Displaying publications 1 - 20 of 43 in total

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  1. From waste to wealth: The "Blue Circle" vision for a sustainable ocean future
    Yu H, Zahidi I, Fai CM, Liang D, Madsen DØ
    Sci Bull (Beijing), 2024 Apr 30;69(8):993-996.
    PMID: 38433031 DOI: 10.1016/j.scib.2024.02.024
  2. Fulltext Sungai Lembing's green tourism: Pioneering the future of resource-based urban renewal
    Yu H, Gunaratna G, Zahidi I, Fai CM
    Innovation (Camb), 2024 Mar 04;5(2):100578.
    PMID: 38445020 DOI: 10.1016/j.xinn.2024.100578
  3. Tunability of Pickering particle features of whey protein isolate via remodeling partial unfolding during ultrasonication-assisted complexation with chitosan/chitooligosaccharide
    Yu H, Zheng Y, Zhou C, Liu L, Wang L, Cao J, et al.
    Carbohydr Polym, 2024 Feb 01;325:121583.
    PMID: 38008470 DOI: 10.1016/j.carbpol.2023.121583
    The potential of ultrasonication-driven molecular self-assembly of whey protein isolate (WPI) with chitosan (CS)/chitooligosaccharide (COS) to stabilize Pickering emulsions was examined, based on CS/COS ligands-induced partial unfolding in remodeling the Pickering particles features. Multi-spectral analysis suggested obvious changes in conformational structures of WPI due to interaction with CS/COS, with significantly higher unfolding degrees of WPI induced by COS. Non-covalent interactions were identified as the major forces for WPI-CS/COS conjugates. Ultrasonication enhanced electrostatic interaction between CS's -NH3 groups and WPI's -COO- groups which improved emulsification activity and storability of WPI-COS stabilized Pickering emulsion. This was attributed to increased surface hydrophobicity and decreased particle size compared to WPI-CS associated with differential unfolding degrees induced by different saccharide ligands. CLSM and SEM consistently observed smaller emulsion droplets in WPI-COS complexes than WPI-CS/COS particles tightly adsorbed at the oil-water interface. The electrostatic self-assembly of WPI with CS/COS greatly enhanced the encapsulation efficiency of quercetin than those stabilized by WPI alone and ultrasound further improved encapsulation efficiency. This corresponded well with the quantitative affinity parameters between quercetin and WPI-CS/COS complexes. This investigation revealed the great potential of glycan ligands-induced conformational transitions of extrinsic physical disruption in tuning Pickering particle features.
  4. Fulltext Crosstalk Between circRNA and Tumor Microenvironment of Hepatocellular Carcinoma: Mechanism, Function and Applications
    Xie C, Hao X, Yuan H, Wang C, Sharif R, Yu H
    Onco Targets Ther, 2024;17:7-26.
    PMID: 38283733 DOI: 10.2147/OTT.S437536
    Hepatocellular carcinoma (HCC) is one of the most common aggressive tumors in the world. Despite the availability of various treatments, its prognosis remains poor due to the lack of specific diagnostic indicators and the high heterogeneity of HCC cases. CircRNAs are noncoding RNAs with stable and highly specific expression. Extensive research evidence suggests that circRNAs mediate the pathogenesis and progression of HCC through acting as miRNA sponges, protein modulators, and translation templates. Tumor microenvironment (TME) has become a hotspot of immune-related research in recent years due to its effects on metabolism, secretion and immunity of HCC. Accordingly, understanding the role played by circRNAs in TME is important for the study of HCC. This review will discuss the crosstalk between circRNAs and TME in HCC. In addition, we will discuss the current deficiencies and controversies in research on circRNAs and predict future research directions.
  5. Fulltext Online Binge-Watching Among Chinese College Students: Implications for Loneliness, Anxiety, and Depression
    Yu H, Alizadeh F
    Psychol Res Behav Manag, 2024;17:295-303.
    PMID: 38292254 DOI: 10.2147/PRBM.S447311
    PURPOSE: This study aimed to investigate binge-watching behavior and addiction among a sample of 446 Chinese college students and assess its consequences for mental health, with a particular focus on feelings of loneliness, anxiety, and depression.

