Protocol to estimate cell type proportions from bulk RNA-seq using DAISM-DNNXMBD.

Computational protocols for cell type deconvolution from bulk RNA-seq data have been used to understand cellular heterogeneity in disease-related samples, but their performance can be impacted by batch effect among datasets. Here, we present a DAISM-DNN protocol to achieve robust cell type proportion estimation on the target dataset. We describe the preparation of calibrated samples from human blood samples. We then detail steps to train a dataset-specific deep neural network (DNN) model and cell type proportion estimation using the trained model. For complete details on the use and execution of this protocol, please refer to Lin et al. (2022).

DAISM-DNNXMBD: Highly accurate cell type proportion estimation with in silico data augmentation and deep neural networks.

Understanding the immune cell abundance of cancer and other disease-related tissues has an important role in guiding disease treatments. Computational cell type proportion estimation methods have been previously developed to derive such information from bulk RNA sequencing data. Unfortunately, our results show that the performance of these methods can be seriously plagued by the mismatch between training data and real-world data. To tackle this issue, we propose the DAISM-DNNXMBD (XMBD: Xiamen Big Data, a biomedical open software initiative in the National Institute for Data Science in Health and Medicine, Xiamen University, China.) (denoted as DAISM-DNN) pipeline that trains a deep neural network (DNN) with dataset-specific training data populated from a certain amount of calibrated samples using DAISM, a novel data augmentation method with an in silico mixing strategy. The evaluation results demonstrate that the DAISM-DNN pipeline outperforms other existing methods consistently and substantially for all the cell types under evaluation in real-world datasets.

A dichoptic custom-made action video game as a treatment for adult amblyopia.

Previous studies have employed different experimental approaches to enhance visual function in adults with amblyopia including perceptual learning, videogame play, and dichoptic training. Here, we evaluated the efficacy of a novel dichoptic action videogame combining all three approaches. This experimental intervention was compared to a conventional, yet unstudied method of supervised occlusion while watching movies. Adults with unilateral amblyopia were assigned to either play the dichoptic action game (n=23; 'game' group), or to watch movies monocularly while the fellow eye was patched (n=15; 'movies' group) for a total of 40hours. Following training, visual acuity (VA) improved on average by ≈0.14logMAR (≈28%) in the game group, with improvements noted in both anisometropic and strabismic patients. This improvement is similar to that obtained following perceptual learning, video game play or dichoptic training. Surprisingly, patients with anisometropic amblyopia in the movies group showed similar improvement, revealing a greater impact of supervised occlusion in adults than typically thought. Stereoacuity, reading speed, and contrast sensitivity improved more for game group participants compared with movies group participants. Most improvements were largely retained following a 2-month no-contact period. This novel video game, which combines action gaming, perceptual learning and dichoptic presentation, results in VA improvements equivalent to those previously documented with each of these techniques alone. Our game intervention led to greater improvement than control training in a variety of visual functions, thus suggesting that this approach has promise for the treatment of adult amblyopia.

Segregation of human immunodeficiency virus type 1 subtypes by risk factor in Australia.

The aim of this study was to determine which human immunodeficiency virus type 1 (HIV-1) subtypes were circulating in Australia and to correlate the subtypes with risk factors associated with the acquisition of HIV-1 infection. DNA was extracted from peripheral blood mononuclear cells, and HIV-1 env genes were amplified and subtyped using heteroduplex mobility analysis, with selected samples sequenced and phylogenetic analysis performed. The HIV-1 env subtypes were determined for 141 samples, of which 40 were from female patients and 101 were from male patients; 13 samples were from children. Forty-seven patients were infected by homosexual or bisexual contact, 46 were infected through heterosexual contact, 21 were infected from injecting drug use (IDU), 13 were infected by vertical transmission, 8 were infected from nosocomial exposure, and 6 were infected by other modes of transmission, including exposure to blood products, ritualistic practices, and two cases of intrafamilial transmission. Five subtypes were detected; B (n = 104), A (n = 5), C (n = 17), E (CRF01_AE; n = 13), and G (n = 2). Subtype B predominated in HIV-1 acquired homosexually (94% of cases) and by IDU (100%), whereas non-subtype B infections were mostly seen in heterosexually (57%) or vertically (22%) acquired HIV-1 infections and were usually imported from Africa and Asia. Subtype B strains of group M viruses predominate in Australia in HIV-1 transmitted by homosexual or bisexual contact and IDU. However, non-B subtypes have been introduced, mostly acquired via heterosexual contact.

