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1.
Rheumatol Int ; 2024 Aug 13.
Article in English | MEDLINE | ID: mdl-39136786

ABSTRACT

Magnetic resonance imaging (MRI) is increasingly used in the classification and evaluation of osteoarthritis (OA). Many studies have focused on knee OA, investigating the association between MRI-detected knee structural abnormalities and knee pain. Hip OA differs from knee OA in many aspects, but little is known about the role of hip structural abnormalities in hip pain. This study aimed to systematically evaluate the association of hip abnormalities on MRI, such as cartilage defects, bone marrow lesions (BMLs), osteophytes, paralabral cysts, effusion-synovitis, and subchondral cysts, with hip pain. We searched electronic databases from inception to February 2024, to identify publications that reported data on the association between MRI features in the hip joint and hip pain. The quality of the included studies was scored using the Newcastle-Ottawa Scale (NOS). The levels of evidence were evaluated according to the Cochrane Back Review Group Method Guidelines and classified into five levels: strong, moderate, limited, conflicting, and no evidence. A total of nine studies were included, comprising five cohort studies, three cross-sectional studies, and one case-control study. Moderate level of evidence suggested a positive association of the presence and change of BMLs with the severity and progress of hip pain, and evidence for the associations between other MRI features and hip pain were limited or even conflicting. Only a few studies with small to modest sample sizes evaluated the association between hip structural changes on MRI and hip pain. BMLs may contribute to the severity and progression of hip pain. Further studies are warranted to uncover the role of hip MRI abnormalities in hip pain. The protocol for the systematic review was registered with PROSPERO ( https://www.crd.york.ac.uk/PROSPERO/ , CRD42023401233).

2.
Placenta ; 155: 32-41, 2024 Jul 29.
Article in English | MEDLINE | ID: mdl-39121585

ABSTRACT

INTRODUCTION: Preeclampsia is a pregnancy-specific disorder characterized by de novo development of hypertension and proteinuria over 20 weeks gestation that has been associated with the dysfunction of trophoblasts. Current evidence suggests that syncytin-1 plays an important role in the non-fusogenic biological activity of trophoblasts, except for specific fusogenic function. However, the underlying mechanism remains unclear. METHODS: The expression and location of syncytin-1 in normal and the late-onset preeclampsia placentas were detected by quantitative real-time PCR, western blotting and immunofluorescence. Morphological and apoptosis analysis were processed in placentas. The ex vivo extravillous explant culture model was used to explore the effect of syncytin-1 on EVT outgrowths. Real-time quantitative PCR and immunoblotting were used to calculate syncytin-1 levels in the trophoblast cells before and after syncytin-1 knockdown or overexpression. CCK-8 assay was used to detect the cell viability. TUNEL staining and immunoblotting were processed in trophoblast cells. Transwell assays and wound healing assays were utilize to assess the invasion and migration of trophoblastic cells. Conditional knockout of syncytin-a mouse model was conducted to present the change of placentas in vivo. The ex vivo extravillous explant culture model was used to explore the effect of syncytin-1 on EVT outgrowths. Western blotting was used to identify the key proteins of PI3K/Akt pathways and invasion-related proteins in trophoblast cells. RESULTS AND DISCUSSION: Here, reduced syncytin-1 was identified in the late-onset preeclampsia placentas. Reduced syncytin-1 may attenuates the EMT process by promoting apoptosis, inhibiting proliferation and invasion by suppressed PI3K/Akt pathway in trophoblast cells. Our findings provide novel insights into the non-fusogenic biological function of reduced syncytin-1 that may be involves in the pathogenesis of preeclampsia.