    PARTICIPANTS AND METHODS: We conducted an online survey to gather data, examining participants' binge-watching habits and preferred platforms. We also utilized regression analysis to assess the impact of binge-watching addiction on mental health, exploring the associations between binge-watching addiction and feelings of loneliness, anxiety, and depression.

    RESULTS: Our findings revealed that the Chinese college students in our study typically defined binge-watching sessions as lasting approximately 7.22 hours, with an average of 10.83 episodes. Regarding the self-assessment of binge-watching, the average duration of participants was 5.76 hours, and the average number of episodes was 7.42. Tencent Video, iQIYI, and Bilibili emerged as the dominant platforms for binge-watching among the respondents. Regression analysis demonstrated a significant link between binge-watching addiction and mental health, with positive associations observed between binge-watching addiction and increased feelings of loneliness, anxiety, and depression.

    CONCLUSION: The results of this study reinforce previous findings regarding the detrimental effects of excessive media consumption on mental well-being. Moreover, they provide valuable insights into the global prevalence of binge-watching and its impact on the psychological health of young adults in the digital age, emphasizing the need for proactive measures to address this issue.

  6. Research on the descaling characteristics of a new electrochemical water treatment device
    Wei Y, Wang D, Li G, Yu H, Dong X, Jiang H
    Water Sci Technol, 2023 Nov;88(10):2566-2580.
    PMID: 38017678 DOI: 10.2166/wst.2023.365
    In recent years, chemical water treatment equipment has gained significant attention due to its environmental-friendly features, multifunctionality, and broad applicability. Recognizing the limitations of existing chemical treatment equipment, such as challenges in scale removal and the high water content in scale deposits, we propose a novel drum design for both anode and cathode, enabling simultaneous scale suction and dehydration. We constructed a small experimental platform to validate the equipment's performance based on our model. Notably, under the optimal operating parameters, the hardness removal rate for circulating water falls within the range of 19.6-24.46%. Moreover, the scale accumulation rate per unit area and unit time reaches 13.7 g h-1 m-2. Additionally, the energy consumption per unit weight of the scale remains impressively low at 0.16 kWh g-1. Furthermore, the chemical oxygen demand (COD) concentration decreased from an initial 106.0 mg L-1 to a mere 18.8 mg L-1, resulting in a remarkable total removal rate of 82.26%. In conclusion, our innovative electrochemical water treatment equipment demonstrates exceptional performance in scale removal, organic matter degradation, and water resource conservation, offering valuable insights for future research and development in chemical treatment equipment and electrochemical theory.
  7. Modified prairie dog optimization algorithm for global optimization and constrained engineering problems
    Yu H, Wang Y, Jia H, Abualigah L
    Math Biosci Eng, 2023 Oct 13;20(11):19086-19132.
    PMID: 38052592 DOI: 10.3934/mbe.2023844
    The prairie dog optimization (PDO) algorithm is a metaheuristic optimization algorithm that simulates the daily behavior of prairie dogs. The prairie dog groups have a unique mode of information exchange. They divide into several small groups to search for food based on special signals and build caves around the food sources. When encountering natural enemies, they emit different sound signals to remind their companions of the dangers. According to this unique information exchange mode, we propose a randomized audio signal factor to simulate the specific sounds of prairie dogs when encountering different foods or natural enemies. This strategy restores the prairie dog habitat and improves the algorithm's merit-seeking ability. In the initial stage of the algorithm, chaotic tent mapping is also added to initialize the population of prairie dogs and increase population diversity, even use lens opposition-based learning strategy to enhance the algorithm's global exploration ability. To verify the optimization performance of the modified prairie dog optimization algorithm, we applied it to 23 benchmark test functions, IEEE CEC2014 test functions, and six engineering design problems for testing. The experimental results illustrated that the modified prairie dog optimization algorithm has good optimization performance.
  8. Fulltext Identification and genomic analysis of temperate Halomonas bacteriophage vB_HmeY_H4907 from the surface sediment of the Mariana Trench at a depth of 8,900 m
    Su Y, Zhang W, Liang Y, Wang H, Liu Y, Zheng K, et al.
