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Sample records for molecular diagnostic methods

  1. [New molecular methods in prenatal invasive diagnostics].

    PubMed

    Łaczmańska, Izabela; Stembalska, Agnieszka

    2013-10-01

    New diagnostic techniques employed in laboratories all over the world enable to create new tests for prenatal genetic diagnosis. They include cytogenetics, molecular-cytogenetics and molecular methods. Chromosomal numerical aberrations (aneuploidies) remain to be the most frequent genetic changes diagnosed prenatally Therefore, our paper presents the latest methods used mainly in prenatal diagnosis of the most common chromosome numerical changes, as well as other methods applicable in detecting chromosome structural changes or gene mutations. One of the main advantages of these new approaches is the short period of time needed to obtain a result. Some of these techniques are used world-wide: QF-PCR (Fluorescence Quantitive Polymerase Chain Reaction)--based on the analysis of the short polymorphic sequences characteristic for each individual; MLPA (Multiplex Ligation-dependent Probe Amplification)--based on the probes ligation to complementary genomic fragments in patient DNA; microarray CGH (Comparative Genomic Hybridization)--based on genomic hybridization to microarray, which enables analysis of the entire genome. Other new methods are also gradually introduced to invasive prenatal diagnosis: NGS (Next-generation DNA sequencing)--for the analysis of the whole genome at the DNA level; BoBs (BACS-on-Beads)--molecular-cytogenetic technique based on hybridization of probes immobilized on polystyrene microspheres with fetal DNA. Nowadays, rapid diagnosis of the most common chromosomal aneuploidies is not a standard procedure in Poland, as opposed to cytogenetics (karyotyping). However, for specific clinical indications, fast and reliable methods of genetic analysis present are likely to become standard procedures in prenatal diagnosis.

  2. Potentials and limitations of molecular diagnostic methods in food safety

    PubMed Central

    Mariani, Paola O.

    2008-01-01

    Molecular methods allow the detection of pathogen nucleic acids (DNA and RNA) and, therefore, the detection of contamination in food is carried out with high selectivity and rapidity. In the last 2 decades molecular methods have accompanied traditional diagnostic methods in routine pathogen detection, and might replace them in the upcoming future. In this review the implementation in diagnostics of four of the most used molecular techniques (PCR, NASBA, microarray, LDR) are described and compared, highlighting advantages and limitations of each of them. Drawbacks of molecular methods with regard to traditional ones and the difficulties encountered in pathogen detection from food or clinical specimen are also discussed. Moreover, criteria for the choice of the target sequence for a secure detection and classification of pathogens and possible developments in molecular diagnostics are also proposed. PMID:19067016

  3. Molecular Diagnostic Methods for Detection and Characterization of Human Noroviruses

    PubMed Central

    Chen, Haifeng; Hu, Yuan

    2016-01-01

    Human noroviruses are a group of viral agents that afflict people of all age groups. The viruses are now recognized as the most common causative agent of nonbacterial acute gastroenteritis and foodborne viral illness worldwide. However, they have been considered to play insignificant roles in the disease burden of acute gastroenteritis for the past decades until the recent advent of new and more sensitive molecular diagnostic methods. The availability and application of the molecular diagnostic methods have led to enhanced detection of noroviruses in clinical, food and environmental samples, significantly increasing the recognition of noroviruses as an etiologic agent of epidemic and sporadic acute gastroenteritis. This article aims to summarize recent efforts made for the development of molecular methods for the detection and characterization of human noroviruses. PMID:27335620

  4. Molecular and Nonmolecular Diagnostic Methods for Invasive Fungal Infections

    PubMed Central

    Arvanitis, Marios; Anagnostou, Theodora; Fuchs, Beth Burgwyn; Caliendo, Angela M.

    2014-01-01

    SUMMARY Invasive fungal infections constitute a serious threat to an ever-growing population of immunocompromised individuals and other individuals at risk. Traditional diagnostic methods, such as histopathology and culture, which are still considered the gold standards, have low sensitivity, which underscores the need for the development of new means of detecting fungal infectious agents. Indeed, novel serologic and molecular techniques have been developed and are currently under clinical evaluation. Tests like the galactomannan antigen test for aspergillosis and the β-glucan test for invasive Candida spp. and molds, as well as other antigen and antibody tests, for Cryptococcus spp., Pneumocystis spp., and dimorphic fungi, have already been established as important diagnostic approaches and are implemented in routine clinical practice. On the other hand, PCR and other molecular approaches, such as matrix-assisted laser desorption ionization (MALDI) and fluorescence in situ hybridization (FISH), have proved promising in clinical trials but still need to undergo standardization before their clinical use can become widespread. The purpose of this review is to highlight the different diagnostic approaches that are currently utilized or under development for invasive fungal infections and to identify their performance characteristics and the challenges associated with their use. PMID:24982319

  5. [CONTEMPORARY MOLECULAR-GENETIC METHODS USED FOR ETIOLOGIC DIAGNOSTICS OF SEPSIS].

    PubMed

    Gavrilov, S N; Skachkova, T S; Shipulina, O Yu; Savochkina, Yu A; Shipulin, G A; Maleev, V V

    2016-01-01

    Etiologic diagnostics of sepsis is one of the most difficult problems of contemporary medicine due to a wide variety of sepsis causative agents, many of which are components of normal human microflora. Disadvantages of contemporary "golden standard" of microbiologic diagnostics of sepsis etiology by seeding of blood for sterility are duration of cultivation, limitation in detection of non-cultivable forms of microorganisms, significant effect of preliminary empiric antibiotics therapy on results of the analysis. Methods of molecular diagnostics that are being actively developed and integrated during the last decade are deprived of these disadvantages. Main contemporary methods of molecular-biological diagnostics are examined in the review, actualdata on their diagnostic characteristic are provided. Special attention is given to methods of PCR-diagnostics, including novel Russian developments. Methods of nucleic acid hybridization and proteomic analysis are examined in comparative aspect. Evaluation of application and perspectives of development of methods of molecular diagnostics of sepsis is given.

  6. Molecular diagnostic methods for invasive fungal disease: the horizon draws nearer?

    PubMed

    Halliday, C L; Kidd, S E; Sorrell, T C; Chen, S C-A

    2015-04-01

    Rapid, accurate diagnostic laboratory tests are needed to improve clinical outcomes of invasive fungal disease (IFD). Traditional direct microscopy, culture and histological techniques constitute the 'gold standard' against which newer tests are judged. Molecular diagnostic methods, whether broad-range or fungal-specific, have great potential to enhance sensitivity and speed of IFD diagnosis, but have varying specificities. The use of PCR-based assays, DNA sequencing, and other molecular methods including those incorporating proteomic approaches such as matrix-assisted laser desorption ionisation-time of flight mass spectroscopy (MALDI-TOF MS) have shown promising results. These are used mainly to complement conventional methods since they require standardisation before widespread implementation can be recommended. None are incorporated into diagnostic criteria for defining IFD. Commercial assays may assist standardisation. This review provides an update of molecular-based diagnostic approaches applicable to biological specimens and fungal cultures in microbiology laboratories. We focus on the most common pathogens, Candida and Aspergillus, and the mucormycetes. The position of molecular-based approaches in the detection of azole and echinocandin antifungal resistance is also discussed.

  7. Why cannot a β-lactamase gene be detected using an efficient molecular diagnostic method?

    PubMed Central

    Park, Kwang Seung; Lee, Jung Hun; Park, Moonhee; Karim, Asad Mustafa; Lee, Sang Hee

    2016-01-01

    Objective: Fast detection of β-lactamase (bla) genes can minimize the spread of antibiotic resistance. Although several molecular diagnostic methods have been developed to detect limited bla gene types, these methods have significant limitations, such as their failure to detect almost all clinically available bla genes. We have evaluated a further refinement of our fast and accurate molecular method, developed to overcome these limitations, using clinical isolates. Methods: We have recently developed the efficient large-scale bla detection method (large-scaleblaFinder) that can detect bla gene types including almost all clinically available 1,352 bla genes with perfect specificity and sensitivity. Using this method, we have evaluated a further refinement of this method using clinical isolates provided by International Health Management Associates, Inc. (Schaumburg, Illinois, USA). Results were interpreted in a blinded manner by researchers who did not know any information on bla genes harbored by these isolates. Results: With only one exception, the large-scaleblaFinder detected all bla genes identified by the provider using microarray and multiplex PCR. In one of the Escherichia coli test isolates, a blaDHA-1 gene was detected using the multiplex PCR assay but it was not detected using the large-scaleblaFinder. Conclusion: The truncation of a blaDHA-1 gene is an important reason for an efficient molecular diagnostic method (large-scaleblaFinder) not to detect the bla gene. PMID:27882043

  8. Current status and future perspectives on molecular and serological methods in diagnostic mycology.

    PubMed

    Lau, Anna; Chen, Sharon; Sleiman, Sue; Sorrell, Tania

    2009-11-01

    Invasive fungal infections are an important cause of infectious morbidity. Nonculture-based methods are increasingly used for rapid, accurate diagnosis to improve patient outcomes. New and existing DNA amplification platforms have high sensitivity and specificity for direct detection and identification of fungi in clinical specimens. Since laboratories are increasingly reliant on DNA sequencing for fungal identification, measures to improve sequence interpretation should support validation of reference isolates and quality control in public gene repositories. Novel technologies (e.g., isothermal and PNA FISH methods), platforms enabling high-throughput analyses (e.g., DNA microarrays and Luminex xMAP) and/or commercial PCR assays warrant further evaluation for routine diagnostic use. Notwithstanding the advantages of molecular tests, serological assays remain clinically useful for patient management. The serum Aspergillus galactomannan test has been incorporated into diagnostic algorithms of invasive aspergillosis. Both the galactomannan and the serum beta-D-glucan test have value for diagnosing infection and monitoring therapeutic response.

  9. Combined Use of Cytogenetic and Molecular Methods in Prenatal Diagnostics of Chromosomal Abnormalities

    PubMed Central

    Stomornjak-Vukadin, Meliha; Kurtovic-Basic, Ilvana; Mehinovic, Lejla; Konjhodzic, Rijad

    2015-01-01

    Aim: The aim of prenatal diagnostics is to provide information of the genetic abnormalities of the fetus early enough for the termination of pregnancy to be possible. Chromosomal abnormalities can be detected in an unborn child through the use of cytogenetic, molecular- cytogenetic and molecular methods. In between them, central spot is still occupied by cytogenetic methods. In cases where use of such methods is not informative enough, one or more molecular cytogenetic methods can be used for further clarification. Combined use of the mentioned methods improves the quality of the final findings in the diagnostics of chromosomal abnormalities, with classical cytogenetic methods still occupying the central spot. Material and methods: Conducted research represent retrospective-prospective study of a four year period, from 2008 through 2011. In the period stated, 1319 karyotyping from amniotic fluid were conducted, along with 146 FISH analysis. Results: Karyotyping had detected 20 numerical and 18 structural aberrations in that period. Most common observed numerical aberration were Down syndrome (75%), Klinefelter syndrome (10%), Edwards syndrome, double Y syndrome and triploidy (5% each). Within observed structural aberrations more common were balanced chromosomal aberrations then non balanced ones. Most common balanced structural aberrations were as follows: reciprocal translocations (60%), Robertson translocations (13.3%), chromosomal inversions, duplications and balanced de novo chromosomal rearrangements (6.6% each). Conclusion: With non- balanced aberrations observed in the samples of amniotic fluid, non- balanced translocations, deletions and derived chromosomes were equally represented. Number of detected aneuploidies with FISH, prior to obtaining results with karyotyping, were 6. PMID:26005269

  10. [Molecular diagnostics in pathology].

    PubMed

    Stenzinger, A; Penzel, R; Endris, V; Weichert, W

    2013-05-01

    Tissue-based molecular diagnostics is a fast growing diagnostic field, which already complements morphologic classifications in many cases. Pathology based molecular diagnosis is performed almost exclusively on paraffin embedded material and always in conjunction with histopathology. Besides the classic field of tissue based detection of pathogenic organisms such as bacteria, viruses and fungi, molecular diagnostics of tumor tissue is one of the current hot topics in oncology. In this context the detection of predictive molecular biomarkers, such as specific mutations, allows patient stratification for individually tailored treatment strategies and thereby is one of the key components of individualized patient care in oncology. The rapidly growing number of clinically relevant predictive biomarkers together with impressive technical advances, specifically the development of massive parallel sequencing, will modify the care of patients with malignant diseases. Pathology, therefore, has returned in the very center of interdisciplinary patient care.

  11. [Molecular diagnostics in neuropathology].

    PubMed

    Dietmaier, W; Lorenz, J; Riemenschneider, M J

    2015-03-01

    As in only few other areas of oncology, molecular markers in neurooncology have become an integral part of clinical decision-making. This development is driven by a bustling scientific activity exploring the molecular basis and pathogenesis of human brain tumors. In addition, a high percentage of brain tumor patients are included in clinical studies in which molecular markers are assessed and linked with clinical informativeness. First steps towards more differentiated therapeutic strategies against brain tumors have thus been taken. The implementation in the clinical and diagnostic routine requires a detailed knowledge and a close collaboration between all medical disciplines involved.

  12. Molecular diagnostics of neurodegenerative disorders.

    PubMed

    Agrawal, Megha; Biswas, Abhijit

    2015-01-01

    Molecular diagnostics provide a powerful method to detect and diagnose various neurological diseases such as Alzheimer's and Parkinson's disease. The confirmation of such diagnosis allows early detection and subsequent medical counseling that help specific patients to undergo clinically important drug trials. This provides a medical pathway to have better insight of neurogenesis and eventual cure of the neurodegenerative diseases. In this short review, we present recent advances in molecular diagnostics especially biomarkers and imaging spectroscopy for neurological diseases. We describe advances made in Alzheimer's disease (AD), Parkinson's disease (PD), Amyotrophic lateral sclerosis (ALS) and Huntington's disease (HD), and finally present a perspective on the future directions to provide a framework for further developments and refinements of molecular diagnostics to combat neurodegenerative disorders.

  13. Molecular diagnostics and parasitic disease.

    PubMed

    Vasoo, Shawn; Pritt, Bobbi S

    2013-09-01

    Molecular parasitology represents an emerging field in microbiology diagnostics. Although most assays use nonstandardized, laboratory-developed methods, a few commercial systems have recently become available and are slowly being introduced into larger laboratories. In addition, a few methodologies show promise for use in field settings in which parasitic infections are endemic. This article reviews the available techniques and their applications to major parasitic diseases such as malaria, leishmaniasis, and trichomoniasis.

  14. Method for improved selectivity in photo-activation and detection of molecular diagnostic agents

    DOEpatents

    Wachter, Eric A.; Fisher, Walter G.; Dees, H. Craig

    1998-01-01

    A method for the imaging of a particular volume of plant or animal tissue, wherein the plant or animal tissue contains at least one photo-active molecular agent. The method includes the steps of treating the particular volume of the plant or animal tissue with light sufficient to promote a simultaneous two-photon excitation of the photo-active molecular agent contained in the particular volume of the plant or animal tissue, photo-activating at least one of the at least one photo-active molecular agent in the particular volume of the plant or animal tissue, thereby producing at least one photo-activated molecular agent, wherein the at least one photo-activated molecular agent emits energy, detecting the energy emitted by the at least one photo-activated molecular agent, and producing a detected energy signal which is characteristic of the particular volume of plant or animal tissue. The present invention is also a method for the imaging of a particular volume of material, wherein the material contains at least one photo-active molecular agent.

  15. Methods for improved selectivity in photo-activation and detection of molecular diagnostic agents

    DOEpatents

    Wachter, Eric A [Oak Ridge, TN; Fisher, Walter G [Knoxville, TN; Dees, H Craig [Knoxville, TN

    2008-03-18

    A method for the imaging of a particular volume of plant or animal tissue, wherein the plant or animal tissue contains at least one photo-active molecular agent. The method comprises the steps of treating the particular volume of the plant or animal tissue with light sufficient to promote a simultaneous two-photon excitation of the photo-active molecular agent contained in the particular volume of the plant or animal tissue, photo-activating at least one of the at least one photo-active molecular agent in the particular volume of the plant or animal tissue, thereby producing at least one photo-activated molecular agent, wherein the at least one photo-activated molecular agent emits energy, detecting the energy emitted by the at least one photo-activated molecular agent, and producing a detected energy signal which is characteristic of the particular volume of plant or animal tissue. The present invention also provides a method for the imaging of a particular volume of material, wherein the material contains at least one photo-active molecular agent.

  16. Method for improved selectivity in photo-activation and detection of molecular diagnostic agents

    DOEpatents

    Wachter, E.A.; Fisher, W.G.; Dees, H.C.

    1998-11-10

    A method for the imaging of a particular volume of plant or animal tissue, wherein the plant or animal tissue contains at least one photo-active molecular agent. The method includes the steps of treating the particular volume of the plant or animal tissue with light sufficient to promote a simultaneous two-photon excitation of the photo-active molecular agent contained in the particular volume of the plant or animal tissue, photo-activating at least one of the at least one photo-active molecular agent in the particular volume of the plant or animal tissue, thereby producing at least one photo-activated molecular agent, wherein the at least one photo-activated molecular agent emits energy, detecting the energy emitted by the at least one photo-activated molecular agent, and producing a detected energy signal which is characteristic of the particular volume of plant or animal tissue. The present invention is also a method for the imaging of a particular volume of material, wherein the material contains at least one photo-active molecular agent. 13 figs.

  17. Small business development for molecular diagnostics.

    PubMed

    Anagostou, Anthanasia; Liotta, Lance A

    2012-01-01

    Molecular profiling, which is the application of molecular diagnostics technology to tissue and blood -specimens, is an integral element in the new era of molecular medicine and individualized therapy. Molecular diagnostics is a fertile ground for small business development because it can generate products that meet immediate demands in the health-care sector: (a) Detection of disease risk, or early-stage disease, with a higher specificity and sensitivity compared to previous testing methods, and (b) "Companion diagnostics" for stratifying patients to receive a treatment choice optimized to their individual disease. This chapter reviews the promise and challenges of business development in this field. Guidelines are provided for the creation of a business model and the generation of a marketing plan around a candidate molecular diagnostic product. Steps to commercialization are outlined using existing molecular diagnostics companies as learning examples.

  18. Molecular methods for pathogen and microbial community detection and characterization: current and potential application in diagnostic microbiology.

    PubMed

    Sibley, Christopher D; Peirano, Gisele; Church, Deirdre L

    2012-04-01

    Clinical microbiology laboratories worldwide have historically relied on phenotypic methods (i.e., culture and biochemical tests) for detection, identification and characterization of virulence traits (e.g., antibiotic resistance genes, toxins) of human pathogens. However, limitations to implementation of molecular methods for human infectious diseases testing are being rapidly overcome allowing for the clinical evaluation and implementation of diverse technologies with expanding diagnostic capabilities. The advantages and limitation of molecular techniques including real-time polymerase chain reaction, partial or whole genome sequencing, molecular typing, microarrays, broad-range PCR and multiplexing will be discussed. Finally, terminal restriction fragment length polymorphism (T-RFLP) and deep sequencing are introduced as technologies at the clinical interface with the potential to dramatically enhance our ability to diagnose infectious diseases and better define the epidemiology and microbial ecology of a wide range of complex infections.

  19. Molecular IR Spectroscopy: New Trends and Methods of Noninvasive Diagnostics of Tissue IN VIVO

    NASA Astrophysics Data System (ADS)

    Afanasyeva, Natalia; Bruch, Reinhard

    1998-05-01

    Fiberoptic evanescent wave Fourier transform infrared (FEW-FTIR) spectroscopy using fiberoptic sensors operated in the attenuated total reflection (ATR) regime in the middle infrared (IR) region of the spectrum (850-1850 cm-1) has recently been applied to the diagnostics of tissues. The method is suitable for noninvasive and rapid (seconds) direct measurements of the spectra of normal and pathological tissues in vitro, ex vivo and in vivo. The aim of our studies is the express testing of various tumor tissues at the early stages of their development. The method is expected to be further developed for endoscopic and biopsy applications. We measured the normal skin and malignant tissues in vivo on the surface (directly on patients) in various cases of basaloma, melanoma and nevus. The experiments were performed in the operating room to measure the skin in the depth (under/in the layers of epidermis) of human breast, stomach, lung, and kidney tissues. The breast and skin tissues at different stages of tumor or cancer were distinguished very clearly in spectra of amide, side cyclic and noncyclic hydrogen bonded fragments of aminoacid residuals, phosphate groups and sugars. Computer monitoring is being developed for diagnostics.

  20. The use of digital PCR to improve the application of quantitative molecular diagnostic methods for tuberculosis.

    PubMed

    Devonshire, Alison S; O'Sullivan, Denise M; Honeyborne, Isobella; Jones, Gerwyn; Karczmarczyk, Maria; Pavšič, Jernej; Gutteridge, Alice; Milavec, Mojca; Mendoza, Pablo; Schimmel, Heinz; Van Heuverswyn, Fran; Gorton, Rebecca; Cirillo, Daniela Maria; Borroni, Emanuele; Harris, Kathryn; Barnard, Marinus; Heydenrych, Anthenette; Ndusilo, Norah; Wallis, Carole L; Pillay, Keshree; Barry, Thomas; Reddington, Kate; Richter, Elvira; Mozioğlu, Erkan; Akyürek, Sema; Yalçınkaya, Burhanettin; Akgoz, Muslum; Žel, Jana; Foy, Carole A; McHugh, Timothy D; Huggett, Jim F

    2016-08-03

    Real-time PCR (qPCR) based methods, such as the Xpert MTB/RIF, are increasingly being used to diagnose tuberculosis (TB). While qualitative methods are adequate for diagnosis, the therapeutic monitoring of TB patients requires quantitative methods currently performed using smear microscopy. The potential use of quantitative molecular measurements for therapeutic monitoring has been investigated but findings have been variable and inconclusive. The lack of an adequate reference method and reference materials is a barrier to understanding the source of such disagreement. Digital PCR (dPCR) offers the potential for an accurate method for quantification of specific DNA sequences in reference materials which can be used to evaluate quantitative molecular methods for TB treatment monitoring. To assess a novel approach for the development of quality assurance materials we used dPCR to quantify specific DNA sequences in a range of prototype reference materials and evaluated accuracy between different laboratories and instruments. The materials were then also used to evaluate the quantitative performance of qPCR and Xpert MTB/RIF in eight clinical testing laboratories. dPCR was found to provide results in good agreement with the other methods tested and to be highly reproducible between laboratories without calibration even when using different instruments. When the reference materials were analysed with qPCR and Xpert MTB/RIF by clinical laboratories, all laboratories were able to correctly rank the reference materials according to concentration, however there was a marked difference in the measured magnitude. TB is a disease where the quantification of the pathogen could lead to better patient management and qPCR methods offer the potential to rapidly perform such analysis. However, our findings suggest that when precisely characterised materials are used to evaluate qPCR methods, the measurement result variation is too high to determine whether molecular quantification

  1. Microfluidic technology for molecular diagnostics.

    PubMed

    Robinson, Tom; Dittrich, Petra S

    2013-01-01

    Molecular diagnostics have helped to improve the lives of millions of patients worldwide by allowing clinicians to diagnose patients earlier as well as providing better ongoing therapies. Point-of-care (POC) testing can bring these laboratory-based techniques to the patient in a home setting or to remote settings in the developing world. However, despite substantial progress in the field, there still remain many challenges. Progress in molecular diagnostics has benefitted greatly from microfluidic technology. This chapter aims to summarise the more recent advances in microfluidic-based molecular diagnostics. Sections include an introduction to microfluidic technology, the challenges of molecular diagnostics, how microfluidic advances are working to solve these issues, some alternative design approaches, and detection within these systems.

  2. [Molecular diagnostic methods of respiratory infections. Has the scheme diagnosis changed?].

    PubMed

    Vila Estapé, Jordi; Zboromyrska, Yuliya; Vergara Gómez, Andrea; Alejo Cancho, Izaskun; Rubio García, Elisa; Álvarez-Martínez, Miriam José; la Bellacasa Brugada, Jorge Puig de; Marcos Maeso, M Ángeles

    2016-07-01

    Lower respiratory tract infections remain one of the most common causes of mortality worldwide, which is why early diagnosis is crucial. Traditionally the microbiological diagnosis of these infections has been based on conventional methods including culture on artificial media for isolation of bacteria and fungi and cell cultures for virus and antibody or antigen detection using antigen-antibody reactions. The main drawback of the above mentioned methods is the time needed for an etiological diagnosis of the infection. The techniques based on molecular biology have drawn much attention in recent decades as tools for rapid diagnosis of infections. Some techniques are very expensive, especially those that can detect various microorganisms in the same reaction, therefore the question that arises is whether the cost of such testing is justified by the information obtained and by the clinical impact that its implementation will determine. In this article we make a review of the various techniques of molecular biology applied to the diagnosis of pneumonia and focus primarily on analysing the impact they may have on the management of patients with acute respiratory tract infections. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

  3. Conventional and molecular cytogenetic diagnostic methods in stem cell research: a concise review.

    PubMed

    Catalina, Purificación; Cobo, Fernando; Cortés, José L; Nieto, Ana I; Cabrera, Carmen; Montes, Rosa; Concha, Angel; Menendez, Pablo

    2007-09-01

    Regenerative medicine and cell therapy are emerging clinical disciplines in the field of stem cell biology. The most important sources for cell transplantation are human embryonic and adult stem cells. The future use of these human stem cell lines in humans requires a guarantee of exhaustive control with respect to quality control, safety and traceability. Genetic instability and chromosomal abnormalities represent a potential weakness in basic studies and future therapeutic applications based on these stem cell lines, and may explain, at least in part, their usual tumourigenic properties. So, the introduction of the cytogenetic programme in the determination of the chromosomal stability is a key point in the establishment of the stem cell lines. The aim of this review is to provide readers with an up-to-date overview of all the cytogenetic techniques, both conventional methods and molecular fluorescence methods, to be used in a stem cell bank or other stem cell research centres. Thus, it is crucial to optimize and validate their use in the determination of the chromosomal stability of these stem cell lines, and assess the advantages and limitations of these cutting-edge cytogenetic technologies.

  4. [Novel methods for dementia diagnostics].

    PubMed

    Wiltfang, J

    2015-04-01

    Novel diagnostic methods, such as cerebrospinal fluid-based neurochemical dementia diagnostics (CSF-NDD) and [18F] amyloid positron emission tomography (PET) are meanwhile recommended for specific indications by international guidelines for the improved early and differential diagnostics of multigenic (sporadic) Alzheimer's dementia (AD). In the case of CSF-NDD the German neuropsychiatric guidelines have already been validated on the S3 level of evidence (http://www.DGPPN.de) and the additional consideration of [18F] amyloid-PET in the current update of the guidelines is to be expected. By means of CSF-NDD and/or [18F] amyloid-PET a predictive diagnosis of incipient (preclinical) AD is also possible for patients at high risk for AD who are in prodromal stages, such as mild cognitive impairment (MCI). As accompanying (secondary) preventive therapy of AD cannot be offered a predictive molecular dementia diagnostics is not recommended by the German neuropsychiatric dementia guidelines (http://www.DGPPN.de). However, novel diagnostic approaches, which offer molecular positive diagnostics of AD have already gained high relevance in therapy research as they allow promising preventive treatment avenues to be validated directly in the clinical trial. Moreover, future blood-based dementia diagnostics by means of multiplex assays is becoming increasingly more feasible; however, so far corresponding proteomic or epigenetic assays could not be consistently validated in independent studies.

  5. [Molecular diagnostics in endocrine diseases].

    PubMed

    Berg, Jens P; Bjerknes, Robert

    2005-11-03

    Molecular diagnostic techniques provide an unsurpassed opportunity to understand the pathophysiological basis of endocrine disorders. Diseases have been associated with mutations in almost every gene known to have a role in either the production or secretion of a hormone or the mediators of hormone signalling. Even though most of these mutations are rare and account for only a small fraction of endocrine diseases, molecular diagnostics offers a valuable tool for the clinician in these cases. The most common endocrine disorders such as autoimmune thyroiditis, type 2 diabetes mellitus, osteoporosis, growth disorders, and obesity have all major genetic components, but these are mostly unknown. In this review the clinical implications of molecular diagnostics are illustrated for some endocrine diseases: congenital adrenal hyperplasia, congenital hypothyroidism, thyroid hormone resistance, familial hypocalciuric hypercalcaemia, growth hormone deficiency and resistance, and monogenic obesity. Improved diagnostic specificity has direct implications for treatment and follow up in these syndromes. Molecular diagnostics in endocrine tumours and diabetes are presented in two other articles in this series.

  6. Towards a rapid molecular diagnostic for melioidosis: comparison of DNA extraction methods from clinical specimens

    PubMed Central

    Richardson, Leisha J; Kaestli, Mirjam; Mayo, Mark; Bowers, Jolene R; Tuanyok, Apichai; Schupp, Jim; Engelthaler, David; Wagner, David M; Keim, Paul S; Currie, Bart J

    2011-01-01

    Optimising DNA extraction from clinical samples for Burkholderia pseudomallei Type III secretion system real-time PCR in suspected melioidosis patients confirmed that urine and sputum are useful diagnostic samples. Direct testing on blood remains problematic; testing DNA extracted from plasma was superior to DNA from whole blood or buffy coat. PMID:22108495

  7. Proteomics, nanotechnology and molecular diagnostics.

    PubMed

    Johnson, Christopher J; Zhukovsky, Nikolay; Cass, Anthony E G; Nagy, Judit M

    2008-02-01

    Sequencing of the human genome opened the way to the exploration of the proteome and this has lead to the identification of large numbers of proteins in complex biological samples. The identification of diagnostic patterns in samples taken from patients to aid diagnosis is in the early stages of development. The solution to many of the technical challenges in proteomics and protein based molecular diagnostics will be found in new applications of nanomaterials. This review describes some of the physical and chemical principles underlying nanomaterials and devices and outlines how they can be used in proteomics; developments which are establishing nanoproteomics as a new field. Nanoproteomics will provide the platform for the discovery of next generation biomarkers. The field of molecular diagnostics will then come of age.

  8. Molecular method for the detection of Andes hantavirus infection: validation for clinical diagnostics

    PubMed Central

    Vial, Cecilia; Martinez-Valdebenito, Constanza; Rios, Susana; Martinez, Jessica; Vial, Pablo; Ferres, Marcela; Rivera, Juan Carlos; Perez, Ruth; Valdivieso, Francisca

    2016-01-01

    Hantavirus Cardiopulmonary Syndrome is a severe disease caused by exposure to New World hantaviruses. Early diagnosis is difficult due to the lack of specific initial symptoms. Anti-hantavirus antibodies are usually negative until late in the febrile prodrome or the beginning of cardiopulmonary phase while Andes hantavirus (ANDV) RNA genome can be detected before symptoms onset. We analyzed the effectiveness of RTqPCR as a diagnostic tool detecting ANDV-Sout genome in peripheral blood cells from 78 confirmed hantavirus patients and 166 negative controls. Our results indicate that RTqPCR had a low detection limit (~10 copies), with a specificity of 100% and a sensitivity of 94.9%. This suggests the potential for establishing RT-qPCR as the assay of choice for early diagnosis, promoting early effective care of patients and improve other important aspects of ANDV infection management, such as compliance of biosafety recommendations for health personnel in order to avoid nosocomial transmission. PMID:26508102

  9. Molecular method for the detection of Andes hantavirus infection: validation for clinical diagnostics.

    PubMed

    Vial, Cecilia; Martinez-Valdebenito, Constanza; Rios, Susana; Martinez, Jessica; Vial, Pablo A; Ferres, Marcela; Rivera, Juan C; Perez, Ruth; Valdivieso, Francisca

    2016-01-01

    Hantavirus cardiopulmonary syndrome is a severe disease caused by exposure to New World hantaviruses. Early diagnosis is difficult due to the lack of specific initial symptoms. Antihantavirus antibodies are usually negative until late in the febrile prodrome or the beginning of cardiopulmonary phase, while Andes hantavirus (ANDV) RNA genome can be detected before symptoms onset. We analyzed the effectiveness of quantitative reverse transcription polymerase chain reaction (RT-qPCR) as a diagnostic tool detecting ANDV-Sout genome in peripheral blood cells from 78 confirmed hantavirus patients and 166 negative controls. Our results indicate that RT-qPCR had a low detection limit (~10 copies), with a specificity of 100% and a sensitivity of 94.9%. This suggests the potential for establishing RT-qPCR as the assay of choice for early diagnosis, promoting early effective care of patients, and improving other important aspects of ANDV infection management, such as compliance of biosafety recommendations for health personnel in order to avoid nosocomial transmission.

  10. Molecular Diagnostic Tests for Microsporidia

    PubMed Central

    Ghosh, Kaya; Weiss, Louis M.

    2009-01-01

    The Microsporidia are a ubiquitous group of eukaryotic obligate intracellular parasites which were recognized over 100 years ago with the description of Nosema bombycis, a parasite of silkworms. It is now appreciated that these organisms are related to the Fungi. Microsporidia infect all major animal groups most often as gastrointestinal pathogens; however they have been reported from every tissue and organ, and their spores are common in environmental sources such as ditch water. Several different genera of these organisms infect humans, but the majority of infections are due to either Enterocytozoon bieneusi or Encephalitozoon species. These pathogens can be difficult to diagnose, but significant progress has been made in the last decade in the development of molecular diagnostic reagents for these organisms. This report reviews the molecular diagnostic tests that have been described for the identification of the microsporidia that infect humans. PMID:19657457

  11. Molecular methods

    SciTech Connect

    1993-12-31

    Chapter 5, describes some of the most important molecular methods used in the study of chromosome structure and function. The methods discussed include fragmentation of DNA, cloning, flow cytometry and chromosome sorting, is situ hybridization, polymerase chain reaction (PCR), and yeast artificial chromosomes (YACs). 18 refs., 3 figs., 1 tab.

  12. Rapid diagnostic tests for molecular surveillance of Plasmodium falciparum malaria -assessment of DNA extraction methods and field applicability.

