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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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Hepatocellular Tumors:Immunohistochemical Analyses for Classification and Prognostication

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Chinese Journal of Cancer Research 2011年第4期23卷 245-253页

作者： Regina Cheuk-lam lo Irene oi-lin Ng Department of Pathology and State Key laboratory for liver Research The University of Hong Kong

Following the classification of hepatocellular nodules by the International Working Party in 1995 and further elaboration by the International Consensus Group for Hepatocellular Neoplasia in 2009, entities under the spectrum of hepatocellular nodules have been better characterized. Research work hence has been done to answer questions such as distinguishing high-grade dysplastic nodules from early hepatocellular carcinoma (HCC), delineating the tumor cell origin of HCC, identifying its prognostic markers, and subtyping hepatocellular adenomas. As a result, a copious amount of data at immunohistochemical and molecular levels has emerged. A panel of immunohistochemical markers including glypican-3, heat shock protein 70 and glutamine synthetase has been found to be of use in the diagnosis of small, well differentiated hepatocellular tumors and particularly of HCC. The use of liver fatty acid binding protein (l-FABP), β-catenin, glutamine synthetase, serum amyloid protein and C-reactive protein is found to be helpful in the subtyping of hepatocellular adenomas. The role of tissue biomarkers for prognostication in HCC and the use of biomarkers in subclassifying HCC based on tumor cell origin are also discussed.

关键词： Hepatocellular tumors Immunohistochemical Classification

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Differential Expression of Rice Genes Under Different Nitrogen Forms and Their Relationship with Sulfur Metabolism

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Journal of Integrative Plant Biology 2006年第10期48卷 1177-1184页

作者： Guo-Hui Zhu Chu-Xiong Zhuang Yu-oi Wang lin-Rong Jiang Xin-Xiang Peng College of life Sciences South China Agricultural University Guangzhou 510642 China

Microarray analysis was initially performed to screen for differentially expressed genes between nitrate-and ammonium-fed rice （Oryza sativa l.） leaves, in total, 198 genes were shown to have a unique expression response to each treatment and most of the genes for which function is known were involved in signal transduction, plant stress resistance, transcriptional regulation, and basic metabolism. Northern blotting analysis confirmed that expression of the MT and PCS genes was highly upregulated in ammonium-fed leaves compared with expression in nitrate-fed leaves and it was further revealed that ammonium-fed leaves accumulated more cysteine and glutathione. The upregulated expressions of the MTand PCS genes and the higher levels of cysteine and glutathione in ammonium-fed leaves indicate that ammonium may be able to accelerate sulfur assimilation metabolism in rice leaves. Unexpectedly, Northern blotting analysis showed that the expression of the two key enzymes in the sulfur assimilation pathway, namely adenosine 5＇-phosphosulfate reductase and O-acetylserine（thiol）lyase, was not upregulated by ammonium treatment. It was found that the total content of free amino acids was much higher in ammonium-fed leaves compared with nitrate-fed leaves, mainly resulting from an increase in several amino acids such as serine, asparagine, glutamine, and arginine. The increased amino acids, in particular serine （as a central substrate for the synthesis of the thioi metabolites）, may have promoted sulfur assimilation metabolism under conditions of ammonium nutrition.

关键词： gene expression nitrogen forms rice sulfur assimilation

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Bilateral Multi-level Pedicle Fractures in the lumbar Spine Secondary to Trauma: A Case Report and literature Review

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Open Journal of Modern Neurosurgery 2020年第4期10卷 422-426页

作者： Noukhoum koné Department of Neurosurgery Kiffa Hospital Center Kiffa Mauritania

Pedicle fractures are among the least common;those involving bilateral pedicle fractures are rare. To our knowledge, there are no previous reports of bilateral multi-level pedicle fractures in the lumbar spine secondary to trauma concerning adolescents. We report a 14-year-old male with bilateral multi-level traumatic pedicle fractures (BMTPF) of lumbar spine (lS) three and five (l3, l5) and spondylolisthesis of l3 on l4 (classified Meyerding grade II). Posterior lumbar instrumentation from l1 to S1 was performed. Postoperative recovery was uneventful. The aims of the study were to provide the first documentation of this pattern of injury in adolescents lS secondary to trauma and to review literature. The patient’s parents were informed that non-identifying information from the case would be submitted for publication, and they provided consent.