3.
bioRxiv ; 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-39091791

ABSTRACT

Many remarkable innovations have repeatedly occurred across vast evolutionary distances. When convergent traits emerge on the tree of life, they are sometimes driven by the same underlying gene families, while other times many different gene families are involved. Conversely, a gene family may be repeatedly recruited for a single trait or many different traits. To understand the general rules governing convergence at both genomic and phenotypic levels, we systematically tested associations between 56 binary metabolic traits and gene count in 14,710 gene families from 993 species of Saccharomycotina yeasts. Using a recently developed phylogenetic approach that reduces spurious correlations, we discovered that gene family expansion and contraction was significantly linked to trait gain and loss in 45/56 (80%) of traits. While 601/746 (81%) of significant gene families were associated with only one trait, we also identified several 'keystone' gene families that were significantly associated with up to 13/56 (23%) of all traits. These results indicate that metabolic innovations in yeasts are governed by a narrow set of major genetic elements and mechanisms.

4.
Curr Microbiol ; 81(9): 283, 2024 Jul 27.
Article in English | MEDLINE | ID: mdl-39066927

ABSTRACT

A novel bacterium designated as SSA5.23T was isolated from seawater. Cells of SSA5.23T are Gram-stain-negative, short, rod-shaped, and exhibit motility via numerous peritrichous flagella. The strain could grow at temperatures ranging from 15 to 35 °C (optimum at 25 °C), in a salinity range of 0-5.0% (w/v) NaCl, and within a pH range of 6.0-9.0 (optimum at pH 7.0). The predominant cellular fatty acid of SSA5.23T was C18:1 ω7c/C18:1 ω6c, and the major respiratory quinones were Q-9 and Q-10. Diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol were identified as the primary polar lipids. The complete genome (5.47 Mb) of SSA5.23T comprises of a circular chromosome of 3.64 Mb and three plasmids, specifically sized at 59.73 kb, 227.82 kb, and 1.54 Mb, respectively. Certain genes located on the plasmids play roles in denitrification, oxidative stress resistance, and osmotic tolerance, which likely contribute to the adaptability of this strain in marine conditions. Core-proteome average amino acid identity analysis effectively identified the strain's affiliation with the genus Affinirhizobium, showing the highest value (89.9%) with Affinirhizobium pseudoryzae DSM 19479T. This classification was further supported by the phylogenetic analysis of concatenated alignment of 170 single-copy orthologous proteins. When compared to related reference strains, SSA5.23T displayed an average nucleotide identity ranging from 74.9 to 80.3% and digital DNA-DNA hybridization values ranging from 19.9 to 23.9%. Our findings confirmed that strain SSA5.23T represents a novel species of the genus Affinirhizobium, for which the name Affinirhizobium gouqiense sp. nov. (type strain SSA5.23T = LMG 32560T = MCCC 1K07165T) was suggested.


Subject(s)
DNA, Bacterial , Fatty Acids , Genome, Bacterial , Phylogeny , Seawater , Seawater/microbiology , China , Fatty Acids/analysis , DNA, Bacterial/genetics , Rhizobium/genetics , Rhizobium/classification , Rhizobium/isolation & purification , Base Composition , Bacterial Typing Techniques , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Islands , Genomics
5.
BMC Musculoskelet Disord ; 25(1): 586, 2024 Jul 26.
Article in English | MEDLINE | ID: mdl-39061027

ABSTRACT

BACKGROUND: To identify physical activity (PA) trajectories in adults with or at risk of knee osteoarthritis and to evaluate the association of PA trajectories with incident knee replacement (KR). METHODS: This study used data from the Osteoarthritis Initiative. The Physical Activity Scale for the Elderly and the KR were assessed annually from baseline to 9 years. Individuals were included if they did not undergo KR surgery at baseline and had data on PA at ≥ 1 visit before KR. Latent class growth mixture Modeling was used to identify the optimal trajectories of PA before KR. Log-binomial regression models were used to assess the association between PA trajectories and the risk of KR. Data analyses were conducted in all individuals and those with radiographic osteoarthritis (ROA) and significant knee pain (Western Ontario and McMaster Osteoarthritis Index pain score of ≥ 5 on a 0-20 scale) at baseline, respectively. RESULTS: Of 4731 participants (mean age 61.1 years, 58.5% female), four distinct and slightly declined PA trajectories were identified. Compared to individuals with a "Low" PA trajectory, those with "Medium-low", "Medium-high", or "High" PA trajectories were not significantly associated with the risk of KR (risk ratios: 0.97-1.19, all p > 0.05). Similar PA trajectories and associations with the risk of KR were observed in the subgroups of individuals with radiographic osteoarthritis and those with significant knee pain at baseline, respectively. CONCLUSION: In participants with or at risk of knee osteoarthritis, PA slightly declines over time and may play no role in the risk of KR.


