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Using Nvivo to Analyze the Impact of Computer Simulation of Parent-Child Cooperative Art Activities on the Growth of Preschool Children

Xie E, Wong SC, Bai Y

J Autism Dev Disord, 2023 Sep 15.
PMID: 37713171 DOI: 10.1007/s10803-023-06124-1

Psychology originally defined parent-child conflict in terms of interpersonal relationships, where parent-child conflict is a process of inconsistent attitudes between parents and children that occurs in a family setting. For this end, we aims to investigate the influence of parental awareness on preschoolers' perception of parent-child conflict and the mediating role of preschoolers' self-esteem. This paper proposes a dynamic parent-child relationship discovery algorithm based on the impact of parent-child cooperation activities on preschool children's development. We applied SPSS and Mplus statistical software for data processing and analysis, and Nvivo 11.0 qualitative software for validation and analysis. The reliability of preschool children's perceived parent-child conflict and sub-dimensions were: 0.901, 0.799, 0.791, 0.811, 0.729; the total scale and the retest reliability of each dimension were: 0.914, 0.837, 0.836, 0.792, 0.711. Validated factor analysis using Mplus: RMSEA = 0.075, TLI = 0.856, CFI = 0.876, SRMR = 0.064.
A systematic review of research on sitting and working furniture ergonomic from 2012 to 2022: Analysis of assessment approaches

Bai Y, Kamarudin KM, Alli H

Heliyon, 2024 Apr 15;10(7):e28384.
PMID: 38571611 DOI: 10.1016/j.heliyon.2024.e28384

This study analyses which aspects of sitting and working furniture ergonomics that may be influenced and how they are assessed. To gather information on the types and assessment techniques connected with influencing furniture ergonomics, a systematic review of the literature was conducted. The papers in the systematic review were published between 2012 and 2022. The articles applied the Systematic Reviews and Meta-Analyses (PRISMA) statement guidelines to limit the 41 papers that were eventually included (N = 41) to those containing keywords like ergonomics, human factors, comfort, working furniture, Chair, assessment and evaluation. The research objective of this systematic review is to provide a comprehensive overview of sitting and working furniture and the main findings, obtaining common assessment techniques for this type of furniture and their suitability. According to the relevant studies, the publications were categorized by summarizing factors like region, gender, research methods, ergonomic assessment techniques and methods used, correlation between assessment techniques and methods, etc. Summaries of the data extracted from the included papers are provided and the applicability of some approaches are assessed. Only a small number of authors have evaluated the ergonomics of furniture used in homes. One of the research gaps is the paucity of research on gender segregation, secular trends, and cultural contexts. These studies heavily rely on quantitative research techniques, and the articles may lack credibility due to the homogeneity of the evaluation techniques. Finally, the authors offer some suggestions for the appropriate ergonomic analysis of furniture.
An overview of signaling pathways regulating YAP/TAZ activity

Heng BC, Zhang X, Aubel D, Bai Y, Li X, Wei Y, et al.

Cell Mol Life Sci, 2021 Jan;78(2):497-512.
PMID: 32748155 DOI: 10.1007/s00018-020-03579-8

YAP and TAZ are ubiquitously expressed homologous proteins originally identified as penultimate effectors of the Hippo signaling pathway, which plays a key role in maintaining mammalian tissue/organ size. Presently, it is known that YAP/TAZ also interact with various non-Hippo signaling pathways, and have diverse roles in multiple biological processes, including cell proliferation, tissue regeneration, cell lineage fate determination, tumorigenesis, and mechanosensing. In this review, we first examine the various microenvironmental cues and signaling pathways that regulate YAP/TAZ activation, through the Hippo and non-Hippo signaling pathways. This is followed by a brief summary of the interactions of YAP/TAZ with TEAD1-4 and a diverse array of other non-TEAD transcription factors. Finally, we offer a critical perspective on how increasing knowledge of the regulatory mechanisms of YAP/TAZ signaling might open the door to novel therapeutic applications in the interrelated fields of biomaterials, tissue engineering, regenerative medicine and synthetic biology.
Fulltext The International Diet-Health Index: a novel tool to evaluate diet quality for cardiometabolic health across countries