关键词： Pedicle Traumatic Fracture lumbar Spine Scews

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Epidemioclinical Profile of Premature Infants at the Neonatology Unit of the Mali Hospital 2012-2015

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Open Journal of Pediatrics 2021年第3期11卷 490-502页

作者： Bourama Kané Mamadou Berthé Guédiouma Dembélé Korotoumou Wélé Diallo Diakaridia koné Fatou Diawara Fanta Sidibé Oumou koné Mamadou Coulibaly Mariam Maiga Mariam Sylla Department of Pediatrics Mali Hospital Bamako Mali National Institute of Public Health Bamako Mali Reference Health Centre of the Commune I Bamako Mali Gynaecological and Obstetric Service Mali Hospital Bamako Mali Paediatrics Department of the Centre de Santé de Référence de la Commune VI Bamako Mali Gabriel TOURE University Hospital Bamako Mali

Introduction: A newborn is preterm when it is born before 37 weeks of amenorrhoea. Preterm births account for 11.1% of live births worldwide, 60% of which are in South Asia and sub-Saharan Africa. Preterm birth is the leading cause of neonatal mortality and the second leading cause of mortality in children under 5 years of age. The aim of this study was to investigate prematurity in the neonatology unit of the Mali Hospital. Materials and Methods: This was a cross-sectional, descriptive study from January 2012 to December 2015 of premature newborns from 28 to 36 weeks of amenorrhea in the neonatology unit of Mali Hospital. Results: le="font-family:Verdana;">From January 2012 to December 2015, we recorded 1692 inpatient newborns, including 614 preterm newborns, a frequency of 36.29%. The sex ratio was 1.43 in favor of boys. The average age of the mothers was 23.9 years with a minimum of 15 and a maximum of 47 years. The majority were housewives (92.7%). The pregnancy was poorly monitored in 51.8% of the mothers. The average gestational age was 32.9 days with extremes of 25 and 36 days. The most frequent mode of delivery was vaginal delivery (93.2%), with late prematurity in 51.5%, moderate prematurity (24.4%), extreme prematurity (18.7%) and very premature (5.4%). The mean birth weight was 1464 g with a standard deviation of 485 g and 2751 g. Prematurity was associated with neonatal infection in 49.4% of newborns, perinatal anoxia (13.9%) and hypotrophy (2.6%). The most frequent maternal risk factors were fever (83.4%), twinship (38.9%) and high blood pressure (8.6%). The average length of hospitalization was 9.75 days with extremes of 0 and 68 days. We recorded a cure rate of 57.7%, a death rate of 35.7% and a dropout rate

关键词： Epidemioclinical Profile Prematurity Mali Hospital

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Space-Time Multi-Block Codes with linear MMSE Receivers: A Scheme Achieving High Diversity Gain with low Complexity

Space-Time Multi-Block Codes with Linear MMSE Receivers: A S...

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第八届国际信号处理国际会议

作者： kon Max Wong Department of Electrical and Computer Engineering McMaster University Hamilton Ontario Canada.

＜正＞We consider a multi-input multi-output （MIMO） communication system equipped with a linear minimum mean-square error （MMSE） receiver. We design a full-rate linear space-time block code （STBC） for blocks of data that span several realizations of a block-static fading channel to achieve high diversity gain. The proposed code structures are necessary and sufficient to minimize the detection error probability. They are information lossless when analyzed from information theory view point. They also enable the detection computations to be partitioned into separate blocks such that the normalized complexity is reduced to little more than that for a single block. The additional complexity grows only linearly with l, the number of blocks for which the code design covers. Analysis shows that the diversity gain achieved by the code also grows linearly with l.

