公开(公告)号：US20070197773A1

公开(公告)日：2007-08-23

申请号：US11561266

申请日：2006-11-17

Applicant: Gregory Stephanopoulos ,  Kyle Jensen ,  Christopher Loose

Inventor： Gregory Stephanopoulos ,  Kyle Jensen ,  Christopher Loose

IPC: G06F19/00 ,  C07K14/16 ,  C07K14/195

CPC classification number: C07K7/08 ,  A61K38/00 ,  C07K14/001 ,  C07K14/4723 ,  C40B50/02 ,  G06F19/18 ,  G06F19/22 ,  G06F19/24 ,  G06F19/28

Abstract: A method has been developed to create databases of peptides having a desirable property, such as antimicrobial activity, based on analyzing a database of known peptides for a pattern statistically associated with an activity. One can determine a set of patterns that may be representative of a peptide having a desired characteristic or property, and evaluate a set of sequences against the set of patterns (grammars) to determine if the peptide sequence being evaluated has similar patterns to those of a peptide having the desired characteristic or property. The set of sequences being evaluated may include peptide sequences of a desired length comprising all or substantially all combinations of amino acids that conform to at least one of the set of patterns. Once the database is identified the database may be processed in a pattern recognition procedure that identifies a set of patterns that could be understood as representative of a peptide having the characteristic of interest. A set of newly generated peptides sequences may then be processed to score these new sequences against the identified patterns to correlate the patterns to the sequences and determine a degree of association or a similarity between a respective one of the new sequences and the set of identified patterns. The method is used to provide a database of sequences that are expected to have one or more desired activities, specific sequences within the database proven to have the desired activity, and the patterns or grammars used to create the database of sequences. Although described with reference to antimicrobial peptides, a database of peptides may be identified that contains peptides that have antiviral properties, wound response properties, or some other property of interest.

Abstract translation: 已经开发了一种基于分析与活性统计相关的模式的已知肽的数据库来创建具有所需性质（例如抗微生物活性）的肽的数据库的方法。 可以确定可以代表具有期望特征或性质的肽的一组模式，并且针对该组模式（语法）评估一组序列，以确定被评估的肽序列是否具有与 肽具有所需的特性或性质。 正在评估的序列集合可以包括期望长度的肽序列，其包含符合该组模式中的至少一个的氨基酸的全部或基本上全部组合。 一旦数据库被识别，数据库可以在识别可以被理解为具有感兴趣特征的肽的代表的一组模式的模式识别过程中被处理。 然后可以对一组新产生的肽序列进行处理，以针对所识别的模式对这些新序列进行评估，以将模式与序列相关联，并确定新序列中的相应一个和所识别的模式集合之间的关联程度或相似度 。 该方法用于提供预期具有一个或多个期望活动的序列的数据库，被证明具有期望活动的数据库中的特定序列，以及用于创建序列数据库的模式或语法。 尽管参考抗微生物肽描述了，但是可以鉴定出含有具有抗病毒性质，伤口应答性质或感兴趣的其它性质的肽的肽数据库。

公开(公告)号：US07739055B2

公开(公告)日：2010-06-15

申请号：US11561266

申请日：2006-11-17

Applicant: Gregory Stephanopoulos ,  Kyle Jensen ,  Christopher Loose

Inventor： Gregory Stephanopoulos ,  Kyle Jensen ,  Christopher Loose

IPC: G06F19/00

CPC classification number: C07K7/08 ,  A61K38/00 ,  C07K14/001 ,  C07K14/4723 ,  C40B50/02 ,  G06F19/18 ,  G06F19/22 ,  G06F19/24 ,  G06F19/28

Abstract: Methods to create databases of peptides having a desirable property, such as antimicrobial activity, involving analyzing a database of known peptides for a pattern statistically associated with the desirable property are described herein, The set of sequences being analyzed may include sequences of a desired length containing all or substantially all combinations of amino acids that conform to at least one of the set of patterns. Once the database is identified, the database may be processed in a pattern recognition procedure that identifies a set of patterns that may be representative of a peptide having the desirable property. A set of newly generated peptides sequences may then be processed to score these new sequences against the identified patterns to correlate the patterns to the sequences and determine a degree of association or similarity between one or more of the new sequences and the set of identified patterns.

