Facile preparation of high-efficiency peroxidase mimics: modulation of the catalytic microenvironment of LDH nanozymes through defect engineering induced by amino acid intercalation

Nanozymes have gained much attention as a replacement for natural enzymes duo to their unique advantages. Two-dimensional layered double hydroxide (LDH) nanomaterials with high physicochemical plasticity are emerging as the main forces for the construction of nanozymes. Unfortunately, high-performance LDH nanozymes are still scarce. Recently, defects in nanomaterials have been verified to play a significant role in modulating the catalytic microenvironment, thereby improving catalytic performances of nanozymes. Therefore, the marriage between defect engineering and LDH nanozymes is expected to spark new possibilities. In this work, twenty kinds of natural amino acids were separately inserted into the interlayer of CoFe-LDH to obtain defect-rich CoFe-LDH nanozymes. The peroxidase (POD)-like activity and catalytic mechanism of the as-prepared LDH nanozymes were systematically studied. The results showed that the intercalation of amino acids can effectively enhance the POD-like activity of LDH nanozymes owing to the increasing oxygen/metal vacancies. And l-cysteine intercalated LDH exhibited the highest catalytic activity ascribed to its thiol group. As a proof of concept, LDH nanozymes with superb POD-like activity were used in biosensing and antibacterial applications. This work suggests that modulating the catalytic microenvironment through defect engineering is an effective way to obtain high-efficiency POD mimics.

[Analysis of the progress in the field of oral microbiology and regenerative medicine from 2014 to 2023]

Objective: To analyze the trends in literature related to oral microbiology and regenerative medicine from 2014 to 2023. By identifying key research countries, institutions, and their collaboration networks, as well as exploring research hotspots and development directions, the study seeks to provide references for researchers and decision-makers in the field of oral microbiology and regenerative medicine, thereby guiding the direction of future research. Methods: Relevant literature was retrieved using the Web of Science Core Collection database, with data processing and analysis conducted using CiteSpace 6.2.R6 software. Time slicing, node type selection, and the application of the g-index (g-index) were used for filtering, analyzing countries, institutions, authors, journals, and keywords. Results: The volume of literature in the field of oral microbiology and regenerative medicine has steadily increased from 2014 to 2023, with the number of publications first exceeding one hundred in 2020 and reaching 134 in 2022, accompanied by a citation frequency of 3 363 times. China and the United States have been at the forefront in terms of the volume of publications, while the United States and Germany lead in terms of intermediary centrality. The research primarily spans disciplines such as oral medicine, interdisciplinary studies, materials science, and immunology. High-frequency keywords include stem cells, scaffold materials, and gut microbiota, while cluster analysis indicates that inflammation, drug delivery, and antimicrobial activity remain consistent research themes. In recent years, the research heat in "tissue regeneration""gut microbiota " and "maxillofacial surgery" has risen, suggesting these may become focal points of future research. Conclusions: Over the past decade, the volume of literature published in the fields of oral microbiology and regenerative medicine, along with their citation frequencies, has increased annually. The research focus has shifted over time. Understanding the interactions between oral and gut microbiomes is crucial for developing innovative regenerative treatment strategies.

MagicalRsq-X: A cross-cohort transferable genotype imputation quality metric

Since genotype imputation was introduced, researchers have been relying on the estimated imputation quality from imputation software to perform post-imputation quality control (QC). However, this quality estimate (denoted as Rsq) performs less well for lower-frequency variants. We recently published MagicalRsq, a machine-learning-based imputation quality calibration, which leverages additional typed markers from the same cohort and outperforms Rsq as a QC metric. In this work, we extended the original MagicalRsq to allow cross-cohort model training and named the new model MagicalRsq-X. We removed the cohort-specific estimated minor allele frequency and included linkage disequilibrium scores and recombination rates as additional features. Leveraging whole-genome sequencing data from TOPMed, specifically participants in the BioMe, JHS, WHI, and MESA studies, we performed comprehensive cross-cohort evaluations for predominantly European and African ancestral individuals based on their inferred global ancestry with the 1000 Genomes and Human Genome Diversity Project data as reference. Our results suggest MagicalRsq-X outperforms Rsq in almost every setting, with 7.3%-14.4% improvement in squared Pearson correlation with true R2, corresponding to 85-218 K variant gains. We further developed a metric to quantify the genetic distances of a target cohort relative to a reference cohort and showed that such metric largely explained the performance of MagicalRsq-X models. Finally, we found MagicalRsq-X saved up to 53 known genome-wide significant variants in one of the largest blood cell trait GWASs that would be missed using the original Rsq for QC. In conclusion, MagicalRsq-X shows superiority for post-imputation QC and benefits genetic studies by distinguishing well and poorly imputed lower-frequency variants.

Compared with soil fungal diversity and microbial network complexity, soil bacterial diversity drives soil multifunctionality during the restoration process

Understanding factors driving soil multifunctionality can help with terrestrial ecosystem restoration. Soil microbial diversity and network complexity are two important factors influencing ecosystem multifunctionality. However, their effects on soil multifunctionality are still unclear. Based on high-throughput sequencing, we analyzed soil microbial alpha diversity and network complexity and their relative impacts on soil multifunctionality during the aerial seeding restoration process from 1983 to 2017 in Mu Us sandy land, China, a region threatened by desertification. Our results showed soil bacterial and fungal alpha diversity and multifunctionality increased with aerial seeding restoration. We found the community composition of soil bacteria and fungi changed with restoration periods. The keystone species of the soil bacterial network changed during restoration, while those of the soil fungal network remained unchanged. Soil bacterial and fungal species mainly maintained positive associations throughout the restoration periods. Soil bacterial network complexity initially decreased before increasing with restoration, while soil fungal network complexity increased continuously. Soil multifunctionality was found to have significantly positive correlations with soil fungal network complexity and soil bacterial alpha diversity. Compared with soil fungal alpha diversity and soil microbial network complexity, soil bacterial alpha diversity significantly promoted soil multifunctionality. Our research highlights the critical impact that soil bacterial alpha diversity plays in soil multifunctionality in restored ecosystems threatened by desertification.

Inflammatory factors mediated the effect of air pollution on ischemic stroke: a two-step, mediation Mendelian randomization study

OBJECTIVE

Numerous investigations have indicated a correlation between air pollution (AP) and an elevated ischemic stroke (IS) likelihood. The existing literature does not provide a consensus about the possible link between AP and IS. A two-sample Mendelian randomization (MR) analysis was utilized to systematically measure the causal link between AP and ischemic stroke. Furthermore, the mediating impact of inflammatory factors was also performed by a two-step MR.

MATERIALS AND METHODS

A two-sample MR analysis was utilized to examine the AP impact on the incidence of IS. Additionally, a two-step MR approach was carried out to account for possible mediating variables. The indirect impact was determined by employing the product approach, which included multiplying the AP impact on inflammatory factors by the inflammatory factors' impacts on IS. The MR effect was identified through inverse variance-weighted (IVW) meta-analysis of each Wald Ratio. Additionally, complementary studies were conducted using the weighted median and MR-egger approaches.

RESULTS

The IVW method with random effects showed that the per unit increase in genetically predicted PM2.5 was linked to the 0.362-fold elevated ischemic stroke risk (OR: 1.362, 95% CI: 1.032-1.796, p=0.029). Furthermore, the IVM technique, incorporating random effects, demonstrated that the per unit increase in genetically predicted PM2.5 was related to an elevated Interleukin (IL)-1β risk (OR: 1.529, 95% CI: 1.191-1.963, p=0.001), IL-6 (OR: 1.498, 95% CI: 1.094-2.052, p=0.012) and IL-17 (OR: 1.478, 95% CI: 1.021-2.139, p=0.038). IL-1β, IL-6, and IL-17 modulated the PM2.5 impact on ischemic stroke, while the proportion mediated by them was 59.5%.

CONCLUSIONS

A positive correlation between genetically predicted PM2.5 levels and elevated ischemic stroke risk is mediated by IL-1β, IL-6, and IL-17.

A subunit vaccine based on Brucella melitensis rBP26 induces Th1 immune responses and M1 macrophage activation

Brucellosis is a global zoonotic infection caused by Brucella bacteria, which poses a significant burden on society. While transmission prevention is currently the most effective method, the absence of a licenced vaccine for humans necessitates the urgent development of a safe and effective vaccine. Recombinant protein-based subunit vaccines are considered promising options, and in this study, the Brucella BP26 protein is expressed using prokaryotic expression systems. The immune responses are evaluated using the well-established adjuvant CpG-ODN. The results demonstrate that rBP26 supplemented with a CpG adjuvant induces M1 macrophage polarization and stimulates cellular immune responses mediated by Th1 cells and CD8 + T cells. Additionally, it generates high levels of rBP26-specific antibodies in immunized mice. Furthermore, rBP26 immunization activates, proliferates, and produces cytokines in T lymphocytes while also maintaining immune memory for an extended period of time. These findings shed light on the potential biological function of rBP26, which is crucial for understanding brucellosis pathogenesis. Moreover, rBP26 holds promise as an effective subunit vaccine candidate for use in endemic areas.