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Relationship between the Guinea Current and the Coastal Upwelling in Northern of Gulf of Guinea

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Open Journal of Marine Science 2024年第4期14卷 63-77页

作者： Sandrine Djakouré Youssouf konaté Vamara koné Kouacou Bosson Mamadou koné Kouassi Yves Kouadio laboratory of Matter Sciences Environment and Solar Energy (LASMES) University Felix Houphouet Boigny of Cocody-Abidjan Abidjan Cte dIvoire UFR of Marine Sciences University of San-Pdro San-Pdro Cte dIvoire laboratory of Environmental Sciences and Techniques (lSTE) University Jean-Lorougnon Gud Daloa Cte dIvoire

The variability of ocean circulation and sea surface temperature (SST) in the tropical Atlantic, especially in the Gulf of Guinea (GG), defines this region as exceptionally rich from an oceanographic perspective. The Guinea Current (GC), as the major surface current, plays a significant role in marine productivity and coastal upwelling in the GG. This coastal upwelling is known to influence the climate of the surrounding region, primary productivity and local fisheries. Studies on GC variability and its impact on this coastal upwelling have highlighted that the upwelling downstream of Cape Palmas is influenced by GC detachment, topographic variations and advective processes leading to significant vertical mixing. This study aims to analyze the interannual variability of the GC and its impact on coastal upwelling using the Coastal and Regional Ocean COmmunity model (CROCO). The model’s evaluation is conducted using observational data, specifically Geostrophic and EKman Current Observatory (GEKCO) and Ocean Surface Current Analysis (OSCAR) for currents, and Air-sea Fluxes for the global Tropic ocean-description (TROPFlUX) and Optimum Interpolation-Sea Surface Temperature (oi-SST) for temperature. Thus, the model evaluation indicates that it accurately replicates ocean circulation and SST patterns in the tropical Atlantic and the GG. The joint analysis of upwelling indices (surface and intensity) and the position of the GC core allowed us to conclude that the displacement of the GC core does indeed influence the upwelling indices in the northern part of GG. However, other oceanic and atmospheric mechanisms such as vertical diffusion and horizontal advection as proposed by previous studies may also affect the year-by-year variability of coastal upwelling in the northern GG.

关键词： Guinea Current Sea Surface Temperature Coastal Upwelling Gulf of Guinea Tropical Atlantic Ocean

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Monitoring the Physico-Chemical Quality of the Davo River (South-West of Côte d’Ivoire)

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Open Journal of Applied Sciences 2022年第8期12卷 1402-1415页

作者： Natchia Aka Yao Dakro Albert Gboko Kéiba Noël Keumean oi Adjiri Adjiri Nagnin Soro Département Environnement Centre de Recherches Océanologiques Abidjan C&ocirc te d’Ivoire laboratoire des Sciences et Techniques de l’Eau et l’Environnement (lSTEE) UFR-STRM Université Félix Houphou&euml t Boigny Abidjan C&ocirc te d’Ivoire laboratoire des Sciences et Technologies de l’Environnement (lSTE) UFR Environnement-Université Jean Lorougnon Guédé Daloa C&ocirc te d’Ivoire

The Davo River, an affluent of the Sassandra River, like other rivers in Côte d’Ivoire, is subject to anthropogenic activities likely to deteriorate its quality which could affect its use as drinking water and also the health of aquatic organisms. This study aims at monitoring the temporal evolution of the physico-chemical quality of the waters of the Davo River at the Dakpadou hydrometric station. Twelve monthly field missions were carried out to sample water, measure temperature, pH, Electrical Conductivity and analyse turbidity, Suspended solids, major elements (Cl-, NO3-,HCO3-, SO42-, Mg2+, Ca2+, Na+, and K+) and Trace Metallic Elements (Hg, Fe, Cu, Cr, and Pb). Results show that the waters of the Davo river are poorly mineralized. They are also acidic during periods of low water and slightly basic during flooding periods. The average turbidity value of 10.18 NTU places these waters in the slightly turbid class. The waters have calcic bicarbonate facies during low water periods and sodium bicarbonate facies with low concentrations of major elements during flood months. The average TME concentrations of the Davo river indicate that the waters are not harmful for the health of the population and the aquatic environment.

