Mining Related Articles for Automatic Journal Cataloging

Purpose： This paper is an investigation of the effectiveness of the method of clustering biomedical journals through mining the content similarity of journal articles. Design/methodology/approach： 3,265 journals in Pub Med are analyzed based on article content similarity and Web usage, respectively. Comparisons of the two analysis approaches and a citation-based approach are given.Findings： Our results suggest that article content similarity is useful for clustering biomedical journals, and the content-similarity-based journal clustering method is more robust and less subject to human factors compared with the usage-based approach and the citation-based approach. Research limitations： Our paper currently focuses on clustering journals in the biomedical domain because there are a large volume of freely available resources such as Pub Med and Me SH in this field. Further investigation is needed to improve this approach to fit journals in other domains.Practical implications： Our results show that it is feasible to catalog biomedical journals by mining the article content similarity. This work is also significant in serving practical needs in research portfolio analysis.Originality/value： To the best of our knowledge, we are among the first to report on clustering journals in the biomedical field through mining the article content similarity. This method can be integrated with existing approaches to create a new paradigm for future studies of journal clustering.

Molecular epidemiological study of animal rabies in Kazakhstan

Rabies is a serious public health issue in Kazakhstan, with high economic impact and social burden. As part of a routine surveillance, 31 rabies-positive brain specimens taken from livestock(cattle) and carnivores(dogs, foxes, and cats)during 2013–2021 were subject to viral sequencing. Phylogenetic and Bayesian analysis were performed using obtained rabies virus(RABV) sequences. All 31 strains of RABV candidate belonged to the Cosmopolitan clade, of which 30strains belonged to steppe-type subclade, and 1 dog strain belonged to Other subclade. The 31 strains did not diverge from RABV strains in Kazakhstan and neighboring countries, including Russia, Mongolia, and China, suggesting that animal rabies has close relationship and transmission between borders. Fox-originated strains and cattle strains shared similar sequence signature, and some animal rabies cases had space–time intersection, showing that infected foxes were a major transmission source of cattle rabies in different Kazakhstan regions. Besides, free-roaming dogs played a pivotal role in rabies epizootics of cattle in Kazakhstan. The recent spread of animal rabies presents an increasing threat to public health, and provides updated information for improving current control and prevention strategies at the source for Kazakhstan and neighboring countries.

Lack of evidence for germline WWP1 pathogenic variants in gastrointestinal polyposis and other phenotypes suggestive of PTEN-hamartoma-tumor syndrome

Germline activating variants in WWP1,which encodes an E3 ubiquitin ligase that antagonizes PTEN tumor suppressive function,have been proposed as an alternative mechanism of PTEN inactivation in PTEN-hamartoma-tumor syndrome(PHTS)-like patients with wildtype PTEN.1 More specifically,heterozygous,potentially activating wwP1 variants were first identified by Lee et al in patients affected with gastrointestinal oligopolyposis,including adenomatous,hyperplastic/serrated,and hamartomatous polyps,and occasionally with colorectal cancer(Table 1).Subsequently,based on the PHTS phenotypic features,wWP1 mutational screening was performed in patients with thyroid nodules,2 or normocephalic autism spectrum disorder(ASD),3 where germline WWP1 variants were also identified(Table S1).

中国生物医药产业技术创新战略联盟发展思路与对策(英文)

1 Introduction Modern biotechnology has significantly propelledthe development of global economy and has a majorimpact on our life[1-2].According to the report releasedin March 2011 by IMS Health,

Analysis of active patents to investigate the frequency and patterns of Chinese herbal extract combinations claiming to treat heart disease

Objective:Using Chinese patents in force to investigate the frequency and patterns of Chinese herbal extract combinations claiming to treat heart disease.Methods:Patent documents were retrieved from the official website of the State Intellectual Property Office of the People’s Republic China.Cluster,frequency,and fuzzy cluster analyses were applied.Results:A high number of patents in force included high-frequency herbs such as Salvia miltiorrhiza,Panax ginseng,and Panax notoginseng,as well as high-frequency herbal families such as Araliaceae,Leguminosae,Labiatae,and Umbelliferae.Herb pairs such as P.ginsengþOphiopogon japonicus,S.miltiorrhizaþDalbergia odorifera,and P.ginsengþSchisandra chinensis are also commonly used,as well as herbal family pairs such as AraliaceaeþLiliaceae,LauraceaeþLeguminosae,and AraliaceaeþSchisandraceae.Traditional treatment principles for preventing and treating heart diseases was most-commonly based on simultaneously treating the liver and heart and treating the lung and spleen secondarily for choosing herbal combinations.Conclusion:Most of the high-frequency Chinese herbs in the patents investigated belong to the high-frequency herbal families,and herb pairs were commonly selected to coincide with the commonly-used herbal family pairs.Low-frequency Chinese herbs were also used,but generally belonged to the high-frequency herbal families,and were therefore similar to the highfrequency herbs in terms of traditional categories of taste and channel entered.The results reflect the use of traditional principles of formula composition,and suggest that these principles may indeed be an effective guide for further research and development of Chinese herbal extract combinations to prevent and treat heart diseases.

