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At least 325 records · Page 18Linked to original sources

AutoDimer: a screening tool for primer-dimer and hairpin structures.

The ability to select short DNA oligonucleotide sequences capable of binding solely to their intended target is of great importance in developing nucleic acid based detection technologies. Applications such as multiplex PCR rely on primers binding to unique regions in a genome. Competing side reactions with other primer pairs or template DNA decrease PCR efficiency: Freely available primer design software such as Primer3 screens for potential hairpin and primer-dimer interactions while selecting a single primer pair. The development of multiplex PCR assays (in the range of 5 to 20 loci) requires the screening of all primer pairs for potential cross-reactivity. However, a logistical problem results due to the number of total number of comparisons required. Comparing the primer set for a 10-plex assay (20 total primer sequences) results in 210 primer-primer combinations that must be screened. The ability to screen sets of candidate oligomers rapidly for potential cross-reactivity reduces overall assay devlelopment time. Here we report the application of a familiar sliding algorithm for comparing two strands of DNA in an overlapping fashion. The algorithm has been employed in a software package wherein the user can compare multiple sequences in a single computational run. After the screening is completed, a score is assigned to potential duplex interactions exceeding a user-defined threshold. Additional criteria of predicted melting temperature (Tm) and free energy of melting (deltaG) are included for further ranking. Sodium counterion and total stand concentrations can be adjusted for the Tm and deltaG calculations. The predicted interactions are saved in a text file for further evaluation.

Algorithms↗

Limitations and practical procedure in BclII-Ig heavy chain gene rearrangement real-time quantitative polymerase chain reaction.

Follicular lymphoma is characterized by the t(14;18)(q32;q21) translocation, which juxtaposes Ig heavy chain gene (IgH) sequences with the BclII gene. Several publications have highlighted the importance of molecular follow-up in follicular lymphoma, demonstrating that the detection of cells bearing the BclII-IgH rearrangement by real-time quantitative polymerase chain reaction (RQ-PCR) can anticipate a clinical relapse. In this context, we developed a BclII-IgH RQ-PCR. We began with SYBR Green I detection technology but observed that this system does not allow an accurate measurement of the tumor load when working with genomic DNA. While we were designing the assay using Taqman technology, Moppett et al (Moppett J, van der Velden VHJ, Wijkhuijs AJM, Hancock J, van Dongen JJM, Goulden N: Inhibition affecting RQ-PCR-based assessment of minimal residual disease in acute lymphoblastic leukemia: reversal by addition of bovine serum albumin. Leukemia 2003, 17:268-270) reported PCR inhibition problems in around 15% of blood and bone marrow samples, affecting the DNA quantification and thus the assessment of minimal residual disease. They demonstrated that this PCR inhibition could be partially resolved by adding nonacetylated bovine serum albumin. In our studies, we observed the same phenomenon in a single follicular lymphoma case and extended our study to other available cases. As a result, we suggest a new RQ-PCR procedure that is based on Taqman probe technology and that takes into account the PCR inhibition problems, making this assay more reliable in a routine molecular laboratory.

Aged↗

[Detection of bcr/abl fusion gene from K562 cell line and mononuclear cells of CML patients by DNA-PCR].

OBJECTIVE: To detect bcr/abl fusion gene at DNA level in K562 cell line and mononuclear cells from patients with chronic myelogenous leukemia (CML). METHODS: Based on previous research, a set of DNA-PCR primers was redesigned. DNA from K562 cells and mononuclear cells of CML patients was extracted respectively. After DNA-PCR for bcr/abl fusion gene the amplified fragments were then sequenced. RESULT: At DNA level the bcr/abl fusion gene in K562 cells and mononuclear cells of 2 CML patients was amplified. Furthermore, the DNA breakpoint of fusion gene in the above samples through sequencing of amplified fragments was localized. CONCLUSION: DNA-PCR offers a new detection technology for bcr/abl fusion without the expression of fusion gene.