    Microbiol Spectr, 2023 Sep 20;11(5):e0191223.
    PMID: 37728551 DOI: 10.1128/spectrum.01912-23
    Viruses play crucial roles in the ecosystem by modulating the host community structure, mediating biogeochemical cycles, and compensating for the metabolism of host cells. Mariana Trench, the world's deepest hadal habitat, harbors a variety of unique microorganisms that have adapted to its extreme conditions of low temperatures, high pressure, and nutrient scarcity. However, our knowledge about isolated hadal phage strains in the hadal trench is still limited. This study reported the discovery of a temperate phage, vB_HmeY_H4907, infecting Halomonas meridiana H4907, isolated from surface sediment from the Mariana Trench at a depth of 8,900 m. To our best knowledge, it is the deepest isolated siphovirus from the ocean. Its 40,452 bp linear dsDNA genome has 57.64% GC content and 55 open reading frames, and it is highly homologous to its host. Phylogenetic analysis and average nucleotide sequence identification reveal that vB_HmeY_H4907 is separated from the isolated phages and represents a new family, Suviridae, with eight predicted proviruses and six uncultured viral genomes. They are widely distributed in the ocean, suggesting a prevalence of this viral family in the deep sea. These findings expand our understanding of the phylogenetic diversity and genomic features of hadal lysogenic phages, provide essential information for further studies of phage-host interactions and evolution, and may reveal new insights into the lysogenic lifestyles of viruses inhabiting the hadal ocean. IMPORTANCE Halomonas phage vB_HmeY_H4907 is the deepest isolated siphovirus from the ocean, and it represents a novel abundant viral family in the ocean. This study provides insights into the genomic, phylogenetic, and ecological characteristics of the new viral family, namely, Suviridae.
  9. Fulltext Vegetation as an ecological indicator in assessing environmental restoration in mining areas
    Yu H, Zahidi I, Chow MF
    iScience, 2023 Sep 15;26(9):107667.
    PMID: 37680487 DOI: 10.1016/j.isci.2023.107667
    As global demand for natural resources escalates, the environmental impact stemming from resource extraction has risen to the forefront of contemporary discussions. This paper probed the potential of using vegetation cover as an ecological barometer to gauge the level of environmental damage and restoration in mining areas: a decline in vegetation cover may signify detrimental impacts from intense mining activities, while an increase may indicate effective local environmental stewardship. Therefore, this paper undertook an assessment and discussion of mining damage and environmental management at China's Ta'ershan Mining Area since 2007, calculating and visualizing FVC (Fractional Vegetation Cover) of the Ta'ershan Mining Area to track changes in vegetation cover between 2007 and 2021. Changes in vegetation cover in the Ta'ershan Mining Area could act as a reflection of both mining-induced damage and subsequent successful environmental management by local authorities, providing a practical way to evaluate ecological effects in resource development.
  10. Fulltext Reclaiming abandoned mine tailings ponds for agricultural use: Opportunities and challenges
    Yu H, Zahidi I, Fai CM
    Environ Res, 2023 Sep 01;232:116336.
    PMID: 37321336 DOI: 10.1016/j.envres.2023.116336
    Tailings ponds, large man-made structures conceived during the mining process for waste storage, often become deserted post-mining, leaving behind a stark, contaminated landscape. This paper posits that these forsaken tailings ponds can be rejuvenated into fertile agricultural land through adept reclamation efforts. Serving as a discussion paper, it engages in a stimulating exploration of the environmental and health risks linked to tailings ponds. It sheds light on the potential and impediments in the transformation of these ponds into agricultural land. The discussion concludes that despite the substantial hurdles in repurposing tailings ponds for agriculture, there are encouraging prospects with the application of multifaceted efforts.
  11. Regulating tumor microenvironments by a lymph node-targeting adjuvant via tumor-specific CTL-derived IFNγ
    Xu X, Yi C, Feng T, Ge Y, Liu M, Wu C, et al.
    Clin Immunol, 2023 Aug;253:109685.
