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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.
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.
Fulltext Genome-wide meta-analysis identifies five new susceptibility loci for pancreatic cancer

Klein AP, Wolpin BM, Risch HA, Stolzenberg-Solomon RZ, Mocci E, Zhang M, et al.

Nat Commun, 2018 02 08;9(1):556.
PMID: 29422604 DOI: 10.1038/s41467-018-02942-5

In 2020, 146,063 deaths due to pancreatic cancer are estimated to occur in Europe and the United States combined. To identify common susceptibility alleles, we performed the largest pancreatic cancer GWAS to date, including 9040 patients and 12,496 controls of European ancestry from the Pancreatic Cancer Cohort Consortium (PanScan) and the Pancreatic Cancer Case-Control Consortium (PanC4). Here, we find significant evidence of a novel association at rs78417682 (7p12/TNS3, P = 4.35 × 10-8). Replication of 10 promising signals in up to 2737 patients and 4752 controls from the PANcreatic Disease ReseArch (PANDoRA) consortium yields new genome-wide significant loci: rs13303010 at 1p36.33 (NOC2L, P = 8.36 × 10-14), rs2941471 at 8q21.11 (HNF4G, P = 6.60 × 10-10), rs4795218 at 17q12 (HNF1B, P = 1.32 × 10-8), and rs1517037 at 18q21.32 (GRP, P = 3.28 × 10-8). rs78417682 is not statistically significantly associated with pancreatic cancer in PANDoRA. Expression quantitative trait locus analysis in three independent pancreatic data sets provides molecular support of NOC2L as a pancreatic cancer susceptibility gene.
Fulltext Three new pancreatic cancer susceptibility signals identified on chromosomes 1q32.1, 5p15.33 and 8q24.21

Zhang M, Wang Z, Obazee O, Jia J, Childs EJ, Hoskins J, et al.

Oncotarget, 2016 Oct 11;7(41):66328-66343.
PMID: 27579533 DOI: 10.18632/oncotarget.11041

Genome-wide association studies (GWAS) have identified common pancreatic cancer susceptibility variants at 13 chromosomal loci in individuals of European descent. To identify new susceptibility variants, we performed imputation based on 1000 Genomes (1000G) Project data and association analysis using 5,107 case and 8,845 control subjects from 27 cohort and case-control studies that participated in the PanScan I-III GWAS. This analysis, in combination with a two-staged replication in an additional 6,076 case and 7,555 control subjects from the PANcreatic Disease ReseArch (PANDoRA) and Pancreatic Cancer Case-Control (PanC4) Consortia uncovered 3 new pancreatic cancer risk signals marked by single nucleotide polymorphisms (SNPs) rs2816938 at chromosome 1q32.1 (per allele odds ratio (OR) = 1.20, P = 4.88x10 -15), rs10094872 at 8q24.21 (OR = 1.15, P = 3.22x10 -9) and rs35226131 at 5p15.33 (OR = 0.71, P = 1.70x10 -8). These SNPs represent independent risk variants at previously identified pancreatic cancer risk loci on chr1q32.1 ( NR5A2), chr8q24.21 ( MYC) and chr5p15.33 ( CLPTM1L- TERT) as per analyses conditioned on previously reported susceptibility variants. We assessed expression of candidate genes at the three risk loci in histologically normal ( n = 10) and tumor ( n = 8) derived pancreatic tissue samples and observed a marked reduction of NR5A2 expression (chr1q32.1) in the tumors (fold change -7.6, P = 5.7x10 -8). This finding was validated in a second set of paired ( n = 20) histologically normal and tumor derived pancreatic tissue samples (average fold change for three NR5A2 isoforms -31.3 to -95.7, P = 7.5x10 -4-2.0x10 -3). Our study has identified new susceptibility variants independently conferring pancreatic cancer risk that merit functional follow-up to identify target genes and explain the underlying biology.
Fulltext A Transcriptome-Wide Association Study Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer

Zhong J, Jermusyk A, Wu L, Hoskins JW, Collins I, Mocci E, et al.

