The Change Rate of the Gene and the Amino Acid Composition of Its Protein Correlate with the Species-Specific Lifespan in Placental Mammals.

This article proposes a methodology for establishing a relationship between the change rate of a given gene (relative to a given taxon) together with the amino acid composition of the proteins encoded by this gene and the traits of the species containing this gene. The methodology is illustrated based on the mammalian genes responsible for regulating the circadian rhythms that underlie a number of human disorders, particularly those associated with aging. The methods used are statistical and bioinformatic ones.

Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster.

Accuracy and efficiency are fundamental to mRNA translation. Codon usage bias is widespread across species. Despite the long-standing association between optimized codon usage and improved translation, our understanding of its evolutionary basis and functional effects remains limited.

Assessment of the reversibility of resistance in the absence of antibiotics and its relationship with the resistance gene's fitness cost: a genetic study with mcr-1.

Background: The intensive use of antibiotics has resulted in strong natural selection for the evolution of antimicrobial resistance (AMR), but whether, and under what circumstances, the removal of antibiotics would result in a rapid reduction in AMR has been insufficiently explored. We aimed to test the hypothesis that in the simple, yet common, case of AMR conferred by a single gene, removing antibiotics would quickly reduce the prevalence of resistance if the AMR gene imposes a high fitness cost and costless resistance is extremely rare among its proximal mutants.

Methods: In this genetic study, to test our hypothesis, we used the mcr-1 gene in Escherichia coli, which confers resistance to the last-resort antibiotic colistin, as a model.

A Prediction Model for Clinical Outcomes of COVID-19 Hospitalized Patients: Construction and Accuracy Assessment.

Background: The coronavirus disease 2019 (COVID-19) pandemic spread rapidly with considerable morbidity nationwide since China's liberalization in December 2022. Our work has focused on identifying different predictive factors from the laboratory examination of critically ill patients, and forecasting the unfavorable outcome of critically ill patients with COVID-19 through a combined diagnosis of biological markers.

Methods: We conducted a retrospective study at the Department of First Affiliated Hospital of Wenzhou Medical University, China, from December 24, 2022, to January 10, 2023, where 434 critically ill patients who met the inclusion criteria were involved.

SIVA-1 enhances acquired chemotherapeutic drug resistance of gastric cancer in vivo by regulating the ARF/MDM2/p53 pathway.

SIVA-1 has been shown to affect apoptotic processes in various different cell lines, and SIVA-1 significantly contributes to the decreased responsiveness of cancer cells to some chemotherapy agents. However, whether SIVA-1 has potential application in gastric cancer remains unknown. Therefore, the objective of this investigation was to clarify the distinct function of SIVA-1 in chemotherapeutic drug resistance within a living murine model with gastric malignancy, and initially elucidate the underlying mechanisms.

Results of the inoperable and operable with aortic valve endocarditis.

Objectives: To evaluate the results of the inoperable and operable with aortic valve endocarditis, focus on risk factors, significance, and management of destruction of the aortic annulus in aortic valve endocarditis.

Methods: The retrospective study was completed to investigate patients with aortic valve endocarditis undergoing cardiac surgery between January 2006 and November 2022 at our hospital.

Results: 512 patients were divided into group with destruction of the aortic annulus ( = 80) and without destruction of the aortic annulus ( = 432).

Risk factors of prolonged intensive care unit stay following cardiac surgery for infective endocarditis.

Introduction: Prolonged intensive care unit (ICU) stay is common in serious patients undergoing cardiac surgery. Prolonged ICU stay is associated with increased mortality and worse prognosis. This study was conducted to determine the risk factors for prolonged ICU stay after cardiac surgery for infective endocarditis (IE) and we try to decrease the operative risk of mortality and morbidity of cardiac surgery for IE.

Surgical treatment of left-sided infective endocarditis with symptomatic neurological complications before surgery in China.

Introduction: We aimed to investigate surgical treatment of left-sided infective endocarditis with symptomatic neurological complications before surgery.

Methods: This was a retrospective study of patients with left-sided infective endocarditis and symptomatic neurological complications before surgery undergoing cardiac surgery between January 2006 and November 2022 at our hospital.

