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Measurement of very low-molecular weight metabolites by traveling wave ion mobility and its use in human urine samples

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Journal of Pharmaceutical Analysis 2024年第5期14卷 733-743页

作者： Alongkorn Kurilung Suphitcha Limjiasahapong Khwanta Kaewnarin Pattipong Wisanpitayakorn Narumol Jariyasopit Kwanjeera Wanichthanarak Sitanan Sartyoungkul Stephen Choong Chee Wong Nuankanya Sathirapongsasuti Chagriya Kitiyakara Yongyut Sirivatanauksorn Sakda Khoomrung Siriraj Center of Research Excellent in Metabolomics and Systems Biology(SiCORE-MSB) Faculty of Medicine Siriraj HospitalMahidol UniversityBangkok10700Thailand Siriraj Metabolomics and Phenomics Center Faculty of Medicine Siriraj HospitalMahidol UniversityBangkok10700Thailand Department of Biomedical Informatics University of Arkansas for Medical SciencesLittle RockAR72205USA SingHealth Duke-NUS Institute of Biodiversity Medicine National Cancer Centre Singapore168583Singapore Waters Pacific Pte. Ltd.Singapore117528Singapore program in Translational Medicine Faculty of Medicine Ramathibodi HospitalMahidol UniversityBangkok10400Thailand Chakri Naruebodindra Medical Institute Faculty of Medicine Ramathibodi HospitalMahidol UniversitySamut Prakan10540Thailand Department of Medicine Ramathibodi HospitalMahidol UniversityBangkok10400Thailand Department of Biochemistry Faculty of Medicine Siriraj HospitalMahidol UniversityBangkok10700Thailand Center of Excellence for Innovation in Chemistry(PERCH-CIC) Faculty of ScienceMahidol UniversityBangkok10400Thailand

The collision cross-sections(CCS)measurement using ion mobility spectrometry(IMS)in combination with mass spectrometry(MS)offers a great opportunity to increase confidence in metabolite ***,owing to the lack of sensitivity and resolution,IMS has an analytical challenge in studying the CCS values of very low-molecular-weight metabolites(VLMs250 Da).Here,we describe an analytical method using ultrahigh-performance liquid chromatography(UPLC)coupled to a traveling wave ion mobility-quadrupole-time-of-flight mass spectrometer optimized for the measurement of VLMs in human urine *** experimental CCS values,along with mass spectral properties,were reported for the 174 *** experimental data included the mass-to-charge ratio(m/z),retention time(RT),tandem MS(MS/MS)spectra,and CCS *** the studied metabolites,263 traveling wave ion mobility spectrometry(TWIMS)-derived CCS values(TWCCSN2)were reported for the first time,and more than 70%of these were CCS values of *** TWCCSN2 values were highly repeatable,with inter-day variations of<1%relative standard deviation(RSD).The developed method revealed excellent TWCCSN2 accuracy with a CCS difference(DCCS)within±2%of the reported drift tube IMS(DTIMS)and TWIMS CCS *** complexity of the urine matrix did not affect the precision of the method,as evidenced by DCCS within±1.92%.According to the Metabolomics Standards Initiative,55 urinary metabolites were identified with a confidence level of *** these 55 metabolites,53(96%)were *** larger number of confirmed compounds found in this study was a result of the addition of TWCCSN2 values,which clearly increased metabolite identification confidence.

关键词： Very low-molecular-weight metabolites Traveling wave ion mobility Collision cross-section human urine

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The evolving roles of Wnt signaling in stem cell proliferation and differentiation, the development of human diseases, and therapeutic opportunities

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Genes & Diseases 2024年第3期11卷 155-187页