    PubMed

    Morris, Ulrika; Aydin-Schmidt, Berit; Shakely, Delér; Mårtensson, Andreas; Jörnhagen, Louise; Ali, Abdullah S; Msellem, Mwinyi I; Petzold, Max; Gil, José P; Ferreira, Pedro E; Björkman, Anders

    2013-03-19

    The need for new malaria surveillance tools and strategies is critical, given improved global malaria control and regional elimination efforts. High quality Plasmodium falciparum DNA can reliably be extracted from malaria rapid diagnostic tests (RDTs). Together with highly sensitive molecular assays, wide scale collection of used RDTs may serve as a modern tool for improved malaria case detection and drug resistance surveillance. However, comparative studies of DNA extraction efficiency from RDTs and the field applicability are lacking. The aim of this study was to compare and evaluate different methods of DNA extraction from RDTs and to test the field applicability for the purpose of molecular epidemiological investigations. DNA was extracted from two RDT devices (Paracheck-Pf® and SD Bioline Malaria Pf/Pan®), seeded in vitro with 10-fold dilutions of cultured 3D7 P. falciparum parasites diluted in malaria negative whole blood. The level of P. falciparum detection was determined for each extraction method and RDT device with multiple nested-PCR and real-time PCR assays. The field applicability was tested on 855 paired RDT (Paracheck-Pf) and filter paper (Whatman® 3MM) blood samples (734 RDT negative and 121 RDT positive samples) collected from febrile patients in Zanzibar 2010. RDT positive samples were genotyped at four key single nucleotide polymorphisms (SNPs) in pfmdr1 and pfcrt as well as for pfmdr1 copy number, all associated with anti-malarial drug resistance. The P. falciparum DNA detection limit varied with RDT device and extraction method. Chelex-100 extraction performed best for all extraction matrixes. There was no statistically significant difference in PCR detection rates in DNA extracted from RDTs and filter paper field samples. Similarly there were no significant differences in the PCR success rates and genotyping outcomes for the respective SNPs in the 121 RDT positive samples. The results support RDTs as a valuable source of parasite DNA and

  13. Huntington Disease: Molecular Diagnostics Approach.

    PubMed

    Bastepe, Murat; Xin, Winnie

    2015-10-06

    Huntington disease (HD) is caused by expansion of a CAG trinucleotide repeat in the first exon of the Huntingtin (HTT) gene. Molecular testing of Huntington disease for diagnostic confirmation and disease prediction requires detection of the CAG repeat expansion. There are three main types of HD genetic testing: (1) diagnostic testing to confirm or rule out disease, (2) presymptomatic testing to determine whether an at-risk individual inherited the expanded allele, and (3) prenatal testing to determine whether the fetus has inherited the expanded allele. This unit includes protocols that describe the complementary use of polymerase chain reactions (PCR) and Southern blot hybridization to accurately measure the CAG trinucleotide repeat size and interpret the test results. In addition, an indirect linkage analysis that does not reveal the unwanted parental HD status in a prenatal testing will also be discussed.

  14. Molecular diagnostics of myeloproliferative neoplasms.

    PubMed

    Langabeer, Stephen E; Andrikovics, Hajnalka; Asp, Julia; Bellosillo, Beatriz; Carillo, Serge; Haslam, Karl; Kjaer, Lasse; Lippert, Eric; Mansier, Olivier; Oppliger Leibundgut, Elisabeth; Percy, Melanie J; Porret, Naomi; Palmqvist, Lars; Schwarz, Jiri; McMullin, Mary F; Schnittger, Susanne; Pallisgaard, Niels; Hermouet, Sylvie

    2015-10-01

    Since the discovery of the JAK2 V617F mutation in the majority of the myeloproliferative neoplasms (MPN) of polycythemia vera, essential thrombocythemia and primary myelofibrosis ten years ago, further MPN-specific mutational events, notably in JAK2 exon 12, MPL exon 10 and CALR exon 9 have been identified. These discoveries have been rapidly incorporated into evolving molecular diagnostic algorithms. Whilst many of these mutations appear to have prognostic implications, establishing MPN diagnosis is of immediate clinical importance with selection, implementation and the continual evaluation of the appropriate laboratory methodology to achieve this diagnosis similarly vital. The advantages and limitations of these approaches in identifying and quantitating the common MPN-associated mutations are considered herein with particular regard to their clinical utility. The evolution of molecular diagnostic applications and platforms has occurred in parallel with the discovery of MPN-associated mutations, and it therefore appears likely that emerging technologies such as next-generation sequencing and digital PCR will in the future play an increasing role in the molecular diagnosis of MPN.

  15. Quantum Dots for Molecular Diagnostics of Tumors

    PubMed Central

    Zdobnova, T.A.; Lebedenko, E.N.; Deyev, S.М.

    2011-01-01

    Semiconductor quantum dots (QDs) are a new class of fluorophores with unique physical and chemical properties, which allow to appreciably expand the possibilities for the current methods of fluorescent imaging and optical diagnostics. Here we discuss the prospects of QD application for molecular diagnostics of tumors ranging from cancer-specific marker detection on microplates to non-invasive tumor imagingin vivo. We also point out the essential problems that require resolution in order to clinically promote QD, and we indicate innovative approaches to oncology which are implementable using QD. PMID:22649672

  16. 2012 HIV Diagnostics Conference: the molecular diagnostics perspective.

    PubMed

    Branson, Bernard M; Pandori, Mark

    2013-04-01

    2012 HIV Diagnostic Conference Atlanta, GA, USA, 12-14 December 2012. This report highlights the presentations and discussions from the 2012 National HIV Diagnostic Conference held in Atlanta (GA, USA), on 12-14 December 2012. Reflecting changes in the evolving field of HIV diagnostics, the conference provided a forum for evaluating developments in molecular diagnostics and their role in HIV diagnosis. In 2010, the HIV Diagnostics Conference concluded with the proposal of a new diagnostic algorithm which included nucleic acid testing to resolve discordant screening and supplemental antibody test results. The 2012 meeting, picking up where the 2010 meeting left off, focused on scientific presentations that assessed this new algorithm and the role played by RNA testing and new developments in molecular diagnostics, including detection of total and integrated HIV-1 DNA, detection and quantification of HIV-2 RNA, and rapid formats for detection of HIV-1 RNA.

  17. Graphene-based nanoprobes for molecular diagnostics.

    PubMed

    Chen, Shixing; Li, Fuwu; Fan, Chunhai; Song, Shiping

    2015-10-07

    In recent years, graphene has received widespread attention owing to its extraordinary electrical, chemical, optical, mechanical and structural properties. Lately, considerable interest has been focused on exploring the potential applications of graphene in life sciences, particularly in disease-related molecular diagnostics. In particular, the coupling of functional molecules with graphene as a nanoprobe offers an excellent platform to realize the detection of biomarkers, such as nucleic acids, proteins and other bioactive molecules, with high performance. This article reviews emerging graphene-based nanoprobes in electrical, optical and other assay methods and their application in various strategies of molecular diagnostics. In particular, this review focuses on the construction of graphene-based nanoprobes and their special advantages for the detection of various bioactive molecules. Properties of graphene-based materials and their functionalization are also comprehensively discussed in view of the development of nanoprobes. Finally, future challenges and perspectives of graphene-based nanoprobes are discussed.

  18. Fundamentals of quality assessment of molecular amplification methods in clinical diagnostics. International Federation of Clinical Chemistry Scientific Division Committee on Molecular Biology Techniques.

    PubMed

    Neumaier, M; Braun, A; Wagener, C

    1998-01-01

    The increasing interest in molecular biology diagnostics is a result of the tremendous gain of scientific knowledge in genetics, made possible especially since the introduction of amplification techniques. High expectations have been placed on genetic testing, and the number of laboratories now using the relevant technology is rapidly increasing--resulting in an obvious need for standardization and definition of laboratory organization. This communication is an effort towards that end. We address aspects that should be considered when structuring a new molecular diagnostic laboratory, and we discuss individual preanalytical and analytical procedures, from sampling to evaluation of assay results. In addition, different means of controlling contamination are discussed. Because the methodology is in constant change, no general standards can be defined. Accordingly, this publication is intended to serve as a recommendation for good laboratory practice and internal quality control and as a guide to troubleshooting, primarily in amplification techniques.

  19. Contribution of the TA repeats on melting temperature (T(m)) in a double strand DNA: comparison of two methods and implications in molecular diagnostics.

    PubMed

    Minucci, Angelo; Mello, Enrica; Tripodi, Domenico; Zuppi, Cecilia; Capoluongo, Ettore

    2011-06-01

    The present paper is aimed to discuss and revise a not recent molecular laboratory protocol describing the behavior of UGT1A1 gene melting curves. Since some problems in the standardization of this already published molecular protocol were found, we tried to improve this method in order to correctly set up the amplification and melting profile steps. Under our standardized conditions, we were able to perfectly distinguish the three different UGT1A1 genotypes since each one showed a peculiar melting behavior, as compared with those previously published by another group. Finally, some suggestions and indications are provided for laboratory specialists interested in Gilbert syndrome diagnostics. Based on these results, we underline the need of more standardized protocols above all when they are used for clinical diagnostics. Copyright © 2011. Published by Elsevier Inc.

  20. [Molecular diagnostics of infectious diseases for the ambulatory practice].

    PubMed

    Dumoulin, A

    2014-10-08

    Molecular diagnostics methods are not limited to specialized centers anymore. They play an important role for the diagnostic of infections commonly encountered in the clinical practice. Especially the detection of pathogens difficult to cultivate, such as viruses, has been greatly improved by these methods. Often, PCR has become the gold standard for the diagnostics of these pathogens. However, PCR cannot be used in any case, and it is not fail proof. Therefore, it is important to know when to use molecular methods and what are their strengths and weaknesses, in order to prescribe them rationally. This article reviews the characteristics of molecular tests and their main indications in the ambulatory setting.

  1. Molecular diagnostics for low resource settings

    NASA Astrophysics Data System (ADS)

    Weigl, Bernhard H.

    2010-03-01

    As traditional high quality diagnostic laboratories are not widely available or affordable in developing country health care settings, microfluidics-based point-of-care diagnostics may be able to address the need to perform complex assays in under-resourced areas. Many instrument-based as well as non-instrumented microfluidic prototype diagnostics are currently being developed. In addition to various engineering challenges, the greatest remaining issue is the search for truly low-cost disposable manufacturing methods. Diagnostics for global health, and specifically microfluidics and molecular-based low resource diagnostics, have become a very active research area over the last five years, thanks in part to new funding that became available from the Bill and Melinda Gates Foundation, the National Institutes of Health, and other sources. This has led to a number of interesting prototype devices that are now in advanced development or clinical validation. These devices include disposables and instruments that perform multiplexed PCR-based lab-on-a-chips for enteric, febrile, and vaginal diseases, as well as immunoassays for diseases such as malaria, HIV, and various sexually transmitted diseases. More recently, instrument-free diagnostic disposables based on isothermal nucleic acid amplification have been developed as well. Regardless of platform, however, the search for truly low-cost manufacturing methods that would result in cost of goods per disposable of around US1/unit at volume remains a big challenge. This talk will give an overview over existing platform development efforts as well as present some original research in this area at PATH.

  2. A method to compare the performance of two molecular diagnostic tools in the absence of a gold standard.

    PubMed

    Xue, Xiaonan; Oktay, Maja; Goswami, Sumanta; Kim, Mimi Y

    2017-01-01

    The paper is motivated by the problem of comparing the accuracy of two molecular tests in detecting genetic mutations in tumor samples when there is no gold standard test. Commonly used sequencing methods require a large number of tumor cells in the tumor sample and the proportion of tumor cells with mutation positivity to be above a threshold level whereas new tests aim to reduce the requirement for number of tumor cells and the threshold level. A new latent class model is proposed to compare these two tests in which a random variable is used to represent the unobserved proportion of mutation positivity so that these two tests are conditionally dependent; furthermore, an independent random variable is included to address measurement error associated with the reading from each test, while existing latent class models often assume conditional independence and do not allow measurement error. In addition, methods for calculating the sample size for a study that is sufficiently powered to compare the accuracy of two molecular tests are proposed and compared. The proposed methods are then applied to a study which aims to compare two molecular tests for detecting EGFR mutations in lung cancer patients.

  3. Next-generation molecular diagnostics.

    PubMed

    Aldape, Kenneth; Pfister, Stefan M

    2016-01-01

    The classification of brain tumors is based on the time-honored tradition of histologic examination, coupled with clinicopathologic correlation, and is based on the fundamental importance of microscopic morphologic interpretation. Supplementation by immunohistochemical markers is of substantial value to distinguish related entities and to confirm morphologic impressions. The use of techniques such as fluorescent in situ hybridization (FISH) is also critical in specific situations. However, with these practices, it is clear that the use of state-of-the-art molecular techniques has great promise to add to classification to (1) reduce the subjectivity inherent in interobserver discordance, particularly with specific entities; and (2) elucidate the biologic diversity of entities that are not resolvable by routine methods. In this chapter, we discuss these possibilities, focusing on several tumor types affecting the central nervous system, including diffuse glioma and ependymoma.

  4. Comparison of molecular diagnostic methods for the detection of Acanthamoeba spp. from clinical specimens submitted for keratitis.

    PubMed

    Khairnar, Krishna; Tamber, Gurdip S; Ralevski, Filip; Pillai, Dylan R

    2011-08-01

    Acanthamoeba spp. are responsible for a significant annual number of keratitis (AK) cases leading to vision-threatening disease worldwide. Current methods rely on direct examination of specimens by microscopy and/or culture. The former lacks sensitivity and the latter suffers from a poor turnaround time. We undertook a comparison of all published molecular methods, evaluating performance characteristics such as analytical sensitivity, specificity, limit of detection (LOD), reproducibility, accuracy, and cost of test. The study population comprised 128 patients. Eligible specimens were tested prospectively between April 2007 and May 2010 by microscopy and/or culture. Eleven different specimen types were used including corneal scrapings (51.5%), corneal swab (17.9%), and contact lens material (10.9%). Results of 2 published gel-based polymerase chain reaction (PCR) and 2 published real-time quantitative (Q) PCR methods were compared in a blinded manner to direct microscopic examination and/or culture for the detection of Acanthamoeba in clinical specimens. QPCR (Riviere method) had the highest sensitivity at 89.3%, excellent accuracy using ROC analysis (AUC ∼0.90), lowest LOD down to 0.1 organism per microliter, and superior linear correlation with parasite density (R(2) = 0.9965) when compared with microscopy, culture, and other molecular methods. Phylogenetic analysis using a sequence-based typing method revealed that clinical isolates in this population with AK were genetically distinct from granulomatous amebic encephalitis or environmental isolates. The QPCR method was more expensive ($14.80) than traditional methods such as culture ($2.50) or microscopy ($2.50). However, 13 culture- and microscopy-negative specimens were positive by QPCR during the study period, suggesting that detection using QPCR may result in reduced complications and health care costs associated with misdiagnosed AK.

  5. Molecular Diagnostics for Soil-Transmitted Helminths.

    PubMed

    O'Connell, Elise M; Nutman, Thomas B

    2016-09-07

    Historically, the diagnosis of soil-transmitted helminths (STHs) (e.g., Strongyloides stercoralis, Trichuris trichiura, Ancylostoma duodenale, Necator americanus, and Ascaris lumbricoides) has relied on often-insensitive microscopy techniques. Over the past several years, there has been an effort to use molecular diagnostics, particularly quantitative polymerase chain reaction (qPCR), to detect intestinal pathogens. While some platforms have been approved by regulatory bodies (e.g., Food and Drug Administration) to detect intestinal bacteria, viruses, and protozoa, there are no approved tests currently available for STH. Although studies comparing qPCR to microscopy methods for STH are imperfect, due in large part to a lack of a sufficient gold standard, they do show a significant increase in sensitivity and specificity of qPCR compared with microscopic techniques. These studies, as well as the advantages and disadvantages of using qPCR for STH diagnosis, are discussed. Guidelines for those designing future studies utilizing qPCR are proposed for optimizing results, as is the proposition for using standardized molecular diagnostics routinely for STH in clinical laboratories and for field-based studies when possible.

  6. Molecular Diagnostics for Soil-Transmitted Helminths

    PubMed Central

    O'Connell, Elise M.; Nutman, Thomas B.

    2016-01-01

    Historically, the diagnosis of soil-transmitted helminths (STHs) (e.g., Strongyloides stercoralis, Trichuris trichiura, Ancylostoma duodenale, Necator americanus, and Ascaris lumbricoides) has relied on often-insensitive microscopy techniques. Over the past several years, there has been an effort to use molecular diagnostics, particularly quantitative polymerase chain reaction (qPCR), to detect intestinal pathogens. While some platforms have been approved by regulatory bodies (e.g., Food and Drug Administration) to detect intestinal bacteria, viruses, and protozoa, there are no approved tests currently available for STH. Although studies comparing qPCR to microscopy methods for STH are imperfect, due in large part to a lack of a sufficient gold standard, they do show a significant increase in sensitivity and specificity of qPCR compared with microscopic techniques. These studies, as well as the advantages and disadvantages of using qPCR for STH diagnosis, are discussed. Guidelines for those designing future studies utilizing qPCR are proposed for optimizing results, as is the proposition for using standardized molecular diagnostics routinely for STH in clinical laboratories and for field-based studies when possible. PMID:27481053

  7. Laboratory Information Systems in Molecular Diagnostics: Why Molecular Diagnostics Data are Different.

    PubMed

    Lee, Roy E; Henricks, Walter H; Sirintrapun, Sahussapont J

    2016-03-01

    Molecular diagnostic testing presents new challenges to information management that are yet to be sufficiently addressed by currently available information systems for the molecular laboratory. These challenges relate to unique aspects of molecular genetic testing: molecular test ordering, informed consent issues, diverse specimen types that encompass the full breadth of specimens handled by traditional anatomic and clinical pathology information systems, data structures and data elements specific to molecular testing, varied testing workflows and protocols, diverse instrument outputs, unique needs and requirements of molecular test reporting, and nuances related to the dissemination of molecular pathology test reports. By satisfactorily addressing these needs in molecular test data management, a laboratory information system designed for the unique needs of molecular diagnostics presents a compelling reason to migrate away from the current paper and spreadsheet information management that many molecular laboratories currently use. This paper reviews the issues and challenges of information management in the molecular diagnostics laboratory.

  8. Comparison of diagnostic potential of serological, molecular and cell culture methods for detection of Q fever in ruminants.

    PubMed

    Niemczuk, Krzysztof; Szymańska-Czerwińska, Monika; Śmietanka, Krzysztof; Bocian, Łukasz

    2014-06-25

    Q fever is an infectious disease caused by Coxiella burnetii. Diagnosis of Q fever based on clinical symptoms is unattainable; thus, different laboratory techniques are used to detect the infection. The aim of the study was to compare the diagnostic potential of ELISA, CFT, conventional PCR, real-time PCR and cell culture. The tests were carried out on 2251 serum samples from ruminants. Moreover, 668 placentas, 1277 vaginal swabs and 306 specimens of the internal organs of aborted foetuses were examined by PCR and cell culture. Pearson's chi-square test was used to compare the results obtained by ELISA, CFT, PCR, real-time PCR and isolation in cell culture. The χ(2) test confirmed that in most cases the results obtained by means of the different methods were correlated with each other (P<0.05). The highest correlation coefficients (r=0.76-0.87) were observed in the case of real-time PCR and conventional PCR. ELISA and CFT were moderately correlated (r=0.43-0.45). When the comparison was made between the results of tests run on samples from swabs and aborted foetuses, the r values between ELISA and CFT were lower than those between ELISA and PCRs. A negligible, or weak to moderate relationship was mostly observed when the method of cell culture isolation was compared with all the other analytical techniques investigated. The use of a combination of different laboratory methods, preferably ELISA for serology and polymerase chain reactions for the agent detection, is suggested to achieve the correct diagnosis of Q fever.

  9. Molecular Diagnostic Testing for Aspergillus

    PubMed Central

    Powers-Fletcher, Margaret V.

    2016-01-01

    The direct detection of Aspergillus nucleic acid in clinical specimens has the potential to improve the diagnosis of aspergillosis by offering more rapid and sensitive identification of invasive infections than is possible with traditional techniques, such as culture or histopathology. Molecular tests for Aspergillus have been limited historically by lack of standardization and variable sensitivities and specificities. Recent efforts have been directed at addressing these limitations and optimizing assay performance using a variety of specimen types. This review provides a summary of standardization efforts and outlines the complexities of molecular testing for Aspergillus in clinical mycology. PMID:27487954

  10. Calculation of diagnostic parameters of advanced serological and molecular tissue-print methods for detection of Citrus tristeza virus: a model for other plant pathogens.

    PubMed

    Vidal, E; Yokomi, R K; Moreno, A; Bertolini, E; Cambra, M

    2012-01-01

    Citrus tristeza virus (CTV) is one of the most important virus diseases that affect citrus. Control of CTV is achieved by grafting selected virus-free citrus scions onto CTV-tolerant or -resistant rootstocks. Quarantine and certification programs are essential for avoiding the entry and propagation of severe strains of CTV. Citrus nurseries in Spain and central California (United States) maintain zero-tolerance policies for CTV that require sensitive, specific, and reliable pathogen-detection methods. Tissue-print (TP) real-time reverse-transcriptase polymerase chain reaction (RT-PCR) assay was compared with the validated TP enzyme-linked immunosorbent assay (ELISA), using the CTV-specific monoclonal antibodies 3DF1 and 3CA5, for CTV detection. In total, 1,395 samples from healthy and CTV-infected nursery and mature tree plants were analyzed with both methods. The total agreement between both detection methods was substantial (Cohen's kappa index of 0.77 ± 0.03). The diagnostic parameters of each technique (i.e., the sensitivity, specificity, and likelihood ratios) were evaluated in a second test involving 658 Citrus macrophylla nursery plants. Mexican lime indexing was used to evaluate samples with discrepant results in the analysis. For TP-ELISA, a sensitivity of 0.8015, a specificity of 0.9963, and a positive and negative likelihood ratio of 216.42 and 0.199, respectively, were estimated. For TP real-time RT-PCR, a sensitivity of 0.9820, a specificity of 0.8519, and a positive and negative likelihood ratio of 6.63 and 0.021, respectively, were estimated. These diagnostic parameters show that TP real-time RT-PCR was the most sensitive technique, whereas TP-ELISA showed the highest specificity, validating the use of the molecular technique for routine CTV-detection purposes. In addition, our results show that the combination of both techniques can accurately substitute for the conventional biological Mexican lime index for the detection of CTV. The calculation of

  11. Standing footprint diagnostic method

    NASA Astrophysics Data System (ADS)

    Fan, Y. F.; Fan, Y. B.; Li, Z. Y.; Newman, T.; Lv, C. S.; Fan, Y. Z.

    2013-10-01

    Center of pressure is commonly used to evaluate standing balance. Even though it is incomplete, no better evaluation method has been presented. We designed our experiment with three standing postures: standing with feet together, standing with feet shoulder width apart, and standing with feet slightly wider than shoulder width. Our platform-based pressure system collected the instantaneous plantar pressure (standing footprint). A physical quantity of instantaneous standing footprint principal axis was defined, and it was used to construct an index to evaluate standing balance. Comparison between results from our newly established index and those from the center of pressure index to evaluate the stability of different standing postures revealed that the standing footprint principal axis index could better respond to the standing posture change than the existing one. Analysis indicated that the insensitive response to the relative position between feet and to the standing posture change from the center of pressure could be better detected by the standing footprint principal axis index. This predicts a wide application of standing footprint principal axis index when evaluating standing balance.

  12. Improving validation methods for molecular diagnostics: application of Bland-Altman, Deming and simple linear regression analyses in assay comparison and evaluation for next-generation sequencing.

    PubMed

    Misyura, Maksym; Sukhai, Mahadeo A; Kulasignam, Vathany; Zhang, Tong; Kamel-Reid, Suzanne; Stockley, Tracy L

    2017-07-26

    A standard approach in test evaluation is to compare results of the assay in validation to results from previously validated methods. For quantitative molecular diagnostic assays, comparison of test values is often performed using simple linear regression and the coefficient of determination (R(2)), using R(2) as the primary metric of assay agreement. However, the use of R(2) alone does not adequately quantify constant or proportional errors required for optimal test evaluation. More extensive statistical approaches, such as Bland-Altman and expanded interpretation of linear regression methods, can be used to more thoroughly compare data from quantitative molecular assays. We present the application of Bland-Altman and linear regression statistical methods to evaluate quantitative outputs from next-generation sequencing assays (NGS). NGS-derived data sets from assay validation experiments were used to demonstrate the utility of the statistical methods. Both Bland-Altman and linear regression were able to detect the presence and magnitude of constant and proportional error in quantitative values of NGS data. Deming linear regression was used in the context of assay comparison studies, while simple linear regression was used to analyse serial dilution data. Bland-Altman statistical approach was also adapted to quantify assay accuracy, including constant and proportional errors, and precision where theoretical and empirical values were known. The complementary application of the statistical methods described in this manuscript enables more extensive evaluation of performance characteristics of quantitative molecular assays, prior to implementation in the clinical molecular laboratory. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  13. Molecular diagnostics: Molecular Med Tri-Con 2013.

    PubMed

    Klein, Roger D

    2013-07-01

    The 20th annual Molecular Med Tri-Con conference, sponsored by Cambridge Health Institute (MA, USA), consisted of over 250 presentations within five parallel 'channels': 'Diagnostics, Therapeutics, Clinical, Informatics and Cancer', along with five preliminary symposia, 15 short courses, a plenary keynote session entitled 'Personalized Oncology - Fulfilling the Promise for Today's Patients' and a keynote panel entitled, 'Emerging Technologies and Industry Perspectives'. Over 3000 individuals from academia, clinical laboratories and industry were in attendance. This article will focus on the Keynote Session of 'Molecular Diagnostics' track within the Diagnostics Channel.

  14. Challenges for rapid molecular HIV diagnostics.

    PubMed

    Schito, Marco L; D'Souza, M Patricia; Owen, S Michele; Busch, Michael P

    2010-04-15

    The introduction of serological point-of-care assays 10 years ago dramatically changed the way that human immunodeficiency virus (HIV) infection was identified and diagnosed. Testing at the point of care has lead to a dramatic increase in the number of individuals who are screened and, most importantly, receive their HIV test result. As the AIDS epidemic continues to mature and scientific advances in prevention and treatment are evaluated and implemented, there is a need to identify acute (viremic preseroconversion) infections and to discriminate "window phase" infections from those that are serologically positive, especially in resource-limited settings, where the majority of vulnerable populations reside and where the incidence of HIV infection is highest. Rapid testing methods are now at a crossroads. There is opportunity to implement and evaluate the incremental diagnostic usefulness of new test modalities that are based on sophisticated molecular diagnostic technologies and that can be performed in settings where laboratory infrastructure is minimal. The way forward requires sound scientific judgment and an ability to further develop and implement these tests despite a variety of technical, social, and operational hurdles, to declare success.

  15. Trends in Laboratory Diagnostic Methods in Periodontology.

    PubMed

    Bolerázska, Beáta; Mareková, Mária; Markovská, Neda

    2016-01-01

    This work presents a summary of current knowledge on the laboratory diagnosis of periodontitis. It focuses on the theoretical foundations and is supplemented with new knowledge. It subsequently describes specifically the laboratory diagnosis methods of periodontitis: the protein expression of inflammation, oral microbiology and molecular diagnostics. Periodontitis is a serious disease worldwide and its confirmed association with systemic diseases means its severity is increasing. Its laboratory diagnosis has the potential to rise to the level of clinical and diagnostic imaging. The transfer of diagnostic methods from laboratory to clinical use is increasingly used in the prevention and monitoring of the exacerbation and treatment of periodontal disease, as well as of its impact on systemic disease.

  16. Modeling Complex Workflow in Molecular Diagnostics

    PubMed Central

    Gomah, Mohamed E.; Turley, James P.; Lu, Huimin; Jones, Dan

    2010-01-01

    One of the hurdles to achieving personalized medicine has been implementing the laboratory processes for performing and reporting complex molecular tests. The rapidly changing test rosters and complex analysis platforms in molecular diagnostics have meant that many clinical laboratories still use labor-intensive manual processing and testing without the level of automation seen in high-volume chemistry and hematology testing. We provide here a discussion of design requirements and the results of implementation of a suite of lab management tools that incorporate the many elements required for use of molecular diagnostics in personalized medicine, particularly in cancer. These applications provide the functionality required for sample accessioning and tracking, material generation, and testing that are particular to the evolving needs of individualized molecular diagnostics. On implementation, the applications described here resulted in improvements in the turn-around time for reporting of more complex molecular test sets, and significant changes in the workflow. Therefore, careful mapping of workflow can permit design of software applications that simplify even the complex demands of specialized molecular testing. By incorporating design features for order review, software tools can permit a more personalized approach to sample handling and test selection without compromising efficiency. PMID:20007844

  17. Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study

    PubMed Central

    Liu, Jie; Platts-Mills, James A; Juma, Jane; Kabir, Furqan; Nkeze, Joseph; Okoi, Catherine; Operario, Darwin J; Uddin, Jashim; Ahmed, Shahnawaz; Alonso, Pedro L; Antonio, Martin; Becker, Stephen M; Blackwelder, William C; Breiman, Robert F; Faruque, Abu S G; Fields, Barry; Gratz, Jean; Haque, Rashidul; Hossain, Anowar; Hossain, M Jahangir; Jarju, Sheikh; Qamar, Farah; Iqbal, Najeeha Talat; Kwambana, Brenda; Mandomando, Inacio; McMurry, Timothy L; Ochieng, Caroline; Ochieng, John B; Ochieng, Melvin; Onyango, Clayton; Panchalingam, Sandra; Kalam, Adil; Aziz, Fatima; Qureshi, Shahida; Ramamurthy, Thandavarayan; Roberts, James H; Saha, Debasish; Sow, Samba O; Stroup, Suzanne E; Sur, Dipika; Tamboura, Boubou; Taniuchi, Mami; Tennant, Sharon M; Toema, Deanna; Wu, Yukun; Zaidi, Anita; Nataro, James P; Kotloff, Karen L; Levine, Myron M; Houpt, Eric R

    2017-01-01

    Summary Background Diarrhoea is the second leading cause of mortality in children worldwide, but establishing the cause can be complicated by diverse diagnostic approaches and varying test characteristics. We used quantitative molecular diagnostic methods to reassess causes of diarrhoea in the Global Enteric Multicenter Study (GEMS). Methods GEMS was a study of moderate to severe diarrhoea in children younger than 5 years in Africa and Asia. We used quantitative real-time PCR (qPCR) to test for 32 enteropathogens in stool samples from cases and matched asymptomatic controls from GEMS, and compared pathogen-specific attributable incidences with those found with the original GEMS microbiological methods, including culture, EIA, and reverse-transcriptase PCR. We calculated revised pathogen-specific burdens of disease and assessed causes in individual children. Findings We analysed 5304 sample pairs. For most pathogens, incidence was greater with qPCR than with the original methods, particularly for adenovirus 40/41 (around five times), Shigella spp or enteroinvasive Escherichia coli (EIEC) and Campylobactor jejuni or C coli (around two times), and heat-stable enterotoxin-producing E coli ([ST-ETEC] around 1·5 times). The six most attributable pathogens became, in descending order, Shigella spp, rotavirus, adenovirus 40/41, ST-ETEC, Cryptosporidium spp, and Campylobacter spp. Pathogen-attributable diarrhoeal burden was 89·3% (95% CI 83·2–96·0) at the population level, compared with 51·5% (48·0–55·0) in the original GEMS analysis. The top six pathogens accounted for 77·8% (74·6–80·9) of all attributable diarrhoea. With use of model-derived quantitative cutoffs to assess individual diarrhoeal cases, 2254 (42·5%) of 5304 cases had one diarrhoea-associated pathogen detected and 2063 (38·9%) had two or more, with Shigella spp and rotavirus being the pathogens most strongly associated with diarrhoea in children with mixed infections. Interpretation A

  18. Towards in vitro molecular diagnostics using nanostructures.

    PubMed

    Kurkina, Tetiana; Balasubramanian, Kannan

    2012-02-01

    Nanostructures appear to be promising for a number of applications in molecular diagnostics, mainly due to the increased surface-to-volume ratio they can offer, the very low limit of detection achievable, and the possibility to fabricate point-of-care diagnostic devices. In this paper, we review examples of the use of nanostructures as diagnostic tools that bring in marked improvements over prevalent classical assays. The focus is laid on the various sensing paradigms that possess the potential or have demonstrated the capability to replace or augment current analytical strategies. We start with a brief introduction of the various types of nanostructures and their physical properties that determine the transduction principle. This is followed by a concise collection of various functionalization protocols used to immobilize biomolecules on the nanostructure surface. The sensing paradigms are discussed in two contexts: the nanostructure acting as a label for detection, or the nanostructure acting as a support upon which the molecular recognition events take place. In order to be successful in the field of molecular diagnostics, it is important that the nanoanalytical tools be evaluated in the appropriate biological environment. The final section of the review compiles such examples, where the nanostructure-based diagnostic tools have been tested on realistic samples such as serum, demonstrating their analytical power even in the presence of complex matrix effects. The ability of nanodiagnostic tools to detect ultralow concentrations of one or more analytes coupled with portability and the use of low sample volumes is expected to have a broad impact in the field of molecular diagnostics.

  19. Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study.