[The association between body mass index and in-hospital major adverse cardiovascular and cerebral events in patients with acute coronary syndrome]

Objective: To assess the association between body mass index (BMI) and major adverse cardiovascular and cerebrovascular events (MACCE) among patients with acute coronary syndrome (ACS). Methods: This was a multicenter prospective cohort study, which was based on the Improving Care for Cardiovascular Disease in China (CCC) project. The hospitalized patients with ACS aged between 18 and 80 years, registered in CCC project from November 1, 2014 to December 31, 2019 were included. The included patients were categorized into four groups based on their BMI at the time of admission: underweight (BMI<18.5 kg/m2), normal weight (BMI between 18.5 and 24.9 kg/m2), overweight (BMI between 25.0 and 29.9 kg/m2), and obese (BMI≥30.0 kg/m2). Multivariate logistic regression models was used to analyze the relationship between BMI and the risk of in-hospital MACCE. Results: A total of 71 681 ACS inpatients were included in the study. The age was (63.4±14.7) years, and 26.5% (18 979/71 681) were female. And the incidence of MACCE for the underweight, normal weight, overweight, and obese groups were 14.9% (322/2 154), 9.5% (3 997/41 960), 7.9% (1 908/24 140) and 7.0% (240/3 427), respectively (P<0.001). Multivariate logistic regression analysis showed a higher incidence of MACCE in the underweight group compared to the normal weight group (OR=1.30, 95%CI 1.13-1.49, P<0.001), while the overweight and obese groups exhibited no statistically significant difference in the incidence of MACCE compared to the normal weight group (both P>0.05). Conclusion: ACS patients with BMI below normal have a higher risk of in-hospital MACCE, suggesting that BMI may be an indicator for evaluating short-term prognosis in ACS patients.

Genome-wide study investigating effector genes and polygenic prediction for kidney function in persons with ancestry from Africa and the Americas

Chronic kidney disease is a leading cause of death and disability globally and impacts individuals of African ancestry (AFR) or with ancestry in the Americas (AMS) who are under-represented in genome-wide association studies (GWASs) of kidney function. To address this bias, we conducted a large meta-analysis of GWASs of estimated glomerular filtration rate (eGFR) in 145,732 AFR and AMS individuals. We identified 41 loci at genome-wide significance (p < 5 × 10-8), of which two have not been previously reported in any ancestry group. We integrated fine-mapped loci with epigenomic and transcriptomic resources to highlight potential effector genes relevant to kidney physiology and disease, and reveal key regulatory elements and pathways involved in renal function and development. We demonstrate the varying but increased predictive power offered by a multi-ancestry polygenic score for eGFR and highlight the importance of population diversity in GWASs and multi-omics resources to enhance opportunities for clinical translation for all.

Fabrication of Hollow and Hierarchical CuO Micro-Nano Cubes Wrapped by Reduced Graphene Oxide as a Prospective Anode for SIBs

In this study, hollow and hierarchical CuO micro-nano cubes wrapped by reduced graphene oxide (H-CuO MNCs@rGO) were designed and successfully fabricated via a novel three-step wet-chemical method. Benefiting from its unique hollow and hierarchical micro-nano structures, H-CuO MNCs@rGO exhibited significantly enhanced electrochemical Na+ storage performance when utilized as anode material for sodium-ion batteries (SIBs). Specifically, H-CuO MNCs@rGO demonstrated a specific capacity of 380.9 mAh g-1 in the initial reversible cycle and a capacity retention of 218.9 mAh g-1 after 150 cycles at a current density of 300 mA g-1. Furthermore, through the dominant pseudocapacitive behavior, an optimized rate capability of 221.2 mAh g-1 at 800 mA g-1 can be obtained for H-CuO MNCs@rGO. The comprehensive Na+ storage properties of H-CuO MNCs@rGO obviously exceeded those of hollow CuO cubes (H-CuO MNCs) and bulk CuO anodes. Such enhanced Na+ storage performances of H-CuO MNCs@rGO can be attributed to its reasonable hollow and hierarchical micro-nano structures, which provide abundant redox active sites, shorten Na+ migration pathway, buffer volume expansion, and improve electronic/ionic conductivity during sodiation/desodiation process. Our strategy provides a facile and innovative approach for the design of CuO with rational micro-nano structure as a high-performance anode for SIBs, which would also be a guiding way for tailoring transition metal oxides in other scalable and functional applications.

Chromothripsis orchestrates leukemic transformation in blast phase MPN through targetable amplification of DYRK1A

Chromothripsis, the process of catastrophic shattering and haphazard repair of chromosomes, is a common event in cancer. Whether chromothripsis might constitute an actionable molecular event amenable to therapeutic targeting remains an open question. We describe recurrent chromothripsis of chromosome 21 in a subset of patients in blast phase of a myeloproliferative neoplasm (BP-MPN), which alongside other structural variants leads to amplification of a region of chromosome 21 in ∼25% of patients ('chr21amp'). We report that chr21amp BP-MPN has a particularly aggressive and treatment-resistant phenotype. The chr21amp event is highly clonal and present throughout the hematopoietic hierarchy. DYRK1A , a serine threonine kinase and transcription factor, is the only gene in the 2.7Mb minimally amplified region which showed both increased expression and chromatin accessibility compared to non-chr21amp BP-MPN controls. We demonstrate that DYRK1A is a central node at the nexus of multiple cellular functions critical for BP-MPN development, including DNA repair, STAT signalling and BCL2 overexpression. DYRK1A is essential for BP-MPN cell proliferation in vitro and in vivo , and DYRK1A inhibition synergises with BCL2 targeting to induce BP-MPN cell apoptosis. Collectively, these findings define the chr21amp event as a prognostic biomarker in BP-MPN and link chromothripsis to a druggable target.

Genome-wide association study identifies variants associated with semen volume in white-feathered broilers

Semen is a measure of the reproductive efficiency of roosters, which affects the economic benefits of white-feathered broilers. Over the years, research in this field has mainly focused on hens, while there have been fewer studies on the reproductive traits of roosters. To identify the genes related to the semen traits of roosters, we used a chicken 55 K SNP chip to genetically type the white-feathered population (220) and performed imputation with resequencing data from 97 roosters. In total, 1 048 576 SNPs were obtained and used for genome-wide association analysis of semen volume, from which 197 genome-wide significant markers were identified, all within the interval of 13.82-16.12 Mb on chromosome 7. By combining our results with the biological functions of genes in the interval, four candidate genes were identified that potentially relate to semen volume: FAPP1, OSBPL6, SESTD1 and SSFA2. Our findings may provide a basis for further research on the genetic mechanism and marker-assisted selection of semen volume in white-feathered broilers.

A high-cholesterol zebrafish diet promotes hypercholesterolemia and fasting-associated liver triglycerides accumulation

Zebrafish are an ideal model organism to study lipid metabolism and to elucidate the molecular underpinnings of human lipid-associated disorders. In this study, we provide an improved protocol to assay the impact of a high-cholesterol diet (HCD) on zebrafish lipid deposition and lipoprotein regulation. Fish fed HCD developed hypercholesterolemia as indicated by significantly elevated ApoB-containing lipoproteins (ApoB-LP) and increased plasma levels of cholesterol and cholesterol esters. Feeding of the HCD to larvae (8 days followed by a 1 day fast) and adult female fish (2 weeks, followed by 3 days of fasting) was also associated with a fatty liver phenotype that presented as severe hepatic steatosis. The HCD feeding paradigm doubled the levels of liver triacylglycerol (TG), which was striking because our HCD was only supplemented with cholesterol. The accumulated liver TG was unlikely due to increased de novo lipogenesis or inhibited β-oxidation since no differentially expressed genes in these pathways were found between the livers of fish fed the HCD versus control diets. However, fasted HCD fish had significantly increased lipogenesis gene fasn in adipose tissue and higher free fatty acids (FFA) in plasma. This suggested that elevated dietary cholesterol resulted in lipid accumulation in adipocytes, which supplied more FFA during fasting, promoting hepatic steatosis. In conclusion, our HCD zebrafish protocol represents an effective and reliable approach for studying the temporal characteristics of the physiological and biochemical responses to high levels of dietary cholesterol and provides insights into the mechanisms that may underlie fatty liver disease.