Results: Eight hundred thirty-two patients were divided into group with symptomatic neurological complications before surgery ( = 112) and without symptomatic neurological complications before surgery ( = 720).

Genome-wide probing of eukaryotic nascent RNA structure elucidates cotranscriptional folding and its antimutagenic effect.

The transcriptional intermediates of RNAs fold into secondary structures with multiple regulatory roles, yet the details of such cotranscriptional RNA folding are largely unresolved in eukaryotes. Here, we present eSPET-seq (Structural Probing of Elongating Transcripts in eukaryotes), a method to assess the cotranscriptional RNA folding in Saccharomyces cerevisiae. Our study reveals pervasive structural transitions during cotranscriptional folding and overall structural similarities between nascent and mature RNAs.

Single-cell immune profiling of mouse liver aging reveals Cxcl2+ macrophages recruit neutrophils to aggravate liver injury.

Background And Aims: Immune cells play a crucial role in liver aging. However, the impact of dynamic changes in the local immune microenvironment on age-related liver injury remains poorly understood. We aimed to characterize intrahepatic immune cells at different ages to investigate key mechanisms associated with liver aging.

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations.

Background: It is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid contents of proteins. Recently, evidence has accumulated that significant evolutionary transformations could also be associated with the loss/emergence of whole genes. The targeted identification of such genes is a challenging problem for both bioinformatics and evo-devo research.

Impact of Vegetation Length on Clinical Complications During Surgical Intervention and Long-Term Survival in Infective Endocarditis.

We aimed to investigate the impact of vegetation length on clinical complications during surgical intervention and long-term survival in infective endocarditis. This was a retrospective study of patients with infective endocarditis who underwent cardiac surgery between January 2006 and November 2022 at our hospital. 896 patients were divided into 2 groups: group I (vegetation length <10 mm, n = 448) and group II (vegetation length ≥10 mm, n = 448).

Reconstructing cell lineage trees with genomic barcoding: approaches and applications.

In multicellular organisms, developmental history of cell divisions and functional annotation of terminal cells can be organized into a cell lineage tree (CLT). The reconstruction of the CLT has long been a major goal in developmental biology and other related fields. Recent technological advancements, especially those in editable genomic barcodes and single-cell high-throughput sequencing, have sparked a new wave of experimental methods for reconstructing CLTs.

Single-cell transcriptomics reveals heterogeneity and intercellular crosstalk in human intervertebral disc degeneration.

The complexity of the human intervertebral disc (IVD) has hindered the elucidation of the microenvironment and mechanisms underlying IVD degeneration (IVDD). Here we determined the landscapes of nucleus pulposus (NP), annulus fibrosus (AF), and immunocytes in human IVD by scRNA-seq. Six NP subclusters and seven AF subclusters were identified, whose functional differences and distribution during different stages of degeneration (Pfirrmann I-V) were investigated.

Phylogenetic Comparative Analysis of Single-Cell Transcriptomes Reveals Constrained Accumulation of Gene Expression Heterogeneity during Clonal Expansion.

In the same way that a phylogeny summarizes the evolutionary history of species, a cell lineage tree describes the process of clonal expansion, in which gene expression differences between cells naturally accrue as a result of stochastic partitioning and imperfect expression control. How is functional homeostasis, a key factor in the biological function of any population of cells, maintained in the face of such continuous accumulation of transcriptomic heterogeneity remains largely unresolved. To answer this question, we experimentally determined the single-cell transcriptomes and lineage relationships of up to 50% cells in single-HEK293-seeded colonies.

Risk factors of non-sentinel lymph node metastasis in breast cancer with 1-2 sentinel lymph node macrometastases underwent total mastectomy: a case-control study.

Background: The randomized trials which include ACOSOG Z0011 and IBCSG 23-01 had found that the survival rates were not different in patients with cT1/2N0 and 1-2 sentinel lymph node (SLN)-positive, macro/micrometastases who underwent breast-conserving therapy, and micrometastases who underwent total mastectomy (TM), when axillary lymph node dissection (ALND) was omitted. However, for patients with cT1/2N0 and 1-2 SLN macrometastases who underwent TM; there was still insufficient evidence from clinical studies to support whether ALND can be exempted. This study aimed to investigate the risk factors of non-sentinel lymph node (nSLN) metastasis in breast cancer patients with 1-2 SLN macrometastases undergoing TM.

