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1. 发明申请

WO2007031556A2 MEANS AND METHODS TO ENHANCE THE PRODUCTION OF VINBLASTINE AND VINCRISTINE IN CATHARANTHUS ROSEUS 审中-公开
标题翻译：意大利语和葡萄牙语在加拿大罗马尼亚生产VINBLASTINE和VINCRISTINE的方法和方法
公开(公告)号：WO2007031556A2
公开(公告)日：2007-03-22
申请号：PCT/EP2006/066366
申请日：2006-09-14
申请人： VIB VZW , UNIVERSITEIT GENT , VALTION TEKNILLINEN TUTKIMUSKESKUS , GOOSSENS, Alain , RISCHER, Heiko , INZE, Dirk, Gustaaf , ORESIC, Matej , OKSMAN-CALDENTEY, Kirsi-Marja
发明人： GOOSSENS, Alain , RISCHER, Heiko , INZE, Dirk, Gustaaf , ORESIC, Matej , OKSMAN-CALDENTEY, Kirsi-Marja
IPC分类号： C12N15/82
CPC分类号： C12N15/8243 , C07K14/415 , C12N15/52 , C12P17/182 , C12P17/188
摘要： The present invention relates to the field of plant secondary metabolites, particularly terpenoid indole alkaloids. More particularly the present invention relates to the production of the anti- cancer metabolites vincristine and vinblastine. The invention provides novel polynucleotide sequences derived from Catharanthus roseus and the use of said polynucleotide sequences to stimulate the production of vinblastine and/or vincristine in plants of Catharanthus roseus and plant cell lines derived thereof. The invention further relates to recombinant plants, plant cells, tissue and organ cultures obtainable by the process of the invention.
摘要翻译：本发明涉及植物次生代谢物，特别是萜类吲哚生物碱的领域。更具体地说，本发明涉及抗癌代谢物长春新碱和长春花碱的生产。本发明提供了源自长春花的新型多核苷酸序列，以及使用所述多核苷酸序列来刺激长春花的植物中长春花碱和/或长春新碱的产生及其衍生的植物细胞系。本发明还涉及可通过本发明的方法获得的重组植物，植物细胞，组织和器官培养物。

2. 发明申请

WO2008031917A1 BIOFLUID METABOLITE PROFILING AS A TOOL FOR EARLY PREDICTION OF AUTOIMMUNITY AND TYPE 1 DIABETES RISK 审中-公开
标题翻译：作为早期预测自身免疫和1型糖尿病风险的工具的生物流动代谢物分析
公开(公告)号：WO2008031917A1
公开(公告)日：2008-03-20
申请号：PCT/FI2007/000227
申请日：2007-09-10
申请人： VALTION TEKNILLINEN TUTKIMUSKESKUS , ORESIC, Matej , SIMELL, Olli , SEPPÄNEN-LAAKSO, Tuulikki , SYSI-AHO, Marko
发明人： ORESIC, Matej , SIMELL, Olli , SEPPÄNEN-LAAKSO, Tuulikki , SYSI-AHO, Marko
IPC分类号： G01N33/50 , G01N33/92
CPC分类号： G01N33/6893 , G01N33/38 , G01N33/92 , G01N2405/04 , G01N2800/042 , Y10T436/203332
摘要： The invention concerns a method for diagnosing a child's susceptibility for developing type 1 diabetes by using a serum metabolite as biomarker. The invention concerns also a method for prevention of the onset of type 1 diabetes in a child.
摘要翻译：本发明涉及通过使用血清代谢物作为生物标志物诊断儿童易发生1型糖尿病的方法。本发明还涉及一种预防儿童1型糖尿病发病的方法。

