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| 1 | 863 genomes reveal the origin and domestication of chicken显示文摘Despite the substantial role that chickens have played in human societies across the world,both the geographic and temporal origins of their domestication remain controversial.To address this issue,we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl(RJF).Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China,northern Thailand and Myanmar.Following their domestication,chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species.In addition,our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF.Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls,our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral,morphological and reproductive traits.Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal. | Ming-Shan Wang Mukesh Thakur Min-Sheng Peng Yu Jiang Laurent Alain Francois Frantz Ming Li Jin-Jin Zhang Sheng Wang Joris Peters Newton Otieno Otecko Chatmongkon Suwannapoom Xing Guo Zhu-Qing Zheng Ali Esmailizadeh Nalini Yasoda Hirimuthugoda Hidayat Ashari Sri Suladari Moch Syamsul Arifin Zein Szilvia Kusza Saeed Sohrabi Hamed Kharrati-Koopaee Quan-Kuan Shen Lin Zeng Min-Min Yang Ya-Jiang Wu Xing-Yan Yang Xue-Mei Lu Xin-Zheng Jia Qing-Hua Nie Susan Joy Lamont Emiliano Lasagna Simone Ceccobelli Humpita Gamaralalage Thilini Nisanka Gunwardana Thilina Madusanka Senasige Shao-Hong Feng Jing-Fang Si Hao Zhang Jie-Qiong Jin Ming-Li Li Yan-Hu Liu Hong-Man Chen Cheng Ma Shan-Shan Dai Abul Kashem Fazlul Haque Bhuiyan Muhammad Sajjad Khan Gamamada Liyanage Lalanie Pradeepa Silva Thi-Thuy Le Okeyo Ally Mwai Mohamed Nawaz Mohamed Ibrahim Megan Supple Beth Shapiro Olivier Hanotte Guojie Zhang Greger Larson Jian-Lin Han Dong-Dong Wu Ya-Ping Zhang | 2020 | Cell Research2020，30，8： | 7 |
| 2 | Clinical characteristics and outcome of hepatocellular carcinoma in alcohol related and cryptogenic cirrhosis: a prospective study显示文摘BACKGROUND: Non-alcoholic fatty liver disease(NAFLD) is becoming a leading cause of chronic liver disease. Hepatocellular carcinoma(HCC) is one of its complications. Although the pathophysiology is unclear, it is reasonable to expect that cryptogenic cirrhosis related HCC(cryptogenic HCC) behaves differently to other types of HCC. This study prospectively compared patients with cryptogenic HCC and those with HCC related to alcoholic cirrhosis. METHODS: A total of 150 consecutive patients with HCC(89 cryptogenic HCC and 61 alcohol related HCC) referred to our unit over a 23-month period were studied. Their demographic data, liver function, tumor characteristics and outcomes were compared.RESULTS: Alcohol related HCC was seen only in males. Compared with cryptogenic HCC, alcohol related HCC had significantly higher aspartate aminotransferase/alanine aminotransferase(AST/ALT) ratio(1.7 vs 1.4, P=0.002), model for endstage liver disease score(13 vs 11, P=0.018) and Child's score(7 vs 6, P=0.037). No significant difference was seen in platelet counts, serum sodium and AST to platelet ratio index. Single nodular tumors were more common in cryptogenic HCC,while diffuse type tumors and macroscopic vascular invasion were common in alcohol related HCC. In patients who could not be offered any treatment because of advanced tumors or poor liver function, alcohol related HCC had a significantly lower median survival(5.3 months) compared with cryptogenic HCC(9.3 months, P=0.034).CONCLUSIONS: Compared with cryptogenic HCC, alcohol related HCC had worse liver function and aggressive tumor morphology at presentation, and a higher proportion was untreatable. In patients who could not be treated, median survival was lower in patients with alcohol related HCC than in those with cryptogenic HCC. | Rohan C Siriwardana Maduni A Niriella Anuradha S Dassanayake Chandika Liyanage Bhagya Gunathilaka Subani Jayathunge Hithanadura J de Silva | 2015 | Hepatobiliary & Pancreatic Diseases International2015，14，4： | 5 |