    PMID: 37406980 DOI: 10.1016/j.clim.2023.109685
    Inducing tumor-specific T cell responses and regulating suppressive tumor microenvironments have been a challenge for effective tumor therapy. CpG (ODN), the Toll-like receptor 9 agonist, has been widely used as adjuvants of cancer vaccines to induce T cell responses. We developed a novel adjuvant to improve the targeting of lymph nodes. CpG were modified with lipid and glycopolymers by the combination of photo-induced RAFT polymerization and click chemistry, and the novel adjuvant was termed as lipid-glycoadjuvant@AuNPs (LCpG). OVA protein was used as model antigen and melanoma model was established to test the immunotherapy effect of the adjuvant. In tumor model, the antitumor effect and mechanism of LCpG on the response of CTLs were examined by flow cytometry and cell cytotoxicity assay. The effects of LCpG on macrophage polarization and Tregs differentiation in tumor microenvironment were also studied by cell depletion assay and cytokine neutralization assay. We also tested the therapeutic effect of the combination of the adjuvant and anti-PD-1 treatment. LCpG could be rapidly transported to and retained longer in the lymphoid nodes than unmodified CpG. In melanoma model, LCpG controlled both primary tumor and its metastasis, and established long-term memory. In spleen and tumor draining lymphoid nodes, LCpG activated tumor-specific Tc1 responses, with increased CD8+ T-cell proliferation, antigen-specific Tc1 cytokine production and specific-tumor killing capacity. In tumor microenvironments, antigen-specific Tc1 induced by the LCpG promoted CTL infiltration, skewed tumor associated macrophages to M1 phenotype, regulated Treg and induced proinflammatory cytokines production in a CTL-derived IFN-γ-dependent manner. In vivo cell depletion and adoptive transfer experiments confirmed that antitumor activity of LCpG included vaccine was mainly dependent on CTL-derived IFN-γ. The anti-tumor efficacy of LCpG was dramatically enhanced when combined with anti-PD1 immunotherapy. LCpG was a promising adjuvant for vaccine formulation which could augment tumor-specific Tc1 activity, and regulate tumor microenvironments.
  12. Spatiotemporal variation of vegetation cover in mining areas of Dexing City, China
    Yu H, Zahidi I, Liang D
    Environ Res, 2023 May 15;225:115634.
    PMID: 36889570 DOI: 10.1016/j.envres.2023.115634
    Dexing City is an important mining city in China, abounding in copper ore, lead ore, zinc ore, and other metal resources, and there are two large open-pit mines in its territory, Dexing Copper Mine and Yinshan Mine. The two open-pit mines have been expanding their mining production scale since 2005, with frequent mining activities; and the expansion of the pits and the discharge of solid waste will undoubtedly increase the land use and cause the destruction of vegetation. Therefore, we plan to visualize the change in vegetation cover in Dexing City from 2005 to 2020 and the expansion of the two open-pit mines by calculating changes of the Fractional Vegetation Cover (FVC) in the mining area using remote sensing technology. In this study, we calculated the FVC of Dexing City in 2005, 2010, 2015 and 2020 using data from NASA Landsat Database via ENVI image analysis software, plotted the FVC reclassified maps via ArcGIS, and conducted field investigations in the mining areas of Dexing City. In this way, we can visualize the spatial and temporal changes of vegetation cover in Dexing City from 2005 to 2020, and appreciate the situation of mining expansion and its solid waste discharge in Dexing City. The results of this study showed that the vegetation cover of Dexing City remained stable from 2005 to 2020, as the expansion of mining scale and mine pits was accompanied by active environmental management and land reclamation, setting a positive example for other mining cities.
  13. Mine land reclamation, mine land reuse, and vegetation cover change: An intriguing case study in Dartford, the United Kingdom
    Yu H, Zahidi I, Liang D
    Environ Res, 2023 May 15;225:115613.
