Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these data to address challenges in transcript isoform detection, quantification and de novo transcript detection. The study revealed that libraries with longer, more accurate sequences produce more accurate transcripts than those with increased read depth, whereas greater read depth improved quantification accuracy. In well-annotated genomes, tools based on reference sequences demonstrated the best performance. Incorporating additional orthogonal data and replicate samples is advised when aiming to detect rare and novel transcripts or using reference-free approaches. This collaborative study offers a benchmark for current practices and provides direction for future method development in transcriptome analysis.

Flexiplex: a versatile demultiplexer and search tool for omics data.

MOTIVATION: The process of analyzing high throughput sequencing data often requires the identification and extraction of specific target sequences. This could include tasks, such as identifying cellular barcodes and UMIs in single-cell data, and specific genetic variants for genotyping. However, existing tools, which perform these functions are often task-specific, such as only demultiplexing barcodes for a dedicated type of experiment, or are not tolerant to noise in the sequencing data. RESULTS: To overcome these limitations, we developed Flexiplex, a versatile and fast sequence searching and demultiplexing tool for omics data, which is based on the Levenshtein distance and thus allows imperfect matches. We demonstrate Flexiplex's application on three use cases, identifying cell-line-specific sequences in Illumina short-read single-cell data, and discovering and demultiplexing cellular barcodes from noisy long-read single-cell RNA-seq data. We show that Flexiplex achieves an excellent balance of accuracy and computational efficiency compared to leading task-specific tools. AVAILABILITY AND IMPLEMENTATION: Flexiplex is available at https://davidsongroup.github.io/flexiplex/.

High-Entropy Fluorite Oxide-Modified CaO-Based Sorbent Pellets for Enhanced High-Temperature CO2 Capture.

The calcium looping technology employing CaO-based sorbents is pivotal for capturing CO2 from flue gas. However, the intrinsic low thermodynamic stability of CaO-based sorbents and the requisite molding step induce severe sintering issues, diminishing their cyclic stability. Herein, a high-entropy fluorite oxide (HEFO) inert stabilizer premised on entropy stabilization and synergistic effect strategies is introduced. HEFO-modified, CaO-based sorbent pellets are synthesized via a rapid cigarette butt-assisted combustion process (15 min) combined with the graphite molding method. Post-multiple cycles, their CO2 capture capacity reaches 0.373 g g-1, which is 2.6-fold superior to that of pure CaO, demonstrating markedly enhanced anti-sintering properties. First, the subtle morphological and crystallographic modifications suggest that the inherent entropy stability of HEFO imparts robust thermal resistance. Concurrently, the disordered structure of single-phase HEFO exhibits a high affinity for CaO, resulting in an interface binding energy of -1.83 eV, in sharp contrast to the -0.112 eV of pure CaO, thereby restricting CaO migration. Additionally, the multi-element synergistic effect of HEFO reduces the energy barrier by 0.15 eV, leading to a 40% and 140% increase in carbonation and calcination rates, respectively. This work presents highly efficient and rapidly synthesized CaO-based sorbent pellets, showcasing promising potential for industrial application.

Effect of particle size on liver MRI R 2 * relaxometry: Monte Carlo simulation and phantom studies.

PURPOSE: To investigate the effect of particle size on liver R 2 * $$ {\mathrm{R}}_2^{\ast } $$ by Monte Carlo simulation and phantom studies at both 1.5 T and 3.0 T. METHODS: Two kinds of particles (i.e., iron sphere and fat droplet) with varying sizes were considered separately in simulation and phantom studies. MRI signals were synthesized and analyzed for predicting R 2 * $$ {\mathrm{R}}_2^{\ast } $$ , based on simulations by incorporating virtual liver model, particle distribution, magnetic field generation, and proton movement into phase accrual. In the phantom study, iron-water and fat-water phantoms were constructed, and each phantom contained 15 separate vials with combinations of five particle concentrations and three particle sizes. R 2 * $$ {\mathrm{R}}_2^{\ast } $$ measurements in the phantom were made at both 1.5 T and 3.0 T. Finally, differences in R 2 * $$ {\mathrm{R}}_2^{\ast } $$ predictions or measurements were evaluated across varying particle sizes. RESULTS: In the simulation study, strong linear and positively correlated relationships were observed between R 2 * $$ {\mathrm{R}}_2^{\ast } $$ predictions and particle concentrations across varying particle sizes and magnetic field strengths ( r ≥ 0.988 $$ r\ge 0.988 $$ ). The relationships were affected by iron sphere size ( p < 0.001 $$ p<0.001 $$ ), where smaller iron sphere size yielded higher predicted R 2 * $$ {\mathrm{R}}_2^{\ast } $$ , whereas fat droplet size had no effect on R 2 * $$ {\mathrm{R}}_2^{\ast } $$ predictions ( p ≥ 0.617 $$ p\ge 0.617 $$ ) for constant total fat concentration. Similarly, the phantom study showed that R 2 * $$ {\mathrm{R}}_2^{\ast } $$ measurements were relatively sensitive to iron sphere size ( p ≤ 0.004 $$ p\le 0.004 $$ ) unlike fat droplet size ( p ≥ 0.223 $$ p\ge 0.223 $$ ). CONCLUSION: Liver R 2 * $$ {\mathrm{R}}_2^{\ast } $$ is affected by iron sphere size, but is relatively unaffected by fat droplet size. These findings may lead to an improved understanding of the underlying mechanisms of R 2 * $$ {\mathrm{R}}_2^{\ast } $$ relaxometry in vivo, and enable improved quantitative MRI phantom design.