Wang J, Masters WA, Bai Y, Mozaffarian D, Naumova EN, Singh GM

BMJ Glob Health, 2020 07;5(7).
PMID: 32694217 DOI: 10.1136/bmjgh-2019-002120

INTRODUCTION: Diet is a major modifiable risk factor for cardiometabolic disease; however, interpretable measures capturing impacts of overall diet on health that can be easily used by policymakers at the global/national levels are not readily available.
METHODS: We developed the International Diet-Health Index (IDHI) to measure health impacts of dietary intake across 186 countries in 2010, using age-specific and sex-specific data on country-level dietary intake, effects of dietary factors on cardiometabolic diseases and country-specific cardiometabolic disease profiles. The index encompasses the impact of 11 foods/nutrients on 12 cardiometabolic diseases, the mediation of health effects of specific dietary intakes through blood pressure and body mass index and background disease prevalence in each country-age-sex group. We decomposed the index into IDHIbeneficial for risk-reducing factors, and IDHIadverse for risk-increasing factors. The flexible functional form of the IDHI allows inclusion of additional risk factors and diseases as data become available.
RESULTS: By sex, women experienced smaller detrimental cardiometabolic effects of diet than men: (females IDHIadverse range: -0.480 (5th percentile, 95th percentile: -0.932, -0.300) to -0.314 (-0.543, -0.213); males IDHIadverse range: (-0.617 (-1.054, -0.384) to -0.346 (-0.624, -0.222)). By age, middle-aged adults had highest IDHIbeneficial (females: 0.392 (0.235, 0.763); males: 0.415 (0.243, 0.949)) and younger adults had most extreme IDHIadverse (females: -0.480 (-0.932, -0.300); males: -0.617 (-1.054, -0.384)). Regionally, Central Latin America had the lowest IDHIoverall (-0.466 (-0.892, -0.159)), while Southeast Asia had the highest IDHIoverall (0.272 (-0.224, 0.903)). IDHIoverall was highest in low-income countries and lowest in upper middle-income countries (-0.039 (-0.317, 0.227) and -0.146 (-0.605, 0.303), respectively). Among 186 countries, Honduras had lowest IDHIoverall (-0.721 (-0.916, -0.207)), while Malaysia had highest IDHIoverall (0.904 (0.435, 1.190)).
CONCLUSION: IDHI encompasses dietary intakes, health effects and country disease profiles into a single index, allowing policymakers a useful means of assessing/comparing health impacts of diet quality between populations.
Molecular cloning and characterization of a novel aspartyl aminopeptidase from Trichinella spiralis

Sun XY, Ma KN, Bai Y, Liu RD, Long SR, Zhang X, et al.

Trop Biomed, 2021 Sep 01;38(3):420-434.
PMID: 34608116 DOI: 10.47665/tb.38.3.085

Trichinellosis is an important zoonotic parasitic disease worldwide and is principally caused by ingesting animal meat containing Trichinella infective larvae. Aspartyl aminopeptidase is an intracytoplasmic metalloproteinase that specifically hydrolyzes the N-terminus of polypeptides free of acidic amino acids (aspartic acid and glutamate), and plays an important role in the metabolism, growth and development of organisms. In this study, a novel T. spiralis aspartyl aminopeptidase (TsAAP) was cloned and expressed, and its biological properties and roles in worm growth and development were investigated. The results revealed that TsAAP transcription and expression in diverse T. spiralis stages were detected by RT-PCR and Western blotting, and primarily localized at cuticle, stichosome and intrauterine embryos of this nematode by immunofluorescence test. rTsAAP has the enzymatic activity of native AAP to hydrolyze the substrate H-Glu-pNA. There was a specific binding between rTsAAP and murine erythrocyte, and the binding site was localized in erythrocyte membrane proteins. Silencing of TsAAP gene by specific dsRNA significantly reduced the TsAAP expression, enzymatic activity, intestinal worm burdens and female fecundity. The results demonstrated that TsAAP participates in the growth, development and fecundity of T. spiralis and it might be a potential target molecule for anti-Trichinella vaccines.
A novel mutation in the mouse Pcsk1 gene showing obesity and diabetes

Muhsin NIA, Bentley L, Bai Y, Goldsworthy M, Cox RD

Mamm. Genome, 2020 Feb;31(1-2):17-29.
PMID: 31974728 DOI: 10.1007/s00335-020-09826-4

