Comparison of imaging-based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed, paraffin-embedded tumor samples.

Imaging-based spatial transcriptomics (ST) is evolving rapidly as a pivotal technology in studying the biology of tumors and their associated microenvironments. However, the strengths of the commercially available ST platforms in studying spatial biology have not been systematically evaluated using rigorously controlled experiments. In this study, we used serial 5-µm sections of formalin-fixed, paraffin-embedded surgically resected lung adenocarcinoma and pleural mesothelioma tumor samples in tissue microarrays to compare the performance of the single cell ST platforms CosMx, MERFISH, and Xenium (uni/multi-modal) platforms in reference to bulk RNA sequencing, multiplex immunofluorescence, GeoMx Digital Spatial Profiler, and hematoxylin and eosin staining data for the same samples.

Leaflet Perforation Using Cor-Knot in Minimally Invasive Aortic Valve Replacement.

A 38-year-old woman underwent minimally invasive aortic valve replacement with a 21-mm Inspiris aortic valve and Cor-Knot for type 0 bicuspid valve and severe aortic stenosis. Postoperative transthoracic echocardiography was uneventful. Four months later, she experienced shortness of breath.

Comparison of imaging-based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed, paraffin-embedded tumor samples.

Imaging-based spatial transcriptomics (ST) is evolving rapidly as a pivotal technology in studying the biology of tumors and their associated microenvironments. However, the strengths of the commercially available ST platforms in studying spatial biology have not been systematically evaluated using rigorously controlled experiments. In this study, we used serial 5-m sections of formalin-fixed, paraffin-embedded surgically resected lung adenocarcinoma and pleural mesothelioma tumor samples in tissue microarrays to compare the performance of the single cell ST platforms CosMx, MERFISH, and Xenium (uni/multi-modal) platforms in reference to bulk RNA sequencing, multiplex immunofluorescence, GeoMx Digital Spatial Profiler, and hematoxylin and eosin staining data for the same samples.

Dietary and lifestyle oxidative balance score was negatively associated with the risk of diabetic kidney disease: NHANES 2005-2020.

Aims: There is a potential association between oxidative stress and the development of diabetic kidney disease (DKD). The Oxidative Balance Score (OBS), derived from dietary and lifestyle factors, acts as a comprehensive marker of oxidative stress. Research examining the relationship between OBS and DKD is scarce.

A statistical approach for systematic identification of transition cells from scRNA-seq data.

Decoding cellular state transitions is crucial for understanding complex biological processes in development and disease. While recent advancements in single-cell RNA sequencing (scRNA-seq) offer insights into cellular trajectories, existing tools primarily study expressional rather than regulatory state shifts. We present CellTran, a statistical approach utilizing paired-gene expression correlations to detect transition cells from scRNA-seq data without explicitly resolving gene regulatory networks.

Adaptive fabric with emissivity regulation for thermal management of humans.

The heat generation of the human body dramatically varies between resting and active status, so dynamic heat dissipation is required to ensure optimal thermal comfort. Herein, we propose a spectrally self-adaptive smart fabric (SSSF) by covering polyester fabric with silver nanowires, which autonomously adjusts its emissivity in response to the body's movement status from dry to wet states. During periods of inactivity, the SSSF maintains radiative heat insulation with a low emissivity state of 0.

Risk of mortality and complications in people with depressive disorder and diabetes mellitus: A 20-year population-based propensity score-matched cohort study.

People with depression have increased premature mortality and elevated prevalence of diabetes-mellitus compared to general population. However, risk of mortality and diabetes-related complications among patients with depression and co-occurring diabetes is under-studied. This population-based propensity score-matched (1:10) cohort study identified 12,175 patients with pre-existing depression and incident-diabetes (depression-diabetes group) and 117,958 patients with incident-diabetes only (diabetes-only group) between 2002 and 2021 in Hong-Kong, using territory-wide medical-record database of public-healthcare services, to investigate whether depression increased the risk of overall mortality, complications and post-complication mortality in people with diabetes.

Prognostic impact and reasons for variability by tumor location in gastric cancer.

