Most of the current alternative splicing (AS) analysis tools are powerless to analyse complex splicing. To address this, we developed SUVA (Splice sites Usage Variation Analysis) that decomposes complex splicing events into five types of splice junction pairs. By analysing real and simulated data, SUVA showed higher sensitivity and accuracy in detecting AS events than the compared methods. Notably, SUVA detected extensive complex AS events and screened out 69 highly conserved and dominant AS events...

Most of the current alternative splicing (AS) analysis tools are powerless to analyse complex splicing. To address this, we developed SUVA (Splice sites Usage Variation Analysis) that decomposes complex splicing events into five types of splice junction pairs. By analysing real and simulated data, SUVA showed higher sensitivity and accuracy in detecting AS events than the compared methods. Notably, SUVA detected extensive complex AS events and screened out 69 highly conserved and dominant AS events...

Immune checkpoint inhibitors (ICIs) -induced adverse events (AEs) have been reported affecting almost all human organs. However, studies about ocular AEs are few. A meta-analysis was performed to evaluate the risks of ICI-related ophthalmic AEs compare to chemotherapy. Methods: Eligible studies were selected from phase II/III randomized controlled trials investigating ICIs. The data were analyzed by R software and Stata. Odds ratio of treatment-related AE (trAEs) and nonspecific ophthalmic trAEs (NS-trAEs) were lower for PD-1/PD-L1...

Soluble pyridine nucleotide transhydrogenase (STH), catalyzes a reversible hydrogen transfer between NADH and NADPH, is widely utilized in cofactor engineering. In the present study, we expanded the distribution range of STH to more unreported bacteria. Meanwhile, STH was mainly found in α, γ, δ-proteobacteria, acidobacteria, actinobacteria and planctomycetes. The enzymological properties of two novel STHs from Acidobacteria bacterium KBS 146 (AbSTH) and Nocardia jiangxiensis (NjSTH) were characterized. The optimum temperature and pH of AbSTH and...

Subcellular localization of transcripts is highly associated with regulation of gene expression, synthesis of protein, and also the development of the human brain cortex. Although many mechanisms are prevalent in the occurrence of neuroinflammation, the mechanisms based on differences in subcellular localization of transcripts have not been explored. To characterize the dynamic profile of nuclear and cytoplasmic transcripts during the progress of haemorrhage-induced neuroinflammation, we isolated nucleo-cytoplasmic RNA fractions of oxyhaemoglobin (oxy-Hb) treated microglia cells...

Mafic microgranular enclaves (MMEs) are hosted by the Early Cretaceous granitic plutons from the Jiaodong Peninsula and are crucial for constraining the petrogenesis of these plutons and understanding the lithospheric evolution in the eastern North China Craton (NCC). This paper presents new geochronological, bulk-rock geochemistry, and Sr-Nd-Hf isotope data for Yashan granodiorite and its MMEs in an effort to build an integrated model of the geodynamic setting during the Early Cretaceous. Zircon U–Pb dating indicates...

Additional file 1. Genomic sequences and their corresponding annotations of 25 flowering plants.

Additional file 6. The collected transcriptome analysis data.

Additional file 4 Significant enrichment functions (n = 39) of conserved lncRNA set (n = 196).

The second human pegivirus HPgV-2 is a novel blood-borne virus that is strongly associated with the hepatitis C virus (HCV) infection. However, the molecular evidence for their association as well as the natural history and tissue tropism of HPgV-2 remain to be elucidated. In this longitudinal study, a total of 753 patients including 512 HIV-1 and HCV co-infected patients were enrolled to characterize the natural history of HPgV-2 infection. Peripheral blood mononuclear cells (PBMCs) 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...

Single nucleotide polymorphisms (SNPs) include the transition and transversion of a single base. In this study, we found two cSNPs (rs110757796 and rs110652478) in the FABP4 (fatty acid-binding protein 4) gene and tested their population genetic parameters in five Chinese cattle breeds. FABP4 is a key marker molecule for lipid production. It plays a crucial role in the growth and development of animals. Thus, we also analyze the association between the two cSNPs of FABP4...

Complement receptor 3 (CD11b/CD18) is an important receptor that mediates adhesion, phagocytosis and chemotaxis in various immunocytes. The conidia of the medically-important pathogenic fungus, Aspergillus fumigatus can be internalized into alveolar epithelial cells to disseminate its infection in immunocompromised host; however, the role of CR3 in this process is poorly understood. In the present study, we investigated the potential role of CR3 on A. fumigatus internalization into type II alveolar epithelial cells and its effect...