InvasionDB: A genome and gene database of invasive alien species

Invasive alien species(IAS) are species whose introduction to areas outside of their native range cause harm to economics, biodiversity, and the environment. Understanding the genetic basis of invasiveness is critical for preventing invasion by an alien species and managing IAS with eco-friendly control methods. In addition, uncovering the genomic features of IAS is essential for accurately predicting invasiveness. However, even though increasing efforts have been devoted to sequencing the genomes of IAS, there is still not an integrated genome database for the invasive biology community. Here, we first determined a list of invasive plants and animals by mining references and databases. Then, we retrieved the genomic and gene data of these IAS, and constructed a database, Invasion DB. Invasion DB encompasses 131 IAS genomes, 76 annotated IAS assemblies, and links these data to conventional functions such as searching for gene coding sequences and Pfam, KEGG, NR annotations, BLAST server, JBrowse, and downloads services. Next, we analyzed 19 invasivenessrelated gene families which confer invasiveness in insects. To study the roles of noncoding RNA in invasiveness, we also annotated 135 494 mi RNAs, 89 294 r RNAs, and 2 671 941 t RNAs from these IAS. In summary, Invasion DB is useful for studying the invasiveness at the genomic level, and thus helps to develop novel management strategies to control IAS.

流产布鲁氏菌的Cu/Zn超氧化物歧化酶的表达及其特性分析(英文)

本研究体外表达了流产布鲁氏菌的Cu/Zn超氧化物歧化酶(Cu/Zn-SOD)并对表达产物进行了免疫原性分析。扩增编码Cu/Zn-SOD的基因,并将其克隆连接到pET-22b(+)载体中。SDS-PAGE结果显示诱导细菌的裂解物有重组Cu/Zn-SOD表达,分子量为20.8 kDa。Western blot结果显示重组Cu/Zn-SOD均与鼠、牛的阳性血清反应。由此,说明体外表达的重组Cu/ZnSOD具有很好的抗原性,为今后疫苗开发及诊断试剂的开发奠定了物质基础。

BioNano Genome Map Resource for Oryza sativa ssp.japonica and indica and Its Application in Rice Genome Sequence Correction and Gap Filling

Dear Editor As one of the most important staple food crops worldwide, rice is among the first plant species whose genomes were sequenced. The reference genome for Oryza sativa ssp. japonica variety Nipponbare was completed by the International Rice Genome Sequencing Project （IRGSP） using a bacterial artificial chromosome （BAC）-based cloning strategy （Matsumoto et al., 2005）.

Cryo-EM structure of a tetrameric photosystem I from Chroococcidiopsis TS-821, a thermophilic, unicellular, non-heterocyst-forming cyanobacterium

Photosystem I(PSI)is one of two photosystems involved in oxygenic photosynthesis.PSI of cyanobacteria exists in monomeric,trimeric,and tetrameric forms,in contrast to the strictly monomeric form of PSI in plants and algae.The tetrameric organization raises questions about its structural,physiological,and evolutionary significance.Here we report the3.72 A˚resolution cryo-electron microscopy structure of tetrameric PSI from the thermophilic,unicellular cyanobacterium Chroococcidiopsis sp.TS-821.The structure resolves 44 subunits and 448 cofactor molecules.We conclude that the tetramer is arranged via two different interfaces resulting from a dimer-of-dimers organization.The localization of chlorophyll molecules permits an excitation energy pathway within and between adjacent monomers.Bioinformatics analysis reveals conserved regions in the PsaL subunit that correlate with the oligomeric state.Tetrameric PSI may function as a key evolutionary step between the trimeric and monomeric forms of PSI organization in photosynthetic organisms.