    PubMed

    Liu, Jie; Platts-Mills, James A; Juma, Jane; Kabir, Furqan; Nkeze, Joseph; Okoi, Catherine; Operario, Darwin J; Uddin, Jashim; Ahmed, Shahnawaz; Alonso, Pedro L; Antonio, Martin; Becker, Stephen M; Blackwelder, William C; Breiman, Robert F; Faruque, Abu S G; Fields, Barry; Gratz, Jean; Haque, Rashidul; Hossain, Anowar; Hossain, M Jahangir; Jarju, Sheikh; Qamar, Farah; Iqbal, Najeeha Talat; Kwambana, Brenda; Mandomando, Inacio; McMurry, Timothy L; Ochieng, Caroline; Ochieng, John B; Ochieng, Melvin; Onyango, Clayton; Panchalingam, Sandra; Kalam, Adil; Aziz, Fatima; Qureshi, Shahida; Ramamurthy, Thandavarayan; Roberts, James H; Saha, Debasish; Sow, Samba O; Stroup, Suzanne E; Sur, Dipika; Tamboura, Boubou; Taniuchi, Mami; Tennant, Sharon M; Toema, Deanna; Wu, Yukun; Zaidi, Anita; Nataro, James P; Kotloff, Karen L; Levine, Myron M; Houpt, Eric R

    2016-09-24

    Diarrhoea is the second leading cause of mortality in children worldwide, but establishing the cause can be complicated by diverse diagnostic approaches and varying test characteristics. We used quantitative molecular diagnostic methods to reassess causes of diarrhoea in the Global Enteric Multicenter Study (GEMS). GEMS was a study of moderate to severe diarrhoea in children younger than 5 years in Africa and Asia. We used quantitative real-time PCR (qPCR) to test for 32 enteropathogens in stool samples from cases and matched asymptomatic controls from GEMS, and compared pathogen-specific attributable incidences with those found with the original GEMS microbiological methods, including culture, EIA, and reverse-transcriptase PCR. We calculated revised pathogen-specific burdens of disease and assessed causes in individual children. We analysed 5304 sample pairs. For most pathogens, incidence was greater with qPCR than with the original methods, particularly for adenovirus 40/41 (around five times), Shigella spp or enteroinvasive Escherichia coli (EIEC) and Campylobactor jejuni o C coli (around two times), and heat-stable enterotoxin-producing E coli ([ST-ETEC] around 1·5 times). The six most attributable pathogens became, in descending order, Shigella spp, rotavirus, adenovirus 40/41, ST-ETEC, Cryptosporidium spp, and Campylobacter spp. Pathogen-attributable diarrhoeal burden was 89·3% (95% CI 83·2-96·0) at the population level, compared with 51·5% (48·0-55·0) in the original GEMS analysis. The top six pathogens accounted for 77·8% (74·6-80·9) of all attributable diarrhoea. With use of model-derived quantitative cutoffs to assess individual diarrhoeal cases, 2254 (42·5%) of 5304 cases had one diarrhoea-associated pathogen detected and 2063 (38·9%) had two or more, with Shigella spp and rotavirus being the pathogens most strongly associated with diarrhoea in children with mixed infections. A quantitative molecular diagnostic approach improved population

  20. Democratizing molecular diagnostics for the developing world.

    PubMed

    Abou Tayoun, Ahmad N; Burchard, Paul R; Malik, Imran; Scherer, Axel; Tsongalis, Gregory J

    2014-01-01

    Infectious diseases that are largely treatable continue to pose a tremendous burden on the developing world despite the availability of highly potent drugs. The high mortality and morbidity rates of these diseases are largely due to a lack of affordable diagnostics that are accessible to resource-limited areas and that can deliver high-quality results. In fact, modified molecular diagnostics for infectious diseases were rated as the top biotechnology to improve health in developing countries. In this review, we describe the characteristics of accessible molecular diagnostic tools and discuss the challenges associated with implementing such tools at low infrastructure sites. We highlight our experience as part of the "Grand Challenge" project supported by the Gates Foundation for addressing global health inequities and describe issues and solutions associated with developing adequate technologies or molecular assays needed for broad access in the developing world. We believe that sharing this knowledge will facilitate the development of new molecular technologies that are extremely valuable for improving global health.

  1. Multidisciplinary molecular diagnostics: the 9th European meeting on molecular diagnostics.

    PubMed

    Loonen, Anne J M; Schuurman, Rob; van den Brule, Adriaan J C

    2016-01-01

    This report presents a summary of the 9th European Meeting on Molecular Diagnostics held in Noordwijk, The Netherlands, 14-16 October 2015. This 3-day conference covered many relevant topics in the field of molecular diagnostics in humans, including infectious disease, oncology, outbreak management, population-based cancer screening, standardization and quality control, chronic diseases and pharmacogenetics. Beyond these different areas, shared values are new technologies and novel technical and clinical applications. Approximately 450 participants, the majority coming from European countries, attended the meeting. Besides high quality scientific presentations, more than 35 diagnostic companies presented their latest innovations, altogether in an informal and inspiring scientific ambience.

  2. Diagnostic molecular microbiology: a 2013 snapshot.

    PubMed

    Fairfax, Marilynn Ransom; Salimnia, Hossein

    2013-12-01

    Molecular testing has a large and increasing role in the diagnosis of infectious diseases. It has evolved significantly since the first probe tests were FDA approved in the early 1990s. This article highlights the uses of molecular techniques in diagnostic microbiology, including "older," as well as innovative, probe techniques, qualitative and quantitative RT-PCR, highly multiplexed PCR panels, some of which use sealed microfluidic test cartridges, MALDI TOF, and nuclear magnetic resonance. Tests are grouped together by technique and target. Tests with similar roles for similar analytes are compared with respect to benefits, drawbacks, and possible problems.

  3. Rendering of mycobacteria safe for molecular diagnostic studies and development of a lysis method for strand displacement amplification and PCR.

    PubMed Central

    Zwadyk, P; Down, J A; Myers, N; Dey, M S

    1994-01-01

    Two criteria must be met before mycobacterial specimens can be tested by DNA amplification methods: (i) the sample must be rendered noninfectious, and (ii) the organisms must be lysed to free the DNA. Previous publications reporting DNA amplification of mycobacteria have concentrated on lysis and amplification procedures and have not addressed the issue of sample safety. We have shown that heating of samples below 100 degrees C may not consistently kill mycobacteria; however, heating at 100 degrees C in a boiling-water bath or a forced-air oven for a minimum of 5 min kills mycobacteria, including Mycobacterium thermoresistibile. Furthermore, heating at 100 degrees C for 30 min consistently lyses mycobacteria to produce short fragments of DNA that are suitable for amplification by PCR and strand displacement amplification. This procedure works with clinical samples digested by the n-acetyl cysteine-NaOH method as well as with suspensions of organisms in phosphate buffer. This paper also demonstrates the feasibility of using strand displacement amplification with clinical specimens. Images PMID:7814537

  4. Diagnostic Accuracy of a Molecular Drug Susceptibility Testing Method for the Antituberculosis Drug Ethambutol: a Systematic Review and Meta-Analysis

    PubMed Central

    Cheng, Song; Cui, Zhenling; Li, Yuanyuan

    2014-01-01

    Ethambutol (EMB) is a first-line antituberculosis drug; however, drug resistance to EMB has been increasing. Molecular drug susceptibility testing (DST), based on the embB gene, has recently been used for rapid identification of EMB resistance. The aim of this meta-analysis was to establish the accuracy of molecular assay for detecting drug resistance to EMB. PubMed, Embase, and Web of Science were searched according to a written protocol and explicit study selection criteria. Measures of diagnostic accuracy were pooled using a random effects model. A total of 34 studies were included in the meta-analysis. The respective pooled sensitivities and specificities were 0.57 and 0.93 for PCR-DNA sequencing that targeted the embB 306 codon, 0.76 and 0.89 for PCR-DNA sequencing that targeted the embB 306, 406, and 497 codons, 0.64 and 0.70 for detecting Mycobacterium tuberculosis isolates, 0.55 and 0.78 for detecting M. tuberculosis sputum specimens using the GenoType MTBDRsl test, 0.57 and 0.87 for pyrosequencing, and 0.35 and 0.98 for PCR-restriction fragment length polymorphism. The respective pooled sensitivities and specificities were 0.55 and 0.92 when using a lower EMB concentration as the reference standard, 0.67 and 0.73 when using a higher EMB concentration as the reference standard, and 0.60 and 1.0 when using multiple reference standards. PCR-DNA sequencing using multiple sites of the embB gene as detection targets, including embB 306, 406, and 497, can be a rapid method for preliminarily screening for EMB resistance, but it does not fully replace phenotypic DST. Of the reference DST methods examined, the agreement rates were the best using MGIT 960 for molecular DST and using the proportion method on Middlebrook 7H10 media. PMID:24899018

  5. [Molecular and immunohistochemical diagnostics in melanoma].

    PubMed

    Schilling, B; Griewank, K G

    2016-07-01

    To provide appropriate therapy and follow-up to patients with malignant melanoma, proper diagnostics are of critical importance. Targeted therapy of advanced melanoma is based on the molecular genetic analyses of tumor tissue. In addition, sequencing of genes and other genetic approaches can provide insight into the origin of melanocytic tumors and can aid in distinguishing benign from malignant lesions. In this regard, spizoid neoplasms remain a challenging entity. Aside from genetic analyses of tumor tissue, immunohistochemistry remains an essential tool in melanoma diagnostics and TNM classification. With new immunotherapies being approved for advanced melanoma, immunohistochemistry to determine PD-L1 expression has gained clinical interest. While PD-L1 expression is associated with response to PD-1 blockade, a substantial number of patients without PD-L1 expression can still experience tumor remission upon treatment. In this review, current and future developments in melanoma diagnostics with regard to molecular genetics and immunohistochemistry are summarized. The utilization of such analyses in clinical decision making is also discussed.

  6. Myasthenia Gravis: Tests and Diagnostic Methods

    MedlinePlus

    ... Focus on MG Newsletter E-Update Test & Diagnostic methods In addition to a complete medical and neurological ... How can I help? About MGFA Test & Diagnostic methods Treatment for MG FAQ's Upcoming Events 2017 MG ...

  7. Development and Evaluation of a Molecular Diagnostic Method for Rapid Detection of Histoplasma capsulatum var. farciminosum, the Causative Agent of Epizootic Lymphangitis, in Equine Clinical Samples

    PubMed Central

    Pinchbeck, G. L.; Loughnane, P.; Aklilu, N.; Ashine, T.; Stringer, A. P.; Gordon, L.; Marshall, M.; Christley, R. M.

    2016-01-01

    Histoplasma capsulatum var. farciminosum, the causative agent of epizootic lymphangitis (EZL), is endemic in parts of Africa. Diagnosis based on clinical signs and microscopy lacks specificity and is a barrier to further understanding this neglected disease. Here, a nested PCR method targeting the internal transcribed spacer (ITS) region of the rRNA operon was validated for application to equine clinical samples. Twenty-nine horses with signs of EZL from different climatic regions of Ethiopia were clinically examined. Blood samples and aspirates of pus from cutaneous nodules were taken, along with blood from a further 20 horses with no cutaneous EZL lesions. Among the 29 horses with suspected cases of EZL, H. capsulatum var. farciminosum was confirmed by extraction of DNA from pus and blood samples from 25 and 17 horses, respectively. Positive PCR results were also obtained with heat-inactivated pus (24 horses) and blood (23 horses) spotted onto Whatman FTA cards. Two positive results were obtained among blood samples from 20 horses that did not exhibit clinical signs of EZL. These are the first reports of the direct detection of H. capsulatum var. farciminosum in equine blood and at high frequency among horses exhibiting cutaneous lesions. The nested PCR outperformed conventional microscopic diagnosis, as characteristic yeast cells could be observed only in 14 pus samples. The presence of H. capsulatum var. farciminosum DNA was confirmed by sequencing the cloned PCR products, and while alignment of the ITS amplicons showed very little sequence variation, there was preliminary single nucleotide polymorphism-based evidence for the existence of two subgroups of H. capsulatum var. farciminosum. This molecular diagnostic method now permits investigation of the epidemiology of EZL. PMID:27707938

  8. Development and Evaluation of a Molecular Diagnostic Method for Rapid Detection of Histoplasma capsulatum var. farciminosum, the Causative Agent of Epizootic Lymphangitis, in Equine Clinical Samples.

    PubMed

    Scantlebury, C E; Pinchbeck, G L; Loughnane, P; Aklilu, N; Ashine, T; Stringer, A P; Gordon, L; Marshall, M; Christley, R M; McCarthy, A J

    2016-12-01

    Histoplasma capsulatum var. farciminosum, the causative agent of epizootic lymphangitis (EZL), is endemic in parts of Africa. Diagnosis based on clinical signs and microscopy lacks specificity and is a barrier to further understanding this neglected disease. Here, a nested PCR method targeting the internal transcribed spacer (ITS) region of the rRNA operon was validated for application to equine clinical samples. Twenty-nine horses with signs of EZL from different climatic regions of Ethiopia were clinically examined. Blood samples and aspirates of pus from cutaneous nodules were taken, along with blood from a further 20 horses with no cutaneous EZL lesions. Among the 29 horses with suspected cases of EZL, H. capsulatum var. farciminosum was confirmed by extraction of DNA from pus and blood samples from 25 and 17 horses, respectively. Positive PCR results were also obtained with heat-inactivated pus (24 horses) and blood (23 horses) spotted onto Whatman FTA cards. Two positive results were obtained among blood samples from 20 horses that did not exhibit clinical signs of EZL. These are the first reports of the direct detection of H. capsulatum var. farciminosum in equine blood and at high frequency among horses exhibiting cutaneous lesions. The nested PCR outperformed conventional microscopic diagnosis, as characteristic yeast cells could be observed only in 14 pus samples. The presence of H. capsulatum var. farciminosum DNA was confirmed by sequencing the cloned PCR products, and while alignment of the ITS amplicons showed very little sequence variation, there was preliminary single nucleotide polymorphism-based evidence for the existence of two subgroups of H. capsulatum var. farciminosum This molecular diagnostic method now permits investigation of the epidemiology of EZL.

  9. Diagnostic methods for detection of bone metastases.

    PubMed

    Łukaszewski, Bartosz; Nazar, Jerzy; Goch, Maciej; Łukaszewska, Marta; Stępiński, Adrian; Jurczyk, Mieczysława U

    2017-01-01

    Skeletal metastases are severe complications in the course of cancer, and they indicate a worse prognosis. The use of modern imaging techniques allows rapid diagnosis of bone metastases. Properly selected diagnostic imaging (scintigraphy, positron emission tomography, whole body MRI) allows us to evaluate the number of metastatic foci in the skeletal system. Complementary imaging examinations (X-ray, computed tomography, magnetic resonance imaging) determine the extent of metastasis and its character: osteolytic, osteoblast, mixed). Hypercalcaemia is a symptom of low specificity for metastatic bone disease (a result of osteolysis); nevertheless, it is a significant complication in oncological treatment and worsens the prognosis of the patient. A biopsy is the final stage of the diagnostic process, which allows us to assess cell and tissue changes. Guided biopsies are performed under the control of musculoskeletal imaging methods (CT, MRI) and they are the most promising tools in bone metastases diagnosis. The development of guided biopsy techniques has led to the conclusion that they should be standard in diagnosing bone metastases. Liquid biopsy (LB) seems to be the most promising diagnostic method for detection of bone metastases. LB based on tumour-specific DNA mutation gives an opportunity for early detection and assessment of the molecular heterogeneity of the overall disease.

  10. Molecular diagnostics and therapeutics for ectopic pregnancy.

    PubMed

    Tong, Stephen; Skubisz, Monika M; Horne, Andrew W

    2015-02-01

    Ectopic pregnancies are a serious gynaecological emergency that can be fatal. As such, prompt diagnosis and safe timely treatment is essential. Here, we review the literature on the development of molecularly targeted diagnostics and therapeutics for ectopic pregnancy. A blood-based biomarker that accurately identifies an ectopic pregnancy could be used to offer early diagnostic certainty in cases where ultrasound cannot determine the location of the embryo ('a pregnancy of unknown location'). Molecules examined so far can be broadly grouped into biological themes of relevance to reproduction: (i) Fallopian tube (dys)function, (ii) embryo/trophoblast growth, (iii) corpus luteum function, (iv) inflammation, (v) uterine function and (vi) angiogenesis. While a sensitive and specific biomarker for ectopic pregnancy has yet to be identified, it is possible that improvements in platform technologies or a multi-modal biomarker approach may yield an accurate diagnostic biomarker test. Furthermore, with the advent of better imaging technology, the need for a blood-based biomarker test may be superseded by improvements in ultrasound or magnetic resonance imaging technology. There have been some recent preclinical studies describing molecularly targeted therapeutic approaches for ectopic pregnancy. Notably, bench-to-bedside studies have examined the use of combination gefitinib (orally available epidermal growth factor receptor inhibitor) and methotrexate. Preclinical studies suggest that combination gefitinib and methotrexate is highly effective in inducing placental cell death, and is significantly more effective than methotrexate alone. In early human trials, encouraging preliminary efficacy data have shown that combination gefitinib and methotrexate can rapidly resolve tubal ectopic pregnancies, and large extra-tubal ectopic pregnancies. If a large clinical randomized controlled trial confirms these findings, combination gefitinib and methotrexate could become a new

  11. Cancer diagnostics: The journey from histomorphology to molecular profiling

    PubMed Central

    Ahmed, Atif A.; Abedalthagafi, Malak

    2016-01-01

    Although histomorphology has made significant advances into the understanding of cancer etiology, classification and pathogenesis, it is sometimes complicated by morphologic ambiguities, and other shortcomings that necessitate the development of ancillary tests to complement its diagnostic value. A new approach to cancer patient management consists of targeting specific molecules or gene mutations in the cancer genome by inhibitory therapy. Molecular diagnostic tests and genomic profiling methods are increasingly being developed to identify tumor targeted molecular profile that is the basis of targeted therapy. Novel targeted therapy has revolutionized the treatment of gastrointestinal stromal tumor, renal cell carcinoma and other cancers that were previously difficult to treat with standard chemotherapy. In this review, we discuss the role of histomorphology in cancer diagnosis and management and the rising role of molecular profiling in targeted therapy. Molecular profiling in certain diagnostic and therapeutic difficulties may provide a practical and useful complement to histomorphology and opens new avenues for targeted therapy and alternative methods of cancer patient management. PMID:27509178

  12. Highlights from the 7th European meeting on molecular diagnostics.

    PubMed

    Loonen, Anne Jm; Schuurman, Rob; van den Brule, Adriaan Jc

    2012-01-01

    This report presents the highlights of the 7th European Meeting on Molecular Diagnostics held in Scheveningen, The Hague, The Netherlands, 12-14 October 2011. The areas covered included molecular diagnostics applications in medical microbiology, virology, pathology, hemato-oncology, clinical genetics and forensics. Novel real-time amplification approaches, novel diagnostic applications and new technologies, such as next-generation sequencing, PCR electrospray-ionization TOF mass spectrometry and techniques based on the detection of proteins or other molecules, were discussed. Furthermore, diagnostic companies presented their future visions for molecular diagnostics in human healthcare.

  13. Benefits and challenges of molecular diagnostics for childhood tuberculosis.

    PubMed

    Gutierrez, Cristina

    2016-12-01

    Expanding tuberculosis (TB)-diagnostic services, including access to rapid tests, is a World Health Organization (WHO) strategy to accelerate progress toward ending TB. Faster and more sensitive molecular tests capable of diagnosing TB and drug-resistant TB have the technical capacity to address limitations associated with smears and cultures by increasing accuracy and shortening turnaround times as compared with those of these conventional laboratory methods. Nucleic acid amplification assays used to detect and analyze Mycobacterium tuberculosis (MTB)-complex nucleic acids can be used directly on specimens from patients suspected of having TB. Recently, several commercial molecular tests were developed to detect MTB and determine the drug resistance (DR) based on detection of specific genetic mutations conferring resistance. The first to be endorsed by the WHO was molecular line-probe assay technology. This test uses polymerase chain reaction (PCR) and reverse-hybridization methods to rapidly identify MTB and DR-related mutations simultaneously. More recently, the WHO endorsed Xpert MTB/RIF, Cepheid Inc, CA, USA, a fully automated assay used for TB diagnosis that relies upon PCR techniques for detection of TB and rifampicin resistance-related mutations. Other promising molecular TB assays for simplifying PCR-based testing protocols and increasing their accuracy are under development and evaluation. Although we lack a practical gold standard for the diagnosis of childhood TB, its bacteriological confirmation is always recommended to be sought whenever possible prior to a diagnostic decision being made. Conventional diagnostic laboratory TB tests are less efficient for children as compared with adults, because sufficient sputum samples are more difficult to collect from infants and young children, and their disease is often paucibacillary, resulting in smear-negative disease. These inherent challenges associated with childhood TB are due to immunological- and

  14. Implementation of Rapid Molecular Infectious Disease Diagnostics: the Role of Diagnostic and Antimicrobial Stewardship.

    PubMed

    Messacar, Kevin; Parker, Sarah K; Todd, James K; Dominguez, Samuel R

    2017-03-01

    New rapid molecular diagnostic technologies for infectious diseases enable expedited accurate microbiological diagnoses. However, diagnostic stewardship and antimicrobial stewardship are necessary to ensure that these technologies conserve, rather than consume, additional health care resources and optimally affect patient care. Diagnostic stewardship is needed to implement appropriate tests for the clinical setting and to direct testing toward appropriate patients. Antimicrobial stewardship is needed to ensure prompt appropriate clinical action to translate faster diagnostic test results in the laboratory into improved outcomes at the bedside. This minireview outlines the roles of diagnostic stewardship and antimicrobial stewardship in the implementation of rapid molecular infectious disease diagnostics.

  15. Quantum Dot Enabled Molecular Sensing and Diagnostics

    PubMed Central

    Zhang, Yi; Wang, Tza-Huei

    2012-01-01

    Since its emergence, semiconductor nanoparticles known as quantum dots (QDs) have drawn considerable attention and have quickly extended their applicability to numerous fields within the life sciences. This is largely due to their unique optical properties such as high brightness and narrow emission band as well as other advantages over traditional organic fluorophores. New molecular sensing strategies based on QDs have been developed in pursuit of high sensitivity, high throughput, and multiplexing capabilities. For traditional biological applications, QDs have already begun to replace traditional organic fluorophores to serve as simple fluorescent reporters in immunoassays, microarrays, fluorescent imaging applications, and other assay platforms. In addition, smarter, more advanced QD probes such as quantum dot fluorescence resonance energy transfer (QD-FRET) sensors, quenching sensors, and barcoding systems are paving the way for highly-sensitive genetic and epigenetic detection of diseases, multiplexed identification of infectious pathogens, and tracking of intracellular drug and gene delivery. When combined with microfluidics and confocal fluorescence spectroscopy, the detection limit is further enhanced to single molecule level. Recently, investigations have revealed that QDs participate in series of new phenomena and exhibit interesting non-photoluminescent properties. Some of these new findings are now being incorporated into novel assays for gene copy number variation (CNV) studies and DNA methylation analysis with improved quantification resolution. Herein, we provide a comprehensive review on the latest developments of QD based molecular diagnostic platforms in which QD plays a versatile and essential role. PMID:22916072

  16. Supramolecular Nanoparticles for Molecular Diagnostics and Therapeutics

    NASA Astrophysics Data System (ADS)

    Chen, Kuan-Ju

    single SNP for both diagnosis and therapy were generated. The results show that this type of theranostic SNPs may have a great contribution in the optimization of therapeutic efficacy for individual patients in clinical translation in the near future. It is anticipated that our supramolecular synthetic approach could be adopted to assemble various SNP-based delivery agents for molecular diagnostics and therapeutics that pave the way toward personalized medicine.

  17. Molecular diagnostics of CNS embryonal tumors.

    PubMed

    Pfister, Stefan M; Korshunov, Andrey; Kool, Marcel; Hasselblatt, Martin; Eberhart, Charles; Taylor, Michael D

    2010-11-01

    Tremendous progress has recently been made in both molecular subgrouping, and the establishment of prognostic biomarkers for embryonal brain tumors, particularly medulloblastoma. Several prognostic biomarkers that were initially identified in retrospective cohorts of medulloblastoma, including MYC and MYCN amplification, nuclear β-catenin accumulation, and chromosome 17 aberrations have now been validated in clinical trials. Moreover, molecular subgroups based on distinct transcriptome profiles have been consistently reported from various groups on different platforms demonstrating that the concept of distinct medulloblastoma subgroups is very robust. Well-described subgroups of medulloblastomas include tumors showing wingless signaling pathway (Wnt) activation, and another characterized by sonic hedgehog pathway activity. Two or more additional subgroups were consistently reported to contain the vast majority of high-risk tumors, including most tumors with metastatic disease at diagnosis and/or large cell/anaplastic histology. Several years ago, atypical teratoid rhabdoid tumor (AT/RT) was recognized as a separate entity based on its distinct biology and particularly aggressive clinical behavior. These tumors may occur supra or infratentorially and are usually found to have genetic alterations of SMARCB1 (INI1/hSNF5), a tumor suppressor gene located on chromosome 22q. Subsequent loss of SMARCB1 protein expression comprises a relatively specific and sensitive diagnostic marker for AT/RT. For CNS primitive neuroectodermal tumors (CNS PNETs), a consistent finding has been that they are molecularly distinct from medulloblastoma. Furthermore, a distinct fraction of CNS PNETs with particularly poor prognosis only occurring in young children was delineated, which was previously labeled ependymoblastoma or embryonal tumor with abundant neuropil and true rosettes (ETANTR) and which is morphologically characterized by the presence of multilayered "ependymoblastic" rosettes

  18. Emerging diagnostic and therapeutic molecular imaging applications in vascular disease

    PubMed Central

    Eraso, Luis H; Reilly, Muredach P; Sehgal, Chandra; Mohler, Emile R

    2013-01-01

    Assessment of vascular disease has evolved from mere indirect and direct measurements of luminal stenosis to sophisticated imaging methods to depict millimeter structural changes of the vasculature. In the near future, the emergence of multimodal molecular imaging strategies may enable robust therapeutic and diagnostic (‘theragnostic’) approaches to vascular diseases that comprehensively consider structural, functional, biological and genomic characteristics of the disease in individualized risk assessment, early diagnosis and delivery of targeted interventions. This review presents a summary of recent preclinical and clinical developments in molecular imaging and theragnostic applications covering diverse atherosclerosis events such as endothelial activation, macrophage infammatory activity, plaque neovascularization and arterial thrombosis. The main focus is on molecular targets designed for imaging platforms commonly used in clinical medicine including magnetic resonance, computed tomography and positron emission tomography. A special emphasis is given to vascular ultrasound applications, considering the important role this imaging platform plays in the clinical and research practice of the vascular medicine specialty. PMID:21310769

  19. Nematode molecular diagnostics: from bands to barcodes.

    PubMed

    Powers, Tom

    2004-01-01

    Nematodes are considered among the most difficult animals to identify. DNA-based diagnostic methods have already gained acceptance in applications ranging from quarantine determinations to assessments of biodiversity. Researchers are currently in an information-gathering mode, with intensive efforts applied to accumulating nucleotide sequence of 18S and 28S ribosomal genes, internally transcribed spacer regions, and mitochondrial genes. Important linkages with collateral data such as digitized images, video clips and specimen voucher web pages are being established on GenBank and NemATOL, the nematode-specific Tree of Life database. The growing DNA taxonomy of nematodes has lead to their use in testing specific short sequences of DNA as a "barcode" for the identification of all nematode species.

  20. Polymerase chain reaction: A molecular diagnostic tool in periodontology.

    PubMed

    Maheaswari, Rajendran; Kshirsagar, Jaishree Tukaram; Lavanya, Nallasivam

    2016-01-01

    This review discusses the principles of polymerase chain reaction (PCR) and its application as a diagnostic tool in periodontology. The relevant MEDLINE and PubMed indexed journals were searched manually and electronically by typing PCR, applications of PCR, PCR in periodontics, polymorphism studies in periodontitis, and molecular techniques in periodontology. The searches were limited to articles in English language and the articles describing PCR process and its relation to periodontology were collected and used to prepare a concise review. PCR has now become a standard diagnostic and research tool in periodontology. Various studies reveal that its sensitivity and specificity allow it as a rapid, efficient method of detecting, identifying, and quantifying organism. Different immune and inflammatory markers can be identified at the mRNA expression level, and also the determination of genetic polymorphisms, thus providing the deeper insight into the mechanisms underlying the periodontal disease.

  1. Polymerase chain reaction: A molecular diagnostic tool in periodontology

    PubMed Central

    Maheaswari, Rajendran; Kshirsagar, Jaishree Tukaram; Lavanya, Nallasivam

    2016-01-01

    This review discusses the principles of polymerase chain reaction (PCR) and its application as a diagnostic tool in periodontology. The relevant MEDLINE and PubMed indexed journals were searched manually and electronically by typing PCR, applications of PCR, PCR in periodontics, polymorphism studies in periodontitis, and molecular techniques in periodontology. The searches were limited to articles in English language and the articles describing PCR process and its relation to periodontology were collected and used to prepare a concise review. PCR has now become a standard diagnostic and research tool in periodontology. Various studies reveal that its sensitivity and specificity allow it as a rapid, efficient method of detecting, identifying, and quantifying organism. Different immune and inflammatory markers can be identified at the mRNA expression level, and also the determination of genetic polymorphisms, thus providing the deeper insight into the mechanisms underlying the periodontal disease. PMID:27143822

  2. Recent advances in molecular diagnostics of hepatitis B virus.

    PubMed

    Datta, Sibnarayan; Chatterjee, Soumya; Veer, Vijay

    2014-10-28

    Hepatitis B virus (HBV) is one of the important global health problems today. Infection with HBV can lead to a variety of clinical manifestations including severe hepatic complications like liver cirrhosis and hepatocellular carcinoma. Presently, routine HBV screening and diagnosis is primarily based on the immuno-detection of HBV surface antigen (HBsAg). However, identification of HBV DNA positive cases, who do not have detectable HBsAg has greatly encouraged the use of nucleic acid amplification based assays, that are highly sensitive, specific and are to some extent tolerant to sequence variation. In the last few years, the field of HBV molecular diagnostics has evolved rapidly with advancements in the molecular biology tools, such as polymerase chain reaction (PCR) and real-time PCR. Recently, apart of PCR based amplification methods, a number of isothermal amplification assays, such as loop mediated isothermal amplification, transcription mediated amplification, ligase chain reaction, and rolling circle amplification have been utilized for HBV diagnosis. These assays also offer options for real time detection and integration into biosensing devices. In this manuscript, we review the molecular technologies that are presently available for HBV diagnostics, with special emphasis on isothermal amplification based technologies. We have also included the recent trends in the development of biosensors and use of next generation sequencing technologies for HBV.

  3. Multispectral optical tweezers for molecular diagnostics of single biological cells

    NASA Astrophysics Data System (ADS)

    Butler, Corey; Fardad, Shima; Sincore, Alex; Vangheluwe, Marie; Baudelet, Matthieu; Richardson, Martin

    2012-03-01

    Optical trapping of single biological cells has become an established technique for controlling and studying fundamental behavior of single cells with their environment without having "many-body" interference. The development of such an instrument for optical diagnostics (including Raman and fluorescence for molecular diagnostics) via laser spectroscopy with either the "trapping" beam or secondary beams is still in progress. This paper shows the development of modular multi-spectral imaging optical tweezers combining Raman and Fluorescence diagnostics of biological cells.

  4. Molecular diagnostics: the changing culture of medical microbiology.

    PubMed

    Bullman, Susan; Lucey, Brigid; Sleator, Roy D

    2012-01-01

    Diagnostic molecular biology is arguably the fastest growing area in current laboratory-based medicine. Growth of the so called 'omics' technologies has, over the last decade, led to a gradual migration away from the 'one test, one pathogen' paradigm, toward multiplex approaches to infectious disease diagnosis, which have led to significant improvements in clinical diagnostics and ultimately improved patient care.

  5. Integrating molecular diagnostics into histopathology training: the Belfast model.

    PubMed

    Flynn, C; James, J; Maxwell, P; McQuaid, S; Ervine, A; Catherwood, M; Loughrey, M B; McGibben, D; Somerville, J; McManus, D T; Gray, M; Herron, B; Salto-Tellez, M

    2014-07-01

    Molecular medicine is transforming modern clinical practice, from diagnostics to therapeutics. Discoveries in research are being incorporated into the clinical setting with increasing rapidity. This transformation is also deeply changing the way we practise pathology. The great advances in cell and molecular biology which have accelerated our understanding of the pathogenesis of solid tumours have been embraced with variable degrees of enthusiasm by diverse medical professional specialties. While histopathologists have not been prompt to adopt molecular diagnostics to date, the need to incorporate molecular pathology into the training of future histopathologists is imperative. Our goal is to create, within an existing 5-year histopathology training curriculum, the structure for formal substantial teaching of molecular diagnostics. This specialist training has two main goals: (1) to equip future practising histopathologists with basic knowledge of molecular diagnostics and (2) to create the option for those interested in a subspecialty experience in tissue molecular diagnostics to pursue this training. It is our belief that this training will help to maintain in future the role of the pathologist at the centre of patient care as the integrator of clinical, morphological and molecular information. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  6. Molecular diagnostic assays for infectious diseases in cats.

    PubMed

    Veir, Julia K; Lappin, Michael R

    2010-11-01

    With the advent of more accessible polymerase chain reaction panels, the use of molecular techniques for the detection of infectious organisms has become more routine in veterinary medicine. The use of molecular diagnostics is best reserved for the detection of organisms that are difficult to detect or identify expediently. In this article, the fundamentals of molecular techniques are reviewed along with an examination of specific feline infectious diseases in which diagnosis via molecular techniques is advantageous.

  7. Methods in Molecular Biophysics

    NASA Astrophysics Data System (ADS)

    Serdyuk, Igor N.; Zaccai, Nathan R.; Zaccai, Joseph

    2001-12-01

    Our knowledge of biological macromolecules and their interactions is based on the application of physical methods, ranging from classical thermodynamics to recently developed techniques for the detection and manipulation of single molecules. These methods, which include mass spectrometry, hydrodynamics, microscopy, diffraction and crystallography, electron microscopy, molecular dynamics simulations, and nuclear magnetic resonance, are complementary; each has its specific advantages and limitations. Organised by method, this textbook provides descriptions and examples of applications for the key physical methods in modern biology. It is an invaluable resource for undergraduate and graduate students of molecular biophysics in science and medical schools, as well as research scientists looking for an introduction to techniques beyond their specialty. As appropriate for this interdisciplinary field, the book includes short asides to explain physics aspects to biologists and biology aspects to physicists. Comprehensive coverage and up-to-date treatment of the latest physical methods in modern biology Each method includes a brief historical introduction, theoretical principles, applications, advantages and limitations, and concludes with a checklist of key ideas Interdisciplinary and accessible to biologists, physicists, and those with medical backgrounds

  8. Molecular Diagnostics of Ageing and Tackling Age-related Disease.

    PubMed

    Timmons, James A

    2017-01-01

    As average life expectancy increases there is a greater focus on health-span and, in particular, how to treat or prevent chronic age-associated diseases. Therapies which were able to control 'biological age' with the aim of postponing chronic and costly diseases of old age require an entirely new approach to drug development. Molecular technologies and machine-learning methods have already yielded diagnostics that help guide cancer treatment and cardiovascular procedures. Discovery of valid and clinically informative diagnostics of human biological age (combined with disease-specific biomarkers) has the potential to alter current drug-discovery strategies, aid clinical trial recruitment and maximize healthy ageing. I will review some basic principles that govern the development of 'ageing' diagnostics, how such assays could be used during the drug-discovery or development process. Important logistical and statistical considerations are illustrated by reviewing recent biomarker activity in the field of Alzheimer's disease, as dementia represents the most pressing of priorities for the pharmaceutical industry, as well as the chronic disease in humans most associated with age. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Tomographic methods in flow diagnostics

    NASA Technical Reports Server (NTRS)

    Decker, Arthur J.