Fusion Proteins, bcr-abl↗

Review of the U.S. Army's health risk assessments for oral exposure to six chemical-warfare agents. Introduction.

The U.S. Army is under a congressional mandate and the Chemical Weapons Convention of January 1993 to destroy its entire stockpile of chemical munitions. In addition to stockpiled munitions, nonstockpile chemical materiel (NSCM) has been identified for destruction. NSCM includes a host of lethal wastes from past disposal efforts, unserviceable munitions, chemically contaminated containers, chemical-production facilities, newly located chemical munitions, known sites containing substantial quantities of buried chemical weapons and wastes, and binary weapons and components. There are eight stockpile sites located in the continental United States and one on an island in the Pacific Ocean, and 82 NSCM locations have been identified. There are concerns, based on storage and past disposal practices, about soil and groundwater contamination at those sites. Six of the most commonly found chemical-warfare agents at stockpile and NSCM sites are the nerve agents GA, GB, GD, and VX and the vesicating (blistering) agents sulfur mustard and lewisite. To ensure that chemical contamination is reduced to safe concentrations at stockpile and NSCM sites before they are used for residential, occupational, or wildlife purposes, the U.S. Army requested that health-based exposure limits for GA, GB, GD, VX, sulfur mustard, and lewisite be developed to protect the public and the environment. Oak Ridge National Laboratory (ORNL) was asked to conduct the health risk assessments and propose chronic oral reference doses (RfDs) and, where appropriate, oral slope factors (SFs) for the six agents. RfDs are toxicological values developed for noncancer effects and used as reference points to limit human oral exposure to potentially hazardous concentrations of chemicals thought to have thresholds for their effects. RfDs are estimates (with uncertainty spanning an order of magnitude or greater) of daily oral chemical exposures that are unlikely to have deleterious effects during a human lifetime. For chemicals identified as carcinogens (e.g., sulfur mustard), SFs are also calculated. SFs are estimates of upper-bound lifetime cancer risk from chronic exposure to an agent. The Army's Surgeon General adopted the proposed RfDs and SFs developed by ORNL as interim values to ensure that consistent health-based criteria were applied in ongoing initiatives requiring decisions on the safety of contaminated sites. The Army's Surgeon General also requested that the National Research Council (NRC) independently review the scientific validity of these values. The NRC assigned this task to the Committee on Toxicology (COT), and a multidisciplinary subcommittee of experts was convened to assess the scientific validity of the interim RfDs developed for GA, GB, GD, VX, sulfur mustard, and lewisite and the SF developed for sulfur mustard. Specifically, the subcommittee was asked to (1) determine whether all the relevant toxicity data were considered appropriately; (2) review the uncertainty, variability, and quality of the data; (3) determine the appropriateness of the assumptions used to derive the RfDs (e.g., the application of uncertainty factors); and (4) identify data gaps and make recommendations for future research. Although multiple agents are present at stockpile and NSCM sites, the subcommittee was asked to evaluate the agents only on an individual basis. Furthermore, although the most likely routes of exposure to chemical-warfare agents at these sites are the inhalation and dermal routes, the subcommittee was only asked to evaluate toxicological risk from the oral route at this time. The Army is in the process of developing inhalation exposure guidelines. The subcommittee was also not asked to address issues related to risk management, such as technology, detection, and feasibility.

Administration, Oral↗

Renal cell carcinoma: presentation, staging, and surgical treatment.

