Publications by authors named "Tao Ma"

872 Publications

Pomegranate-Inspired Graphene Parcel Enables High-Performance Dendrite-Free Lithium Metal Anodes.

Adv Sci (Weinh) 2022 Aug 9:e2203178. Epub 2022 Aug 9.

Department of Chemistry, Institute of Biomimetic Materials & Chemistry, Anhui Engineering Laboratory of Biomimetic Materials, Division of Nanomaterials & Chemistry, Hefei National Research Center for Physical Sciences at the Microscale, Institute of Energy, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei, 230026, P. R. China.

Uncontrolled lithium dendrites seriously hinder the commercialization of lithium metal batteries in comparison to the durable lithium-ion batteries. Herein, inspired by squashy pomegranate structure, a novel loading strategy of metallic lithium (Li) is introduced to construct dendrite-free Li metal anodes through porous reduced graphene oxide/Au (PRGO/Au) composite microrods (MRs) as unique storage parcels. The abundant internal voids and robust host structure are capable of achieving high mass loading of Li metal and effectively alleviating the conceivable volume change during cycling, accompanied by the preferential selective plating/stripping of Li inside the graphene-based MRs with the embedded Au nanonuclei. As a result, the obtained PRGO/Au-Li anodes deliver a long-lifespan stable cycling up to 600 h with a high specific capacity of ≈2140 mA h g and voltage hysteresis as low as 20 mV in the absence of dendrites. The assembled full cells exhibit excellent rate capability and cycling stability. This work provides an alternative strategy to construct advanced high-energy-density lithium batteries via the unique 1D bioinspired graphene-based packaging strategy.
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http://dx.doi.org/10.1002/advs.202203178DOI Listing
August 2022

Adjuvant therapy with gemcitabine and stereotactic body radiation therapy versus gemcitabine alone for resected stage II pancreatic cancer: a prospective, randomized, open-label, single center trial.

BMC Cancer 2022 Aug 8;22(1):865. Epub 2022 Aug 8.

Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital of Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 31003, China.

Background: The role of adjuvant radiation in pancreatic adenocarcinoma (PDAC) remains unclear. We aimed to investigate the efficacy of gemcitabine combined with stereotactic body radiation therapy (SBRT) as adjuvant therapy for resected stage II PDAC.

Methods: In this single-center randomized controlled trial, patients with stage II PDAC that underwent margin-negative resection were randomly assigned to gemcitabine-alone adjuvant chemotherapy or adjuvant SBRT followed by gemcitabine chemotherapy. The primary endpoint was recurrence-free survival (RFS). Secondary endpoints included locoregional recurrence-free survival (LRFS), overall survival (OS), and incidence of adverse events.

Results: Forty patients were randomly assigned to treatment between Sep 1, 2015 and Mar 31, 2018. Of these, 38 were included in the intention-to-treat analysis (20 in gemcitabine arm and 18 in gemcitabine plus SBRT arm). The median RFS and OS were 9.70, 28.0 months in the gemcitabine arm and 5.30, 15.0 months in the gemcitabine plus SBRT arm (RFS, P = 0.53; OS, P = 0.20), respectively. The median LRFS in both arms was unreached (P = 0.81). Grade 3 or 4 adverse events were all comparable between the two arms. Evaluation of data from the enrolled patients indicated that the addition of adjuvant SBRT was not associated with either better local disease control or recurrence-free survival.

Conclusions: Adjuvant SBRT neither provided a survival benefit nor improved local disease control in resected stage II PDAC.

Trial Registration: ClinicalTrials.gov, NCT02461836 . Registered 03/06/2015.
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http://dx.doi.org/10.1186/s12885-022-09974-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9361660PMC
August 2022

Association between height growth patterns in puberty and stature in late adolescence: A longitudinal analysis in chinese children and adolescents from 2006 to 2016.

Front Endocrinol (Lausanne) 2022 22;13:882840. Epub 2022 Jul 22.

Institute of Child and Adolescent Health, School of Public Health, Peking University; National Health Commission Key Laboratory of Reproductive Health, Beijing, China.

Introduction: The relationship between the characteristics of puberty growth and the stature (height and overweight and obesity) in late adolescence was not clear. We aimed to explore the effects of puberty growth patterns on the stature in late adolescence.

Methods: A total of 13,143 children from a longitudinal cohort from 2006 to 2016 in Zhongshan city of China were included. The Preece-Baines growth curve was fitted for each individual child, and the age at peak height velocity (APHV), peak height velocity (PHV), and age at take-off (TOA) were obtained from the Preece-Baines model. To compare the difference in height in late adolescence (at 18 years old) at different pubertal height growth patterns (height spurt timing, intensity, and duration), the height at baseline was matched by using the propensity score matching. The log-binomial model was applied to assess the association between the three pubertal height growth patterns (timing, intensity, and duration) and overweight and obesity status in late adolescence, controlling the urbanity and body mass index (BMI) at baseline.

Results: After matching the baseline height, boys and girls in three pubertal patterns with early timing ( < 0.01), small intensity ( < 0.01), and short duration ( < 0.01) of height spurt had the lowest final height in the late adolescence. A 16% increase and 45% increase of risk for overweight and obesity were significantly associated with the early APHV in boys and girls, respectively, () in boys, 1.16(95% confidence interval, CI: 1.03-1.30), = 0.011; in girls, 1.45(1.21-1.75), < 0.001. 21% increase and 59% increase of risk for overweight and obesity were significantly associated with small PHV in boys and girls, respectively, in boys, 1.21(1.07-1.36), < 0.001; in girls, 1.59(1.30-1.95), < 0.001; and an 80% increase of risk for overweight and obesity with small spurt duration in girls ( = 1.80; 95% CI: 1.49, 2.18; < 0.001).

Conclusion: Pubertal growth patterns, including earlier puberty onset timing, smaller puberty intensity, and shorter puberty spurt duration, had a positive association with lower height risks and higher overweight and obesity risks in late adolescence.
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http://dx.doi.org/10.3389/fendo.2022.882840DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9354934PMC
August 2022

Optimize Lithium Deposition at Low Temperature by Weakly Solvating Power Solvent.

Angew Chem Int Ed Engl 2022 Aug 4. Epub 2022 Aug 4.