作者： Michael Yu Kevin Qin Jiaming Fan Guozhi Zhao Piao Zhao Wei Zeng Connie Chen Annie Wang Yonghui Wang jiamin Zhong Yi Zhu William Wagstaff Rex C.Haydon Hue H.Luu Sherwin Ho Michael J.Lee Jason Strelzow Russell R.Reid Tong-Chuan He School of Medicine Rosalind Franklin University of Medicine and ScienceNorth ChicagoIL 60064USA Molecular Oncology Laboratory Department of Orthopedic Surgery and Rehabilitation MedicineThe University of Chicago Medical CenterChicagoIL 60637USA Ministry of Education Key Laboratory of Diagnostic Medicine and Department of Clinical BiochemistryThe School of Laboratory MedicineChongqing Medical UniversityChongqing 400016China Department of Orthopedic Surgery The First Affliated Hospital of Chongqing Medical UniversityChongqing 400016China Department of Urology The First Affiliated Hospital of Chongqing Medical UniversityChongqing 400016China Department of Clinical Laboratory Medicine Shanghai Jiaotong University School of MedicineShanghai 200000China Department of Orthopaedic Surgery Chinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100730China Laboratory of Craniofacial Suture Biology and Development Department of Surgery Section of Plastic SurgeryThe University of Chicago Medical CenterChicagoIL 60637USA Department of Neurology The First Dongguan Affiliated HospitalGuangdong Medical UniversityDongguanGuangdong 523475China

The evolutionarily conserved Wnt signaling pathway plays a central role in develop-ment and adult tissue homeostasis across *** proteins are secreted,lipid-modified signaling molecules that activate the canonical(β-catenin dependent)and non-canonical(β-catenin independent)Wnt signaling *** behaviors such as proliferation,differ-entiation,maturation,and proper body-axis specification are carried out by the canonical pathway,which is the best characterized of the known Wnt signaling *** signaling has emerged as an important factor in stem cell biology and is known to affect the self-renewal of stem cells in various *** includes but is not limited to embryonic,hematopoietic,mesenchymal,gut,neural,and epidermal stem *** signaling has also been implicated in tumor cells that exhibit stem cell-like *** signaling is crucial for bone formation and presents a potential target for the development of therapeutics for bone *** surprisingly,aberrant Wnt signaling is also associated with a wide variety of diseases,including *** of Wnt pathway members in cancer can lead to unchecked cell proliferation,epithelial-mesenchymal transition,and ***,advances in the understand-ing of dysregulated Wnt signaling in disease have paved the way for the development of novel therapeutics that target components of the Wnt *** with a brief overview of the mechanisms of canonical and non-canonical Wnt,this review aims to summarize the cur-rent knowledge of Wnt signaling in stem cells,aberrations to the Wnt pathway associated with diseases,and novel therapeutics targeting the Wnt pathway in preclinical and clinical studies.

关键词： β-Catenin Cancer Canonical Wnt Disease Non-canonical Wnt Stem cells Targeted therapy Wnt signaling

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Canonical and noncanonical Wnt signaling: Multilayered mediators, signaling mechanisms and major signaling crosstalk

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Genes & Diseases 2024年第1期11卷 103-134页

作者： Kevin Qin Michael Yu Jiaming Fan Hongwei Wang Piao Zhao Guozhi Zhaoo Wei Zeng Connie Chen Yonghui Wang Annie Wang Zander Schwartz Jeffrey Hong Lily Song William Wagstaff Rex C.Haydon Hue H.Luu Sherwin H.Ho Jason Strelzow Russell R.Reid Tong-Chuan He Lewis L.Shi Chicago Medical School Rosalind Franklin University of Medicine and ScienceNorth ChicagoIL 60064USA Molecular Oncology Laboratory Department of Orthopaedic Surgery and Rehabilitation MedicineThe University of Chicago Medical CenterChicagoIL 60637USA Ministry of Education Key Laboratory of Diagnostic Medicine and Department of Clinical BiochemistryThe School of Laboratory MedicineChongqing Medical UniversityChongqing 400016China Departments of Orthopaedic Surgery and Urology The First Affiliated Hospital of Chongqing Medical UniversityChongqing 400016China Department of Interventional Neurology The First Dongguan Affiliated HospitalGuangdong Medical UniversityDongguanGuangdong 523475China Department of Clinical Laboratory Medicine Shanghai Jiaotong University School of MedicineShanghai 200000China School of Biomedical Engineering Vanderbilt UniversityNashvilleTN 37235USA Laboratory of Craniofacial Biology and Development Department of Surgery Section of Plastic SurgeryThe University of Chicago Medical CenterChicagoIL 60637USA