3. 发明申请

WO2006125865A1 ANALYSIS TECHNIQUES FOR LIQUID CHROMATOGRAPHY/MASS SPECTROMETRY 审中-公开
标题翻译：液相色谱/质谱分析技术
公开(公告)号：WO2006125865A1
公开(公告)日：2006-11-30
申请号：PCT/FI2006/050210
申请日：2006-05-24
申请人： VALTION TEKNILLINEN TUTKIMUSKESKUS , ORESIC, Matej , KATAJAMAA, Mikko
发明人： ORESIC, Matej , KATAJAMAA, Mikko
IPC分类号： G01N30/72
CPC分类号： G01N30/8675 , G01N30/7233 , G01N30/8631
摘要： A method for analyzing liquid chromatography/mass spectrometry [="LC/MS”] data comprises: preparing (1-2) a plurality of sample runs; processing (1-4) each of the prepared sample runs in an LC/MS spectrometer to obtain a spectrum in respect of each processed sample run; internally representing (1-10) each spectrum as a layout of mass/charge versus retention time; performing a first peak detection (1 -12) to detect peaks of each spectrum; searching (1-18) for the standard compound peak closest to a peak being analyzed and normalizing (1-20) the peak being analyzed based on a distance measure of the distance between the peak being analyzed and said closest standard compound peak.
摘要翻译：分析液相色谱/质谱法[=“LC / MS”]数据的方法包括：制备（1-2）多个样品流程; 处理（1-4）每个所制备的样品在LC / MS光谱仪中运行以获得关于每个处理的样品运行的光谱; 内部代表（1-10）每个频谱作为质量/电荷与保留时间的布局; 执行第一峰检测（1 -12）以检测每个光谱的峰值; 搜索（1-18）最接近正在分析峰的标准化合物峰，并根据待分析峰与所述最接近的标准化合物峰之间的距离的距离测量来归一化（1-20）所分析的峰。

4. 发明申请

WO2007147938A1 NORMALIZING SPECTROSCOPY DATA WITH MULTIPLE INTERNAL STANDARDS 审中-公开
标题翻译：通过多种内部标准对光谱数据进行正规化处理
公开(公告)号：WO2007147938A1
公开(公告)日：2007-12-27
申请号：PCT/FI2007/050356
申请日：2007-06-14
申请人： VALTION TEKNILLINEN TUTKIMUSKESKUS , ORESIC, Matej
发明人： ORESIC, Matej
IPC分类号： G01N30/86 , G01N30/72 , G06F17/18
CPC分类号： G01N30/8624 , G01N30/7233
摘要： Normalization of spectra, comprising: preparing (1-2) experiment runs; processing (1-4) them in an LC/MS spectrometer to obtain a spectrum for each experiment run; internally representing (1-10) each spectrum as mass/charge (m/z) versus retention time (rt); performing a peak detection (1-12) of each spectrum; internally aligning (1-14) the detected peaks; and normalizing (1-18) the spectra, which comprises modelling variation of Y i j , denoted δY ij , as a function of variability of Ω , denoted f(δΩ) . δ denotes variability of a quantity, (the quantity's deviation from an average value of the quantity over the sample runs); X = X ij = intensity matrix for ail peaks, mapped to Y via a first transformation function / such that Y = f 1 (X); Z = Z ij = intensity matrix for internal standard peaks (IS 1 - IS 4 ), mapped to Ω via a second transformation function t such that Ω = f 1 (Z). i denotes peaks: i → {m/z, rt} and i = 1... N ; and j denotes experiment runs.
摘要翻译：光谱的归一化，包括：制备（1-2）实验运行; 在LC / MS光谱仪中处理（1-4）它们以获得每个实验运行的光谱; 内部表示（1-10）每个光谱作为质量/电荷（m / z）对保留时间（rt）; 执行每个频谱的峰值检测（1-12）; 内部校准（1-14）检测到的峰; 并且归一化（1-18）光谱，其包括作为表示为f（SO）的O的变异性的函数的表示为Y ij ij的Y Y ij的建模变化。 d表示量的变异性（数量与样品运行数量的平均值的偏差）; X = X ij =用于通过第一变换函数映射到Y的所述峰的强度矩阵，使得Y = f 1（X）; Z = Z ij ij =用于内部标准峰（IS 1 -I 4）的强度矩阵，经由第二变换函数t映射到O 那么O = f 1（Z）。我表示峰：i？ {m / z，rt}和i = 1 ... N; j表示实验运行。