In vivo generation of dendritic cells by intramuscular codelivery of FLT3 ligand and GM-CSF plasmids.

Dendritic cells (DCs) are the major cells responsible for the uptake and the transport of antigens to regional lymphoid tissues and for the presentation of antigenic peptides to T cells. They are highly effective in immunotherapy. However, in lymphoid and other tissues, DCs constitute only a small population and are difficult to isolate in large numbers. Our objective was to devise a method with which to rapidly expand splenic DCs in vivo. We accomplished this by intramuscular injection of plasmids encoding mouse granulocyte-macrophage colony stimulating factor (GM-CSF) and fms-like tyrosine kinase 3-ligand (FLT3-L). Gene transfer was amplified by electroporation. Both cytokine vectors significantly increased DC numbers, but they were more effective in combination. When either control plasmid (Blank), or FLT3-L or GM-CSF expression plasmids were injected individually, the mean numbers of CD11c(+)/MHC II(+) DCs in spleen cell suspensions were, respectively, 6, 11, and 23 million. When FLT3-L and GM-CSF plasmids were codelivered, this increased to 36 million. Peak levels occurred 7 days postinjection of DNA. To further characterize these DCs, we stained them with myeloid (CD11b, F4/80)- and lymphoid (CD8alpha)-related markers. FLT3-L cDNA favored lymphoid DC expansion and GM-CSF cDNA favored myeloid DC expansion, whereas combined treatment expanded both types with a myeloid predominance. We confirm the ability of these DCs to present antigen to CD4(+) T cells and to stimulate in mixed lymphocyte cultures. We demonstrate that DCs can be rapidly expanded by this simple gene transfer method, which has numerous potential applications.

New technology for deep light distribution in tissue for phototherapy.

Photodynamic therapy is one of several techniques developed for phototherapy for solid cancers and hematologic malignancies. Photodynamic therapy is a treatment that utilizes a molecular energy exchange between visible light and a photosensitive drug, which results in the production of 1O2, a highly reactive cytocidal oxygen species. The effect is limited to the region where light and drug are combined so that malignant tissue is destroyed and the usual side effects associated with standard cancer therapies are avoided. The light component of photodynamic therapy is customarily generated via dye-pumped or diode lasers. The cost and the complexity of lasers have seriously limited the clinical use of photodynamic therapy for malignancies. A new device technology, based on light-emitting diodes, has been developed (Light Sciences Corporation, Issaquah, WA) that allows light production inside the target tissue. This new technology will expand the current range of indications that are treatable with photodynamic therapy to include moderate- and large-volume refractorytumors. Conventional photodynamic therapy utilizes the delivery of intense light for seconds or minutes. The new approach differs from conventional photodynamic therapy in that it combines a novel interstitial light delivery system with prolonged photoactivation of photosensitive drugs. Prolonging photoactivation time in order to deliver a higher light dose results in an amplification effect, whereby the repeated activation of each photosensitive drug molecule leads to the generation of many thousands of 1O2 molecules. The production of overwhelming numbers of these powerful oxidants in individual cells and the vascular supply of tumors leads to irreversible damage and death of the targeted lesions. Results of preclinical studies have indicated a significant correlation between increased duration of photoactivation and increased volume and depth of photodynamic therapy-induced necrosis. The new developments will enable photodynamic therapy to be used effectively against refractory bulky disease as frontline therapy or in combination with chemotherapy, radiation therapy, or biologics. Perhaps most promising, many patients with advanced refractory disease may now be relieved of symptoms or may return to the treatable population.