The widespread availability of abdominal ultrasound, magnetic resonance imaging (MRI), and computed tomography (CT) scanning has increased the diagnosis of incidental renal tumors, which now comprise the vast majority of the new cases diagnosed each year. With the detection of renal tumors at an earlier stage, partial nephrectomy and nephron-sparing surgery have evolved as effective alternatives to radical nephrectomy. The poor prognostic findings of involved regional lymph nodes or ipsilateral adrenal metastases has led to more selective operations on those sites in the face of incidental tumor detection. Technological advances have allowed for the development by committed surgical investigators of techniques of laparoscopic and laparoscopically assisted nephrectomy. Although not widely employed, further improvements in technology may widen the appeal of these approaches to selected renal tumors. Advances in cardiovascular surgical techniques have made resection of renal cell carcinoma (RCC) with tumor thrombi involving the inferior vena cava (IVC) possible, although this approach is still associated with significant perioperative mortality depending on the degree of caval involvement. In highly selected cases, resection of limited metastatic disease is recommended, particularly if the disease-free interval is greater than 12 months and there is a only a single site of metastatic disease. Whether metastectomy is therapeutic or fits within the realm of the often long and unpredictable natural history of RCC is not known. Strategies for follow-up are based primarily on the pathologic stage of the operated tumor. Small incidental tumors have an excellent prognosis and require little in the way of postoperative imaging. As the pathologic stage increases, the likelihood of developing metastatic disease increases, necessitating biannual chest x-ray in addition to history and physical examination. Symptom-directed bone scans and CT scans are effective in identifying most recurrences in patients with large, poorly differentiated tumors. Patients requiring specialized follow-up programs include those treated by partial nephrectomy, and those with end-stage renal disease, acquired cystic disease of the kidney, or von Hippel-Lindau (VHL) disease.

Adrenalectomy↗

Nanobeads as a solid phase in a solute homogeneous assay format.

The measurement of numerous samples as in drug screening or diagnostics has been improved significantly over recent years. The processing of a great number of carriers with 96, 384 or 1536 wells is not the limiting step anymore and more than 100,000 samples can be analyzed within 24 h. New challenges arise in optimizing data quality and assay volume in order to gain more reliable results with a reduced consumption of assay reagents. Both are addressed with an approach using dispersed nanoparticles analyzed by a new detection technology, fluorescence intensity distribution analysis. This homogeneous assay is a generic format holding great potential in expanding the assay strategy portfolio for diagnostic and screening applications.

Automation↗

Enabling high-throughput discovery.

During the past few years, the introduction of ultra-high-throughput screening and new assay design and detection technologies has exponentially increased the amount and complexity of screening data. Effective use of this data implies a process that begins with assay design. An effective data management system should control a range of processes, from the initial selection of compounds and storage and mining of the assay result to more complex tasks, such as extracting patterns from these data. Remarkable advances have been made during the last year to increase efficiency at different phases of the screening, shifting the bottleneck of this process to data analysis. The challenge facing drug discovery today is to extract knowledge from these data. Knowledge discovery is defined as 'the non-trivial extraction of implicit, unknown, and potentially useful information from data'. A large amount of research is being devoted to optimize the extraction of knowledge from screening data. In this review, we discuss the screening process and its progress during the last year. Some of the challenges for the future, such as optimization of the knowledge discovery process and the sharing of data across an organization, will also be presented.

Databases, Factual↗

[Cystic fibrosis from the exocrine pancreatic point of view].

Cystic fibrosis (CF) is the most common life-limiting autosomal recessive genetic disorder in Caucasians and is characterized by a wide variability of clinical expression. The vast majority of patients with CF have pancreatic insufficiency (PI) requiring exogenous pancreatic enzyme replacement therapy with meals. It is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which encodes a protein that functions as a chloride channel and is regulated by cAMP. CFTR gene mutations may be classified as severe or mild with respect to pancreatic function status. Patients homozygous for two severe mutations experience severe clinical presentation including PI. Patients carrying at least one mild mutation are considered to be pancreatic sufficient (PS) and carry an overall prognosis that is vastly superior to CF patients with PI. Thus mild mutations appear to be dominant, providing enough functional CFTR to avoid PI. Five general mechanisms have been proposed which describe how CFTR gene mutations influence CFTR-mediated chloride secretion. Classes 1, 2, and 3. that confer little or no chloride channel function, confer the PI phenotype. In contrast, classes 4 and 5 allow CFTR residual function, that are expected to confer the less severe PS phenotype. Recent advances in mutation detection technology and the demonstration of characteristic abnormalities in trans-epithelial potential difference measurements, have expanded the spectrum of diseases associated with the CFTR mutant genes, and paradoxically, in some ways complicated rather than simplified CF diagnosis. Until new diagnostic criteria is conclusively determined, CF diagnosis should be made on clinical rather than laboratory grounds.