    1993-01-01

    This report presents a viewpoint of tomography that should be well adapted to currently available optical measurement technology as well as the needs of computational and experimental fluid dynamists. The goals in mind are to record data with the fastest optical array sensors; process the data with the fastest parallel processing technology available for small computers; and generate results for both experimental and theoretical data. An in-depth example treats interferometric data as it might be recorded in an aeronautics test facility, but the results are applicable whenever fluid properties are to be measured or applied from projections of those properties. The paper discusses both computed and neural net calibration tomography. The report also contains an overview of key definitions and computational methods, key references, computational problems such as ill-posedness, artifacts, missing data, and some possible and current research topics.

  10. Nutritional Lipidomics: Molecular Metabolism, Analytics, and Diagnostics

    PubMed Central

    Smilowitz, Jennifer T.; Zivkovic, Angela M.; Wan, Yu-Jui Yvonne; Watkins, Steve M.; Nording, Malin L.; Hammock, Bruce D.; German, J. Bruce

    2013-01-01

    The field of lipidomics is providing nutritional science a more comprehensive view of lipid intermediates. Lipidomics research takes advantage of the increase in accuracy and sensitivity of mass detection of mass spectrometry with new bioinformatics toolsets to characterize the structures and abundances of complex lipids. Yet, translating lipidomics to practice via nutritional interventions is still in its infancy. No single instrumentation platform is able to solve the varying analytical challenges of the different molecular lipid species. Biochemical pathways of lipid metabolism remain incomplete and the tools to map lipid compositional data to pathways are still being assembled. Biology itself is dauntingly complex and simply separating biological structures remains a key challenge to lipidomics. Nonetheless, the strategy of combining tandem analytical methods to perform the sensitive, high-throughput, quantitative and comprehensive analysis of lipid metabolites of very large numbers of molecules is poised to drive the field forward rapidly. Among the next steps for nutrition to understand the changes in structures, compositions and function of lipid biomolecules in response to diet is to describe their distribution within discrete functional compartments-lipoproteins. Additionally, lipidomics must tackle the task of assigning the functions of lipids as signaling molecules, nutrient sensors, and intermediates of metabolic pathways. PMID:23818328

  11. Nutritional lipidomics: molecular metabolism, analytics, and diagnostics.

    PubMed

    Smilowitz, Jennifer T; Zivkovic, Angela M; Wan, Yu-Jui Yvonne; Watkins, Steve M; Nording, Malin L; Hammock, Bruce D; German, J Bruce

    2013-08-01

    The field of lipidomics is providing nutritional science a more comprehensive view of lipid intermediates. Lipidomics research takes advantage of the increase in accuracy and sensitivity of mass detection of MS with new bioinformatics toolsets to characterize the structures and abundances of complex lipids. Yet, translating lipidomics to practice via nutritional interventions is still in its infancy. No single instrumentation platform is able to solve the varying analytical challenges of the different molecular lipid species. Biochemical pathways of lipid metabolism remain incomplete and the tools to map lipid compositional data to pathways are still being assembled. Biology itself is dauntingly complex and simply separating biological structures remains a key challenge to lipidomics. Nonetheless, the strategy of combining tandem analytical methods to perform the sensitive, high-throughput, quantitative, and comprehensive analysis of lipid metabolites of very large numbers of molecules is poised to drive the field forward rapidly. Among the next steps for nutrition to understand the changes in structures, compositions, and function of lipid biomolecules in response to diet is to describe their distribution within discrete functional compartments lipoproteins. Additionally, lipidomics must tackle the task of assigning the functions of lipids as signaling molecules, nutrient sensors, and intermediates of metabolic pathways. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Malignant Catarrhal Fever: Understanding Molecular Diagnostics in Context of Epidemiology

    PubMed Central

    Li, Hong; Cunha, Cristina W.; Taus, Naomi S.

    2011-01-01

    Malignant catarrhal fever (MCF) is a frequently fatal disease, primarily of ruminants, caused by a group of gammaherpesviruses. Due to complexities of pathogenesis and epidemiology in various species, which are either clinically-susceptible or reservoir hosts, veterinary clinicians face significant challenges in laboratory diagnostics. The recent development of specific assays for viral DNA and antibodies has expanded and improved the inventory of laboratory tests and opened new opportunities for use of MCF diagnostics. Issues related to understanding and implementing appropriate assays for specific diagnostic needs must be addressed in order to take advantage of molecular diagnostics in the laboratory. PMID:22072925

  13. Cryptosporidiosis: multiattribute evaluation of six diagnostic methods.

    PubMed Central

    MacPherson, D W; McQueen, R

    1993-01-01

    Six diagnostic methods (Giemsa staining, Ziehl-Neelsen staining, auramine-rhodamine staining, Sheather's sugar flotation, an indirect immunofluorescence procedure, and a modified concentration-sugar flotation method) for the detection of Cryptosporidium spp. in stool specimens were compared on the following attributes: diagnostic yield, cost to perform each test, ease of handling, and ability to process large numbers of specimens for screening purposes by batching. A rank ordering from least desirable to most desirable was then established for each method by using the study attributes. The process of decision analysis with respect to the laboratory diagnosis of cryptosporidiosis is discussed through the application of multiattribute utility theory to the rank ordering of the study criteria. Within a specific health care setting, a diagnostic facility will be able to calculate its own utility scores for our study attributes. Multiattribute evaluation and analysis are potentially powerful tools in the allocation of resources in the laboratory. PMID:8432802

  14. Molecular diagnostics in medical microbiology: yesterday, today and tomorrow.

    PubMed

    van Belkum, Alex

    2003-10-01

    Clinical microbiology is clearly on the move, and various new diagnostic technologies have been introduced into laboratory practice over the past few decades. However, Henri D Isenberg recently stated that molecular biology techniques promised to revolutionise the diagnosis of infectious disease, but that, to date, this promise is still in its infancy. Molecular diagnostics have now surpassed these early stages and have definitely reached puberty. Currently, a second generation of automated molecular approaches is already within the microbiologists' reach. Quantitative amplification tests in combination with genomics, transcriptomics, proteomics and related methodologies will pave the way to further enhancement of innovative microbial detection and identification.

  15. Aspects of molecular diagnostics and therapy in obstetrics and gynecology.

    PubMed

    Beckmann, Matthias W; Strick, Reiner; Strissel, Pamela L; Fasching, Peter A; Oppelt, Peter; Pöhls, Uwe D; Malur, Sabine U; Ackermann, Sven

    2003-05-01

    Scientific progress and information relating to the theoretical and clinical work being carried out in the field of obstetrics and gynecology has dramatically increased due to recent developments in molecular biology. Molecular obstetrics and gynecology is therefore the link between the different sections in obstetrics and gynecology. At present, the molecular understanding of cellular pathways is much greater than that of the direct integration of molecular diagnostics and therapy in routine clinical practice. The use of molecular diagnostics, such as preimplantation diagnostics or predictive genetic testing, still has technical problems as well as novel, and to date unclear, social, ethical and legal implications. To date, the technical elements of molecular therapy have not yet fulfilled their expectations. In the broad spectrum of obstetrics and gynecology, new molecular discoveries are influenced not only by technical but also by socioeconomic and political considerations. These include, for example, free access to genetic testing, patents for genes and the financial monopoly over molecular medication. Society must propose rules for the potential integration of the knowledge of molecular obstetrics and gynecology into the daily care of those seeking aid or advice.

  16. Achieving molecular diagnostics for Lyme disease.

    PubMed

    Eshoo, Mark W; Schutzer, Steven E; Crowder, Christopher D; Carolan, Heather E; Ecker, David J

    2013-11-01

    Early Lyme disease is often difficult to diagnose. Left untreated, symptoms can last for many years leading to chronic health problems. Serological tests for the presence of antibodies that react to Borrelia burgdorferi antigens are generally used to support a clinical diagnosis. Due to the biologically delayed antibody response, serology is negative in many patients in the initial 3 weeks after infection and a single test cannot be used to demonstrate active disease, although certain specialized tests provide strong correlation. Because of these limitations there exists a need for better diagnostics for Lyme disease that can detect Borrelia genomic material at the onset of symptoms.

  17. Molecular malaria diagnostics: A systematic review and meta-analysis.

    PubMed

    Roth, Johanna M; Korevaar, Daniël A; Leeflang, Mariska M G; Mens, Pètra F

    2016-01-01

    Accurate diagnosis of malaria is essential for identification and subsequent treatment of the disease. Currently, microscopy and rapid diagnostic tests are the most commonly used diagnostics, next to treatment based on clinical signs only. These tests are easy to deploy, but have a relatively high detection limit. With declining prevalence in many areas, there is an increasing need for more sensitive diagnostics. Molecular tools may be a suitable alternative, although costs and technical requirements currently hamper their implementation in resource limited settings. A range of (near) point-of-care diagnostics is therefore under development, including simplifications in sample preparation, amplification and/or read-out of the test. Accuracy data, in combination with technical characteristics, are essential in determining which molecular test, if any, would be the most promising to be deployed. This review presents a comprehensive overview of the currently available molecular malaria diagnostics, ranging from well-known tests to platforms in early stages of evaluation, and systematically evaluates their published accuracy. No important difference in accuracy was found between the most commonly used PCR-based assays (conventional, nested and real-time PCR), with most of them having high sensitivity and specificity, implying that there are no reasons other than practical ones to choose one technique over the other. Loop-mediated isothermal amplification and other (novel) diagnostics appear to be highly accurate as well, with some offering potential to be used in resource-limited settings.

  18. Hybrid opto-electric techniques for molecular diagnostics

    SciTech Connect

    Haque, Aeraj Ul

    2012-01-01

    Hybrid optoelectric techniques reflect a new paradigm in microfluidics. In essence, these are microfluidic techniques that employ a synergistic combination of optical and electrical forces to enable noninvasive manipulation of fluids and/or particle-type entities at the micro/nano-scale [1]. Synergy between optical and electrical forces bestows these techniques with several unique features that are promising to bring new opportunities in molecular diagnostics. Within the scope of molecular diagnostics, several aspects of optoelectric techniques promise to play a relevant role. These include, but are not limited to, sample preparation, sorting, purification, amplification and detection.

  19. Low-pressure plasma diagnostic methods

    SciTech Connect

    Eddy, T.L.

    1989-01-01

    Diagnostic techniques have been recently developed that permit the determination of the deviation from local thermal equilibrium (LTE) in subatmospheric electric arcs and plasma jets. A review is presented of the methods that are applicable to MPD and arcjet thruster plasmas but that have not been used in space propulsion research. Appropriate plasma diagnostics can lead to increased thrust, better nozzle design, and improved modeling capabilities. These methods include nonintrusive techniques, and can determine the electron, gas, and total excitation, temperatures, as well as the electron and atom densities, without using LTE or partial LTE assumptions. General relations for analysis and experimental results for argon constricted arcs, an arc in a rotating magnetic field, and plasma torch jets are presented. The methods discussed can also be applied to plasma mixtures. 23 refs.

  20. Molecular Diagnostics and Genetic Counseling in Primary Congenital Glaucoma.

    PubMed

    Faiq, Muneeb; Mohanty, Kuldeep; Dada, Rima; Dada, Tanuj

    2013-01-01

    Primary congenital glaucoma (PCG) is a childhood irreversible blinding disorder with onset at birth or in the first year of life. It is characterized by the classical traid of symptoms viz. epiphora (excessive tearing), photophobia (hypersensitivity to light) and blepharospasm (inflammation of eyelids). The only anatomical defect seen in PCG is trabecular meshwork dysgenesis. PCG shows autosomal recessive mode of inheritance with considerable number of sporadic cases. The etiology of this disease has not been fully understood but some genes like CYP1B1, MYOC, FOXC1, LTBP2 have been implicated. Various chromosomal aberrations and mutations in mitochondrial genome have also been reported. Molecular biology has developed novel techniques in order to do genetic and biochemical characterization of many genetic disorders including PCG. Techniques like polymerase chain reaction, single strand conformational polymorphism and sequencing are already in use for diagnosis of PCG and other techniques like protein truncation testing and functional genomics are beginning to find their way into molecular workout of this disorder. In the light of its genetic etiology, it is important to develop methods for genetic counseling for the patients and their families so as to bring down its incidence. In this review, we ought to develop a genetic insight into PCG with possible use of molecular biology and functional genomics in understanding the disease etiology, pathogenesis, pathology and mechanism of inheritance. We will also discuss the possibilities and use of genetic counseling in this disease. How to cite this article: Faiq M, Mohanty K, Dada R, Dada T. Molecular Diagnostics and Genetic Counseling in Primary Congenital Glaucoma. J Current Glau Prac 2013;7(1):25-35.

  1. The rapid evolution of molecular genetic diagnostics in neuromuscular diseases.

    PubMed

    Volk, Alexander E; Kubisch, Christian

    2017-10-01

    The development of massively parallel sequencing (MPS) has revolutionized molecular genetic diagnostics in monogenic disorders. The present review gives a brief overview of different MPS-based approaches used in clinical diagnostics of neuromuscular disorders (NMDs) and highlights their advantages and limitations. MPS-based approaches like gene panel sequencing, (whole) exome sequencing, (whole) genome sequencing, and RNA sequencing have been used to identify the genetic cause in NMDs. Although gene panel sequencing has evolved as a standard test for heterogeneous diseases, it is still debated, mainly because of financial issues and unsolved problems of variant interpretation, whether genome sequencing (and to a lesser extent also exome sequencing) of single patients can already be regarded as routine diagnostics. However, it has been shown that the inclusion of parents and additional family members often leads to a substantial increase in the diagnostic yield in exome-wide/genome-wide MPS approaches. In addition, MPS-based RNA sequencing just enters the research and diagnostic scene. Next-generation sequencing increasingly enables the detection of the genetic cause in highly heterogeneous diseases like NMDs in an efficient and affordable way. Gene panel sequencing and family-based exome sequencing have been proven as potent and cost-efficient diagnostic tools. Although clinical validation and interpretation of genome sequencing is still challenging, diagnostic RNA sequencing represents a promising tool to bypass some hurdles of diagnostics using genomic DNA.

  2. Molecular diagnostics of cardiovascular diseases in sudden unexplained death.

    PubMed

    Tang, Yingying; Stahl-Herz, Jay; Sampson, Barbara A

    2014-01-01

    The most challenging type of sudden cardiac death is sudden unexplained death. The etiologies for sudden unexplained death are diverse and not necessarily confined to the cardiovascular system. Nevertheless, certain cardiovascular diseases, particularly cardiac channelopathies and cardiomyopathies, are known to play significant roles in sudden deaths. The purpose of the review is to provide autopsy pathologists with an actionable guide through illuminating the clinically relevant molecular basis of cardiac channelopathies and cardiomyopathies, as well as the changing landscape of molecular diagnostics.

  3. Personalized Cancer Medicine: Molecular Diagnostics, Predictive biomarkers, and Drug Resistance

    PubMed Central

    Gonzalez de Castro, D; Clarke, P A; Al-Lazikani, B; Workman, P

    2013-01-01

    The progressive elucidation of the molecular pathogenesis of cancer has fueled the rational development of targeted drugs for patient populations stratified by genetic characteristics. Here we discuss general challenges relating to molecular diagnostics and describe predictive biomarkers for personalized cancer medicine. We also highlight resistance mechanisms for epidermal growth factor receptor (EGFR) kinase inhibitors in lung cancer. We envisage a future requiring the use of longitudinal genome sequencing and other omics technologies alongside combinatorial treatment to overcome cellular and molecular heterogeneity and prevent resistance caused by clonal evolution. PMID:23361103

  4. Improving the treatment of musculoskeletal infections with molecular diagnostics.

    PubMed

    Tarkin, Ivan S; Dunman, Paul M; Garvin, Kevin L

    2005-08-01

    Molecular diagnostic strategies have been implemented to enhance the treatment of musculoskeletal infections. Once primarily a research tool, molecular-based assays, have become accepted clinical tests for the genomic detection of certain pathogens involved in bone and joint infections. Currently, culture remains the gold standard for identifying most organisms causing infection. However, molecular assays are beneficial in clinical cases in which standard culture-based tests are unreliable or untimely. We will review current clinical utility of this emerging technology and roles for assays in the future.

  5. Molecular engineering of antibodies for therapeutic and diagnostic purposes

    PubMed Central

    Ducancel, Frédéric; Muller, Bruno H.

    2012-01-01

    During the past ten years, monoclonal antibodies (mAbs) have taken center stage in the field of targeted therapy and diagnosis. This increased interest in mAbs is due to their binding accuracy (affinity and specificity) together with the original molecular and structural rules that govern interactions with their cognate antigen. In addition, the effector properties of antibodies constitute a second major advantage associated with their clinical use. The development of molecular and structural engineering and more recently of in vitro evolution of antibodies has opened up new perspectives in the de novo design of antibodies more adapted to clinical and diagnostic use. Thus, efforts are regularly made by researchers to improve or modulate antibody recognition properties, to adapt their pharmacokinetics, engineer their stability, and control their immunogenicity. This review presents the latest molecular engineering results on mAbs with therapeutic and diagnostic applications. PMID:22684311

  6. The impact of new trends in POCTs for companion diagnostics, non-invasive testing and molecular diagnostics.

    PubMed

    Huckle, David

    2015-06-01

    Point-of-care diagnostics have been slowly developing over several decades and have taken on a new importance in current healthcare delivery for both diagnostics and development of new drugs. Molecular diagnostics have become a key driver of technology change and opened up new areas in companion diagnostics for use alongside pharmaceuticals and in new clinical approaches such as non-invasive testing. Future areas involving smartphone and other information technology advances, together with new developments in molecular biology, microfluidics and surface chemistry are adding to advances in the market. The focus for point-of-care tests with molecular diagnostic technologies is focused on advancing effective applications.

  7. Non-invasive diagnostic methods in dentistry

    NASA Astrophysics Data System (ADS)

    Todea, Carmen

    2016-03-01

    The paper, will present the most important non-invasive methods for diagnostic, in different fields of dentistry. Moreover, the laser-based methods will be emphasis. In orthodontics, 3D laser scanners are increasingly being used to establish database for normative population and cross-sectional growth changes but also to asses clinical outcomes in orthognatic surgical and non-surgical treatments. In prevention the main methods for diagnostic of demineralization and caries detection in early stages are represented by laser fluorescence - Quantitative Light Florescence (QLF); DiagnoDent-system-655nm; FOTI-Fiberoptic transillumination; DIFOTI-Digital Imaging Fiberoptic transillumination; and Optical Coherence Tomography (OCT). In odontology, Laser Doppler Flowmetry (LDF) is a noninvasive real time method used for determining the tooth vitality by monitoring the pulp microcirculation in traumatized teeth, fractured teeth, and teeth undergoing different conservative treatments. In periodontology, recently study shows the ability of LDF to evaluate the health of gingival tissue in periodontal tissue diseases but also after different periodontal treatments.

  8. Intelligent DNA-based molecular diagnostics using linked genetic markers

    SciTech Connect

    Pathak, D.K.; Perlin, M.W.; Hoffman, E.P.

    1994-12-31

    This paper describes a knowledge-based system for molecular diagnostics, and its application to fully automated diagnosis of X-linked genetic disorders. Molecular diagnostic information is used in clinical practice for determining genetic risks, such as carrier determination and prenatal diagnosis. Initially, blood samples are obtained from related individuals, and PCR amplification is performed. Linkage-based molecular diagnosis then entails three data analysis steps. First, for every individual, the alleles (i.e., DNA composition) are determined at specified chromosomal locations. Second, the flow of genetic material among the individuals is established. Third, the probability that a given individual is either a carrier of the disease or affected by the disease is determined. The current practice is to perform each of these three steps manually, which is costly, time consuming, labor-intensive, and error-prone. As such, the knowledge-intensive data analysis and interpretation supersede the actual experimentation effort as the major bottleneck in molecular diagnostics. By examining the human problem solving for the task, we have designed and implemented a prototype knowledge-based system capable of fully automating linkage-based molecular diagnostics in X-linked genetic disorders, including Duchenne Muscular Dystrophy (DMD). Our system uses knowledge-based interpretation of gel electrophoresis images to determine individual DNA marker labels, a constraint satisfaction search for consistent genetic flow among individuals, and a blackboard-style problem solver for risk assessment. We describe the system`s successful diagnosis of DMD carrier and affected individuals from raw clinical data.

  9. Multiple biomarkers in molecular oncology. I. Molecular diagnostics applications in cervical cancer detection.

    PubMed

    Malinowski, Douglas P

    2007-03-01

    The screening for cervical carcinoma and its malignant precursors (cervical neoplasia) currently employs morphology-based detection methods (Papanicolaou [Pap] smear) in addition to the detection of high-risk human papillomavirus. The combination of the Pap smear with human papillomavirus testing has achieved significant improvements in sensitivity for the detection of cervical disease. Diagnosis of cervical neoplasia is dependent upon histology assessment of cervical biopsy specimens. Attempts to improve the specificity of cervical disease screening have focused on the investigation of molecular biomarkers for adjunctive use in combination with the Pap smear. Active research into the genomic and proteomic alterations that occur during human papillomavirus-induced neoplastic transformation have begun to characterize some of the basic mechanisms inherent to the disease process of cervical cancer development. This research continues to demonstrate the complexity of multiple genomic and proteomic alterations that accumulate during the tumorigenesis process. Despite this diversity, basic patterns of uncontrolled signal transduction, cell cycle deregulation, activation of DNA replication and altered extracellular matrix interactions are beginning to emerge as common features inherent to cervical cancer development. Some of these gene or protein expression alterations have been investigated as potential biomarkers for screening and diagnostics applications. The contribution of multiple gene alterations in the development of cervical cancer suggests that the application of multiple biomarker panels has the potential to develop clinically useful molecular diagnostics. In this review, the application of biomarkers for the improvement of sensitivity and specificity of the detection of cervical neoplasia within cytology specimens will be discussed.

  10. Molecular diagnostics: harmonization through reference materials, documentary standards and proficiency testing.

    PubMed

    Holden, Marcia J; Madej, Roberta M; Minor, Philip; Kalman, Lisa V

    2011-09-01

    There is a great need for harmonization in nucleic acid testing for infectious disease and clinical genetics. The proliferation of assay methods, the number of targets for molecular diagnostics and the absence of standard reference materials contribute to variability in test results among laboratories. This article provides a comprehensive overview of reference materials, related documentary standards and proficiency testing programs. The article explores the relationships among these resources and provides necessary information for people practicing in this area that is not taught in formal courses and frequently is obtained on an ad hoc basis. The aim of this article is to provide helpful tools for molecular diagnostic laboratories.

  11. Molecular diagnostic and surveillance tools for global malaria control.

    PubMed

    Erdman, Laura K; Kain, Kevin C

    2008-01-01

    Malaria is the most devastating parasitic infection in the world, annually causing over 1 million deaths and extensive morbidity. The global burden of malaria has increased over the last several decades, as have rates of imported malaria into non-endemic regions. Rapid and accurate diagnostics are a crucial component of malaria control strategies, and epidemiological surveillance is required to monitor trends in malaria prevalence and antimalarial drug resistance. Conventional malaria diagnostic and surveillance tools can be cumbersome and slow with limitations in both sensitivity and specificity. New molecular techniques have been developed in an attempt to overcome these restrictions. These molecular techniques are discussed with regard to their technical advantages and disadvantages, with an emphasis on the practicality of implementation in malaria-endemic and non-endemic regions.

  12. Something old and something new about molecular diagnostics in gliomas

    PubMed Central

    Horbinski, Craig

    2012-01-01

    Synopsis Progress in our understanding of the molecular biology of neoplasms has been driven by remarkable improvements in molecular biology techniques. This has created a rapidly moving field in which even subspecialists struggle to keep abreast of the current literature. Nowhere is this more clearly demonstrated than in neuro-oncology, wherein molecular diagnostics can now wring more clinically useful information out of very small biopsies than ever before. Herein the biologic and practical aspects of four key molecular biomarkers in gliomas are discussed, including two that have been known for some time (1p/19q codeletion and EGFR amplification) as well as two whose relevance was discovered via advanced whole-genome assays (IDH1/2 mutations and BRAF alterations). PMID:23459421

  13. A new molecular diagnostic tool for quantitatively detecting and genotyping “Candidatus Liberibacter species”

    USDA-ARS?s Scientific Manuscript database

    A new molecular diagnostic method was developed for quantitative detection of “Candidatus Liberibacter” species associated with citrus Huanglongbing (“Ca. Liberibacter asiaticus”, “Ca. Liberibacter africanus” and “Ca. Liberibacter americanus”) and potato zebra chip disorder (“Ca. Liberibacter solana...

  14. Methods in molecular cardiology

    PubMed Central

    de Theije, C.C.; de Windt, L.J.; Doevendans, P.A.

    2002-01-01

    Sequencing is one the major breakthroughs in molecular cardiology. The development of this technique has made it possible to determine the exact order of the nucleotides in DNA. The exact order is relevant for the formation of proteins, through the genetic code. Sequencing is even more important for the identification of genetic variation and disease-causing mutations. The elucidation of the human genome is based on the continuous improvement of this technique, reducing the cost and increasing efficiency. Initially, complex chemical reactions were performed using isotopes to unravel the base sequence in genes. Nowadays, fluorescent capillary-based techniques are available to determine the genetic information. Here, the historical development of the technique is described. In addition, examples are provided on how sequencing is used in clinical medicine. ImagesFigure 2Figure 3Figure 8Figure 9 PMID:25696079

  15. Paper-based sample-to-answer molecular diagnostic platform for point-of-care diagnostics.

    PubMed

    Choi, Jane Ru; Tang, Ruihua; Wang, ShuQi; Wan Abas, Wan Abu Bakar; Pingguan-Murphy, Belinda; Xu, Feng

    2015-12-15

    Nucleic acid testing (NAT), as a molecular diagnostic technique, including nucleic acid extraction, amplification and detection, plays a fundamental role in medical diagnosis for timely medical treatment. However, current NAT technologies require relatively high-end instrumentation, skilled personnel, and are time-consuming. These drawbacks mean conventional NAT becomes impractical in many resource-limited disease-endemic settings, leading to an urgent need to develop a fast and portable NAT diagnostic tool. Paper-based devices are typically robust, cost-effective and user-friendly, holding a great potential for NAT at the point of care. In view of the escalating demand for the low cost diagnostic devices, we highlight the beneficial use of paper as a platform for NAT, the current state of its development, and the existing challenges preventing its widespread use. We suggest a strategy involving integrating all three steps of NAT into one single paper-based sample-to-answer diagnostic device for rapid medical diagnostics in the near future.

  16. Current status of diagnostic methods for henipavirus.

    PubMed

    Tamin, A; Rota, P A

    2013-01-01

    Hendra virus (HeV) and Nipah virus (NiV) are the causative agents of emerging transboundary animal disease in pigs and horses. They also cause fatal disease in humans. NiV has a case fatality rate of 40 - 100%. In the initial NiV outbreak in Malaysia in 1999, about 1.1 million pigs had to be culled. The economic impact was estimated to be approximately US$450 million. Worldwide, HeV has caused more than 60 deaths in horses with 7 human cases and 4 deaths. Since the initial outbreak, HeV spillovers from Pteropus bats to horses and humans continue. This article presents a brief review on the currently available diagnostic methods for henipavirus infections, including advances achieved since the initial outbreak, and a gap analysis of areas needing improvement.

  17. Molecular Pathogenesis and Diagnostic, Prognostic and Predictive Molecular Markers in Sarcoma.

    PubMed

    Mariño-Enríquez, Adrián; Bovée, Judith V M G

    2016-09-01

    Sarcomas are infrequent mesenchymal neoplasms characterized by notable morphological and molecular heterogeneity. Molecular studies in sarcoma provide refinements to morphologic classification, and contribute diagnostic information (frequently), prognostic stratification (rarely) and predict therapeutic response (occasionally). Herein, we summarize the major molecular mechanisms underlying sarcoma pathogenesis and present clinically useful diagnostic, prognostic and predictive molecular markers for sarcoma. Five major molecular alterations are discussed, illustrated with representative sarcoma types, including 1. the presence of chimeric transcription factors, in vascular tumors; 2. abnormal kinase signaling, in gastrointestinal stromal tumor; 3. epigenetic deregulation, in chondrosarcoma, chondroblastoma, and other tumors; 4. deregulated cell survival and proliferation, due to focal copy number alterations, in dedifferentiated liposarcoma; 5. extreme genomic instability, in conventional osteosarcoma as a representative example of sarcomas with highly complex karyotype. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. New approaches to sepsis: molecular diagnostics and biomarkers.

    PubMed

    Reinhart, Konrad; Bauer, Michael; Riedemann, Niels C; Hartog, Christiane S

    2012-10-01

    Sepsis is among the most common causes of death in hospitals. It arises from the host response to infection. Currently, diagnosis relies on nonspecific physiological criteria and culture-based pathogen detection. This results in diagnostic uncertainty, therapeutic delays, the mis- and overuse of antibiotics, and the failure to identify patients who might benefit from immunomodulatory therapies. There is a need for new sepsis biomarkers that can aid in therapeutic decision making and add information about screening, diagnosis, risk stratification, and monitoring of the response to therapy. The host response involves hundreds of mediators and single molecules, many of which have been proposed as biomarkers. It is, however, unlikely that one single biomarker is able to satisfy all the needs and expectations for sepsis research and management. Among biomarkers that are measurable by assays approved for clinical use, procalcitonin (PCT) has shown some usefulness as an infection marker and for antibiotic stewardship. Other possible new approaches consist of molecular strategies to improve pathogen detection and molecular diagnostics and prognostics based on transcriptomic, proteomic, or metabolic profiling. Novel approaches to sepsis promise to transform sepsis from a physiologic syndrome into a group of distinct biochemical disorders and help in the development of better diagnostic tools and effective adjunctive sepsis therapies.

  19. New Approaches to Sepsis: Molecular Diagnostics and Biomarkers

    PubMed Central

    Bauer, Michael; Riedemann, Niels C.; Hartog, Christiane S.

    2012-01-01

    Summary: Sepsis is among the most common causes of death in hospitals. It arises from the host response to infection. Currently, diagnosis relies on nonspecific physiological criteria and culture-based pathogen detection. This results in diagnostic uncertainty, therapeutic delays, the mis- and overuse of antibiotics, and the failure to identify patients who might benefit from immunomodulatory therapies. There is a need for new sepsis biomarkers that can aid in therapeutic decision making and add information about screening, diagnosis, risk stratification, and monitoring of the response to therapy. The host response involves hundreds of mediators and single molecules, many of which have been proposed as biomarkers. It is, however, unlikely that one single biomarker is able to satisfy all the needs and expectations for sepsis research and management. Among biomarkers that are measurable by assays approved for clinical use, procalcitonin (PCT) has shown some usefulness as an infection marker and for antibiotic stewardship. Other possible new approaches consist of molecular strategies to improve pathogen detection and molecular diagnostics and prognostics based on transcriptomic, proteomic, or metabolic profiling. Novel approaches to sepsis promise to transform sepsis from a physiologic syndrome into a group of distinct biochemical disorders and help in the development of better diagnostic tools and effective adjunctive sepsis therapies. PMID:23034322

  20. [Molecular Genetics as Best Evidence in Glioma Diagnostics].

    PubMed

    Masui, Kenta; Komori, Takashi

    2016-03-01

    The development of a genomic landscape of gliomas has led to the internally consistent, molecularly-based classifiers. However, development of a biologically insightful classification to guide therapy is still ongoing. Further, tumors are heterogeneous, and they change and adapt in response to drugs. The challenge of developing molecular classifiers that provide meaningful ways to stratify patients for therapy remains a major challenge for the field. Therefore, by incorporating molecular markers into the new World Health Organization (WHO) classification of tumors of the central nervous system, the traditional principle of diagnosis based on histologic criteria will be replaced by a multilayered approach combining histologic features and molecular information in an "integrated diagnosis", to define tumor entities as narrowly as possible. We herein review the current status of diagnostic molecular markers for gliomas, focusing on IDH mutation, ATRX mutation, 1p/19q co-deletion, and TERT promoter mutation in adult tumors, as well as BRAF and H3F3A aberrations in pediatric gliomas, the combination of which will be a promising endeavor to render molecular genetics as a best evidence in the glioma diagnositics.

  1. Health Technology Assessment for Molecular Diagnostics: Practices, Challenges, and Recommendations from the Medical Devices and Diagnostics Special Interest Group.

    PubMed

    Garfield, Susan; Polisena, Julie; S Spinner, Daryl; Postulka, Anne; Y Lu, Christine; Tiwana, Simrandeep K; Faulkner, Eric; Poulios, Nick; Zah, Vladimir; Longacre, Michael

    2016-01-01

    Health technology assessments (HTAs) are increasingly used to inform coverage, access, and utilization of medical technologies including molecular diagnostics (MDx). Although MDx are used to screen patients and inform disease management and treatment decisions, there is no uniform approach to their evaluation by HTA organizations. The International Society for Pharmacoeconomics and Outcomes Research Devices and Diagnostics Special Interest Group reviewed diagnostic-specific HTA programs and identified elements representing common and best practices. MDx-specific HTA programs in Europe, Australia, and North America were characterized by methodology, evaluation framework, and impact. Published MDx HTAs were reviewed, and five representative case studies of test evaluations were developed: United Kingdom (National Institute for Health and Care Excellence's Diagnostics Assessment Programme, epidermal growth factor receptor tyrosine kinase mutation), United States (Palmetto's Molecular Diagnostic Services Program, OncotypeDx prostate cancer test), Germany (Institute for Quality and Efficiency in Healthcare, human papillomavirus testing), Australia (Medical Services Advisory Committee, anaplastic lymphoma kinase testing for non-small cell lung cancer), and Canada (Canadian Agency for Drugs and Technologies in Health, Rapid Response: Non-invasive Prenatal Testing). Overall, the few HTA programs that have MDx-specific methods do not provide clear parameters of acceptability related to clinical and analytic performance, clinical utility, and economic impact. The case studies highlight similarities and differences in evaluation approaches across HTAs in the performance metrics used (analytic and clinical validity, clinical utility), evidence requirements, and how value is measured. Not all HTAs are directly linked to reimbursement outcomes. To improve MDx HTAs, organizations should provide greater transparency, better communication and collaboration between industry and HTA

  2. Ultrasensitive microanalytical diagnostic methods for rickettsial pathogens

    SciTech Connect

    Hatch, A. V.

