59 results about "Cycle threshold" patented technology

The invention discloses a method for detecting lncRNA in plasma. Through steps of TrizolLS pretreatment of theplasma, chloroform and isoamyl alcohol mixed liquid extraction, isopropanol precipitation, ethanol washing, RNA RT (reverse transcription), PCR (polymerase chain reaction) detection and the like, a TrizolLSreagentcan well remove impurities such as polysaccharide, mucoprotein and the like in blood, RNA degradation is less, the phenomenon thattrichloromethane is easy to emulsify under the TrizolLS strong acid condition is effectively eliminated by a chloroform and isoamyl alcohol mixed liquid, high-quality and high-content extraction of RNA in the plasma is realized, fluorescence quantitative RT-PCR detection is performed on the quality of lncRNA, and meanwhile, a reference Ct (cycle threshold) value of the total RNA (that is, cDNA) mass can be detected.

An apparatus, system, and method are disclosed for migrating wear spots in solid-state drives. A count module counts lifetime write cycles for logical units of a plurality of solid-state memories. Each logical unit has a logical address. An identification module identifies a wear spot on a first logical unit of a first solid-state memory if a count for the first logical unit exceeds a cycle threshold. A migration module dynamically migrates data of the first logical unit to a second solid-state memory, wherein the data is continuously available at an original logical address.

Processes and methods for the simultaneous quantification of nucleic acids in diseased cells that are based on real-time PCR are provided. The real-time PCR protocol is an excellent tool for reliable quantification of in vitro drug screening and evaluation protocols to determine the efficacy of potential anti-viral agents. Quantification using these simultaneous PCR cycle threshold (Ct) detection techniques during one-step real-time RT-PCR (Applied Biosystems, CA) eliminates the variability resulting from quantification of end-point RT-PCR products. In addition, the mitochondrial toxicity assay is an added tool to assess potential side-effects for these chemotherapeutic agents.

Systems and methods for determining characteristic transition values such as elbow values in sigmoid or growth-type curves, such as the cycle threshold (Ct) value in PCR amplification curves. A double sigmoid function with parameters determined by a Levenberg-Marquardt (LM) regression process is used to find an approximation to a curve that fits a PCR dataset. Once the parameters have been determined, the curve can be normalized using one or more of the determined parameters. Normalization is advantageous for determining the Ct value if one chooses the arbitrary fluorescence level (AFL) approach to calculating Ct values for amplification curves. After normalization, the normalized curve is processed by applying a root-finding algorithm to determine the root of the function representing the normalized curve, which root corresponds to the Ct value. The Ct value is then returned and may be displayed or otherwise used for further processing.

Systems and methods for determining the elbow or Ct value in a real-time, or kinetic, PCR amplification curve data set. The PCR data set may be visualized in a two-dimensional plot of fluorescence intensity (y-axis) vs. cycle number (x-axis). The data set is transformed to produce a partition table of data points with one column including the fluorescence at cycle (n) and a second column including the fluorescence at cycle (n+i), where i is typically 1 or greater. A cluster analysis process is applied to the partition table data set to determine a plurality of clusters in the partition table data set. In one aspect, the clustering process used includes a k-means clustering algorithm, where k≧3. The data point representing the elbow or Ct value of the PCR curve is identified as an end point of one of the identified clusters, and the cycle number corresponding to this data point is returned or displayed.

Systems and methods for determining characteristic transition values such as elbow values in sigmoid or growth-type curves, such as the cycle threshold (Ct) value in PCR amplification curves. A double sigmoid function with parameters determined by a Levenberg-Marquardt (LM) regression process is used to find an approximation to a curve that fits a PCR dataset. Once the parameters have been determined, the curve can be normalized using one or more of the determined parameters. After normalization, the normalized curve is processed to determine the curvature of the curve at some or all points along the curve, e.g., to produce a dataset or plot representing the curvature v. the cycle number. The cycle number at which the maximum curvature occurs corresponds to the Ct value. The Ct value is then returned and may be displayed or otherwise used for further processing.

Described herein are methods and kits for detecting the presence or absence of gene dysregulations such as those arising from gene fusions and / or chromosomal abnormalities, e.g. translocations, insertions, inversions and deletions. The methods, compositions and kits are useful for detecting mutations that cause the differential expression of a 5′ portion of a target gene relative to the 3′ region of the target gene. The average expression of the 5′ portion of the target gene is compared with the average expression of the 3′ portion of the target gene to determine an intragenic differential expression (IDE). The IDE can then be used to determine if a dysregulation or a particular disease (or susceptibility to a disease) is present or absent in a subject or sample.

The influence of transgenic crops on rhizospheric microorganisms in soil is an important aspect in environmental biosafety research. The invention establishes a detection system of Real-Time QPCR (Real-Time Fluorescent Quantitative Polymerase Chain Reaction)) by carrying out absolute quantification on the quantity of pseudomonas fluorescens in rhizospheric soil during the growth period of transgenic disease-resistant wheat. By virtue of application of the reaction system, the absolute quantification is carried out on the copy number of the pseudomonas fluorescens in the rhizospheric soil during the whole growth period of the transgenic wheat. A result shows that the designed primer has better specificity; the intervals of cycle thresholds (Ct values) of plasmids with various gradient standards in an amplification curve of Real-Time QPCR are uniform, the peak value of a melting curve is more obvious, and for the standard curve, the correlation coefficient R2 is equal to 0.99905, the slope is minus 3.203, and the amplification efficiency E is equal to 100%. In the seeding stage, seedling establishment stage, watery stage and mature stage of the transgenic wheat, the quantity of the pseudomonas fluorescens in the rhizospheric soil takes on a trend of gradually rising.

