The Influence of Embedded Properties on the Liberation Characteristics of Macerals in Subbituminous Coal.

The utilization pathways of coal macerals exhibit a significant variability. The efficient separation of active and inert components in coal is critical for realizing their high value-added applications. The liberation efficiency of coal macerals directly influences the accuracy of subsequent separation processes.

Systemic immune-inflammatory complex index as a novel predictor of sepsis prognosis: a retrospective cohort study using MIMIC-IV.

Purpose: Sepsis is a life-threatening condition with high mortality and morbidity, making its early detection is critical. Current diagnosis relies on the Sequential [sepsis-related] Organ Failure Assessment score, which is complex and time-consuming to determine. Herein, we proposed a novel index, the systemic immune-inflammatory complex index (SIICI), defined as (neutrophil × monocyte count) × 10/(platelet × lymphocyte count), to predict illness severity, and we verified its prognostic value.

Emotion regulation strategies and mental wellbeing among Chinese college students during COVID-19: the moderating roles of confinement and attentional bias.

Background: During COVID-19, confinement measures were implemented to curb the epidemic spread. While effective in reducing infections, these measures likely deteriorated the psychological wellbeing of students due to school closures and isolation.

Methods: This study analyzed 13,109 valid questionnaires from individuals aged 18-24 years (mean 20.

Single-cell transcriptomic and chromatin dynamics of the human brain in PTSD.

Post-traumatic stress disorder (PTSD) is a polygenic disorder occurring after extreme trauma exposure. Recent studies have begun to detail the molecular biology of PTSD. However, given the array of PTSD-perturbed molecular pathways identified so far, it is implausible that a single cell type is responsible.

scMODAL: a general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links.

Recent advancements in single-cell technologies have enabled comprehensive characterization of cellular states through transcriptomic, epigenomic, and proteomic profiling at single-cell resolution. These technologies have significantly deepened our understanding of cell functions and disease mechanisms from various omics perspectives. As these technologies evolve rapidly and data resources expand, there is a growing need for computational methods that can integrate information from different modalities to facilitate joint analysis of single-cell multi-omics data.

Interpretable Differential Abundance Signature (iDAS).

Single-cell technologies have revolutionized the understanding of cellular dynamics by allowing researchers to investigate individual cell responses under various conditions, such as comparing diseased versus healthy states. Many differential abundance methods have been developed in this field, however, the understanding of the gene signatures obtained from those methods is often incomplete, requiring the integration of cell type information and other biological factors to yield interpretable and meaningful results. To better interpret the gene signatures generated in the differential abundance analysis, iDAS is developed to classify the gene signatures into multiple categories.

Stress hyperglycemia ratio as a predictor of acute kidney injury and its outcomes in critically ill patients.

This study investigated stress hyperglycemia ratio (SHR) for acute kidney injury (AKI) and clinical outcomes in intensive care unit (ICU). Key outcomes were AKI within 48 h after ICU admission, acute kidney disease (AKD), ICU mortality, 28-day mortality, 90-day mortality and 1-year mortality. The associations between SHR and outcomes was estimated logistic regression, Cox proportional hazards regression, and restricted cubic spline (RCS) analyses.

VISTA Uncovers Missing Gene Expression and Spatial-induced Information for Spatial Transcriptomic Data Analysis.

Characterizing cell activities within a spatially resolved context is essential to enhance our understanding of spatially-induced cellular states and features. While single-cell RNA-seq (scRNA-seq) offers comprehensive profiling of cells within a tissue, it fails to capture spatial context. Conversely, subcellular spatial transcriptomics (SST) technologies provide high-resolution spatial profiles of gene expression, yet their utility is constrained by the limited number of genes they can simultaneously profile.

A CD26 tendon stem progenitor cell population contributes to tendon repair and heterotopic ossification.

Inadequate tendon healing and heterotopic bone formation result in substantial pain and disability, yet the specific cells responsible for tendon healing remain uncertain. Here we identify a CD26 tendon stem/progenitor cells residing in peritendon, which constitutes a primitive stem cell population with self-renewal and multipotent differentiation potentials. CD26 tendon stem/progenitor cells migrate into the tendon midsubstance and differentiation into tenocytes during tendon healing, while ablation of these cells led to insufficient tendon healing.

Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels.

Summary: With the recent advancement in single-cell RNA-sequencing technologies and the increased availability of integrative tools, challenges arise in easy and fast access to large collections of cell atlas. Existing cell atlas portals rarely are open sourced and adaptable, and do not support meta-analysis at cell level. Here, we present an open source, highly optimized and scalable architecture, named Scope+, to allow quick access, meta-analysis and cell-level selection of the atlas data.

Genetically defined causal effects of natural killer cells related traits in risk of infection: a Mendelian randomization study.

Background: The intricate interplay between genetics and immunology often dictates the host's susceptibility to various diseases. This study explored the genetic causal relationship between natural killer (NK) cell-related traits and the risk of infection.

Methods: Single-nucleotide polymorphisms (SNPs) significantly associated with NK cell-related traits were selected as instrumental variables to estimate their genetic causal effects on infection.

Leveraging single-cell RNA-seq for uncovering naïve B cells associated with better prognosis of hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is a typical highly heterogeneous solid tumor with high morbidity and mortality worldwide, especially in China; however, the immune microenvironment of HCC has not been clarified so far. Here, we employed single-cell RNA sequencing (scRNA-seq) on diethylnitrosamine (DEN)-induced mouse HCC model to dissect the immune cell dynamics during tumorigenesis. Our findings reveal distinct immune profiles in both precancerous and cancerous lesions, indicating early tumor-associated immunological alterations.

Single-cell RNA sequencing reveals melanoma cell state-dependent heterogeneity of response to MAPK inhibitors.

Background: Melanoma is a heterogeneous cancer influenced by the plasticity of melanoma cells and their dynamic adaptations to microenvironmental cues. Melanoma cells transition between well-defined transcriptional cell states that impact treatment response and resistance.

Methods: In this study, we applied single-cell RNA sequencing to interrogate the molecular features of immunotherapy-naive and immunotherapy-resistant melanoma tumours in response to ex vivo BRAF/MEK inhibitor treatment.

Spatial dynamics of mammalian brain development and neuroinflammation by multimodal tri-omics mapping.

The ability to spatially map multiple layers of the omics information over different time points allows for exploring the mechanisms driving brain development, differentiation, arealization, and alterations in disease. Herein we developed and applied spatial tri-omic sequencing technologies, DBiT ARP-seq (spatial ATAC-RNA-Protein-seq) and DBiT CTRP-seq (spatial CUT&Tag-RNA-Protein-seq) together with multiplexed immunofluorescence imaging (CODEX) to map spatial dynamic remodeling in brain development and neuroinflammation. A spatiotemporal tri-omic atlas of the mouse brain was obtained at different stages from postnatal day P0 to P21, and compared to the regions of interest in the human developing brains.

Spatial dynamics of mammalian brain development and neuroinflammation by multimodal tri-omics mapping.

The ability to spatially map multiple layers of the omics information over different time points allows for exploring the mechanisms driving brain development, differentiation, arealization, and alterations in disease. Herein we developed and applied spatial tri-omic sequencing technologies, DBiT ARP-seq (spatial ATAC-RNA-Protein-seq) and DBiT CTRP-seq (spatial CUT&Tag-RNA-Protein-seq) together with multiplexed immunofluorescence imaging (CODEX) to map spatial dynamic remodeling in brain development and neuroinflammation. A spatiotemporal tri-omic atlas of the mouse brain was obtained at different stages from postnatal day P0 to P21, and compared to the regions of interest in the human developing brains.

SANTO: a coarse-to-fine alignment and stitching method for spatial omics.

With the flourishing of spatial omics technologies, alignment and stitching of slices becomes indispensable to decipher a holistic view of 3D molecular profile. However, existing alignment and stitching methods are unpractical to process large-scale and image-based spatial omics dataset due to extreme time consumption and unsatisfactory accuracy. Here we propose SANTO, a coarse-to-fine method targeting alignment and stitching tasks for spatial omics.