Promoting effects of soil C and N and limiting effect of soil P jointly determine the plant diversity during the aerial seeding restoration process in Mu Us sandy land, China

Introduction

Exploring the change and maintaining mechanism of plant diversity is of great significance for guiding the restoration of degraded ecosystems. However, how plant taxonomic, functional, and phylogenetic diversity change during long-term ecosystem restoration process and their driving factors remain unclear.

Methods

Based on the 35-year time gradient of aerial seeding restoration in Mu Us sandy land, this study explored the changes in plant taxonomic, functional, and phylogenetic diversity and the driving factors.

Results

The results showed that plant taxonomic, functional, and phylogenetic diversity showed consistent response with the aerial seeding restoration, all of which increased first and then tended to a saturation state in the middle of restoration (14 years). TN, TOC, and NO3 --N increased with aerial seeding restoration and showed a significant positive correlation with plant diversity of the three dimensions, while AP showed a negative correlation. Soil nitrogen and carbon promoted the increase of diversity of three dimensions in the early restoration period, while phosphorus limited the increase of diversity of three dimensions in the middle and late restoration periods. The diversity of three dimensions was mainly affected by restoration time, soil nutrients, and climate factors, and the coupling effect of restoration time and soil nutrients was dominant.

Discussion

These findings indicate that the plant diversity in different dimensions and soil nutrients are improved by aerial seeding restoration. Our study highlights that aerial seeding restoration mainly improves plant diversity by increasing soil nutrients, and the relative effects of different soil nutrients on plant diversity during restoration are inconsistent.

[Application effects of 3D visualization reconstruction technique in pheochromocytoma/ paraganglioma surgery]

To investigate the value of 3D visualization reconstruction technology in pheochromocytoma/paraganglioma surgery.The clinical data of 87 patients with pheochromocytoma/paraganglioma admitted to the Department of Urology of Peking Union Medical College Hospital between January 2019 and December 2022 were retrospectively analyzed, and 3D visualization model reconstruction was performed preoperatively in 47 patients [Group A:males was 24 cases,the age M(Q1, Q3)42.00(30.00, 54.00)]. while the remaining 40 patients [Group B: males was 23 cases,the age M(Q1, Q3) 44.00(30.25, 53.75)] was not. The maximum tumor diameter, operation time, intraoperative bleeding, drain retention time and postoperative hospital stay were compared between the two groups. Surgery was successfully completed in both groups. 37 (78.7%) patients in group A underwent laparoscopic surgery, 7 (14.9%) patients underwent open surgery, and 3 (6.4%) patients underwent laparoscopic-to-open surgery. Thirty-one (77.5%) patients in group B underwent laparoscopic surgery, 5 (12.5%) patients underwent open surgery, and 4 (10.0%) patients underwent laparoscopic to open surgery. There was a difference in the maximum diameter of the tumor between the two groups [(6.09±3.02) cm vs (5.32±1.76) cm, P<0.05], the retention time of the drainage tube was significantly shorter in group A compared with group B [(3.20±1.38) d vs (4.02±1.98) d, P<0.05], and the length of the hospital stay after surgery was significantly shorter [(5.75±2.12) d vs (6.49±3.37) d, P<0.05]. Comparison of operation time and intraoperative bleeding between the two groups showed no statistically significant difference (P>0.05).Two cases of postoperative anemia and one case of pulmonary atelectasis in group B patients improved before discharge. Conclusion when the tumor diameter is>6 cm or has a close relationship with the surrounding organs and blood vessels, the use of 3D visual reconstruction technology can formulate and implement a more accurate and safe surgical plan, shorten the retention time of the drainage tube and postoperative hospitalization time, which is conducive to the patient's postoperative recovery and reduce postoperative complications.

Highly efficient removal of Cr(VI) from wastewater using electronegative SA/EGCG@Ti/SA/PVDF sandwich membrane

The use of green, non-toxic raw materials is of great significance to the sustainable development of the environment, among which epigallocatechin gallate (EGCG) is a renewable carbon source from plants. At present, there is a lack of research on the metal-polyphenol nanomaterials their use in water decontamination. In this study, a novel SA/EGCG@Ti/SA/PVDF (SESP) sandwich membrane was prepared to effectively solve the problems of difficult recovery of nanomaterials and the leaching of metal ions. The membrane was made by scraping SA on the surface of the PVDF substrate as the bottom protective layer, depositing EGCG@Ti NPs as the functional layer, then coating SA as the surface isolation layer, and finally cross-linking with anhydrous calcium chloride. Results showed that EGCG@Ti NPs dispersed well on the surface of the SA/PVDF basement membrane. SESP sandwich membrane had good hydrothermal and acid-base stability, and it can be applied to wastewater with multiple co-existing heavy metals (e.g., Cu, Pb, Cd, and Ni). The contact angle and pure water flux of the SESP sandwich membrane with a negatively charged surface were 14.0-15.6° and 171.40 L/m2 h, respectively. The pure water flux of the regenerated membrane after BSA pollution recovered to 98.68 L/m2 h, and the interception efficiency and the interception flux of Cr(VI) were 100 % and 72.92 L/m2 h at 40 min of interception, respectively. Additionally, the removal efficiency of Cr(VI) by SESP sandwich membrane was maintained above 83 % for simulated wastewater and 100 % for actual wastewater after five adsorption-desorption cycles. Cr(VI) and Cr(III) can be removed simultaneously with the negatively charged SESP sandwich membrane. EDS and XPS analysis showed that the removal of Cr(VI) was controlled by the Donnan effect, anion exchange, chelation/complexation, and reduction mechanism. In contrast, Cr(III) was mainly influenced by electrostatic attraction and chelation/complexation mechanisms. In conclusion, the newly prepared sandwich membrane has good application potential in treating Cr(VI) wastewater.

A study evaluating liquid-based endometrial cytology test and transvaginal ultrasonography as a screening tool for endometrial cancer in 570 postmenopausal women

OBJECTIVE

To evaluate the combination of transvaginal ultrasonography (TVS) and endometrial cytology test (ECT) as a potential diagnostic strategy for endometrial cancer and endometrial precancerous lesions in postmenopausal patients.

METHODS

570 postmenopausal patients admitted in our hospital due to abnormal bleeding or other symptoms and/or with endometrium thickness over 5 mm on ultrasound. The endometrial thickness was evaluated by TVS. Following obtainment with written consent, all patients underwent ECT, hysteroscopy and then dilatation and curettage (D&C). Cytological sampling was conducted by scratching the uterus cavity using SAP-1 and the samples were prepared as liquid-based smear using SurePath technology. The samples were stained using Papanicolaou method. The correlation between cytological diagnosis and TVS results with the D&C histological diagnosis was analyzed. The WHO classification was used for diagnosis.

RESULTS

Sensitivity of ECT, TVS, ECT or TVS positive, ECT and TVS positive to diagnose atypical hyperplasia or worse were estimated at 80.7%, 86.8%, 97.4%, 70.2%, specificity at 94.7%, 20.4%, 17.5%, 88.4%, positive predictive value at 58.2%, 21.1%, 22.8%, 60.2%, negative predictive value at 94.4%, 86.1%, 96.4%, 92.2%, and accuracy at 84.6%, 33.7%, 33.5%, 84.7%, respectively.

CONCLUSIONS

Transvaginal ultrasonography and Endometrial cytology test may be regarded as a effective first-line method in endometrial pathology detection in postmenopausal women.

Functional characterization of Alzheimer's disease genetic variants in microglia

Candidate cis-regulatory elements (cCREs) in microglia demonstrate the most substantial enrichment for Alzheimer's disease (AD) heritability compared to other brain cell types. However, whether and how these genome-wide association studies (GWAS) variants contribute to AD remain elusive. Here we prioritize 308 previously unreported AD risk variants at 181 cCREs by integrating genetic information with microglia-specific 3D epigenome annotation. We further establish the link between functional variants and target genes by single-cell CRISPRi screening in microglia. In addition, we show that AD variants exhibit allelic imbalance on target gene expression. In particular, rs7922621 is the effective variant in controlling TSPAN14 expression among other nominated variants in the same cCRE and exerts multiple physiological effects including reduced cell surface ADAM10 and altered soluble TREM2 (sTREM2) shedding. Our work represents a systematic approach to prioritize and characterize AD-associated variants and provides a roadmap for advancing genetic association to experimentally validated cell-type-specific phenotypes and mechanisms.