    PMID: 36870554 DOI: 10.1016/j.envres.2023.115613
    Dartford, a town in England, heavily relied on industrial production, particularly mining, which caused significant environmental pollution and geological damage. However, in recent years, several companies have collaborated under the guidance of the local authorities to reclaim the abandoned mine land in Dartford and develop it into homes, known as the Ebbsfleet Garden City project. This project is highly innovative as it not only focuses on environmental management but also provides potential economic benefits, employment opportunities, builds a sustainable and interconnected community, fosters urban development and brings people closer together. This paper presents a fascinating case that employs satellite imagery, statistical data, and Fractional Vegetation Cover (FVC) calculations to analyse the re-vegetation progress of Dartford and the development of the Ebbsfleet Garden City project. The findings indicate that Dartford has successfully reclaimed and re-vegetated the mine land, maintaining a high vegetation cover level while the Ebbsfleet Garden City project has advanced. This suggests that Dartford is committed to environmental management and sustainable development while pursuing construction projects.
  14. Environmental hazards posed by mine dust, and monitoring method of mine dust pollution using remote sensing technologies: An overview
    Yu H, Zahidi I
    Sci Total Environ, 2023 Mar 15;864:161135.
    PMID: 36566867 DOI: 10.1016/j.scitotenv.2022.161135
    The over-exploitation of mineral resources has led to increasingly serious dust pollution in mines, resulting in a series of negative impacts on the environment, mine workers (occupational health) and nearby residents (public health). For the environment, mine dust pollution is considered a major threat on surface vegetation, landscapes, weather conditions and air quality, leading to serious environmental damage such as vegetation reduction and air pollution; for occupational health, mine dust from the mining process is also regarded as a major threat to mine workers' health, leading to occupational diseases such as pneumoconiosis and silicosis; for public health, the pollutants contained in mine dust may pollute surrounding rivers, farmlands and crops, which poses a serious risk to the domestic water and food security of nearby residents who are also susceptible to respiratory diseases from exposure to mine dust. Therefore, the second section of this paper combines literature research, statistical studies, and meta analysis to introduce the public mainly to the severity of mine dust pollution and its hazards to the environment, mine workers (occupational health), and residents (public health), as well as to present an outlook on the management of mine dust pollution. At the same time, in order to propose a method for monitoring mine dust pollution on a regional scale, based on the Dense Dark Vegetation (DDV) algorithm, the third section of this paper analysed the aerosol optical depth (AOD) change in Dexing City of China using the data of 2010, 2014, 2018 and 2021 from the NASA MCD19A2 Dataset to explore the mine dust pollution situation and the progress of pollution treatment in Dexing City from 2010 to 2021. As a discussion article, this paper aims to review the environmental and health risks caused by mine dust pollution, to remind the public to take mine dust pollution seriously, and to propose the use of remote sensing technologies to monitor mine dust pollution, providing suggestions for local governments as well as mines on mine dust monitoring measures.
  15. Spatial and temporal variation of vegetation cover in the main mining area of Qibaoshan Town, China: Potential impacts from mining damage, solid waste discharge and land reclamation
    Yu H, Zahidi I
    Sci Total Environ, 2023 Feb 10;859(Pt 2):160392.
    PMID: 36423851 DOI: 10.1016/j.scitotenv.2022.160392
    The increasing frequency of mining activities in the world has led to many environmental pollution problems, such as mine wastewater discharge, mine solid waste dumps, and mine dust dispersion. These problems have negative implications for the environment and the public health of people living nearby the mining areas. Despite this, there are few methods to determine the state of mine pollution on a regional scale. Therefore, we applied remote sensing technologies to assess the mine pollution situation, especially the mine solid waste pollution, of a mining area, taking Qibaoshan Town, Liuyang City, Hunan Province, China, as an example. In our research, we have calculated the vegetation cover change of the Qibaoshan Town over the years (2000-2020), charted the vegetation coverage grade maps, and analysed the tendency of vegetation cover changes, to infer the mine pollution situation, the progress of pollution treatment and the efforts made by the local government and the mines on mine pollution disposal and the land reclamation. Additionally, mining damage can bring about geological hazards such as surface subsidence leading to vegetation destruction, while mining solid waste pollution and discharge can occupy a large amount of land and thus lead to vegetation reduction. As a result, this method of calculating FVC changes in a mining area is particularly suitable for assessing the extent of mining damage, the status of solid waste pollution and discharge, and the progress of land reclamation. In the abstract, we claim that this short communication article serves as a guide to start a conversation, and encourages experts and scholars to engage in this area of research.