Abstract translation: 本文描述了创建具有期望性质（例如抗微生物活性）的肽的数据库的方法，其涉及分析已知肽的数据库以获得与所需性质统计学相关的模式。所分析的一组序列可以包含期望长度的序列，其含有 所有或基本上所有符合该组图案中的至少一个的氨基酸组合。 一旦识别了数据库，就可以在模式识别程序中处理数据库，该模式识别程序识别可以代表具有所需性质的肽的一组模式。 然后可以处理一组新产生的肽序列以针对所识别的模式对这些新序列进行评估，以将模式与序列相关联，并确定一个或多个新序列与所识别的模式集合之间的关联度或相似度。

公开(公告)号：US09285501B2

公开(公告)日：2016-03-15

申请号：US12612375

申请日：2009-11-04

Applicant: Colin Christy ,  Paul Drummond ,  Giyoung Kweon ,  Chase Maxton ,  Kenton Dreiling ,  Kyle Jensen ,  Eric Lund

Inventor： Colin Christy ,  Paul Drummond ,  Giyoung Kweon ,  Chase Maxton ,  Kenton Dreiling ,  Kyle Jensen ,  Eric Lund

IPC: G01N31/00 ,  G01N33/24 ,  G01V11/00 ,  G01N21/359 ,  G01N21/85 ,  G01N21/3563

CPC classification number: G01V11/00 ,  G01N21/3563 ,  G01N21/359 ,  G01N21/8507

Abstract: A multi-sensor system rapidly measures diffuse reflectance of soil, soil conductivity, and other soil properties in situ, in three dimensions. The system includes a tractor-drawn implement containing a sensor shank used for X-Y axis measurements, a hydraulic probe implement containing a sensor probe for −Z axis measurements, and a set of visible and near-infrared spectrometers, controls, and firmware that are shared by each implement. Both implements include optical sensors and soil electrical conductivity sensors. The probe implement incorporates a sensor that measures insertion force, and the shank implement includes a soil temperature sensor. These combinations of sensors are used to calibrate the system and to characterize the soil properties within a field or area. Geo-referenced soil measurements are collected with the shank implement to identify optimal locations for conducting sensor probe insertions. The probe implement is then used for sensor probing and for collecting soil core samples for lab analysis.

Abstract translation: 多传感器系统在三维方面快速测量土壤，土壤电导率和其他土壤性质的漫反射。 该系统包括一个拖拉机牵引工具，其中包含用于XY轴测量的传感器柄，包含用于-Z轴测量的传感器探头的液压探头工具以及共享的一组可见光和近红外光谱仪，控制和固件 由每个工具。 两种工具都包括光学传感器和土壤电导率传感器。 探头工具包括测量插入力的传感器，并且柄部件包括土壤温度传感器。 传感器的这些组合用于校准系统和表征场或区域内的土壤性质。 采用柄部工具收集地质参考土壤测量，以确定传感器探针插入的最佳位置。 然后将探头工具用于传感器探测和收集土壤样品进行实验室分析。

公开(公告)号：US20100184693A1

公开(公告)日：2010-07-22

申请号：US12685522

申请日：2010-01-11

Applicant: Gregory Stephanopoulos ,  Kyle Jensen ,  Christopher Loose

Inventor： Gregory Stephanopoulos ,  Kyle Jensen ,  Christopher Loose

IPC: A61K38/10 ,  C07K14/00 ,  C07K2/00 ,  A61K38/00 ,  A61P31/00

CPC classification number: C07K7/08 ,  A61K38/00 ,  C07K14/001 ,  C07K14/4723 ,  G16B20/00 ,  G16B30/00 ,  G16B35/00 ,  G16B40/00 ,  G16B50/00 ,  G16C20/60

