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Large-scale genome-wide SNP analysis reveals the rugged(and ragged)landscape of global ancestry,phylogeny,and demographic history in chicken breeds

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2024年第4期25卷 324-340页

作者： Natalia V.DEMENTIEVA Yuri S.SHCHERBAKOV Olga I.STANISHEVSKAYA Anatoly B.VAKHRAMEEV Tatiana A.LARKINA Artem P.DYSIN Olga A.NIKOLAEVA Anna E.RYABOVA Anastasiia I.AZOVTSEVA Olga V.MITROFANOVA Grigoriy K.PEGLIVANYAN Natalia R.REINBACH Darren K.GRIFFIN Michael N.ROMANOV Russian research Institute of Farm Animal Genetics and Breeding-Branch of the L.K.Ernst federal research Centre for Animal Husbandry.Pushkin St.Petersburg196601Russia School of Biosciences University of KentCanterburyCT27NJUK L.K.Ernst federal research center for Animal Husbandry DubrovitsyPodolskMoscow Oblast142132Russia

The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse *** study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 *** populations represent a significant sample of the world's chicken breeds from Europe(Russia,Czech Republic,France,Spain,UK,etc.),Asia(China),North America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism(SNP)chip,a bioinformatic analysis was carried *** included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population *** also included assessment of linkage disequilibrium and construction of phylogenetic *** multidimensional scaling,principal component analysis,and ADMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each *** overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous *** a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry *** general,whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.

关键词： Chicken genome diversity Single nucleotide polymorphism(SNP)analysis Gene pool Global ancestry Phylogeny Demographic history

Reactivation of hepatitis B virus infection – an important aspect of multifaceted problem

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World Journal of Gastroenterology 2024年第26期30卷 3193-3197页

作者： Sergey Morozov Sergey Batskikh Department of Gastroenterology Hepatology and NutritionFederal Research Center of NutritionBiotechnology and Food SafetyMoscow 115446Russia Department of Hepatology Moscow Clinical Scientific Center N.A.A.S.LoginovMoscow 111123Russia

In this editorial we comment on the article published in the recent issue of the W orld Journal of *** focus specifically on the problem of occult hepatitis B virus(HBV)infection,that is a result of previous hepatitis B(PHB)and a source for reactivation of *** prevalence of PHB is underestimated due to the lack of population testing ***,this condition not only com-plicate anticancer treatment,but may be responsible for the development of other diseases,like cancer or autoimmune *** we unveil possible mecha-nisms responsible for realization of these processes and suggest practical approa-ches for diagnosis and treatment.

关键词： Occult hepatitis B virus infection Hepatitis B virus reactivation Previous hepatitis B Cancer Autoimmune disorders

Parasites of the liver:A global problem?

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World Journal of Gastroenterology 2024年第30期30卷 3554-3559页

作者： Vladislav V Tsukanov Alexander V Vasyutin Julia L Tonkikh Clinical Department of the Digestive System Pathology of Adults and Children Federal Research Center“Krasnoyarsk Science Center”of the Siberian Branch of the Russian Academy of SciencesScientific Research Institute of Medical Problems of the NorthKrasnoyarsk 660022Russia

Parasitic liver diseases can be caused by trematodes,cestodes,nematodes,and *** pathology is significant because millions of people in different parts of the world have liver parasites,which can manifest themselves in the development of inflammation,liver cysts,cholecystitis,cholelithiasis,pancreatitis and liver cirrhosis that are often threatening their *** International Agency for research on Cancer considers three species of trematodes,Schistosoma haematobium,Opisthorchis viverrini and Clonorchis sinensis,to be *** modern examination methods,in some cases including extensive screening of large populations,are required for diagnosing liver *** of parasitic liver diseases is differentiated and can involve a combination of surgical and therapeutic *** is no doubt that the clinical and epidemiological scale allows one to regard parasitic liver diseases as a global healthcare problem.

关键词： Liver Parasites Epidemiology Diagnosis Clinics Treatment Echinococcosis Opisthorchiasis Fascioliasis Schistosomiasis

Determining the effective elastic thickness through cross-correlation between isostatic disturbances

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Geodesy and Geodynamics 2024年第3期15卷 241-251页

作者： Nelson Ribeiro-Filho Cristiano Mendel Martins Raissa Moraes Baldez Ivaldevingles Rodrigues de Souza Júnior Franck Eitel Kemgang Ghomsi Instituto federal do Pará(IFPA) AltamiraParáBrazil Universidade federal do Pará(UFPA) BelemParáBrazil Nansen-Tutu center for Marine Environmental research Department of OceanographyUniversity of Cape TownSouth Africa Geodesy research Laboratory National Institute of CartographyYaoundeCameroon