Subject(s)
Arthroplasty, Replacement, Knee , Exercise , Osteoarthritis, Knee , Humans , Osteoarthritis, Knee/surgery , Osteoarthritis, Knee/epidemiology , Osteoarthritis, Knee/physiopathology , Arthroplasty, Replacement, Knee/trends , Female , Male , Middle Aged , Aged , Exercise/physiology , Risk Factors , Longitudinal Studies , Time Factors
6.
Future Oncol ; : 1-11, 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-39041580

ABSTRACT

Aim: This multicenter retrospective study aimed to develop a novel prognostic system for extranodal natural killer/T-cell lymphoma (ENKTL) patients in the era of pegaspargase/L-asparaginase. Materials & methods: A total of 844 newly diagnosed ENKTL patients were included. Results: Multivariable analysis confirmed that Eastern Cooperative Oncology Group performance status, lactate dehydrogenase, Chinese Southwest Oncology Group and Asia Lymphoma Study Group ENKTL (CA) system, and albumin were independent prognostic factors. By rounding up the hazard ratios from four significant variables, a maximum of 7 points were assigned. The model of Huaihai Lymphoma Working Group-Natural killer/T-cell Lymphoma prognostic index (NPI) was identified with four risk groups and the 5-year overall survival was 88.2, 66.7, 54.3 and 30.5%, respectively. Conclusion: Huaihai Lymphoma Working Group-NPI provides a feasible stratification system for patients with ENKTL in the era of pegaspargase/L-asparaginase.


[Box: see text].

7.
Angew Chem Int Ed Engl ; : e202410666, 2024 Jul 15.
Article in English | MEDLINE | ID: mdl-39007416

ABSTRACT

Near-infrared region (NIR; 650-1700 nm) dyes offer many advantages over traditional dyes with absorption and emission in the visible region. However, developing new NIR dyes, especially organic dyes with long wavelengths, small molecular weight, and excellent stability and biocompatibility, is still quite challenging. Herein, we present a general method to enhance the absorption and emission wavelengths of traditional fluorophores by simply appending a charge separation structure, dihydropyridopyrazine. These novel NIR dyes not only exhibited greatly redshifted wavelengths compared to their parent dyes, but also displayed a small molecular weight increase together with retained stability and biocompatibility. Specifically, dye NIR-OX, a dihydropyridopyra-zine derivative of oxazine with a molecular mass of 386.2 Da, exhibited an absorption at 822 nm and an emission extending to 1200 nm, making it one of the smallest molecular-weight NIR-II emitting dyes. Thanks to its rapid metabolism and long wave-length, NIR-OX enabled high-contrast bioimaging and assessment of cholestatic liver injury in vivo and also facilitated the evalua-tion of the efficacy of liver protection medicines against cholestatic liver injury.

8.
Contemp Clin Trials ; 145: 107646, 2024 Jul 30.
Article in English | MEDLINE | ID: mdl-39084407

ABSTRACT

In medical research, publication bias (PB) poses great challenges to the conclusions from systematic reviews and meta-analyses. The majority of efforts in methodological research related to classic PB have focused on examining the potential suppression of studies reporting effects close to the null or statistically non-significant results. Such suppression is common, particularly when the study outcome concerns the effectiveness of a new intervention. On the other hand, attention has recently been drawn to the so-called inverse publication bias (IPB) within the evidence synthesis community. It can occur when assessing adverse events because researchers may favor evidence showing a similar safety profile regarding an adverse event between a new intervention and a control group. In comparison to the classic PB, IPB is much less recognized in the current literature; methods designed for classic PB may be inaccurately applied to address IPB, potentially leading to entirely incorrect conclusions. This article aims to provide a collection of accessible methods to assess IPB for adverse events. Specifically, we discuss the relevance and differences between classic PB and IPB. We also demonstrate visual assessment through contour-enhanced funnel plots tailored to adverse events and popular quantitative methods, including Egger's regression test, Peters' regression test, and the trim-and-fill method for such cases. Three real-world examples are presented to illustrate the bias in various scenarios, and the implementations are illustrated with statistical code. We hope this article offers valuable insights for evaluating IPB in future systematic reviews of adverse events.