    2012-03-01

    A strategic CRADA was established between Sandia National Laboratories (SNL) and the University of Texas Medical Branch (UTMB) at Galveston to address pressing needs for US protection against biological weapons of mass destruction (WMD) and emerging infectious diseases. The combination of unique expertise and facilities at UTMB and SNL enabled interdisciplinary research efforts in the development of rapid and accurate diagnostic methods for early detection of trace priority pathogen levels. Outstanding postdoctoral students were also trained at both institutions to help enable the next generation of scientists to tackle the challenging interdisciplinary problems in the area of biodefense and emerging infectious diseases. Novel approaches to diagnostics were developed and the both the speed of assays as well as the detection sensitivity were improved by over an order of magnitude compared to traditional methods. This is a significant step toward more timely and specific detection of dangerous infections. We developed in situ polymerized porous polymer monoliths that can be used as (1) size exclusion elements for capture and processing of rickettsial infected cells from a sample, (2) photopatternable framework for grafting high densities of functionalized antibodies/fluorescent particles using novel monolith chemistry. Grafting affinity reagents specific to rickettsial particles enables rapid, ultra-sensitive assays by overcoming transport limitations of traditional planar assay approaches. We have selectively trapped particles and bacteria at the cell trap and have also detected picomolar mouse IL-6 captured with only 20 minutes total incubation times using the densely patterned monolith framework. As predicted, the monolith exhibits >10x improvements in both capture speed and capture density compared to traditional planar approaches. The most significant advancements as part of this CRADA is the optimization of techniques allowing the detection of <10 rickettsial

  3. The role of molecular genetic analysis within the diagnostic haemato-oncology laboratory.

    PubMed

    Bench, A J

    2012-02-01

    The identification of the molecular genetic basis to many haematological malignancies along with the increased use of molecularly targeted therapy has heralded an increasing role for molecular genetic-based techniques. Demonstration of acquired changes such as the JAK2 V617F mutation within myeloproliferative neoplasms has quickly moved from a research setting to the diagnostic laboratory. Disease-specific genetic markers, such as the BCR-ABL1 fusion gene in chronic myeloid leukaemia, enable sensitive molecular genetic methods to be applied for the detection and quantification of low-level residual disease, allowing early identification of relapse. Consequently, molecular genetics now plays a crucial role in diagnosis, the identification of prognostic markers and monitoring of haematological malignancies. The development of high-throughput whole-genome approaches offers the potential to rapidly screen newly diagnosed patients for all disease-associated molecular genetic changes.

  4. Recent advances in the molecular diagnostics of gastric cancer

    PubMed Central

    Kanda, Mitsuro; Kodera, Yasuhiro

    2015-01-01

    Gastric cancer (GC) is the third most common cause of cancer-related death in the world, representing a major global health issue. Although the incidence of GC is declining, the outcomes for GC patients remain dismal because of the lack of effective biomarkers to detect early GC and predict both recurrence and chemosensitivity. Current tumor markers for GC, including serum carcinoembryonic antigen and carbohydrate antigen 19-9, are not ideal due to their relatively low sensitivity and specificity. Recent improvements in molecular techniques are better able to identify aberrant expression of GC-related molecules, including oncogenes, tumor suppressor genes, microRNAs and long non-coding RNAs, and DNA methylation, as novel molecular markers, although the molecular pathogenesis of GC is complicated by tumor heterogeneity. Detection of genetic and epigenetic alterations from gastric tissue or blood samples has diagnostic value in the management of GC. There are high expectations for molecular markers that can be used as new screening tools for early detection of GC as well as for patient stratification towards personalized treatment of GC through prediction of prognosis and drug-sensitivity. In this review, the studies of potential molecular biomarkers for GC that have been reported in the publicly available literature between 2012 and 2015 are reviewed and summarized, and certain highlighted papers are examined. PMID:26379391

  5. Molecular Diagnostic Experience of Whole-Exome Sequencing in Adult Patients

    PubMed Central

    Posey, Jennifer E.; Rosenfeld, Jill A.; James, Regis A.; Bainbridge, Matthew; Niu, Zhiyv; Wang, Xia; Dhar, Shweta; Wiszniewski, Wojciech; Akdemir, Zeynep H.C.; Gambin, Tomasz; Xia, Fan; Person, Richard E.; Walkiewicz, Magdalena; Shaw, Chad A.; Sutton, V. Reid; Beaudet, Arthur L.; Muzny, Donna; Eng, Christine M.; Yang, Yaping; Gibbs, Richard A.; Lupski, James R.; Boerwinkle, Eric; Plon, Sharon E.

    2015-01-01

    Purpose Whole exome sequencing (WES) is increasingly used as a diagnostic tool in medicine, but prior reports focus on predominantly pediatric cohorts with neurologic or developmental disorders. We describe the diagnostic yield and characteristics of whole exome sequencing in adults. Methods We performed a retrospective analysis of consecutive WES reports for adults from a diagnostic laboratory. Phenotype composition was determined using Human Phenotype Ontology terms. Results Molecular diagnoses were reported for 17.5% (85/486) of adults, lower than a primarily pediatric population (25.2%; p=0.0003); the diagnostic rate was higher (23.9%) in those 18–30 years of age compared to patients over 30 years (10.4%; p=0.0001). Dual Mendelian diagnoses contributed to 7% of diagnoses, revealing blended phenotypes. Diagnoses were more frequent among individuals with abnormalities of the nervous system, skeletal system, head/neck, and growth. Diagnostic rate was independent of family history information, and de novo mutations contributed to 61.4% of autosomal dominant diagnoses. Conclusion Early WES experience in adults demonstrates molecular diagnoses in a substantial proportion of patients, informing clinical management, recurrence risk and recommendations for relatives. A positive family history was not predictive, consistent with molecular diagnoses often revealed by de novo events, informing the Mendelian basis of genetic disease in adults. PMID:26633545

  6. Molecular diagnostics clinical utility strategy: a six-part framework.

    PubMed

    Frueh, Felix W; Quinn, Bruce

    2014-09-01

    The clinical utility of a molecular test rises proportional to a favorable regulatory risk/benefit assessment, and clinical utility is the driver of payer coverage decisions. Although a great deal has been written about clinical utility, debates still center on its 'definition.' We argue that the definition (an impact on clinical outcomes) is self-evident, and improved communications should focus on sequential steps in building and proving an adequate level of confidence for the diagnostic test's clinical value proposition. We propose a six-part framework to facilitate communications between test developers and health technology evaluators, relevant to both regulatory and payer decisions.

  7. Closing the diarrhoea diagnostic gap in Indian children by the application of molecular techniques.

    PubMed

    Ajjampur, S S R; Rajendran, P; Ramani, S; Banerjee, I; Monica, B; Sankaran, P; Rosario, V; Arumugam, R; Sarkar, R; Ward, H; Kang, G

    2008-11-01

    A large proportion of diarrhoeal illnesses in children in developing countries are ascribed to an unknown aetiology because the only available methods, such as microscopy and culture, have low sensitivity. This study was aimed at decreasing the diagnostic gap in diarrhoeal disease by the application of molecular techniques. Faecal samples from 158 children with and 99 children without diarrhoea in a hospital in South India were tested for enteric pathogens using conventional diagnostic methods (culture, microscopy and enzyme immunoassays) and molecular methods (six PCR-based assays). The additional use of molecular techniques increased identification to at least one aetiological agent in 76.5 % of diarrhoeal specimens, compared with 40.5 % using conventional methods. Rotavirus (43.3 %), enteropathogenic Escherichia coli (15.8 %), norovirus (15.8 %) and Cryptosporidium spp. (15.2 %) are currently the most common causes of diarrhoea in hospitalized children in Vellore, in contrast to a study conducted two decades earlier in the same hospital, where bacterial pathogens such as Shigella spp., Campylobacter spp. and enterotoxigenic E. coli were more prevalent. Molecular techniques significantly increased the detection rates of pathogens in children with diarrhoea, but a more intensive study, testing for a wider range of infectious agents and including more information on non-infectious causes of diarrhoea, is required to close the diagnostic gap in diarrhoeal disease.

  8. Sudden unexpected death in epilepsy genetics: Molecular diagnostics and prevention.

    PubMed

    Goldman, Alica M; Behr, Elijah R; Semsarian, Christopher; Bagnall, Richard D; Sisodiya, Sanjay; Cooper, Paul N

    2016-01-01

    Epidemiologic studies clearly document the public health burden of sudden unexpected death in epilepsy (SUDEP). Clinical and experimental studies have uncovered dynamic cardiorespiratory dysfunction, both interictally and at the time of sudden death due to epilepsy. Genetic analyses in humans and in model systems have facilitated our current molecular understanding of SUDEP. Many discoveries have been informed by progress in the field of sudden cardiac death and sudden infant death syndrome. It is becoming apparent that SUDEP genomic complexity parallels that of sudden cardiac death, and that there is a pauci1ty of analytically useful postmortem material. Because many challenges remain, future progress in SUDEP research, molecular diagnostics, and prevention rests in international, collaborative, and transdisciplinary dialogue in human and experimental translational research of sudden death. Wiley Periodicals, Inc. © 2016 International League Against Epilepsy.

  9. Sudden unexpected death in epilepsy genetics: Molecular diagnostics and prevention

    PubMed Central

    Goldman, Alica M.; Behr, Elijah R.; Semsarian, Christopher; Bagnall, Richard D.; Sisodiya, Sanjay; Cooper, Paul N.

    2016-01-01

    Summary Epidemiologic studies clearly document the public health burden of sudden unexpected death in epilepsy (SUDEP). Clinical and experimental studies have uncovered dynamic cardiorespiratory dysfunction, both interictally and at the time of sudden death due to epilepsy. Genetic analyses in humans and in model systems have facilitated our current molecular understanding of SUDEP. Many discoveries have been informed by progress in the field of sudden cardiac death and sudden infant death syndrome. It is becoming apparent that SUDEP genomic complexity parallels that of sudden cardiac death, and that there is a pauci1ty of analytically useful postmortem material. Because many challenges remain, future progress in SUDEP research, molecular diagnostics, and prevention rests in international, collaborative, and transdisciplinary dialogue in human and experimental translational research of sudden death. PMID:26749013

  10. [Valuation of diagnostic methods of pneumonia alveolitis].

    PubMed

    Makhmudova, S Iu

    2010-05-01

    The aim of this study was to identify effectiveness of modern complex of roentgenological, endoscopic, functional, citomorphologic and immunological methods in diagnosis of alveolitis. Between May-June 2002 and July-August 2003 the single-stage diagnosis was conducted among 1192 workers (400 - Siasan broiler, 391 - Baku flour mill and 401 - tobacco from Gabala zone). The patients with the diagnosis of various forms alveolitis were examined. 89 patients with symptoms of tympanal, acrocyanosis, tachycardia, tarnished glass effect, vascular lungs deformation were selected. Cough, short breath, crackling, infiltrative and cystous changes in lungs, acceleration of erythrocyte sedimentation rate (ESR) up to 27-36 mm/hour on average, decrease of total lung capacity, lymphocyte reaction, opacity, symptom of honeycomb lung and alteration in mucous of lung were considered as auxiliary factors. The investigation proofed that computed tomography was an effective technique for the diagnosis of alveolitis; the diagnostic reliability of computed tomography for the evaluation of various forms of alveolitis was 100%.

  11. Impact of gene patents on the development of molecular diagnostics.

    PubMed

    Toneguzzo, Frances

    2011-07-01

    There is a widely held view that gene patents in particular and patents in general, because of the exclusionary rights that they provide, are inhibiting the development of and access to critical molecular diagnostic testing. This is a highly relevant issue for healthcare delivery as we move towards personalized medicine, which relies heavily on genetic testing to tailor treatments that are specific for individual characteristics. Critics of the patent system hope to void or diminish the exclusionary aspect of patents by removing genes from the definition of what is patentable, by increasing the number of activities that fall within the research use exemption, or by compelling patent holders to license their rights non-exclusively. Although a re-examination of what constitutes patentable subject matter is an important undertaking, narrowing the definition of patentable subject matter is at best only a partial solution. Erosion of the patent system through compulsory licensing or expansion of the research use exemption runs the risk of destroying important incentives without also fully addressing the problem. To promote solutions that truly address the issues, this article distinguishes documented facts from perceptions and suggests alternative approaches to explore. The author believes that efforts to undermine the patent system are simply counterproductive and that time would be better spent addressing the real issues that lie within molecular diagnostic development.

  12. Molecular Diagnostic and Drug Delivery Agents based on Aptamer-Nanomaterial Conjugates

    PubMed Central

    Lee, Jung Heon; Yigit, Mehmet V.; Mazumdar, Debapriya; Lu, Yi

    2010-01-01

    Recent progress in an emerging area of designing aptamer and nanomaterial conjugates as molecular diagnostic and drug delivery agents in biomedical applications is summarized. Aptamers specific for a wide range of targets are first introduced and compared to antibodies. Methods of integrating these aptamers with a variety of nanomaterials, such as gold nanoparticles, quantum dots, carbon nanotubes, and superparamagnetic iron oxide nanoparticles, each with unique optical, magnetic, and electrochemical properties, are reviewed. Applications of these systems as fluorescent, colorimetric, magnetic resonance imaging, and electrochemical sensors in medical diagnostics are given, along with new applications as smart drug delivery agents. PMID:20338204

  13. Molecular diagnostic and drug delivery agents based on aptamer-nanomaterial conjugates.

    PubMed

    Lee, Jung Heon; Yigit, Mehmet V; Mazumdar, Debapriya; Lu, Yi

    2010-04-30

    Recent progress in an emerging area of designing aptamer and nanomaterial conjugates as molecular diagnostic and drug delivery agents in biomedical applications is summarized. Aptamers specific for a wide range of targets are first introduced and compared to antibodies. Methods of integrating these aptamers with a variety of nanomaterials, such as gold nanoparticles, quantum dots, carbon nanotubes, and superparamagnetic iron oxide nanoparticles, each with unique optical, magnetic, and electrochemical properties, are reviewed. Applications of these systems as fluorescent, colorimetric, magnetic resonance imaging, and electrochemical sensors in medical diagnostics are given, along with new applications as smart drug delivery agents.

  14. Diagnostic Profiles: A Standard Setting Method for Use with a Cognitive Diagnostic Model

    ERIC Educational Resources Information Center

    Skaggs, Gary; Hein, Serge F.; Wilkins, Jesse L. M.

    2016-01-01

    This article introduces the Diagnostic Profiles (DP) standard setting method for setting a performance standard on a test developed from a cognitive diagnostic model (CDM), the outcome of which is a profile of mastered and not-mastered skills or attributes rather than a single test score. In the DP method, the key judgment task for panelists is a…

  15. Increasing role of arthropod bites in tularaemia transmission in Poland - case reports and diagnostic methods.

    PubMed

    Formińska, Kamila; Zasada, Aleksandra A; Rastawicki, Waldemar; Śmietańska, Karolina; Bander, Dorota; Wawrzynowicz-Syczewska, Marta; Yanushevych, Mariya; Niścigórska-Olsen, Jolanta; Wawszczak, Marek

    2015-01-01

    The study describes four cases of tularaemia - one developed after contact with rabbits and three developed after an arthropod bite. Due to non-specific clinical symptoms, accurate diagnosis of tularaemia may be difficult. The increasing contribution of the arthropod vectors in the transmission of the disease indicates that special effort should be made to apply sensitive and specific diagnostic methods for tularaemia, and to remind health-care workers about this route of Francisella tularensis infections. The advantages and disadvantages of various diagnostic methods - molecular, serological and microbiological culture - are discussed. The PCR as a rapid and proper diagnostic method for ulceroglandular tularaemia is presented.

  16. Electron-Beam Diagnostic Methods for Hypersonic Flow Diagnostics

    NASA Technical Reports Server (NTRS)

    1994-01-01

    The purpose of this work was the evaluation of the use of electron-bean fluorescence for flow measurements during hypersonic flight. Both analytical and numerical models were developed in this investigation to evaluate quantitatively flow field imaging concepts based upon the electron beam fluorescence technique for use in flight research and wind tunnel applications. Specific models were developed for: (1) fluorescence excitation/emission for nitrogen, (2) rotational fluorescence spectrum for nitrogen, (3) single and multiple scattering of electrons in a variable density medium, (4) spatial and spectral distribution of fluorescence, (5) measurement of rotational temperature and density, (6) optical filter design for fluorescence imaging, and (7) temperature accuracy and signal acquisition time requirements. Application of these models to a typical hypersonic wind tunnel flow is presented. In particular, the capability of simulating the fluorescence resulting from electron impact ionization in a variable density nitrogen or air flow provides the capability to evaluate the design of imaging instruments for flow field mapping. The result of this analysis is a recommendation that quantitative measurements of hypersonic flow fields using electron-bean fluorescence is a tractable method with electron beam energies of 100 keV. With lower electron energies, electron scattering increases with significant beam divergence which makes quantitative imaging difficult. The potential application of the analytical and numerical models developed in this work is in the design of a flow field imaging instrument for use in hypersonic wind tunnels or onboard a flight research vehicle.

  17. From morphologic to molecular: established and emerging molecular diagnostics for breast carcinoma.

    PubMed

    Portier, Bryce P; Gruver, Aaron M; Huba, Michael A; Minca, Eugen C; Cheah, Alison L; Wang, Zhen; Tubbs, Raymond R

    2012-09-15

    Diagnostics in the field of breast carcinoma are constantly evolving. The recent wave of molecular methodologies, both microscope and non-microscope based, have opened new ways to gain insight into this disease process and have moved clinical diagnostics closer to a 'personalized medicine' approach. In this review we highlight some of the advancements that laboratory medicine technology is making toward guiding the diagnosis, prognosis, and therapy selection for patients affected by breast carcinoma. The content of the article is largely structured by methodology, with a distinct emphasis on both microscope based and non-microscope based diagnostic formats. Where possible, we have attempted to emphasize the potential benefits as well as limitations to each of these technologies. Successful molecular diagnostics, applied in concert within the morphologic context of a patient's tumor, are what will lay the foundation for personalized therapy and allow a more sophisticated approach to clinical trial stratification. The future of breast cancer diagnostics looks challenging, but it is also a field of great opportunity. Never before have there been such a plethora of new tools available for disease investigation or candidate therapy selection.

  18. Optimization of capillary array electrophoresis single-strand conformation polymorphism analysis for routine molecular diagnostics.

    PubMed

    Jespersgaard, Cathrine; Larsen, Lars Allan; Baba, Shingo; Kukita, Yoji; Tahira, Tomoko; Christiansen, Michael; Vuust, Jens; Hayashi, Kenshi; Andersen, Paal Skytt

    2006-10-01

    Mutation screening is widely used for molecular diagnostics of inherited disorders. Furthermore, it is anticipated that the present and future identification of genetic risk factors for complex disorders will increase the need for high-throughput mutation screening technologies. Capillary array electrophoresis (CAE) SSCP analysis is a low-cost, automated method with a high throughput and high reproducibility. Thus, the method fulfills many of the demands to be met for application in routine molecular diagnostics. However, the need for performing the electrophoresis at three temperatures between 18 degrees C and 35 degrees C for achievement of high sensitivity is a disadvantage of the method. Using a panel of 185 mutant samples, we have analyzed the effect of sample purification, sample medium and separation matrix on the sensitivity of CAE-SSCP analysis to optimize the method for molecular diagnostic use. We observed different effects from sample purification and sample medium at different electrophoresis temperatures, probably reflecting the complex interplay between sequence composition, electrophoresis conditions and sensitivity in SSCP analysis. The effect on assay sensitivity from three different polymers was tested using a single electrophoresis temperature of 27 degrees C. The data suggest that a sensitivity of 98-99% can be obtained using a 10% long chain poly-N,N-dimethylacrylamide polymer.

  19. [Molecular biology methods in immunohematology].

    PubMed

    Tournamille, C

    2013-05-01

    The molecular basis of almost all antigens of the 33 blood group systems are known. These knowledge and the advent of the PCR technology have allowed the DNA-based genotyping in order to predict the presence or absence of a blood group antigen on the cell membrane of red blood cells. DNA genotyping is required in cases where red blood cells patient cannot be used for serological typing either after a recent transfusion or because of the presence of autoantibodies on the red blood cells. Numerous DNA assays are available to detect any nucleotide polymorphism on the genes encoding blood group antigens. The technologies have improved to answer quickly to any case of transfusion emergency and to limit the risk of DNA contamination in a molecular diagnostic laboratory. Some technologies are ready for high-throughput blood group genotyping. They will be used in the future to obtain a fully typed blood group card of each donor but also to detect blood donors with rare phenotypes to register them to the Banque Nationale de Sang de Phénotype Rare (BNSPR).

  20. Method and apparatus for holographic wavefront diagnostics

    DOEpatents

    Toeppen, J.S.

    1995-04-25

    A wavefront diagnostic apparatus has an optic and a measuring system. The optic forms a holographic image in response to a beam of light striking a hologram formed on a surface of the optic. The measuring system detects the position of the array of holographic images and compares the positions of the array of holographic images to a reference holographic image. 3 figs.

  1. Method and apparatus for holographic wavefront diagnostics

    DOEpatents

    Toeppen, John S.

    1995-01-01

    A wavefront diagnostic apparatus has an optic and a measuring system. The optic forms a holographic image in response to a beam of light striking a hologram formed on a surface of the optic. The measuring system detects the position of the array of holographic images and compares the positions of the array of holographic images to a reference holographic image.

  2. Current advances in diagnostic methods of Acanthamoeba keratitis.

    PubMed

    Wang, Yuehua; Feng, Xianmin; Jiang, Linzhe

    2014-01-01

    The objective of this article was to review the current advances in diagnostic methods for Acanthamoeba keratitis (AK). Data used in this review were retrieved from PubMed (1970-2013). The terms "Acanthamoeba keratitis" and "diagnosis" were used for the literature search. Data from published articles regarding AK and diagnosis in clinical trials were identified and reviewed. The diagnostic methods for the eight species implicated in AK were reviewed. Among all diagnostic procedures, corneal scraping and smear examination was an essential diagnostic method. Polymerase chain reaction was the most sensitive and accurate detection method. Culturing of Acanthamoeba was a reliable method for final diagnosis of AK. Confocal microscopy to detect Acanthamoeba was also effective, without any invasive procedure, and was helpful in the early diagnosis of AK. Clinically, conjunction of various diagnostic methods to diagnose AK was necessary.

  3. Cell and molecular biology for diagnostic and therapeutic technology

    NASA Astrophysics Data System (ADS)

    Tan, M. I.

    2016-03-01

    Our body contains 100 trillion cells. However, each cell has certain function and structure. For maintaining their integrity, cells will be collaborating with each other and with extracellular matrix surround them to form a tissue. These interactions effect internally on many networks or pathway such as signalling pathway, metabolic pathway and transport network in the cell. These networks interact with each other to maintain cell survival, cell structure and function and moreover the tissue as well as the organ which the cells built. Therefore, as part of a tissue, genetic and epigenetic abnormality of a cell can also alter these networks, and moreover disturb the function of the tissue itself. Hence, condition of genetic and epigenetic of the cell may affect other conditions in omics level such as transcriptomic, proteomic, metabolomics characteristics which can be differentiated by a particular unique molecular profile from each level, which can be used for diagnostic as well as for targeted therapy.

  4. Molecular separation method and apparatus

    DOEpatents

    Villa-Aleman, E.

    1996-04-09

    A method and apparatus are disclosed for separating a gaseous mixture of chemically identical but physically different molecules based on their polarities. The gaseous mixture of molecules is introduced in discrete quantities into the proximal end of a porous glass molecular sieve. The molecular sieve is exposed to microwaves to excite the molecules to a higher energy state from a lower energy state, those having a higher dipole moment being excited more than those with a lower energy state. The temperature of the sieve kept cold by a flow of liquid nitrogen through a cooling jacket so that the heat generated by the molecules colliding with the material is transferred away from the material. The molecules thus alternate between a higher energy state and a lower one, with the portion of molecules having the higher dipole moment favored over the others. The former portion can then be extracted separately from the distal end of the molecular sieve. 2 figs.

  5. Molecular separation method and apparatus

    DOEpatents

    Villa-Aleman, Eliel

    1996-01-01

    A method and apparatus for separating a gaseous mixture of chemically identical but physically different molecules based on their polarities. The gaseous mixture of molecules is introduced in discrete quantities into the proximal end of a porous glass molecular. The molecular sieve is exposed to microwaves to excite the molecules to a higher energy state from a lower energy state, those having a higher dipole moment being excited more than those with a lower energy state. The temperature of the sieve kept cold by a flow of liquid nitrogen through a cooling jacket so that the heat generated by the molecules colliding with the material is transferred away from the material. The molecules thus alternate between a higher energy state and a lower one, with the portion of molecules having the higher dipole moment favored over the others. The former portion can then be extracted separately from the distal end of the molecular sieve.

  6. A Refined QSO Selection Method Using Diagnostics

    NASA Astrophysics Data System (ADS)

    Kim, Dae-Won; Protopapas, Pavlos; Trichas, Markos; Rowan-Robinson, Michael; Khardon, Roni; Alcock, Charles; Byun, Yong-Ik

    2012-04-01

    We present 663 QSO candidates in the Large Magellanic Cloud (LMC) that were selected using multiple diagnostics. We started with a set of 2,566 QSO candidates selected using the methodology presented in our previous work based on time variability of the MACHO LMC light curves. We then obtained additional information for the candidates by cross-matching them with the Spitzer SAGE, the 2MASS, the Chandra, the XMM, and an LMC UBVI catalogues. Using that information, we specified diagnostic features based on mid-IR colours, photometric redshifts using SED template fitting, and X-ray luminosities, in order to discriminate more high-confidence QSO candidates in the absence of spectral information. We then trained a one-class Support Vector Machine model using those diagnostics features. We applied the trained model to the original candidates, and finally selected 663 high-confidence QSO candidates. We cross-matched those 663 QSO candidates with 152 newly-confirmed QSOs and 275 non-QSOs in the LMC fields, and found that the false positive rate was less than 1%.

  7. Recombinase polymerase amplification: Emergence as a critical molecular technology for rapid, low-resource diagnostics.

    PubMed

    James, Ameh; Macdonald, Joanne

    2015-01-01

    Isothermal molecular diagnostics are bridging the technology gap between traditional diagnostics and polymerase chain reaction-based methods. These new techniques enable timely and accurate testing, especially in settings where there is a lack of infrastructure to support polymerase chain reaction facilities. Despite this, there is a significant lack of uptake of these technologies in developing countries where they are highly needed. Among these novel isothermal technologies, recombinase polymerase amplification (RPA) holds particular potential for use in developing countries. This rapid nucleic acid amplification approach is fast, highly sensitive and specific, and amenable to countries with a high burden of infectious diseases. Implementation of RPA technology in developing countries is critically required to assess limitations and potentials of the diagnosis of infectious disease, and may help identify impediments that prevent adoption of new molecular technologies in low resource- and low skill settings. This review focuses on approaching diagnosis of infectious disease with RPA.

  8. Molecular filter-based diagnostics in high speed flows

    NASA Technical Reports Server (NTRS)

    Elliott, Gregory S.; Samimy, MO; Arnette, Stephen A.

    1993-01-01

    The use of iodine molecular filters in nonintrusive planar velocimetry methods is examined. Detailed absorption profiles are obtained to highlight the effects that determine the profile shape. It is shown that pressure broadening induced by the presence of a nonabsorbing vapor can be utilized to significantly change the slopes bounding the absorbing region while remaining in the optically-thick regime.

  9. [Acute myeloid leukemia. Genetic diagnostics and molecular therapy].

    PubMed

    Schlenk, R F; Döhner, K; Döhner, H

    2013-02-01

    Acute myeloid leukemia (AML) is a genetically heterogeneous disease. The genetic diagnostics have become an essential component in the initial work-up for disease classification, prognostication and prediction. More and more promising molecular targeted therapeutics are becoming available. A prerequisite for individualized treatment strategies is a fast pretherapeutic molecular screening including the fusion genes PML-RARA, RUNX1-RUNX1T1 and CBFB-MYH11 as well as mutations in the genes NPM1, FLT3 and CEBPA. Promising new therapeutic approaches include the combination of all- trans retinoic acid and arsentrioxid in acute promyelocytic leukemia, the combination of intensive chemotherapy with KIT inhibitors in core-binding factor AML and FLT3 inhibitors in AML with FLT3 mutation, as well as gemtuzumab ozogamicin therapy in patients with low and intermediate cytogenetic risk profiles. With the advent of the next generation sequencing technologies it is expected that new therapeutic targets will be identified. These insights will lead to a further individualization of AML therapy.

  10. COLD-PCR: improving the sensitivity of molecular diagnostics assays

    PubMed Central

    Milbury, Coren A; Li, Jin; Liu, Pingfang; Makrigiorgos, G Mike

    2011-01-01

    The detection of low-abundance DNA variants or mutations is of particular interest to medical diagnostics, individualized patient treatment and cancer prognosis; however, detection sensitivity for low-abundance variants is a pronounced limitation of most currently available molecular assays. We have recently developed coamplification at lower denaturation temperature-PCR (COLD-PCR) to resolve this limitation. This novel form of PCR selectively amplifies low-abundance DNA variants from mixtures of wild-type and mutant-containing (or variant-containing) sequences, irrespective of the mutation type or position on the amplicon, by using a critical denaturation temperature. The use of a lower denaturation temperature in COLD-PCR results in selective denaturation of amplicons with mutation-containing molecules within wild-type mutant heteroduplexes or with a lower melting temperature. COLD-PCR can be used in lieu of conventional PCR in several molecular applications, thus enriching the mutant fraction and improving the sensitivity of downstream mutation detection by up to 100-fold. PMID:21405967

  11. Spinal Muscular Atrophy: Overview of Molecular Diagnostic Approaches.

    PubMed

    Prior, Thomas W; Nagan, Narasimhan

    2016-01-01

    Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disease and the most common genetic cause of infant mortality, affecting ∼1 in 10,000 live births. The disease is characterized by progressive symmetrical muscle weakness resulting from the degeneration and loss of anterior horn cells in the spinal cord and brain stem nuclei. The disease is classified on the basis of age of onset and clinical course. SMA is caused by mutations in the telomeric copy of the survival motor neuron 1 (SMN1) gene, but all patients retain a centromeric copy of the gene, SMN2. The homozygous absence of the SMN1 exon 7 has been observed in the majority of patients and is being utilized as a reliable and sensitive SMA diagnostic test. In the majority of cases, the disease severity correlates inversely with an increased SMN2 gene copy number. Carrier detection, in the deletion cases, relies on the accurate determination of the SMN1 gene copies. Since SMA is one of the most common lethal genetic disorders, with a carrier frequency of 1 in 40 to 1 in 60, direct carrier dosage testing has been beneficial to many families. This unit attempts to highlight the molecular genetics of SMA with a focus on the advantages and limitations of the current molecular technologies. Copyright © 2016 John Wiley & Sons, Inc.

  12. Aircraft Engine Gas Path Diagnostic Methods: Public Benchmarking Results

    NASA Technical Reports Server (NTRS)

    Simon, Donald L.; Borguet, Sebastien; Leonard, Olivier; Zhang, Xiaodong (Frank)

    2013-01-01

    Recent technology reviews have identified the need for objective assessments of aircraft engine health management (EHM) technologies. To help address this issue, a gas path diagnostic benchmark problem has been created and made publicly available. This software tool, referred to as the Propulsion Diagnostic Method Evaluation Strategy (ProDiMES), has been constructed based on feedback provided by the aircraft EHM community. It provides a standard benchmark problem enabling users to develop, evaluate and compare diagnostic methods. This paper will present an overview of ProDiMES along with a description of four gas path diagnostic methods developed and applied to the problem. These methods, which include analytical and empirical diagnostic techniques, will be described and associated blind-test-case metric results will be presented and compared. Lessons learned along with recommendations for improving the public benchmarking processes will also be presented and discussed.

  13. [Positron emission tomography: diagnostic imaging on a molecular level].

    PubMed

    Allemann, K; Wyss, M; Wergin, M; Bley, C Rohrer; Ametamay, S; Bruehlmeier, M; Kaser-Hotz, B

    2004-08-01

    In human medicine positron emission tomography (PET) is a modern diagnostic imaging method. In the present paper we outline the physical principles of PET and give an overview over the main clinic fields where PET is being used, such as neurology, cardiology and oncology. Moreover, we present a current project in veterinary medicine (in collaboration with the Paul Scherrer Institute and the University Hospital Zurich), where a hypoxia tracer is applied to dogs and cats suffering from spontaneous tumors. Finally new developments in the field of PET were discussed.

  14. Simultaneous Extraction of Viral and Bacterial Nucleic Acids for Molecular Diagnostic Applications.

    PubMed

    Kajiura, Lauren N; Stewart, Scott D; Dresios, John; Uyehara, Catherine F T

    2015-12-01

    Molecular detection of microbial pathogens in clinical samples requires the application of efficient sample lysis protocols and subsequent extraction and isolation of their nucleic acids. Here, we describe a simple and time-efficient method for simultaneous extraction of genomic DNA from gram-positive and -negative bacteria, as well as RNA from viral agents present in a sample. This method compared well with existing bacterial- and viral-specialized extraction protocols, worked reliably on clinical samples, and was not pathogen specific. This method may be used to extract DNA and RNA concurrently from viral and bacterial pathogens present in a sample and effectively detect coinfections in routine clinical diagnostics.

  15. Diagnostic methods for CW laser damage testing

    NASA Astrophysics Data System (ADS)

    Stewart, Alan F.; Shah, Rashmi S.

    2004-06-01

    High performance optical coatings are an enabling technology for many applications - navigation systems, telecom, fusion, advanced measurement systems of many types as well as directed energy weapons. The results of recent testing of superior optical coatings conducted at high flux levels will be presented. The diagnostics used in this type of nondestructive testing and the analysis of the data demonstrates the evolution of test methodology. Comparison of performance data under load to the predictions of thermal and optical models shows excellent agreement. These tests serve to anchor the models and validate the performance of the materials and coatings.

  16. Diffusion of molecular diagnostic lung cancer tests: a survey of german oncologists.

    PubMed

    Steffen, Julius Alexander

    2014-03-21

    This study was aimed at examining the diffusion of diagnostic lung cancer tests in Germany. It was motivated by the high potential of detecting and targeting oncogenic drivers. Recognizing that the diffusion of diagnostic tests is a conditio sine qua non for the success of personalized lung cancer therapies, this study analyzed the diffusion of epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) tests in Germany. Qualitative and quantitative research strategies were combined in a mixed-method design. A literature review and subsequent Key Opinion Leader interviews identified a set of qualitative factors driving the diffusion process, which were then translated into an online survey. The survey was conducted among a sample of 961 oncologists (11.34% response rate). The responses were analyzed in a multiple linear regression which identified six statistically significant factors driving the diffusion of molecular diagnostic lung cancer tests: reimbursement, attitude towards R&D, information self-assessment, perceived attitudes of colleagues, age and test-pathway strategies. Besides the important role of adequate reimbursement and relevant guidelines, the results of this study suggest that an increasing usage of test-pathway strategies, especially in an office-based setting, can increase the diffusion of molecular diagnostic lung cancer tests in the future.