Inhibition of inflammation and apoptosis through the cyclic GMP-AMP synthase-stimulator of interferon genes pathway by stress granules after ALKBH5 demethylase activation during diabetic myocardial ischaemia-reperfusion injury.

AIM: Post-transcriptional modifications and their specific mechanisms are the focus of research on the regulation of myocardial damage. Stress granules (SGs) can inhibit the inflammatory response by inhibiting the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway. This study investigated whether alkylation repair homologue protein 5 (ALKBH5) could affect myocardial inflammation and apoptosis during diabetic myocardial ischaemia-reperfusion injury (IRI) through the cGAS-STING pathway via SGs. METHODS: A diabetes ischaemia-reperfusion rat model and a high glucose hypoxia/reoxygenation cell model were established. Adeno-associated virus (AAV) and lentivirus (LV) were used to overexpress ALKBH5, while the SG agonist arsenite (Ars) and the SG inhibitor anisomycin were used as interventions. Then, the levels of apoptosis and related indicators in the cell and rat models were measured. RESULTS: In the in vivo experiment, compared with the normal sham group, the degree of myocardial tissue damage, creatine kinase-MB and cardiac troponin I in serum, and myocardial apoptosis, the infarcted area of myocardium, and the level of B-cell lymphoma 2 associated X protein, cGAS-STING pathway and inflammatory factors in the diabetes ischaemia-reperfusion group were significantly increased. However, the expression of SGs and the levels of ALKBH5, rat sarcoma-GTPase-activating protein-binding protein 1, T-cell intracellular antigen-1 and Bcl2 were significantly decreased. After AAV-ALKBH5 intervention, the degree of myocardial tissue damage, degree of myocardial apoptosis, and extent of myocardial infarction in myocardial tissue were significantly decreased. In the in vitro experiment, compared with those in the normal control group, the levels of lactate dehydrogenase, inflammation and apoptosis were significantly greater, and cell viability and the levels of ALKBH5 and SGs were decreased in the high glucose and hypoxia/reoxygenation groups. In the high glucose hypoxia/reoxygenation cell model, the degree of cell damage, inflammation, and apoptosis was greater than those in the high glucose and hypoxia/reoxygenation models, and the levels of ALKBH5 and SGs were further decreased. LV-ALKBH5 and Ars alleviated the degree of cell damage and inhibited inflammation and cell apoptosis. The inhibition of SGs could partly reverse the protective effect of LV-ALKBH5. The cGAS agonist G140 antagonized the inhibitory effects of the SG agonist Ars on cardiomyocyte apoptosis, inflammation and the cGAS-STING pathway. CONCLUSION: Both ALKBH5 and SGs inhibited myocardial inflammation and apoptosis during diabetic myocardial ischaemia-reperfusion. Mechanistically, ALKBH5 might inhibit the apoptosis of cardiomyocytes by promoting the expression of SGs through the cGAS-STING pathway.

Clinical value and mechanistic analysis of HIIT on modulating risk and symptoms of depression: A systematic review.