9.
Int J Ophthalmol ; 17(7): 1337-1343, 2024.
Article in English | MEDLINE | ID: mdl-39026904

ABSTRACT

AIM: To investigate Omicron's impact on clinical presentation of acute primary angle closure (APAC) in China. METHODS: A consecutive case series with historical controls was conducted at Shenzhen Eye Hospital, the largest specialized hospital in Shenzhen, China. Medical records from a two-month period during the Omicron pandemic (December 1, 2022, to January 31, 2023) were compared with records from two control groups (12/2018-1/2019 and 12/2021-1/2022) before pandemic. Patients with APAC were included, and the prevalence of APAC and demographic characteristics in Omicron-infected and non-infected patients were compared. RESULTS: Seventy-one (23.43%) out of 303 patients were diagnosed with APAC in the pandemic cohort, which was 2.98 and 2.61 times higher than that in control cohorts (7.87% in 2019, 8.96% in 2022, P<0.001). The pandemic cohort has significantly higher Omicron-infected rate (78.87% vs 0 vs 0; P<0.001), lower proportion of glaucoma history (16.90% vs 42.86% vs 41.67%, P=0.005), higher surgical rate (95.77% vs 83.33% vs 78.57%, P=0.024), higher total medical costs and larger pupil diameter (5.63±0.15 vs 4.68±0.15 vs 4.69±0.22 mm, P<0.01). In 83% Omicron-infected patients, ocular symptoms appeared within 3d after systemic symptoms onset. In multivariate analysis, Omicron infection (P<0.001) was the only independent predictor of pupil diameter. CONCLUSION: In the Omicron epidemic in China, there is an increase of prevalence and severity of APAC, particularly focusing on the first 3d following infection.

10.
J Cancer ; 15(12): 3760-3765, 2024.
Article in English | MEDLINE | ID: mdl-38911370

ABSTRACT

Background: The association of socioeconomic status and individual behavior (SES/IB) with human health is receiving increasing attention. However, the causal effects between SES/IB and lymphomas remain unclear. Methods: A two-sample Mendelian randomization (MR) study was used to assess the causal effects of 25 SES/IB traits (dietary habits, physical activity, smoking/drinking behaviors, sleeping behaviors, leisure sedentary behaviors, risky behaviors, and reproductive behaviors) on six distinct types of lymphomas, including Hodgkin lymphoma (HL), follicular lymphoma (FL), diffuse large B-cell lymphoma (DLBCL), mature T/NK-cell lymphomas, marginal zone B-cell lymphoma (MZL), and mantle cell lymphoma (MCL). The inverse variance weighted (IVW) method was the primary approach used for the MR analysis. A series of sensitivity analyses were also conducted to ensure the robustness of the findings. Results: Two-sample MR revealed six SES/IB traits causally associated with lymphomas, including relative fat intake, drive time, television watching time, computer use time, vigorous physical activity, and number of children ever born. After false discovery rate (FDR) correction, the causal associations between longer television watching time and DLBCL (OR: 4.048, 95% CI: 1.688 to 9.708, P fdr=0.009), and the number of children ever born with both FL (OR: 0.008, 95% CI: 1.412E-04 to 0.484, P fdr=0.021) and DLBCL (OR: 0.001, 95% CI:1.587E-05 to 0.081, P fdr=0.002) were identified. Conclusions: These findings suggest that certain lifestyle and behavioral factors have a measurable impact on specific lymphoma types.

