Abstract Background Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy, particularly with regard to visualization of read mapping location, normalization options, growth dynamics and functional gene repertoires. Current read classification tools use non-standard output formats, or do not fully show information on mapping location. As reference datasets are not perfect, portrayal of mapping information is critical for judging results effectively. Results Our alignment-based...

Additional file 1: Fig. S1. A schematic showing the experimental design, milk feeding, and fecal sample collection of the two trials.

Additional file 2: Fig. S2. Heatmap of the ASVs associated with diarrheic status in stage 4 of trial 1. The ASVs were identified based on fold change and analysis using LEfSe or DESeq2.

Additional file 5: Fig. S4. Heatmap of the ASVs that identified to be diarrheic status transition-associated in trial 2. The ASVs were identified based on fold change and analysis using LEfSe or DESeq2.

Abstract Background Nowadays, 3D planning and static for dynamic aids play an increasing role in oral rehabilitation of the masticatory apparatus with dental implants. The aim of this study is to compare the accuracy of implant placement using a 3D-printed drilling guide and an intraoral real-time dynamic navigation system. Methods A total of 60 implants were placed on 12 partially edentulous lower jaw models. 30 were placed with pilot drilling guides, the other half with...

Richmond agitation-sedation scale (RASS) is a simple and widely used tool for evaluating sedation and agitation in adult ICU patients. Early deep sedation has been shown to be an important independent predictor of death, however, studies on the role of RASS in the prognostic assessment of neurocritical patients are lacking. The purpose of this study was to investigate the relationship between RASS and in-hospital mortality in neurocritical patients, and to develop and validate an effective...

Patients with R/M HNSCC treated with palliative first-line therapy at Hannover Medical School between October 2005 and December 2016 have been included to show changes in survival following broad utilization of cetuximab. Treatment periods were defined from 10/2005 to 12/2008 (Period A) and 01/2009 to 12/2016. Overall survival did not improve over time. However, in subgroup analysis cetuximab utilized at any time vs. never showed a significant improve of overall survival (11.3 vs. 6.3 months,...

Supplementary Material 2

Supplementary Material 1

Supplementary Material 3

Additional file 1: Fig. S1. A schematic showing the experimental design, milk feeding, and fecal sample collection of the two trials.

Additional file 2: Fig. S2. Heatmap of the ASVs associated with diarrheic status in stage 4 of trial 1. The ASVs were identified based on fold change and analysis using LEfSe or DESeq2.

Additional file 3: Table S1. The ASVs in co-occurrence pattern of trial 1 stage 4.

Additional file 4: Fig. S3. Principal coordinates analysis (PCoA) plot of fecal microbiotas among ages in trial 2. The fecal microbiotas differences (P values) between diarrheic and non-diarrheic calves within the same age were compared.

The organoid is a 3D cell architecture formed by self-organized tissues or cells in vitro with similar cell types, histological structures, and biological functions of the native organ. Depending on the unique organ structures and cell types, producing organoids requires individualized design and is still challenging. Organoids of some tissues, including adipose tissue, remain to generate to be more faithful to their original organ in structure and function. We previously established a new model of...

Supplemental Material for Epidemiological and clinical characteristics of vaccinated COVID-19 patients: A meta-analysis and systematic review by Wen Tian, Xingxiang Ren, Mei Han, Yuanyuan Zhang, Xu Gao, Zhihai Chen, and Wei Zhang in International Journal of Immunopathology and Pharmacology

Additional file 2: Fig. S2. Differential methylation of CpG loci in the SOCS3 promoter in T-LGL samples. Comparison of CpG methylation (beta-value) for CpGs in the SOCS3 promoter between CD8+ memory cells (CD8mem) and T-LGLL samples (LGL). On top, adjusted p val of differential methylation analysis (dmpFDR, top left) and adjusted p value of differential variability analysis (dmVar, top right).

Additional file 3: Fig. S2. Differential methylation of CpG loci in the SOCS3 promoter in T-LGL samples. Comparison of CpG methylation (beta-value) for CpGs in the SOCS3 promoter between CD8+ memory cells (CD8mem) and T-LGLL samples (LGL). On top, adjusted p val of differential methylation analysis (dmpFDR, top left) and adjusted p value of differential variability analysis (dmVar, top right).

Additional file 6: Fig. S4. Differential gene expression of IL6 between T-LGL and healthy donor-derived CD8+ memory T cells. Differential gene expression for IL6 was measured by qPCR. Bulk CD8+ cells from two healthy donors were used for comparison. In line with previous publications, the T-LGLL cohort analyzed exhibits a higher IL6 expression compared to healthy donor-derived C8+ cells. HD Healthy donor.

Additional file 9: Fig. S1. Correlation of bisulfite Pyrosequencing (BPS) and methylation Array DNA methylation levels. The correlation matrix shows the Pearson correlation coefficient (r: 1 (red) to − 1 (blue) among all CpG loci analyzed by BPS. The candidate genes LINC01550 and BCL11B contained multiple CpG sites. Columns and rows represent one CpG loci of the listed candidate gene.

Additional file 9: Fig. S1. Correlation of bisulfite Pyrosequencing (BPS) and methylation Array DNA methylation levels. The correlation matrix shows the Pearson correlation coefficient (r: 1 (red) to − 1 (blue) among all CpG loci analyzed by BPS. The candidate genes LINC01550 and BCL11B contained multiple CpG sites. Columns and rows represent one CpG loci of the listed candidate gene.

Abstract Background The molecular pathogenesis of T-cell large granular lymphocytic leukemia (T-LGLL), a mature T-cell leukemia arising commonly from T-cell receptor αβ-positive CD8+ memory cytotoxic T cells, is only partly understood. The role of deregulated methylation in T-LGLL is not well known. We analyzed the epigenetic profile of T-LGLL cells of 11 patients compared to their normal counterparts by array-based DNA methylation profiling. For identification of molecular events driving the pathogenesis of T-LGLL, we compared...

Supplemental material, sj-docx-1-opp-10.1177_10781552221144303 for Knowledge and practices about safe handling regarding the risk of exposure to antineoplastic drugs for caregivers in compounding units and in operating rooms performing HIPEC/PIPAC by Clémence Delafoy, Hubert Benoist, Alex Patin, Michèle Vasseur, Sonia Guillouet, Clarisse Eveno, Jean-Marc Guilloit, Pascal Odou, Nicolas Simon and Guillaume Saint-Lorant in Journal of Oncology Pharmacy Practice

Abstract Objective Pregnancy is characterized by well-defined immunological adaptions within the maternal immune cell compartment allowing the survival of a genetically disparate individual in the maternal womb. Phenotype and function of immune cells are largely determined by intracellular processing of external stimuli. Ubiquitinating and deubiquitinating enzymes are known to critically regulate immune signaling either by modulating the stability or the interaction of the signaling molecules. Accordingly, if absent, critical physiological processes may be perturbed such...

Abstract Background Diarrhea is a major cause of morbidity and mortality in young calves, resulting in considerable economic loss for dairy farms. To determine if some gut microbes might have resistance to dysbiotic process with calf diarrhea by dictating the microbial co-occurrence patterns from birth to post-weaning, we examined the dynamic development of the gut microbiota and diarrhea status using two animal trials, with the first trial having 14 Holstein dairy calves whose fecal samples...