  17. Clinical Significance of Molecular Diagnostic Tools for Bacterial Bloodstream Infections: A Systematic Review

    PubMed Central

    Nyirahabimana, Therese

    2016-01-01

    Bacterial bloodstream infection (bBSI) represents any form of invasiveness of the blood circulatory system caused by bacteria and can lead to death among critically ill patients. Thus, there is a need for rapid and accurate diagnosis and treatment of patients with septicemia. So far, different molecular diagnostic tools have been developed. The majority of these tools focus on amplification based techniques such as polymerase chain reaction (PCR) which allows the detection of nucleic acids (both DNA and small RNAs) that are specific to bacterial species and sequencing or nucleic acid hybridization that allows the detection of bacteria in order to reduce delay of appropriate antibiotic therapy. However, there is still a need to improve sensitivity of most molecular techniques to enhance their accuracy and allow exact and on time antibiotic therapy treatment. In this regard, we conducted a systematic review of the existing studies conducted in molecular diagnosis of bBSIs, with the main aim of reporting on clinical significance and benefits of molecular diagnosis to patients. We searched both Google Scholar and PubMed. In total, eighteen reviewed papers indicate that shift from conventional diagnostic methods to molecular tools is needed and would lead to accurate diagnosis and treatment of bBSI. PMID:27974890

  18. Primary diagnostic approaches of invasive aspergillosis--molecular testing.

    PubMed

    Bretagne, Stéphane

    2011-04-01

    The PCR methods published for the diagnosis of invasive aspergillosis (IA) are diverse in terms of amplification protocols and methods, equipment, fluorescent detection dyes, PCR chemistries, and clinical specimens used. This explains why PCR is still not included in the revised EORTC/MSG definitions of IA despite encouraging results. Therefore, achieving consensual PCR procedures at the international level is mandatory. When using PCR as a diagnostic tool, emphasis must be put on limiting false positive results due to contamination either with previously amplified products or with environmental commensals. Internal amplification controls are compulsory to evidence false negative results. For most of these aspects, quantitative PCR (qPCR) should improve both the results' reliability and the clinicians' confidence. A checklist of items (Minimum information for publication of quantitative real-time PCR experiments) has been proposed to help scientists and reviewers. Currently, the main limitation relies in the DNA extraction procedure the choice of which dramatically depends on the still unknown origin of the Aspergillus DNA to amplify. There is an urgent need for basic studies to elucidate the origin and kinetics of Aspergillus DNA in blood. Once a technical consensus is achieved, clinical studies should be initiated to integrate qPCR in the diagnostic armentarium of IA.

  19. Juvenile retinoschisis: a model for molecular diagnostic testing of X-linked ophthalmic disease.

    PubMed Central

    Sieving, P A; Yashar, B M; Ayyagari, R

    1999-01-01

    BACKGROUND AND PURPOSE: X-linked juvenile retinoschisis (RS) provides a starting point to define clinical paradigms and understand the limitations of diagnostic molecular testing. The RS phenotype is specific, but the broad severity range is clinically confusing. Molecular diagnostic testing obviates unnecessary examinations for boys at-risk and identifies carrier females who otherwise show no clinical signs. METHODS: The XLRS1 gene has 6 exons of 26-196 base-pair size. Each exon is amplified by a single polymerase chain reaction and then sequenced, starting with exons 4 through 6, which contain mutation "hot spots." RESULTS: The 6 XLRS1 exons are sequenced serially. If alterations are found, they are compared with mutations in our > 120 XLRS families and with the > 300 mutations reported worldwide. Point mutations, small deletions, or rearrangements are identified in nearly 90% of males with a clinical diagnosis of RS. XLRS1 has very few sequence polymorphisms. Carrier-state testing produces 1 of 3 results: (1) positive, in which the woman has the same mutation as an affected male relative or known in other RS families; (2) negative, in which she lacks the mutation of her affected male relative; and (3) uninformative, in which no known mutation is identified or no information exists about the familial mutation. CONCLUSIONS: Molecular RS screening is an effective diagnostic tool that complements the clinician's skills for early detection of at-risk males. Useful outcomes of carrier testing depend on several factors: (1) a male relative with a clear clinical diagnosis; (2) a well-defined inheritance pattern; (3) high disease penetrance; (4) size and organization of the gene; and (5) the types of disease-associated mutations. Ethical questions include molecular diagnostic testing of young at-risk females before the age of consent, the impact of this information on the emotional health of the patient and family, and issues of employability and insurance coverage

  20. Enabling Equal Access to Molecular Diagnostics: What Are the Implications for Policy and Health Technology Assessment?

    PubMed

    Plun-Favreau, Juliette; Immonen-Charalambous, Kaisa; Steuten, Lotte; Strootker, Anja; Rouzier, Roman; Horgan, Denis; Lawler, Mark

    2016-01-01

    Molecular diagnostics can offer important benefits to patients and are a key enabler of the integration of personalised medicine into health care systems. However, despite their promise, few molecular diagnostics are embedded into clinical practice (especially in Europe) and access to these technologies remains unequal across countries and sometimes even within individual countries. If research translation and the regulatory environments have proven to be more challenging than expected, reimbursement and value assessment remain the main barriers to providing patients with equal access to molecular diagnostics. Unclear or non-existent reimbursement pathways, together with the lack of clear evidence requirements, have led to significant delays in the assessment of molecular diagnostics technologies in certain countries. Additionally, the lack of dedicated diagnostics budgets and the siloed nature of resource allocation within certain health care systems have significantly delayed diagnostics commissioning. This article will consider the perspectives of different stakeholders (patients, health care payers, health care professionals, and manufacturers) on the provision of a research-enabled, patient-focused molecular diagnostics platform that supports optimal patient care. Through the discussion of specific case studies, and building on the experience from countries that have successfully integrated molecular diagnostics into clinical practice, this article will discuss the necessary evolutions in policy and health technology assessment to ensure that patients can have equal access to appropriate molecular diagnostics.

  1. How can molecular diagnostics contribute to the elimination of human African trypanosomiasis?

    PubMed

    Büscher, Philippe; Deborggraeve, Stijn

    2015-05-01

    A variety of molecular diagnostic tests for human African trypanosomiasis (HAT) (sleeping sickness) has been developed. Some are effectively used for research and confirmation diagnosis in travel medicine, usually following non-standardized protocols. Others have become commercially available as diagnostic kits. WHO aims to eliminate HAT as a public health problem by the year 2020, and zero transmission by the year 2030. This article gives an overview of the recent progress in molecular diagnostics for sleeping sickness, including the most recent data on test performances. Also discussed is how molecular diagnostics can play an important role in the process toward the elimination of HAT.

  2. Numerical methods for molecular dynamics

    SciTech Connect

    Skeel, R.D.

    1991-01-01

    This report summarizes our research progress to date on the use of multigrid methods for three-dimensional elliptic partial differential equations, with particular emphasis on application to the Poisson-Boltzmann equation of molecular biophysics. This research is motivated by the need for fast and accurate numerical solution techniques for three-dimensional problems arising in physics and engineering. In many applications these problems must be solved repeatedly, and the extremely large number of discrete unknowns required to accurately approximate solutions to partial differential equations in three-dimensional regions necessitates the use of efficient solution methods. This situation makes clear the importance of developing methods which are of optimal order (or nearly so), meaning that the number of operations required to solve the discrete problem is on the order of the number of discrete unknowns. Multigrid methods are generally regarded as being in this class of methods, and are in fact provably optimal order for an increasingly large class of problems. The fundamental goal of this research is to develop a fast and accurate numerical technique, based on multi-level principles, for the solutions of the Poisson-Boltzmann equation of molecular biophysics and similar equations occurring in other applications. An outline of the report is as follows. We first present some background material, followed by a survey of the literature on the use of multigrid methods for solving problems similar to the Poisson-Boltzmann equation. A short description of the software we have developed so far is then given, and numerical results are discussed. Finally, our research plans for the coming year are presented.

  3. DNA detection and single nucleotide mutation identification using SERS for molecular diagnostics and global health

    NASA Astrophysics Data System (ADS)

    Ngo, Hoan T.; Gandra, Naveen; Fales, Andrew M.; Taylor, Steve M.; Vo-Dinh, Tuan

    2017-02-01

    Nucleic acid-based molecular diagnostics at the point-of-care (POC) and in resource-limited settings is still a challenge. We present a sensitive yet simple DNA detection method with single nucleotide polymorphism (SNP) identification capability. The detection scheme involves sandwich hybridization of magnetic beads conjugated with capture probes, target sequences, and ultrabright surface-enhanced Raman Scattering (SERS) nanorattles conjugated with reporter probes. Upon hybridization, the sandwich probes are concentrated at the detection focus controlled by a magnetic system for SERS measurements. The ultrabright SERS nanorattles, consisting of a core and a shell with resonance Raman reporters loaded in the gap space between the core and the shell, serve as SERS tags for ultrasensitive signal detection. Specific DNA sequences of the malaria parasite Plasmodium falciparum and dengue virus 1 (DENV1) were used as the model marker system. Detection limit of approximately 100 attomoles was achieved. Single nucleotide polymorphism (SNP) discrimination of wild type malaria DNA and mutant malaria DNA, which confers resistance to artemisinin drugs, was also demonstrated. The results demonstrate the molecular diagnostic potential of the nanorattle-based method to both detect and genotype infectious pathogens. The method's simplicity makes it a suitable candidate for molecular diagnosis at the POC and in resource-limited settings.

  4. Gold-based hybrid nanomaterials for biosensing and molecular diagnostic applications.

    PubMed

    Kim, Jung Eun; Choi, Ji Hye; Colas, Marion; Kim, Dong Ha; Lee, Hyukjin

    2016-06-15

    The properties of gold nanomaterials are particularly of interest to many researchers, since they show unique physiochemical properties such as optical adsorption of specific wavelength of light, high electrical conductance with rich surface electrons, and facile surface modification with sulfhydryl groups. These properties have facilitated the use of gold nanomaterials in the development of various hybrid systems for biosensors and molecular diagnostics. Combined with various synthetic materials such as fluorescence dyes, polymers, oligonucleotides, graphene oxides (GO), and quantum dots (QDs), the gold-based hybrid nanomaterials offer multi-functionalities in molecular detection with high specificity and sensitivity. These two aspects result in the increase of detection speed as well as the lower detection limits, having shown that this diagnosis method is more effective than other conventional ones. In this review, we have highlighted various examples of nanomaterials for biosensing and molecular diagnostics. The gold-based hybrid systems are categorized by three distinct detection approaches, in which include (1) optical, such as surface plasmon resonance (SPR), RAMAN, and surface-enhanced Raman scattering (SERS), (2) fluorescence, such as förster resonance energy transfer (FRET) and nanomaterial surface energy transfer (NSET), and (3) electrochemical, such as potentiometic, amperometric, and conductometric. Each example provides the detailed mechanism of molecular detection as well as the supporting experimental result with the limit of detection (LOD). Lastly, future perspective on novel development of gold-based hybrid nanomaterials is discussed as well as their challenges.

  5. Companion diagnostics: a regulatory perspective from the last 5 years of molecular companion diagnostic approvals.

    PubMed

    Roscoe, Donna M; Hu, Yun-Fu; Philip, Reena

    2015-01-01

    Companion diagnostics are essential for the safe and effective use of the corresponding therapeutic products. The US FDA has approved a number of companion diagnostics used to select cancer patients for treatment with contemporaneously approved novel therapeutics. The processes of co-development and co-approval of a therapeutic product and its companion diagnostic have been a learning experience that continues to evolve. Using several companion diagnostics as examples, this article describes the challenges associated with the scientific, clinical and regulatory hurdles faced by FDA and industry alike. Taken together, this discussion is intended to assist manufacturers toward a successful companion diagnostics development plan.

  6. Dextran-coated iron oxide nanoparticles: a versatile platform for targeted molecular imaging, molecular diagnostics, and therapy.

    PubMed

    Tassa, Carlos; Shaw, Stanley Y; Weissleder, Ralph

    2011-10-18

    Advances in our understanding of the genetic basis of disease susceptibility coupled with prominent successes for molecular targeted therapies have resulted in an emerging strategy of personalized medicine. This approach envisions risk stratification and therapeutic selection based on an individual's genetic makeup and physiologic state (the latter assessed through cellular or molecular phenotypes). Molecularly targeted nanoparticles can play a key role in this vision through noninvasive assessments of molecular processes and specific cell populations in vivo, sensitive molecular diagnostics, and targeted delivery of therapeutics. A superparamagnetic iron oxide nanoparticle with a cross-linked dextran coating, or CLIO, is a powerful and illustrative nanoparticle platform for these applications. These structures and their derivatives support diagnostic imaging by magnetic resonance (MRI), optical, and positron emission tomography (PET) modalities and constitute a versatile platform for conjugation to targeting ligands. A variety of conjugation methods exist to couple the dextran surface to different functional groups; in addition, a robust bioorthogonal [4 + 2] cycloaddition reaction between 1,2,4,5-tetrazene (Tz) and trans-cyclooctene (TCO) can conjugate nanoparticles to targeting ligands or label pretargeted cells. The ready availability of conjugation methods has given rise to the synthesis of libraries of small molecule modified nanoparticles, which can then be screened for nanoparticles with specificity for a specific cell type. Since most nanoparticles display their targeting ligands in a multivalent manner, a detailed understanding of the kinetics and affinity of a nanoparticle's interaction with its target (as determined by surface plasmon resonance) can yield functionally important insights into nanoparticle design. In this Account, we review applications of the CLIO platform in several areas relevant to the mission of personalized medicine. We demonstrate

  7. Method and system for diagnostics of apparatus

    NASA Technical Reports Server (NTRS)

    Gorinevsky, Dimitry (Inventor)

    2012-01-01

    Proposed is a method, implemented in software, for estimating fault state of an apparatus outfitted with sensors. At each execution period the method processes sensor data from the apparatus to obtain a set of parity parameters, which are further used for estimating fault state. The estimation method formulates a convex optimization problem for each fault hypothesis and employs a convex solver to compute fault parameter estimates and fault likelihoods for each fault hypothesis. The highest likelihoods and corresponding parameter estimates are transmitted to a display device or an automated decision and control system. The obtained accurate estimate of fault state can be used to improve safety, performance, or maintenance processes for the apparatus.

  8. The Far Infrared Lines of OH as Molecular Cloud Diagnostics

    NASA Technical Reports Server (NTRS)

    Smith, Howard A.

    2004-01-01

    Future IR missions should give some priority to high resolution spectroscopic observations of the set of far-IR transitions of OH. There are 15 far-IR lines arising between the lowest eight rotational levels of OH, and ISO detected nine of them. Furthermore, ISO found the OH lines, sometimes in emission and sometimes in absorption, in a wide variety of galactic and extragalactic objects ranging from AGB stars to molecular clouds to active galactic nuclei and ultra-luminous IR galaxies. The ISO/LWS Fabry-Perot resolved the 119 m doublet line in a few of the strong sources. This set of OH lines provides a uniquely important diagnostic for many reasons: the lines span a wide wavelength range (28.9 m to 163.2 m); the transitions have fast radiative rates; the abundance of the species is relatively high; the IR continuum plays an important role as a pump; the contribution from shocks is relatively minor; and, not least, the powerful centimeter-wave radiation from OH allows comparison with radio and VLBI datasets. The problem is that the large number of sensitive free parameters, and the large optical depths of the strongest lines, make modeling the full set a difficult job. The SWAS montecarlo radiative transfer code has been used to analyze the ISO/LWS spectra of a number of objects with good success, including in both the lines and the FIR continuum; the DUSTY radiative transfer code was used to insure a self-consistent continuum. Other far IR lines including those from H2O, CO, and [OI] are also in the code. The OH lines all show features which future FIR spectrometers should be able to resolve, and which will enable further refinements in the details of each cloud's structure. Some examples are given, including the case of S140, for which independent SWAS data found evidence for bulk flows.

  9. Molecular diagnostics of sepsis--where are we today?

    PubMed

    Bauer, Michael; Reinhart, Konrad

    2010-08-01

    Rapid diagnosis of sepsis is of outstanding significance as each hour of delay of appropriate antimicrobial therapy increases mortality by 5-10%. As a result, antibiotics are started without a definitive microbial result based on clinical signs in concert with "biomarkers" with high sensitivity but a lack of specificity. Diagnostic uncertainty is compensated for by liberal use of broad spectrum antibiotics with inherent resistance as an increasing public-health problem. Blood culture reflects the current gold-standard but is positive only in approximately 20% of cases and even if positive, results are obtained too late to influence decision making. Culture-independent microbial nucleic acid amplification techniques may allow ways out of this dilemma. In addition to diagnosis of infection, "biomarkers" reflecting the host response can provide valuable information regarding prognosis, course, and response to treatment. Among available single protein markers, procalcitonin (PCT) covers these features best and a PCT-based therapeutic strategy carries potential to reduce antibiotic courses even in life-threatening infections. Recent data from transcriptomic and/or proteomic profiling would, however, indicate that marker panels derived from transcriptomic or proteomic profiling are superior to single proteins to differentiate non-infectious from sepsis-associated systemic inflammation. Multiplexed assay systems, e.g. after platform transfer from whole-genomic chips to multiplexed quantitative PCR are currently being developed with potential to improve sensitivity and specificity. Clinical utility of both, molecular tests to identify the pathogen and the ensuing host response, has still to be evaluated in prospective trials.

  10. Point-of-care technologies for molecular diagnostics using a drop of blood.

    PubMed

    Song, Yujun; Huang, Yu-Yen; Liu, Xuewu; Zhang, Xiaojing; Ferrari, Mauro; Qin, Lidong

    2014-03-01

    Molecular diagnostics is crucial for prevention, identification, and treatment of disease. Traditional technologies for molecular diagnostics using blood are limited to laboratory use because they rely on sample purification and sophisticated instruments, are labor and time intensive, expensive, and require highly trained operators. This review discusses the frontiers of point-of-care (POC) diagnostic technologies using a drop of blood obtained from a finger prick. These technologies, including emerging biotechnologies, nanotechnologies, and microfluidics, hold the potential for rapid, accurate, and inexpensive disease diagnostics.

  11. Point-of-care technologies for molecular diagnostics using a drop of blood

    PubMed Central

    Song, Yujun; Huang, Yu-Yen; Liu, Xuewu; Zhang, Xiaojing; Ferrari, Mauro; Qin, Lidong

    2014-01-01

    Molecular diagnostics is critical for prevention, identification, and treatment of disease. Traditional technologies for molecular diagnostics using blood are limited to laboratory use because they rely on sample purification and sophisticated instruments, are labor- and time-intensive and expensive, and require highly trained operators. This review discusses the frontiers of point-of-care diagnostic technologies using a drop of blood obtained from a finger-prick. These technologies, including emerging biotechnologies, nanotechnologies, and microfluidics, hold the potential for rapid, accurate, and inexpensive disease diagnostics. PMID:24525172

  12. [The diagnostic methods applied in mycology].

    PubMed

    Kurnatowska, Alicja; Kurnatowski, Piotr

    2008-01-01

    The systemic fungal invasions are recognized with increasing frequency and constitute a primary cause of morbidity and mortality, especially in immunocompromised patients. Early diagnosis improves prognosis, but remains a problem because there is lack of sensitive tests to aid in the diagnosis of systemic mycoses on the one hand, and on the other the patients only present unspecific signs and symptoms, thus delaying early diagnosis. The diagnosis depends upon a combination of clinical observation and laboratory investigation. The successful laboratory diagnosis of fungal infection depends in major part on the collection of appropriate clinical specimens for investigations and on the selection of appropriate microbiological test procedures. So these problems (collection of specimens, direct techniques, staining methods, cultures on different media and non-culture-based methods) are presented in article.

  13. [Objective diagnostic methods in pediatric audiology].

    PubMed

    Mühler, R; Hoth, S

    2014-10-01

    Objective methods based on the measurement of otoacoustic emissions (OAE) and auditory evoked potentials (AEP) are indispensable in pediatric audiology especially for the early detection and therapy of congenital hearing impairment. The correct and efficient use requires knowledge and skills which are beyond the basic equipment of many users and require continuous updating. In the present review many aspects relevant for the safe handling of the methods and interpretation of the results are addressed. The presentation does not focus on the methods themselves but on the core problem of the practical daily routine, namely the qualitative and quantitative description of hearing loss in terms of its extent, the frequency range affected and the identity with respect to the type and site of the lesion. The certainty of the diagnosis can be optimized by observing few and simple rules. Central importance is attached to the thorough discussion of the interrelated parameters residual noise, signal-to-noise ratio and reproducibility in order to promote their correct use. Further subjects of this article are the recognition of pitfalls, the description of new developments, such as chirp and auditory steady-state responses (ASSR) and finally the consideration of the extraordinarily important aspect of maturation.

  14. Laboratory diagnosis of malaria: conventional and rapid diagnostic methods.

    PubMed

    Wilson, Michael L

    2013-06-01

    The global control of malaria is more challenging than that of many other infectious diseases: malaria is vector borne, it is caused by 5 species of Plasmodium with different geographic distributions, infection is widespread in many regions, drug resistance is common, and the disease overlaps clinically with other infectious diseases. Therefore, malaria control programs, in addition to diagnosis and testing, must also target limiting spread of the disease through vector control. Although malaria control efforts have been successful in some regions, malaria remains one of the most important causes of death in sub-Saharan Africa, particularly in women and children. To review the current literature regarding diagnostic methods available to detect clinical malaria, with an emphasis on comparing the strengths and limitations of each method. Current World Health Organization malaria control report and other information, recent meta-analyses of diagnostic tests, primary literature concerning the performance characteristics of different tests, and primary literature concerning how diagnostic tests are used in daily practice. The most commonly used method for identifying cases of malaria remains microscopic examination of peripheral blood, but there is growing use of malaria rapid diagnostic tests in many regions. One of the most important findings in the recent literature is that despite the widespread use of diagnostic tests, treatment is too often based on clinical findings rather than on results of diagnostic tests.

  15. Differential temperature integrating diagnostic method and apparatus

    DOEpatents

    Doss, James D.; McCabe, Charles W.

    1976-01-01

    A method and device for detecting the presence of breast cancer in women by integrating the temperature difference between the temperature of a normal breast and that of a breast having a malignant tumor. The breast-receiving cups of a brassiere are each provided with thermally conductive material next to the skin, with a thermistor attached to the thermally conductive material in each cup. The thermistors are connected to adjacent arms of a Wheatstone bridge. Unbalance currents in the bridge are integrated with respect to time by means of an electrochemical integrator. In the absence of a tumor, both breasts maintain substantially the same temperature, and the bridge remains balanced. If the tumor is present in one breast, a higher temperature in that breast unbalances the bridge and the electrochemical cells integrate the temperature difference with respect to time.

  16. VUV diagnostics of electron impact processes in low temperature molecular hydrogen plasma

    NASA Astrophysics Data System (ADS)

    Komppula, J.; Tarvainen, O.

    2015-08-01

    Novel methods for diagnostics of molecular hydrogen plasma processes, such as ionization, production of high vibrational levels, dissociation of molecules via excitation to singlet and triplet states and production of metastable states, are presented for molecular hydrogen plasmas in corona equilibrium. The methods are based on comparison of rate coefficients of plasma processes and optical emission spectroscopy of lowest singlet and triplet transitions, i.e. Lyman band ({{B}1}Σ\\text{u}+\\to {{X}1}Σ\\text{g}+ ) and molecular continuum ({{a}3}Σ\\text{g}+\\to {{b}3}Σ\\text{u}+ ), of the hydrogen molecule in the VUV wavelength range. Comparison of rate coefficients of spin-allowed and/or spin-forbidden excitations reduces the uncertainty caused by the non-equilibrium distributions of electron energy and molecular vibrational level, which are typically known poorly in plasma sources. The described methods are applied to estimate the rates of various plasma processes in a filament arc discharge.

  17. [Diagnostic and therapeutic methods in the asthmatic triad].

    PubMed

    Gorichkina, L A; Frolova, M K; Kuria, V F

    1985-01-01

    Comprehensive diagnostic methods used in 48 patients with the asthmatic triad made it possible to select diagnostic methods and means of control of treatment of such patients. Methods of specific diagnosis of the intolerance of pyrazolone drugs and some probable pathogenetic indicators of intolerance of acetylsalicylic acid, pyrazolone drugs and tartrazine containing substances in patients with different forms of bronchial asthma (atopic and infectious-allergic) in combination with nasal polyposis were evaluated. Basing on these materials conditions for specific immunotherapy were worked out.

  18. Optical methods in diagnostics of liver fibrosis via blood observation

    NASA Astrophysics Data System (ADS)

    Kruchinina, Margarita V.; Generalov, Vladimir M.; Atuchin, Victor V.; Kruchinin, Vladimir N.; Volodin, Vladimir A.; Gromov, Andrey A.; Rykhlitsky, Sergey V.

    2016-11-01

    A possible application of optical methods (dielectrophoresis, spectral and imaging ellipsometry, Fourier- transform infrared spectroscopy, Raman spectroscopy) for the early diagnostics in studies of red blood cells and serum in patients with the diffuse liver disease, with varying degrees of fibrosis, has been evaluated. As experimentally confirmed, the combined optical methods significantly improve the sensitivity, specificity and accuracy index in the diagnosis of both severe fibrosis and slight ulterior liver fibrosis. The identified optical methods diagnostic potential can be efficiently utilized in noninvasive screening evaluation of the stages of diffuse liver disease of various genesis.

  19. Application of tissue mesodissection to molecular cancer diagnostics

    PubMed Central

    Krizman, David; Adey, Nils; Parry, Robert

    2015-01-01

    Aims To demonstrate clinical application of a mesodissection platform that was developed to combine advantages of laser-based instrumentation with the speed/ease of manual dissection for automated dissection of tissue off standard glass slides. Methods Genomic analysis for KRAS gene mutation was performed on formalin fixed paraffin embedded (FFPE) cancer patient tissue that was dissected using the mesodissection platform. Selected reaction monitoring proteomic analysis for quantitative Her2 protein expression was performed on FFPE patient tumour tissue dissected by a laser-based instrument and the MilliSect instrument. Results Genomic analysis demonstrates highly confident detection of KRAS mutation specifically in lung cancer cells and not the surrounding benign, non-tumour tissue. Proteomic analysis demonstrates Her2 quantitative protein expression in breast cancer cells dissected manually, by laser-based instrumentation and by MilliSect instrumentation (mesodissection). Conclusions Slide-mounted tissue dissection is commonly performed using laser-based instruments or manually scraping tissue by scalpel. Here we demonstrate that the mesodissection platform as performed by the MilliSect instrument for tissue dissection is cost-effective; it functions comparably to laser-based dissection and which can be adopted into a clinical diagnostic workflow. PMID:25430495

  20. Advances and prospects for molecular diagnostics of fungal infections.

    PubMed

    Bretagne, Stéphane

    2010-11-01

    The polymerase chain reaction (PCR) methods published for the diagnosis of invasive fungal infections are still not included in the revised European Organization for Research and Treatment of Cancer/Invasive Fungal Infections Cooperative Group and the National Institute of Allergy and Infectious Diseases Mycoses Study Group (EORTC/MSG) Consensus Group definitions of IA. This could be achieved with consensual PCR procedures. A checklist of items has been proposed to improve the reliability of the results and clinicians' confidence in them, with emphasis on limiting false-positive results from contamination with either previously amplified products or environmental commensals. Internal amplification controls are mandatory to expose false-negative results. However, our ignorance of the origin and the kinetics of fungal DNA during an infection hamper the choice of the best specimen and DNA extraction protocol. Evidence is increasing that serum could be a good compromise between sensitivity and ease of DNA extraction. Once a technical consensus is achieved, clinical studies should be initiated to integrate quantitative PCR in the diagnostic armamentarium.

  1. An improved molecular diagnostic assay for canine and feline dermatophytosis.

    PubMed

    Cafarchia, Claudia; Gasser, Robin B; Figueredo, Luciana A; Weigl, Stefania; Danesi, Patrizia; Capelli, Gioia; Otranto, Domenico

    2013-02-01

    The few studies attempting to specifically characterize dermatophytes from hair samples of dogs and cats using PCR-based methodology relied on sequence-based analysis of selected genetic markers. The aim of the present investigation was to establish and evaluate a PCR-based approach employing genetic markers of nuclear DNA for the specific detection of dermatophytes on such specimens. Using 183 hair samples, we directly compared the test results of our one-step and nested-PCR assays with those based on conventional microscopy and in vitro culture techniques (using the latter as the reference method). The one step-PCR was highly accurate (AUC > 90) for the testing of samples from dogs, but only moderately accurate (AUC = 78.6) for cats. A nested-PCR was accurate (AUC = 93.6) for samples from cats, and achieved higher specificity (94.1 and 94.4%) and sensitivity (100 and 94.9%) for samples from dogs and cats, respectively. In addition, the nested-PCR allowed the differentiation of Microsporum canis from Trichophyton interdigitale (zoophilic) and geophilic dermatophytes (i.e., Microsporum gypseum or Trichophyton terrestre), which was not possible using the one step-assay. The PCRs evaluated here provide practical tools for diagnostic applications to support clinicians in initiating prompt and targeted chemotherapy of dermatophytoses.

  2. Examinations of electron temperature calculation methods in Thomson scattering diagnostics

    SciTech Connect

    Oh, Seungtae; Lee, Jong Ha; Wi, Hanmin

    2012-10-15

    Electron temperature from Thomson scattering diagnostic is derived through indirect calculation based on theoretical model. {chi}-square test is commonly used in the calculation, and the reliability of the calculation method highly depends on the noise level of input signals. In the simulations, noise effects of the {chi}-square test are examined and scale factor test is proposed as an alternative method.

  3. Gold nanoprobe-based non-crosslinking hybridization for molecular diagnostics.

    PubMed

    Larguinho, Miguel; Canto, Rafaela; Cordeiro, Milton; Pedrosa, Pedro; Fortuna, Andreia; Vinhas, Raquel; Baptista, Pedro V

    2015-01-01

    Non-crosslinking (NCL) approaches using DNA-modified gold nanoparticles for molecular detection constitute powerful tools with potential implications in clinical diagnostics and tailored medicine. From detection of pathogenic agents to identification of specific point mutations associated with health conditions, these methods have shown remarkable versatility and simplicity. Herein, the NCL hybridization assay is broken down to the fundamentals behind its assembly and detection principle. Gold nanoparticle synthesis and derivatization is addressed, emphasizing optimal size homogeneity and conditions for maximum surface coverage, with direct implications in downstream detection. The detection principle is discussed and the advantages and drawbacks of different NCL approaches are discussed. Finally, NCL-based applications for molecular detection of clinically relevant loci and potential integration into more complex biosensing platforms, projecting miniaturization and portability are addressed.

  4. Gene and genetic diagnostic method patent claims: a comparison under current European and US patent law

    PubMed Central

    Huys, Isabelle; Van Overwalle, Geertrui; Matthijs, Gert

    2011-01-01

    The paper focuses on the fundamental debate that is going on in Europe and the United States about whether genes and genetic diagnostic methods are to be regarded as inventions or subject matter eligible for patent protection, or whether they are discoveries or principles of nature and thus excluded from patentability. The study further explores some possible scenarios of American influences on European patent applications with respect to genetic diagnostic methods. Our analysis points out that patent eligibility for genes and genetic diagnostic methods, as discussed in the United States in the Association of Molecular Pathology versus US Patent and Trademark Office decision, is based on a different reasoning compared with the European Patent Convention. PMID:21654725

  5. Gene and genetic diagnostic method patent claims: a comparison under current European and US patent law.

    PubMed

    Huys, Isabelle; Van Overwalle, Geertrui; Matthijs, Gert

    2011-10-01

    The paper focuses on the fundamental debate that is going on in Europe and the United States about whether genes and genetic diagnostic methods are to be regarded as inventions or subject matter eligible for patent protection, or whether they are discoveries or principles of nature and thus excluded from patentability. The study further explores some possible scenarios of American influences on European patent applications with respect to genetic diagnostic methods. Our analysis points out that patent eligibility for genes and genetic diagnostic methods, as discussed in the United States in the Association of Molecular Pathology versus US Patent and Trademark Office decision, is based on a different reasoning compared with the European Patent Convention.

  6. Diagnostic procedures in tularaemia with special focus on molecular and immunological techniques.

    PubMed

    Splettstoesser, W D; Tomaso, H; Al Dahouk, S; Neubauer, H; Schuff-Werner, P

    2005-08-01

    Tularaemia is a severe bacterial zoonosis caused by the highly infectious agent Francisella tularensis. It is endemic in countries of the northern hemisphere ranging from North America to Europe, Asia and Japan. Very recently, Francisella-like strains causing disease in humans were described from tropical northern Australia. In the last decade, efforts have been made to develop sensitive and specific immunological and molecular techniques for the laboratory diagnosis of tularaemia and also for the definite identification of members of the species F. tularensis and its four subspecies. Screening for the keyword 'Francisella' a Medline search over the last decade was performed and articles describing diagnostic methods for tularaemia and its causative agent were selected. Besides classical microbiological techniques (cultivation, biochemical profiling, susceptibility testing) several new immunological and molecular approaches to identify F. tularensis have been introduced employing highly specific antibodies and various polymerase chain reaction (PCR)-based methods. Whereas direct antigen detection by enzyme-linked immunosorbent assay (ELISA) or immunofluorescence might allow early presumptive diagnosis of tularaemia, these methods--like all PCR techniques--still await further evaluation. Therefore, diagnosis of tularaemia still relies mainly on the demonstration of specific antibodies in the host. ELISA and immunoblot methods started to replace the standard tube or micro-agglutination assays. However, the diagnostic value of antibody detection in the very early clinical phase of tularaemia is limited. Francisella tularensis is regarded as a 'highest priority' biological agent (category 'A' according to the CDC, Atlanta, GA, USA), thus rapid and reliable diagnosis of tularaemia is required not only for a timely onset of therapy, the handling of outbreak investigations but also for the surveillance of endemic foci. Only very recently, evaluated test kits for

  7. A method for knowledge acquisition in diagnostic expert system.

    PubMed

    Li, Weishi; Li, Aiping; Li, Shudong

    2015-01-01

    Knowledge acquisition plays very important role in the diagnostic expert system. It usually takes a long period to acquire disease knowledge using the traditional methods. To solve this problem, this paper describes relations between rough set theory and rule-based description of diseases, which corresponds to the process of knowledge acquisition of diagnostic expert system. Then the exclusive rules, inclusive rules and disease images of disease are built based on the PDES diagnosis model, and the definition of probability rule is put forward. At last, the paper presents the rule-based automated induction reasoning method, including exhaustive search, post-processing procedure, estimation for statistic test and the bootstrap and resampling methods. We also introduce automated induction of the rule-based description, which is used in our diseases diagnostic expert system. The experimental results not only show that rough set theory gives a very suitable framework to represent processes of uncertain knowledge extraction, but also that this method induces diagnostic rules correctly. This method can act as the assistant tool for development of diagnosis expert system, and has an extensive application in intelligent information systems.