Nankai University College of Chemistry, Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), CHINA.

  For lithium (Li) metal batteries, the decrease in operating temperature brings severe safety issues by more disordered Li deposition. Here, we demonstrate that the solvating power of solvent is closely related to the reversibility of the Li deposition/stripping process under low-temperature conditions. The electrolyte with weakly solvating power solvent shows lower desolvation energy, allowing for a uniform Li deposition morphology, as well as a high deposition/stripping efficiency (97.87% at -40 °C). Based on a weakly solvating electrolyte, we further built a full cell by coupling the Li metal anode with a sulfurized polyacrylonitrile electrode at a low anode-to-cathode capacity ratio for steady cycling at -40 °C. Our results clarified the relationship between solvating power of solvent and Li deposition behavior at low temperatures.
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http://dx.doi.org/10.1002/anie.202207927DOI Listing
August 2022

A Novel Delivery System of RGD-HSA Loaded GEM/CUR Nanoparticles for the Treatment of Pancreatic Cancer Therapy.

Drug Des Devel Ther 2022 26;16:2395-2406. Epub 2022 Jul 26.

Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, People's Republic of China.

Introduction: Pancreatic cancer is one of the most common malignant tumors and is characterized by high malignancy, occult incidence and poor prognosis. Traditional chemotherapy drugs have limited efficacy and strong side effects. Therefore, there is an urgent need for a better treatment of the malignancy.

Methods: The prepared arginine glycine peptide (RGD)-human serum albumin (HSA)-Gemcitabine (GEM)/Curcumin (CUR) nanoparticles (NPs) were characterized for physicochemical properties, stability and in vitro release. Comparisons of HSA-GEM/CUR NPs and RGD-HSA-GEM/CUR NPs regarding tissue distributions and pharmacodynamics were also carried out using mice as the animal models.

Results: Transmission electron micrographs showed that RGD peptide-conjugated HSA-NPs had an irregular surface, good dispersion (PDI=0.139±0.03) and a uniform size distribution (Mean PS=115.6±5.7 nm). The ζ-potential was -17.3 mV. As regards in vitro release, non RGD modified NPs showed a faster release rate in 24 hours, yielding a release amount of 75% for GEM and 72% for CUR. RGD-HSA-GEM/CUR NPs exhibited 67% of accumulated release of GEM (63% for CUR) in 24 hours. This may be due to the HSA chain covering the surface of NPs, which hindered the drug release. The cytotoxicity of GEM/CUR co-loaded NPs was significantly higher than that of single-drug NPs (P < 0.05). In vivo study results indicated that RGD-HSA-GEM/CUR NPs had notable targeting effect on subcutaneous tumors, with a potential to actively deliver drugs to tumor tissues.

Conclusion: In this study, we prepared RGD-HSA-GEM/CUR NPs that had both good water solubility and tumor-targeting property. The results also showed that the RGD modified NPs had advantages in increasing GEM/CUR concentration at tumor sites and reducing its distribution in peripheral organs.
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http://dx.doi.org/10.2147/DDDT.S366558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9339944PMC
August 2022

CTPS1 suppresses proliferation and migration in colorectal cancer cells.

Cell Cycle 2022 Aug 1:1-12. Epub 2022 Aug 1.

Department of General Surgery, Hepatic-biliary-pancreatic Institute, Lanzhou University Second Hospital, Lanzhou, China.

Colorectal cancer (CRC) is now the third most prevalent tumor and one of the deadliest cancers worldwide, with an increasing prevalence every year. Therefore, we urgently need to understand the mechanisms regulating the progression of colorectal cancer and find potential diagnostic biomarkers. In this study, we performed an analysis using the TCGA and GEO databases to find a molecular biomarker for the diagnosis of CRC, namely CTPS1. The results of this analysis revealed that CTPS1 could promote tumor proliferation and metastasis. Furthermore, bioinformatics analysis revealed that CTPS1 promoted CRC progression through cell cycle and p53 pathways. Further investigation demonstrated that CTPS1 might be involved in the regulation of CCNB1, RRM2, GTSE1, CDK2 and CHEK2 genes. Moreover, PCR confirmed that CTPS1 regulated GTSE1 and CDK2 molecules. Then, western blot was used to verify that CTPS1 promoted the expression of GTSE1 and CDK2 by inhibiting the expression of p53. In summary, we identified an important diagnostic biomarker for CRC, namely CTPS1, and its importance was validated at the cellular level. These results suggest that CTPS1 could serve as a candidate biomarker for CRC and CTPS1 inhibitors may be a potential treatment for CRC.
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http://dx.doi.org/10.1080/15384101.2022.2105084DOI Listing
August 2022

The Role of The Tumor Microbiome in Tumor Development and Its Treatment.

Front Immunol 2022 15;13:935846. Epub 2022 Jul 15.

Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, China.

Commensal bacteria and other microorganisms that reside in the human body are closely associated with the development and treatment of cancers. Recently, tumor microbiome (TM) has been identified in a variety of cancers such as pancreatic, lung, and breast cancers. TM has different compositions in different tumors and has different effects on tumors. TM plays an important role in the formation of the tumor microenvironment, regulation of local immunity, and modification of tumor cell biology, and directly affects the efficacy of drug treatment for tumors. TM is expected to be a biomarker for tumors, and engineered tumor-targeting bacteria and anti-cancer microbial agents (GEN-001) have an important role in the treatment of tumors. This paper reviews the relevant studies on TM in recent years and describes its distribution in different tumors, its correlation with clinical features, its effect on local immunity, and the research directions of TM in tumor treatment.
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http://dx.doi.org/10.3389/fimmu.2022.935846DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9334697PMC
August 2022

Effects of Different Environment-Friendly Gibberellic Acid Microcapsules on Herbicide Injury of Wheat.

Front Plant Sci 2022 11;13:915506. Epub 2022 Jul 11.

College of Plant Protection, Shanxi Agricultural University, Jinzhong, China.