Effective removal of Cr(VI) in water by bulk-size polyaniline/polyvinyl alcohol/amyloid fibril composite beads

With the rapid expansion of industrial activities, chromium ions are discharged into the environment and cause water and soil pollution of various extents, which seriously endangers the natural ecological environment and human health. In this study, polyaniline/polyvinyl alcohol/amyloid fibril (PANI/PVA/AFL) composite gel beads (PPA) were prepared from polyaniline and amyloid fibrils with HCl as doping acid and PVA as a cross-linking agent. The results showed that PPA was an irregular composite bead with a diameter of 6 mm. The adsorption of Cr(VI) on the PPA gel beads followed the pseudo-second-order kinetics model, suggesting that chemical reactions were the controlling step in the Cr(VI) adsorption process. Though the Redlich-Peterson isotherm model had the best fit for the adsorption data, the isothermal adsorption process can be simplified using the Langmuir model. The maximum adsorption capacity for Cr(VI) in water was 51.5 mg g-1, comparable to or even higher than some PANI-based nanomaterials. Thermodynamic parameters showed that the adsorption process was a spontaneous, endothermic, and entropy-increasing process. Microscopic analysis revealed that the capture of Cr(VI) on PPA was mainly governed by electrostatic attraction, reduction, and complexation reactions. PPA can be used as a kind of effective remediation agent to remove Cr(VI) in water.

Preliminary results of the 105 GHz collective Thomson scattering system on HL-2A

A 105 GHz collective Thomson scattering (CTS) diagnostic has been successfully developed for fast-ion measurements on the HL-2A tokamak, and it has been deployed during an experimental campaign. Enhanced signals exhibiting synchronous modulation characteristics have been observed across all CTS channels upon the launch of a modulated probe wave. Results show that the intensity of the CTS signal increases with Neutral Beam Injection (NBI) power and is proportional to neutron count, indicating that the scattering signal contains a contribution from fast ions. Compared with the signal without NBI, the enhanced scattering spectrum due to NBI is slightly wider than the predicted fast ion range. Such broadening might be attributed to the heating effects of the gyrotron.

Expression quantitative trait methylation analysis elucidates gene regulatory effects of DNA methylation: the Framingham Heart Study

Expression quantitative trait methylation (eQTM) analysis identifies DNA CpG sites at which methylation is associated with gene expression. The present study describes an eQTM resource of CpG-transcript pairs derived from whole blood DNA methylation and RNA sequencing gene expression data in 2115 Framingham Heart Study participants. We identified 70,047 significant cis CpG-transcript pairs at p < 1E-7 where the top most significant eGenes (i.e., gene transcripts associated with a CpG) were enriched in biological pathways related to cell signaling, and for 1208 clinical traits (enrichment false discovery rate [FDR] ≤ 0.05). We also identified 246,667 significant trans CpG-transcript pairs at p < 1E-14 where the top most significant eGenes were enriched in biological pathways related to activation of the immune response, and for 1191 clinical traits (enrichment FDR ≤ 0.05). Independent and external replication of the top 1000 significant cis and trans CpG-transcript pairs was completed in the Women's Health Initiative and Jackson Heart Study cohorts. Using significant cis CpG-transcript pairs, we identified significant mediation of the association between CpG sites and cardiometabolic traits through gene expression and identified shared genetic regulation between CpGs and transcripts associated with cardiometabolic traits. In conclusion, we developed a robust and powerful resource of whole blood eQTM CpG-transcript pairs that can help inform future functional studies that seek to understand the molecular basis of disease.

[Effects of growth patterns and years on quality of Saposhnikoviae Radix samples]

This study aims to reveal the effects of different growth patterns and years on the quality of Saposhnikoviae Radix samples. The apparent colors of the powder samples were quantified by a colorimeter, and the total color values(E~*ab) were calculated. The content of prim-O-glucosylcimifugin, cimifugin, 4'-O-β-D-glucosyl-5-O-methylvisamminol, sec-O-glucosylhamaudol, and 3'-O-angeloylhamaudol in the samples was simultaneously determined by high performance liquid chromatography(HPLC). Cluster analysis, principal component analysis, partial least squares discriminant analysis, and Pearson correlation analysis were performed to analyze the powder chromatic values and the content of 5 components. The results showed that the E~*ab values of the samples were in the order of wild group<multiple-year-old group<one-year-old group. The content of cimifugin, sec-O-glucosylhamaudol, and 3'-O-angeloylhamaudol in the wild group was significantly higher than that in the multiple-year-old and one-year-old groups. The results of multivariate statistical analysis showed that the quality of multiple-year-old group varied greatly. The quality of the multiple-year-old samples was close to that of the wild group and better than that of the one-year-old group. The variable importance in the projection(VIP) values of b~*, 3'-O-angeloylhamaudol content, E~*ab, and L~* were all larger than 1, and that of cimifugin content was close to 1. The E~*ab value was negatively correlated with the content of prim-O-glucosylcimifugin, cimifugin, sec-O-glucosylhamaudol, and 3'-O-angeloylhamaudol, while it had no linear correlation with the 4'-O-β-D-glucosyl-5-O-methylvisamminol content. The growth patterns and years had different effects on the quality of Saposhnikoviae Radix samples. The chromatic values of Saposhnikoviae Radix and the content of 5 components can be used to evaluate the quality of Saposhnikoviae Radix, and 3'-O-angeloylhamaudol and cinmifugin can be considered as markers for the quality control of Saposhnikovia divaricata during the growing process.

Novel efficient capture of hexavalent chromium by polyethyleneimine/amyloid fibrils/polyvinyl alcohol aerogel beads: Functional design, applicability, and mechanisms

The harmful effects of hexavalent chromium (Cr(VI)) on the environment and human health have aroused wide public concern. In this study, bulk spherical aerogel beads (PAP) were synthesized from polyethyleneimine (PEI), protein amyloid fibrils (AFL), and polyvinyl alcohol (PVA) through green technology and its removal of Cr(VI) from wastewater was comprehensively studied. The results showed that although the bulk PAP beads (∼ 5 mm) only had an average pore size of 16.88 nm and a BET surface area of 12 m²/g, its maximum adsorption capacity for Cr(VI) reached 121.44 mg/g (at 298 K). Cr(VI) adsorption onto PAP conformed to pseudo-second-order adsorption kinetics and was endothermic. The adsorption of Cr(VI) decreased stepwise with the increase of solution alkalinity (pH = 2: 91.97%; pH = 10: 0.04%). Importantly, PAP showed high selectivity towards Cr(VI) in mixed heavy metal solutions (Cr(VI) > Pb(II) > Ni(II) > Cu(II) > Cd(II)) and good reusability (removal efficiency > 88% after 5 cycles). PAP had excellent anti-interference ability against FA and HCO₃^- with the overall removal rate exceeding 87% in the presence of 5 - 25 mg/L of these ions. Cations such as Na⁺, Mg²⁺, and other heavy metal ions at high concentrations could promote the removal efficiency of Cr(VI). The removal rates of Cr(VI) and Cr(III) by PAP in a tannery wastewater were 34.4% and 59.3%, respectively. Meanwhile, the removal rates of Cr(VI) in a electroplating wastewater and a contaminated soil leachate reached 84.4∼89.7%, showing high practicability. Mechanism studies revealed that electrostatic attraction, hydrogen bonding, reduction, and complexation were the main reactions for Cr(VI) removal by PAP. In general, the study of PAP provides a new insight into using bulk monolith materials for treating Cr(VI) contaminated wastewater.

Increased Prevalence of Rare Copy Number Variants in Treatment-Resistant Psychosis

BACKGROUND

It remains unknown why ~30% of patients with psychotic disorders fail to respond to treatment. Previous genomic investigations of treatment-resistant psychosis have been inconclusive, but some evidence suggests a possible link between rare disease-associated copy number variants (CNVs) and worse clinical outcomes in schizophrenia. Here, we identified schizophrenia-associated CNVs in patients with treatment-resistant psychotic symptoms and then compared the prevalence of these CNVs to previously published schizophrenia cases not selected for treatment resistance.

METHODS

CNVs were identified using chromosomal microarray (CMA) and whole exome sequencing (WES) in 509 patients with treatment-resistant psychosis (a lack of clinical response to ≥3 adequate antipsychotic medication trials over at least 5 years of psychiatric hospitalization). Prevalence of schizophrenia-associated CNVs in this sample was compared to that in a previously published large schizophrenia cohort study.

RESULTS

Integrating CMA and WES data, we identified 47 cases (9.2%) with at least one CNV of known or possible neuropsychiatric risk. 4.7% (n = 24) carried a known neurodevelopmental risk CNV. The prevalence of well-replicated schizophrenia-associated CNVs was 4.1%, with duplications of the 16p11.2 and 15q11.2-q13.1 regions, and deletions of the 22q11.2 chromosomal region as the most frequent CNVs. Pairwise loci-based analysis identified duplications of 15q11.2-q13.1 to be independently associated with treatment resistance.

