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DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

genomics, Proteomics & Bioinformatics 2020年第2期18卷 104-119页

作者： Tiansheng Zhu Yi Zhu Yue Xuan Huanhuan gao Xue Cai Sander R.Piersma Thang V.Pham Tim Schelfhorst Richard R.g.D.Haas Irene V.Bijnsdorp Rui Sun Liang Yue guan Ruan Qiushi Zhang Mo Hu Yue Zhou Winan J.Van Houdt Tessa Y.S.Le Large Jacqueline Cloos Anna Wojtuszkiewicz Danijela Koppers-Lalic Franziska Bottger Chantal Scheepbouwer Ruud H.Brakenhoff geert J.L.H.van Leenders Jan N.M.Ijzermans John W.M.Martens Renske D.M.Steenbergen Nicole C.grieken Sathiyamoorthy Selvarajan Sangeeta Mantoo Sze S.Lee Serene J.Y.Yeow Syed M.F.Alkaff Nan Xiang Yaoting Sun Xiao Yi Shaozheng Dai Wei Liu Tian Lu Zhicheng Wu Xiao Liang Man Wang Yingkuan Shao Xi Zheng Kailun Xu Qin Yang Yifan Meng Cong Lu Jiang Zhu Jin'e Zheng Bo Wang Sai Lou Yibei Dai Chao Xu Chenhuan Yu Huazhong Ying Tony K.Lim Jianmin Wu Xiaofei gao Zhongzhi Luan Xiaodong Teng Peng Wu Shi'ang Huang Zhihua Tao narayanan g.iyer Shuigeng Zhou Wenguang Shao Henry Lam Ding Ma Jiafu Ji Oi L.Kon Shu Zheng Ruedi Aebersold Connie R.Jimenez Tiannan guo Zhejiang Provincial Laboratory of Life Sciences and Biomedicine Westlake UniversityHangzhou 310024China Key Laboratory of Structural Biology of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzhou 310024China School of Computer Science Shanghai Key Laboratory of Intelligent Information ProcessingFudan UniversityShanghai 200433China Thermo Fisher Scientific(BREMEN)gmbH Bremen 28195Germany OncoProteomics Laboratory Department of Medical OncologyVU University Medical CenterVU UniversityAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamUrologyCancer Center AmsterdamAmsterdam 1011The Netherlands Thermo Fisher Scientific Shanghai 201206China The Netherlands Cancer Institute Surgical OncologyAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamSurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPediatric Oncology/HematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamHematologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamMedical OncologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamNeurosurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamPathologyCancer Center AmsterdamAmsterdam 1011The Netherlands Amsterdam UMC Vrije Universiteit AmsterdamOtolaryngology/Head and Neck SurgeryCancer Center AmsterdamAmsterdam 1011The Netherlands Erasmus MC University Medical Center PathologyRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center SurgeryRotterdam 1016LVThe Netherlands Erasmus MC University Medical Center Medical OncologyRotterdam 1016LVThe Netherlands Department of Anatomical Pathology Singapore General HospitalSingapore 169608Singapore Division of Medical Scie

To address the increasing need for detecting and validating protein biomarkers in clinical specimens,mass spectrometry(MS)-based targeted proteomic techniques,including the selected reaction monitoring(SRM),parallel reaction monitoring(PRM),and massively parallel dataindependent acquisition(DIA),have been *** optimal performance,they require the fragment ion spectra of targeted peptides as prior *** this report,we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue *** build the spectral resource,we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on *** then applied the workflow to generate DPHL,a comprehensive DIA pan-human library,from 1096 data-dependent acquisition(DDA)MS raw files for 16 types of cancer *** extensive spectral resource was then applied to a proteomic study of 17 prostate cancer(PCa)***,PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was *** a second application,the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma(DLBCL)patients and 18 healthy control *** expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by *** data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker *** is freely accessible at https://***/page/***?id=IPX0001400000.