J Natl Cancer Inst, 2020 Oct 01;112(10):1003-1012.
PMID: 31917448 DOI: 10.1093/jnci/djz246

BACKGROUND: Although 20 pancreatic cancer susceptibility loci have been identified through genome-wide association studies in individuals of European ancestry, much of its heritability remains unexplained and the genes responsible largely unknown.
METHODS: To discover novel pancreatic cancer risk loci and possible causal genes, we performed a pancreatic cancer transcriptome-wide association study in Europeans using three approaches: FUSION, MetaXcan, and Summary-MulTiXcan. We integrated genome-wide association studies summary statistics from 9040 pancreatic cancer cases and 12 496 controls, with gene expression prediction models built using transcriptome data from histologically normal pancreatic tissue samples (NCI Laboratory of Translational Genomics [n = 95] and Genotype-Tissue Expression v7 [n = 174] datasets) and data from 48 different tissues (Genotype-Tissue Expression v7, n = 74-421 samples).
RESULTS: We identified 25 genes whose genetically predicted expression was statistically significantly associated with pancreatic cancer risk (false discovery rate < .05), including 14 candidate genes at 11 novel loci (1p36.12: CELA3B; 9q31.1: SMC2, SMC2-AS1; 10q23.31: RP11-80H5.9; 12q13.13: SMUG1; 14q32.33: BTBD6; 15q23: HEXA; 15q26.1: RCCD1; 17q12: PNMT, CDK12, PGAP3; 17q22: SUPT4H1; 18q11.22: RP11-888D10.3; and 19p13.11: PGPEP1) and 11 at six known risk loci (5p15.33: TERT, CLPTM1L, ZDHHC11B; 7p14.1: INHBA; 9q34.2: ABO; 13q12.2: PDX1; 13q22.1: KLF5; and 16q23.1: WDR59, CFDP1, BCAR1, TMEM170A). The association for 12 of these genes (CELA3B, SMC2, and PNMT at novel risk loci and TERT, CLPTM1L, INHBA, ABO, PDX1, KLF5, WDR59, CFDP1, and BCAR1 at known loci) remained statistically significant after Bonferroni correction.
CONCLUSIONS: By integrating gene expression and genotype data, we identified novel pancreatic cancer risk loci and candidate functional genes that warrant further investigation.
Fulltext Mitochondrial Respiration Is Reduced in Atherosclerosis, Promoting Necrotic Core Formation and Reducing Relative Fibrous Cap Thickness

Yu EPK, Reinhold J, Yu H, Starks L, Uryga AK, Foote K, et al.

Arterioscler Thromb Vasc Biol, 2017 12;37(12):2322-2332.
PMID: 28970293 DOI: 10.1161/ATVBAHA.117.310042

OBJECTIVE: Mitochondrial DNA (mtDNA) damage is present in murine and human atherosclerotic plaques. However, whether endogenous levels of mtDNA damage are sufficient to cause mitochondrial dysfunction and whether decreasing mtDNA damage and improving mitochondrial respiration affects plaque burden or composition are unclear. We examined mitochondrial respiration in human atherosclerotic plaques and whether augmenting mitochondrial respiration affects atherogenesis.
APPROACH AND RESULTS: Human atherosclerotic plaques showed marked mitochondrial dysfunction, manifested as reduced mtDNA copy number and oxygen consumption rate in fibrous cap and core regions. Vascular smooth muscle cells derived from plaques showed impaired mitochondrial respiration, reduced complex I expression, and increased mitophagy, which was induced by oxidized low-density lipoprotein. Apolipoprotein E-deficient (ApoE-/-) mice showed decreased mtDNA integrity and mitochondrial respiration, associated with increased mitochondrial reactive oxygen species. To determine whether alleviating mtDNA damage and increasing mitochondrial respiration affects atherogenesis, we studied ApoE-/- mice overexpressing the mitochondrial helicase Twinkle (Tw+/ApoE-/-). Tw+/ApoE-/- mice showed increased mtDNA integrity, copy number, respiratory complex abundance, and respiration. Tw+/ApoE-/- mice had decreased necrotic core and increased fibrous cap areas, and Tw+/ApoE-/- bone marrow transplantation also reduced core areas. Twinkle increased vascular smooth muscle cell mtDNA integrity and respiration. Twinkle also promoted vascular smooth muscle cell proliferation and protected both vascular smooth muscle cells and macrophages from oxidative stress-induced apoptosis.
CONCLUSIONS: Endogenous mtDNA damage in mouse and human atherosclerosis is associated with significantly reduced mitochondrial respiration. Reducing mtDNA damage and increasing mitochondrial respiration decrease necrotic core and increase fibrous cap areas independently of changes in reactive oxygen species and may be a promising therapeutic strategy in atherosclerosis.
Fulltext The schizophrenia genetics knowledgebase: a comprehensive update of findings from candidate gene studies