Environmentally friendly microcapsules are becoming more and more widely used due to the increasing demand for environmental safety in pesticides. To compare the impact of differences in wheat herbicide phytotoxicity of different gibberellic acid microcapsule suspensions, two microcapsule suspensions were separately formulated using the phase transfer method and the polymerization method, and the key performance indicators are the size of microcapsules and the degree of encapsulation. Meanwhile, through field trials, the pharmacological and detoxification effects of different types of microcapsule suspensions on the herbicide methyldisulfuron in wheat fields were compared. The microcapsule suspension was prepared by the phase transfer method and the particle sizes D, D, and D are 0.990, 2.136, and 5.201 μm, respectively; the microcapsule suspension was prepared by the polymerization, the particle sizes D, D, and D are 4.365, 8.547, and 16.782 μm, respectively. The encapsulation rate of the microcapsules prepared by the phase transfer method and the polymerization method was 86.9% and 91.2%, being higher than 80%, the national standard for capsules. Meanwhile, the release rate conforms to first-order release kinetics in 0-4 days and zero-order release kinetics in 5-28 days. The plot trials' result showed that the detoxification effect of the microcapsules prepared by the polymerization method was significantly better than the detoxification effect of the microcapsules prepared by the phase transfer method and the control agent. The growth index of wheat was higher than that of the untreated check after using the agent.
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http://dx.doi.org/10.3389/fpls.2022.915506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9310017PMC
July 2022

The comparative effects of sacubitril/valsartan versus enalapril on pulmonary hypertension due to heart failure with a reduced ejection fraction.

Pulm Circ 2022 Jul 1;12(3):e12034. Epub 2022 Jul 1.

Department of Cardiology Handan Central Hospital Handan Hebei China.

The purpose of this study was to investigate the effects of sacubitril/valsartan on right ventricular (RV) function in patients with pulmonary hypertension (PH) due to heart failure with reduced ejection fraction (HFrEF). We prospectively enrolled patients with HFrEF-induced PH admitted to the Department of Cardiology between August 2018 and December 2019. Patients were randomized to receive oral treatment with sacubitril/valsartan or enalapril. Epidemiological data were recorded before treatment. Echocardiography was performed at admission and 6 months of follow-up, and all parameters were compared. Major adverse cardiac events (MACEs) were compared between baseline and 6 months follow-up. There were no significant differences in the baseline characteristics between the two groups. After 6 months of treatment, both treatment groups improved the following parameters from baseline (mean ± SD): left atrium, left ventricle, the left ventricular ejection function (LVEF), RV systolic function (the tricuspid annular plane systolic excursion [TAPSE], the systolic pulmonary artery pressure [sPAP], and TAPSE/sPAP). After 6 months, sacubitril/valsartan improved significantly the following parameters compared with enalapril (all  < 0.05): LVEF (47.07 ± 6.93% vs. 43.47 ± 7.95%); TAPSE (15.33 ± 1.31 vs. 14.78 ± 1.36 mm); sPAP (36.76 ± 14.32 vs. 42.26 ± 12.07 mmHg); and TAPSE/sPAP ratio (0.50 ± 0.23 vs. 0.39 ± 0.14), respectively. There was no difference in readmissions due to recurrent heart failure. Sacubitril/valsartan seems to provide more beneficial effects among patients with HFrEF-induced PH to improve RV function, along with a decrease in pulmonary pressure.
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http://dx.doi.org/10.1002/pul2.12034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9297686PMC
July 2022

Change in Oxidative Stress and Mitochondrial Dynamics in Response to Elevated Cold-Inducible RNA-Binding Protein in Cardiac Surgery-Associated Acute Kidney Injury.

Oxid Med Cell Longev 2022 9;2022:3576892. Epub 2022 Jul 9.

Department of Blood Purification, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.

Cardiac surgery-associated acute kidney injury (CSA-AKI) is a common yet serious complication that is closely related to cardiopulmonary bypass (CPB). Extracellular cold-inducible RNA-binding protein (eCIRP) can mediate aseptic inflammation and trigger intracellular oxidative stress. In the present study, expression of serum CIRP was significantly elevated post-CPB (785.0 ± 640.5 pg/mL vs. 149.5 ± 289.1 pg/mL, < 0.001) and was positively correlated with CPB duration ( = 0.502, < 0.001). Patients with high expression of CIRP had higher risks of postoperative AKI than patients with low CIRP expression (OR: 1.67, 95% CI 1.04-2.68). In a rat CPB model, the serum CIRP concentration increased significantly after CPB. Similarly, the levels of Scr and BUN significantly increased 4 hours after CPB. KIM-1 and NGAL mRNA levels in the CPB group were 8.2 and 4.3 times higher than the sham group, respectively. In addition, the levels of inflammatory cell infiltration, oxidative stress, and apoptosis in the renal tissue of the CPB group were significantly higher compared to the sham group. The expression levels of serum inflammatory factors at 4 hours post-CPB were also increased. Administration of recombinant human CIRP protein promoted the expression of NADPH oxidase via the TLR-4/MyD88 pathway, aggravated intracellular oxidative stress, mediated mitochondrial dynamics disorder, and eventually increased apoptosis in HK-2 cells. However, the CIRP inhibitor C23 improved the CIRP-mediated oxidative stress and mitochondrial dysfunction in both rat and cell models. In summary, elevated CIRP could mediate oxidative stress and mitochondrial dynamics in the kidney to promote CSA-AKI.
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http://dx.doi.org/10.1155/2022/3576892DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9288297PMC
July 2022

Reference genome assemblies reveal the origin and evolution of allohexaploid oat.

Nat Genet 2022 Aug 18;54(8):1248-1258. Epub 2022 Jul 18.

Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China.

Common oat (Avena sativa) is an important cereal crop serving as a valuable source of forage and human food. Although reference genomes of many important crops have been generated, such work in oat has lagged behind, primarily owing to its large, repeat-rich polyploid genome. Here, using Oxford Nanopore ultralong sequencing and Hi-C technologies, we have generated a reference-quality genome assembly of hulless common oat, comprising 21 pseudomolecules with a total length of 10.76 Gb and contig N50 of 75.27 Mb. We also produced genome assemblies for diploid and tetraploid Avena ancestors, which enabled the identification of oat subgenomes and provided insights into oat chromosomal evolution. The origin of hexaploid oat is inferred from whole-genome sequencing, chloroplast genomes and transcriptome assemblies of different Avena species. These findings and the high-quality reference genomes presented here will facilitate the full use of crop genetic resources to accelerate oat improvement.
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http://dx.doi.org/10.1038/s41588-022-01127-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9355876PMC
August 2022

Guiding significance of anterior-posterior diameter compression ratio of surgical segment of psoas major muscle in the oblique lumbar interbody fusion.