The proprotein convertase subtilisin/Kexin type 1 (PCSK1/PC1) protein processes inactive pro-hormone precursors into biologically active hormones in a number of neuroendocrine and endocrine cell types. Patients with recessive mutations in PCSK1 exhibit a complex spectrum of traits including obesity, diarrhoea and endocrine disorders. We describe here a new mouse model with a point mutation in the Pcsk1 gene that exhibits obesity, hyperphagia, transient diarrhoea and hyperproinsulinaemia, phenotypes consistent with human patient traits. The mutation results in a pV96L amino acid substitution and changes the first nucleotide of mouse exon 3 leading to skipping of that exon and in homozygotes very little full-length transcript. Overexpression of the exon 3 deleted protein or the 96L protein results in ER retention in Neuro2a cells. This is the second Pcsk1 mouse model to display obesity phenotypes, contrasting knockout mouse alleles. This model will be useful in investigating the basis of endocrine disease resulting from prohormone processing defects.
Anticoagulation control in different ethnic groups receiving vitamin K antagonist therapy for stroke prevention in atrial fibrillation

Zulkifly H, Cheli P, Lutchman I, Bai Y, Lip GYH, Lane DA

Thromb Res, 2020 08;192:12-20.
PMID: 32416364 DOI: 10.1016/j.thromres.2020.04.001

BACKGROUND: Efficacy and safety of vitamin K antagonists (VKAs) is optimised in atrial fibrillation (AF) patients when the International Normalised Ratio (INR) is 2.0-3.0. Anticoagulation control comparing different ethnic groups is limited, although epidemiological studies suggest poorer INR control in non-white cohorts.
METHODS: VKA control was assessed retrospectively by time-in-the-therapeutic range (TTR) (Rosendaal method) and percentage INR-in-range (PINRR) in 991 White, Afro-Caribbean and South-Asian AF patients [overall mean (SD) age 71.6 (9.4) years; 55% male; mean (SD) CHA2DS2-VASc score 3.4 (1.6)] over a median (IQR) follow-up of 5.2 (3.2-7.0) years.
RESULTS: Compared to Whites, mean (SD) TTR and PINRR were significantly lower in South-Asians [TTR 67.9% vs. 60.5%; PINRR 58.8% vs. 51.6%, respectively] and Afro-Caribbeans [TTR 67.9% vs. 61.3%; PINRR 58.8% vs. 53.1%, respectively], despite similar INR monitoring intensity. Logistic regression revealed non-white ethnicity [OR 2.62; 95% Confidence Interval [CI] (1.67-4.10) and OR 3.47 (1.44-8.34)] and anaemia [OR 1.65 (1.00-2.70) and OR 6.27 (1.89-20.94)] as independent predictors of both TTR and PINRR
Fulltext Thermal and Mechanical Properties of Concrete Incorporating Silica Fume and Waste Rubber Powder

Lakhiar MT, Kong SY, Bai Y, Susilawati S, Zahidi I, Paul SC, et al.

Polymers (Basel), 2022 Nov 11;14(22).
PMID: 36432983 DOI: 10.3390/polym14224858

Using waste rubber tires for concrete production will reduce the demand for natural aggregate and help to reduce environmental pollution. The main challenge of using waste rubber tires in concrete is the deterioration of mechanical properties, due to poor bonding between rubber and cement matrix. This research aims to evaluate the mechanical and thermal properties of rubberised concrete produced by using different proportions of rubber powder and silica fume. Ordinary Portland cement was partially replaced with silica fume by amounts of 5%, 10%, 15% and 20%, while sand was replaced by 10%, 20% and 30% with waste rubber powder. Tests were carried out in order to determine workability, density, compressive strength, splitting tensile strength, elastic modulus, thermal properties, water absorption and shrinkage of rubberised concrete. The compressive strength and splitting tensile strength of concrete produced using waste rubber powder were reduced by 10-52% and 9-57%, respectively. However, the reduction in modulus of elasticity was 2-36%, less severe than compressive and splitting tensile strengths. An optimum silica fume content of 15% was observed based on the results of mechanical properties. The average shrinkage of concrete containing 15% silica fume increased from -0.051% to -0.085% at 28 days, as the content of waste rubber powder increased from 10% to 30%. While the thermal conductivity of rubberised concrete was reduced by 9-35% compared to the control sample. Linear equations were found to correlate the density, splitting tensile strength, modulus of elasticity and thermal conductivity of concrete with silica fume and waste rubber powder.
Fulltext The bioelectrical properties of bone tissue

Heng BC, Bai Y, Li X, Meng Y, Lu Y, Zhang X, et al.

