: a superfast and scalable single-cell RNA-seq data analysis pipeline powered by GPU.

Summary: The rise of large-scale single-cell RNA-seq data has introduced challenges in data processing due to its slow speed. Leveraging advancements in Graphics Processing Unit (GPU) computing ecosystems, such as and Compute Unified Device Architecture (CUDA), building on and package, we developed , a GPU-accelerated solution for large-scale single-cell data processing. delivers over a 20× speedup through GPU computing and significantly improves scalability, handling datasets of 10-20 million cells with over 1000 batches by overcoming the memory bottleneck on a single A100 card, which far surpasses s capacity of processing only 1 million cells without multi-GPU support.

Therapeutic potentials of Trichinella spiralis in immune disorders: From allergy to autoimmunity.

The incidence of immune system diseases is increasing globally, particularly in developed countries. The hygiene and old friend hypotheses suggest that the decreased incidence of helminth infections in these countries may underlie the rising prevalence of autoimmune, allergic, and inflammatory diseases. The preventive and therapeutic potential of Trichinella spiralis, a helminthic parasite, has been well demonstrated in animal models of immune dysregulation-mediated diseases.

xOmicsShiny: an R Shiny application for cross-omics data analysis and pathway mapping.

Summary: We developed xOmicsShiny, a feature-rich R Shiny-powered application that enables biologists to fully explore omics datasets across experiments and data types, with an emphasis on uncovering biological insights at the pathway level. The data merging feature ensures flexible exploration of cross-omics data, such as transcriptomics, proteomics, metabolomics, and lipidomics. The pathway mapping function covers a broad range of databases, including WikiPathways, Reactome, and KEGG pathways.

Comprehensive visceral transcriptome profiling of three pig breeds along altitudinal gradients in Yunnan.

High-altitude hypoxia acclimatization requires comprehensive physiological regulation in highland immigrants, yet the genetic mechanisms remain unclear. Yunnan's vertical zoning with pig breeds distributed across varying elevations provides an excellent model for investigating hypoxic adaptation. Here, we examined three indigenous Yunnan pig breeds: Diannan small-ear pigs (DSE, 500 m), Baoshan pigs (BS, 1500 m), and Diqing Tibetan pigs (DT, 3200 m).

The effect of polygenic risk score on PD risk and phenotype in G2019S and carriers.

BackgroundWhile and variants are associated with Parkinson's disease (PD), most carriers will not develop the disease.ObjectiveTo test if polygenic risk score (PRS) modifies disease risk and phenotypes in G2019S carriers, carriers, and non-carriers (NC).MethodsWe genotyped 786 participants using Illumina's NeuroBooster-array (NBA) and sequenced the genome of 244, all of Ashkenazi ancestry (AJ), and calculated PRS to test its effects on clinically- and biologically-defined disease risk and phenotypes (n = 715).

Paraoxonase-1 Is a Pivotal Regulator Responsible for Suppressing Allergic Airway Inflammation Through Adipose Stem Cell-Derived Extracellular Vesicles.

Although adipose stem cell (ASC)-derived extracellular vesicles (EVs) are as effective as ASCs in the suppression of Th2 cell-mediated eosinophilic inflammation, the role of identified pulmonary genes has not been well documented. Thus, we assessed the immunomodulatory effects of paraoxonase-1 (PON1) on allergic airway inflammation in a mouse model of asthma. Five-week-old female C57BL/6 mice were sensitized to ovalbumin (OVA) by intraperitoneal injection and challenged intranasally with OVA.

Proteome identification of common immunological proteins of two nematode parasites.

Although helminth parasites have different life cycles, their hosts share similar immune responses involving Th2 cell-type. Here, we extracted proteins from the larvae of Anisakis simplex complex and Trichinella spiralis to identify common and specific antigens (or allergens) associated with the Th2 immune response. We performed two-dimensional electrophoresis analysis and Matrix-assisted laser desorption ionization-time of flight/time of flight (MALDI-TOF/TOF) experiments.

Upregulated solute-carrier family genes in the hippocampus of schizophrenia can be rescued by antipsychotic medications.

Background And Hypothesis: Our previous studies have found that functional changes in the hippocampal circuit from dentate gyrus (DG) to cornu ammonis 3 and 1 (CA3, CA1) are highly associated with schizophrenia (SZ). However, no studies have explored the genetic expression across the three and two human hippocampal subfields (DG-CA3-CA1 and CA3-CA1) between subjects with SZ and healthy controls (CT).

Study Design: We matched cohorts between CT (n = 13) and SZ (n = 13).

Host and venom evolution in parasitoid wasps: does independently adapting to the same host shape the evolution of the venom gland transcriptome?

Background: Venoms have repeatedly evolved over 100 occasions throughout the animal tree of life, making them excellent systems for exploring convergent evolutionary novelty. Growing evidence supports that venom evolution is predominantly driven by prey or host-related selection pressures, and the expression patterns of venom glands reflect adaptive evolution. However, it remains elusive whether the evolution of expression patterns in venom glands is likewise a convergent evolution driven by their prey/host species.

Presence and diversity of free-living amoebae and their potential application as water quality indicators.

Free-living amoebae (FLA) are found in diverse environments, such as soils, rivers, and seas. Hence, they can be used as bioindicators to assess the water quality based solely on their presence. In this study, we determined the presence of FLA in river water by filtering water samples collected from various sites and culturing the resulting filtrates.

Anti-Pseudomonal Effect of Nephrite-Impregnated Contact Lenses.

Purpose: This study compared the anti-pseudomonal effects between nephrite-impregnated contact lenses (CLs) and conventional and cosmetic CLs.

Methods: After inoculation with , we counted the number of bacteria on the CL surface and observed each surface using atomic force microscopy (AFM) and scanning electron microscopy (SEM). To estimate potential harm of nephrite-impregnated CLs, we conducted a safety test using a rabbit model, treated with all CL types.