Wnt signaling plays a major role in regulating cell proliferation and *** Wnt ligands are a family of 19 secreted glycoproteins that mediate their signaling effects via binding to Frizzled receptors and LRP5/6 coreceptors and transducing the signal either throughβ-catenin in the canonical pathway or through a series of other proteins in the nonca-nonical *** of the individual components of both canonical and noncanonical Wnt signaling have additional functions throughout the body,establishing the complex interplay between Wnt signaling and other signaling *** crosstalk between Wnt signaling and other pathways gives Wnt signaling a vital role in many cellular and organ ***-regulation of this system has been implicated in many diseases affecting a wide array of organ systems,including cancer and embryological defects,and can even cause embryonic *** complexity of this system and its interacting proteins have made Wnt signaling a target for many therapeutic ***,both stimulatory and inhibitory treatments come with potential risks that need to be *** review synthesized much of the current knowl-edge on the Wnt signaling pathway,beginning with the history of Wnt *** thoroughly described the different variants of Wnt signaling,including canonical,noncanonical Wnt/PCP,and the noncanonical Wnt/Ca2+*** description involved each of its components and their involvement in other cellular ***,this review explained the various other pathways and processes that crosstalk with Wnt signaling.

关键词： β-catenin Canonical Wnt Noncanonical Wnt Signal transduction Signaling crosstalk

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Dynamics of self-hybridized exciton–polaritons in 2D halide perovskites

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Light(science & Applications) 2024年第1期13卷 13-22页

作者： Surendra B.Anantharaman Jason Lynch Christopher E.Stevens Christopher Munley Chentao Li Jin Hou Hao Zhang Andrew Torma Thomas Darlington Francis Coen Kevin Li Arka Majumdar PJames Schuck Aditya Mohite Hayk Harutyunyan Joshua R.Hendrickson Deep Jariwala Department of Electrical and Systems Engineering University of PennsylvaniaPhiladelphiaPA19104USA KBR Inc. BeavercreekOH45431USA Air Force Research Laboratory Sensors DirectorateWright-Patterson Air Force BaseOH45433USA Department of Physics University of WashingtonSeattleWA98195USA Department of Physics Emory UniversityAtlantaGA30322USA Department of Chemical and Biomolecular Engineering Rice UniversityHoustonTX77005USA Department of Materials science and Nanoengineering Rice UniversityHoustonTX77005USA Applied Physics program Smalley‐Curl InstituteRice UniversityHoustonTX77005USA Department of Mechanical Engineering Columbia UniversityNew YorkNY10027USA Department of Electrical and Computer Engineering University of WashingtonSeattleWA98195USA

Excitons,bound electron–hole pairs,in two-dimensional hybrid organic inorganic perovskites(2D HOIPs)are capable of forming hybrid light-matter states known as exciton-polaritons(E–Ps)when the excitonic medium is confined in an optical *** the case of 2D HOIPs,they can self-hybridize into E–Ps at specific thicknesses of the HOIP crystals that form a resonant optical cavity with the ***,the fundamental properties of these self-hybridized E–Ps in 2D HOIPs,including their role in ultrafast energy and/or charge transfer at interfaces,remain ***,we demonstrate that>0.5µm thick 2D HOIP crystals on Au substrates are capable of supporting multiple-orders of self-hybridized E–P *** E–Ps have high Q factors(>100)and modulate the optical dispersion for the crystal to enhance sub-gap absorption and *** varying excitation energy and ultrafast measurements,we also confirm energy transfer from higher energy E–Ps to lower energy E–***,we also demonstrate that E–Ps are capable of charge transport and transfer at *** findings provide new insights into charge and energy transfer in E–Ps opening new opportunities towards their manipulation for polaritonic devices.