  16. Robotic Level IV Inferior Vena Cava Thrombectomy Using an Intrapericardial Control Technique: Is It Safe Without Cardiopulmonary Bypass?
    Huang Q, Zhao G, Chen Y, Wu P, Li S, Peng C, et al.
    J Urol, 2023 Jan;209(1):99-110.
    PMID: 36194169 DOI: 10.1097/JU.0000000000002952
    PURPOSE: We introduce an intrapericardial control technique using a robotic approach in the surgical treatment of renal tumor with level IV inferior vena cava thrombus to decrease the severe complications associated with cardiopulmonary bypass and deep hypothermic circulatory arrest.

    MATERIALS AND METHODS: Eight patients with level IV inferior vena cava thrombi not extending into the atrium underwent transabdominal-transdiaphragmatic robot-assisted inferior vena cava thrombectomy obviating cardiopulmonary bypass/deep hypothermic circulatory arrest (cardiopulmonary bypass-free group) by an expert team comprising urological, hepatobiliary, and cardiovascular surgeons. The central diaphragm tendon and pericardium were transabdominally dissected until the intrapericardial inferior vena cava were exposed and looped proximal to the cranial end of the thrombi under intraoperative ultrasound guidance. As controls, 14 patients who underwent robot-assisted inferior vena cava thrombectomy with cardiopulmonary bypass (cardiopulmonary bypass group) and 25 patients who underwent open thrombectomy with cardiopulmonary bypass/deep hypothermic circulatory arrest (cardiopulmonary bypass/deep hypothermic circulatory arrest group) were included. Clinicopathological, operative, and survival outcomes were retrospectively analyzed.

    RESULTS: Eight robot-assisted inferior vena cava thrombectomies were successfully performed without cardiopulmonary bypass, with 1 open conversion. The median operation time and first porta hepatis occlusion time were shorter, and estimated blood loss was lower in the cardiopulmonary bypass-free group as compared to the cardiopulmonary bypass group (540 vs 586.5 minutes, 16.5 vs 38.5. minutes, and 2,050 vs 3,500 mL, respectively). Severe complications (level IV-V) were also lower in the cardiopulmonary bypass-free group than in cardiopulmonary bypass and cardiopulmonary bypass/deep hypothermic circulatory arrest groups (25% vs 50% vs 40%). Oncologic outcomes were comparable among the 3 groups in short-term follow-up.

    CONCLUSIONS: Pure transabdominal-transdiaphragmatic robot-assisted inferior vena cava thrombectomy without cardiopulmonary bypass/deep hypothermic circulatory arrest represents as an alternative minimally invasive approach for selected level IV inferior vena cava thrombi.

  17. Fulltext Disease Progression of WHIM Syndrome in an International Cohort of 66 Pediatric and Adult Patients
    Geier CB, Ellison M, Cruz R, Pawar S, Leiss-Piller A, Zmajkovicova K, et al.
    J Clin Immunol, 2022 Nov;42(8):1748-1765.
    PMID: 35947323 DOI: 10.1007/s10875-022-01312-7
    Warts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome (WS) is a combined immunodeficiency caused by gain-of-function mutations in the C-X-C chemokine receptor type 4 (CXCR4) gene. We characterize a unique international cohort of 66 patients, including 57 (86%) cases previously unreported, with variable clinical phenotypes. Of 17 distinct CXCR4 genetic variants within our cohort, 11 were novel pathogenic variants affecting 15 individuals (23%). All variants affect the same CXCR4 region and impair CXCR4 internalization resulting in hyperactive signaling. The median age of diagnosis in our cohort (5.5 years) indicates WHIM syndrome can commonly present in childhood, although some patients are not diagnosed until adulthood. The prevalence and mean age of recognition and/or onset of clinical manifestations within our cohort were infections 88%/1.6 years, neutropenia 98%/3.8 years, lymphopenia 88%/5.0 years, and warts 40%/12.1 years. However, we report greater prevalence and variety of autoimmune complications of WHIM syndrome (21.2%) than reported previously. Patients with versus without family history of WHIM syndrome were diagnosed earlier (22%, average age 1.3 years versus 78%, average age 5 years, respectively). Patients with a family history of WHIM syndrome also received earlier treatment, experienced less hospitalization, and had less end-organ damage. This observation reinforces previous reports that early treatment for WHIM syndrome improves outcomes. Only one patient died; death was attributed to complications of hematopoietic stem cell transplantation. The variable expressivity of WHIM syndrome in pediatric patients delays their diagnosis and therapy. Early-onset bacterial infections with severe neutropenia and/or lymphopenia should prompt genetic testing for WHIM syndrome, even in the absence of warts.