Supplemental material, sj-pdf-1-prf-10.1177_02676591211031468 for Establishment of a venovenous extracorporeal membrane oxygenation in a rat model of acute respiratory distress syndrome by Yongnan Li, Jian Huang, Rongzhi Zhang, Shixiong Wang, Xingdong Cheng, Pengbin Zhang, Kerong Zhai, Wei Wang, Debin Liu and Bingren Gao in Perfusion

Supplemental material, sj-pdf-1-prf-10.1177_02676591211031468 for Establishment of a venovenous extracorporeal membrane oxygenation in a rat model of acute respiratory distress syndrome by Yongnan Li, Jian Huang, Rongzhi Zhang, Shixiong Wang, Xingdong Cheng, Pengbin Zhang, Kerong Zhai, Wei Wang, Debin Liu and Bingren Gao in Perfusion

This study proposes a memory-based search strategy for the fruit fly optimization algorithm (FOA) to enrich its search ability, and utilizes an improved Deb (IDeb) rule to tackle the constraints and increase the computational efficiency of the FOAs. Unlike other FOAs that employ a predefined search radius, the proposed search strategy mines the knowledge of both the swarm and the individuals to adaptively determine the vision search radius of each fruit fly. The improved Deb...

This study proposes a memory-based search strategy for the fruit fly optimization algorithm (FOA) to enrich its search ability, and utilizes an improved Deb (IDeb) rule to tackle the constraints and increase the computational efficiency of the FOAs. Unlike other FOAs that employ a predefined search radius, the proposed search strategy mines the knowledge of both the swarm and the individuals to adaptively determine the vision search radius of each fruit fly. The improved Deb...

Changes in the intestinal microbiota indirectly impact the health of mucosa distal to the intestine, particularly the respiratory tract. However, the effects of intestinal microbiota dysbiosis on the regulation of respiratory syncytial virus (RSV) infection are not clear. In this study, we examined the effects of altering the intestinal microbiota on the pulmonary immune response against RSV infection. BALB/c mice were treated with streptomycin before infection with RSV to study the altered immune response. The...

Curcumin (Cur) is a flavonoid derived from Curcuma longa L. that has been shown to have a variety of biological activities, but some previous studies have described its non-negligible negative effects on female reproduction and embryo development. To further explore the toxic stress effect, this study investigated apoptosis and autophagy of healthy buffalo (Bubalus bubalis) derived granulosa cells (GCs) exposed to Cur and/or autophagy inhibitors. Results showed that Cur declined viability of GCs in a...

Hsa_circ_0101432 promotes the development of hepatocellular carcinoma (HCC) by adsorbing miR-1258 and miR-622 We, the Editors and Publisher of the journal Cell Cycle, have retracted the following article: Haibo Zou, Xiangang Xu, Lanyun Luo, Yu Zhang, Le Luo, Yutong Yao, Guangming Xiang, Xiaolun Huang, and Guan Wang. Hsa_circ_0101432 promotes the development of hepatocellular carcinoma (HCC) by adsorbing miR-1258 and miR-622. Cell Cycle. 2019;18(19):2398-2413. doi: 10.1080/15384101.2019.1618120. Since publication, significant concerns have been raised about the integrity...

Numerous studies have reported the regulatory effects of miR-21-5p and reversine in human breast cancer (HBC). However, the mechanism of reversine and miR-21-5p has not been fully investigated in HBC. The aim of the current study was to assess the mechanism of action of reversine, with or without miR-21-5p, in HBC progression. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and Western blot results confirmed the upregulation of miR-21-5p and downregulation of sprouty RTK signaling antagonist 2...

Regarding the extremely high mortality caused by sepsis-induced acute respiratory distress syndrome (ARDS), it is urgent to develop new biomarkers of sepsis-induced ARDS for treatment. Here, 532 differential expression genes (DEGs) related to sepsis and 433 DEGs related to sepsis-induced ARDS were screened in the GSE32707 dataset. Compared with sepsis samples, sepsis ARDS samples showed a higher infiltration of activated memory CD4 T cells and naive B cells, but a relatively lower infiltration of CD8...

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,...

Adhesives with properties of low-temperature and water-resistance are important in manufacturing. In this work, dopamine hydrochloride (DA), containing catechol groups, was introduced into the polymer by covalent grafting to obtain water-resistant films. Films with low-temperature and water-resistance properties were obtained through layer-by-layer assembly of branched polyethyleneimine (bPEI) and chemically cross-linked hyaluronate (HA)-DA (denoted HA-D). The film surfaces were wetted with moisture generated from low-temperature pretreatment, and the resulting films, named as bPEI/HA-D multilayer films, could...

Heat stress is an environmental challenge that reduces plant productivity and growth. Plants have developed corresponding mechanisms to survive this adverse environmental stress. To demonstrate the mechanisms of how plants adapt to the environmental challenge, the heat response experiments involving Arabidopsis thaliana were retrieved from the GEO database. After quantile normalization of the GEO raw data, the differentially expressed genes (DEGs) in response to heat stress were identified by robust rank aggregation (RRA) algorithm, including...