Background: Gastric cancer (GC) is a highly prevalent gastrointestinal tract tumor. Several trials have demonstrated that the location of GC can affect patient prognosis. However, the factors determining tumor location remain unclear.

Temporal recording of mammalian development and precancer.

Temporal ordering of cellular events offers fundamental insights into biological phenomena. Although this is traditionally achieved through continuous direct observations, an alternative solution leverages irreversible genetic changes, such as naturally occurring mutations, to create indelible marks that enables retrospective temporal ordering. Using a multipurpose, single-cell CRISPR platform, we developed a molecular clock approach to record the timing of cellular events and clonality in vivo, with incorporation of cell state and lineage information.

Stem cell activity-coupled suppression of endogenous retrovirus governs adult tissue regeneration.

Mammalian retrotransposons constitute 40% of the genome. During tissue regeneration, adult stem cells coordinately repress retrotransposons and activate lineage genes, but how this coordination is controlled is poorly understood. Here, we observed that dynamic expression of histone methyltransferase SETDB1 (a retrotransposon repressor) closely mirrors stem cell activities in murine skin.

Comparing neoantigen cancer vaccines and immune checkpoint therapy unveils an effective vaccine and anti-TREM2 macrophage-targeting dual therapy.

The goal of therapeutic cancer vaccines and immune checkpoint therapy (ICT) is to promote T cells with anti-tumor capabilities. Here, we compared mutant neoantigen (neoAg) peptide-based vaccines with ICT in preclinical models. NeoAg vaccines induce the most robust expansion of proliferating and stem-like PD-1TCF-1 neoAg-specific CD8 T cells in tumors.

A Deep Learning Method for Human Sleeping Pose Estimation with Millimeter Wave Radar.

Recognizing sleep posture is crucial for the monitoring of people with sleeping disorders. Existing contact-based systems might interfere with sleeping, while camera-based systems may raise privacy concerns. In contrast, radar-based sensors offer a promising solution with high penetration ability and the capability to detect vital bio-signals.

BATF is a major driver of NK cell epigenetic reprogramming and dysfunction in AML.

Myelodysplastic syndrome and acute myeloid leukemia (AML) belong to a continuous disease spectrum of myeloid malignancies with poor prognosis in the relapsed/refractory setting necessitating novel therapies. Natural killer (NK) cells from patients with myeloid malignancies display global dysfunction with impaired killing capacity, altered metabolism, and an exhausted phenotype at the single-cell transcriptomic and proteomic levels. In this study, we identified that this dysfunction was mediated through a cross-talk between NK cells and myeloid blasts necessitating cell-cell contact.

VCAT: an integrated variant function annotation tools.

The development of sequencing technology has promoted discovery of variants in the human genome. Identifying functions of these variants is important for us to link genotype to phenotype, and to diagnose diseases. However, it usually requires researchers to visit multiple databases.

Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma.

Somatic mutation phasing informs our understanding of cancer-related events, like driver mutations. We generated linked-read whole genome sequencing data for 23 samples across disease stages from 14 multiple myeloma (MM) patients and systematically assigned somatic mutations to haplotypes using linked-reads. Here, we report the reconstructed cancer haplotypes and phase blocks from several MM samples and show how phase block length can be extended by integrating samples from the same individual.

Interleukin-21 engineering enhances NK cell activity against glioblastoma via CEBPD.

Glioblastoma (GBM) is an aggressive brain cancer with limited therapeutic options. Natural killer (NK) cells are innate immune cells with strong anti-tumor activity and may offer a promising treatment strategy for GBM. We compared the anti-GBM activity of NK cells engineered to express interleukin (IL)-15 or IL-21.

Phase II study of talazoparib in advanced cancers with BRCA1/2, DNA repair, and PTEN alterations.

Cancer cells with BRCA1/2 deficiencies are sensitive to poly (ADP-ribose) polymerase (PARP) inhibitors. We evaluated the efficacy of talazoparib in DNA-Damage Repair (DDR)-altered patients. In this phase II trial, patients were enrolled onto one of four cohorts based on molecular alterations: (1) somatic BRCA1/2, (2) other homologous recombination repair pathway, (3) PTEN and (4) germline BRCA1/2.