关键词： Data-independent acquisition Parallel reaction monitoring Spectral library Prostate cancer Diffuse large B cell lymphoma

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Linking stemness with colorectal cancer initiation, progression, and therapy

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World Journal of Stem Cells 2019年第8期11卷 519-534页

作者： Deepak narayanan iyer Wai-Yan Sin Lui Ng Department of Surgery Li Ka Shing Faculty of Medicine The University of Hong Kong

The discovery of cancer stem cells caused a paradigm shift in the concepts of origin and development of colorectal cancer. Several unresolved questions remain in this field though. Are colorectal cancer stem cells the cause or an effect of the disease? How do cancer stem cells assist in colorectal tumor dissemination to distant organs? What are the molecular or environmental factors affecting the roles of these cells in colorectal cancer? Through this review, we investigate the key findings until now and attempt to elucidate the origins, physical properties, microenvironmental niches, as well as the molecular signaling network that support the existence, self-renewal, plasticity, quiescence, and the overall maintenance of cancer stem cells in colorectal cancer. Increasing data show that the cancer stem cells play a crucial role not only in the establishment of the primary colorectal tumor but also in the distant spread of the disease. Hence, we will also look at the mechanisms adopted by cancer stem cells to influence the development of metastasis and evade therapeutic targeting and its role in the overall disease prognosis. Finally, we will illustrate the importance of understanding the biology of these cells to develop improved clinical strategies to tackle colorectal cancer.

关键词： Cancer stem cell Colorectal cancer Tumor microenvironment Metastasis Extracellular matrix Tumor heterogeneity Resistance Stemness Quiescence Recurrence

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Matrisomal genes in squamous cell carcinoma of head and neck influence tumor cell motility and response to cetuximab treatment

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Cancer Communications 2022年第4期42卷 355-359页

作者： Kah Yee goh Kah Weng Lau Terence You De Cheng Su Chin Tham Chwee Teck Lim narayanan gopalakrishna iyer Su Bin Lim Darren Wan-Teck Lim Division of Medical Oncology National Cancer Centre SingaporeSingapore 169610 Department of Pathology National University HospitalSingapore 119074 A*STAR ProteosInstitute of Molecular and Cell BiologySingapore 138673 Department of Biomedical Engineering Mechanobiology InstituteNational University of SingaporeT-LabSingapore 117411 Institute for Health Innovation and Technology(iHealthtech) National University of SingaporeMD6Singapore 117599 Department of Head and Neck Surgery National Cancer Centre Singapore11 Hospital CrescentSingapore 169610 Office of Academic and Clinical Development Duke-NUS Medical SchoolSingapore 169857 Department of Biochemistry and Molecular Biology Ajou University School of MedicineYeongtong-GuSuwon 16499South Korea

Dear Editor,Head and neck squamous cell carcinoma(HNSCC)is the sixth most common cancer globally[1,2].Despite the improvement in treatment modalities,up to 50%of HNSCC patients still develop recurrent/metastatic(R/M)disease[3],and platinum-based chemotherapy with cetuximab and/or pembrolizumab has become the standard of care[4].However,R/M HNSCC is challenging to treat,the prognosis is poor,and there is an unmet need for new therapeutic targets.

关键词： chemotherapy cetuximab treatment

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Z-scheme mechanism for methylene blue degradation over Fe_(2)O_(3)/g-C_(3)N_(4) nanocomposite prepared via one-pot exfoliation and magnetization of g-C_(3)N_(4)

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Frontiers of Materials Science 2022年第3期16卷 203-218页

作者： Shemeena MULLAKKATTUTHODI Vijayasree HARIDAS Sankaran SUgUNAN Binitha N.narayanan Department of Chemistry Sree Neelakanta Government Sanskrit College(Affiliated to University of Calicut)PattambiPalakkad 679306KeralaIndia Department of Applied Chemistry Cochin University of Science and TechnologyCochin 22KeralaIndia Department of Chemistry University of CalicutMalappuramKerala 673635India

The low surface area,high recombination rate of photogenerated charge carriers,narrow visible range activity,and difficulty in the separation from cleaned solutions limit the wide application of g-C_(3)N_(4) as a ***,we have succeeded in developing a one-pot strategy to overcome the above-mentioned difficulties of g-C_(3)N_(4).The broadening of the visible-light response range and inducing magnetic nature to g-C_(3)N_(4) was succeeded by preparing a nanocomposite with Fe_(2)O_(3) via a facile solvothermal *** preparation method additionally imparted layer exfoliation of g-C_(3)N_(4) as evident from the XRD patterns and TEM *** strong interaction between the components is revealed from the XPS *** broadened visible-light absorbance of Fe_(2)O_(3)/g-C_(3)N_(4) with a Z-scheme photocatalytic degradation mechanism is well evident from the UV-Vis DRS analysis and PL measurement of the composite with terephthalic *** active species of photocatalysis were further investigated using scavenging studies in methylene blue degradation that revealed hydroxyl radicals and holes as the major contributors to the activity of Fe_(2)O_(3)/g-C_(3)N_(4).

