderly Patients With Newly Diagnosed Multiple Myeloma Ineligible for High Dose Chemotherapy With Autologous Stem-Cell Transplantation
Authors: Buda Gabriele , Del Giudice Maria Livia , Antonioli Elisabetta , Ghio Francesco , Orciuolo Enrico , Morganti Riccardo , Martini Francesca , Staderini Michela , Galimberti Sara , Petrini Mario 
Published: September 2021

Introduction: Currently, the regimen with bortezomib plus melphalan and prednisone (VMP) is a standard treatment for multiple myeloma and it is recommended as the first-line therapy for patients with multiple myeloma (MM) ineligible for high-dose chemotherapy with autologous stem-cell transplantation.Objectives: Participants of the clinical trial are highly selected populations; therefore, the aim of this study was to present observations from real practice that can provide important information for practitioners and to investigate clinical outcomes of VMP regimen in elderly patients with newly diagnosed MM.Patients and Methods: We retrospectively analyzed the data on the efficacy and survival parameters, such as overall survival (OS) and event-free survival (EFS), with attention to the effect of gender, age and International Staging System (ISS) stage, of VMP regimen in 164 patients with newly diagnosed MM not eligible for high-dose chemotherapy with autologous stem-cell transplantation (median age, 75 years; range, 60–86 years).Results: Patients aged 75 years or older constituted 50.6% of the study cohort. Frail patients were 10.36%, according to the clinical frailty scale of geriatric assessment (GA). A total of 1203 courses of VMP regimen (mainly VMP 1–29, 99.16 %) were administered. The median cumulative delivered dose of bortezomib was 46.8 mg/m2. The overall response rate (ORR), including all patients with a partial response or better, was 81.7% and the complete response rate (CRR) was 10.36 %. After a median 38.51 months of follow-up, the median overall survival (OS) was 34.33 months; the median event-free survival (EFS) after VMP and second-line therapy (mainly Rd, 56.31%) were 18.51 and 10.75 months, respectively. In the subgroup of patients with 75 years or older the median OS was 29.76 months; the median EFS after first and second-line therapy were 17.76 and 8.93 months, respectively. The hazard ratio for OS was 2.276 (p-value 0.046) and for EFS was 1.507 (p-value 0.055) for the ISS stage II and III group. Age and gender were not negative predictors of survival.Conclusions: VMP treatment is highly effective in the first-line therapy of elderly patients with multiple myeloma ineligible for HDT with auto-SCT.
Ultra-Rapid Drug Susceptibility Testing for Klebsiella pneumoniae Clinical Isolates in 60 Min by SYBR Green I/Propidium Iodide Viability Assay
Authors: Chen Jiazhen , Wang Xuyang , Wang Shiyong , Chen Chen , Zhang Wenhong , Zhang Ying 
Published: September 2021

BackgroundWe aimed to optimize and validate the drug susceptibility test (DST) assay by SYBR Green I/PI (SG-PI) method using a panel of 89 Klebsiella pneumoniae clinical isolates in comparison with the conventional DST method to three most important antibiotics used for treatment of this bacterial infection, including imipenem, cefmetazole, and gentamicin.MethodsBy staining with SYBR Green I and PI dyes, green fluorescence and red fluorescence, which linearly correlated with the percentages of live and dead or membrane damaged cells, respectively, were used to produce two standard curves to calculate the relative cell membrane impermeable rates for each log and stationary phase cultures. Stationary phase K. pneumoniae cells were used in imipenem and cefmetazole SG-PI DST assay whereas log phase cells were used in the gentamicin assay. The conventional broth microdilution method was used as a gold standard for DST for comparison.ResultsData showed that after antibiotic treatment for 30–60 min, the antibiotic-resistant K. pneumoniae strains had significantly higher numbers of surviving cells than the susceptible strains at different concentrations of imipenem, cefmetazole, and gentamicin, where the average relative membrane impermeable rates were 88.5, 92.5, and 103.8% for resistant clinical strains, respectively, and 9.1, 49.3, and 71.5% for susceptible strains, respectively. Overall, the total concordances between the ultra-rapid SG-PI method and conventional minimal inhibitory concentration assay in diagnosing imipenem, cefmetazole and gentamicin resistance were high and were 96.6% (86/89), 95.4% (83/87), and 95.5% (85/89), respectively.ConclusionWe demonstrate that our novel SG-PI assay can accurately and stably detect resistance to different antibiotics in clinical isolates of K. pneumoniae in an ultra-fast manner in 60–90 min.
Mindfulness Training Improves Cognition and Strengthens Intrinsic Connectivity Between the Hippocampus and Posteromedial Cortex in Healthy Older Adults
Authors: Sevinc Gunes , Rusche Johann , Wong Bonnie , Datta Tanya , Kaufman Robert , Gutz Sarah E. , Schneider Marissa , Todorova Nevyana , Gaser Christian , Thomalla Götz , Rentz Dorene , Dickerson Bradford D. , Lazar Sara W. 
Published: September 2021