5. 发明申请

WO2007128882A1 INFORMATION MANAGEMENT TECHNIQUES FOR METABOLISM-RELATED DATA 审中-公开
标题翻译：代谢相关数据的信息管理技术
公开(公告)号：WO2007128882A1
公开(公告)日：2007-11-15
申请号：PCT/FI2007/050261
申请日：2007-05-09
申请人： VALTION TEKNILLINEN TUTKIMUSKESKUS , ORESIC, Matej
发明人： ORESIC, Matej
IPC分类号： G06F19/00 , G01N30/72 , G01N33/50 , G01N33/92 , G01N33/487
CPC分类号： G06F19/28 , G06F19/12 , G06F19/26 , G06F19/703 , G06F19/708 , G06F19/709
摘要： A method for processing information on compounds of molecular classes sharing common building blocks. The method comprises maintaining pathway information on the compounds at individual compound level and/or generic class level (13-1); generating a diversity of the compounds based on a set of seed structures, each seed structure describing a lipid compound having a higher- than-average likelihood to occur in nature (13-2); using a formal description language to express the seed structures (13-3); using the structural elements to generate expected spectra for each compound, by using known experimental conditions for mass spectrometry (13-4); performing one or more spectroscopy experiments to obtain compound information (13-5); and linking the obtained compound information to existing information on the molecular classes (13-6).
摘要翻译：用于处理分享共同共同构件的分子类化合物信息的方法。该方法包括在个体化合物水平和/或一般类别水平上维持化合物的途径信息（13-1）; 基于一组种子结构产生多种化合物，每个种子结构描述了具有高于平均可能性的自然界中的脂质化合物（13-2）; 使用正式的描述语言来表达种子结构（13-3）; 通过使用已知的质谱实验条件（13-4），使用结构元件产生每种化合物的预期光谱; 执行一个或多个光谱实验以获得化合物信息（13-5）; 并将获得的化合物信息与分子级别上的现有信息（13-6）连接。

6. 发明申请

WO2006125864A1 ANALYSIS TECHNIQUES FOR LIQUID CHROMATOGRAPHY/MASS SPECTROMETRY 审中-公开
标题翻译：液相色谱/质谱分析技术
公开(公告)号：WO2006125864A1
公开(公告)日：2006-11-30
申请号：PCT/FI2006/050209
申请日：2006-05-24
申请人： VALTION TEKNILLINEN TUTKIMUSKESKUS , ORESIC, Matej , KATAJAMAA, Mikko
发明人： ORESIC, Matej , KATAJAMAA, Mikko
IPC分类号： G01N30/72
CPC分类号： G01N30/8675 , G01N30/7233 , G01N30/8631
摘要： Α method for analyzing liquid chromatography/spectrometry [=”LC/MS”] data comprising the following steps: preparing (1-2) a plurality of sample runs; processing (1-4) each of the prepared sample runs in an LC/MS spectrometer to obtain a spectrum in respect of each processed sample run; internally representing (1-10) each spectrum as a layout of mass/charge versus retention time; performing a first peak detection (1-12) to detect peaks of each spectrum; internally aligning (1-14) the detected peaks of each spectrum; and performing a second peak detection (1-16) to detect peaks missed in the first peak detection.
摘要翻译：？分析液相色谱/光谱法的方法[=“LC / MS”]数据，包括以下步骤：制备（1-2）多个样品流程; 处理（1-4）每个所制备的样品在LC / MS光谱仪中运行以获得关于每个处理的样品运行的光谱; 内部代表（1-10）每个频谱作为质量/电荷与保留时间的布局; 执行第一峰值检测（1-12）以检测每个频谱的峰值; 内部对齐（1-14）每个光谱的检测峰; 以及执行第二峰值检测（1-16）以检测在第一峰值检测中丢失的峰值。

7. 发明申请

WO2006125863A1 ANALYSIS TECHNIQUES FOR LIQUID CHROMATOGRAPHY/MASS SPECTROMETRY 审中-公开
标题翻译：液相色谱/质谱分析技术
公开(公告)号：WO2006125863A1
公开(公告)日：2006-11-30
申请号：PCT/FI2006/050208
申请日：2006-05-24
申请人： VALTION TEKNILLINEN TUTKIMUSKESKUS , ORESIC, Matej , KATAJAMAA, Mikko
发明人： ORESIC, Matej , KATAJAMAA, Mikko
IPC分类号： G01N30/72
CPC分类号： G01N30/8675 , G01N30/7233 , G01N30/8631
摘要： A method for analyzing liquid chromatography/mass spectrometry [=”CL/MS”] data comprises: preparing (1-2) a plurality of sample runs; processing (1-4) each of the prepared sample runs in an LC/MS spectrometer to obtain a spectrum in respect of each processed sample run; internally representing (1-10) each spectrum as a layout of mass/charge versus retention time; performing a first peak detection (1-12) to detect peaks of each spectrum; visualizing peaks of each spectrum, wherein the visualizing step comprises: mapping (1-22) each peak to be visualized to a coordinate system in which a first coordinate indicates mass/charge ratio and a second coordinate indicates retention time; and assigning (1-24) a specific visual attribute to each peak to be visualized.
摘要翻译：分析液相色谱/质谱法[=“CL / MS”]数据的方法包括：制备（1-2）多个样品流程; 处理（1-4）每个所制备的样品在LC / MS光谱仪中运行以获得关于每个处理的样品运行的光谱; 内部代表（1-10）每个频谱作为质量/电荷与保留时间的布局; 执行第一峰值检测（1-12）以检测每个频谱的峰值; 每个光谱的可视化峰值，其中可视化步骤包括：将要显现的每个峰映射（1-22）到其中第一坐标表示质量/电荷比的坐标系，而第二坐标表示保留时间; 并为每个需要可视化的峰分配（1-24）特定的视觉属性。

