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    Process and Kit for Predicting Antibiotic Resistance and Susceptibility of Bacteria
    2.
    发明申请
    Process and Kit for Predicting Antibiotic Resistance and Susceptibility of Bacteria 有权
    用于预测抗生素耐药性和细菌易感性的方法和试剂盒

    公开(公告)号：US20160251702A1

    公开(公告)日：2016-09-01

    申请号：US15055376

    申请日：2016-02-26

    申请人： Sujay Chattopadhyay ,  Pavel Aprikian ,  Evgeni Sokurenko

    发明人： Sujay Chattopadhyay ,  Pavel Aprikian ,  Evgeni Sokurenko

    IPC分类号： C12Q1/68

    CPC分类号： C12Q1/689 ,  C12Q2600/106 ,  C12Q2600/156 ,  C12Q2600/158 ,  C12Q2600/16

    摘要： There is disclosed a PCR-based test kit and PCR process for identification of multiple clonal sub-species lineages of infectious bacteria, such as uropathogenic E. coli causing cystitis, pyelonephritis and urosepsis, for the purposes of predicting antibiotic resistance of the bacteria. More specifically, there is further disclosed a SNP (single nucleotide polymorphism) identification process that simultaneously detect compilations of the presence of absence of predictive SNPs within mutated loci of infectious bacterial clonal subspecies variants, such as the fumC/fimH loci of the E. coli bacterium. This disclosure provides a PCR detection kit incorporating a SNP compilation that forms a BFC (Binary Footprint Code) that allows for rapid identification of multiple infectious bacterial clonotypes based on their SNP footprint. More specifically there is disclosed a clonotyping method for clonal typing E. coli and predicting antibiotic susceptibility, comprising (a) providing forward primers and reverse primers for at least seven SNPs (single nucleotide polymorphisms) selected from the group consisting of fumC-63, fumC-248, fumC-380, fimH-162, fimH-233, fimH-483, and fimH-483, (b) measuring the presence or absence of each SNP, and (c) determining antibiotic susceptibility from Lookup Table 1.

    摘要翻译： 公开了一种基于PCR的测试试剂盒和PCR方法，用于鉴定感染性细菌的多个克隆亚种谱系，如致病性大肠杆菌引起的膀胱炎，肾盂肾炎和泌尿系，以预测细菌的抗生素抗性。 更具体地，还公开了SNP（单核苷酸多态性）鉴定过程，其同时检测在感染性细菌克隆亚种变体（例如大肠杆菌的fumC / fimH基因座）的突变位点内是否存在预测性SNP的缺失 细菌。 本公开提供了一种PCR检测试剂盒，其包含形成BFC（二进制足迹码）的SNP编码，其允许基于其SNP足迹快速鉴定多种感染性细菌克隆型。 更具体地，公开了克隆型大肠杆菌的克隆分型方法和预测抗生素敏感性，其包括（a）向至少七个选自以下的SNP（单核苷酸多态性）提供正向引物和反向引物，所述SNP（单核苷酸多态性）选自fumC-63， -248，fumC-380，fimH-162，fimH-233，fimH-483和fimH-483，（b）测量每个SNP的存在或不存在，以及（c）从查找表1确定抗生素敏感性。

    Conserved-Element Vaccines and Methods for Designing Conserved-Element Vaccines
    7.
    发明申请
    Conserved-Element Vaccines and Methods for Designing Conserved-Element Vaccines 审中-公开
    保守元素疫苗和设计保护性元素疫苗的方法

    公开(公告)号：US20110269937A1

    公开(公告)日：2011-11-03

    申请号：US13097592

    申请日：2011-04-29

    申请人： James Mullins ,  David Nickle ,  Morgane Rolland

    发明人： James Mullins ,  David Nickle ,  Morgane Rolland

    IPC分类号： C07K7/08 ,  C07K7/06 ,  G06N5/00 ,  C07H21/04

    CPC分类号： G16B30/00 ,  G16B20/00

    摘要： Embodiments of the present invention include conserved-element vaccines and methods for designing and producing conserved-element vaccines. A conserved-element vaccine (“CEVac”) is a recombinant and/or synthetic vaccine that incorporates only highly conserved epitopes from an observed set of pathogen variants. The conserved epitopes are identified computationally by aligning biopolymer sequences, such as concatenated polypeptide sequences that together represent a pathogen proteome, corresponding to an observed set of pathogen variants, and computationally selecting conserved subsequences according to a number of subsequence-selection criteria. These subsequence-selection criteria may include a minimum conserved-subsequence length, a threshold frequency of occurrence of a particular monomer at each conserved, single-monomer position within a conserved subsequence, a threshold combined occurrence for a set of allowable variant monomers at a particular conserved, variable position within a conserved subsequence, and a maximum number of variable positions within a subsequence. A set of conserved subsequences identified according to the subsequence-selection criteria are then filtered to remove subsequences identical to, or too similar to, naturally-occurring host subsequences, and are then assembled into expression vectors for incorporation into microbial hosts for biosynthesis of a recombinant CEVac or assembled into one or more synthetic constructs for a synthetic CEVac.