Liu C, Kanazawa T, Tian Y, Mohamed Saini S, Mancuso S, Mostaid MS, et al.

Transl Psychiatry, 2019 08 27;9(1):205.
PMID: 31455759 DOI: 10.1038/s41398-019-0532-4

Over 3000 candidate gene association studies have been performed to elucidate the genetic underpinnings of schizophrenia. However, a comprehensive evaluation of these studies' findings has not been undertaken since the decommissioning of the schizophrenia gene (SzGene) database in 2011. As such, we systematically identified and carried out random-effects meta-analyses for all polymorphisms with four or more independent studies in schizophrenia along with a series of expanded meta-analyses incorporating published and unpublished genome-wide association (GWA) study data. Based on 550 meta-analyses, 11 SNPs in eight linkage disequilibrium (LD) independent loci showed Bonferroni-significant associations with schizophrenia. Expanded meta-analyses identified an additional 10 SNPs, for a total of 21 Bonferroni-significant SNPs in 14 LD-independent loci. Three of these loci (MTHFR, DAOA, ARVCF) had never been implicated by a schizophrenia GWA study. In sum, the present study has provided a comprehensive summary of the current schizophrenia genetics knowledgebase and has made available all the collected data as a resource for the research community.
Fulltext LGR5 Activates Noncanonical Wnt Signaling and Inhibits Aldosterone Production in the Human Adrenal

Shaikh LH, Zhou J, Teo AE, Garg S, Neogi SG, Figg N, et al.

J Clin Endocrinol Metab, 2015 Jun;100(6):E836-44.
PMID: 25915569 DOI: 10.1210/jc.2015-1734

CONTEXT: Aldosterone synthesis and cellularity in the human adrenal zona glomerulosa (ZG) is sparse and patchy, presumably due to salt excess. The frequency of somatic mutations causing aldosterone-producing adenomas (APAs) may be a consequence of protection from cell loss by constitutive aldosterone production.
OBJECTIVE: The objective of the study was to delineate a process in human ZG, which may regulate both aldosterone production and cell turnover.
DESIGN: This study included a comparison of 20 pairs of ZG and zona fasciculata transcriptomes from adrenals adjacent to an APA (n = 13) or a pheochromocytoma (n = 7).
INTERVENTIONS: Interventions included an overexpression of the top ZG gene (LGR5) or stimulation by its ligand (R-spondin-3).
MAIN OUTCOME MEASURES: A transcriptome profile of ZG and zona fasciculata and aldosterone production, cell kinetic measurements, and Wnt signaling activity of LGR5 transfected or R-spondin-3-stimulated cells were measured.
RESULTS: LGR5 was the top gene up-regulated in ZG (25-fold). The gene for its cognate ligand R-spondin-3, RSPO3, was 5-fold up-regulated. In total, 18 genes associated with the Wnt pathway were greater than 2-fold up-regulated. ZG selectivity of LGR5, and its absence in most APAs, were confirmed by quantitative PCR and immunohistochemistry. Both R-spondin-3 stimulation and LGR5 transfection of human adrenal cells suppressed aldosterone production. There was reduced proliferation and increased apoptosis of transfected cells, and the noncanonical activator protein-1/Jun pathway was stimulated more than the canonical Wnt pathway (3-fold vs 1.3-fold). ZG of adrenal sections stained positive for apoptosis markers.
CONCLUSION: LGR5 is the most selectively expressed gene in human ZG and reduces aldosterone production and cell number. Such conditions may favor cells whose somatic mutation reverses aldosterone inhibition and cell loss.
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.
Fulltext Defining the disease liability of variants in the cystic fibrosis transmembrane conductance regulator gene

Sosnay PR, Siklosi KR, Van Goor F, Kaniecki K, Yu H, Sharma N, et al.