Abstract: A method has been developed to create databases of peptides having a desirable property, such as antimicrobial activity, based on analyzing a database of known peptides for a pattern statistically associated with an activity. One can determine a set of patterns that may be representative of a peptide having a desired characteristic or property, and evaluate a set of sequences against the set of patterns (grammars) to determine if the peptide sequence being evaluated has similar patterns to those of a peptide having the desired characteristic or property. The set of sequences being evaluated may include peptide sequences of a desired length comprising all or substantially all combinations of amino acids that conform to at least one of the set of patterns. Once the database is identified, the database may be processed in a pattern recognition procedure that identifies a set of patterns that could be understood as representative of a peptide having the characteristic of interest. A set of newly generated peptides sequences may then be processed to score these new sequences against the identified patterns to correlate the patterns to the sequences and determine a degree of association or a similarity between a respective one of the new sequences and the set of identified patterns. The method is used to provide a database of sequences that are expected to have one or more desired activities, specific sequences within the database proven to have the desired activity, and the patterns or grammars used to create the database of sequences. Although described with reference to antimicrobial peptides, a database of peptides may be identified that contains peptides that have antiviral properties, wound response properties, or some other property of interest.

Abstract translation: 已经开发了一种基于分析与活性统计相关的模式的已知肽的数据库来创建具有所需性质（例如抗微生物活性）的肽的数据库的方法。 可以确定可以代表具有期望特征或性质的肽的一组模式，并且针对该组模式（语法）评估一组序列，以确定被评估的肽序列是否具有与 肽具有所需的特性或性质。 正在评估的序列集合可以包括期望长度的肽序列，其包含符合该组模式中的至少一个的氨基酸的全部或基本上全部组合。 一旦数据库被识别，数据库就可以在模式识别程序中进行处理，该模式识别程序识别可以被理解为代表具有感兴趣特征的肽的一组模式。 然后可以对一组新产生的肽序列进行处理，以针对所识别的模式对这些新序列进行评估，以将模式与序列相关联，并确定新序列中的相应一个和所识别的模式集合之间的关联程度或相似度 。 该方法用于提供预期具有一个或多个期望活动的序列的数据库，被证明具有期望活动的数据库中的特定序列，以及用于创建序列数据库的模式或语法。 尽管参考抗微生物肽描述了，但是可以鉴定出含有具有抗病毒性质，伤口应答性质或感兴趣的其它性质的肽的肽数据库。

公开(公告)号：US20100076173A1

公开(公告)日：2010-03-25

申请号：US12548211

申请日：2009-08-26

Applicant: Gregory Stephanopoulos ,  Christopher R. Loose ,  Kyle Jensen

Inventor： Gregory Stephanopoulos ,  Christopher R. Loose ,  Kyle Jensen

IPC: C07K14/00 ,  C07K7/06 ,  C07K7/08

CPC classification number: C07K1/00 ,  G16B30/00 ,  G16B40/00

Abstract: Antimicrobial peptides are small proteins used by the innate immune system to combat bacterial infection in multicellular eukaryotes. There is mounting evidence that these peptides are less susceptible to bacterial resistance than traditional antibiotics and that they may form the basis for a novel class of therapeutics. Systems and methods may treat the amino acid sequences of these peptides as a formal language and build a set of right-linear grammars that describe this language. These grammars may allow for rationally designed novel antimicrobial peptides in silico. These peptides conform to the syntax of natural antimicrobial peptides lack significant homology to any natural sequences, thus populating a previously unexplored region of protein sequence space. Synthesis of these peptides, leads to de novo AmPs.

Abstract translation: 抗微生物肽是先天免疫系统用于防治多细胞真核生物细菌感染的小蛋白质。 有越来越多的证据表明，这些肽比传统抗生素对细菌耐药性较不敏感，并且它们可能形成新型治疗剂的基础。 系统和方法可以将这些肽的氨基酸序列视为形式语言，并构建描述此语言的一组右线性语法。 这些语法可以允许合理设计的新型抗微生物肽。 这些肽符合天然抗微生物肽的语法，与任何天然序列缺乏显着的同源性，从而填充了以前未探索的蛋白质序列空间区域。 这些肽的合成，导致从头AmPs。

公开(公告)号：US20060144783A1

公开(公告)日：2006-07-06

申请号：US11277070

申请日：2006-03-21

Applicant: Kyle Jensen

Inventor： Kyle Jensen

IPC: C02F3/32

CPC classification number: C02F9/00 ,  C02F1/001 ,  C02F1/283 ,  C02F1/32 ,  C02F1/52 ,  C02F1/78 ,  C02F3/327 ,  C02F2103/007 ,  C02F2201/782 ,  Y02W10/18 ,  Y10S210/908

