Additional file 6: Table S6. The GSVA results of GSE70769 dataset.

Additional file 6: Table S6. The GSVA results of GSE70769 dataset.

Autophagy is an important protein degradation pathway in eukaryotes and is involved in multiple processes. To date, many autophagy-related genes had been studied in various plants, but a few studies have been reported on the role of autophagy in seed development. For centuries, seedlessness has been one of the most valuable characteristics of grapes. In this study, we identified a total of 33 ATG genes in the grape. Tissue-specific expression analysis showed that VvATGs expressed...

Autophagy is an important protein degradation pathway in eukaryotes and is involved in multiple processes. To date, many autophagy-related genes had been studied in various plants, but a few studies have been reported on the role of autophagy in seed development. For centuries, seedlessness has been one of the most valuable characteristics of grapes. In this study, we identified a total of 33 ATG genes in the grape. Tissue-specific expression analysis showed that VvATGs expressed...

Additional file 17: Table S12. The cluster of functional annotations enriched by differential methylated and expressed genes (MetGDE genes).

Additional file 7: Table S2. Read mapping statistics of whole-genome bisulfite sequencing data and RNA sequencing data of six cows.

Additional file 7: Table S2. Targeted transcriptome analysis reveals new neuronal nuclear calcium-regulated mediators of neuro–glia crosstalk upon TBI. All significantly differentially regulated genes between the PV.NLS TBI (PT) and Control TBI (CT) /PV.NLS Sham (PS) are listed with name, log FC and their adjusted p-value.

Additional file 7: Table S2. Targeted transcriptome analysis reveals new neuronal nuclear calcium-regulated mediators of neuro–glia crosstalk upon TBI. All significantly differentially regulated genes between the PV.NLS TBI (PT) and Control TBI (CT) /PV.NLS Sham (PS) are listed with name, log FC and their adjusted p-value.

Supplemental material, sj-xlsx-2-cix-10.1177_11769351221136056 for Optimizing Drug Response Study Design in Patient-Derived Tumor Xenografts by Jessica Weiss, Nhu-An Pham, Melania Pintilie, Ming Li, Geoffrey Liu, Frances A Shepherd, Ming-Sound Tsao and Wei Xu in Cancer Informatics

This systematic review aimed to identify the referral criteria for palliative care in patients with Parkinson’s disease. We conducted an electronic search for publications on referral criteria for palliative care in patients with Parkinson’s disease in six electronic databases. The articles were thoroughly reviewed by two independent reviewers for inclusion using a predefined data extraction list. The referral criteria were thematically classified using a coding methodology. This systematic review included 36 publications. We identified 14...

Supplemental material, sj-rar-1-mac-10.1177_00202940221135917 for Fault detection and classification of the rotor unbalance based on dynamics features and support vector machine by Lan Lan, Xiao Liu and Qian Wang in Measurement and Control

Soft tissue sarcomas (STSs) are rare, heterogeneous mesenchymal neoplasias. Understanding the tumor microenvironment (TME) and identifying potential biomarkers for prognosis associated with the TME of STS might provide effective clues for immune therapy. We evaluated the immune scores and stromal scores of STS patients by using the RNA sequencing dataset from The Cancer Genome Atlas (TCGA) database and the ESTIMATE algorithm. Then, the differentially expressed mRNAs (DEGs), miRNAs (DEMs) and lncRNAs (DELs) were identified after...

More and more circular RNAs (circRNAs) revealed to play a critical role in the initiation and progression of cancer, however, the effects of circRNAs on non-small cell lung cancer (NSCLC) remain largely undetermined. In the present study, we screened the dysregulated circRNAs in paired NSCLC and normal samples from GEO database and identified circ_0043278 was to be significantly up-regulated in NSCLC and demonstrated it promotes NSCLC progression in vitro and in vivo. Then, we revealed...

More and more circular RNAs (circRNAs) revealed to play a critical role in the initiation and progression of cancer, however, the effects of circRNAs on non-small cell lung cancer (NSCLC) remain largely undetermined. In the present study, we screened the dysregulated circRNAs in paired NSCLC and normal samples from GEO database and identified circ_0043278 was to be significantly up-regulated in NSCLC and demonstrated it promotes NSCLC progression in vitro and in vivo. Then, we revealed...

Our previous studies have elucidated a possible connection between long intergenic non-protein coding RNA 2570 (LINC02570) and nasopharyngeal carcinoma (NPC). However, the precise mechanism by which LINC02570 promotes NPC remains unknown. We used quantitative polymerase chain reaction (qPCR) to detect LINC02570 expression in nasopharyngeal cell lines, NPC tissues, and chronic rhinitis tissues. Subcellular LINC02570 localization was confirmed by fluorescence in situ hybridization (FISH). The effects of LINC02570 stable knockdown and overexpression on viabillity, proliferation, migration,...