Web search and data mining of natural products and their bioactivities in PubChem

Natural products,as major resources for drug discovery historically,are gaining more attentions recently due to the advancement in genomic sequencing and other technologies,which makes them attractive and amenable to drug candidate screening.Collecting and mining the bioactivity information of natural products are extremely important for accelerating drug development process by reducing cost.Lately,a number of publicly accessible databases have been established to facilitate the access to the chemical biology data for small molecules including natural products.Thus,it is imperative for scientists in related fields to exploit these resources in order to expedite their researches on natural products as drug leads/candidates for disease treatment.PubChem,as a public database,contains large amounts of natural products associated with bioactivity data.In this review,we introduce the information system provided at PubChem,and systematically describe the applications for a set of PubChem web services for rapid data retrieval,analysis,and downloading of natural products.We hope this work can serve as a starting point for the researchers to perform data mining on natural products using PubChem.

Pleosporales

One hundred and five generic types of Pleosporales are described and illustrated.A brief introduction and detailed history with short notes on morphology,molecular phylogeny as well as a general conclusion of each genus are provided.For those genera where the type or a representative specimen is unavailable,a brief note is given.Altogether 174 genera of Pleosporales are treated.Phaeotrichaceae as well as Kriegeriella,Zeuctomorpha and Muroia are excluded from Pleosporales.Based on the multigene phylogenetic analysis,the suborder Massarineae is emended to accommodate five families,viz.Lentitheciaceae,Massarinaceae,Montagnulaceae,Morosphaeriaceae and Trematosphaeriaceae.

Comparison of caspase-3 activation in tumor cells upon treatment of chemotherapeutic drugs using capillary electrophoresis

Caspases play important roles in cell apoptosis.Meas-urement of the dynamics of caspase activation in tumor cells not only facilitates understanding of the molecular mechanisms of apoptosis but also contributes to the development,screening,and evaluation of anticancer drugs that target apoptotic pathways.The fluorescence resonance energy transfer(FRET)technique provides a valuable approach for defining the dynamics of apop-tosis with high spatio-temporal resolution.However,FRET generally functions in the single-cell level and becomes ineffective when applied in the high throughput detection of caspase activation.In the cur-rent study,a FRET sensor was combined with capillary electrophoresis(CE)to achieve a high throughput method for cellular caspase detection.The FRET-based CE system is composed of a homemade CE system and a laser source for detecting the dynamics of caspase-3 in various cells expressing sensors of caspase-3 that have been treated with anticancer drugs,such as cell cycle-independent drug cisplatin and specific cell cycle drugs camptothecin and etoposide,as well as their combination with tumor necrosis factor(TNF).A posi-tive correlation between the caspase-3 activation ve-locity and drug concentration was observed when the cells were treated with cisplatin,but cells induced by camptothecin and etoposide did not show any apparent correlation with their concentrations.Moreover,differ-ent types of cells presented distinct sensitivities under the same drug treatment,and the combination treat-ment of TNF and anticancer drugs significantly accel-erated the caspase-3 activation process.Its high throughput capability and detection sensitivity make the FRET-based CE system a useful tool for investi-gating the mechanisms of anticancer drugs and anti-cancer drug screening.

Perspectives on the management of synthetic biological and gene edited foods

Synthetic biology,gene editing and transgene technologies that involving gene manipulation are widely used in food research and development.In recent decades,China has formulatedmany policies and regulations to govern the safety of genetically modified agricultural organisms.Based on the comparative analysis of technical connotations on synthetic biology,gene editing and transgenes and related risksregarding the safety of food,environment and the management of genetically modified agricultural organisms,this paper puts forward the following suggestions on 1)management of synthetic biological and gene-edited foods(in this paper,“food”refers to“edible agricultural products and food”),2)promoting the gradual process of industrialization on gene-edited and synthetic biological foods through lessons learned from the practice on genetically modified crops,3)speeding up the industrialization of gene-edited foods and prudently promoting the application of synthetic biological foods,4)urgently establishing and updating policies and regulations related to gene-edited and synthetic biological foods,5)unifying the legislation and supervision of synthetic biological,gene-edited and genetically modified foods 6)establishing ethical principles and bottom lines for genetically manipulated foods.