11.
Ann Hematol ; 103(8): 3033-3042, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38886192

ABSTRACT

BACKGROUND: The interaction between CD47 and signal-regulatory protein-alpha (SIRPα) inhibits phagocytosis, and their clinicopathological characteristics have been evaluated in various diseases. However, the significance of CD47 and SIRPα expression, as well as the combined effect, in Extranodal Natural killer/T-cell Lymphoma (ENKTL) remains uncertain. METHODS: In total, 76 newly diagnosed ENKTL patients (mean age 49.9 years, 73.7% male) were included in this study. CD47 and SIRPα expression were examined by immunohistochemistry. Survival analyses were conducted through Kaplan-Meier curves and the Cox regression model. RESULTS: Seventy-one (93.4%) cases were categorized as the CD47 positive group and 59 (77.6%) cases were categorized as the SIRPα positive group. CD47-negative cases had more advanced-stage illness (P = 0.001), while SIRPα-positive cases showed significantly lower levels of high-density lipoprotein (P < 0.001). In univariable analysis, CD47, SIRPα expression, and their combination were significantly associated with prognosis (P < 0.05). In multivariable analysis, only positive SIRPα expression remained significantly associated with superior overall survival (Hazard ratio [HR] 0.446; 95% confidence interval [CI] 0.207-0.963; P = 0.004). Furthermore, SIRPα expression could re-stratify the survival of patients in ECOG (< 2), advanced CA stage, PINK (HR), CD38-positive, PD1-positive, and CD30-positive groups. CONCLUSIONS: SIRPα status was a potential independent prognostic factor for ENKTL. The prognostic significance of CD47 expression and the interaction between CD47 and SIRPα in ENKTL need further investigation.


Subject(s)
CD47 Antigen , Lymphoma, Extranodal NK-T-Cell , Receptors, Immunologic , Humans , CD47 Antigen/metabolism , CD47 Antigen/analysis , CD47 Antigen/biosynthesis , Male , Middle Aged , Female , Receptors, Immunologic/metabolism , Receptors, Immunologic/biosynthesis , Lymphoma, Extranodal NK-T-Cell/metabolism , Lymphoma, Extranodal NK-T-Cell/pathology , Lymphoma, Extranodal NK-T-Cell/mortality , Adult , Aged , Antigens, Differentiation/biosynthesis , Antigens, Differentiation/analysis , Immunohistochemistry , Prognosis , Survival Rate
12.
Adv Mater ; 36(30): e2401960, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38843807

ABSTRACT

Preorganizing molecular drugs within a microenvironment is crucial for the development of efficient and controllable therapeutic systems. Here, the use of tetrahedral DNA framework (TDF) is reported to preorganize antiarrhythmic drugs (herein doxorubicin, Dox) in 3D for catheter ablation, a minimally invasive treatment for fast heartbeats, aiming to address potential complications linked to collateral tissue damage and the post-ablation atrial fibrillation (AF) recurrence resulting from incomplete ablation. Dox preorganization within TDF transforms its random distribution into a confined, regular spatial arrangement governed by DNA. This, combined with the high affinity between Dox and DNA, significantly increases local Dox concentration. The exceptional capacity of TDF for cellular internalization leads to a 5.5-fold increase in intracellular Dox amount within cardiomyocytes, effectively promoting cellular apoptosis. In vivo investigations demonstrate that administering TDF-Dox reduces the recurrence rate of electrical conduction after radiofrequency catheter ablation (RFCA) to 37.5%, compared with the 77.8% recurrence rate in the free Dox-treated group. Notably, the employed Dox dosage exhibits negligible adverse effects in vivo. This study presents a promising treatment paradigm that strengthens the efficacy of catheter ablation and opens a new avenue for reconciling the paradox of ablation efficacy and collateral damage.