CONCLUSIONS

These findings suggest that CNVs may uniquely impact clinical phenotypes beyond increasing risk for schizophrenia and may potentially serve as biological entry points for studying treatment resistance. Further investigation will be necessary to elucidate the spectrum of phenotypic characteristics observed in adult psychiatric patients with disease-associated CNVs.

Plasma position measurements by O-mode and X-mode reflectometry systems in tokamak plasmas

Plasma Position Reflectometry (PPR) is planned to provide plasma position and shape information for plasma operation in future fusion reactors. Its primary function is to calibrate the drift of the magnetic signals due to the integral nature of magnetic measurement. Here, we attempt to measure plasma position using ordinary mode (O-mode) and extraordinary mode (X-mode) reflectometry systems on two tokamaks. A new physical model based on the phase shift is proposed to deduce the relative movement of the cut-off layer without density inversion. We demonstrate the plasma position measurements by absolute measurement from density profile inversion and relative measurement from phase shift. The combination of X-mode and O-mode reflectometers can minimize the limitations of single polarization reflectometry and further increase the accuracy of plasma position measurement. These results could provide an important technical basis for the further development of a real-time control system based on PPR.

Genetic Modifiers of Cystic Fibrosis Lung Disease Severity: Whole-Genome Analysis of 7,840 Patients

Rationale: Lung disease is the major cause of morbidity and mortality in persons with cystic fibrosis (pwCF). Variability in CF lung disease has substantial non-CFTR (CF transmembrane conductance regulator) genetic influence. Identification of genetic modifiers has prognostic and therapeutic importance. Objectives: Identify genetic modifier loci and genes/pathways associated with pulmonary disease severity. Methods: Whole-genome sequencing data on 4,248 unique pwCF with pancreatic insufficiency and lung function measures were combined with imputed genotypes from an additional 3,592 patients with pancreatic insufficiency from the United States, Canada, and France. This report describes association of approximately 15.9 million SNPs using the quantitative Kulich normal residual mortality-adjusted (KNoRMA) lung disease phenotype in 7,840 pwCF using premodulator lung function data. Measurements and Main Results: Testing included common and rare SNPs, transcriptome-wide association, gene-level, and pathway analyses. Pathway analyses identified novel associations with genes that have key roles in organ development, and we hypothesize that these genes may relate to dysanapsis and/or variability in lung repair. Results confirmed and extended previous genome-wide association study findings. These whole-genome sequencing data provide finely mapped genetic information to support mechanistic studies. No novel primary associations with common single variants or rare variants were found. Multilocus effects at chr5p13 (SLC9A3/CEP72) and chr11p13 (EHF/APIP) were identified. Variant effect size estimates at associated loci were consistently ordered across the cohorts, indicating possible age or birth cohort effects. Conclusions: This premodulator genomic, transcriptomic, and pathway association study of 7,840 pwCF will facilitate mechanistic and postmodulator genetic studies and the development of novel therapeutics for CF lung disease.

The accumulation and toxicity of ZIF-8 nanoparticles in Corbicula fluminea

Metal-organic frameworks (MOFs) are promising new materials that have been intensively studied and possibly applied to various environmental remediation. However, little is known about the fate and risk of MOFs to living organisms in the water environment. Here, the toxic effects of ZIF-8 nanoparticles (NPs) on benthic organisms were confirmed by sub-chronic toxicity experiments (7 and 14 days) using Corbicula fluminea as the model organism. With exposure doses ranging from 0 to 50 mg/L, ZIF-8 NPs induced oxidative stress behaviors similar to the hormesis effect in the tissues of C. fluminea. The oxidative stress induced by ZIF-8 NPs and the released Zn²⁺ was the crucial cause of the toxic effects. Besides, we also found that the ZIF-8 NPs and dissolved Zn²⁺ may result in different mechanisms of toxicity and accumulation depending on the dosages. The Zn²⁺ release rate of ZIF-8 NPs was high at low dosages, leading to a higher proportion of Zn²⁺ taken up by C. fluminea than the particulate ZIF-8. Conversely, at high dosages, C. fluminea mainly ingested the ZIF-8 NPs and resulted in increased mortality. The results have important implications for understanding the fate and biological effects of ZIF-8 in natural aquatic environments.

Gene Expression and Splicing QTL Analysis of Blood Cells in African American Participants from the Jackson Heart Study

Most gene expression and alternative splicing quantitative trait loci (eQTL/sQTL) studies have been biased toward European ancestry individuals. Here, we performed eQTL and sQTL analysis using TOPMed whole genome sequencing-derived genotype data and RNA sequencing data from stored peripheral blood mononuclear cells in 1,012 African American participants from the Jackson Heart Study (JHS). At a false discovery rate (FDR) of 5%, we identified 4,798,604 significant eQTL-gene pairs, covering 16,538 unique genes; and 5,921,368 sQTL-gene-cluster pairs, covering 9,605 unique genes. About 31% of detected eQTL and sQTL variants with a minor allele frequency (MAF) > 1% in JHS were rare (MAF < 0.1%), and therefore unlikely to be detected, in European ancestry individuals. We also generated 17,630 eQTL credible sets and 24,525 sQTL credible sets for genes (gene-clusters) with lead QTL p < 5e-8. Finally, we created an open database, which is freely available online, allowing fast query and bulk download of our QTL results.

Leveraging base-pair mammalian constraint to understand genetic variation and human disease

Thousands of genomic regions have been associated with heritable human diseases, but attempts to elucidate biological mechanisms are impeded by an inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function, agnostic to cell type or disease mechanism. Single-base phyloP scores from 240 mammals identified 3.3% of the human genome as significantly constrained and likely functional. We compared phyloP scores to genome annotation, association studies, copy-number variation, clinical genetics findings, and cancer data. Constrained positions are enriched for variants that explain common disease heritability more than other functional annotations. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.

COVID-19 pandemic and neonatal birth weight: a systematic review and meta-analysis

OBJECTIVES

Lockdown was implemented in many countries during the pandemic, which led to myriad changes in pregnant women's lives. However, the potential impacts of the COVID-19 pandemic on neonatal outcomes remain unclear. We aimed to evaluate the association between the pandemic and neonatal birth weight.

STUDY DESIGN

This was a systematic review and meta-analysis of the previous literature.

METHODS

We searched the MEDLINE and Embase databases up to May 2022 and extracted 36 eligible studies that compared neonatal birth weight between the pandemic and the prepandemic period. The following outcomes were included: mean birth weight, low birth weight (LBW), very low birth weight (VLBW), macrosomia, small for gestational age (SGA), very small for gestational age (VSGA), and large for gestational age (LGA). Statistical heterogeneity among studies was assessed to determine whether a random effects model or fixed effects model was conducted.

RESULTS

Of the 4514 studies identified, 36 articles were eligible for inclusion. A total of 1,883,936 neonates during the pandemic and 4,667,133 neonates during the prepandemic were reported. We identified a significant increase in mean birth weight (pooled mean difference [95% confidence interval (CI)] = 15.06 [10.36, 19.76], I² = 0.0%, 12 studies) and a reduction in VLBW (pooled OR [95% CI] = 0.86 [0.77, 0.97], I² = 55.4%, 12 studies). No overall effect was identified for other outcomes: LBW, macrosomia, SGA, VSGA, and LGA. There was publication bias for mean birth weight with a borderline significance (Egger's P = 0.050).

CONCLUSION

Pooled results showed the pandemic was significantly associated with an increase in mean birth weight and a reduction in VLBW, but not for other outcomes. This review provided clues about the indirect effects of the pandemic on neonatal birth weight and more healthcare measures needed to improve neonatal long-term health.

Immunogenicity of peptide-based vaccine composed of epitopes from Echinococcus granulosus rEg.P29

Echinococcus granulosus is one of the main causes of economic loss in the livestock industry because of its food-borne transmission. Cutting off the transmission route is a valid prevention method, and vaccines are the most effective means of controlling and eliminating infectious diseases. However, no human-related vaccine has been yet marketed. As a genetic engineering vaccine, recombinant protein P29 of E. granulosus (rEg.P29) could provide protection against deadly challenges. In this study, we generated peptide vaccines (rEg.P29_T , rEg.P29_B , and rEg.P29_T+B ) based on rEg.P29 and an immunized model was established by subcutaneous immunization. Further evaluation showed that peptide vaccine immunization in mice induced T helper type 1 (Th1)-mediated cellular immune responses, leading to high levels of rEg.P29 or rEg.P29_B -specific antibodies. In addition, rEg.P29_T+B immunization can induce a higher antibody and cytokine production level than single-epitope vaccines, and immune memory is also longer. Collectively, these results suggest that rEg.P29_T+B has the potential to be developed as an efficient subunit vaccine for use in areas where E. granulosus is endemic.