Animal Model Exp Med, 2023 Apr;6(2):120-130.
PMID: 36856186 DOI: 10.1002/ame2.12300

Understanding the bioelectrical properties of bone tissue is key to developing new treatment strategies for bone diseases and injuries, as well as improving the design and fabrication of scaffold implants for bone tissue engineering. The bioelectrical properties of bone tissue can be attributed to the interaction of its various cell lineages (osteocyte, osteoblast and osteoclast) with the surrounding extracellular matrix, in the presence of various biomechanical stimuli arising from routine physical activities; and is best described as a combination and overlap of dielectric, piezoelectric, pyroelectric and ferroelectric properties, together with streaming potential and electro-osmosis. There is close interdependence and interaction of the various electroactive and electrosensitive components of bone tissue, including cell membrane potential, voltage-gated ion channels, intracellular signaling pathways, and cell surface receptors, together with various matrix components such as collagen, hydroxyapatite, proteoglycans and glycosaminoglycans. It is the remarkably complex web of interactive cross-talk between the organic and non-organic components of bone that define its electrophysiological properties, which in turn exerts a profound influence on its metabolism, homeostasis and regeneration in health and disease. This has spurred increasing interest in application of electroactive scaffolds in bone tissue engineering, to recapitulate the natural electrophysiological microenvironment of healthy bone tissue to facilitate bone defect repair.
Fulltext Electroactive Biomaterials for Facilitating Bone Defect Repair under Pathological Conditions

Heng BC, Bai Y, Li X, Lim LW, Li W, Ge Z, et al.

Adv Sci (Weinh), 2023 Jan;10(2):e2204502.
PMID: 36453574 DOI: 10.1002/advs.202204502

Bone degeneration associated with various diseases is increasing due to rapid aging, sedentary lifestyles, and unhealthy diets. Living bone tissue has bioelectric properties critical to bone remodeling, and bone degeneration under various pathological conditions results in significant changes to these bioelectric properties. There is growing interest in utilizing biomimetic electroactive biomaterials that recapitulate the natural electrophysiological microenvironment of healthy bone tissue to promote bone repair. This review first summarizes the etiology of degenerative bone conditions associated with various diseases such as type II diabetes, osteoporosis, periodontitis, osteoarthritis, rheumatoid arthritis, osteomyelitis, and metastatic osteolysis. Next, the diverse array of natural and synthetic electroactive biomaterials with therapeutic potential are discussed. Putative mechanistic pathways by which electroactive biomaterials can mitigate bone degeneration are critically examined, including the enhancement of osteogenesis and angiogenesis, suppression of inflammation and osteoclastogenesis, as well as their anti-bacterial effects. Finally, the limited research on utilization of electroactive biomaterials in the treatment of bone degeneration associated with the aforementioned diseases are examined. Previous studies have mostly focused on using electroactive biomaterials to treat bone traumatic injuries. It is hoped that this review will encourage more research efforts on the use of electroactive biomaterials for treating degenerative bone conditions.
Fulltext Role of YAP/TAZ in Cell Lineage Fate Determination and Related Signaling Pathways

Heng BC, Zhang X, Aubel D, Bai Y, Li X, Wei Y, et al.

Front Cell Dev Biol, 2020;8:735.
PMID: 32850847 DOI: 10.3389/fcell.2020.00735

The penultimate effectors of the Hippo signaling pathways YAP and TAZ, are transcriptional co-activator proteins that play key roles in many diverse biological processes, ranging from cell proliferation, tumorigenesis, mechanosensing and cell lineage fate determination, to wound healing and regeneration. In this review, we discuss the regulatory mechanisms by which YAP/TAZ control stem/progenitor cell differentiation into the various major lineages that are of interest to tissue engineering and regenerative medicine applications. Of particular interest is the key role of YAP/TAZ in maintaining the delicate balance between quiescence, self-renewal, proliferation and differentiation of endogenous adult stem cells within various tissues/organs during early development, normal homeostasis and regeneration/healing. Finally, we will consider how increasing knowledge of YAP/TAZ signaling might influence the trajectory of future progress in regenerative medicine.
Biochar from pyrolyzed Tibetan Yak dung as a novel additive in ensiling sweet sorghum: An alternate to the hazardous use of Yak dung as a fuel in the home

Bai Y, Rafiq MK, Li S, Degen AA, Mašek O, Sun H, et al.