Subject(s)
Anti-Arrhythmia Agents , Catheter Ablation , DNA , Doxorubicin , Doxorubicin/pharmacology , Doxorubicin/chemistry , Anti-Arrhythmia Agents/pharmacology , Anti-Arrhythmia Agents/chemistry , Animals , DNA/chemistry , DNA/metabolism , Atrial Fibrillation/drug therapy , Myocytes, Cardiac/drug effects , Myocytes, Cardiac/metabolism , Myocytes, Cardiac/cytology , Apoptosis/drug effects , Rats , Humans
13.
Zhongguo Shi Yan Xue Ye Xue Za Zhi ; 32(3): 708-717, 2024 Jun.
Article in Chinese | MEDLINE | ID: mdl-38926957

ABSTRACT

OBJECTIVE: To investigate the effectiveness, safety, and related prognostic factors of the treatment of follicular lymphoma (FL) with a regimen containing Bendamustine. METHODS: The clinical data of 129 FL patients who were treated with Bendamustine containing regimen were collected from January 1,2020 to October 30,2022 in the Hematology Department of Lianyungang Second People's Hospital and Jiangsu Provincial People's Hospital. The patients were divided into three groups: Bendamustine plus Rituximab (BR), Bendamustine plus Obinutuzumab (GB), Rituximab + Cyclophosphamide + Epirubicin / Doxorubicin + Vindesine + Prednisone (R-CHOP). The efficacy, safety and related prognostic factors of the treatment of FL with a regimen based on Bendamustine were retrospectively analyzed. RESULTS: The ORR was 98% for the BR group, 94% for the GB group, and 72.3% for the R-CHOP group, while the CR rate was 61.2%,70% and 40.4%, respectively. The ORR and CR rates of the R-CHOP group were statistically different from those of the BR group and GB group (P < 0.05). The 3-year PFS rate of the BR group, GB group, and R-CHOP group was 89.6%, 90.9%, 48.9%, respectively. There was a statistically significant difference in 3-year PFS between the R-CHOP group, BR group, and GB group (P < 0.05), while there was no statistically significant difference in 3-year OS(P >0.05). Hematological adverse reactions were mainly bone marrow suppression. Lymphocytes and CD4+T lymphocytes decreased to the lowest level about 6 months after treatment, and the incidence of lymphopenia in BR group and GB group was higher than that in R-CHOP group, with a statistical difference (P < 0.05). The higher incidence of non-Hematological adverse reactions were pulmonary infection, EB virus infection, hepatitis B virus reactivation, and gastrointestinal reactions without statistical difference in 3 groups (P >0.05), and were all controllable. The Receiver operating characteristic of CD4+T lymphocyte count showed that AUC of BR group was 0.802, and the critical value was 258/uL; AUC of GB group was 0.754 with a critical value of 322/uL. CONCLUSION: The treatment of FL with the Bendamustine containing regimen has good efficacy and controllable adverse reactions, but lymphocytopenia was significant after treatment, and the curative efficacy in combination with various CD20 monoclonal antibodies was different. The lowest CD4+T lymphocyte count can be used as a predictive factor for the occurrence of infection and efficacy of the Bendamustine containing regimen for FL.


Subject(s)
Antineoplastic Combined Chemotherapy Protocols , Bendamustine Hydrochloride , CD4-Positive T-Lymphocytes , Lymphoma, Follicular , Rituximab , Humans , Bendamustine Hydrochloride/administration & dosage , Lymphoma, Follicular/drug therapy , Male , Female , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Retrospective Studies , Middle Aged , Rituximab/administration & dosage , Doxorubicin/administration & dosage , Cyclophosphamide , Prednisone/administration & dosage , Adult , Prognosis , Infections , Treatment Outcome , Vincristine
14.
Geriatr Nurs ; 58: 336-343, 2024.
Article in English | MEDLINE | ID: mdl-38875760

ABSTRACT

OBJECTIVE: This study aims to examine the trends and correlates in multiple hospitalizations among older adults in China. METHODS: The data were from the China Health and Retirement Longitudinal Study (CHARLS), and generalized ordered logit model (GOLM) was used to identify the correlates of multiple hospitalizations among older adults aged≥60 years old. RESULTS: Between 2011 and 2018, the proportion of older adults having multiple hospitalizations in the past year showed an increasing trend in the total sample (p value for trend = 0.014). Being older, male, illiterate, living in the middle/western region, having higher annual per capita household expenditure, health insurance, multimorbidity, and being depressed were associated with increased odds of multiple hospitalizations. CONCLUSIONS: Our findings indicated that older adults with multiple hospitalizations may expect an increasing burden on healthcare system. More efforts are needed to improve health insurance and primary healthcare to reduce avoidable hospitalizations.