Gut microbiota are the candidate biomarkers for neurogenic bowel dysfunction (NBD) in patients with spinal cord injury (SCI). We aimed to identify the common features between patients with varying degree of thoracic SCI and healthy individuals and subpopulations of microbiota correlated with the serum biomarkers. Twenty-one patients with complete thoracic SCI (CTSCI), 24 with incomplete thoracic SCI (ITSCI), and 24 healthy individuals (HC) were enrolled in this study. Fresh stool samples and clinical data were...

Gut microbiota are the candidate biomarkers for neurogenic bowel dysfunction (NBD) in patients with spinal cord injury (SCI). We aimed to identify the common features between patients with varying degree of thoracic SCI and healthy individuals and subpopulations of microbiota correlated with the serum biomarkers. Twenty-one patients with complete thoracic SCI (CTSCI), 24 with incomplete thoracic SCI (ITSCI), and 24 healthy individuals (HC) were enrolled in this study. Fresh stool samples and clinical data were...

Although long noncoding RNAs (lncRNAs) in lung adenocarcinoma (LUAD) have been increasingly studied, LINC01426 has not been fully investigated in LUAD. The GEPIA database revealed that LINC01426 was upregulated in LUAD tissues. In our study, we further verified the significantly high expression of LINC01426 in LUAD tissues and cell lines. We also analyzed the LINC01426 expression level and LUAD clinical features and found that high LINC01426 expression was associated with tumor diameter; tumor, node, and...

This study was designed to explore the relationship between the deterioration of sea cucumbers and intestinal flora’s diversity change during preservation using 16S rRNA gene sequencing. We show that the body wall of sea cucumber develops white spots on day 4, and the epidermis dissolves on day 7. The distinctive OTUs remain relatively low during four days of storage but increase on day 7. The potential gut microbiota biomarkers are Psychrobacter-cibarius, Ralstonia-pickettii, and Clostridiales during...

Chemoresistance is a major challenge for the treatment of breast cancer (BC). Previous studies showed that miR-145 level decreases in chemoresistant BC tissues. Nevertheless, the biological function of miR-145 on docetaxel resistance of BC cells remains unclear, which is what our research attempted to clarify. RT-qPCR analyzed miR-145 level, and cell viability and colony formation assays assessed the impact of miR-145 on docetaxel resistance. Molecular mechanisms of miR-145-mediated docetaxel sensitivity were examined by Luciferase reporter...

The impact of quaternary glaciation in eastern China on local fanua and flora has been a topic of considerable interest. We used mitochondrial DNA (mtDNA) sequence data and coalescent simulations to test two general biogeographic hypothesis related to the effects of Pleistocene climatic fluctuations for a widespread ophidian species (Gloydius brevicaudus) in eastern China and Korean Peninsula. The phylogenetic analysis revealed three major lineages, the southeast Coastal, Yangtze and North Lineages. The latter two are...

1. The biodiversity-ecosystem functioning debate is a central topic in ecology. Recently, there has been a growing interest in size diversity because body size is sensitive to environmental changes and is one of the fundamental characteristics of organisms linking many ecosystem properties. However, how size diversity affects ecosystem functioning is an important yet unclear issue. 2. To fill the gap, with large-scale field data from the East China Sea, we tested the novel hypothesis that...

The emerging COVID-19 caused by SARS-CoV-2 infection poses severe challenges to global public health. Serum antibody testing is becoming one of the critical methods for the diagnosis of COVID-19 patients. We investigated IgM and IgG responses against SARS-CoV-2 nucleocapsid (N) and spike (S) protein after symptom onset in the intensive care unit (ICU) and non-ICU patients. 130 blood samples from 38 COVID-19 patients were collected. The levels of IgM and IgG specific to N and...

The emerging COVID-19 caused by SARS-CoV-2 infection poses severe challenges to global public health. Serum antibody testing is becoming one of the critical methods for the diagnosis of COVID-19 patients. We investigated IgM and IgG responses against SARS-CoV-2 nucleocapsid (N) and spike (S) protein after symptom onset in the intensive care unit (ICU) and non-ICU patients. 130 blood samples from 38 COVID-19 patients were collected. The levels of IgM and IgG specific to N and...

Streptococcus suis (S. suis), more specifically serotype 2, is a bacterial pathogen that threatens the lives of pigs and humans. Like many other pathogens, S. suis exhibits quorum sensing (QS) system-controlled virulence factors, such as biofilm formation that complicates treatment. Therefore, impairing the QS involving LuxS/AI-2 cycle in S. suis, may be a promising alternative strategy for overcoming S. suis infections. In this study, we investigated paeoniflorin (PF), a monoterpenoid glycoside compound extracted from peony,...