J Hazard Mater, 2021 02 05;403:123647.
PMID: 33264862 DOI: 10.1016/j.jhazmat.2020.123647

Yak dung is used as fuel in Tibetan homes; however, this use is hazardous to health. An alternative use of the dung that would be profitable and offset the loss as a fuel would be very beneficial. Sweet sorghum silage with yak dung biochar as an additive was compared with a control silage with no additives and three silages with different commercial additives, namely Lactobacillus buchneri, Lactobacillus plantarum and Acremonium cellulase. Biochar-treated silage had a significantly greater concentration of water-soluble carbohydrates than the other silages (76 vs 12.4-45.8 g/kg DM) and a greater crude protein content (75.5 vs 61.4 g/kg DM), lactic acid concentration (40.7 vs 27.7 g/kg DM) and gross energy yield (17.8 vs 17.4 MJ/kg) than the control silage. Biochar-treated and control silages did not differ in in vitro digestibility and in total gas (507 vs 511 L/kg DM) and methane production (57.9 vs 57.1 L/kg DM). Biochar inhibited degradation of protein and water-soluble carbohydrates and enhanced lactic acid production, which improved storability of feed. It was concluded that yak dung biochar is an efficient, cost-effective ensiling additive. The profit could offset the loss of dung as fuel and improve the health of Tibetan people.
Biochar amendment improves alpine meadows growth and soil health in Tibetan plateau over a three year period

Rafiq MK, Bai Y, Aziz R, Rafiq MT, Mašek O, Bachmann RT, et al.

Sci Total Environ, 2020 May 15;717:135296.
PMID: 31839318 DOI: 10.1016/j.scitotenv.2019.135296

Previous biochar research has primarily focused on agricultural annual cropping systems with very little attention given to highly fragile, complex and diverse natural alpine grassland ecosystems. The present study investigated the effect of biochar on the growth of alpine meadows and soil health. This study was conducted in the Qinghai Tibetan Plateau over a three year period to investigate the effect of three rice husk biochar application rates alone and combination with high and low NPK fertilizer dosages on alpine meadow productivity, soil microbial diversity as well as pH, carbon and nitrogen content at 0-10 cm and 10-20 cm depth. At the end of the 3rd year soil samples were analysed and assessed by combined analysis of variance. The results showed that biochar application in combination with nitrogen (N), phosphorus (P) and potassium (K) fertilizer had a significant increase in fresh and dry biomass during the second and third year of the study as compared to control and alone biochar application (p ≤ 0.05). Biochar alone and in combination with NPK fertilizer resulted in a significant increase in the soil pH and carbon contents of the soil. XPS results, the SEM imaging and EDS analysis of aged biochar demonstrated that the biochar has undergone complex changes over the 3 years as compared to fresh biochar. This research suggests that biochar has positive effect on alpine meadow growth and soil health and may be an effective tool for alpine meadow restoration.
Pembrolizumab versus paclitaxel for previously treated advanced gastric or gastroesophageal junction cancer (KEYNOTE-063): A randomized, open-label, phase 3 trial in Asian patients

Chung HC, Kang YK, Chen Z, Bai Y, Wan Ishak WZ, Shim BY, et al.

