For spatially dependent functional data, a generalized Karhunen-Loève expansion is commonly used to decompose data into an additive form of temporal components and spatially correlated coefficients. This structure provides a convenient model to investigate the space-time interactions, but may not hold for complex spatio-temporal processes. In this work, we introduce the concept of weak separability, and propose a formal test to examine its validity for non-replicated spatially stationary functional field. The asymptotic distribution of the...

For spatially dependent functional data, a generalized Karhunen-Loève expansion is commonly used to decompose data into an additive form of temporal components and spatially correlated coefficients. This structure provides a convenient model to investigate the space-time interactions, but may not hold for complex spatio-temporal processes. In this work, we introduce the concept of weak separability, and propose a formal test to examine its validity for non-replicated spatially stationary functional field. The asymptotic distribution of the...

Subtropical forests act as a carbon sink and play an important role in mitigating global warming. However, the understanding of the effects of stand characteristics and climatic factors on forest carbon sequestration capacity remains limited. Based on multiple regression analyses using structural equation modeling and plot-level data of coniferous and broadleaf forests from the national forest resource inventories, our study quantified vegetation carbon accumulation rate (VCAR) and the underlying influence pattern in Zhejiang Province, Southeastern...

In eukaryotes, calcium not only is an essential mineral nutrient but also serves as an intracellular second messenger that is necessary for many physiological processes. Previous studies showed that the protein phosphatase-calcineurin protects fungi from toxicity caused by the extracellular calcium; however, little is known about how calcineurin mediates the cellular physiology process for this function. In this study, by monitoring intracellular calcium, particularly by tracking vacuolar calcium dynamics in living cells through a novel...

Our previous studies found that the C-X-C motif chemokine receptor 5 (CXCR5) loss leads to retinal pigment epithelium (RPE) dysfunction and AMD pathogenesis. The current study aimed to characterize the G protein-coupled receptor (GPCR) structure of CXCR5 and analyze its interactions with AMD-related risk genes. The sequence alignments, homology model of CXCR5 and structural assessment analysis were performed. Data and text mining were then performed to identify AMD-related risk genes and their interaction with CXCR5...

The fungal pathogen Candida auris has emerged as a new threat to human health. We previously reported the first isolate of C. auris (BJCA001) in China, which belongs to the South Asian clade (I) and was susceptible to all antifungals tested. In this study, we report the isolation of a drug-resistant C. auris strain (BJCA002) from the same city (Beijing). Strain BJCA002 belongs to the South African clade (III) and is resistant to fluconazole and...

In plants, recent studies have revealed that N6-methyladenosine (m6A) methylation of mRNA has potential regulatory functions of this mRNA modification in many biological processes. m6A methyltransferase, m6A demethylase and m6A-binding proteins can cause differential phenotypes, indicating that m6A may have critical roles in the plant. In this study, we depicted the m6A map of sea buckthorn (Hippophae rhamnoides Linn.) transcriptome. Similar to A. thaliana, m6A sites of sea buckthorn transcriptome is significantly enriched around the...

Colorectal cancer (CRC) is a common malignancy of the gastrointestinal tract, which has the second highest incidence among gastrointestinal tumors. At present, due to the limitations of current CRC treatment strategies, there is an urgent need for developing more effective therapies. B7 family member H4 (B7-H4) is associated with the progression of a wide spectrum of cancers, but its functional role in CRC is unknown. The purpose of this study is to clarify the role...

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).

Mosquito-transmitted flaviviruses cause widespread disease across the world. To provide better molecular tools for drug screens and pathogenesis studies, we report a new approach to produce stable NanoLuc-tagged flaviviruses, including dengue virus serotypes 1-4, Japanese encephalitis virus, yellow fever virus, West Nile virus, and Zika virus. Since the reporter gene is often engineered at the capsid gene region, the capsid sequence must be duplicated to flank the reporter gene; such capsid duplication is essential for...

Although members of the Mycobacterium tuberculosis complex (MTBC) exhibit high similarity, they are characterized by differences with respect to virulence, immune response, and transmissibility. To understand the virulence of these bacteria and identify potential novel therapeutic targets, we systemically investigated the total cell protein contents of virulent H37Rv, attenuated H37Ra, and avirulent M. bovis BCG vaccine strains at the log and stationary phases, based on tandem mass tag (TMT) quantitative proteomics. Data analysis revealed 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...

Additional file 1: Table S1. Expression of known miRNAs identified in wheat crown tissues.

Additional file 3: Table S2. Expression of wheat new miRNAs in crown tissues.

Additional file 5: Table S4. Expression of differentially expressed miRNAs in wheat crown tissues.

Additional file 5: Table S4. Expression of differentially expressed miRNAs in wheat crown tissues.

The three-dimensional (3D) structure of RNA usually plays an important role in the recognition with RNA-binding protein. Along with the discovering of RNAs, several RNA databases are developed to study the functions of RNA based on sequence, secondary structure, local 3D structural motif and global structure. Based on RNA function and structure, different RNAs are classified and stored in SCOR and DARTS, respectively. The classification of RNA structures is useful in RNA structure prediction and...

We, the Editors and Publisher of the journal Cell Cycle, have retracted the following article: Qicai Han, Jie Yang, Hao Yang, Chao Li, Juan Li & Yuan Cao (2020) KIAA1429 promotes osteosarcoma progression by promoting stem cell properties and is regulated by miR-143-3p, Cell Cycle, 19:10, 1172-1185, DOI: 10.1080/15384101.2020.1749465 Since publication, concerns have been raised about similarity of the data in another published article: Yang J, Han Q, Li C, Yang H, Chen X, Wang...

The current level of knowledge on transcriptome responses triggered by endotoxins and glucocorticoids in immune cells in pigs is limited. Therefore, in the present study, we treated porcine peripheral blood mononuclear cells (PBMCs) with lipopolysaccharide (LPS) and dexamethasone (DEX) separately or combined for 2 hours. The resultant transcriptional responses were examined by mRNA sequencing. We found that the LPS treatment triggered pronounced inflammatory responses as evidenced by upregulation of pro-inflammatory cytokines, chemokines, and related signaling...

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,...

Although members of the Mycobacterium tuberculosis complex (MTBC) exhibit high similarity, they are characterized by differences with respect to virulence, immune response, and transmissibility. To understand the virulence of these bacteria and identify potential novel therapeutic targets, we systemically investigated the total cell protein contents of virulent H37Rv, attenuated H37Ra, and avirulent M. bovis BCG vaccine strains at the log and stationary phases, based on tandem mass tag (TMT) quantitative proteomics. Data analysis revealed that...

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...

Dengue virus infection mainly causes dengue hemorrhagic fever (DHF) and/or dengue shock syndrome (DSS). However, ADE (antibody-dependent enhancement) is one of the main pathogenic factors, and its pathogenic mechanism has not been fully elucidated. Recently, with the development of high-throughput sequencing, an increased number of RNAs have been confirmed to play a vital regulatory role in the process of virus infection. However, there is a lack of research on dengue virus infection and ADE. In...