Cystic Fibrosis↗

[Single nucleotide polymorphism and its use in chicken QTL mapping].

Single nucleotide polymorphism (SNP) refers to the change of single nucleotide in DNA sequence. Because of its high density in genomes and easy in detection and analysis statistically,SNP can be used in genetic linkage map construction and QTL mapping.Here,the characters and detecting technology of SNP,as well as the status and foreground of the use of candidate gene SNP in chicken QTL mapping are introduced.

English Abstract↗

[Fetal ECG monitoring system based on MCU processing].

In order to monitor the fetus in labor, the signal characteristic from fetal scalp electrode is researched, An adaptation algorithm and a peak to peak detecting technology are adopted in signal processing, and an adaptation gain control method is used to eliminate disturber from base-line shift. A fetal ECG monitoring system is designed on the basis of C8051F020 MCU.

Adult↗

Intrauterine infections and birth defects.

Intrauterine infection is an important cause of some birth defects worldwide. The most common pathogens include rubella virus, cytomegaloviurs, ureaplasma urealyticum, toxoplasma, etc. General information about these pathogens in epidemiology, consequence of birth defects, and the possible mechanisms in the progress of birth defects, and the interventions to prevent or treat these pathogens' infections are described. The infections caused by rubella virus, cytomegaloviurs, ureaplasma urealyticum, toxoplasma, etc. are common, yet they are proved to be fatal during the pregnant period, especially during the first trimester. These infections may cause sterility, abortion, stillbirth, low birth weight, and affect multiple organs that may induce loss of hearing and vision, even fetal deformity and the long-term effects. These pathogens' infections may influence the microenvironment of placenta, including levels of enzymes and cytokines, and affect chondriosome that may induce the progress of birth defect. Early diagnosis of infections during pregnancy should be strengthened. There are still many things to be settled, such as the molecular mechanisms of birth defects, the effective vaccines to certain pathogens. Birth defect researches in terms of etiology and the development of applicable and sensitive pathogen detection technology and methods are imperative.

Animals↗

[Photoelectron decay time-resolved spectrum of AgCl crystals doped with K4Ru(CN)6 complex].

Microwave absorption and film dielectric spectrum detection technology was used to study the influence of complex K4Ru (CN)6 on the photoelectron decay time-resolved spectrum of cubic AgCl crystals illuminated in this paper. The results indicate that the influence of the doping content and doping position of the complex K4Ru(CN)6 on the photoelectron decay time-resolved spectrum is evident. The photoelectron decay process of this emulsion is slowest, and the photoelectron lifetime is longest when doped with K4Ru (CN)6 of 2.45 x 10(-5) mol x (mol Ag)(-1) at doping positions of 75% Ag.

Crystallization↗

[The design and applications of a non-invasive intelligent detector for cardiovascular functions].

An apparatus based on a high sensitive sensor which detects cardiovascular functions is introduced in this paper. Some intelligent detecting technologies, such as syntactic pattern recognition and a medical expert system are used in this detector. Its embedded single-chip microcomputer processes and analyzes pulse signals for gaining automatically the parameters about heart, blood vessel and blood etc., so as to get the health evaluation, correct medical diagnosis and prediction of cardiovascular diseases.

Algorithms↗

A comparison of costs and effectiveness of the BACTEC NR-730 system and a conventional method of blood culture.