Subject(s)
Hospitalization , Humans , Male , China/epidemiology , Aged , Hospitalization/statistics & numerical data , Hospitalization/trends , Female , Longitudinal Studies , Middle Aged , Insurance, Health/statistics & numerical data , Aged, 80 and over
15.
bioRxiv ; 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38895429

ABSTRACT

Gene gains and losses are a major driver of genome evolution; their precise characterization can provide insights into the origin and diversification of major lineages. Here, we examined gene family evolution of 1,154 genomes from nearly all known species in the medically and technologically important yeast subphylum Saccharomycotina. We found that yeast gene family and genome evolution are distinct from plants, animals, and filamentous ascomycetes and are characterized by small genome sizes and smaller gene numbers but larger gene family sizes. Faster-evolving lineages (FELs) in yeasts experienced significantly higher rates of gene losses-commensurate with a narrowing of metabolic niche breadth-but higher speciation rates than their slower-evolving sister lineages (SELs). Gene families most often lost are those involved in mRNA splicing, carbohydrate metabolism, and cell division and are likely associated with intron loss, metabolic breadth, and non-canonical cell cycle processes. Our results highlight the significant role of gene family contractions in the evolution of yeast metabolism, genome function, and speciation, and suggest that gene family evolutionary trajectories have differed markedly across major eukaryotic lineages.

17.
bioRxiv ; 2024 May 24.
Article in English | MEDLINE | ID: mdl-38826271

ABSTRACT

Codon usage bias, or the unequal use of synonymous codons, is observed across genes, genomes, and between species. The biased use of synonymous codons has been implicated in many cellular functions, such as translation dynamics and transcript stability, but can also be shaped by neutral forces. The Saccharomycotina, the fungal subphylum containing the yeasts Saccharomyces cerevisiae and Candida albicans , has been a model system for studying codon usage. We characterized codon usage across 1,154 strains from 1,051 species to gain insight into the biases, molecular mechanisms, evolution, and genomic features contributing to codon usage patterns across the subphylum. We found evidence of a general preference for A/T-ending codons and correlations between codon usage bias, GC content, and tRNA-ome size. Codon usage bias is also distinct between the 12 orders within the subphylum to such a degree that yeasts can be classified into orders with an accuracy greater than 90% using a machine learning algorithm trained on codon usage. We also characterized the degree to which codon usage bias is impacted by translational selection. Interestingly, the degree of translational selection was influenced by a combination of genome features and assembly metrics that included the number of coding sequences, BUSCO count, and genome length. Our analysis also revealed an extreme bias in codon usage in the Saccharomycodales associated with a lack of predicted arginine tRNAs. The order contains 24 species, and 23 are computationally predicted to lack tRNAs that decode CGN codons, leaving only the AGN codons to encode arginine. Analysis of Saccharomycodales gene expression, tRNA sequences, and codon evolution suggests that extreme avoidance of the CGN codons is associated with a decline in arginine tRNA function. Codon usage bias within the Saccharomycotina is generally consistent with previous investigations in fungi, which show a role for both genomic features and GC bias in shaping codon usage. However, we find cases of extreme codon usage preference and avoidance along yeast lineages, suggesting additional forces may be shaping the evolution of specific codons.