Asian J Surg 2022 Jul 15. Epub 2022 Jul 15.

Department of Orthopedics, The Affiliated Changzhou No.2 People's Hospital with Nanjing Medical University, Changzhou, 213003, China. Electronic address:

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http://dx.doi.org/10.1016/j.asjsur.2022.07.028DOI Listing
July 2022

General Synthesis of Tube-like Nanostructured Perovskite Oxides with Tunable Transition Metal-Oxygen Covalency for Efficient Water Electrooxidation in Neutral Media.

J Am Chem Soc 2022 Jul 18;144(29):13163-13173. Epub 2022 Jul 18.

Department of Chemistry, Institute of Biomimetic Materials & Chemistry, Anhui Engineering Laboratory of Biomimetic Materials, Division of Nanomaterials & Chemistry, Hefei National Research Center for Physical Sciences at the Microscale, Institute of Energy, Hefei Comprehensive National Science Center, University of Science and Technology of China, Hefei 230026, China.

Hydrogen production from water electrolysis in neutral-pH electrolytes can not only avoid the corrosion and safety issues and expand the catalyst option but also potentially integrate with artificial photosynthesis and bioelectrocatalysis. However, heterogeneous catalysts that can efficiently negotiate the sluggish oxygen evolution reaction (OER) in neutral solutions are considerably lacking. Herein, we report a template-assisted strategy for the synthesis of 13 kinds of tube-like nanostructured perovskite oxides (TNPOs) with markedly high Brunauer-Emmett-Teller surface areas. By systematic examination of these TNPOs, we found that the OER activity of TNPOs in neutral solution exhibits a volcano shape as a function of the covalency of transition metal-oxygen bonds. Consequently, our designed Sm-doped LaCoO catalyst yields a geometric current density of 8.5 mA cm at 1.75 V versus the reversible hydrogen electrode in 1 M phosphate buffer solution (pH 7) due to the optimized covalency of Co 3d and O 2p states, representing the most active noble-metal-free OER catalyst in neutral electrolytes reported as yet.
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http://dx.doi.org/10.1021/jacs.2c02989DOI Listing
July 2022

High-Efficiency, Mass-Producible, and Colored Solar Photovoltaics Enabled by Self-Assembled Photonic Glass.

ACS Nano 2022 Jul 18. Epub 2022 Jul 18.

Engineering Research Centre for Solar Energy and Refrigeration of MOE, School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China.

Building-integrated photovoltaics is a crucial technology for developing zero-energy buildings and sustainable cities, while great efforts are required to make photovoltaic (PV) panels aesthetically pleasing. This places an urgent demand on PV colorization technology that has a low impact on power conversion efficiency (PCE) and is simultaneously mass-producible at a low cost. To address this challenge, this study contributes a colorization strategy for solar PVs based on short-range correlated dielectric microspheres, .., photonic glass. Through theoretical studies, first we demonstrate that the photonic glass self-assembled by high-index microspheres could enable both colored solar cells and modules, with easily variable colors and negligible parasitic absorption. By a fast spray coating process of colloidal monodisperse ZnS microspheres, we show the photonic glass layer could be easily deposited on silicon solar cells, enabling them to have structural colors. Through varying microsphere sizes, solar cells with different colors are achieved, showing low PCE loss compared to normal black cells. These colored solar cells are also encapsulated with a general lamination process to produce PV modules with various colors and patterns at a stunning PCE approaching 21%. Moreover, the long-term stability is subsequently verified by aging tests including an outdoor exposure for 10 days and a damp-heat test for 1000 h, and the mass producibility is demonstrated by presenting a colored PV panel with an output power over 108 W. These results confirm photonic glass as a promising strategy for colored PVs possessing high efficiency and practical applicability.
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http://dx.doi.org/10.1021/acsnano.2c05840DOI Listing
July 2022

Excimer laser ablation combined with drug-coated balloon versus drug-coated balloon in the treatment of de novo atherosclerotic lesions in lower extremities (ELABORATE): study protocol for a real-world clinical trial.

BMC Cardiovasc Disord 2022 07 16;22(1):317. Epub 2022 Jul 16.

Department of Vascular Surgery, Institute of Vascular Surgery, Zhongshan Hospital, Fudan University, National Clinical Research Center for Interventional Medicine, 180 Fenglin Road, Shanghai, 200032, China.

Background: The efficacy and validity of excimer laser ablation (ELA) in the in-stent restenosis (ISR) has been confirmed. However, its application in de novo atherosclerotic lesions of lower extremity artery disease (LEAD) has not been clearly defined and its procedure has not been standardized.

Methods: ELABORATE is a prospective, multicenter, real-world study designed to evaluate the efficacy and safety between ELA combined with drug-coated balloon (DCB) and DCB alone in de novo atherosclerotic lesions of LEAD.

Discussion: ELABORATE is a prospective, multicenter, real-world study designed to assess the efficacy and safety between ELA combined with drug-coated balloon (DCB) and DCB alone in patients with de novo atherosclerotic lesions of LEAD. According to the real-world situation, eligible patients will be allocated to ELA + DCB group (group E) and DCB group (group C). Baseline and follow-up information (at 3, 6, and 12 months) will be collected. The primary efficacy point is primary patency at 12-months, and the secondary efficacy points include clinically driven target lesion reintervention (CD-TLR), change of Rutherford class, ankle-brachial index and ulcer healing rate. These indexes will be assessed and recorded at 3, 6, and 12-month follow-up. Also, safety evaluation, including major adverse event, all-cause mortality through 30-day follow-up, unplanned major amputation, bailout stent and distal embolization, will also be evaluated by an independent core laboratory. All the data will be collected and recorded by the electric data capture system. This study will be finished in 3 years and the 12-month results will be available in 2023. All the patients will be followed for 5 years. Trial registration number Chinese Clinical Trial Registry (ChiCTR2100051263). Registered 17 September 2019. http://www.chictr.org.cn/listbycreater.aspx .
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http://dx.doi.org/10.1186/s12872-022-02751-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9287897PMC
July 2022

Risk Factors of Brain Metastasis and Prognosis in HER2-Positive Breast Cancer: A Single-Institution Retrospective Analysis from China.