  8. Validation of the Ion Torrent PGM sequencing for the prospective routine molecular diagnostic of colorectal cancer.

    PubMed

    Belardinilli, Francesca; Capalbo, Carlo; Buffone, Amelia; Petroni, Marialaura; Colicchia, Valeria; Ferraro, Sergio; Zani, Massimo; Nicolussi, Arianna; D'Inzeo, Sonia; Coppa, Anna; Screpanti, Isabella; Gulino, Alberto; Giannini, Giuseppe

    2015-09-01

    Treatment individualization based on specific molecular biomarkers is becoming increasingly important in oncology. In colorectal cancer (CRC), the molecular characterization of RAS and BRAF mutation status for prognostic and predictive purposes is commonly performed by different validated methods. However, as the number of clinically relevant mutations to be analyzed increases, the definition of new approaches for more sensitive, rapid and economic patient selection urges. To this aim, we evaluated the Ion Semiconductor sequencing using the Ion Torrent Personal Genome Machine (IT-PGM) in our routine molecular diagnostics for CRC in comparison with the gold standard direct Sanger sequencing. Formalin-fixed and paraffin-embedded tumor tissues obtained by surgery or biopsy of 66 CRCs were collected. DNA was extracted and sequenced by IT-PGM and Sanger method. The proposed IT-PGM sequencing strategy exceeded the 500 reads of coverage for all clinically relevant RAS/BRAF amplicons in most samples and thus guaranteed optimal determination. Indeed, the frequencies and the mutational spectrum of RAS and BRAF mutations were in agreement with literature data and revealed 100% concordance between the IT-PGM and routine Sanger sequencing approaches. Turnaround time and cost evaluation indicate that the IT-PGM sequencing permits the characterization of the clinically relevant mutational spots at lower cost and turnaround time compared to Sanger sequencing and allows inclusion of additional amplicons whose characterization may acquire significance in the very next future. The IT-PGM is a valid, flexible, sensitive and economical method alternative to the Sanger sequencing in routine diagnostics to select patients for anti-epidermal growth factor receptor therapy for metastatic CRC. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  9. Sodium and T1ρ MRI for molecular and diagnostic imaging of articular cartilage†

    PubMed Central

    Borthakur, Arijitt; Mellon, Eric; Niyogi, Sampreet; Witschey, Walter; Kneeland, J. Bruce; Reddy, Ravinder

    2010-01-01

    In this article, both sodium magnetic resonance (MR) and T1ρ relaxation mapping aimed at measuring molecular changes in cartilage for the diagnostic imaging of osteoarthritis are reviewed. First, an introduction to structure of cartilage, its degeneration in osteoarthritis (OA) and an outline of diagnostic imaging methods in quantifying molecular changes and early diagnostic aspects of cartilage degeneration are described. The sodium MRI section begins with a brief overview of the theory of sodium NMR of biological tissues and is followed by a section on multiple quantum filters that can be used to quantify both bi-exponential relaxation and residual quadrupolar interaction. Specifically, (i) the rationale behind the use of sodium MRI in quantifying proteoglycan (PG) changes, (ii) validation studies using biochemical assays, (iii) studies on human OA specimens, (iv) results on animal models and (v) clinical imaging protocols are reviewed. Results demonstrating the feasibility of quantifying PG in OA patients and comparison with that in healthy subjects are also presented. The section concludes with the discussion of advantages and potential issues with sodium MRI and the impact of new technological advancements (e.g. ultra-high field scanners and parallel imaging methods). In the theory section on T1ρ, a brief description of (i) principles of measuring T1ρ relaxation, (ii) pulse sequences for computing T1ρ relaxation maps, (iii) issues regarding radio frequency power deposition, (iv) mechanisms that contribute to T1ρ in biological tissues and (v) effects of exchange and dipolar interaction on T1ρ dispersion are discussed. Correlation of T1ρ relaxation rate with macromolecular content and biomechanical properties in cartilage specimens subjected to trypsin and cytokine-induced glycosaminoglycan depletion and validation against biochemical assay and histopathology are presented. Experimental T1ρ data from osteoarthritic specimens, animal models, healthy human

  10. Molecular diagnostic testing for inherited thrombophilia using Invader.

    PubMed

    Keller, Margaret A

    2005-01-01

    Physicians in the United States and Europe began testing patients who had idiopathic thrombotic events for inherited risk factors in 1990s. The College of American Pathologists (CAP) offered proficiency testing for molecular genetic screening for thrombophilia in 1997. Today, a hypercoagulable workup including screening for inherited thrombophilia defects is becoming part of the standard of care in many parts of the world (1). Who, what, and when to test continue to be controversial and challenging questions (2); however, laboratories developing new or improved mutation detection methodologies have used the most commonly screened inherited thrombophilia polymorphism, factor V Leiden (R506Q), for many years (3). In the most recent CAP survey (MGL-A 2003), the most commonly employed method used in one-third of all participating clinical laboratories testing for factor V Leiden and prothrombin G20210A was the non-PCR-based method called Invader, developed by Third Wave Technologies. The remainder of the clinical laboratories reported testing for these variants using PCR-restriction fragment length polymorphism (RFLP), allele-specific PCR, and allele-specific hybridization. Emerging mutation detection technologies include DNA resequencing approaches such as pyrosequencing (4) fluorescence polarization detection (5), genotyping on microelectronic DNA chips like Nanogen's nanochip (6), and oligonucleotide hybridization with photocrosslinking (7). Invader technology is currently a medium-throughput, 96-well plate format assay that is sufficient for most hospital clinical laboratories. Although this assay format is not currently performed in a microarray format, Invader is amenable to performance on a solid support; specifically, the reaction can be performed on the surface of microspheres and the resulting fluorescence measured using flow cytometry (8). This chapter presents the method as well as some suggestions for utilizing the Invader system for mutation

  11. Current trends in molecular diagnostics of chronic myeloid leukemia.

    PubMed

    Vinhas, Raquel; Cordeiro, Milton; Pedrosa, Pedro; Fernandes, Alexandra R; Baptista, Pedro V

    2017-08-01

    Nearly 1.5 million people worldwide suffer from chronic myeloid leukemia (CML), characterized by the genetic translocation t(9;22)(q34;q11.2), involving the fusion of the Abelson oncogene (ABL1) with the breakpoint cluster region (BCR) gene. Early onset diagnosis coupled to current therapeutics allow for a treatment success rate of 90, which has focused research on the development of novel diagnostics approaches. In this review, we present a critical perspective on current strategies for CML diagnostics, comparing to gold standard methodologies and with an eye on the future trends on nanotheranostics.

  12. Multifunctional Nanomaterials Utilizing Hybridization Chain Reaction for Molecular Diagnostics and Bioanalytical Applications

    NASA Astrophysics Data System (ADS)

    Rana, Md. Muhit

    DNA nanotechnology has shown great promise in molecular diagnostic, bioanalytical and biomedical applications. The great challenge of detecting target analytes, biomarkers and small molecules, in molecular diagnostics is low yield sensitivity. To address this challenge, different nanomaterials have been used for a long time and to date there is no such cost-effective bioanalytical technique which can detect these target biomarkers (DNA, RNA, circulating DNA/miRNA) or environmental heavy metal ions (Hg2+ and Ag+) in a cost-effective and efficient manner. Herein, we initially discuss two possible bioanalytical detection methods- a) colorimetric and b) fluorometric assays which are very popular nowadays due to their distinctive spectroscopic properties. Finally, we report the promising colorimetric assay using a novel DNA based amplification strategy know as hybridization chain reaction (HCR) for potential application in the visual detection of low copies of biomarkers (miRNAs as little as 20 femtomole in an RNA pool and cell extracts in seven different combinations and Ebola virus DNA as low as 400 attomoles in liquid biopsy mimics in sixteen different combinations), environmental and biological heavy metal ions (mercury and silver concentrations as low as 10 pM in water, soil and urine samples) and also successfully applied to a molecular logic gate operation to distinguish OR and AND logic gates. No results showed any false-positive or false-negative information. On the other hand, we also discuss the future possibilities of HCR amplification technology, which is very promising for fluorometric bioanalysis. The HCR based nanoprobe technology has numerous remarkable advantages over other methods. It is re-programmable, simple, inexpensive, easy to assemble and operate and can be performed with visual and spectroscopic read-outs upon recognition of the target analytes. This rapid, specific and sensitive approach for biomarkers and heavy metal ion detection generates

  13. The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae

    PubMed Central

    Diaz, Maureen H.; Winchell, Jonas M.

    2016-01-01

    Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen. PMID:27014191

  14. The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae.

    PubMed

    Diaz, Maureen H; Winchell, Jonas M

    2016-01-01

    Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen.

  15. Epigenetics, copy number variation, and other molecular mechanisms underlying neurodevelopmental disabilities: new insights and diagnostic approaches.

    PubMed

    Gropman, Andrea L; Batshaw, Mark L

    2010-09-01

    The diagnostic evaluation of children with intellectual disability (ID) and other neurodevelopmental disabilities (NDD) has become increasingly complex in recent years owing to a number of newly recognized genetic mechanisms and sophisticated methods to diagnose them. Previous studies have attempted to address the diagnostic yield of finding a genetic cause in ID. The results have varied widely from 10% to 81%, with the highest percentage being found in studies using new array comparative genomic hybridization methodology especially in autism. Although many cases of ID/NDD result from chromosomal aneuploidy or structural rearrangements, single gene disorders and new categories of genome modification, including epigenetics and copy number variation play an increasingly important role in diagnosis and testing. Epigenetic mechanisms, such as DNA methylation and modifications to histone proteins, regulate high-order DNA structure and gene expression. Aberrant epigenetic and copy number variation mechanisms are involved in several neurodevelopmental and neurodegenerative disorders including Rett syndrome, fragile X syndrome, and microdeletion syndromes. This review will describe a number of the molecular genetic mechanisms that play a role in disorders leading to ID/NDD and will discuss the categories and technologies for diagnostic testing of these conditions.

  16. Novel methods for molecular dynamics simulations.

    PubMed

    Elber, R

    1996-04-01

    In the past year, significant progress was made in the development of molecular dynamics methods for the liquid phase and for biological macromolecules. Specifically, faster algorithms to pursue molecular dynamics simulations were introduced and advances were made in the design of new optimization algorithms guided by molecular dynamics protocols. A technique to calculate the quantum spectra of protein vibrations was introduced.

  17. Method to directly radiolabel antibodies for diagnostic imaging and therapy

    SciTech Connect

    Thakur, M.L.

    1991-04-30

    This patent describes a method for directly labeling proteins with radionuclides for use in diagnostic imaging and therapy. It comprises: the steps of incubating a protein-containing solution with a solution of sodium ascorbate; adding a required quantity of reduced radionuclide to the incubated protein-containing solution and incubating.

  18. MOLECULAR DIAGNOSTICS - ANOTHER PIECE IN THE ENVIRONMENTAL PUZZLE

    EPA Science Inventory

    Molecular biology offers sensitive and expedient tools for the detection of exposure to environmental stressors. Molecular approaches provide the means for detection of the "first cellular event(s)" in response to environmental changes-specifically, immediate changes in gene expr...

  19. A Diagnostic Assessment for Introductory Molecular and Cell Biology

    ERIC Educational Resources Information Center

    Shi, Jia; Wood, William B.; Martin, Jennifer M.; Guild, Nancy A.; Vicens, Quentin; Knight, Jennifer K.

    2010-01-01

    We have developed and validated a tool for assessing understanding of a selection of fundamental concepts and basic knowledge in undergraduate introductory molecular and cell biology, focusing on areas in which students often have misconceptions. This multiple-choice Introductory Molecular and Cell Biology Assessment (IMCA) instrument is designed…

  20. A Diagnostic Assessment for Introductory Molecular and Cell Biology

    ERIC Educational Resources Information Center

    Shi, Jia; Wood, William B.; Martin, Jennifer M.; Guild, Nancy A.; Vicens, Quentin; Knight, Jennifer K.

    2010-01-01

    We have developed and validated a tool for assessing understanding of a selection of fundamental concepts and basic knowledge in undergraduate introductory molecular and cell biology, focusing on areas in which students often have misconceptions. This multiple-choice Introductory Molecular and Cell Biology Assessment (IMCA) instrument is designed…

  1. MOLECULAR DIAGNOSTICS - ANOTHER PIECE IN THE ENVIRONMENTAL PUZZLE

    EPA Science Inventory

    Molecular biology offers sensitive and expedient tools for the detection of exposure to environmental stressors. Molecular approaches provide the means for detection of the "first cellular event(s)" in response to environmental changes-specifically, immediate changes in gene expr...

  2. Companion diagnostics and molecular imaging-enhanced approaches for oncology clinical trials.

    PubMed

    Van Heertum, Ronald L; Scarimbolo, Robert; Ford, Robert; Berdougo, Eli; O'Neal, Michael

    2015-01-01

    In the era of personalized medicine, diagnostic approaches are helping pharmaceutical and biotechnology sponsors streamline the clinical trial process. Molecular assays and diagnostic imaging are routinely being used to stratify patients for treatment, monitor disease, and provide reliable early clinical phase assessments. The importance of diagnostic approaches in drug development is highlighted by the rapidly expanding global cancer diagnostics market and the emergent attention of regulatory agencies worldwide, who are beginning to offer more structured platforms and guidance for this area. In this paper, we highlight the key benefits of using companion diagnostics and diagnostic imaging with a focus on oncology clinical trials. Nuclear imaging using widely available radiopharmaceuticals in conjunction with molecular imaging of oncology targets has opened the door to more accurate disease assessment and the modernization of standard criteria for the evaluation, staging, and treatment responses of cancer patients. Furthermore, the introduction and validation of quantitative molecular imaging continues to drive and optimize the field of oncology diagnostics. Given their pivotal role in disease assessment and treatment, the validation and commercialization of diagnostic tools will continue to advance oncology clinical trials, support new oncology drugs, and promote better patient outcomes.

  3. Companion diagnostics and molecular imaging-enhanced approaches for oncology clinical trials

    PubMed Central

    Van Heertum, Ronald L; Scarimbolo, Robert; Ford, Robert; Berdougo, Eli; O’Neal, Michael

    2015-01-01

    In the era of personalized medicine, diagnostic approaches are helping pharmaceutical and biotechnology sponsors streamline the clinical trial process. Molecular assays and diagnostic imaging are routinely being used to stratify patients for treatment, monitor disease, and provide reliable early clinical phase assessments. The importance of diagnostic approaches in drug development is highlighted by the rapidly expanding global cancer diagnostics market and the emergent attention of regulatory agencies worldwide, who are beginning to offer more structured platforms and guidance for this area. In this paper, we highlight the key benefits of using companion diagnostics and diagnostic imaging with a focus on oncology clinical trials. Nuclear imaging using widely available radiopharmaceuticals in conjunction with molecular imaging of oncology targets has opened the door to more accurate disease assessment and the modernization of standard criteria for the evaluation, staging, and treatment responses of cancer patients. Furthermore, the introduction and validation of quantitative molecular imaging continues to drive and optimize the field of oncology diagnostics. Given their pivotal role in disease assessment and treatment, the validation and commercialization of diagnostic tools will continue to advance oncology clinical trials, support new oncology drugs, and promote better patient outcomes. PMID:26392755

  4. Method of azimuthally stable Mueller-matrix diagnostics of blood plasma polycrystalline films in cancer diagnostics

    NASA Astrophysics Data System (ADS)

    Ushenko, Yu. A.; Prysyazhnyuk, V. P.; Gavrylyak, M. S.; Gorsky, M. P.; Bachinskiy, V. T.; Vanchuliak, O. Ya.

    2015-02-01

    A new information optical technique of diagnostics of the structure of polycrystalline films of blood plasma is proposed. The model of Mueller-matrix description of mechanisms of optical anisotropy of such objects as optical activity, birefringence, as well as linear and circular dichroism is suggested. The ensemble of informationally topical azimuthally stable Mueller-matrix invariants is determined. Within the statistical analysis of such parameters distributions the objective criteria of differentiation of films of blood plasma taken from healthy and patients with liver cirrhosis were determined. From the point of view of probative medicine the operational characteristics (sensitivity, specificity and accuracy) of the information-optical method of Mueller-matrix mapping of polycrystalline films of blood plasma were found and its efficiency in diagnostics of liver cirrhosis was demonstrated. Prospects of application of the method in experimental medicine to differentiate postmortem changes of the myocardial tissue was examined.

  5. ACOG Technology Assessment No. 11: Genetics and molecular diagnostic testing.

    PubMed

    2014-02-01

    Human genetics and molecular testing are playing an increasingly important role in medicine, including obstetric and gynecologic practice. As the genetic basis for reproductive disorders, common diseases, and cancer is elucidated with improved molecular technology, genetic testing opportunities are expanding and influencing treatment options and prevention strategies. It is essential that obstetrician-gynecologists be aware of advances in the understanding of genetic disease and the fundamental principles of genetic screening and molecular testing as genetics becomes a more integral part of routine medical practice. This document reviews the basics of genetic transmission and genetic technologies in current use.

  6. Exhaled breath analysis: physical methods, instruments, and medical diagnostics

    NASA Astrophysics Data System (ADS)

    Vaks, V. L.; Domracheva, E. G.; Sobakinskaya, E. A.; Chernyaeva, M. B.

    2014-07-01

    This paper reviews the analysis of exhaled breath, a rapidly growing field in noninvasive medical diagnostics that lies at the intersection of physics, chemistry, and medicine. Current data are presented on gas markers in human breath and their relation to human diseases. Various physical methods for breath analysis are described. It is shown how measurement precision and data volume requirements have stimulated technological developments and identified the problems that have to be solved to put this method into clinical practice.

  7. Method to directly radiolabel antibodies for diagnostic imaging and therapy

    SciTech Connect

    Thakur, M.L.

    1994-05-03

    The invention is a novel method and kit for directly radiolabeling proteins such as antibodies or antibody fragments for diagnostic and therapeutic purposes. The method comprises incubating a protein-containing solution with a solution of sodium ascorbate; adding a required quantity of reduced radionuclide to the incubated protein. A kit is also provided wherein the protein and/or reducing agents may be in lyophilized form. No Drawings

  8. Method to directly radiolabel antibodies for diagnostic imaging and therapy

    DOEpatents

    Thakur, Mathew L.

    1991-01-01

    The invention is a novel method and kit for directly radiolabeling proteins such as antibodies or antibody fragments for diagnostic and therapeutic purposes. The method comprises incubating a protein-containing solution with a solution of sodium ascorbate; adding a required quantity of reduced radionuclide to the incubated protein. A kit is also provided wherein the protein and/or reducing agents may be in lyophilized form.

  9. Method to directly radiolabel antibodies for diagnostic imaging and therapy

    DOEpatents

    Thakur, Mathew L.

    1994-01-01

    The invention is a novel method and kit for directly radiolabeling proteins such as antibodies or antibody fragments for diagnostic and therapeutic purposes. The method comprises incubating a protein-containing solution with a solution of sodium ascorbate; adding a required quantity of reduced radionuclide to the incubated protein. A kit is also provided wherein the protein and/or reducing agents may be in lyophilized form.

  10. Toward molecular parasitologic diagnosis: enhanced diagnostic sensitivity for filarial infections in mobile populations.

    PubMed

    Fink, Doran L; Fahle, Gary A; Fischer, Steven; Fedorko, Daniel F; Nutman, Thomas B

    2011-01-01

    The diagnosis of filarial infections among individuals residing in areas where the disease is not endemic requires both strong clinical suspicion and expert training in infrequently practiced parasitological methods. Recently developed filarial molecular diagnostic assays are highly sensitive and specific but have limited availability and have not been closely evaluated for clinical use outside populations residing in areas of endemicity. In this study, we assessed the performance of a panel of real-time PCR assays for the four most common human filarial pathogens among blood and tissue samples collected from a cohort of patients undergoing evaluation for suspected filarial infections. Compared to blood filtration, real-time PCR was equally sensitive for the detection of microfilaremia due to Wuchereria bancrofti (2 of 46 samples positive by both blood filtration and PCR with no discordant results) and Loa loa (24 of 208 samples positive by both blood filtration and PCR, 4 samples positive by PCR only, and 3 samples positive by blood filtration only). Real-time PCR of skin snip samples was significantly more sensitive than microscopic examination for the detection of Onchocerca volvulus microfiladermia (2 of 218 samples positive by both microscopy and PCR and 12 samples positive by PCR only). The molecular assays required smaller amounts of blood and tissue than conventional methods and could be performed by laboratory personnel without specialized parasitology training. Taken together, these data demonstrate the utility of the molecular diagnosis of filarial infections in mobile populations.

  11. Toward Molecular Parasitologic Diagnosis: Enhanced Diagnostic Sensitivity for Filarial Infections in Mobile Populations▿

    PubMed Central

    Fink, Doran L.; Fahle, Gary A.; Fischer, Steven; Fedorko, Daniel F.; Nutman, Thomas B.

    2011-01-01

    The diagnosis of filarial infections among individuals residing in areas where the disease is not endemic requires both strong clinical suspicion and expert training in infrequently practiced parasitological methods. Recently developed filarial molecular diagnostic assays are highly sensitive and specific but have limited availability and have not been closely evaluated for clinical use outside populations residing in areas of endemicity. In this study, we assessed the performance of a panel of real-time PCR assays for the four most common human filarial pathogens among blood and tissue samples collected from a cohort of patients undergoing evaluation for suspected filarial infections. Compared to blood filtration, real-time PCR was equally sensitive for the detection of microfilaremia due to Wuchereria bancrofti (2 of 46 samples positive by both blood filtration and PCR with no discordant results) and Loa loa (24 of 208 samples positive by both blood filtration and PCR, 4 samples positive by PCR only, and 3 samples positive by blood filtration only). Real-time PCR of skin snip samples was significantly more sensitive than microscopic examination for the detection of Onchocerca volvulus microfiladermia (2 of 218 samples positive by both microscopy and PCR and 12 samples positive by PCR only). The molecular assays required smaller amounts of blood and tissue than conventional methods and could be performed by laboratory personnel without specialized parasitology training. Taken together, these data demonstrate the utility of the molecular diagnosis of filarial infections in mobile populations. PMID:20980560

  12. [Mass spectrometry analysis of blood plasma lipidome as method of disease diagnostics, evuation of effectiveness and optimization of drug therapy].

    PubMed

    Lokhov, P G; Maslov, D L; Balashova, E E; Trifonova, O P; Medvedeva, N V; Torkhovskaya, T I; Ipatova, O M; Archakov, A I; Malyshev, P P; Kukharchuk, V V; Shestakova, E A; Shestakova, M V; Dedov, I I

    2015-01-01

    A new method for the analysis of blood lipid based on direct mass spectrometry of lipophilic low molecular weight fraction of blood plasma has been considered. Such technique allows quantification of hundreds of various types of lipids and this changes existing concepts on diagnostics of lipid disorders and related diseases. The versatility and quickness of the method significantly simplify its wide use. This method is applicable for diagnostics of atherosclerosis, diabetes, cancer and other diseases. Detalization of plasma lipid composition at the molecular level by means of mass spectrometry allows to assess the effectiveness of therapy and to optimize the drug treatment of cardiovascular diseases by phospholipid preparations.

  13. Molecular diagnostics for infectious disease in small animal medicine: an overview from the laboratory.

    PubMed

    Daniels, Joshua B

    2013-11-01

    Molecular diagnostic tests have augmented the way in which veterinary practitioners approach the diagnosis of infectious disease. The technical bases of these tests are explained in addition to the general clinical applications for which they are most aptly suited, as individual assays are best discussed in the context of their respective diseases. In this article, an emphasis is placed on validation of molecular tests so that practitioners can be educated consumers of molecular diagnostics. The relationships between disease prevalence and positive and negative predictive values are discussed. Finally, examples of the pitfalls of multiplex polymerase chain reaction testing are illustrated.

  14. Systems diagnostics: the systems approach to molecular imaging.

    PubMed

    Lee, Daniel Y; Li, King C P

    2009-08-01

    Molecular imaging has emerged as a powerful technology that has already changed the practice of modern medicine. During this same period, the monumental genome project has sequenced man's entire genetic content. Now the postgenomic aim is to understand the dynamic interactions of the encoded components and their regulatory mechanisms. Molecular imaging is well positioned to play a major role in this massive effort as we move toward a comprehensive paradigm for assessing health and disease.

  15. Comprehensive Carrier Screening and Molecular Diagnostic Testing for Recessive Childhood Diseases

    PubMed Central

    Kingsmore, Stephen

    2012-01-01

    Of 7,028 disorders with suspected Mendelian inheritance, 1,139 are recessive and have an established molecular basis. Although individually uncommon, Mendelian diseases collectively account for ~20% of infant mortality and ~18% of pediatric hospitalizations. Molecular diagnostic testing is currently available for only ~300 recessive disorders. Preconception screening, together with genetic counseling of carriers, has resulted in remarkable declines in the incidence of several severe recessive diseases including Tay-Sachs disease and cystic fibrosis. However, extension of preconception screening and molecular diagnostic testing to most recessive disease genes has hitherto been impractical. Recently, we reported a preconception carrier screen / molecular diagnostic test for 448 recessive childhood diseases. The current status of this test is reviewed here. Currently, this reports analytical validity of the comprehensive carrier test. As the clinical validity and clinical utility in the contexts described is ascertained, this article will be updated. PMID:22872815

  16. Molecular microbiological methods in the diagnosis of neonatal sepsis

    PubMed Central

    Venkatesh, Mohan; Flores, Angela; Luna, Ruth Ann; Versalovic, James

    2010-01-01

    Neonatal sepsis is a major cause of neonatal mortality and morbidity. The current gold standard for diagnosis of sepsis, namely blood culture, suffers from low sensitivity and a reporting delay of approximately 48–72 h. Rapid detection of sepsis and institution of antimicrobial therapy may improve patient outcomes. Rapid and sensitive tests that can inform clinicians regarding the institution or optimization of antimicrobial therapy are urgently needed. The ideal diagnostic test should have adequate specificity and negative predictive value to reliably exclude sepsis and avoid unnecessary antibiotic therapy. We comprehensively searched for neonatal studies that evaluated molecular methods for diagnosis of sepsis. We identified 19 studies that were assessed with respect to assay methodology and diagnostic characteristics. In addition, we also reviewed newer molecular microbiological assays of relevance that have not been fully evaluated in neonates. Molecular methods offer distinct advantages over blood cultures, including increased sensitivity and rapid diagnosis. However, diagnostic accuracy and cost–effectiveness should be established before implementation in clinical practice. PMID:20818947

  17. Integration methods for molecular dynamics

    SciTech Connect

    Leimkuhler, B.J.; Reich, S.; Skeel, R.D.

    1996-12-31

    Classical molecular dynamics simulation of a macromolecule requires the use of an efficient time-stepping scheme that can faithfully approximate the dynamics over many thousands of timesteps. Because these problems are highly nonlinear, accurate approximation of a particular solution trajectory on meaningful time intervals is neither obtainable nor desired, but some restrictions, such as symplecticness, can be imposed on the discretization which tend to imply good long term behavior. The presence of a variety of types and strengths of interatom potentials in standard molecular models places severe restrictions on the timestep for numerical integration used in explicit integration schemes, so much recent research has concentrated on the search for alternatives that possess (1) proper dynamical properties, and (2) a relative insensitivity to the fastest components of the dynamics. We survey several recent approaches. 48 refs., 2 figs.

  18. [Molecular and immunological methods applied in diagnosis of mycoses].

    PubMed

    Kuba, Katarzyna

    2008-01-01

    The diagnosis of fungal infections remains a problem for the management of fungal diseases, particularly in the immunocompromised patients. Systemic Candida infections and invasive aspergillosis can be a serious problem for individuals who need intensive care. Traditional methods used for the identification and typing of medically important fungi, such as morphological and biochemical analysis, are time-consuming. For the diagnosis of mycoses caused by pathogenic fungi faster and more specific methods, especially after the dramatic increase in nosocomial invasive mycoses are needed. New diagnostic tools to detect circulating fungal antigens in biological fluids and PCR-based methods to detect species or genus-specific DNA or RNA have been developed. Antigen detection is limited to searching only one genus. Molecular genetic methods, especially PCR analysis, are becoming increasingly important as a part of diagnostics in the clinical mycology laboratory. Various modifications of the PCR method are used to detect DNA in clinical material, particularly multiple, nested and real-time PCR. Molecular methods may be used to detection of nucleic acids of fungi in clinical samples, to identify fungal cultures at the species level or to evaluate strain heterogeneity differences within the species. This article reviews some of the recent advances in the possibility of molecular diagnosis of fungal infections.

  19. Hemlock woolly adelgid biological control: molecular methods to distinguish Laricobius nigrinus, L. rubidus, and their hybrids

    Treesearch

    Nathan P. Havill; Gina Davis; Joanne Klein; Adalgisa Caccone; Scott. Salom

    2011-01-01

    Molecular diagnostics use DNA-based methods to assign unknown organisms to species. As such, they rely on a priori species designation by taxonomists and require validation with enough samples to capture the variation within species for accurately selecting diagnostic characters.

  20. A new molecular diagnostic tool for surveying and monitoring Triops cancriformis populations.

    PubMed

    Sellers, Graham S; Griffin, Larry R; Hänfling, Bernd; Gómez, Africa

    2017-01-01

    The tadpole shrimp, Triops cancriformis, is a freshwater crustacean listed as endangered in the UK and Europe living in ephemeral pools. Populations are threatened by habitat destruction due to land development for agriculture and increased urbanisation. Despite this, there is a lack of efficient methods for discovering and monitoring populations. Established macroinvertebrate monitoring methods, such as net sampling, are unsuitable given the organism's life history, that include long lived diapausing eggs, benthic habits and ephemerally active populations. Conventional hatching methods, such as sediment incubation, are both time consuming and potentially confounded by bet-hedging hatching strategies of diapausing eggs. Here we develop a new molecular diagnostic method to detect viable egg banks of T. cancriformis, and compare its performance to two conventional monitoring methods involving diapausing egg hatching. We apply this method to a collection of pond sediments from the Wildfowl & Wetlands Trust Caerlaverock National Nature Reserve, which holds one of the two remaining British populations of T. cancriformis. DNA barcoding of isolated eggs, using newly designed species-specific primers for a large region of mtDNA, was used to estimate egg viability. These estimates were compared to those obtained by the conventional methods of sediment and isolation hatching. Our method outperformed the conventional methods, revealing six ponds holding viable T. cancriformis diapausing egg banks in Caerlaverock. Additionally, designed species-specific primers for a short region of mtDNA identified degraded, inviable eggs and were used to ascertain the levels of recent mortality within an egg bank. Together with efficient sugar flotation techniques to extract eggs from sediment samples, our molecular method proved to be a faster and more powerful alternative for assessing the viability and condition of T. cancriformis diapausing egg banks.

  1. A new molecular diagnostic tool for surveying and monitoring Triops cancriformis populations

    PubMed Central

    Griffin, Larry R.; Hänfling, Bernd; Gómez, Africa

    2017-01-01

    The tadpole shrimp, Triops cancriformis, is a freshwater crustacean listed as endangered in the UK and Europe living in ephemeral pools. Populations are threatened by habitat destruction due to land development for agriculture and increased urbanisation. Despite this, there is a lack of efficient methods for discovering and monitoring populations. Established macroinvertebrate monitoring methods, such as net sampling, are unsuitable given the organism’s life history, that include long lived diapausing eggs, benthic habits and ephemerally active populations. Conventional hatching methods, such as sediment incubation, are both time consuming and potentially confounded by bet-hedging hatching strategies of diapausing eggs. Here we develop a new molecular diagnostic method to detect viable egg banks of T. cancriformis, and compare its performance to two conventional monitoring methods involving diapausing egg hatching. We apply this method to a collection of pond sediments from the Wildfowl & Wetlands Trust Caerlaverock National Nature Reserve, which holds one of the two remaining British populations of T. cancriformis. DNA barcoding of isolated eggs, using newly designed species-specific primers for a large region of mtDNA, was used to estimate egg viability. These estimates were compared to those obtained by the conventional methods of sediment and isolation hatching. Our method outperformed the conventional methods, revealing six ponds holding viable T. cancriformis diapausing egg banks in Caerlaverock. Additionally, designed species-specific primers for a short region of mtDNA identified degraded, inviable eggs and were used to ascertain the levels of recent mortality within an egg bank. Together with efficient sugar flotation techniques to extract eggs from sediment samples, our molecular method proved to be a faster and more powerful alternative for assessing the viability and condition of T. cancriformis diapausing egg banks. PMID:28507815

  2. Molecular diagnostics in soft tissue sarcomas and gastrointestinal stromal tumors.

    PubMed

    Smith, Stephen M; Coleman, Joshua; Bridge, Julia A; Iwenofu, O Hans

    2015-04-01

    Soft tissue sarcomas are rare malignant heterogenous tumors of mesenchymal origin with over fifty subtypes. The use of hematoxylin and eosin stained sections (and immunohistochemistry) in the morphologic assessment of these tumors has been the bane of clinical diagnosis until recently. The last decade has witnessed considerable progress in the understanding and application of molecular techniques in refining the current understanding of soft tissue sarcomas and gastrointestinal stromal tumors beyond the limits of traditional approaches. Indeed, the identification of reciprocal chromosomal translocations and fusion genes in some subsets of sarcomas with potential implications in the pathogenesis, diagnosis and treatment has been revolutionary. The era of molecular targeted therapy presents a platform that continues to drive biomarker discovery and personalized medicine in soft tissue sarcomas and gastrointestinal stromal tumors. In this review, we highlight how the different molecular techniques have enhanced the diagnosis of these tumors with prognostic and therapeutic implications.

  3. [Physical methods and molecular biology].