Abstract: A method of treating water includes exposing influent comprising water desired to be treated to ozone in sufficient quantity to disrupt cell walls of undesired microorganisms therein, thereby releasing nutrients from within the microorganisms in a form amenable to bioassimilation. The ozone is further in sufficient quantity to oxidize toxic, humic substances to a form amenable to plant bioassimilation. Aquatic plants are contacted with the ozone-exposed water, the aquatic plants being adapted to remove the released and oxidized nutrients therefrom. Water emerging from the aquatic plants is then again exposed to ozone in sufficient quantity to further purify the water.

Abstract translation: 一种处理水的方法包括将期望待处理的水的流入物充分暴露于臭氧中以破坏其中不期望的微生物的细胞壁，从而以适于生物同化的形式从微生物中释放营养物质。 臭氧进一步足够的量将有毒的腐殖质氧化成适于植物生物同化的形式。 水生植物与暴露于臭氧的水接触，水生植物适于从其中除去释放和氧化的营养物质。 然后从水生植物出来的水再次以足够的量暴露于臭氧，以进一步净化水。

公开(公告)号：US09743574B1

公开(公告)日：2017-08-29

申请号：US13277208

申请日：2011-10-19

Applicant: Chase Maxton ,  Paul Drummond ,  Eric Lund ,  Kyle Jensen

Inventor： Chase Maxton ,  Paul Drummond ,  Eric Lund ,  Kyle Jensen

IPC: G01V3/38 ,  G01N31/00 ,  A01B79/00 ,  G01S17/89 ,  G01N21/31 ,  G01N21/3563

CPC classification number: A01B79/005 ,  A01C21/007 ,  G01N21/15 ,  G01N21/276 ,  G01N21/31 ,  G01N21/3563 ,  G01N21/359 ,  G01N2201/0625 ,  G01S17/89 ,  G01V8/02

Abstract: A soil mapping system for collecting and mapping soil reflectance data in a field includes an implement having a furrow opener for creating a furrow and an optical module. The optical module is arranged to collect soil reflectance data at a predetermined depth within the furrow as the implement traverses a field. The optical module includes two monochromatic light sources, a window arranged to press against the soil, and a photodiode for receiving light reflected back from the soil through the window. The two light sources have different wavelengths and are modulated at different frequencies. The photodiode provides a modulated voltage output signal that contains reflectance data from both of the light sources. Additional measurement devices are carried by the implement for collecting additional soil property data, such as electrical conductivity, pH, and elevation, which can be used together with the optical data to determine variations in soil organic matter.

公开(公告)号：US20110106451A1

公开(公告)日：2011-05-05

申请号：US12612375

申请日：2009-11-04

Applicant: Colin Christy ,  Paul Drummond ,  Giyoung Kweon ,  Chase Maxton ,  Kenton Dreiling ,  Kyle Jensen ,  Eric Lund

Inventor： Colin Christy ,  Paul Drummond ,  Giyoung Kweon ,  Chase Maxton ,  Kenton Dreiling ,  Kyle Jensen ,  Eric Lund

IPC: G01V3/38

CPC classification number: G01V11/00 ,  G01N21/3563 ,  G01N21/359 ,  G01N21/8507

Abstract: A multi-sensor system rapidly measures diffuse reflectance of soil, soil conductivity, and other soil properties in situ, in three dimensions. The system includes a tractor-drawn implement containing a sensor shank used for X-Y axis measurements, a hydraulic probe implement containing a sensor probe for −Z axis measurements, and a set of visible and near-infrared spectrometers, controls, and firmware that are shared by each implement. Both implements include optical sensors and soil electrical conductivity sensors. The probe implement incorporates a sensor that measures insertion force, and the shank implement includes a soil temperature sensor. These combinations of sensors are used to calibrate the system and to characterize the soil properties within a field or area. Geo-referenced soil measurements are collected with the shank implement to identify optimal locations for conducting sensor probe insertions. The probe implement is then used for sensor probing and for collecting soil core samples for lab analysis.