关键词： charge polar excitation

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Minimizing the ratio of ionizable lipid in lipid nanoparticles for in vivo base editing

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National science Review 2024年第6期11卷 285-293页

作者： Qiubing Chen Xuebin Wang Yizhou Zhang Ming Tian Junyi Duan Ying Zhang Hao Yin Departments of Urology and Laboratory Medicine Frontier Science Center for Immunology and Metabolism Medical Research InstituteZhongnan Hospital of Wuhan UniversityWuhan University State Key Laboratory of Virology Tai Kang Center for Life and Medical Sciences Tai Kang Medical SchoolWuhan University Department of Rheumatology and Immunology Zhongnan Hospital of Wuhan UniversityWuhan University Wuhan Research Center for Infectious Diseases and Cancer Chinese Academy of Medical Sciences RNA Institute Wuhan University

Lipid nanoparticles(LNPs) have gained clinical approval as carriers for both siRNA and mRNA. Among the crucial components of LNPs, ionizable lipids play a pivotal role in determining the efficiency of RNA delivery. In this study, we synthesized a series of ionizable lipids, denoted as HTO, with a higher count of hydroxyl groups compared to SM-102. Remarkably, LNPs based on HTO12 lipid demonstrated comparable mRNA delivery efficiency and biosafety to those based on SM-102. However, the former reduced the ratio of ionizable lipid/total lipids to mRNA in LNPs by 2.5 times compared to SM-102. The HTO12 LNP efficiently encapsulated adenine base editor mRNA and sgRNA targeting Pcsk9, leading to substantial gene editing within the liver of mice and effective reduction of the target protein. Our study underscores that ionizable lipids with multiple hydroxyl groups may facilitate an improved lipid-to-mRNA ratio to minimize the dosage of ionizable lipids for in vivo delivery.

关键词： ionizable lipid lipid nanoparticle mRNA delivery base editor delivery Pcsk9

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Machine learning predicts atomistic structures of multielement solid surfaces for heterogeneous catalysts in variable environments

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The Innovation 2024年第2期5卷 79-87页

作者： Huan Ma Yueyue Jiao Wenping Guo Xingchen Liu Yongwang Li Xiaodong Wen State Key Laboratory of Coal Conversion Institute of Coal ChemistryChinese Academy of SciencesTaiyuan 030001China University of Chinese Academy of sciences Beijing 100049China National Energy Center for Coal to Liquids Synfuels China Co.Ltd.Beijing 101400China Beijing Advanced Innovation Center for Materials Genome Engineering IndustryUniversity Cooperation Base between Beijing Information S&T University and Synfuels China Co.Ltd.Beijing 100101China

Solid surfaces usually reach thermodynamic equilibrium through particle exchange with their environment under reactive conditions.A prerequisite for understanding their functionalities is detailed knowledge of the surface composition and atomistic geometry under working *** to the large number of possible Miller indices and terminations involved in multielement solids,extensive sampling of the compositional and conformational space needed for reliable surface energy estimation is beyond the scope of ab initio ***,we demonstrate,using the case of iron carbides in environments with varied carbon chemical potentials,that the stable surface composition and geometry of multielement solids under reactive conditions,which involve large compositional and conformational spaces,can be predicted at ab initio accuracy using an approach that combines the bond valence model,Gaussian process regression,and ab initio *** the atomistic structure of surfaces under working conditions paves the way toward identifying the true active sites of multielement catalysts in heterogeneous catalysis.