Comprehensive landscape of the IPAF inflammasomes in pan-cancer: A bulk omics research and single-cell sequencing validation.

Background: IPAF (ICE-protease Activating Factor) is a nucleotide-binding/leucine-rich repeat (NLR) protein known as the cysteine-associated recruitment domain 12 (CARD12). Previous studies only discuss the role of IPAF inflammasomes in specific tumors. The role of IPAF inflammasomes in pan-cancer is still unclear.

Incomplete Pericardial Dissection, Fluid Overload, Delayed Diagnosis And Treatment, And Tuberculosis Pericarditis Are Associated With Low Cardiac Output Syndrome Following Pericardiectomy.

Background: We aimed to investigate risk factors of LCOS following pericardiectomy.

Methods: This was a retrospective study of patients undergoing pericardiectomy at three hospitals between January 1994 and May 2021.

Results: A total of 826 patients were divided into two groups: group with LCOS (N = 126) and group without LCOS (N = 700).

Lack of evolutionary convergence in multiple primary lung cancer suggests insufficient specificity of personalized therapy.

Multiple primary lung cancer (MPLC) is an increasingly prevalent subtype of lung cancer. According to recent genomic studies, the different lesions of a single MPLC patient exhibit functional similarities that may reflect evolutionary convergence. We perform whole-exome sequencing for a unique cohort of MPLC patients with multiple samples from each lesion found.

Analysis of risk factors of multiorgan failure after pericardiectomy for constrictive pericarditis.

Background: We aimed to investigate risk factors of multiorgan failure following pericardiectomy.

Methods: This was a retrospective study of patients undergoing pericardiectomy between January 1994 and May 2021 at three hospitals.

Results: 826 patients were included in the study and divided into two groups: group with multiorgan failure (n = 86) and group without multiorgan failure (n = 740).

Rectal nonsteroidal anti-inflammatory drugs, glyceryl trinitrate, or combinations for prophylaxis of post-endoscopic retrograde cholangiopancreatography pancreatitis: A network meta-analysis.

Background: Acute pancreatitis is the most common and severe complication of endoscopic retrograde cholangiopancreatography (ERCP). Recent evidence suggests that combinations based on rectal nonsteroidal anti-inflammatory drugs (NSAIDs) are more beneficial in preventing post-ERCP pancreatitis (PEP). Randomized controlled trials (RCTs) have also demonstrated the efficacy of glyceryl trinitrate (GTN).

Prediction of Antibiotic Resistance Evolution by Growth Measurement of All Proximal Mutants of Beta-Lactamase.

The antibiotic resistance crisis continues to threaten human health. Better predictions of the evolution of antibiotic resistance genes could contribute to the design of more sustainable treatment strategies. However, comprehensive prediction of antibiotic resistance gene evolution via laboratory approaches remains challenging.

Analysis of Risk Factors of Early Mortality After Pericardiectomy For Constrictive Pericarditis.

Background: We aimed to investigate risk factors of early mortality following pericardiectomy.

Methods: This was a retrospective study of patients undergoing pericardiectomy between January 1994 and May 2021 at The People's Hospital of Guangxi Zhuang Autonomous Region, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, and The People's Hospital of Liuzhou City.

Results: This study included 826 patients, who were divided into two groups: group with operative deaths (N = 66) and group without operative deaths (N = 760).

Distinct codon usage bias evolutionary patterns between weakly and strongly virulent respiratory viruses.

Human respiratory viruses are of vastly different virulence, giving rise to symptoms ranging from common cold to severe pneumonia or even death. Although this most likely impacts molecular evolution of the corresponding viruses, the specific differences in their evolutionary patterns remain largely unknown. By comparing structural and nonstructural genes within respiratory viruses, greater similarities in codon usage bias (CUB) between nonstructural genes and humans were observed in weakly virulent viruses, whereas in strongly virulent viruses, it was structural genes whose CUBs were more similar to that of humans.