| 3 | A secondary bile acid from microbiota metabolism attenuates ileitis and bile acid reduction in subclinical necrotic enteritis in chickens显示文摘Background:Clostridium perfringens-induced chicken necrotic enteritis(NE)is responsible for substantial economic losses worldwide annually.Recently,as a result of antibiotic growth promoter prohibition,the prevalence of NE in chickens has reemerged.This study was aimed to reduce NE through titrating dietary deoxycholic acid(DCA)as an effective antimicrobial alternative.Materials and methods:Day-old broiler chicks were assigned to six groups and fed diets supplemented with 0(basal diet),0.8,1.0 and 1.5 g/kg(on top of basal diet)DCA.The birds were challenged with Eimeria maxima(20,000 oocysts/bird)at d 18 and C.perfringens(109 CFU/bird per day)at d 23,24,and 25 to induce NE.The birds were sacrificed at d 26 when ileal tissue and digesta were collected for analyzing histopathology,mRNA accumulation and C.perfringens colonization by real-time PCR,targeted metabolomics of bile acids,fluorescence in situ hybridization(FISH),or terminal deoxynucleotidyl transferase dUTP nick end labeling(TUNEL)assay.Results:At the cellular level,birds infected with E.maxima and C.perfringens developed subclinical NE and showed shortening villi,crypt hyperplasia and immune cell infiltration in ileum.Dietary DCA alleviated the NE-induced ileal inflammation in a dose-dependent manner compared to NE control birds.Consistent with the increased histopathological scores,subclinical NE birds suffered body weight gain reduction compared to the uninfected birds,an effect attenuated with increased doses of dietary DCA.At the molecular level,the highest dose of DCA at 1.5 g/kg reduced C.perfringens luminal colonization compared to NE birds using PCR and FISH.Furthermore,the dietary DCA reduced subclinical NE-induced intestinal inflammatory gene expression and cell apoptosis using PCR and TUNEL assays.Upon further examining ileal bile acid pool through targeted metabolomics,subclinical NE reduced the total bile acid level in ileal digesta compared to uninfected birds.Notably,dietary DCA increased total bile acid and DCA levels in a dose-dependent manner compared to NE birds.Conclusion:These results indicate that DCA attenuates NE-induced intestinal inflammation and bile acid reduction and could be an effective antimicrobial alternative against the intestinal disease. | Mohit Bansal Ying Fu Bilal Alrubaye Mussie Abraha Ayidh Almansour Anamika Gupta Rohana Liyanage Hong Wang Billy Hargis Xiaolun Sun | 2020 | Journal of Animal Science and Biotechnology2020，11，3： | 3 |
| 4 | Molecular characterization of cyanobacterial diversity in Lake Gregory, Sri Lanka显示文摘Eutrophication or the process of nutrient enrichment of stagnant waters due to excessive use of fertilizer is becoming a critical issue worldwide. Lake Gregory, an artificial lake situated in Nuwara Eliya, Sri Lanka was once a very attractive landscape feature and recreational area attracting a large number of visitors. Rapid urbanization in surrounding areas and the consequent intensification of agricultural and industrial activities led to eutrophication and siltation in the lake. Present study was conducted to detect cyanobacterial diversity and their ability to produce hepatotoxic microcystins using polymerase chain reaction (PCR)-based techniques. Twenty five water samples (surface and bottom) were collected from the lake and total nitrogen and total carbon were estimated. Cyanobacterial cultures were grown in appropriate media and microscopic observations were used to determine the morphological diversity of cyanobacteria isolated from different sites. Genomic DNA was isolated and purified from cyanobacteria using Boom's method. DNA samples were analyzed by PCR with oligonucleotide primers for 16S rRNA gene and mcyA gene of the operon that encodes a microcystin synthetase. The 16S rRNA gene sequences revealed the presences of cyanobacteria belong to Synechococcus sp., Microcystis aeruginosa, Calothrix sp., Leptolyngbya sp., Limnothrix sp., order Oscillatoriales and order Chroococcales. The sequences obtained from this study were deposited in the database under the accession numbers (GenBank: GU368104-GU368116). PCR amplification of mcyA primers indicated the potential for toxin formation of isolated M. aeruginosa from Lake Gregory. This preliminary study shows that the Lake Gregory is under the potential risk of cyanobacterial toxicity. Clearly more work is needed to extend this finding and clarify if other cyanobacterial isolates have genetic potential to produce microcystin since this lake is utilized for recreational activities. | Dhammika MAGANA-ARACHCHI Rasika WANIGATUNGE Madhushankha LIYANAGE | 2011 | Chinese Journal of Oceanology and Limnology2011，29，4： | 3 |