Front Oncol 2022 27;12:905065. Epub 2022 Jun 27.

Department of Oncological Surgery, Provincial Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China.

Background: Brain metastasis (BM) frequently occurs in HER2-positive breast cancer (BC) patients, but the risk factors of BM in this type of patients are still unknown. Our study aims to assess the risk factors of BM and prognostic analysis in HER2-positive BC patients.

Methods: Univariate analysis used -test, chi-square test, and Fisher's exact test to find out the risk factors for BM, and multivariable analysis was done with stepwise logistic regression analysis. Prognostic data analysis was estimated by the Kaplan-Meier method.

Results: A total of 228 HER2-positive BC patients were included, of whom 214 patients were postoperative metastatic patients and 14 patients were stage IV patients. Through comparing the stratified variables between 51 postoperative metastatic patients with BM and 163 postoperative metastatic patients without BM, the multivariate analysis showed that age ≤40 years (OR 2.321, 95% CI: 1.089 to 4.948) and first metastatic site with lung metastasis (OR 2.168, 95% CI: 1.099 to 4.274) were independent risk factors for BM in HER2-positive BC patients. Prognostic data of all 65 HER2-positive BC patients with BM showed that the time from the diagnosis of BC to the development of breast cancer brain metastasis (BCBM) was 36.3 months (95% CI: 30.0 to 42.1 months). The time from the diagnosis of first recurrence and metastasis stage to the diagnosis of BCBM was 11.35 months (95% CI: 7.1 to 18.4 months). The time from the diagnosis of BCBM to the time of follow-up was 24.1 months (95% CI: 13.9 to 37.5 months). Up until the time of follow-up data, a total of 38 patients had died, and the time from the diagnosis of BM of these 38 patients to death was 11.0 months (95% CI: 9.0 to 20.4 months).

Conclusion: The prognosis of HER2-positive BC patients with BM was poor due to the lack of effective treatments for BM. Age ≤40 years and first metastatic site with lung metastasis were the independent risk factors for BM in HER2-positive BC patients. Future research about pre-emptive medical interventions may help to improve the prognosis of HER2-positive BC patients with high risk to develop BM.
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http://dx.doi.org/10.3389/fonc.2022.905065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9271963PMC
June 2022

Massively targeted evaluation of therapeutic CRISPR off-targets in cells.

Nat Commun 2022 Jul 13;13(1):4049. Epub 2022 Jul 13.

Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, BGI-Shenzhen, Qingdao, China.

Methods for sensitive and high-throughput evaluation of CRISPR RNA-guided nucleases (RGNs) off-targets (OTs) are essential for advancing RGN-based gene therapies. Here we report SURRO-seq for simultaneously evaluating thousands of therapeutic RGN OTs in cells. SURRO-seq captures RGN-induced indels in cells by pooled lentiviral OTs libraries and deep sequencing, an approach comparable and complementary to OTs detection by T7 endonuclease 1, GUIDE-seq, and CIRCLE-seq. Application of SURRO-seq to 8150 OTs from 110 therapeutic RGNs identifies significantly detectable indels in 783 OTs, of which 37 OTs are found in cancer genes and 23 OTs are further validated in five human cell lines by targeted amplicon sequencing. Finally, SURRO-seq reveals that thermodynamically stable wobble base pair (rG•dT) and free binding energy strongly affect RGN specificity. Our study emphasizes the necessity of thoroughly evaluating therapeutic RGN OTs to minimize inevitable off-target effects.
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http://dx.doi.org/10.1038/s41467-022-31543-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9279339PMC
July 2022

Effects of lipid type and toxicological properties on the digestion of cellulose nanocrystals in simulated gastrointestinal tract.

Food Chem 2022 Jul 8;396:133653. Epub 2022 Jul 8.

College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; National Engineering Research Center for Fruits and Vegetables Processing, Beijing 100193, China; Key Laboratory of Fruits and Vegetables Processing, Ministry of Agriculture, Beijing 100193, China.

This study aimed to understand the impact of different oil types on the cellulose nanocrystals (CNCs) to modulate lipid digestion and the in vitro gastrointestinal toxicity of CNCs in food systems. We explored the ability of CNCs to modulate lipid digestion in a simulated gastrointestinal system and monitored the gastrointestinal fate of CNC-based emulsions with different oil types. Finally, a small intestine epithelial model was used to evaluate the influence of cytotoxicity. The results suggested that the addition of 0.6 wt% CNCs in the high-fat food model reduced the hydrolysis of free fatty acids (FFAs) from triglycerides by 37.8% after the small intestine phase. CNCs showed the best effect in reducing lipid digestion in emulsions with high unsaturation triglycerides. In addition, the toxicology results suggest that 0.6 wt% CNCs had only a slight effect on reactive oxygen species and cytotoxicity, and no significant change in cell-layer integrity.
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http://dx.doi.org/10.1016/j.foodchem.2022.133653DOI Listing
July 2022

Human periodontal ligament stem cell encapsulation in alginate-fibrin-platelet lysate microbeads for dental and craniofacial regeneration.

J Dent 2022 Jul 8;124:104219. Epub 2022 Jul 8.

Department of Trauma and Joint Surgery, Shunde Hospital, Southern Medical University, Foshan, Guangdong, China; Member, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, United States of America; Center for Stem Cell Biology & Regenerative Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, United States of America.

Objective: Tissue engineering is promising for dental and craniofacial regeneration. The objectives of this study were to develop a novel xeno-free alginate-fibrin-platelet lysate hydrogel with human periodontal ligament stem cells (hPDLSCs) for dental regeneration, and to investigate the proliferation and osteogenic differentiation of hPDLSCs using hPL as a cell culture nutrient supplement.