    摘要翻译： 本发明的实施方案包括保守元件疫苗和用于设计和生产保守元件疫苗的方法。 保守元件疫苗（“CEVac”）是重组和/或合成疫苗，其仅包含观察到的一组病原体变体的高度保守的表位。 通过对齐生物聚合物序列，例如一起代表病原体蛋白质组的连接多肽序列，对应于观察到的一组病原体变体，并且根据多个子序列选择标准计算选择保守的亚序列，可以计算地鉴定保守的表位。 这些子序列选择标准可以包括最小保守序列长度，在保守子序列内的每个保守的单个单体位置处特定单体出现的阈值频率，特定的一组允许的变体单体的阈值组合发生 保守的子序列内的保守的，可变的位置，以及子序列内可变位置的最大数目。 然后将根据子序列选择标准鉴定的一组保守的亚序列过滤以去除与天然存在的宿主亚序列相同或类似于的天然存在的宿主亚序列的亚序列，然后将其组装到表达载体中，以结合到微生物宿主中用于生物合成重组 CEVac或组装成合成CEVac的一种或多种合成构建体。

    Methods and compositions for predicting drug responses
    9.
    发明授权
    Methods and compositions for predicting drug responses 有权
    用于预测药物反应的方法和组合物

    公开(公告)号：US07829282B2

    公开(公告)日：2010-11-09

    申请号：US11687123

    申请日：2007-03-16

    申请人： Mark J. Rieder ,  Allan Rettie

    发明人： Mark J. Rieder ,  Allan Rettie

    IPC分类号： C12Q1/68 ,  C12P19/34 ,  C07H21/02 ,  C07H21/04

    CPC分类号： C12Q1/6883 ,  C12Q1/6876 ,  C12Q2600/156

    摘要： The present invention relates to methods and compositions for predicting drug responses. In particular, the present invention provides methods and compositions for determining individualized Warfarin dosages based on genotype of DNA polymorphisms and haplotypes derived from them in the VKORC1 gene.

    摘要翻译： 本发明涉及用于预测药物反应的方法和组合物。 特别地，本发明提供了基于VKORC1基因中DNA多态性和从它们衍生的单元型的基因型确定个体化华法林剂量的方法和组合物。

    Plasma-based EUV light source
    10.
    发明授权
    Plasma-based EUV light source 有权
    基于等离子体的EUV光源

    公开(公告)号：US07825391B2

    公开(公告)日：2010-11-02

    申请号：US12101083

    申请日：2008-04-10

    申请人： Uri Shumlak ,  Raymond Golingo ,  Brian A. Nelson

    发明人： Uri Shumlak ,  Raymond Golingo ,  Brian A. Nelson

    IPC分类号： A61N5/06

    CPC分类号： H05G2/003

    摘要： Various mechanisms are provided relating to plasma-based light source that may be used for lithography as well as other applications. For example, a device is disclosed for producing extreme ultraviolet (EUV) light based on a sheared plasma flow. The device can produce a plasma pinch that can last several orders of magnitude longer than what is typically sustained in a Z-pinch, thus enabling the device to provide more power output than what has been hitherto predicted in theory or attained in practice. Such power output may be used in a lithography system for manufacturing integrated circuits, enabling the use of EUV wavelengths on the order of about 13.5 nm. Lastly, the process of manufacturing such a plasma pinch is discussed, where the process includes providing a sheared flow of plasma in order to stabilize it for long periods of time.

    摘要翻译： 提供了关于可用于光刻以及其它应用的基于等离子体的光源的各种机构。 例如，公开了一种基于剪切等离子体流产生极紫外（EUV）光的装置。 该装置可以产生比通常在Z夹中持续几个数量级的等离子体夹点，从而使得该装置能够提供比迄今为止在理论上所预期的或实践中获得的功率输出更多的功率输出。 这种功率输出可以用于制造集成电路的光刻系统中，使得能够使用约13.5nm量级的EUV波长。 最后，讨论了制造这种等离子体夹紧的过程，其中该方法包括提供剪切的等离子体流，以便使其长时间稳定。