| 5 | Probability Enhanced Entropy(PEE) Novel Feature for Improved Bird Sound Classification显示文摘Identification of bird species from their sounds has become an important area in biodiversity-related research due to the relative ease of capturing bird sounds in the commonly challenging habitat. Audio features have a massive impact on the classification task since they are the fundamental elements used to differentiate classes. As such, the extraction of informative properties of the data is a crucial stage of any classification-based application. Therefore, it is vital to identify the most significant feature to represent the actual bird sounds. In this paper, we propose a novel feature that can advance classification accuracy with modified features, which are most suitable for classifying birds from its audio sounds. Modified Gammatone frequency cepstral coefficient(GTCC) features have been extracted with their frequency banks adjusted to suit bird sounds. The features are then used to train and test a support vector machine(SVM) classifier. It has been shown that the modified GTCC features are able to give 86% accuracy with twenty Bornean birds. Furthermore, in this paper, we are proposing a novel probability enhanced entropy(PEE) feature, which, when combined with the modified GTCC features, is able to improve accuracy further to 89.5%. These results are significant as the relatively low-resource intensive SVM with the proposed modified GTCC, and the proposed novel PEE feature can be implemented in a real-time system to assist researchers,scientists, conservationists, and even eco-tourists in identifying bird species in the dense forest. | Ramashini Murugaiya Pg Emeroylariffion Abas Liyanage Chandratilak De Silva | 2022 | Machine Intelligence Research2022，19，1： | 2 |
| 6 | SEAR update on mea- sles mortality reduction and elimination, 2003 -2008 显示文摘 | O'Connor PM Liyanage JB Mach O | 2011 | J Infect Dis2011，200，1： | 1 |
| 7 | Prevalence of regulatory T cells is increased in peripheral blood and tumor microenvironment of patients with pancreas or breast adenocarcinoma显示文摘 | Liyanage U K Moore T T Joo H G | 2002 | J Immunol2002，169，： | 1 |
| 8 | The agrin/muscle-specific kinase pathway:new targets for autoimmune and genetic disorders at the neuromuscular junction显示文摘 | Liyanage Y Hoch W Beeson D | 2002 | Muscle Nerve2002，25，1： | 1 |
| 9 | Prevalence of regulatory T ceils is increased in peripheral blood and tumor microenviron- ment of patients with pancreas or breast adenocarcinoma显示文摘 | Liyanage UK Moore TT Joo HG | 2002 | J Im- munol2002，169，5： | 1 |
| 10 | Myeloid-derived vascular endothelial growth factor and hypoxia-inducible factor are dispensable for ocular neovascularization-briefreport显示文摘 | Liyanage SE Fantin A Villacampa P | 2016 | Arterioscler Thromb Vase Bioi2016，36，1： | 1 |
| 11 | The agrin/musclespecific kinase pathway: new targets for autoimmune and genetic disorders at the neuromuscular junction显示文摘 | Liyanage Y Hoch W Beeson D | 2002 | Muscle Nerve2002，25，： | 1 |
| 12 | A thinning-based algorits for evaluating somatic embryos显示文摘 | Kurata K Komine M Liyanage KH | 1993 | Transactions of the ASAE1993，，： | 1 |
| 13 | Prevalence of regulatory T cells is increased in peripheral blood and tumor microenvironment of patients with pancreas or breast adenocarcinoma 显示文摘 | Liyanage UK Moore TT Joo HG | 2002 | J Immunol2002，169，： | 1 |
| 14 | Synthesisand characterization of low-generation polyamidoamine ( PAMAM )dendrimer-sodium montmorillonite ( Na-MMT )clay nanocomposites显示文摘 | AmilaU Liyanage sther U Ikhuoria Adeniyi A | 2013 | Inorganic chemistry2013，52，8： | 1 |
| 15 | DNA modifications:function and applications in normal and disease states显示文摘 | Liyanage VR Jarmasz JS Murugeshan N Del Bigio MR Rastegar M Davie JR | 2014 | Biology(Basel)2014，3，4： | 1 |
| 16 | A detergent-insoluble membrane compartment contains A-beta in vivo显示文摘 | Lee S J Liyanage U Bickel P E | 1998 | Nat Med1998，4，： | 1 |
| 17 | A practical invento- ry control policy using operational statistics显示文摘 | Liyanage L H Shanthikumar J G | 2005 | Opera- tions Research Letters2005，33，4： | 1 |
| 18 | Hazardous waste generation and processing显示文摘 | CHONGRAK P LIYANAGE L R J | 1996 | Resources Conservation and Recycling1996，16，： | 1 |
| 19 | Prevalence of regulatory T cells is increased in peripheral blood and tumor microenvironment of patients with pancreas or breast adenocarcinoma 显示文摘 | Liyanage UK Moore TT Joo HG | 2002 | J Immunol2002，169，5： | 1 |
| 20 | Worldwide ac- cess to treatment for end-stage kidney disease a sys tematic review显示文摘 | Liyanage T Ninomiya T Jha V | 2015 | Lancet2015，385，9981： | 1 |
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