Modified transcrestal sinus floor elevation with concomitant implant placement in edentulous posterior maxillae with residual bone height of 5 mm or less: a non-controlled prospective study

The aim of this study was to describe a modified transcrestal sinus floor elevation (mTSFE) technique and to evaluate its clinical effectiveness and reliability when residual bone height is severely reduced. Forty-three maxillary edentulous patients who met the inclusion criteria were enrolled. All patients underwent the mTSFE technique; 66 dental implants were inserted simultaneously. Patient-reported outcomes were assessed 2 weeks after surgery. Prosthetic crowns were placed 6 months after surgery. Radiographic analyses and clinical analyses were conducted to assess the clinical effectiveness and feasibility of mTSFE during a follow-up period of 2-8 years. The mean vertical bone increase after surgery was 8.09 mm, and it decreased to 6.56 mm at 6 months after surgery. Two cases of membrane perforation occurred during surgery and one implant was lost in the third year after surgery; the survival rate at the implant level was 98.48%. No severe postoperative complication was reported and the subjective feeling of patients was acceptable. This mTSFE technique could simplify the operative procedure and might be helpful to reduce intraoperative trauma, as well as to alleviate postoperative discomfort.

MHD instability dynamics and turbulence enhancement towards the plasma disruption at the HL-2A tokamak

The evolutions of MHD instability behaviors and enhancement of both electrostatic and electromagnetic turbulence towards the plasma disruption have been clearly observed in the HL-2A plasmas. Two types of plasma disruptive discharges have been investigated for similar equilibrium parameters: one with a distinct stage of a small central temperature collapse ([Formula: see text] 5-10%) around 1 millisecond before the thermal quench (TQ), while the other without. For both types, the TQ phase is preceded by a rotating 2/1 tearing mode, and it is the development of the cold bubble from the inner region of the 2/1 island O-point along with its inward convection that causes the massive energy loss. In addition, the micro-scale turbulence, including magnetic fluctuations and density fluctuations, increases before the small collapse, and more significantly towards the TQ. Also, temperature fluctuations measured by electron cyclotron emission imaging enhances dramatically at the reconnection site and expand into the island when approaching the small collapse and TQ, and the expansion is more significant close to the TQ. The observed turbulence enhancement near the X-point cannot be fully interpreted by the linear stability analysis by GENE. Evidences suggest that nonlinear effects, such as the reduction of local [Formula: see text] shear and turbulence spreading, may play an important role in governing turbulence enhancement and expansion. These results imply that the turbulence and its interaction with the island facilitate the stochasticity of the magnetic flux and formation of the cold bubble, and hence, the plasma disruption.

Clinical characteristics and prognostic characterization of endometrial carcinoma: a comparative analysis of molecular typing protocols

BACKGROUND

Endometrial carcinoma (EC) is one of the most common gynecological malignancies in China and globally, accounting for the fourth-prevalent cancer in women. Although numerous studies have confirmed prognostic value of The Cancer Genome Atlas (TCGA) molecular subgroups, it is unclear how they are combined with histological features. The main objective of this study was to compare ProMisE and TCGA classification for the rapid and accurate prediction of prognosis within EC patients, together with the provision of a revised strategy for individualized diagnosis and treatment of patients.

METHODS

Within this study, 70 patients with EC from Beijing Tsinghua Changgeng Hospital (affiliated to Tsinghua University) were retrospectively examined between July 2015 and December 2021. Samples were processed for determination of clinical markers, together with ProMisE and TCGA classification.

RESULTS

Comparative analysis across four TCGA types (POLE, Low-CN, High-CN, and MSI-H) and age, was statistically significant (χ²= 7.000, p = 0.029). There was no significant difference observed among the four TCGA types and FIGO stage, vascular invasion and depth of invasion, or lymph node metastasis and tumor area. There was no significant association between the expression of Vimentin, Ki-67, PTEN, MSH2, PAX-8, β-catenin, CD10, ER, PR, P16, MLH1, and PMS2 with the four TCGA types. In addition, p63 expression (χ²= 11.09, p = 0.029) and p53 expression (χ²= 11.585, p = 0.005) were statistically significant. Numerous models demonstrated that patients with POLE mutations and low-CN had higher progression free survival (PFS) and overall survival (OS), whereas those with high-CN had lowest values. The log-rank test revealed that the survival rate of PR-positive and ER-positive patients was significantly higher (p < 0.001).

CONCLUSION

Overall, these results can be of additional benefit for clinical applications, in comparison to the ProMisE classification method. In addition, PR, ER, vascular infiltration, hyperlipidemia and atherosclerosis were found to be the key factors affecting EC prognosis.

Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease

Although thousands of genomic regions have been associated with heritable human diseases, attempts to elucidate biological mechanisms are impeded by a general inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function that is agnostic to cell type or disease mechanism. Here, single base phyloP scores from the whole genome alignment of 240 placental mammals identified 3.5% of the human genome as significantly constrained, and likely functional. We compared these scores to large-scale genome annotation, genome-wide association studies (GWAS), copy number variation, clinical genetics findings, and cancer data sets. Evolutionarily constrained positions are enriched for variants explaining common disease heritability (more than any other functional annotation). Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease.

Comparative Genomic and Transcriptomic Analyses Reveal the Impacts of Genetic Admixture in Kazaks, Uyghurs, and Huis

Population admixture results in the combinations of genetic components derived from distinct ancestral populations, which may impact diversity at the genetic, transcriptomic, and phenotypic levels, as well as postadmixture adaptive evolution. Here, we systematically investigated the genomic and transcriptomic diversity in Kazaks, Uyghurs, and Huis-three admixed populations of various Eurasian ancestries living in Xinjiang, China. All three populations showed elevated genetic diversity and closer genetic distance compared with the reference populations across the Eurasian continent. However, we also observed differentiated genomic diversity and inferred different demographic histories among the three populations. Varying ancestry proportions observed in both the global and local aspects corresponded to the population-differentiated genomic diversity, with the most representative signals observed in the genes EDAR, SULT1C4, and SLC24A5. The varying local ancestry partly resulted from the postadmixture local adaptation, with the most significant signals observed in immunity- and metabolism-related pathways. Admixture-shaped genomic diversity further influenced the transcriptomic diversity in the admixed populations; in particular, population-specific regulatory effects were associated with immunity- and metabolism-involved genes such as MTHFR, FCER1G, SDHC, and BDH2. Furthermore, differentially expressed genes between the populations were identified, many of which could be explained by the population-specific regulatory properties, including genes related to health concerns (e.g., AHI1 between Kazak and Uyghurs [P < 6.92 × 10-5] and CTRC between Huis and Uyghurs [P < 2.32 × 10-4]). Our results demonstrate genetic admixture as a driving force in shaping the genomic and transcriptomic diversity of human populations.

Theoretical determination of superior high-temperature thermoelectricity in an n-type doped 2H-ZrI2 monolayer

Two-dimensional materials with a competitive figure of merit zT are extremely desirable for the fabrication of thermoelectric modules. In the present work, we systematically evaluated the thermoelectricity of monolayer 2H-ZrI₂ through first-principles calculations and semiclassical Boltzmann transport theory. Apart from its all-round structural stability and feasibility of experimental preparation, the semiconducting material with a moderate indirect bandgap of 1.07 eV at the HSE06 level exhibits an acceptable lattice thermal conductivity κ_L of 6.69 W m^-1 K^-1 at 900 K contributed dominantly by acoustic modes. The four-phonon scattering is found to exert a minor effect on the κ_L of the monolayer. Moreover, a quite large power factor of up to 147.89 mW m^-1 K^-2 can be achieved due to the conduction band valley degeneracy near the Fermi level. These transport coefficients eventually give rise to a significant optimal n-type zT value as high as 3.57 at 900 K at a certain experimentally achievable electron doping concentration. Our study demonstrates the potential application of monolayer 2H-ZrI₂ in high-temperature thermoelectric devices.