Cancer, 2022 Mar 01;128(5):995-1003.
PMID: 34878659 DOI: 10.1002/cncr.34019

BACKGROUND: KEYNOTE-063 (NCT03019588) investigated pembrolizumab versus paclitaxel as second-line therapy in Asian patients with advanced programmed death ligand 1 (PD-L1)-positive (combined positive score ≥1) gastric/gastroesophageal junction (GEJ) cancer.
METHODS: This randomized, open-label, phase 3 study was conducted at 36 medical centers in China (mainland), Malaysia, South Korea, and Taiwan. Patients were randomly assigned 1:1 to 200 mg of pembrolizumab intravenously every 3 weeks for ≤2 years or 80 mg/m2 of paclitaxel intravenously every week. Primary end points were overall survival (OS) and progression-free survival (PFS). Secondary end points were objective response rate (ORR) per Response Evaluation Criteria in Solid Tumors version 1.1 and safety.
RESULTS: Between February 16, 2017, and March 12, 2018, 94 patients were randomly assigned (47 pembrolizumab/47 paclitaxel) after screening; enrollment was stopped on March 12, 2018, based on the results of the global KEYNOTE-061 study, and patients were followed until the last patient's last visit. Median OS was 8 months (95% confidence interval [CI], 4-10 months) with pembrolizumab versus 8 months (95% CI, 5-11 months) with paclitaxel (hazard ratio [HR], 0.99; 95% CI, 0.63-1.54). Median PFS was 2 months (95% CI, 1-3 months) with pembrolizumab versus 4 months (95% CI, 3-6 months) with paclitaxel (HR, 1.62; 95% CI, 1.04-2.52). ORR was 13% for pembrolizumab versus 19% for paclitaxel. Any-grade treatment-related adverse events occurred in 28 pembrolizumab-treated patients (60%) and 42 paclitaxel-treated patients (96%); grades 3 to 5 events occurred in 5 patients (11%) and 28 patients (64%), respectively.
CONCLUSIONS: Definitive conclusions about the efficacy of second-line pembrolizumab in Asian patients with advanced PD-L1-positive gastric/GEJ cancer are limited because of insufficient power, but pembrolizumab was well tolerated in this patient population. Efficacy followed a trend similar to that observed in the phase 3 KEYNOTE-061 trial.
Fulltext Pembrolizumab Versus Placebo as Second-Line Therapy in Patients From Asia With Advanced Hepatocellular Carcinoma: A Randomized, Double-Blind, Phase III Trial

Qin S, Chen Z, Fang W, Ren Z, Xu R, Ryoo BY, et al.

J Clin Oncol, 2023 Mar 01;41(7):1434-1443.
PMID: 36455168 DOI: 10.1200/JCO.22.00620

PURPOSE: We evaluated the efficacy and safety of pembrolizumab in patients from Asia with previously treated advanced hepatocellular carcinoma (HCC).
METHODS: In a double-blind, phase III trial, 453 patients with advanced HCC and progression during or after treatment with or intolerance to sorafenib or oxaliplatin-based chemotherapy were randomly assigned in a 2:1 ratio to receive pembrolizumab (200 mg) or placebo once every 3 weeks for ≤ 35 cycles plus best supportive care. The primary end point was overall survival (one-sided significance threshold, P = .0193 [final analysis]). Secondary end points included progression-free survival (PFS) and objective response rate (ORR; one-sided significance threshold, P = .0134 and .0091, respectively [second interim analysis]; RECIST version 1.1, by blinded independent central review).
RESULTS: Median overall survival was longer in the pembrolizumab group than in the placebo group (14.6 v 13.0 months; hazard ratio for death, 0.79; 95% CI, 0.63 to 0.99; P = .0180). Median PFS was also longer in the pembrolizumab group than in the placebo group (2.6 v 2.3 months; hazard ratio for progression or death, 0.74; 95% CI, 0.60 to 0.92; P = .0032). ORR was greater in the pembrolizumab group (12.7% [95% CI, 9.1 to 17.0]) than in the placebo group (1.3% [95% CI, 0.2 to 4.6]; P < .0001). Treatment-related adverse events occurred in 66.9% of patients (grade 3, 12.0%; grade 4, 1.3%; grade 5, 1.0%) in the pembrolizumab group and 49.7% of patients (grade 3, 5.9%; grade 4, 0%; grade 5, 0%) in the placebo group.
CONCLUSION: In patients from Asia with previously treated advanced HCC, pembrolizumab significantly prolonged overall survival and PFS, and ORR was greater versus placebo.
Fulltext The Tsinghua-Lancet Commission on Healthy Cities in China: unlocking the power of cities for a healthy China

Yang J, Siri JG, Remais JV, Cheng Q, Zhang H, Chan KKY, et al.

Lancet, 2018 05 26;391(10135):2140-2184.
PMID: 29678340 DOI: 10.1016/S0140-6736(18)30486-0
Fulltext Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1

Klionsky DJ, Abdel-Aziz AK, Abdelfatah S, Abdellatif M, Abdoli A, Abel S, et al.

Autophagy, 2021 Jan;17(1):1-382.
PMID: 33634751 DOI: 10.1080/15548627.2020.1797280

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

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