Methods: hPDLSCs were cultured with Dulbecco's modified eagle medium (DMEM), DMEM + 10% fetal bovine serum (FBS), and DMEM + hPL (1%, 2.5%, and 5%). hPDLSCs were encapsulated in alginate-fibrin microbeads (Alg+Fib), alginate-hPL microbeads (Alg+hPL), or alginate-fibrin-hPL microbeads (Alg+Fib+hPL). hPDLSCs encapsulated in alginate microbeads were induced with an osteogenic medium containing hPL or FBS. Quantitative real-time polymerase chain reaction (qRT-PCR), alkaline phosphatase (ALP) activity, ALP staining, and alizarin red (ARS) staining was investigated.

Results: hPDLSCs were released faster from Alg+Fib+hPL than from Alg+hPL. At 14 days, ALP activity was 44.1 ± 7.61 mU/mg for Alg+Fib+hPL group, higher than 28.07 ± 5.15 mU/mg of Alg+Fib (p<0.05) and 0.95 ± 0.2 mU/mg of control (p<0.01). At 7 days, osteogenic genes (ALP, RUNX2, COL1, and OPN) in Alg+Fib+hPL and Alg+Fib were 3-10 folds those of control. At 21 days, the hPDLSC-synthesized bone mineral amount in Alg+Fib+hPL and Alg+Fib was 7.5 folds and 4.3 folds that of control group, respectively.

Conclusions: The 2.5% hPL was determined to be optimal for hPDLSCs. Adding hPL into alginate hydrogel improved the viability of the hPDLSCs encapsulated in the microbeads. The hPL-based medium enhanced the osteogenic differentiation of hPDLSCs in Alg+Fib+hPL construct, showing a promising xeno-free approach for delivering hPDLSCs to enhance dental, craniofacial and orthopedic regenerations.
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http://dx.doi.org/10.1016/j.jdent.2022.104219DOI Listing
July 2022

PtoNF-YC9-SRMT-PtoRD26 module regulates the high saline tolerance of a triploid poplar.

Genome Biol 2022 07 7;23(1):148. Epub 2022 Jul 7.

Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Science, Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, China.

Background: Sensing and responding to stresses determine the tolerance of plants to adverse environments. The triploid Chinese white poplar is widely cultivated in North China because of its adaptation to a wide range of habitats including highly saline ones. However, its triploid genome complicates any detailed investigation of the molecular mechanisms underlying its adaptations.

Results: We report a haplotype-resolved genome of this triploid poplar and characterize, using reverse genetics and biochemical approaches, a MYB gene, SALT RESPONSIVE MYB TRANSCRIPTION FACTOR (SRMT), which combines NUCLEAR FACTOR Y SUBUNIT C 9 (PtoNF-YC9) and RESPONSIVE TO DESICCATION 26 (PtoRD26), to regulate an ABA-dependent salt-stress response signaling. We reveal that the salt-inducible PtoRD26 is dependent on ABA signaling. We demonstrate that ABA or salt drives PtoNF-YC9 shuttling into the nucleus where it interacts with SRMT, resulting in the rapid expression of PtoRD26 which in turn directly regulates SRMT. This positive feedback loop of SRMT-PtoRD26 can rapidly amplify salt-stress signaling. Interference with either component of this regulatory module reduces the salt tolerance of this triploid poplar.

Conclusion: Our findings reveal a novel ABA-dependent salt-responsive mechanism, which is mediated by the PtoNF-YC9-SRMT-PtoRD26 module that confers salt tolerance to this triploid poplar. These genes may therefore also serve as potential and important modification targets in breeding programs.
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http://dx.doi.org/10.1186/s13059-022-02718-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9264554PMC
July 2022

Long Non-Coding RNA MCM3AP-AS1: A Crucial Role in Human Malignancies.

Pathol Oncol Res 2022 16;28:1610194. Epub 2022 Jun 16.

Department of Hematology, The Affiliated Hospital of Southwest Medical University, Luzhou, China.

The incidence of cancer continues to grow and is one of the leading causes of death in the world. Long noncoding RNAs (LncRNAs) is a group of RNA transcripts greater than 200 nucleotides in length, and although it cannot encode proteins, it can regulate different biological functions by controlling gene expression, transcription factors, etc. LncRNA micro-chromosome maintenance protein 3-associated protein antisense RNA 1 (MCM3AP-AS1) is involved in RNA processing and cell cycle-related functions, and MCM3AP-AS1 is dysregulated in expression in various types of cancers. This biomarker is involved in many processes related to carcinogens, such as cell proliferation, apoptosis, cell cycle, and migration. In this review, we summarize the roles of MCM3AP-AS1 in different human cancers and its biological functions with a view to providing ideas for future research.
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http://dx.doi.org/10.3389/pore.2022.1610194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9243217PMC
July 2022

Preoperative malnutrition as an independent risk factor for the postoperative mortality in elderly Chinese individuals undergoing hip surgery: a single-center observational study.

Ther Adv Chronic Dis 2022 27;13:20406223221102739. Epub 2022 Jun 27.

Department of Cardiology, Hainan Hospital of Chinese People's Liberation Army General Hospital, Sanya, China.

Objective: Malnutrition is prevalent in elderly with hip fracture and higher than in community-dwelling older adults. Scarce studies have examined the association between preoperative malnutrition and postoperative mortality in elderly Chinese individuals with hip fracture. This study was designed to explore the effect of preoperative malnutrition on the postoperative long-term mortality in elderly Chinese individuals undergoing hip surgery.

Methods: As a single-center observational study, this study included 263 consecutive patients above 70 years old with hip fracture and elective surgery. Preoperative nutritional status was evaluated by prognostic nutritional index (PNI). Patients were divided into one group with malnutrition (26 patients with PNI ⩽ 38) and the other group without malnutrition (169 patients with PNI > 38), respectively.

Results: The overall malnutrition rate was 13.3% (26 patients). The postoperative long-term mortality rates of patients with and without malnutrition had statistically significant difference [10 patients (38.5%) and 32 patients (18.9%),  < 0.05]. Cox regression analysis showed that malnutrition (hazard ratio: 0.269, 95% confidence interval: 0.085-0.859,  < 0.05) and partial pressure of carbon dioxide (hazard ratio: 0.873, 95% confidence interval: 0.790-0.964,  < 0.05) were independent risk factors for the postoperative long-term mortality.