Antecedent Cardiac Arrest Status of Donation After Circulatory Determination of Death (DCDD) Kidney Donors and the Risk of Delayed Graft Function After Kidney Transplantation: A Cohort Study.

Background: The number of donors from donation after circulatory determination of death (DCDD) has increased by at least 4-fold over the past decade. This study evaluated the association between the antecedent cardiac arrest status of controlled DCDD donors and the risk of delayed graft function (DGF).

Methods: Using data from the Australia and New Zealand Dialysis and Transplant, the associations between antecedent cardiac arrest status of DCDD donors before withdrawal of cardiorespiratory support, DGF, posttransplant estimated glomerular filtration rate (eGFR), and allograft loss were examined using adjusted logistic, linear mixed modeling, and cox regression, respectively.

Prediction of acute kidney injury after cardiac surgery with fibrinogen-to-albumin ratio: a prospective observational study.

Background: The occurrence of acute kidney injury (AKI) following cardiac surgery is common and linked to unfavorable consequences while identifying it in its early stages remains a challenge. The aim of this research was to examine whether the fibrinogen-to-albumin ratio (FAR), an innovative inflammation-related risk indicator, has the ability to predict the development of AKI in individuals after cardiac surgery.

Methods: Patients who underwent cardiac surgery from February 2023 to March 2023 and were admitted to the Cardiac Surgery Intensive Care Unit of a tertiary teaching hospital were included in this prospective observational study.

Thinking process templates for constructing data stories with SCDNEY.

Background: Globally, scientists now have the ability to generate a vast amount of high throughput biomedical data that carry critical information for important clinical and public health applications. This data revolution in biology is now creating a plethora of new single-cell datasets. Concurrently, there have been significant methodological advances in single-cell research.

Severe Jarisch-Herxheimer Reaction (JHR) in a leptospirosis patient: A case report.

Leptospirosis is a zoonosis that is related to potential respiratory, renal, neurological, and cardiovascular failure. At present, antibiotics are the recommended treatment, but due to the underlying cause of the disease, they may induce the Jarisch-Herxheimer reaction (JHR) within 24 hours. At the same time, we speculate that JHR may aggravate the natural course of leptospirosis.

BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data.

Recent advances in subcellular imaging transcriptomics platforms have enabled high-resolution spatial mapping of gene expression, while also introducing significant analytical challenges in accurately identifying cells and assigning transcripts. Existing methods grapple with cell segmentation, frequently leading to fragmented cells or oversized cells that capture contaminated expression. To this end, we present BIDCell, a self-supervised deep learning-based framework with biologically-informed loss functions that learn relationships between spatially resolved gene expression and cell morphology.

Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE.

Single-cell technologies offer unprecedented opportunities to dissect gene regulatory mechanisms in context-specific ways. Although there are computational methods for extracting gene regulatory relationships from scRNA-seq and scATAC-seq data, the data integration problem, essential for accurate cell type identification, has been mostly treated as a standalone challenge. Here we present scTIE, a unified method that integrates temporal multimodal data and infers regulatory relationships predictive of cellular state changes.

Differential developmental blueprints of organ-intrinsic nervous systems.

The organ-intrinsic nervous system is a major interface between visceral organs and the brain, mediating important sensory and regulatory functions in the body-brain axis and serving as critical local processors for organ homeostasis. Molecularly, anatomically, and functionally, organ-intrinsic neurons are highly specialized for their host organs. However, the underlying mechanism that drives this specialization is largely unknown.

mediates olfactory sensory neuron coalescence during postnatal stages and regeneration.

The mouse olfactory system regenerates constantly throughout life. While genes critical for the initial projection of olfactory sensory neurons (OSNs) to the olfactory bulb have been identified, what genes are important for maintaining the olfactory map during regeneration are still unknown. Here we show a mutation in (), a cell adhesion molecule and member of the cadherin superfamily, leads to defects in OSN coalescence during regeneration.