关键词： Fe_(2)O_(3)/g-C_(3)N_(4)nanocomposite Z-scheme photocatalysis magnetic separation dyedegradation

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genome and clonal hematopoiesis stability contrasts with immune,cfDNA,mitochondrial,and telomere length changes during short duration spaceflight

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Precision Clinical Medicine 2024年第1期7卷 1-13页

作者： J.Sebastian garcia-Medina Karolina Sienkiewicz S.Anand narayanan Eliah g.Overbey Kirill grigorev Krista A.Ryon Marissa Burke Jacqueline Proszynski Braden Tierney Caleb M.Schmidt Nuria Mencia-Trinchant Remi Klotz Veronica Ortiz Jonathan Foox Christopher Chin Deena Najjar Irina Matei Irenaeus Chan Carlos Cruchaga Ashley Kleinman JangKeun Kim Alexander Lucaci Conor Loy Omary Mzava Iwijn De Vlaminck Anvita Singaraju Lynn E.Taylor Julian C.Schmidt Michael A.Schmidt Kelly Blease Juan Moreno Andrew Boddicker Junhua Zhao Bryan Lajoie Andrew Altomare Semyon Kruglyak Shawn Levy Min Yu Duane C.Hassane Susan M.Bailey Kelly Bolton Jaime Mateus Christopher E.Mason Department of Physiology and Biophysics Weill Cornell MedicineCornell UniversityNew YorkNY 10021USA The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine Weill Cornell MedicineNew YorkNY 10021USA Department of Immunology Weill Cornell MedicineCornell UniversityNew YorkNY 10021USA Department of Stem Cell Biology and Regenerative Medicine Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA 90033USA Space Exploration Technologies Corporation HawthomeCA 90250USA Sovaris Aerospace BoulderCO 80302USA Advanced Pattern Analysis&Human Performance group BoulderCO 80302USA Children's Cancer and Blood Foundation Laboratories Departments of Pediatrics and Cell and Developmental BiologyDrukier Institute for Children's HealthMeyer Cancer CenterWeill Cornell MedicineNew YorkNY 10021USA Meyer Cancer Center Weill Cornell MedicineNew YorkNY 10065USA Department of Nutrition and Integrative Physiology Florida State UniversityTallahasseeFL 32306USA Department of Systems Engineering Colorado State UniversityFort CollinsCO 80523USA Element Biosciences San DiegoCA 10055USA Department of Environmental and Radiological Health Sciences Colorado State UniversityFort CollinsCO 80523USA Cell and Molecular Biology Program Colorado State UniversityFort CollinsCO 80523USA BioAstra Inc New YorkNYUSA Washington University St Louis Oncology Division St.LouisMO 63100USA Meinig School of Biomedical Engineering Cornell UniversityIthacaNY 14853USA The Feil Family Brain and Mind Research Institute Weill Cornell MedicineNY 10021USA WorldQuant Initiative for Quantitative Prediction Weill Cornell MedicineNew YorkNY 10021USA

Background The Inspiration4(I4)mission,the first all-civilian orbital flight mission,investigated the physiological effects of short-duration spaceflight through a multi-omic *** advances,there remains much to learn about human adaptation to spaceflight's unique challenges,including microgravity,immune system perturbations,and radiation *** To provide a detailed genetics analysis of the mission,we collected dried blood spots pre-,during,and post-flight for DNA *** length was measured by quantitative PCR,while whole genome and cfDNA sequencing provided insight into genomic stability and immune adaptations.A robust bioinformatic pipeline was used for data analysis,including variant calling to assess mutational *** Telomere elongation occurred during spaceflight and shortened after return to ***-free DNA analysis revealed increased immune cell signatures *** significant clonal hematopoiesis of indeterminate potential(CHIP)or whole-genome instability was *** long-term gene expression changes across immune cells suggested cellular adaptations to the space environment persisting months *** Our findings provide valuable insights into the physiological consequences of short-duration spaceflight,with telomere dynamics and immune cell gene expression adapting to spaceflight and persisting after return to *** sequencing data will serve as a reference point for studying the early development of CHIP in astronauts,an understudied phenomenon as previous studies have focused on career *** study will serve as a reference point for future commercial and non-commercial spaceflight,low Earth orbit(LEO)missions,and deep-space exploration.