Maintaining optimal cognitive functioning throughout the lifespan is a public health priority. Evaluation of cognitive outcomes following interventions to promote and preserve brain structure and function in older adults, and associated neural mechanisms, are therefore of critical importance. In this randomized controlled trial, we examined the behavioral and neural outcomes following mindfulness training (n = 72), compared to a cognitive fitness program (n = 74) in healthy, cognitively normal, older adults (65–80 years old). To assess cognitive functioning, we used the Preclinical Alzheimer Cognitive Composite (PACC), which combines measures of episodic memory, executive function, and global cognition. We hypothesized that mindfulness training would enhance cognition, increase intrinsic functional connectivity measured with magnetic resonance imaging (MRI) between the hippocampus and posteromedial cortex, as well as promote increased gray matter volume within those regions. Following the 8-week intervention, the mindfulness training group showed improved performance on the PACC, while the control group did not. Furthermore, following mindfulness training, greater improvement on the PACC was associated with a larger increase in intrinsic connectivity within the default mode network, particularly between the right hippocampus and posteromedial cortex and between the left hippocampus and lateral parietal cortex. The cognitive fitness training group did not show such effects. These findings demonstrate that mindfulness training improves cognitive performance in cognitively intact older individuals and strengthens connectivity within the default mode network, which is particularly vulnerable to aging affects.Clinical Trial Registration: [https://clinicaltrials.gov/ct2/show/NCT02628548], identifier [NCT02628548].
IV-Thrombolysis in Ischemic Stroke With Unknown Time of Onset—Safety and Outcomes in Posterior vs. Anterior Circulation Stroke
Authors: Macha Kosmas , Hoelter Philip , Siedler Gabriela , Wang Ruihao , Knott Michael , Stoll Svenja , Engelhorn Tobias , Doerfler Arnd , Schwab Stefan , Mühlen Iris , Kallmünzer Bernd 
Published: September 2021

Background: rt-PA for ischemic stroke in the unknown or extended time window beyond the first 4. 5 h after symptom onset is safe and effective for certain patients after selection by multimodal neuroimaging. However, the evidence for this approach comes mainly from patients with anterior circulation stroke (ACS), while the data on posterior circulation stroke (PCS) are scarce.Methods: Ischemic stroke patients treated with IV-thrombolysis in the unknown or extended time window between January 2011 and May 2019 were identified from an institutional registry. The patients were categorized into PCS or ACS based on clinico-radiological findings. We analyzed the hemorrhagic complications, clinical and imaging efficacy outcomes, and mortality rates by comparing the PCS and ACS patient groups. Adjusted outcome analyses were performed after propensity score matching for the relevant factors.Results: Of the 182 patients included, 38 (20.9%) had PCS and 144 (79.1%) had ACS. Symptomatic acute large vessel occlusion (LVO) was present in 123 patients on admission [27 (22.0%) PCS and 96 (78.0%) ACS]. The score on the National Institutes of Health Stroke Scale (NIHSS), the time from last seen normal, and the door-to-needle times were similar in PCS and ACS. In patients with LVO, the NIHSS score was lower [8 (5–15) vs. 14 (9–18), p = 0.005], and infarction visible on follow-up imaging was less common [70.4 vs. 87.5%; aRD, −18.9% (−39.8 to −2.2%)] in the PCS patient group. There was a trend toward a lower risk for intracranial hemorrhage (ICH) following intravenous thrombolysis in PCS vs. ACS, without reaching a statistical significance [5.3 vs. 16.9%; aRD, −10.4% (−20.4 to 4.0%)]. The incidence of symptomatic ICH [according to the ECASS III criteria: 2.6 vs. 3.5%; aRD, −2.9% (−10.3 to 9.2%)], efficacy outcomes, and mortality rates were similar in PCS and ACS patients.Conclusions: In this real-world clinical cohort, the safety and the efficacy of rt-PA for ischemic stroke in the unknown or extended time window did not show relevant differences between PCS and ACS, with a trend toward less hemorrhagic complications in PCS. The findings reconfirm the clinician in the usage of rt-PA beyond the first 4.5 h also in selected patients with PCS.