关键词： Davo River Turbidity Suspended Solids Major Elements Trace Metallic Element

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γ-酮醛清道夫水杨胺对尿毒症ApoE-/-小鼠动脉粥样硬化的作用

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西安交通大学学报（医学版） 2020年第1期41卷 47-52页

作者：申燕陈胜男赵艳 VAlENTINA kon 西安交通大学第一附属医院肾内科陕西西安710061 西安交通大学第一附属医院心血管内科陕西西安710061 美国范德堡大学医学中心儿科肾脏与高血压系田纳西纳什维尔37232

目的观察γ-酮醛清道夫水杨胺(salicylamine,SAM)对尿毒症ApoE-/-小鼠动脉粥样硬化(atherosclerosis,AS)及其表型的影响。方法ApoE-/-小鼠通过5/6肾切除术建立尿毒症模型,对照组仅行假手术。实验动物分为对照组、尿毒症组及尿毒症SAM干... 详细信息

目的观察γ-酮醛清道夫水杨胺(salicylamine,SAM)对尿毒症ApoE-/-小鼠动脉粥样硬化(atherosclerosis,AS)及其表型的影响。方法ApoE-/-小鼠通过5/6肾切除术建立尿毒症模型,对照组仅行假手术。实验动物分为对照组、尿毒症组及尿毒症SAM干预组,分别以SAM或安慰剂干预6周。干预结束后检测体质量、血压、血脂、肾功能、血清SAM浓度、主动脉AS斑块面积及斑块组分。结果与对照组相比,尿毒症组主动脉AS病变面积明显增大,AS斑块组分中坏死面积增大,巨噬细胞含量增多,胶原含量减少。SAM干预6周,尿毒症小鼠AS损伤面积、AS斑块中坏死面积及巨噬细胞含量减少,胶原含量增加,但不影响体质量、血压、血脂和肾功能,未发生药物蓄积和毒性作用。结论SAM能减轻尿毒症ApoE-/-小鼠加速发展的AS病变并使斑块的稳定性增加,这些作用不依赖于对血压、血脂或肾功能的影响,同时不引起药物蓄积及毒性作用。

关键词： γ-酮醛清道夫水杨胺尿毒症 ApoE-/-小鼠动脉粥样硬化水杨胺(salicylamine)

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Quantitative Structure-Activity Relationship Study of a Benzimidazole-Derived Series Inhibiting Mycobacterium tuberculosis H37Rv

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Computational Chemistry 2022年第2期10卷 71-96页

作者： Georges Stéphane Dembélé Mamadou Guy-Richard koné Fandia konate Doh Soro Nahossé Ziao laboratoire de Thermodynamique et de Physico-Chimie du Milieu UFR SFA Université Nangui Abrogoua Abidjan C&#244 te-d’Ivoire Groupe Ivoirien de Recherches en Modélisation des Maladies (GIR2M) Université Nangui Abrogoua Abidjan C&#244 te-d’Ivoire

This work was carried out on a series of twenty-two (22) benzimidazole derivatives with inhibitory activities against Mycobacterium tuberculosis H37Rv by applying the Quantitative Structure-Activity Relationship (QSAR) method. The molecules were optimized at the level DFT/B3lYP/6-31 + G (d, p), to obtain the molecular descriptors. We used three statistical learning tools namely, the linear multiple regression (lMR) method, the nonlinear regression (NlMR) and the artificial neural network (ANN) method. These methods allowed us to obtain three (3) quantitative models from the quantum descriptors that are, chemical potential (μ), polarizability (α), bond length l (C = N), and lipophilicity. These models showed good statistical performance. Among these, the ANN has a significantly better predictive ability R2 = 0.9995;RMSE = 0.0149;F = 31879.0548. The external validation tests verify all the criteria of Tropsha et al. and Roy et al. Also, the internal validation tests show that the model has a very satisfactory internal predictive character and can be considered as robust. Moreover, the applicability range of this model determined from the levers shows that a prediction of the pMIC of the new benzimidazole derivatives is acceptable when its lever value is lower than 1.

关键词： Mycobacterium tuberculosis H37Rv Benzimidazole Derivatives QSAR ANN Applicability Domain

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