关键词： genomes clonal hematopoiesis stability immune mitochondria ribosomes spaceflight

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Thymoquinone as a potential therapeutic for Alzheimer’s disease in transgenic Drosophila melanogaster model

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BIOCELL 2021年第5期45卷 1251-1262页

作者： narayanan NAMPOOTHIRI V.P. VIgNESH SUNDARARAJAN PALLAVI DAN g.DEVANAND VENKATASUBBU SAHABUDEEN SHEIK MOHIDEEN Department of Biotechnology School of BioengineeringSRM Institute of Science and TechnologyKattankulathur603203India Department of Physics and Nanotechnology School of BioengineeringSRM Institute of Science and TechnologyKattankulathur603203India

Alzheimer’s disease(AD)is one of the most common forms of *** dysfunction and memory loss are the two main clinical symptoms of *** melanogaster models of AD,which are based on overexpression of human amyloidβ(Aβ)or human tau(hTau)protein,have been used to study the mechanism underlying AD and to screen potential therapeutic *** that are currently available for AD provide only symptomatic *** unmet medical needs exists to slow,stop,or reverse the progression of ***(TQ)is an active ingredient isolated from Nigella sativa(NS)and possesses various pharmacological activities,and it is also a potential neuropharmacological *** current study was performed to investigate the effect of dietary administration of TQ at concentrations of 12.5μM and 25μM for 15 and 30 days on biochemical and behavioral parameters,gene,and protein expression of hTau,using Drosophila models of *** Drosophila models exhibiting pan-neuronal and eye-specific expression of hTau were generated using the gAL4/UAS *** with TQ at both concentrations resulted in a significant increase in behavioral activity,a significant reduction in the amount of reactive oxygen species(ROS),and restoration of depleted superoxide dismutase(SOD)and acetylcholine esterase(AChE)activities.A significant decrease in gene and protein expression of hTau was also observed at the molecular level for both concentrations of ***,TQ has the potential to be investigated as a potential therapeutic phytochemical for the treatment of AD in future studies.

关键词： hTau gAL4/UAS system Nigella sativa

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Validation of Foreground Emission Model using gALEX Medium Observations

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Research in Astronomy and Astrophysics 2023年第6期23卷 228-237页

作者： Nimmi narayanan Shivashankar S.Menon N.V.Sujatha Department of Physics St.Xavier's College for WomenAluva 683101India Department of Physics Sree Sankara CollegeKaladyErnakulam 683574India CSIS BITS Pilani K.K.Birla Goa CampusZuarinagarGoa 403726India

The study of diffuse ultraviolet(UV)background radiation is vital in the investigation of stellar and galactic ***-based UV observations are comprised of both foreground and background *** foreground emission in an observation is a result of solar contamination in the direction of *** our previous work,we modeled airglow(one of the major constituents of the foreground emission)as a function of10.7 cm Solar Flux and Sun Angle with great accuracy using gALEX deep *** adopt a similar methodology to validate the obtained model and run equivalent experiments here using far-UV(FUV)and nearUV(NUV)gALEX medium imaging surveys(MIS)with a total exposure time greater than 3300 *** obtained a predictive model having excellent compatibility with the earlier *** analysis shows that the total foreground emission varies between 59 and 295 photon units in FUV whereas in NUV,it varies between 671 and1195 photon units depending upon the date and time of *** also noticed a strong correlation between the background emission and optical depth both in FUV and NUV,especially in the low density *** clearly indicates that the major contributor in diffuse background radiation is the starlight scattered by interstellar dust grains.

关键词： instrumentation:detectors Sun:activity ultraviolet:ISM atmospheric effects

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Nonylphenol in bivalves and sediments in the northeast coast of China

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Journal of Environmental Sciences 2010年第11期22卷 1735-1740页

作者： Juan Wang Won-joon Shim Un-hynk Yim narayanan Kannan Donghao Li Key Laboratory of Nature Resources of Changbai Mountain and Functional Molecular Ministry of Education of China Yanbian University Yanji 133002 China. Oil and POPs Research group Korea Ocean Research and Development Institute Geoje-shi 656-834 Korea

To understand nonylphenol （NP） contamination in the northeast coastal environment in China, NP was determined in 19 sediment and 20 bivalve samples collected during November 2005. NP was identified in all sediment samples in the range of 8.8 to 1.0 × 10^3 ng/g dw （dry weight）, with an average of 0.12 × 10^3 ng/g dw. Most of the bivalve samples （oysters and mussels） contained detectable amounts of NP that ranged from ND （not detected） to 7.6 × 10^3 ng/g dw, with an average value of 0.79 × 10^3 ng/g dw. These results indicated that NP is ubiquitous in sediments and bivalves from the northeast coast of China, and are even present in bivalves sold as seafood. Serious contamination with NP was recorded off the coast of Bohai Strait and in semi-enclosed coastal environment such as Jiaozhou Bay and Liaodong Bay. Possible environmental and human health implications were understood in this study.