Conclusion: This study demonstrated that preoperative malnutrition was an independent risk factor for the postoperative long-term mortality and resulted in a more than 2.5-fold increase of the postoperative long-term mortality in elderly Chinese individuals undergoing hip surgery.
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http://dx.doi.org/10.1177/20406223221102739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9243382PMC
June 2022

Adiposity status, trajectories and the earlier puberty onset: Results from a longitudinal cohort study.

J Clin Endocrinol Metab 2022 Jul 2. Epub 2022 Jul 2.

Institute of Child and Adolescent Health, School of Public Health, Peking University, Beijing, China.

Context: Adiposity is associated with earlier puberty onset in girls, but such an association among boys is controversial.

Objective: To estimate the association of prepubertal adiposity status, trajectories, and the earlier puberty onset based on a cohort study.

Design, Setting, And Participants: A total of 1322 children were included in 2017, with a mean age of 8.1±0.6 years for girls and 9.1±0.6 years for boys, and followed up every 6 months until October 2020. Anthropometric profiles, including BMI, WC, and body composition indicators, were used to determine adiposity status. Group-based trajectory model was used to identify trajectory groups of anthropometric profiles. The pubertal development was assessed through clinical inspection and palpation by using The Tanner rating map and Prader orchidometer. Covariate information was obtained through questionnaires.

Main Outcome Measures: The clinical assessment of testicular volume for boys and breast stage for girls was acquired.

Results: Childhood adiposity was associated with an increased risk of earlier puberty onset. Body composition was more sensitive to earlier puberty onset than BMI and WC. Boys and girls with high-level body fat percentage had an increased risk of earlier puberty onset, compared with those with low-level body fat percentage. However, boys and girls with high-level FFM (fat-free mass)/FM (fat mass) had a decreased risk of earlier puberty onset, compared with those with low-level FFM/FM. The high-level trajectories of the rapid increase in anthropometric profiles, in addition to FFM/FM, were also significantly associated with a higher risk of earlier puberty onset.

Conclusions: Prepubertal adiposity and distinct trajectories were associated with earlier puberty onset. It's important to maintain healthy adiposity status in preventing earlier puberty onset in children.
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http://dx.doi.org/10.1210/clinem/dgac395DOI Listing
July 2022

Superior Fast-Charging Lithium-Ion Batteries Enabled by the High-Speed Solid-State Lithium Transport of an Intermetallic Cu Sn Network.

Adv Mater 2022 Aug 7;34(32):e2202688. Epub 2022 Jul 7.

Department of Chemistry, Institute of Biomimetic Materials and Chemistry, Anhui Engineering Laboratory of Biomimetic Materials, Division of Nanomaterials and Chemistry, Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, 230026, China.

Superior fast charging is a desirable capability of lithium-ion batteries, which can make electric vehicles a strong competition to traditional fuel vehicles. However, the slow transport of solvated lithium ions in liquid electrolytes is a limiting factor. Here, a Li Cu Sn intermetallic network is reported to address this issue. Based on electrochemical analysis and X-ray photoelectron spectroscopy mapping, it is demonstrated that the reported intermetallic network can form a high-speed solid-state lithium transport matrix throughout the electrode, which largely reduces the lithium-ion-concentration polarization effect in the graphite anode. Employing this design, superior fast-charging graphite/lithium cobalt oxide full cells are fabricated and tested under strict electrode conditions. At the charging rate of 6 C, the fabricated full cells show a capacity of 145 mAh g with an extraordinary capacity retention of 96.6%. In addition, the full cell also exhibits good electrochemical stability at a high charging rate of 2 C over 100 cycles (96.0% of capacity retention) in comparison to traditional graphite-anode-based cells (86.1% of capacity retention). This work presents a new strategy for fast-charging lithium-ion batteries on the basis of high-speed solid-state lithium transport in intermetallic alloy hosts.
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http://dx.doi.org/10.1002/adma.202202688DOI Listing
August 2022

The latent period of coronavirus disease 2019 with SARS-CoV-2 B.1.617.2 Delta variant of concern in the postvaccination era.

Immun Inflamm Dis 2022 07;10(7):e664

Department of Acute Infectious Disease Control and Prevention, Nanjing Municipal Center for Disease Control and Prevention, Nanjing, China.

Introduction: Emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have resulted in new challenges for epidemic prevention and control worldwide. However, little is known about the latent period of coronavirus disease by the SARS-CoV-2 Delta variant of concern (VOC) in the postvaccination era.

Methods: The epidemiology and clinical data of cases with confirmed SARS-CoV-2 Delta VOC infection were retrospective collected. Dates of the first positive PCR test were collected to estimate the distribution of latent period.

Results: Of the 40 patients, 16 were male (40%). The median age of patients was 47.5 years. The median latent period of patients was 6.0 days (interquartile range [IQR], 4.0-9.0 days) and the longest latent period was 13.0 days after exposure. The latent periods were longer in male patients compared to female patients (median, 8.5 days vs. 5.0 days, p = .041). The median latent period was comparable among fully vaccinated cases (6.5 days), no vaccinated cases (7.5 days), and partially vaccinated cases (5.5 days).

Conclusions: The median latent period of SARS-CoV-2 Delta VOC infection was 6.0 days. The latent period between vaccinated and non-vaccinated patients was not significantly different. The 14-day quarantine program is sufficient to prevent the transmission of COVID-19 by Delta VOC in the postvaccination era.
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http://dx.doi.org/10.1002/iid3.664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9186332PMC
July 2022

Study on the Stability of Functionally Graded Simply Supported Fluid-Conveying Microtube under Multi-Physical Fields.

Authors:
Tao Ma Anle Mu

Micromachines (Basel) 2022 Jun 3;13(6). Epub 2022 Jun 3.

School of Mechanical and Precision Instrument Engineering, Xi'an University of Technology, Xi'an 710048, China.