Nat Genet, 2013 Oct;45(10):1160-7.
PMID: 23974870 DOI: 10.1038/ng.2745

Allelic heterogeneity in disease-causing genes presents a substantial challenge to the translation of genomic variation into clinical practice. Few of the almost 2,000 variants in the cystic fibrosis transmembrane conductance regulator gene CFTR have empirical evidence that they cause cystic fibrosis. To address this gap, we collected both genotype and phenotype data for 39,696 individuals with cystic fibrosis in registries and clinics in North America and Europe. In these individuals, 159 CFTR variants had an allele frequency of ł0.01%. These variants were evaluated for both clinical severity and functional consequence, with 127 (80%) meeting both clinical and functional criteria consistent with disease. Assessment of disease penetrance in 2,188 fathers of individuals with cystic fibrosis enabled assignment of 12 of the remaining 32 variants as neutral, whereas the other 20 variants remained of indeterminate effect. This study illustrates that sourcing data directly from well-phenotyped subjects can address the gap in our ability to interpret clinically relevant genomic variation.
Menstrual and Reproductive Factors, Hormone Use, and Risk of Pancreatic Cancer: Analysis From the International Pancreatic Cancer Case-Control Consortium (PanC4)

Lujan-Barroso L, Zhang W, Olson SH, Gao YT, Yu H, Baghurst PA, et al.

Pancreas, 2016 11;45(10):1401-1410.
PMID: 27088489

OBJECTIVES: We aimed to evaluate the relation between menstrual and reproductive factors, exogenous hormones, and risk of pancreatic cancer (PC).
METHODS: Eleven case-control studies within the International Pancreatic Cancer Case-control Consortium took part in the present study, including in total 2838 case and 4748 control women. Pooled estimates of odds ratios (ORs) and their 95% confidence intervals (CIs) were calculated using a 2-step logistic regression model and adjusting for relevant covariates.
RESULTS: An inverse OR was observed in women who reported having had hysterectomy (ORyesvs.no, 0.78; 95% CI, 0.67-0.91), remaining significant in postmenopausal women and never-smoking women, adjusted for potential PC confounders. A mutually adjusted model with the joint effect for hormone replacement therapy (HRT) and hysterectomy showed significant inverse associations with PC in women who reported having had hysterectomy with HRT use (OR, 0.64; 95% CI, 0.48-0.84).
CONCLUSIONS: Our large pooled analysis suggests that women who have had a hysterectomy may have reduced risk of PC. However, we cannot rule out that the reduced risk could be due to factors or indications for having had a hysterectomy. Further investigation of risk according to HRT use and reason for hysterectomy may be necessary.
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.
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
Phylogeny and evolution of the Drosophila nasuta subgroup based on mitochondrial ND4 and ND4L gene sequences

Yu H, Wang W, Fang S, Zhang YP, Lin FJ, Geng ZC

Mol Phylogenet Evol, 1999 Dec;13(3):556-65.
PMID: 10620413

The sequences of the mitochondrial ND4 gene (1339 bp) and the ND4L gene (290 bp) were determined for all the 14 extant taxa of the Drosophila nasuta subgroup. The average A + T content of ND4 genes is 76.5% and that of ND4L genes is 83.5%. A total of 114 variable sites were scored. The ND4 gene sequence divergence ranged from 0 to 5.4% within the subgroup. The substitution rate of the ND4 gene is about 1.25% per million years. The base substitution of the genes is strongly transition biased. Neighbor-joining and parsimony were used to construct a phylogeny based on the resultant sequence data set. According to these trees, five distinct mtDNA clades can be identified. D. niveifrons represents the most diverged lineage. D. sulfurigaster bilimbata and D. kepulauana form two independent lineages. The other two clades are the kohkoa complex and the albomicans complex. The kohkoa complex consists of D. sulfurigaster sulfurigaster, D. pulaua, D. kohkoa, and Taxon-F. The albomicans complex can be divided into two groups: D. nasuta, D. sulfurigaster neonasuta, D. sulfurigaster albostrigata, and D. albomicans from Chiangmai form one group; and D. pallidifrons, Taxon-I, Taxon-J, and D. albomicans from China form the other group. High genetic differentiation was found among D. albomicans populations. Based on our phylogenetic results, we hypothesize that D. niveifrons diverged first from the D. nasuta subgroup in Papua New Guinea about 3.5 Mya. The ancestral population spread to the north and when it reached Borneo, it diversified sequentially into the kohkoa complex, D. s. bilimbata, and D. kepulauana. About 1 Mya, another radiation occurred when the ancestral populations reached the Indo-China Peninsula, forming the albomicans complex. Discrepancy between morphological groupings and phylogenetic results suggests that the male morphological traits may not be orthologous.
Influence of substrate on ultrafast water transport property of multilayer graphene coatings