  18. Fulltext Genomic evidence for the Chinese mountain cat as a wildcat conspecific (Felis silvestris bieti) and its introgression to domestic cats
    Yu H, Xing YT, Meng H, He B, Li WJ, Qi XZ, et al.
    Sci Adv, 2021 Jun;7(26).
    PMID: 34162544 DOI: 10.1126/sciadv.abg0221
    The Qinghai-Tibet Plateau endemic Chinese mountain cat has a controversial taxonomic status, whether it is a true species or a wildcat (Felis silvestris) subspecies and whether it has contributed to cat (F. s. catus) domestication in East Asia. Here, we sampled F. silvestris lineages across China and sequenced 51 nuclear genomes, 55 mitogenomes, and multilocus regions from 270 modern or museum specimens. Genome-wide analyses classified the Chinese mountain cat as a wildcat conspecific F. s. bieti, which was not involved in cat domestication of China, thus supporting a single domestication origin arising from the African wildcat (F. s. lybica). A complex hybridization scenario including ancient introgression from the Asiatic wildcat (F. s. ornata) to F. s. bieti, and contemporary gene flow between F. s. bieti and sympatric domestic cats that are likely recent Plateau arrivals, raises the prospect of disrupted wildcat genetic integrity, an issue with profound conservation implications.
  19. Fulltext Smoking Modifies Pancreatic Cancer Risk Loci on 2q21.3
    Mocci E, Kundu P, Wheeler W, Arslan AA, Beane-Freeman LE, Bracci PM, et al.
    Cancer Res, 2021 Jun 01;81(11):3134-3143.
    PMID: 33574088 DOI: 10.1158/0008-5472.CAN-20-3267
    Germline variation and smoking are independently associated with pancreatic ductal adenocarcinoma (PDAC). We conducted genome-wide smoking interaction analysis of PDAC using genotype data from four previous genome-wide association studies in individuals of European ancestry (7,937 cases and 11,774 controls). Examination of expression quantitative trait loci data from the Genotype-Tissue Expression Project followed by colocalization analysis was conducted to determine whether there was support for common SNP(s) underlying the observed associations. Statistical tests were two sided and P < 5 × 10-8 was considered statistically significant. Genome-wide significant evidence of qualitative interaction was identified on chr2q21.3 in intron 5 of the transmembrane protein 163 (TMEM163) and upstream of the cyclin T2 (CCNT2). The most significant SNP using the Empirical Bayes method, in this region that included 45 significantly associated SNPs, was rs1818613 [per allele OR in never smokers 0.87, 95% confidence interval (CI), 0.82-0.93; former smokers 1.00, 95% CI, 0.91-1.07; current smokers 1.25, 95% CI 1.12-1.40, P interaction = 3.08 × 10-9). Examination of the Genotype-Tissue Expression Project data demonstrated an expression quantitative trait locus in this region for TMEM163 and CCNT2 in several tissue types. Colocalization analysis supported a shared SNP, rs842357, in high linkage disequilibrium with rs1818613 (r 2 = 0. 94) driving both the observed interaction and the expression quantitative trait loci signals. Future studies are needed to confirm and understand the differential biologic mechanisms by smoking status that contribute to our PDAC findings. SIGNIFICANCE: This large genome-wide interaction study identifies a susceptibility locus on 2q21.3 that significantly modified PDAC risk by smoking status, providing insight into smoking-associated PDAC, with implications for prevention.
  20. 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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