8. 发明申请

WO2006114479A1 VISUALIZATION TECHNIQUE FOR BIOLOGICAL INFORMATION 审中-公开
标题翻译：生物信息可视化技术
公开(公告)号：WO2006114479A1
公开(公告)日：2006-11-02
申请号：PCT/FI2006/050163
申请日：2006-04-26
申请人： VALTION TEKNILLINEN TUTKIMUSKESKUS , ORESIC, Matej , LINDFORS, Erno , PEDDINTI, Gopalacharyulu
发明人： ORESIC, Matej , LINDFORS, Erno , PEDDINTI, Gopalacharyulu
IPC分类号： G06F19/00 , G06F17/30
CPC分类号： G06F17/30545 , G06F19/12 , G06F19/26 , G06F19/28
摘要： Method/system for visualizing biological information. The system receives (2-2) a user query relating to biological information and determines (2-4) which database contains related biological information. A database query is sent (2-6) to the database and the result (2-8) indicates biological/chemical entities and relations. A network is created (2-10) based on the result; biological/chemical entities are mapped to network nodes and relations to network connections. A distance matrix (2-12) indicates a multi-dimensional distance for several pairs of network nodes. A dimensionality reduction function is adjusted (2- 14) based on a research context, to bias the search toward a relevant focus. The number of dimensions in the distance matrix is lowered (2-16) by the dimensionality reduction function. Neighbours of a selected node are searched (2-18) based on the distance matrix to elucidate a biological role of the selected node. A re-created network is visualised (2-20) based on the adjusted dimensionality reduction function.
摘要翻译：用于可视化生物信息的方法/系统系统接收（2-2）与生物信息相关的用户查询，并确定（2-4）哪个数据库包含相关生物信息。数据库查询（2-6）发送到数据库，结果（2-8）表示生物/化学实体和关系。根据结果创建网络（2-10）; 生物/化学实体被映射到网络节点和与网络连接的关系。距离矩阵（2-12）表示多对网络节点的多维距离。基于研究背景调整维数降低函数（2-14），将搜索偏向于相关焦点。距离矩阵中的维数由维度降低函数降低（2-16）。根据距离矩阵搜索所选节点的邻居（2-18），以阐明所选节点的生物学作用。基于经调整的维数降低功能可重构网络（2-20）。

9. 发明申请

WO2007035613A1 CORRELATION ANALYSIS OF BIOLOGICAL SYSTEMS 审中-公开
标题翻译：生物系统的相关分析
公开(公告)号：WO2007035613A1
公开(公告)日：2007-03-29
申请号：PCT/US2006/036247
申请日：2006-09-19
申请人： BG MEDICINE, INC. , ADOURIAN, Aram, S. , ORESIC, Matej , DAMIAN, Doris , NEUMANN, Eric, K. , PLASTERER, Thomas , JENNINGS, Ezra
发明人： ADOURIAN, Aram, S. , ORESIC, Matej , DAMIAN, Doris , NEUMANN, Eric, K. , PLASTERER, Thomas , JENNINGS, Ezra
IPC分类号： G06F19/00
CPC分类号： G06F19/12
摘要： The present teachings relate to gaining insight into biological states, e.g., disease states or drugged states, by gathering, integrating, and combining biomolecular data. More particularly, the present teachings relate to methods and systems for profiling a state of a biological system, finding accessible biomarkers representative of the state of a biological system, and deriving insights into the biochemistry of a biological system for therapeutic, diagnostic, prognostic and other purposes.
摘要翻译：本教导涉及通过收集，整合和组合生物分子数据来了解生物状态，例如疾病状态或药物状态。更具体地，本教导涉及用于分析生物系统的状态，找到代表生物系统的状态的可及性生物标志物的方法和系统，以及用于治疗，诊断，预后等的生物系统的生物化学的见解目的。

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