Results and costs of the first six months experience with BACTEC NR-730 were compared with a series of blood cultures performed by the conventional method previously used. The newer technology detected the growth of 14.1% of significant isolates on the day of receipt of the specimens. The previous method lacked blind subcultures on the day of receipt and therefore detected growth only after overnight incubation. No direct comparison of the sensitivities of the methods was possible, but the percentages of cultures yielding significant isolates were similar for the two methods. With the new method, technicians needed less time for daily screening of blood cultures, fewer subcultures were required and less contamination was observed. The method used to calculate the directly-related variable costs of the two methods is set out. In the particular situation reported, workload and labor costs were such that introduction of BACTEC NR-730 resulted in a saving on variable costs.

Bacteria, Aerobic↗

Breast self-examination by young women: II. Characteristics associated with proficiency.

Studying a stratified random sample of university women (n = 869) we investigated the correlates of proficiency (i.e., the correctness or competence) of breast self-examination (BSE). A 19-item BSE quality index score was developed based on the recommended steps a woman should perform when doing the exam in the three BSE positions. A comprehensive set of independent variables including knowledge, attitudes and perceptions, personal characteristics, and environmental factors were studied. While proficiency scores for both undergraduates and graduates were relatively low, the mean score for graduates was significantly higher than for undergraduates. This study corroborates the few recent studies that indicate that frequency of performance is not highly correlated with proficiency (relationships were r = .14 and .04, respectively, for undergraduate and graduate women). Bivariate and multivariate regression analyses demonstrate that the relevance of such factors varies by age (undergraduate and graduate). Results of the regression model indicate that the skill knowledge variable regarding time of month BSE should be performed, awareness of BSE, perceived effect of cancer detection, and perceived benefit of BSE were predictors of more proficient practice for undergraduates. Knowledge of time of month to do BSE and mammogram as a detection technology and discussion of BSE with others were important for graduate women. The independent variables examined accounted for 22 percent and 30 percent of the variance, respectively, for undergraduate and graduate women.(ABSTRACT TRUNCATED AT 250 WORDS)

Adolescent↗

[Use of a diagnostic prospective algorithm for patients with recurrent miscarriage].

The application of a diagnostic algorithm to couples with recurrent pregnancy loss, was evaluated in this descriptive, prospective, clinical trial, at Infertility Clinic and Assisted Reproduction Unit, Instituto Nacional de Perinatología (INPer), México City. Fifty couples with primary or secondary recurrent pregnancy loss, were studied. A study protocol was applied to evaluate the following factors of miscarriage: anatomic, endocrine, infectious, genetic and immunologic. The frequency of altered factors was determined in the couples including in this trial. There were no cases of diabetes mellitus or impaired glucose tolerance in the studied group. The most common abnormal findings were: luteal phase defects; genital infections (Chlamydia trachomatis, Mycoplasma hominis, Ureaplasma urealyticum) and; an elevated frequency of chromosomal abnormalities. In addition, in 16% of the couples there was not an identified cause of their problem. The applied algorithm find the etiology of the recurrent pregnancy loss in the 84% of the couples studies. The method included new technologies (detection of anti-immunity, allo-immunity and infectious diseases), however, need corrections to increase its diagnostic and prognosis accuracy.

Abortion, Habitual↗

A rapid and quantitative DNA sex test: fluorescence-based PCR analysis of X-Y homologous gene amelogenin.

A rapid, simple and reliable sex test that entails PCR amplification of a segment of the X-Y homologous gene amelogenin has been developed. We used a single pair of primers spanning part of the first intron which generated 106-bp and 112-bp PCR products from the X and Y homologues, respectively, that can be analyzed simply by agarose gel electrophoresis. Less than 1 ng of template DNA is required for gender assignment, and the test has been automated by the fluorescent tagging of the PCR products that are then quantitated during electrophoresis by automated fluorescence-detection technology. Quantitation enables sex chromosome aneuploidy to be determined, and the amelogenin intron sequence can also be co-amplified with several highly polymorphic microsatellite loci, thereby providing a combined gender/identity DNA test.

Amelogenin↗