关键词： nonylphenol Yellow Sea Bohai Sea sediment bivalve

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Machine-learned interatomic potentials by active learning:amorphous and liquid hafnium dioxide

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npj Computational Materials 2020年第1期6卷 803-810页

作者： ganesh Sivaraman Anand narayanan Krishnamoorthy Matthias Baur Christian Holm Marius Stan gábor Csányi Chris Benmore Álvaro Vázquez-Mayagoitia Leadership Computing Facility Argonne National LaboratoryArgonneIL 60439USA Institute for Computational Physics Universität StuttgartAllmandring 3Stuttgart 70569Germany Helmholtz-Institute Münster:Ionics in Energy Storage(IEK-12) Forschungszentrum Jülich GmbHCorrensstrasse 46Münster 48149Germany Applied Materials Division Argonne National LaboratoryArgonneIL 60439USA Department of Engineering University of CambridgeTrumpington StreetCambridge CB21PZUK X-ray Science Division Argonne National LaboratoryArgonneIL 60439USA Computational Science Division Argonne National LaboratoryArgonneIL 60439USA

We propose an active learning scheme for automatically sampling a minimum number of uncorrelated configurations for fitting the gaussian Approximation Potential(gAP).Our active learning scheme consists of an unsupervised machine learning(ML)scheme coupled with a Bayesian optimization technique that evaluates the gAP *** apply this scheme to a Hafnium dioxide(HfO2)dataset generated from a“melt-quench”ab initio molecular dynamics(AIMD)*** results show that the active learning scheme,with no prior knowledge of the dataset,is able to extract a configuration that reaches the required energy fit ***,molecular dynamics(MD)simulations performed using this active learned gAP model on 6144 atom systems of amorphous and liquid state elucidate the structural properties of HfO2 with near ab initio precision and quench rates(i.e.,1.0 K/ps)not accessible via *** melt and amorphous X-ray structural factors generated from our simulation are in good agreement with *** addition,the calculated diffusion constants are in good agreement with previous ab initio studies.

关键词： amorphous dioxide scheme

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Inverted internal limiting membrane flap technique for very large macular hole

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International Journal of Ophthalmology(English edition) 2016年第8期9卷 1230-1232页

作者： Mitali Khodani Pooja Bansal Raja narayanan Jay Chhablani Kanuri Santhamma Retina Vitreous Centre LV Prasad Eye Institute Kallam Anji Reddy Campus Dr. Rajendra Prasad Centre for Ophthalmic Sciences All India Institute of Medical Sciences

AIMTo assess the anatomical and visual outcome of idiopathic macular holes greater than 1000 µm using the inverted internal limiting membrane flap *** retrospective case series included 5 eyes of 5 patients with idiopathic macular hole with base diameter greater than 1000 µm who underwent inverted internal limiting membrane flap technique along with standard 23g pars plans vitrectomy with posterior hyaloid detachment and fluid gas exchange with 12%-14% perfluoropropane (C3F8). Preoperative and postoperative visual acuity and spectral domain optical coherence tomography images were evaluated. The main outcome measures were visual outcome and macular hole *** age was 63.2±8.4y with all 5 subjects being females. Mean duration of symptoms was 11±14mo with a mean postoperative follow up of 13.2±13mo. The mean base diameter of the macular holes was 1420±84.8 µm (1280-1480 µm). Type 1 closure was achieved in four out of five patients, while one patient had type 2 closure using the inverted internal limiting membrane (ILM) flap technique. Median baseline BCVA was 0.79 logMAR (Snellen’s equivalent 20/120) and median final BCVA 0.6 logMAR (Snellen’s equivalent 20/80) with mean visual improvement of approximately three lines improvement. No complications related to surgical procedure were *** inverted internal limiting membrane flap technique may be promising for very large macular holes with high rate of macular closure and good visual outcome.

关键词： inverted internal limiting membrane flap technique vitrectomy macular hole

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