Spatial-linked alignment tool (SLAT) for aligning heterogenous slices.

Spatially resolved omics technologies reveal the spatial organization of cells in various biological systems. Here we propose SLAT (Spatially-Linked Alignment Tool), a graph-based algorithm for efficient and effective alignment of spatial slices. Adopting a graph adversarial matching strategy, SLAT is the first algorithm capable of aligning heterogenous spatial data across distinct technologies and modalities.

Magnetoencephalogram-based brain-computer interface for hand-gesture decoding using deep learning.

Advancements in deep learning algorithms over the past decade have led to extensive developments in brain-computer interfaces (BCI). A promising imaging modality for BCI is magnetoencephalography (MEG), which is a non-invasive functional imaging technique. The present study developed a MEG sensor-based BCI neural network to decode Rock-Paper-scissors gestures (MEG-RPSnet).

Machine Learning Applied to Omics Datasets Predicts Mortality in Patients with Alcoholic Hepatitis.

Alcoholic hepatitis is a major health care burden in the United States due to significant morbidity and mortality. Early identification of patients with alcoholic hepatitis at greatest risk of death is extremely important for proper treatments and interventions to be instituted. In this study, we used gradient boosting, random forest, support vector machine and logistic regression analysis of laboratory parameters, fecal bacterial microbiota, fecal mycobiota, fecal virome, serum metabolome and serum lipidome to predict mortality in patients with alcoholic hepatitis.

Identifying complex motifs in massive omics data with a variable-convolutional layer in deep neural network.

Motif identification is among the most common and essential computational tasks for bioinformatics and genomics. Here we proposed a novel convolutional layer for deep neural network, named variable convolutional (vConv) layer, for effective motif identification in high-throughput omics data by learning kernel length from data adaptively. Empirical evaluations on DNA-protein binding and DNase footprinting cases well demonstrated that vConv-based networks have superior performance to their convolutional counterparts regardless of model complexity.

[Construction of lentiviral mediated CyPA siRNA and its functions in non-small cell lung cancer].

Objective: To construct a lentiviral-vector-mediated CyPA small interference RNA (siRNA) and study its function in non-small cell lung cancer.

Methods: First, four target sequences were selected according to CyPA mRNA sequence, the complementary DNA contained both sense and antisense oligonucleotides were designed, synthesized and cloned into the pGCL-GFP vector, which contained U6 promoter and green fluorescent protein (GFP). The resulting lentiviral vector containing CyPA shRNA was named Lv-shCyPA, and it was confirmed by PCR and sequencing.

[Preventive and therapeutic effects of recombinant IFN-alpha2b nasal spray on SARS-CoV infection in Macaca mulata].

Objective: To study the preventive and therapeutic effects of recombinant IFN-alpha2b for nasal spray on SARS-CoV infection in Macaca mulata (rhesus monkey).

Methods: Ten rhesus monkeys were divided into two groups, 5 in interferon group, and 5 in control group. Before and after SARS-CoV attack, the virus was detected in samples such as pharyngeal swab in all the two groups by Real-time PCR (RT-PCR) and virus isolation was performed.

[Potent neutralization antibody elicited in mice by SARS-associated coronavirus spike protein S1 domain].

Objective: To study the antigenicity of SARS associated coronavirus (CoV) spike S1 (12-672Aa) domain.

Methods: BALB/c mice were immunized with a plasmid bearing codon-optimized SARS-CoV (Tor2 strain) S1 domain and then boosted with purified S1 protein; the SARS-CoV specific IgG antibody was tested by ELISA and neutralization antibody was determined by in vitro microneutralization assay.

Results: S1 domain of SARS-CoV spike, which has been demonstrated harboring the receptor binding domain, successfully elicited SARS-CoV specific IgG antibody in mouse after combined immunization with DNA and purified S1 protein; the antibody elicited solely by S1 could potently neutralize SARS-CoV (HKU-39849) in vitro, 50% of 1 000 TCID50 SARS-CoV challenged cells were protected from viral infection by a 1:1499.