Background: The exact causal mechanisms of depression remain unclear due to the complexity of the triggers, which has led to limitations in treating depression using modern drugs. High-intensity interval training (HIIT) is as effective as medication in treating depression without toxic side effects. Typically, HIIT requires less time commitment (i.e., shorter exercise duration) and exhibits pronounced benefits on depressive symptoms than other forms of physical exercise. This review summarizes the risk reduction and clinical effects of HIIT for depression and discusses the underlying mechanisms, providing a theoretical basis for utilizing HIIT in treating depression. Methods: A database search was conducted in PubMed, Embase, Web of Science, and Scopus from inception up to October 2022. The methodological quality of the included literature was evaluated by the physiotherapy evidence database (PEDro) scale criteria. The review focused on evaluating the changes in depression risk or symptoms of HIIT interventions in healthy individuals, patients with depression, and patients with other disorders co-morbid with depression. Consequently, the mechanisms associated with depression related HIIT were summarized. Results: A total of 586 participants (52 % female; mean age: 43.58±8.93 years) from 22 studies were included. Implementing HIIT using different exercise types alleviates depressive symptoms in individuals with depression and in individuals with depression who have exhibited comorbidities and reduced depression scale scores in subjects immediately after acute exercise. In addition, the long-interval HIIT and short-interval HIIT in the treatment of patients with cardiovascular or psychiatric disorders may reduce depressive symptoms via complex exercise-related changes on several levels, including by effecting the following measures: releasing monoamines, reducing neuronal death, inducing neurogenesis, modulating the functional homeostasis of the HPA axis, and enhancing the level of inflammation in the body. Conclusion: HIIT is a relatively safe and effective antidepressant, which may involve multiple neurobiological mechanisms (release of monoamines, reducing neuronal death, inducing neurogenesis, modulating the functional homeostasis of the HPA axis, and enhancing the level of inflammation in the body), thereby reducing the risk or symptoms of depression in participants.

The development of the neurocritical care specialty in China based on the analysis of neurocritical care unit volume and quality.

PURPOSE: Through three neurocritical care unit (NCCU) surveys in China, we tried to understand the development status of neurocritical care and clarify its future development. METHODS: Using a cross-sectional survey method and self-report questionnaires, the number and quality of NCCUs were investigated through three steps: administering the questionnaire, sorting the survey data, and analyzing the survey data. RESULTS: At the second and third surveys, the number of NCCUs (76/112/206) increased by 47% and 84%, respectively. The NCCUs were located in tertiary grade A hospitals or teaching hospitals (65/100/181) in most provinces (24/28/29). The numbers of full-time doctors (359/668/1337) and full-time nurses (904/1623/207) in the NCCUs increased, but the doctor-bed ratio and nurse-bed ratio were still insufficient (0.4:1 and 1.3:1). CONCLUSION: In the past 20 years, the growth rate of NCCUs in China has accelerated, while the allocation of medical staff has been insufficient. Although most NCCU hospital bed facilities and instruments and equipment tend to be adequate, there are obvious defects in some aspects of NCCUs.

Clinical value and mechanistic analysis of HIIT on modulating risk and symptoms of depression: A systematic review / Valor clínico y análisis mecanicista del HIIT sobre la modulación del riesgo y los síntomas de la depresión: una revisión sistemática

Background: The exact causal mechanisms of depression remain unclear due to the complexity of the triggers, which has led to limitations in treating depression using modern drugs. High-intensity interval training (HIIT) is as effective as medication in treating depression without toxic side effects. Typically, HIIT requires less time commitment (i.e., shorter exercise duration) and exhibits pronounced benefits on depressive symptoms than other forms of physical exercise. This review summarizes the risk reduction and clinical effects of HIIT for depression and discusses the underlying mechanisms, providing a theoretical basis for utilizing HIIT in treating depression. Methods: A database search was conducted in PubMed, Embase, Web of Science, and Scopus from inception up to October 2022. The methodological quality of the included literature was evaluated by the physiotherapy evidence database (PEDro) scale criteria. The review focused on evaluating the changes in depression risk or symptoms of HIIT interventions in healthy individuals, patients with depression, and patients with other disorders co-morbid with depression. Consequently, the mechanisms associated with depression related HIIT were summarized. Results: A total of 586 participants (52 % female; mean age: 43.58±8.93 years) from 22 studies were included. Implementing HIIT using different exercise types alleviates depressive symptoms in individuals with depression and in individuals with depression who have exhibited comorbidities and reduced depression scale scores in subjects immediately after acute exercise. In addition, the long-interval HIIT and short-interval HIIT in the treatment of patients with cardiovascular or psychiatric disorders may reduce depressive symptoms via complex exercise-related changes on several levels, including by effecting the following measures: releasing monoamines, reducing neuronal death, inducing neurogenesis, modulating the functional...(AU)