The invention provides a composition for detecting gastric cancer, wherein the composition comprises: 1) a nucleic acid for detecting a methylation state in at least one region of a target gene, wherein the target gene is selected from an SEPT9 gene or fragments thereof and / or an RNF180 gene or fragments thereof; 2) an agent for detecting a concentration of an MG7 antigen in serum / plasma; the gastric cancer is detected by the methylation state of the target gene and a protein expression level of the target gene. The invention further provides a kit comprising the composition and a method for detecting the gastric cancer in vitro. Therefore, a method for analyzing DNA in a plasma sample by real-time PCR in the invention can conveniently detect the SEPT9 gene or the fragments thereof and / orthe RNF180 gene or the fragments thereof, and can rapidly and conveniently judge whether the sample is positive or not according to a cycle threshold (Ct) of the real-time PCR; further, the inventionprovides an accurate in-vitro detection method for detecting the concentration of the MG7 antigen in the serum / plasma of the sample to be detected.

Systems and methods for determining characteristic transition values such as elbow values in sigmoid or growth-type curves, such as the cycle threshold (Ct) value in PCR amplification curves. A double sigmoid function with parameters determined by a Levenberg-Marquardt (LM) regression process is used to find an approximation to a curve that fits a PCR dataset. Once the parameters have been determined, the curve can be normalized using one or more of the determined parameters. After normalization, the normalized curve is processed to determine the curvature of the curve at some or all points along the curve, e.g., to produce a dataset or plot representing the curvature v. the cycle number. The cycle number at which the maximum curvature occurs corresponds to the Ct value. The Ct value is then returned and may be displayed or otherwise used for further processing.

Systems and methods for determining the cycle threshold (Ct) value in a kinetic PCR amplification curve. The PCR data set may be visualized in a two-dimensional plot of fluorescence intensity (y-axis) vs. cycle number (x-axis). The data set is transformed to produce a partition table of data points with one column including the fluorescence at cycle (n) and a second column including the fluorescence at cycle (n+i), where i is typically 1 or greater. A cluster analysis process is applied to the partition table data set to determine a plurality of clusters in the partition table data set. In one aspect, the clustering process used includes a k-means clustering algorithm, where the number of identified clusters, k, is greater than or equal to three. In another aspect, a Partitioning Around Medoids (PAM) algorithm is used to identify three or more clusters. Using the identified clusters, a linear slope of each of the clusters is determined based on y(n+1) vs. n, and for each cluster, a ratio of the slope of that cluster with the slope of an adjacent cluster is determined. The ratios are then compared. An end point of a cluster having the largest or smallest ratio represents a specific point of interest in the data curve. The data point representing the elbow or Ct value of the PCR curve is identified as an end point of one of the identified clusters, and the cycle number corresponding to this data point is returned or displayed.

Methods, systems and / or apparatus for slowing a patient's breathing by using positive pressure therapy. In certain embodiments, a current interim breathing rate target is set, and periodically the magnitude of a variable pressure waveform that is scaled to the current interim breathing rate target is increased if the patient's breathing rate is greater than the interim breathing rate target in order to lengthen the patient's breath duration. The magnitude of the pressure increase may be a function of the difference between the interim breathing rate target and the patient's breathing rate. The interim breathing rate target may be periodically reduced in response to the patient's breathing rate slowing down toward the current interim breathing rate target. The variable pressure waveform cycles from an inhalation phase to an exhalation phase when the patient airflow decreases to a cycle threshold, the cycle threshold being a function of flow versus time within a breath and generally increasing with time. Different interim breathing rate targets have different cycle threshold functions, and the cycle threshold functions allow easier cycling as the interim breathing rate targets decrease. Similarly, the variable pressure waveform triggers from an exhalation phase to an inhalation phase when the patient airflow increases to a trigger threshold, the trigger threshold being a function of flow versus time within a breath and generally decreasing with time. Different interim breathing rate targets have different trigger threshold functions, and the trigger threshold functions allow easier triggering as the interim breathing rate targets decrease.

The invention discloses a method and a kit for detecting genotypes of a herpes simplex virus (HSV). Primer probes designed on the basis of HSV DNA polymerase gene are adopted, type 1 and type 2 of the HSV are detected simultaneously in a single tube by TaqMan probe dual-wavelength fluorescent PCR technology, and the existence and the type of the HSV in a sample are judged through fluorescent signals and circulating threshold values of amplification templates with different wavelengths. In the kit, a manually constructed internal reference system is used for avoiding false negative of a detection result. The kit comprises nucleic acid extracting solution, PCR buffer solution, Taq enzyme, an internal reference, negative control and positive control; and two steps of sample treatment and amplification detection are adopted. The kit is easy and convenient to operate and high in sensitivity, can avoid false positive caused by PCR product nucleic acid pollution, can solve the problem of false negative caused by a PCR inhibitor in the sample, and can be widely applied to quick detection of the genotypes of the pathogen clinically.

Systems and methods for determining the elbow or Ct value in a real-time, or kinetic, PCR amplification curve data set. The PCR data set may be visualized in a two-dimensional plot of fluorescence intensity vs. cycle number. A rotation transform is applied to the data set to rotate the data about a defined coordinate such as the origin so that the data point representing the Ct value becomes a minimum or a maximum along the intensity axis. The data point representing the elbow or Ct value of the PCR curve is identified, and this data point is then rotated back and the cycle number of the data point is returned or displayed.

A single technique for determining Ct is provided that can be used for standard sigmoidal growth curves and for problematic growth curves, such as parabolic curves. The Ct value can be determined as the intersection of a line tangent to the growth curve at the maximum of the second derivative with a baseline of the growth curve. Such a Ct value is usable for sigmoidal curves and parabolic curves, and can provide linear calibration curves to achieve accuracy in determining initial concentrations of a sample.