Abstract translation: 多传感器系统在三维方面快速测量土壤，土壤电导率和其他土壤性质的漫反射。 该系统包括一个拖拉机牵引工具，其中包含用于XY轴测量的传感器柄，包含用于-Z轴测量的传感器探头的液压探头工具以及共享的一组可见光和近红外光谱仪，控制和固件 由每个工具。 两种工具都包括光学传感器和土壤电导率传感器。 探头工具包括测量插入力的传感器，并且柄部件包括土壤温度传感器。 传感器的这些组合用于校准系统和表征场或区域内的土壤性质。 采用柄部工具收集地质参考土壤测量，以确定传感器探针插入的最佳位置。 然后将探头工具用于传感器探测和收集土壤样品进行实验室分析。

公开(公告)号：US07603239B2

公开(公告)日：2009-10-13

申请号：US11123399

申请日：2005-05-05

Applicant: Gregory Stephanopoulos ,  Christopher R. Loose ,  Kyle Jensen

Inventor： Gregory Stephanopoulos ,  Christopher R. Loose ,  Kyle Jensen

IPC: G06F19/00

CPC classification number: C07K1/00 ,  G06F19/22 ,  G06F19/24

Abstract: Antimicrobial peptides are small proteins used by the innate immune system to combat bacterial infection in multicellular eukaryotes. There is mounting evidence that these peptides are less susceptible to bacterial resistance than traditional antibiotics and that they may form the basis for a novel class of therapeutics. Systems and methods may treat the amino acid sequences of these peptides as a formal language and build a set of right-linear grammars that describe this language. These grammars may allow for rationally designed novel antimicrobial peptides in silico. These peptides conform to the syntax of natural antimicrobial peptides lack significant homology to any natural sequences, thus populating a previously unexplored region of protein sequence space. Synthesis of these peptides, leads to de novo AmPs.

Abstract translation: 抗微生物肽是先天免疫系统用于防治多细胞真核生物细菌感染的小蛋白质。 有越来越多的证据表明，这些肽比传统抗生素对细菌耐药性较不敏感，并且它们可能形成新型治疗剂的基础。 系统和方法可以将这些肽的氨基酸序列视为形式语言，并构建描述此语言的一组右线性语法。 这些语法可以允许合理设计的新型抗微生物肽。 这些肽符合天然抗微生物肽的语法，与任何天然序列缺乏显着的同源性，从而填充了以前未探索的蛋白质序列空间区域。 这些肽的合成，导致从头AmPs。

公开(公告)号：US20050230307A1

公开(公告)日：2005-10-20

申请号：US11061394

申请日：2005-02-18

Applicant: Kyle Jensen

Inventor： Kyle Jensen

IPC: C02F1/32 ,  A01N53/00 ,  A01N59/00 ,  A01N63/00 ,  C02F1/34 ,  C02F1/50 ,  C02F1/78 ,  C02F3/32 ,  C02F3/34 ,  C02F9/00

CPC classification number: C02F3/32 ,  C02F1/32 ,  C02F1/50 ,  C02F1/78 ,  C02F3/327 ,  C02F2201/78 ,  C02F2303/04 ,  C02F2303/18 ,  Y02W10/18 ,  Y02W10/37

Abstract: Periphyton filtration is a known method for performing bioremediation of polluted water, removing nutrients from the influent on which the attached algae thrive. The present system improves upon this method by establishing a water-treatment facility for adding a strong oxidizer to the influent, and, in some cases, to the effluent, to make organically bound nutrients available to a target culture of periphyton or aquatic plants to reduce the population of undesirable microinvertebrates, to make organically bound nutrients available to the periphyton, and to reduce the level of toxic compounds. A particular embodiment comprises ozonating the water. A pesticide may be added to control insect populations.

Abstract translation: Periphyton过滤是一种已知的方法，用于对污染水进行生物修复，从附着的藻类繁殖的流入物中去除营养物质。 本系统通过建立一种用于向流入物中添加强氧化剂的水处理设备，并且在某些情况下，对流出物进行有机结合的营养物，以便可用于周围水体或水生植物的目标培养物以减少 不合需要的微无脊椎动物的群体，使有机结合的营养物质可用于周围环境，并降低有毒化合物的含量。 特定的实施方案包括使水臭氧化。 可以添加农药来控制昆虫种群。