The elastic thickness parameter was estimated using the mobile correlation technique between the observed isostatic disturbance and the gravity disturbance calculated through direct gravimetric modeling. We computed the vertical flexure value of the crust for a specific elastic thickness using a given topographic dataset. The gravity disturbance due to the topography was determined after the calculation. A grid of values for the elastic thickness parameter was generated. Then, a moving correlation was performed between the observed gravity data(representing actual surface data) and the calculated data from the forward modeling. The optimum elastic thickness of the particular point corresponded to the highest correlation coefficient. The methodology was tested on synthetic data and showed that the synthetic depth closely matched the original depth, including the elastic thickness value. To validate the results, the described procedure was applied to a real dataset from the Barreirinhas Basin, situated in the northeastern region of Brazil. The results show that the obtained crustal depth is highly correlated with the depth from known models. Additionally, we noted that the elastic thickness behaves as expected, decreasing from the continent towards the ocean. Based on the results, this method has the potential to be employed as a direct estimate of crustal depth and elastic thickness for any region.

关键词： Isostasy Elastic thickness Isostatic disturbance Moho depth Cross-correlation

Small mammal community composition impacts bank vole (Clethrionomys glareolus) population dynamics and associated seroprevalence of Puumala orthohantavirus

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Integrative Zoology 2024年第1期19卷 52-65页

作者： Felicitas Maria BUJNOCH Daniela REIL Stephan DREWES Ulrike MROSENFELD Rainer G.ULRICH Jens JACOB Christian IMHOLT Julius Kühn-Institute Federal Research Centre for Cultivated PlantsInstitute for Epidemiology and Pathogen DiagnosticsRodent ResearchMünsterGermany University of Münster Institute for Evolution and BiodiversityMünsterGermany Friedrich-Loeffler-Institut Federal Research Institute for Animal HealthInstitute of Novel and Emerging Infectious DiseasesGreifswald-Insel RiemsGermany

Rodents are important reservoirs for zoonotic pathogens that cause diseases in *** is hypoth-esized to be closely related to pathogen prevalence through multiple direct and indirect *** example,the presence of non-host species can reduce contact rates of the main reservoir host and thus reduce the risk of transmission(“dilution effect”).In addition,an overlap in ecological niches between two species could lead to increased interspecific competition,potentially limiting host densities and reducing density-dependent pathogen transmission *** this study,we investigated the relative impact of population-level regulation of direct and indirect drivers of the prevalence of Puumala orthohantavirus(PUUV)in bank voles(Clethrionomys glareolus)during years with high *** compiled data on small mammal community composition from four regions in Germany between 2010 and *** equation modeling revealed a strong seasonality in PUUV control mechanisms in bank *** abundance of shrews tended to have a negative relationship with host abundance,and host abundance positively influenced PUUV seroprevalence,while at the same time increasing the abundance of competing non-hosts like the wood mouse(Apodemus sylvaticus)and the yellow-neckedfield mouse(Apodemusflavicollis)were associated with reduced PUUV seroprevalence in the *** results indicate that for PUUV in bank voles,dilution is associated with increased interspecific *** pressures leading to the decline of Apodemus *** a specific habitat could lead to the amplification of mechanisms promoting PUUV transmission within the host populations.

关键词： bank vole biodiversity Puumala orthohantavirus small mammals

Artificial enhancement of sturgeon stock in freshwater reservoirs:A case study on sterlet Acipenser ruthenus of the Kama reservoir

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Aquaculture and Fisheries 2024年第2期9卷 287-294页

作者： Pavel B.Mikheev Semyon N.Kazarinov Alla G.Melnikova Stanislav V.Ponosov Nikolai G.Petrenko Andrei I.Nikiforov Alexey Yu Puzik Olga N.Elchenkova Perm State National research University Perm614990Russia Khabarovsk Branch of the federal State Budget Scientific Institution“Russian federal research Institute of Fisheries and Oceanography”“KhabarovskNIRO” Khabarovsk680038Russia Perm Branch of the federal State Budget Scientific Institution“Russian federal research Institute of Fisheries and Oceanography”“PermNIRO” Perm614991Russia federal State Budget Scientific Institution“Russian federal research Institute of Fisheries and Oceanography”“VNIRO” Moscow117454Russia Moscow State Institute of International Relations(University)of the Ministry for Foreign Affairs of Russia“MGIMO” Moscow117454Russia Department of State Control Supervision and Protection of Aquatic Biological Resources for Perm KraiMiddle-Volga Regional Office of the Federal Fishery AgencyPerm614990Russia