The Recombinant Profilin from Free-Living Amoebae Induced Allergic Immune Responses via TLR2.

Background: Repeated exposure to recombinant profilin from (rAc-PF) induces allergic airway responses in vitro and in vivo. Based on the role of toll-like receptors (TLRs) in allergic airway diseases, TLRs play a central role in innate immune responses and the adaptive immune system and regulate responses against antigens through antigen-specific receptors. In this study, we attempted to determine the molecular mechanisms underlying rAc-PF-induced allergic inflammatory responses.

Risk factors for scabies in hospital: a systematic review.

Background: Annually, 175.4 million people are infected with scabies worldwide. Although parasitic infections are important nosocomial infections, they are unrecognized compared to bacterial, fungal, and viral infections.

Adipose Tissue Macrophage Polarization Is Altered during Recovery after Exercise: A Large-Scale Flow Cytometric Study.

We performed a large-scale flow cytometric analysis to determine whether M1 macrophage (M1Ø) and M2 macrophage (M2Ø) polarization in white adipose tissue (WAT) was altered immediately after exercise. Additionally, we comprehensively investigated the effects of obesity, exercise intensity, and recovery time on macrophage polarization in WAT. A single exercise bout of various intensities (ND, non-exercise control; -LIE, low-intensity exercise; -MIE, mid-intensity exercise; -HIE, high-intensity exercise) was performed by normal mice (ND) and obese mice (HFD).

Anti-obesity effects by parasitic nematode () total lysates.

Background: Obesity is an inducible factor for the cause of chronic diseases and is described by an increase in the size and number of adipocytes that differentiate from precursor cells (preadipocytes). Parasitic helminths are the strongest natural trigger of type 2 immune system, and several studies have showed that helminth infections are inversely correlated with metabolic syndromes.

Methodology/principal Findings: To investigate whether helminth-derived molecules have therapeutic effects on high-fat diet (HFD)-induced obesity, we isolated total lysates from muscle larvae.

Correction: The amoebicidal effect of Torreya nucifera extract on Acanthamoeba lugdunensis.

[This corrects the article DOI: 10.1371/journal.pone.

Long- and short-read RNA sequencing from five reproductive organs of boar.

The production of semen in boars involves multiple reproductive glands, including the testis (Tes), epididymis (Epi), vesicular gland (VG), prostate gland (PG), and bulbourethral gland (BG). However, previous studies on boar reproduction primarily focused on the testis, with little attention paid to the other glands. Here, we integrated single-molecule long-read sequencing with short-read sequencing to characterize the RNA landscape from five glands of Banna mini-pig inbred line (BMI) and Diannan small-ear pigs (DSE).

Comprehensive isoform-level analysis reveals the contribution of alternative isoforms to venom evolution and repertoire diversity.

Animal venom systems have emerged as valuable models for investigating how novel polygenic phenotypes may arise from gene evolution by varying molecular mechanisms. However, a significant portion of venom genes produce alternative mRNA isoforms that have not been extensively characterized, hindering a comprehensive understanding of venom biology. In this study, we present a full-length isoform-level profiling workflow integrating multiple RNA sequencing technologies, allowing us to reconstruct a high-resolution transcriptome landscape of venom genes in the parasitoid wasp Our findings demonstrate that more than half of the venom genes generate multiple isoforms within the venom gland.

Evaluating the activity of N-89 as an oral antimalarial drug.

Despite the recent progress in public health measures, malaria remains a troublesome disease that needs to be eradicated. It is essential to develop new antimalarial medications that are reliable and secure. This report evaluated the pharmacokinetics and antimalarial activity of 1,2,6,7-tetraoxaspiro[7.

Extract of Pericarps Exhibits a Parasiticidal Effect on the Nematode Parasite, .

Benzimidazole derivatives can effectively treat nematode parasitic infections; however, some derivatives demand distinct administrative strategies depending on plasma concentration and patient conditions. Numerous studies have examined the potential of natural extracts to exert parasiticidal activity with minimal side effects. Herein, we examined the potential parasiticidal effects of extract.

A rapidly evolving single copy histone H1 variant is associated with male fertility in a parasitoid wasp.

The linker histone H1 binds to the nucleosome core particle at the site where DNA enters and exits, and facilitates folding of the nucleosomes into a higher-order chromatin structure in eukaryotes. Additionally, some variant H1s promote specialized chromatin functions in cellular processes. Germline-specific H1 variants have been reported in some model species with diverse roles in chromatin structure changes during gametogenesis.

Antimalarial effect of synthetic endoperoxide on synchronized Plasmodium chabaudi infected mice.

The discovery of new antimalarial drugs can be developed using asynchronized Plasmodium berghei malaria parasites in vivo in mice. Studies on a particular stage are also required to assess the effectiveness and mode of action of drugs. In this report, we used endoperoxide 6-(1,2,6,7-tetraoxaspiro [7.

scRNASequest: an ecosystem of scRNA-seq analysis, visualization, and publishing.

Background: Single-cell RNA sequencing is a state-of-the-art technology to understand gene expression in complex tissues. With the growing amount of data being generated, the standardization and automation of data analysis are critical to generating hypotheses and discovering biological insights.

Results: Here, we present scRNASequest, a semi-automated single-cell RNA-seq (scRNA-seq) data analysis workflow which allows (1) preprocessing from raw UMI count data, (2) harmonization by one or multiple methods, (3) reference-dataset-based cell type label transfer and embedding projection, (4) multi-sample, multi-condition single-cell level differential gene expression analysis, and (5) seamless integration with cellxgene VIP for visualization and with CellDepot for data hosting and sharing by generating compatible h5ad files.