The stability of functionally graded simply supported fluid-conveying microtubes under multiple physical fields was studied in this article. The strain energy of the fluid-conveying microtubes was determined based on strain gradient theory, and the governing equation of the functionally graded, simply supported, fluid-conveying microtube was established using Hamilton's principle. The Galerkin method was used to solve the governing equation, and the effects of the dimensionless microscale parameters, temperature difference, and magnetic field intensity on the stability of the microtube were investigated. The results showed that the dimensionless microscale parameters have a significant impact on the stability of the microtube. The smaller the dimensionless microscale parameters were, the stronger the microscale effect of the material and the better the microtube stability became. The increase in the temperature difference decreased the eigenfrequency and critical velocity of the microtube and reduced the microtube stability. However, the magnetic field had the opposite effect. The greater the magnetic field intensity was, the greater the eigenfrequency and critical velocity were, and the more stable the microtube became.
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http://dx.doi.org/10.3390/mi13060895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9229689PMC
June 2022

The Sweetpotato Voltage-Gated K Channel β Subunit, KIbB1, Positively Regulates Low-K and High-Salinity Tolerance by Maintaining Ion Homeostasis.

Genes (Basel) 2022 Jun 20;13(6). Epub 2022 Jun 20.

College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China.

Voltage-gated K channel β subunits act as a structural component of K channels in different species. The β subunits are not essential to the channel activity but confer different properties through binding the T1 domain or the C-terminal of α subunits. Here, we studied the physiological function of a novel gene, , encoding a voltage-gated K channel β subunit in sweetpotato. The transcriptional level of this gene was significantly higher in the low-K-tolerant line than that in the low-K-sensitive line under K deficiency conditions. In , positively regulated low-K tolerance through regulating K uptake and translocation. Under high-salinity stress, the growth conditions of transgenic lines were obviously better than wild typr (WT). Enzymatic and non-enzymatic reactive oxygen species (ROS) scavenging were activated in transgenic plants. Accordingly, the malondialdehyde (MDA) content and the accumulation of ROS such as HO and O were lower in transgenic lines under salt stress. It was also found that the overexpression of enhanced K uptake, but the translocation from root to shoot was not affected under salt stress. This demonstrates that acted as a positive regulator in high-salinity stress resistance through regulating Na and K uptake to maintain K/Na homeostasis. These results collectively suggest that the mechanisms of in regulating K were somewhat different between low-K and high-salinity conditions.
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http://dx.doi.org/10.3390/genes13061100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9222298PMC
June 2022

Characterization of Early Alzheimer's Disease-Like Pathological Alterations in Non-Human Primates with Aging: A Pilot Study.

J Alzheimers Dis 2022 ;88(3):957-970

Department of Internal Medicine-Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA.

Background: Sporadic or late onset Alzheimer's disease (LOAD) is a multifactorial neurodegenerative disease with aging the most known risk factor. Non-human primates (NHPs) may serve as an excellent model to study LOAD because of their close similarity to humans in many aspects including neuroanatomy and neurodevelopment. Recent studies reveal AD-like pathology in old NHPs.

Objective: In this pilot study, we took advantage of brain samples from 6 Cynomolgus macaques that were divided into two groups: middle aged (average age 14.81 years) and older (average age 19.33 years). We investigated whether AD-like brain pathologies are present in the NHPs.

Methods: We used immunohistochemical method to examine brain Aβ pathology and neuron density. We applied biochemical assays to measure tau phosphorylation and multiple signaling pathways indicated in AD. We performed electron microscopy experiments to study alterations of postsynaptic density and mitochondrial morphology in the brain of NHPs.

Results: We found multiple AD-like pathological alteration in the prefrontal cortex (but not in the hippocampus) of the older NHPs including tau hyperphosphorylation, increased activity of AMP-activated protein kinase (AMPK), decreased expression of protein phosphatase 2A (PP2A), impairments in mitochondrial morphology, and postsynaptic densities formation.

Conclusion: These findings may provide insights into the factors contributing to the development of LOAD, particularly during the early stage transitioning from middle to old age. Future endeavors are warranted to elucidate mechanisms underlying the regional (and perhaps cellular) vulnerability with aging and the functional correlation of such pathological changes in NHPs.
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http://dx.doi.org/10.3233/JAD-215303DOI Listing
August 2022

A chromosome-level Populus qiongdaoensis genome assembly provides insights into tropical adaptation and a cryptic turnover of sex determination.

Mol Ecol 2022 Jun 17. Epub 2022 Jun 17.

Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, China.

Populus species have long been used as model organisms to study the adaptability of trees and the evolution of sex chromosomes. As a species belonging to the section Populus and limited to tropical areas, the P. qiongdaoensis genome contains important information for tropical poplar studies and protection. Here, we report a chromosome-level genome assembly and annotation of a female P. qiongdaoensis. Gene family clustering, positive selection detection and historical reconstruction of population dynamics revealed the tropical adaptation of P. qiongdaoensis, and showed convergent evolution with another tropical poplar, P. ilicifolia, at the molecular level, especially on some functional genes (e.g., PIF3 and PIL1). In addition, we also identified a ZW sex determination system on chromosome 19 of P. qiongdaoensis, and inferred that it seems to have a similar sex determination mechanism to other poplars, controlled by a type-A cytokinin response regulator (RR) gene. However, comparison and phylogenetic analysis of the sex determination regions confirmed a cryptic sex turnover event in the section Populus, which may be caused by the translocation and duplication of the RR gene driven by Helitron-like transposable elements. Our study provides new insights into the environmental adaptation and sex chromosome evolution of poplars, and emphasizes the importance of using long read sequencing in ecological and evolutionary inferences of plants.
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http://dx.doi.org/10.1111/mec.16566DOI Listing
June 2022

Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication.

Syst Biol 2022 Jun 11. Epub 2022 Jun 11.

Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China.

Whole-genome duplication (WGD) occurs broadly and repeatedly across the history of eukaryotes, and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD, however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs-paralogous genes mistakenly identified as orthologs because they are present in single copes within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as a result of gene extinction (or incomplete laboratory sampling) is only recently gaining empirical attention in the phylogenomics community. Moreover, few studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and differential gene loss scenarios following WGD. When gene loss occurs along the terminal branches of the species tree, alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the degree of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of genes increases. Additionally, pseudoorthologs can greatly mislead species tree inference when gene loss occurs along the internal branches of the species tree. Here, both coalescent and concatenation methods yield inconsistent results. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era.
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http://dx.doi.org/10.1093/sysbio/syac040DOI Listing
June 2022
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