Biodegradation of pendimethalin by Bacillus subtilis Y3

A bacterium strain Y3,capable of efficiently degrading pendimethalin,was isolated from activated sludge and identified as Bacillus subtilis according to its phenotypic features and 16 S rRNA phylogenetic analysis.This strain could grow on pendimethalin as a sole carbon source and degrade 99.5%of 100 mg/L pendimethalin within 2.5 days in batch liquid culture,demonstrating a greater efficiency than any other reported strains.Three metabolic products,6-aminopendimethalin,5-amino-2-methyl-3-nitroso-4-（pentan-3-ylamino） benzoic acid,and 8-amino-2-ethyl-5-（hydroxymethyl）-1,2-dihydroquinoxaline-6-carboxylic acid,were identified by HPLC-MS/MS,and a new microbial degradation pathway was proposed.A nitroreductase catalyzing nitroreduction of pendimethalin to 6-aminopendimethalin was detected in the cell lysate of strain Y3.The cofactor was nicotinamide adenine dinucleotide phosphate（NADPH） or more preferably nicotinamide adenine dinucleotide（NADH）.The optimal temperature and pH for the nitroreductase were 30℃ and 7.5,respectively.Hg^（2＋）,Ni^（2＋）,Pb^（2＋）,Co^（2＋）,Mn^（2＋） Cu^（2＋）,Ag~＋,and EDTA severely inhibited the nitroreductase activity,whereas Fe^（2＋）,Mg^（2＋）,and Ca^（2＋） enhanced it.This study provides an efficient pendimethalin-degrading microorganism and broadens the knowledge of the microbial degradation pathway of pendimethalin.

In silico Analysis of the Potential Infection Mechanisms of Magnaporthe grisea from Horizontal Gene Transfer Hypothesis

Horizontal gene transfer （HGT） has long been considered as a principal force for an organism to gain novel genes in genome evolution. Homology search, phylogenetic analysis and nucleotide composition analysis are three major objective approaches to arguably determine the occurrence and directionality of HGT. Here, 21 genes that possess the potential to horizontal transfer were acquired from the whole genome of Magnaporthe grisea according to annotation, among which three candidate genes （corresponding protein accession numbers are EAA55123, EAA47200 and EAA52136） were selected for further analysis. According to BLAST homology results, we subsequently conducted phylogenetic analysis of the three candidate HGT genes. Moreover, nucleotide composition analysis was conducted to further validate these HGTs. In addition, the functions of the three candidate genes were searched in COG database. Consequently, we conclude that the gene encoding protein EAA55123 is transferred from Clostridium perfringens. Another HGT event is between EAA52136 and a certain metazoan＇s corresponding gene, but the direction remains uncertain. Yet, EAA47200 is not a transferred gene.

High cell density and high expression of recombinant human ApoA-I_(Milano) in Escherichia coli by twice temperature-shifted induction

The effect of temperature on the formation of recombinant protein,apolipoprotein A-IMilano was investigated in the present study.The temperature of the initial growth phase was set at 30ºC,while temperature variation in induction phase was arranged in three modes.High cell-density culture of Escherichia coli and high expression of recombinant human by twice temperature-shifted induction were carried out.Experimental results showed that ApoA-IMilano reached 4.8 g/L with the final cell density of OD600,150.It was found that twice temperature-shifted induction could successfully avoid the effect of acetic acid on cell density and the expression of the product.The present study provides a basic procedure for the production of recombinant ApoA-IMilano.

Epidermal growth factor receptor stabilizes programmed death ligand 1 by glycosylation in colorectal cancer with microstatellite instability status

Programmed death ligand-1(PD-L1)is involved in inhibiting of T lymphocyte proliferation,producing cytokine,cytolytic activity,and suppressing of the immune response.Genes with molecular alterations involved in DNA mismatch repair promote cancer initiation and tumor progression.Clinical studies show that colorectal cancer(CRC)patients harboring microsatellite instability(MSI)have a higher anti-programmed cell death protein 1/PD-L1 immunotherapy response ratio compared with microsatellite stable subgroup patients.The underlying mechanism has however remained unclear.Here,we found that compared with microsatellite stable samples,PD-L1 was glycosylated and highly expressed both in MSI CRC cell lines and tissue samples.Specifically,PD-L1 was Nglycosylated at its N35,N192,N200,and N219 sites,and the four glycosylation sites were all responsible for PD-L1 degradation.Additionally,non-glycosylated PD-L1 underwent rapid degradation compared with glycosylated PD-L1 through the 26S proteasome pathway.The faster degradation of the non-glycosylated PD-L1 was ascribed to its binding to glycogen synthase kinase 3b via ubiquitination.This degradation phenotype was,however,not observed for glycosylated PD-L1.Significantly,glycosylated PD-L1 was up-regulated by activated epidermal growth factor receptor in MSI CRC cells.Together,our results indicate that epidermal growth factor receptor stabilized PD-L1 via glycosylation in MSI CRC cells,uncovering a novel role of PD-L1 in MSI CRC immunosuppression and disease progression.The study was approved by the Clinical Ethics Review Committee at the Six Affiliated Hospital of Sun Yat-sen University,China(Approval No.2019ZSLYEC-005).