Simultaneous removal of aqueous same ionic type heavy metals and dyes by a magnetic chitosan/polyethyleneimine embedded hydrophobic sodium alginate composite: Performance, interaction and mechanism

Heavy metals and azo dyes caused huge harm to the aqueous system and human health. A magnetic chitosan/polyethyleneimine embedded hydrophobic sodium alginate composite (MCPS) was designed and prepared to simultaneously remove aqueous same ionic type heavy metals and azo dyes. In mono-polluted system, the optimal pH for Cr(VI), MO (methyl orange), Cu(Ⅱ) and MB (methylene blue) were 3, 2, 6 and 12 with a saturated adsorption capacity of 87.53, 66.41, 351.03 and 286.54 mg/g, respectively. Pseudo-second-order was suitable to describe the adsorption kinetics of them and the adsorption isotherms were more consistent with the Langmuir isotherm model being a spontaneous, endothermic, and entropy-increasing process. In binary-polluted system, MCPS possessed simultaneous adsorption for Cr (Ⅵ)-MO and Cu(Ⅱ)-MB pollutants at their optimal pH, in addition, whether in anionic or cationic solution, the removal of heavy metals were promoted with the add of azo dyes but the removal of azo dyes were suppressed with the add of heavy metals. Both Cr (Ⅵ)-MO and Cu(Ⅱ)-MB pollutants could be effectively adsorbed and desorbed from MCPS by changing the pH of the aqueous solution to realize recyclability. Lastly, removal mechanism was revealed in detail by FT-IR, EDS and XPS.

Exploration on the role of different iron species in the remediation of As and Cd co-contamination by sewage sludge biochar

Numerous studies have explored the adsorption of cadmium (Cd) and arsenic (As) by iron (Fe)-modified biochar, but few studies have examined in-depth the similarities and differences in the adsorption behavior of different iron types on Cd and As. In this study, sewage sludge biochar (BC) was co-pyrolyzed with self-made Fe minerals (magnetite, hematite, ferrihydrite, goethite, and schwertmannite) to treat Cd and As co-contaminated water. The adsorption of Cd and As on the Fe-modified biochar was further analyzed by adsorption kinetics, adsorption isotherms, and adsorption thermodynamics combined with a series of characterization experiments. Both SEM-EDX and XRD results confirmed the successful loading of iron minerals onto BC. Both adsorption kinetics and adsorption isotherms experiments showed that the adsorption of Cd and As by BC and the other five Fe-modified biochar was mainly controlled by chemical interactions. The results also indicated that goethite biochar (GtBC) was the most effective for the adsorption of Cd among the five Fe-modified biochar. Ferrihydrite biochar (FhBC) formed more diverse complexes, coupled with the relatively stronger electrons accepting ability, thus making it more effective for As adsorption than the others. Additionally, GtBC and hematite biochar (HmBC) were found effective for the adsorption of both Cd and As, whereas MBC was not found effective for either metal. Furthermore, combined with XPS results, the adsorption of Cd by the materials was mainly governed by Cd²⁺-π interactions, complexation precipitation, and co-precipitation, while oxidation reactions also existed for As.

Studying the mechanism underlying lipid metabolism in osteosarcoma based on transcriptomic RNA sequencing and single-cell data

BACKGROUND

We aimed to provide a new typing method for osteosarcoma (OS) based on single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data from the perspective of lipid metabolism and examine its potential mechanisms in the onset and progression of OS.

METHODS

Scores for six lipid metabolic pathways were calculated by single-sample gene set enrichment analysis (ssGSEA) based on a scRNA-seq dataset and three microarray expression profiles. Subsequently, cluster typing was conducted using unsupervised consistency clustering. Furthermore, single-cell clustering and dimensionality-reduction analyses identified cell subtypes. Finally, an analysis of cellular receptors was performed using CellphoneDB to identify cellular communication.

RESULTS

OS was classified into three subtypes based on lipid metabolic pathways. Among them, patients in clust3 showed poor prognoses, whereas those in clust1 and clust2 exhibited good prognoses. In addition, ssGSEA analysis showed that patients in clust3 had lower immune cell scores. Moreover, the Th17 cell differentiation pathway was significantly differentially enriched between clust2 and clust3, with lower enrichment scores for metabolic pathways in the former relative to clust1 and clust2. In total, 24 genes were upregulated between clust1 and clust2, whereas 20 were downregulated in clust3. These observations were validated by single-cell data analysis. Finally, through scRNA-seq data analysis, we identified nine ligand-receptor pairs particularly critical for communication between normal and malignant cells.

CONCLUSIONS

Three clusters were identified and the single-cell analysis revealed that malignant cells dominated lipid metabolism patterns in tumors, thereby influencing the tumor microenvironment.

DeepGWAS: Enhance GWAS Signals for Neuropsychiatric Disorders via Deep Neural Network

Genetic dissection of neuropsychiatric disorders can potentially reveal novel therapeutic targets. While genome-wide association studies (GWAS) have tremendously advanced our understanding, we approach a sample size bottleneck (i.e., the number of cases needed to identify >90% of all loci is impractical). Therefore, computationally enhancing GWAS on existing samples may be particularly valuable. Here, we describe DeepGWAS, a deep neural network-based method to enhance GWAS by integrating GWAS results with linkage disequilibrium and brain-related functional annotations. DeepGWAS enhanced schizophrenia (SCZ) loci by ~3X when applied to the largest European GWAS, and 21.3% enhanced loci were validated by the latest multi-ancestry GWAS. Importantly, DeepGWAS models can be transferred to other neuropsychiatric disorders. Transferring SCZ-trained models to Alzheimer's disease and major depressive disorder, we observed 1.3-17.6X detected loci compared to standard GWAS, among which 27-40% were validated by other GWAS studies. We anticipate DeepGWAS to be a powerful tool in GWAS studies.

Construction of a novel mRNAsi-related risk model for predicting prognosis and immunotherapy response in osteosarcoma

Background

Targeting cancer stem cells (CSC) may represent a future therapeutic direction for osteosarcoma (OS), which mainly relies on the identification of CSC markers. This study aimed to classify OS based on messenger ribonucleic acid (mRNA) stemness indices (mRNAsi) and construct a mRNAsi-related risk model to predict the prognosis of OS.

Methods

The one-class logistic regression (OCLR) algorithm was applied to the RNA- sequencing (seq) data of human embryonic stem cells (hESC) and induced pluripotent stem cell (iPSC) lines to calculate mRNAsi. Weighted gene co-expression network analysis (WGCNA) was performed on data obtained from the TARGET database to screen the mRNAsi-related genes. Univariate Cox regression analysis was implemented to screen mRNAsi-related genes with prognostic significance for consensus clustering of OS. The least absolute shrinkage and selection operator (LASSO) and COX regression analysis were conducted to construct a risk model based on mRNAsi-related genes.

Results

Six gene modules were identified in the TARGET database. The yellow module showed the strongest negative correlation with mRNAsi and the strongest significant positive correlation with the immune score and stromal score. OS was divided into three molecular subtypes with significant survival differences based on 73 mRNAsi-related genes with prognostic value for OS. The survival rate was ranked as C3 < C1 < C2 from low to high. The levels of immune components in C2 was significantly higher than those in C1 and C3. HSD11B2, GBP1, RNF130, APBB1IP, and NPC2 in the yellow module were used as variables for building the mRNAsi-related risk model. The survival rate of the high-risk group (as defined by this model) was significantly higher than that of the low-risk group, and it had significant survival prediction ability in 28 types of cancer. In addition, the mRNAsi-related risk model was superior to the Tumor Immune Dysfunction and Exclusion (TIDE) model in predicting the prognosis and immunotherapy response in all three immunotherapy cohorts.

Conclusions

This study classified OS and constructed a mRNAsi-related risk model based on mRNAsi-related genes, which provides a potential tool for more accurate risk stratification of OS and prediction of immunotherapy response.

RUP2 facilitates UVR8 redimerization via two interfaces

The plant UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8) exists as a homodimer in its inactive ground state. Upon UV-B exposure, UVR8 monomerizes and interacts with a downstream key regulator, the CONSTITUTIVE PHOTOMORPHOGENIC 1/SUPPRESSOR OF PHYA (COP1/SPA) E3 ubiquitin ligase complex, to initiate UV-B signaling. Two WD40 proteins, REPRESSOR OF UV-B PHOTOMORPHOGENESIS 1 (RUP1) and RUP2 directly interact with monomeric UVR8 and facilitate UVR8 ground state reversion, completing the UVR8 photocycle. Here, we reconstituted the RUP-mediated UVR8 redimerization process in vitro and reported the structure of the RUP2-UVR8^W285A complex (2.0 Å). RUP2 and UVR8^W285A formed a heterodimer via two distinct interfaces, designated Interface 1 and 2. The previously characterized Interface 1 is found between the RUP2 WD40 domain and the UVR8 C27 subregion. The newly identified Interface 2 is formed through interactions between the RUP2 WD40 domain and the UVR8 core domain. Disruption of Interface 2 impaired UV-B induced photomorphogenic development in Arabidopsis thaliana. Further biochemical analysis indicated that both interfaces are important for RUP2-UVR8 interactions and RUP2-mediated facilitation of UVR8 redimerization. Our findings suggest that the two-interface-interaction mode is adopted by both RUP2 and COP1 when they interact with UVR8, marking a step forward in understanding the molecular basis that underpins the interactions between UVR8 and its photocycle regulators.