关键词： surfaces solids environments

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Versatile multiplexed super-resolution imaging of nanostructures by Quencher-Exchange-PAINT

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Nano Research 2018年第12期11卷 6141-6154页

作者： Tobias Lutz Alexander H.Clowsley Ruisheng Lin Stefano Pagliara Lorenzo Di Michele Christian Soeller Living Systems Institute & Biomedical Physics University of ExeterExeter EX44QDUK Cavendish Laboratory University of CambridgeCambridge CB30HEUK

The optical super-resolution technique DNA-PAINT (Point Accumulation Imaging in Nanoscale Topography) provides a flexible way to achieve imaging of nanoscale structures at ∼10-nanometer resolution. In DNA-PAINT, fluorescently labeled DNA “imager” strands bind transiently and with high specificity to complementary target “docking” strands anchored to the structure of interest. The localization of single binding events enables the assembly of a super-resolution image, and this approach effectively circumvents photobleaching. The solution exchange of imager strands is the basis of Exchange-PAINT, which enables multiplexed imaging that avoids chromatic aberrations. Fluid exchange during imaging typically requires specialized chambers or washes, which can disturb the sample. Additionally, diffusional washout of imager strands is slow in thick samples such as biological tissue slices. Here, we introduce Quencher-Exchange-PAINT—a new approach to Exchange-PAINT in regular open-top imaging chambers—which overcomes the comparatively slow imager strand switching via diffusional imager washout. Quencher-Exchange-PAINT uses “quencher” strands, i.e., oligonucleotides that prevent the imager from binding to the targets, to rapidly reduce unwanted single-stranded imager concentrations to negligible levels, decoupled from the absolute imager concentration. The quencher strands contain an effective dye quencher that reduces the fluorescence of quenched imager strands to negligible levels. We characterized Quencher-Exchange-PAINT when applied to synthetic, cellular, and thick tissue samples. Quencher-Exchange-PAINT opens the way for efficient multiplexed imaging of complex nanostructures, e.g., in thick tissues, without the need for washing steps.

关键词： super-resolution microscopy fluorescence imaging DNA nanotechnology DNA-PAINT fluorescence quencher

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Contribution of Cyclic and Pseudo-cyclic Electron Transport to the Formation of Proton Motive Force in Chloroplasts

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Molecular Plant 2017年第1期10卷 20-29页

作者： Toshiharu Shikanai Hiroshi Yamamoto Department of Botany Graduate School of Science Kyoto University Oiwake-cho Kitashirakawa Sakyo-ku Kyoto 606-8502 Japan CREST Japan Science and Technology Agency Chiyoda-ku Tokyo 102-0076 Japan

Photosynthetic electron transport is coupled to proton translocation across the thylakoid membrane, re- sulting in the formation of a trans-thylakoid proton gradient （△pH） and membrane potential （△ψ）. Ion trans-porters and channels localized to the thylakoid membrane regulate the contribution of each component to the proton motive force （pmf）. Although both △pH and △ψ contribute to ATP synthesis as pmf, only ~pH downregulates photosynthetic electron transport via the acidification of the thylakoid lumen by inducing thermal dissipation of excessive absorbed light energy from photosystem II antennae and slowing down of the electron transport through the cytochrome bsf complex. To optimize the tradeoff between efficient light energy utilization and protection of both photosystems against photodamage, plants have to regulate the pmf amplitude and its components, △pH and △ψ. Cyclic electron transport around photosystem I （PSI） is a major regulator of the pmf amplitude by generating pmf independently of the net production of NADPH by linear electron transport. Chloroplast ATP synthase relaxes pmf for ATP synthesis, and its activity should be finely tuned for maintaining the size of the pmf during steady-state photosynthesis. Pseudo-cyclic electron transport mediated by flavodiiron protein （FIv） forms a large electron sink, which is essential for PSI photoprotection in fluctuating light in cyanobacteria. FIv is conserved from cyanobacteria to gymno- sperms but not in angiosperms. The Arabidopsis proton gradient regulation 50（pgr5） mutant is defective in the main pathway of PSI cyclic electron transport. By introducing Physcomitrella patens genes encoding Flvs, the function of PSI cyclic electron transport was substituted by that of FIv-dependent pseudo-cyclic electron transport. In transgenic plants, the size of the pmf was complemented to the wild-type level but the contribution of △pH to the total pmf was lower than that in the wild type. In the pgr5 mutant, the size of