Kueh TC, Yu H, Soh AK, Wu HA, Hung YM

Nanotechnology, 2020 Sep 11;31(37):375704.
PMID: 32480382 DOI: 10.1088/1361-6528/ab9864

The ultrafast water transport in graphene nanoplatelets (GNPs) coating is attributed to the low friction passages formed by pristine graphene and the hydrophilic functional groups which provide a strong interaction force to the water molecules. Here, we examine the influence of the supporting substrate on the ultrafast water transport property of multilayer graphene coatings experimentally and by computational modelling. Thermally cured GNPs manifesting ultrafast water permeation are coated on different substrate materials, namely aluminium, copper, iron and glass. The physical and chemical structures of the GNPs coatings which are affected by the substrate materials are characterized using various spectroscopy techniques. Experimentally, the water permeation and absorption tests evidence the significant influence of the substrate on the rapid water permeation property of GNPs-coating. The water transport rates of the GNPs coatings correspond to the wettability and the free surface energy of their substrates where the most hydrophilic substrate induces the highest water transport rate. In addition, we conduct molecular dynamics (MD) simulations to investigate the transport rate of water molecules through multilayer GNPs adjacent to different substrate materials. The MD simulations results agree well with the experimental results inferring the strong influence of the substrate materials on the fast water transport of GNPs. Therefore, selection of substrate has to be taken into consideration when the GNPs-coating is placed into applications.
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.
Fulltext Common variation at 2p13.3, 3q29, 7p13 and 17q25.1 associated with susceptibility to pancreatic cancer

Childs EJ, Mocci E, Campa D, Bracci PM, Gallinger S, Goggins M, et al.

Nat Genet, 2015 Aug;47(8):911-6.
PMID: 26098869 DOI: 10.1038/ng.3341

Pancreatic cancer is the fourth leading cause of cancer death in the developed world. Both inherited high-penetrance mutations in BRCA2 (ref. 2), ATM, PALB2 (ref. 4), BRCA1 (ref. 5), STK11 (ref. 6), CDKN2A and mismatch-repair genes and low-penetrance loci are associated with increased risk. To identify new risk loci, we performed a genome-wide association study on 9,925 pancreatic cancer cases and 11,569 controls, including 4,164 newly genotyped cases and 3,792 controls in 9 studies from North America, Central Europe and Australia. We identified three newly associated regions: 17q25.1 (LINC00673, rs11655237, odds ratio (OR) = 1.26, 95% confidence interval (CI) = 1.19-1.34, P = 1.42 × 10(-14)), 7p13 (SUGCT, rs17688601, OR = 0.88, 95% CI = 0.84-0.92, P = 1.41 × 10(-8)) and 3q29 (TP63, rs9854771, OR = 0.89, 95% CI = 0.85-0.93, P = 2.35 × 10(-8)). We detected significant association at 2p13.3 (ETAA1, rs1486134, OR = 1.14, 95% CI = 1.09-1.19, P = 3.36 × 10(-9)), a region with previous suggestive evidence in Han Chinese. We replicated previously reported associations at 9q34.2 (ABO), 13q22.1 (KLF5), 5p15.33 (TERT and CLPTM1), 13q12.2 (PDX1), 1q32.1 (NR5A2), 7q32.3 (LINC-PINT), 16q23.1 (BCAR1) and 22q12.1 (ZNRF3). Our study identifies new loci associated with pancreatic cancer risk.
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.
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.
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.

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