The paper presents the results of the sterlet sturgeon Acipenser ruthenus reintroduction into the Kama Reservoir(Perm Krai,Russia)by sterlet fry from hatcheries into the reservoir since *** effectiveness of hatchery releases was evaluated by monitoring gillnet sampling *** results showed that the species was reported throughout entire Kama Reservoir,which contrasts with 1988-1994 data,when the species was registered only at the upper part of the reservoir near the Kama River *** highest number and biomass values of catch per unit effort(CPUE)of the sterlet were found in submerged river channels-the deepest habitats with flow conditions which are close to the ecological requirements of the *** distribution of the sterlet within the channel biotopes of the reservoir is defined by reduced *** biggest individuals and the widest size range of the sterlet were typical for the upper area of the reservoir and Chusovskoy Bay,which have the greatest *** smallest sizes were typical for fish from catches near the dam of the reservoir,which is consistent with the published data on the distribution of sterlet in reservoir *** presented results may indicate the artificial formation of the sterlet stock in the Kama Reservoir maintained by hatchery *** revealed distribution of the sterlet in the reservoir determines the direction of further research on natural reproduction and thus formation of an artificially formed ***,future studies are required to assess the possibility of hybridization of the sterlet of artificial origin with natural populations of the species,since the low genetic diversity of the sterlet released into the Kama Reservoir which can lead to irreversible loss of genetic individuality of the natural stocks of the species in the catchment of upper course of the Kama River.

关键词： Sterlet Acipenser ruthenus Kama reservoir Hatchery releases CPUE Artificial stock formation

Lattice distortion generates bound states in the continuum

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Science China(Physics,Mechanics & Astronomy) 2024年第3期67卷 166-166页

作者： Almas Sadreev Kirensky Institute of Physics Federal Research Center KSC Siberian BranchRussian Academy of SciencesKrasnoyarsk 660036Russia

High-Q optical cavity is an indispensable component of many photonic devices, such as lasers, sensors, harmonic generation and photon emission, and chiral *** way of realizing ultrahigh Q-factor relies on Fabry-Pérot... 详细信息

关键词： Lattice distortion cavity

Innate IgM antibodies to mannose in patients with gastric cancer

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Cancer Biology & Medicine 2024年第3期21卷 193-197页

作者： Maxim Petrovich Nikulin Nadezhda Vladimirovna Shilova Alexander Dmitrievich Lipatnikov Ivan Sokratovich Stilidi Alexandra Vladimirovna Semyanikhina Nikolai Vladimirovich Bovin Nikolai Nikolaevich Tupitsyn federal State Budgetary Institution"National Medical research center for Oncology Named After N.N.Blokhin"of the Ministry of Health of Russia MoscowRussia State research center"Institute of Bioorganic Chemistry Named After Academicians M.M.Shemyakin and Yu.A.Ovchinnikov"of the Russian Academy of Sciences MoscowRussia National Medical research center for Obstetrics Gynecology and Perinatology Named After Academician VI.Kulakov of the Ministry of Health of Russian FederationMoscowRussia

Gastric cancer(GC) remains one of the most common lethal diseases. Every year, about 1 million people fall ill and almost 800 thousand people die worldwide~1. Surgical treatment has reached its limit. The current advances in immunology and detection of epidermal growth factor molecules(EGFR) in gastric cancer cells allowed to improve the treatment results;however, the metastatic form of this disease is still incurable.

关键词： Gastric cancer gastric

From prediction to prevention:Machine learning revolutionizes hepatocellular carcinoma recurrence monitoring

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World Journal of Gastroenterology 2024年第7期30卷 631-635页

作者： Mariana Michelle Ramírez-Mejía Nahum Méndez-Sánchez Plan of Combined Studies in Medicine Faculty of MedicineNational Autonomous University of MexicoDistrito Federal 04510Mexico Liver research Unit Medica Sur Clinic&FoundationDistrito Federal 14050Mexico Faculty of Medicine National Autonomous University of MexicoDistrito Federal 04510Mexico

In this editorial,we comment on the article by Zhang et al entitled Development of a machine learning-based model for predicting the risk of early postoperative recurrence of hepatocellular *** carcinoma(HCC),which is characterized by high incidence and mortality rates,remains a major global health challenge primarily due to the critical issue of postoperative *** recurrence,defined as recurrence that occurs within 2 years posttreatment,is linked to the hidden spread of the primary tumor and significantly impacts patient *** predictive factors,including both patient-and treatment-related factors,have limited predictive ability with respect to HCC *** integration of machine learning algorithms is fueled by the exponential growth of computational power and has revolutionized HCC *** study by Zhang et al demonstrated the use of a groundbreaking preoperative prediction model for early postoperative HCC *** persist,including sample size constraints,issues with handling data,and the need for further validation and *** study emphasizes the need for collaborative efforts,multicenter studies and comparative analyses to validate and refine the *** these challenges and exploring innovative approaches,such as multi-omics integration,will enhance personalized oncology *** study marks a significant stride toward precise,efficient,and personalized oncology practices,thus offering hope for improved patient outcomes in the field of HCC treatment.

关键词： Hepatocellular carcinoma Early recurrence Machine learning XGBoost model Predictive precision medicine Clinical utility Personalized interventions