关键词： alternative electron transport cyclic electron transport around photosystem I ion channel flavodiironprotein proton motive force pseudo-cyclic electron transport

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CUTIN SYNTHASE 2 Maintains Progressively Developing Cuticular Ridges in Arabidopsis Sepals

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Molecular Plant 2017年第4期10卷 560-574页

作者： Lilan Hong Joel Brown Nicholas A. Segerson Jocelyn K.C. Rose Adrienne H.K. Roeder Weiil institute for Ceil and Molecular Biology Cornell University Ithaca NY 14853 USA Plant Biology Section School of Integrative Plant Science Cornell University Ithaca NY 14853 USA Field of Genetics Genomics and Development Cornell University Ithaca NY 14853 USA

The cuticle is a crucial barrier on the aerial surfaces of land plants, in many plants, including Arabidopsis, the sepals and petals form distinctive nanoridges in their cuticles. However, little is known about how the formation and maintenance of these nanostructures is coordinated with the growth and development of the underlying cells. Here we report the characterization of the Arabidopsis cutin synthase 2 （cus2） mutant, which causes a great reduction in cuticular ridges on the mature sepal epidermis, but only a moderate effect on petal cone cell ridges. Using scanning electron microscopy and confocal live imaging combined with quantification of cellular growth, we find that cuticular ridge formation progresses down the sepal from tip to base as the sepal grows, pCUS2：：GFP-GUS reporter expression coincides with cutic- ular ridge formation, descending the sepal from tip to base. Ridge formation also coincides with the reduction in growth rate and termination of cell division of the underlying epidermal cells. Surprisingly, cuticular ridges at first form normally in the cus2 mutant, but are lost progressively at later stages of sepal development, indicating that CUS2 is crucial for the maintenance of cuticular ridges after they are formed~ Our results reveal the dynamics of both ridge formation and maintenance as the sepal grows.

关键词： Arabidopsis thaliana cellular growth CUTIN SYNTHASE2 (CUS2) cuticular ridges nanoridges sepal

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Fight them or feed them:how the intestinal mucus layer manages the gut microbiota

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Gastroenterology Report 2019年第1期7卷 3-12,I0001页

作者： Bjoern O.Schroeder Wallenberg Laboratory and Sahlgrenska Center for Cardiovascular and Metabolic Research Department of Molecular and Clinical MedicineInstitute of MedicineBruna Stra°ket 16University of GothenburgSE 41345 GothenburgSweden

The intestinal tract is inhabited by a tremendous number of microorganisms,termed the gut *** microorganisms live in a mutualistic relationship with their host and assist in the degradation of complex *** the gut microbiota is generally considered beneficial,the vast number of microbial cells also form a permanent threat to the ***,the intestinal epithelium is covered with a dense layer of mucus to prevent translocation of the gut microbiota into underlying *** mucus is an organized glycoprotein network with a host-specific glycan *** the mucus layer has long been considered a passive,host-designed barrier,recent studies showed that maturation and function of the mucus layer are strongly influenced by the gut *** return,the glycan repertoire of mucins can select for distinct mucosa-associated bacteria that are able to bind or degrade specific mucin glycans as a nutrient *** the intestinal mucus layer is at the crucial interface between host and microbes,its breakdown leads to gut bacterial encroachment that can eventually cause inflammation and ***,a dysfunctional mucus layer has been observed in colitis in mice and ***,the increased consumption of a low-fiber Western-style diet in our modern society has recently been demonstrated to cause bacteria-mediated defects of the intestinal mucus ***,I will review current knowledge on the interaction between gut bacteria and the intestinal mucus layer in health and *** the molecular details of this host–microbe interaction may contribute to the development of novel treatment options for diseases involving a dysfunctional mucus layer,such as ulcerative colitis.

关键词： Dietary fiber gut microbiota host-microbe interaction inflammatory bowel disease mucus mucin mucosal barrier metabolic disease probiotics ulcerative colitis

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