HPTAD: A computational method to identify topologically associating domains from HiChIP and PLAC-seq datasets

High-throughput chromatin conformation capture technologies, such as Hi-C and Micro-C, have enabled genome-wide view of chromatin spatial organization. Most recently, Hi-C-derived enrichment-based technologies, including HiChIP and PLAC-seq, offer attractive alternatives due to their high signal-to-noise ratio and low cost. While a series of computational tools have been developed for Hi-C data, methods tailored for HiChIP and PLAC-seq data are still under development. Here we present HPTAD, a computational method to identify topologically associating domains (TADs) from HiChIP and PLAC-seq data. We performed comprehensive benchmark analysis to demonstrate its superior performance over existing TAD callers designed for Hi-C data. HPTAD is freely available at https://github.com/yunliUNC/HPTAD.

Saponins of ginseng products: a review of their transformation in processing

The primary processed product of Panax ginseng C.A. Meyer (P. ginseng) is red ginseng. As technology advances, new products of red ginseng have arisen. Red ginseng products, e.g., traditional red ginseng, sun ginseng, black ginseng, fermented red ginseng, and puffed red ginseng, are commonly used in herbal medicine. Ginsenosides are the major secondary metabolites of P. ginseng. The constituents of P. ginseng are significantly changed during processing, and several pharmacological activities of red ginseng products are dramatically increased compared to white ginseng. In this paper, we aimed to review the ginsenosides and pharmacological activities of various red ginseng products, the transformation law of ginsenosides in processing, and some clinical trials of red ginseng products. This article will help to highlight the diverse pharmacological properties of red ginseng products and aid in the future development of red ginseng industrialization.

Exploring the common pathogenesis of Alzheimer's disease and type 2 diabetes mellitus via microarray data analysis

Background

Alzheimer's Disease (AD) and Type 2 Diabetes Mellitus (DM) have an increased incidence in modern society. Although more and more evidence has supported that DM is prone to AD, the interrelational mechanisms remain fully elucidated.

Purpose

The primary purpose of this study is to explore the shared pathophysiological mechanisms of AD and DM.

Methods

Download the expression matrix of AD and DM from the Gene Expression Omnibus (GEO) database with sequence numbers GSE97760 and GSE95849, respectively. The common differentially expressed genes (DEGs) were identified by limma package analysis. Then we analyzed the six kinds of module analysis: gene functional annotation, protein-protein interaction (PPI) network, potential drug screening, immune cell infiltration, hub genes identification and validation, and prediction of transcription factors (TFs).

Results

The subsequent analyses included 339 common DEGs, and the importance of immunity, hormone, cytokines, neurotransmitters, and insulin in these diseases was underscored by functional analysis. In addition, serotonergic synapse, ovarian steroidogenesis, estrogen signaling pathway, and regulation of lipolysis are closely related to both. DEGs were input into the CMap database to screen small molecule compounds with the potential to reverse AD and DM pathological functions. L-690488, exemestane, and BMS-345541 ranked top three among the screened small molecule compounds. Finally, 10 essential hub genes were identified using cytoHubba, including PTGS2, RAB10, LRRK2, SOS1, EEA1, NF1, RAB14, ADCY5, RAPGEF3, and PRKACG. For the characteristic Aβ and Tau pathology of AD, RAPGEF3 was associated significantly positively with AD and NF1 significantly negatively with AD. In addition, we also found ADCY5 and NF1 significant correlations with DM phenotypes. Other datasets verified that NF1, RAB14, ADCY5, and RAPGEF3 could be used as key markers of DM complicated with AD. Meanwhile, the immune cell infiltration score reflects the different cellular immune microenvironments of the two diseases.

Conclusion

The common pathogenesis of AD and DM was revealed in our research. These common pathways and hub genes directions for further exploration of the pathogenesis or treatment of these two diseases.

The role of upper and lower genital tract microbiota alterations in term chorionamnionitis: A prospective study

Objective

This study aimed to compare the dynamics of lower and upper genital tract microbiota in normal term pregnancy, histological chorioamnionitis (HCA), and clinical chorioamnionitis (CCA) patients to provide a reference for the diagnosis and treatment of chorioamnionitis (CAM) patients.

Methods

We prospectively collected vaginal and cervical secretions, as well as placenta tissues, fetal membranes, and amniotic fluid from normal-term pregnant women, HCA and CCA patients. Then, we performed genomic DNA extraction and PCR amplification for all samples. The eligible samples were analyzed by 16S ribosomal RNA (16S rRNA) sequencing. Additionally, all placenta tissues were histopathologically examined, and neonatal pharyngeal swabs and placenta tissues from the HCA and CCA groups were subjected to microbial culture.

Results

A total of 85 term pregnant women were enrolled in this study, including 34 in the normal group (N), 37 in the HCA group, and 14 in the CCA group. A total of 171 qualified samples were analyzed by 16S rRNA sequencing. The results suggested that the cervical microbiota was highly similar to the vaginal microbiota in normal term parturients, with Lactobacillus as the dominant bacterium. Moreover, there was no difference in the alpha and beta diversity of vaginal microbiota between the N, HCA, and CCA groups at the genus level. Besides, no significant differences were detected in cervical microbiome among the three groups. Regarding intrauterine microorganisms, the N and HCA groups had similar microbial composition but were different from the CCA group. No microbe was detected in the placental tissue of normal term parturients, while some microorganisms were found in the intrauterine amniotic fluid and fetal membrane samples. Regardless of cultivation or 16S rRNA sequencing, an extremely low microbial positive rate was detected in HCA and CCA intrauterine samples. Compared to the normal group, Lactobacillus was significantly reduced in the CCA group intrauterine, and Ureaplasma and Enterococcus increased with no statistically significant.

Conclusion

The N, HCA and CCA groups had similar composition of vaginal and cervical microflora. Some normal-term pregnant women can harbor non-pathogenic microbiota in the uterine cavity. Sterile inflammation is more frequent than microbial-associated inflammation in term HCA and CCA parturients.

Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program

Genome-wide association studies have identified thousands of single nucleotide variants and small indels that contribute to variation in hematologic traits. While structural variants are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of structural variants to quantitative blood cell trait variation is unknown. Here we utilized whole genome sequencing data in ancestrally diverse participants of the NHLBI Trans Omics for Precision Medicine program (N = 50,675) to detect structural variants associated with hematologic traits. Using single variant tests, we assessed the association of common and rare structural variants with red cell-, white cell-, and platelet-related quantitative traits and observed 21 independent signals (12 common and 9 rare) reaching genome-wide significance. The majority of these associations (N = 18) replicated in independent datasets. In genome-editing experiments, we provide evidence that a deletion associated with lower monocyte counts leads to disruption of an S1PR3 monocyte enhancer and decreased S1PR3 expression.

Impacts of COVID-19 pandemic on preterm birth: a systematic review and meta-analysis

OBJECTIVES

The COVID-19 pandemic has significantly affected healthcare systems and daily well-being. However, the reports of the indirect impacts of the pandemic on preterm birth remain conflicting. We performed a meta-analysis to examine whether the pandemic altered the risk of preterm birth.

STUDY DESIGN

This was a systematic review and meta-analysis of the previous literature.

METHODS

We searched MEDLINE and Embase databases until March 2022 using appropriate keywords and extracted 63 eligible studies that compared preterm between the COVID-19 pandemic period and the prepandemic period. A random effects model was used to obtain the pooled odds of each outcome. The study protocol was registered with PROSPERO (No. CRD42022326717).

RESULTS

The search identified 3827 studies, of which 63 reports were included. A total of 3,220,370 pregnancies during the COVID-19 pandemic period and 6,122,615 pregnancies during the prepandemic period were studied. Compared with the prepandemic period, we identified a significant decreased odds of preterm birth (PTB; <37 weeks' gestation; pooled odds ratio [OR; 95% confidence interval (CI)] = 0.96 [0.94, 0.98]; I² = 78.7%; 62 studies) and extremely PTB (<28 weeks' gestation; pooled OR [95% CI] = 0.92 [0.87, 0.97]; I² = 26.4%; 25 studies) during the pandemic, whereas there was only a borderline significant reduction in the odds of very PTB (<32 weeks' gestation; pooled OR [95% CI] = 0.93 [0.86, 1.01]; I² = 90.1%; 33 studies) between the two periods. There was significant publication bias for PTB.

CONCLUSION

Pooled results suggested the COVID-19 pandemic was associated with preterm birth, although there was only a borderline significant reduction for very PTB during the pandemic compared with the prepandemic period. Large studies showed conflicting results, and further research on whether the change is related to pandemic mitigation measures was warranted.