18.
Nat Aging ; 2024 Jun 04.
Article in English | MEDLINE | ID: mdl-38834883

ABSTRACT

Oxidative phosphorylation, essential for energy metabolism and linked to the regulation of longevity, involves mitochondrial and nuclear genes. The functions of these genes and their evolutionary rate covariation (ERC) have been extensively studied, but little is known about whether other nuclear genes not targeted to mitochondria evolutionarily and functionally interact with mitochondrial genes. Here we systematically examined the ERC of mitochondrial and nuclear benchmarking universal single-copy ortholog (BUSCO) genes from 472 insects, identifying 75 non-mitochondria-targeted nuclear genes. We found that the uncharacterized gene CG11837-a putative ortholog of human DIMT1-regulates insect lifespan, as its knockdown reduces median lifespan in five diverse insect species and Caenorhabditis elegans, whereas its overexpression extends median lifespans in fruit flies and C. elegans and enhances oxidative phosphorylation gene activity. Additionally, DIMT1 overexpression protects human cells from cellular senescence. Together, these data provide insights into the ERC of mito-nuclear genes and suggest that CG11837 may regulate longevity across animals.

19.
Front Oncol ; 14: 1394111, 2024.
Article in English | MEDLINE | ID: mdl-38873258

ABSTRACT

Purpose: We tried to establish the normal tissue complication probability (NTCP) model of temporal lobe injury of recurrent nasopharyngeal carcinoma (NPC) patients after two courses of intensity modulated radiotherapy (IMRT) to provide more reliable dose-volume data reference to set the temporal lobe tolerance dose for recurrent NPC patients in the future. Methods and materials: Recurrent NPC patients were randomly divided into training data set and validation data set in a ratio of 2:1, All the temporal lobes (TLs) were re-contoured as R/L structures and named separately in the MIM system. The dose distribution of the initial IMRT plan was deformed into the second course planning CT via MIM software to get the deformed dose. Equivalent dose of TLs in 2Gy fractions was calculated via linear quadratic model, using an α/ß=3 for temporal lobes. NTCP model that correlated the irradiated volume of the temporal lobe and? the clinical variables were evaluated in a multivariate prediction model using AUC analysis. Results: From Jan. 2010 to Dec. 2020, 78 patients were enrolled into our study. Among which 26 (33.3%) developed TLI. The most important factors affecting TLI was the sum-dose d1.5cc of TL, while the possible clinical factors did not reach statistically significant differences in multivariate analysis. According to NTCP model, the TD5 and TD50 EQD2 dose of sum-dose d1.5cc were 65.26Gy (46.72-80.69Gy) and 125.25Gy (89.51-152.18Gy), respectively. For the accumulated EQD2 dose, the area under ROC shadow was 0.8702 (0.7577-0.9828) in model validation, p<0.001. Conclusion: In this study, a NTCP model of temporal lobe injury after a second course of IMRT for recurrent nasopharyngeal carcinoma was established. TD5 and TD50 doses of temporal lobe injury after re-RT were obtained according to the model, and the model was verified by validation set data.

20.
China CDC Wkly ; 6(25): 597-604, 2024 Jun 21.
Article in English | MEDLINE | ID: mdl-38933041

ABSTRACT

This study aims to perform a systematic review and meta-analysis on the global prevalence of cannabis use to inform drug prevention strategies, policy-making, and resource allocation. This study initially screened 177,843 studies published between January 1, 2000, and January 15, 2024, using peer-reviewed databases including Web of Science, PubMed, Scopus, Embase, and Cochrane Library. Ultimately, 595 studies were identified for data extraction, and 39 of these were selected as country-representative studies. Heterogeneity among the selected studies was assessed using the chi-squared test and I2 statistic, while sensitivity analysis was conducted to evaluate the robustness of the results. The prevalence of cannabis use varied between 0.42% and 43.90% across 33 European countries, 1.40% to 38.12% across 15 North and South American countries, 0.30% to 19.10% across 16 Asian countries, and 1.30% to 48.70% across 18 Oceania and African countries. The pooled prevalence of cannabis use was 12.0% [95% confidence interval (CI): 10.0, 14.3] in countries where cannabis is legalized, compared to 5.4% (95% CI: 4.3, 6.9) in non-legalized countries. Our findings indicate that the prevalence of cannabis use has disproportionately increased in most countries with the implementation of medical or recreational cannabis legalization policies and relevant geographic proximity. Increased efforts are needed to monitor newly cannabis-legalized countries and prevent initial use.

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