    PubMed

    Serdiuk, I N

    2009-01-01

    The review is devoted to the description of the current state of physical and chemical methods used for studying the structural and functional bases of living processes. Special attention is focused on the physical methods that have opened a new page in the research of the structure of biological macromolecules. They include primarily the methods of detecting and manipulating single molecules using optical and magnetic traps. New physical methods, such as two-dimensional infrared spectroscopy, fluorescence correlation spectroscopy and magnetic resonance microscopy are also analyzed briefly in the review. The path that physics and biology have passed for the latest 55 years shows that there is no single method providing all necessary information on macromolecules and their interactions. Each method provides its space-time view of the system. All physical methods are complementary. It is just complementarity that is the fundamental idea justifying the existence in practice of all physical methods, whose description is the aim of the review.

  4. [Dermoscopy for beginners (ii): Dermoscopic structures and diagnostic methods].

    PubMed

    Palacios-Martínez, D; Díaz-Alonso, R A

    2016-01-06

    Dermoscopy (DS) is an in vivo non-invasive diagnostic technique developed to study skin lesions. It improves the diagnostic accuracy of hyperpigmented lesions and early diagnosis of potentially malignant lesions, especially melanoma. It uses a device called a dermoscope to display deeper skin structures not visible to the naked eye, called dermoscopic structures. Only some of them have histological significance, basing them on DS. Many, more or less complex, dermoscopic methods have been developed to aid in the differential diagnosis of skin cancer. The most widespread is 2-step algorithm dermoscopy. But there are some more simple methods, designed to be operated by non-medical experts in DS. Two of them are useful in primary care: the 3-point checklist of DS, and the BLINCK algorithm. This paper focuses on describing the dermoscopic parameters needed to implement these algorithms, as well as their interpretation.

  5. Instrumental methods in the diagnostics of locked-in syndrome.

    PubMed

    Kotchoubey, Boris; Lotze, Martin

    2013-01-01

    The locked-in syndrome (LiS) is typically characterized by a paralysis of almost all body muscles combined with intact cognitive functions. In practice, there are often additional brain damages besides the one directly causing LiS. These damages can lead to cognitive impairment, which substantially complicates the diagnosis of LiS. At the level of behavior, therefore, the disease can be confused with akinetic mutism, vegetative state (syn. unresponsive wakefulness state) and some other conditions. Using instrumental methods in addition to behavioral diagnostics helps to avoid diagnostic errors and to improve prognosis of rehabilitation of such patients. These methods, which include measurements of brain electric or magnetic fields, electrical potential of muscles, blood flow and oxygen consumption in the brain, are reviewed in this paper.

  6. Disorders of sex development: effect of molecular diagnostics.

    PubMed

    Achermann, John C; Domenice, Sorahia; Bachega, Tania A S S; Nishi, Mirian Y; Mendonca, Berenice B

    2015-08-01

    Disorders of sex development (DSDs) are a diverse group of conditions that can be challenging to diagnose accurately using standard phenotypic and biochemical approaches. Obtaining a specific diagnosis can be important for identifying potentially life-threatening associated disorders, as well as providing information to guide parents in deciding on the most appropriate management for their child. Within the past 5 years, advances in molecular methodologies have helped to identify several novel causes of DSDs; molecular tests to aid diagnosis and genetic counselling have now been adopted into clinical practice. Occasionally, genetic profiling of embryos prior to implantation as an adjunct to assisted reproduction, prenatal diagnosis of at-risk pregnancies and confirmatory testing of positive results found during newborn biochemical screening are performed. Of the available genetic tests, the candidate gene approach is the most popular. New high-throughput DNA analysis could enable a genetic diagnosis to be made when the aetiology is unknown or many differential diagnoses are possible. Nonetheless, concerns exist about the use of genetic tests. For instance, a diagnosis is not always possible even using new molecular approaches (which can be worrying for the parents) and incidental information obtained during the test might cause anxiety. Careful selection of the genetic test indicated for each condition remains important for good clinical practice. The purpose of this Review is to describe advances in molecular biological techniques for diagnosing DSDs.

  7. Toward Integrated Molecular Diagnostic System (iMDx): Principles and Applications

    PubMed Central

    Park, Seung-min; Sabour, Andrew F.; Son, Jun Ho; Lee, Sang Hun

    2014-01-01

    Integrated molecular diagnostic systems (iMDx), which are automated, sensitive, specific, user-friendly, robust, rapid, easy-to-use, and portable, can revolutionize future medicine. This review will first focus on the components of sample extraction, preservation, and filtration necessary for all point-of-care devices to include for practical use. Subsequently, we will look for low-powered and precise methods for both sample amplification and signal transduction, going in-depth to the details behind their principles. The final field of total device integration and its application to the clinical field will also be addressed to discuss the practicality for future patient care. We envision that microfluidic systems hold the potential to breakthrough the number of problems brought into the field of medical diagnosis today. PMID:24759281

  8. [Malignant tumours of the eye: Epidemiology, diagnostic methods and radiotherapy].

    PubMed

    Jardel, P; Caujolle, J-P; Gastaud, L; Maschi, C; Sauerwein, W; Thariat, J

    2015-12-01

    Malignant tumours of the eye are not common, barely representing 1 % of all cancers. This article aims to summarise, for each of the main eye malignant diseases, aspects of epidemiology, diagnostic methods and treatments, with a focus on radiation therapy techniques. The studied tumours are: eye metastasis, intraocular and ocular adnexal lymphomas, uveal melanomas, malignant tumours of the conjunctive, of the lids, and retinoblastomas. The last chapter outlines ocular complications of radiation therapy and their management.

  9. Development of Methods for Diagnostics of Discharges in Supersonic Flows

    DTIC Science & Technology

    2004-03-01

    flow, diagnostic methods, electric probe, measurement circuit, propane-air mixture, ignition. Participating Institution : Department of...932-88-20 E-mail: dean@phys.msu.su /ershov@ph-elec.phys.msu.su Partner: The European Office of Aerospace Research and Development (EOARD) Adress...of flight . The gas discharges of a various type can be the perspective tool of the decision of this problem. The definition of the most effective

  10. Molecular diagnostics and personalized medicine in oncology: challenges and opportunities.

    PubMed

    Normanno, Nicola; Rachiglio, Anna Maria; Roma, Cristin; Fenizia, Francesca; Esposito, Claudia; Pasquale, Raffaella; La Porta, Maria Libera; Iannaccone, Alessia; Micheli, Filippo; Santangelo, Michele; Bergantino, Francesca; Costantini, Susan; De Luca, Antonella

    2013-03-01

    Increasing evidence demonstrates that target-based agents are active only in molecularly selected populations of patients. Therefore, the identification of predictive biomarkers has become mandatory to improve the clinical development of these novel drugs. Mutations of the epidermal growth factor receptor (EGFR) or rearrangements of the ALK gene in non-small-cell lung cancer, and BRAF mutations in melanoma are clear examples of driver mutations and predictive biomarkers of response to treatment with specific inhibitors. Predictive biomarkers might also identify subgroups of patients that are not likely to respond to specific drugs, as shown for KRAS mutations and anti-EGFR monoclonal antibodies in colorectal carcinoma. The discovery of novel driver molecular alterations and the availability of drugs capable to selectively block such oncogenic mechanisms are leading to a rapid increase in the number of putative biomarkers that need to be assessed in each single patient. In this respect, two different approaches are being developed to introduce a comprehensive molecular characterization in clinical practice: high throughput genotyping platforms, which allow the detection of recognized genetic aberrations in clinical samples, and next generation sequencing that can provide information on all the different types of cancer-causing alterations. The introduction of these techniques in clinical practice will increase the possibility to identify molecular targets in each individual patient, and will also allow to follow the molecular evolution of the disease during the treatment. By using these approaches, the development of personalized medicine for patients with cancer will finally become possible. Copyright © 2012 Wiley Periodicals, Inc.

  11. Workshop on molecular methods for genetic diagnosis. Final technical report

    SciTech Connect

    Rinchik, E.M.

    1997-07-01

    The Sarah Lawrence College Human Genetics Program received Department of Energy funding to offer a continuing medical education workshop for genetic counselors in the New York metropolitan area. According to statistics from the National Society of Genetic Counselors, there are approximately 160 genetic counselors working in the tri-state area (New York, New Jersey, and Connecticut), and many of them had been working in the field for more than 10 years. Thus, there was a real need to offer these counselors an in-depth opportunity to learn the specifics of the major advances in molecular genetics, and, in particular, the new approaches to diagnostic testing for genetic disease. As a result of the DOE Award DE-FG02-95ER62048 ($20,583), in July 1995 we offered the {open_quotes}Workshop on Molecular Methods for Genetic Diagnosis{close_quotes} for 24 genetic counselors in the New York metropolitan area. The workshop included an initial review session on the basics of molecular biology, lectures and discussions on past and current topics in molecular genetics and diagnostic procedures, and, importantly, daily laboratory exercises. Each counselor gained not only background, but also firsthand experience, in the major techniques of biochemical and molecular methods for diagnosing genetic diseases as well as in mathematical and computational techniques involved in human genetics analyses. Our goal in offering this workshop was not to make genetic counselors experts in these laboratory diagnostic techniques, but to acquaint them, by hands-on experience, about some of the techniques currently in use. We also wanted to provide them a technical foundation upon which they can understand and appreciate new technical developments arising in the near future.

  12. The Utilization of Cytologic Fine-Needle Aspirates of Lung Cancer for Molecular Diagnostic Testing

    PubMed Central

    Roh, Michael H.

    2015-01-01

    In this era of precision medicine, our understanding and knowledge of the molecular landscape associated with lung cancer pathogenesis continues to evolve. This information is being increasingly exploited to treat advanced stage lung cancer patients with tailored, targeted therapy. During the management of these patients, minimally invasive procedures to obtain samples for tissue diagnoses are desirable. Cytologic fine-needle aspirates are often utilized for this purpose and are important not only for rendering diagnoses to subtype patients’ lung cancers, but also for ascertaining molecular diagnostic information for treatment purposes. Thus, cytologic fine-needle aspirates must be utilized and triaged judiciously to achieve both objectives. In this review, strategies in utilizing fine-needle aspirates will be discussed in the context of our current understanding of the clinically actionable molecular aberrations underlying non-small cell lung cancer and the molecular assays applied to these samples in order to obtain treatment-relevant molecular diagnostic information. PMID:26076721

  13. Computational methods for molecular docking

    SciTech Connect

    Klebe, G.; Lengauer, T.

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Recently, it has been demonstrated that the knowledge of the three-dimensional structure of the protein can be used to derive new protein ligands with improved binding properties. This tutorial focuses on the following questions: What is its binding affinity toward a particular receptor? What are putative conformations of a ligand at the binding site? What are the similarities of different ligands in terms of their recognition capabilities? Where and in which orientation will a ligand bind to the active site? How is a new putative protein ligand selected? An overview is presented of the algorithms which are presently used to handle and predict protein-ligand interactions and to dock small molecule ligands into proteins.

  14. Alternative Confidence Interval Methods Used in the Diagnostic Accuracy Studies.

    PubMed

    Erdoğan, Semra; Gülhan, Orekıcı Temel

    2016-01-01

    Background/Aim. It is necessary to decide whether the newly improved methods are better than the standard or reference test or not. To decide whether the new diagnostics test is better than the gold standard test/imperfect standard test, the differences of estimated sensitivity/specificity are calculated with the help of information obtained from samples. However, to generalize this value to the population, it should be given with the confidence intervals. The aim of this study is to evaluate the confidence interval methods developed for the differences between the two dependent sensitivity/specificity values on a clinical application. Materials and Methods. In this study, confidence interval methods like Asymptotic Intervals, Conditional Intervals, Unconditional Interval, Score Intervals, and Nonparametric Methods Based on Relative Effects Intervals are used. Besides, as clinical application, data used in diagnostics study by Dickel et al. (2010) has been taken as a sample. Results. The results belonging to the alternative confidence interval methods for Nickel Sulfate, Potassium Dichromate, and Lanolin Alcohol are given as a table. Conclusion. While preferring the confidence interval methods, the researchers have to consider whether the case to be compared is single ratio or dependent binary ratio differences, the correlation coefficient between the rates in two dependent ratios and the sample sizes.

  15. A step forward in molecular diagnostics of lyssaviruses--results of a ring trial among European laboratories.

    PubMed

    Fischer, Melina; Wernike, Kerstin; Freuling, Conrad M; Müller, Thomas; Aylan, Orhan; Brochier, Bernard; Cliquet, Florence; Vázquez-Morón, Sonia; Hostnik, Peter; Huovilainen, Anita; Isaksson, Mats; Kooi, Engbert A; Mooney, Jean; Turcitu, Mihai; Rasmussen, Thomas B; Revilla-Fernández, Sandra; Smreczak, Marcin; Fooks, Anthony R; Marston, Denise A; Beer, Martin; Hoffmann, Bernd

    2013-01-01

    Rabies is a lethal and notifiable zoonotic disease for which diagnostics have to meet the highest standards. In recent years, an evolution was especially seen in molecular diagnostics with a wide variety of different detection methods published. Therefore, a first international ring trial specifically designed on the use of reverse transcription polymerase chain reaction (RT-PCR) for detection of lyssavirus genomic RNA was organized. The trial focussed on assessment and comparison of the performance of conventional and real-time assays. In total, 16 European laboratories participated. All participants were asked to investigate a panel of defined lyssavirus RNAs, consisting of Rabies virus (RABV) and European bat lyssavirus 1 and 2 (EBLV-1 and -2) RNA samples, with systems available in their laboratory. The ring trial allowed the important conclusion that conventional RT-PCR assays were really robust assays tested with a high concordance between different laboratories and assays. The real-time RT-PCR system by Wakeley et al. (2005) in combination with an intercalating dye, and the combined version by Hoffmann and co-workers (2010) showed good sensitivity for the detection of all RABV samples included in this test panel. Furthermore, all used EBLV-specific assays, real-time RT-PCRs as well as conventional RT-PCR systems, were shown to be suitable for a reliable detection of EBLVs. It has to be mentioned that differences were seen in the performance between both the individual RT-PCR systems and the laboratories. Laboratories which used more than one molecular assay for testing the sample panel always concluded a correct sample result. Due to the markedly high genetic diversity of lyssaviruses, the application of different assays in diagnostics is needed to achieve a maximum of diagnostic accuracy. To improve the knowledge about the diagnostic performance proficiency testing at an international level is recommended before using lyssavirus molecular diagnostics e

  16. Mitochondrial disease: maintenance of mitochondrial genome and molecular diagnostics.

    PubMed

    Kang, Dongchon; Hamasaki, Naotaka

    2006-01-01

    Mitochondrial DNA (mtDNA) is essential for the aerobic ATP synthesis system that is responsible for about 80% of normal cellular energy demands. In addition to rare genetic disorders causing neuromyopathy, alterations of mtDNA have been found also in so-called common diseases such as heart failure, diabetes, and cancer. Although some of these alterations are inherited, some are considered to be generated and/or accumulated in somatic cells with age. One reason for the somatic mutations is that mtDNA is more vulnerable than is nuclear DNA. For example, mitochondrial respiratory chain produces a large amount of reactive oxygen species as inevitable byproducts of oxidative phosphorylation. However, the molecular mechanisms for maintenance of mitochondrial genome are much less elucidated than those for nuclear genome. In spite of its increasing importance, the molecular diagnosis of mitochondrial DNA-related diseases is well done only in very limited expert laboratories. In this chapter, we focus on maintenance of mtDNA in somatic cells, its clinical importance, and recent developments of molecular tests.

  17. A diagnostic assessment for introductory molecular and cell biology.

    PubMed

    Shi, Jia; Wood, William B; Martin, Jennifer M; Guild, Nancy A; Vicens, Quentin; Knight, Jennifer K

    2010-01-01

    We have developed and validated a tool for assessing understanding of a selection of fundamental concepts and basic knowledge in undergraduate introductory molecular and cell biology, focusing on areas in which students often have misconceptions. This multiple-choice Introductory Molecular and Cell Biology Assessment (IMCA) instrument is designed for use as a pre- and posttest to measure student learning gains. To develop the assessment, we first worked with faculty to create a set of learning goals that targeted important concepts in the field and seemed likely to be emphasized by most instructors teaching these subjects. We interviewed students using open-ended questions to identify commonly held misconceptions, formulated multiple-choice questions that included these ideas as distracters, and reinterviewed students to establish validity of the instrument. The assessment was then evaluated by 25 biology experts and modified based on their suggestions. The complete revised assessment was administered to more than 1300 students at three institutions. Analysis of statistical parameters including item difficulty, item discrimination, and reliability provides evidence that the IMCA is a valid and reliable instrument with several potential uses in gauging student learning of key concepts in molecular and cell biology.

  18. A Diagnostic Assessment for Introductory Molecular and Cell Biology

    PubMed Central

    Wood, William B.; Martin, Jennifer M.; Guild, Nancy A.; Vicens, Quentin; Knight, Jennifer K.

    2010-01-01

    We have developed and validated a tool for assessing understanding of a selection of fundamental concepts and basic knowledge in undergraduate introductory molecular and cell biology, focusing on areas in which students often have misconceptions. This multiple-choice Introductory Molecular and Cell Biology Assessment (IMCA) instrument is designed for use as a pre- and posttest to measure student learning gains. To develop the assessment, we first worked with faculty to create a set of learning goals that targeted important concepts in the field and seemed likely to be emphasized by most instructors teaching these subjects. We interviewed students using open-ended questions to identify commonly held misconceptions, formulated multiple-choice questions that included these ideas as distracters, and reinterviewed students to establish validity of the instrument. The assessment was then evaluated by 25 biology experts and modified based on their suggestions. The complete revised assessment was administered to more than 1300 students at three institutions. Analysis of statistical parameters including item difficulty, item discrimination, and reliability provides evidence that the IMCA is a valid and reliable instrument with several potential uses in gauging student learning of key concepts in molecular and cell biology. PMID:21123692

  19. [Anaplastic glioma. Neuropathology, molecular diagnostics and current study concepts].

    PubMed

    Wick, W; Weller, M

    2010-08-01

    According to the current WHO classification anaplastic gliomas comprise pure astrocytomas and oligodendrogliomas and mixed tumors. This review summarizes findings, discusses problems and defines new questions from the phase III trials on anaplastic gliomas. The molecular subgroup analyses of the NOA-04 trial identified three molecular parameters, which predict longer progression-free and overall survival independent from the mode of therapy, radiotherapy or alkylating chemotherapy-. These are 1p/19q codeletion, methylation of the promoter of the O(6)-methylguanyl methyltransferase (MGMT) gene and hot-spot mutations in the isocitrate dehydrogenase 1 (IDH1) gene. The prognostic relevance of these markers is not lower than that of histopathological subclassification but determination is potentially more robust. Therefore, marker profiles should be included into the next WHO brain tumor classification. The current standard of care for first-line treatment in anaplastic gliomas is radiotherapy or chemotherapy. The next steps, e.g. within the international CATNON trial, are to define the role and optimal sequencing of combined modality treatment focusing on radiotherapy and temozolomide. Inclusion in this trial is already based on the WHO grade and the 1p/19q status and not on the histopathological subtype. Furthermore, anaplastic gliomas are an important group of brain tumors for developing future molecular targeted therapies and should therefore be in the main focus of academic and industrial drug development, which aims at improved efficacy and avoiding long-term side-effects.

  20. Role of Serologic and Molecular Diagnostic Assays in Identification and Management of Hepatitis C Virus Infection.

    PubMed

    Cloherty, Gavin; Talal, Andrew; Coller, Kelly; Steinhart, Corklin; Hackett, John; Dawson, George; Rockstroh, Juergen; Feld, Jordan

    2016-02-01

    The drugs available for the treatment of hepatitis C virus (HCV) have evolved to provide shorter treatment duration and higher rates of sustained virologic response (SVR), and the role of HCV infection diagnostic tests has had to evolve in order to meet changing clinical needs. This review gives an overview on the role of HCV infection diagnostic testing (molecular and serological tools) used in the diagnosis and management of HCV infection. All of this critical information guides physician decisions to optimize patient clinical outcomes. Also discussed is the future direction of diagnostic testing in the context of further advances in drug development. Copyright © 2016 Cloherty et al.

  1. Pre-examination factors affecting molecular diagnostic test results and interpretation: A case-based approach.

    PubMed

    Payne, Deborah A; Baluchova, Katarina; Peoc'h, Katell H; van Schaik, Ron H N; Chan, K C Allen; Maekawa, Masato; Mamotte, Cyril; Russomando, Graciela; Rousseau, François; Ahmad-Nejad, Parviz

    2017-04-01

    Multiple organizations produce guidance documents that provide opportunities to harmonize quality practices for diagnostic testing. The International Organization for Standardization ISO 15189 standard addresses requirements for quality in management and technical aspects of the clinical laboratory. One technical aspect addresses the complexities of the pre-examination phase prior to diagnostic testing. The Committee for Molecular Diagnostics of the International Federation for Clinical Chemistry and Laboratory Medicine (also known as, IFCC C-MD) conducted a survey of international molecular laboratories and determined ISO 15189 to be the most referenced guidance document. In this review, the IFCC C-MD provides case-based examples illustrating the value of select pre-examination processes as these processes relate to molecular diagnostic testing. Case-based examples in infectious disease, oncology, inherited disease and pharmacogenomics address the utility of: 1) providing information to patients and users, 2) designing requisition forms, 3) obtaining informed consent and 4) maintaining sample integrity prior to testing. The pre-examination phase requires extensive and consistent communication between the laboratory, the healthcare provider and the end user. The clinical vignettes presented in this paper illustrate the value of applying select ISO 15189 recommendations for general laboratory to the more specialized area of Molecular Diagnostics. Copyright © 2016 Elsevier B.V. All rights reserved.

  2. A defect-driven diagnostic method for machine tool spindles

    PubMed Central

    Vogl, Gregory W.; Donmez, M. Alkan

    2016-01-01

    Simple vibration-based metrics are, in many cases, insufficient to diagnose machine tool spindle condition. These metrics couple defect-based motion with spindle dynamics; diagnostics should be defect-driven. A new method and spindle condition estimation device (SCED) were developed to acquire data and to separate system dynamics from defect geometry. Based on this method, a spindle condition metric relying only on defect geometry is proposed. Application of the SCED on various milling and turning spindles shows that the new approach is robust for diagnosing the machine tool spindle condition. PMID:28065985

  3. A defect-driven diagnostic method for machine tool spindles.

    PubMed

    Vogl, Gregory W; Donmez, M Alkan

    2015-01-01

    Simple vibration-based metrics are, in many cases, insufficient to diagnose machine tool spindle condition. These metrics couple defect-based motion with spindle dynamics; diagnostics should be defect-driven. A new method and spindle condition estimation device (SCED) were developed to acquire data and to separate system dynamics from defect geometry. Based on this method, a spindle condition metric relying only on defect geometry is proposed. Application of the SCED on various milling and turning spindles shows that the new approach is robust for diagnosing the machine tool spindle condition.

  4. Raman background photobleaching as a possible method of cancer diagnostics

    NASA Astrophysics Data System (ADS)

    Brandt, Nikolai N.; Brandt, Nikolai B.; Chikishev, Andrey Y.; Gangardt, Mihail G.; Karyakina, Nina F.

    2001-06-01

    Kinetics of photobleaching of background in Raman spectra of aqueous solutions of plant toxins ricin and ricin agglutinin, ricin binding subunit, and normal and malignant human blood serum were measured. For the excitation of the spectra cw and pulsed laser radiation were used. The spectra of Raman background change upon laser irradiation. Background intensity is lower for the samples with small molecular weight. The cyclization of amino acid residues in the toxin molecules as well as in human blood serum can be a reason of the Raman background. The model of the background photobleaching is proposed. The differences in photobleaching kinetics in the cases of cw and pulsed laser radiation are discussed. It is shown that Raman background photobleaching can be very informative for cancer diagnostics.

  5. Smart Cup: A Minimally-Instrumented, Smartphone-Based Point-of-Care Molecular Diagnostic Device

    PubMed Central

    Liao, Shih-Chuan; Peng, Jing; Mauk, Michael G.; Awasthi, Sita; Song, Jinzhao; Friedman, Harvey; Bau, Haim H.; Liu, Changchun

    2016-01-01

    Nucleic acid amplification-based diagnostics offer rapid, sensitive, and specific means for detecting and monitoring the progression of infectious diseases. However, this method typically requires extensive sample preparation, expensive instruments, and trained personnel. All of which hinder its use in resource-limited settings, where many infectious diseases are endemic. Here, we report on a simple, inexpensive, minimally-instrumented, smart cup platform for rapid, quantitative molecular diagnostics of pathogens at the point of care. Our smart cup takes advantage of water-triggered, exothermic chemical reaction to supply heat for the nucleic acid-based, isothermal amplification. The amplification temperature is regulated with a phase-change material (PCM). The PCM maintains the amplification reactor at a constant temperature, typically, 60-65°C, when ambient temperatures range from 12 to 35°C. To eliminate the need for an optical detector and minimize cost, we use the smartphone’s flashlight to excite the fluorescent dye and the phone camera to record real-time fluorescence emission during the amplification process. The smartphone can concurrently monitor multiple amplification reactors and analyze the recorded data. Our smart cup’s utility was demonstrated by amplifying and quantifying herpes simplex virus type 2 (HSV-2) with LAMP assay in our custom-made microfluidic diagnostic chip. We have consistently detected as few as 100 copies of HSV-2 viral DNA per sample. Our system does not require any lab facilities and is suitable for use at home, in the field, and in the clinic, as well as in resource-poor settings, where access to sophisticated laboratories is impractical, unaffordable, or nonexistent. PMID:26900258

  6. Application of tissue mesodissection to molecular cancer diagnostics.

    PubMed

    Krizman, David; Adey, Nils; Parry, Robert

    2015-02-01

    To demonstrate clinical application of a mesodissection platform that was developed to combine advantages of laser-based instrumentation with the speed/ease of manual dissection for automated dissection of tissue off standard glass slides. Genomic analysis for KRAS gene mutation was performed on formalin fixed paraffin embedded (FFPE) cancer patient tissue that was dissected using the mesodissection platform. Selected reaction monitoring proteomic analysis for quantitative Her2 protein expression was performed on FFPE patient tumour tissue dissected by a laser-based instrument and the MilliSect instrument. Genomic analysis demonstrates highly confident detection of KRAS mutation specifically in lung cancer cells and not the surrounding benign, non-tumour tissue. Proteomic analysis demonstrates Her2 quantitative protein expression in breast cancer cells dissected manually, by laser-based instrumentation and by MilliSect instrumentation (mesodissection). Slide-mounted tissue dissection is commonly performed using laser-based instruments or manually scraping tissue by scalpel. Here we demonstrate that the mesodissection platform as performed by the MilliSect instrument for tissue dissection is cost-effective; it functions comparably to laser-based dissection and which can be adopted into a clinical diagnostic workflow. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  7. [Clinical importance and diagnostic methods of minimal hepatic encephalopathy].

    PubMed

    Stawicka, Agnieszka; Zbrzeźniak, Justyna; Świderska, Aleksandra; Kilisińska, Natalia; Świderska, Magdalena; Jaroszewicz, Jerzy; Flisiak, Robert

    2016-02-01

    Minimal hepatic encephalopathy (MHE) encompasses a number of neuropsychological and neurophysiological disorders in patients suffering from liver cirrhosis, who do not display abnormalities during a medical interview or physical examination. A negative influence of MHE on the quality of life of patients suffering from liver cirrhosis was confirmed, which include retardation of ability of operating motor vehicles and disruption of multiple health-related areas, as well as functioning in the society. The data on frequency of traffic offences and accidents amongst patients diagnosed with MHE in comparison to patients diagnosed with liver cirrhosis without MHE, as well as healthy persons is alarming. Those patients are unaware of their disorder and retardation of their ability to operate vehicles, therefore it is of utmost importance to define this group. The term minimal hepatic encephalopathy (formerly "subclinical" encephalopathy) erroneously suggested the unnecessity of diagnostic and therapeutic procedures in patients with liver cirrhosis. Diagnosing MHE is an important predictive factor for occurrence of overt encephalopathy - more than 50% of patients with this diagnosis develop overt encephalopathy during a period of 30 months after. Early diagnosing MHE gives a chance to implement proper treatment which can be a prevention of overt encephalopathy. Due to continuing lack of clinical research there exist no commonly agreed-upon standards for definition, diagnostics, classification and treatment of hepatic encephalopathy. This article introduces the newest findings regarding the importance of MHE, scientific recommendations and provides detailed descriptions of the most valuable diagnostic methods.

  8. New targeted therapies and diagnostic methods for iron overload diseases.

    PubMed

    Kolnagou, Annita; Kontoghiorghe, Christina N; Kontoghiorghes, George John

    2018-01-01

    Millions of people worldwide suffer from iron overload toxicity diseases such as transfusional iron overload in thalassaemia and hereditary haemochromatosis. The accumulation and presence of toxic focal iron deposits causing tissue damage can also be identified in Friedreich's ataxia, Alzheimer's, Parkinson's, renal and other diseases. Different diagnostic criteria of toxicity and therapeutic interventions apply to each disease of excess or misplaced iron. Magnetic resonance imaging relaxation times T2 and T2* for monitoring iron deposits in organs and iron biomarkers such as serum ferritin and transferrin iron saturation have contributed in the elucidation of iron toxicity mechanisms and pathways, and also the evaluation of the efficacy and mode of action of chelating drugs in the treatment of diseases related to iron overload, toxicity and metabolism. Similarly, histopathological and electron microscopy diagnostic methods have revealed mechanisms of iron overload toxicity at cellular and sub-cellular levels. These new diagnostic criteria and chelator dose adjustments could apply in different or special patient categories e.g. thalassaemia patients with normal iron stores, where iron deficiency and over-chelation toxicity should be avoided.

  9. Molecular Diagnostic and Prognostic Subtyping of Gliomas in Tunisian Population.

    PubMed

    Trabelsi, Saoussen; Chabchoub, Imen; Ksira, Iadh; Karmeni, Nadhir; Mama, Nadia; Kanoun, Samia; Burford, Anna; Jury, Alexa; Mackay, Alan; Popov, Sergey; Bouaouina, Noureddine; Ben Ahmed, Slim; Mokni, Moncef; Tlili, Kalthoum; Krifa, Hedi; Yacoubi, Mohamed Tahar; Jones, Chris; Saad, Ali; H'mida Ben Brahim, Dorra

    2017-05-01

    It has become increasingly evident that morphologically similar gliomas may have distinct clinical phenotypes arising from diverse genetic signatures. To date, glial tumours from the Tunisian population have not been investigated. To address this, we correlated the clinico-pathology with molecular data of 110 gliomas by a combination of HM450K array, MLPA and TMA-IHC. PTEN loss and EGFR amplification were distributed in different glioma histological groups. However, 1p19q co-deletion and KIAA1549:BRAF fusion were, respectively, restricted to Oligodendroglioma and Pilocytic Astrocytoma. CDKN2A loss and EGFR overexpression were more common within high-grade gliomas. Furthermore, survival statistical correlations led us to identify Glioblastoma (GB) prognosis subtypes. In fact, significant lower overall survival (OS) was detected within GB that overexpressed EGFR and Cox2. In addition, IDH1R132H mutation seemed to provide a markedly survival advantage. Interestingly, the association of IDHR132H mutation and EGFR normal status, as well as the association of differentiation markers, defined GB subtypes with good prognosis. By contrast, poor survival GB subtypes were defined by the combination of PTEN loss with PDGFRa expression and/or EGFR amplification. Additionally, GB presenting p53-negative staining associated with CDKN2A loss or p21 positivity represented a subtype with short survival. Thus, distinct molecular subtypes with individualised prognosis were identified. Interestingly, we found a unique histone mutation in a poor survival young adult GB case. This tumour exceptionally associated the H3F3A G34R mutation and MYCN amplification as well as 1p36 loss and 10q loss. Furthermore, by exhibiting a remarkable methylation profile, it emphasised the oncogenic power of G34R mutation connecting gliomagenesis and chromatin regulation.

  10. Role of molecular diagnostics in the management of infectious disease emergencies.

    PubMed

    Krishna, Neel K; Cunnion, Kenji M

    2012-11-01

    In the setting of infectious disease emergencies, rapid and accurate identification of the causative agent is critical to optimizing antimicrobial therapy in a timely manner. It is clearly evident that the age of molecular diagnostics is now upon us, with real-time PCR becoming the standard of diagnosis for many infectious disease emergencies in either monoplex or multiplex format. Other molecular techniques such as whole or partial genome sequencing, microarrays, broad-range PCR, restriction fragment length polymorphisms, and molecular typing are also being used. However, for most small clinical laboratories, implementation of these advanced molecular techniques is not feasible owing to the high cost of instrumentation and reagents. If these tests are not available in-house, samples can be sent to national reference laboratories (eg, Mayo Medical Laboratories and Quest Diagnostics) for real-time PCR assays that can be completed in 1 day. It is anticipated that over time commercial real-time PCR tests and instrumentation will become more standardized and affordable, allowing individual laboratories to conduct tests locally, thus further reducing turnaround time. Although real-time PCR has been proved to expand our diagnostic capability, it must be stressed that such molecular methodology constitutes only an additional tool in the diagnosis of infectious diseases in emergency situations. Phenotypic methodologies (staining, cultures, biochemical tests, and serology) still play a critical role in identifying, confirming, and providing antibiotic susceptibility testing for many microbial pathogens. As multiplex assays become increasingly available, there will be even greater temptation for taking a “shotgun” approach to diagnostic testing. These new technologies will not substitute for a proper history and physical examination leading to a thoughtful differential diagnosis. None the less, these new molecular tests increase the capability of the diagnostician to

  11. New diagnostic methods for laser plasma- and microwave-enhanced combustion

    PubMed Central

    Miles, Richard B; Michael, James B; Limbach, Christopher M; McGuire, Sean D; Chng, Tat Loon; Edwards, Matthew R; DeLuca, Nicholas J; Shneider, Mikhail N; Dogariu, Arthur

    2015-01-01

    The study of pulsed laser- and microwave-induced plasma interactions with atmospheric and higher pressure combusting gases requires rapid diagnostic methods that are capable of determining the mechanisms by which these interactions are taking place. New rapid diagnostics are presented here extending the capabilities of Rayleigh and Thomson scattering and resonance-enhanced multi-photon ionization (REMPI) detection and introducing femtosecond laser-induced velocity and temperature profile imaging. Spectrally filtered Rayleigh scattering provides a method for the planar imaging of temperature fields for constant pressure interactions and line imaging of velocity, temperature and density profiles. Depolarization of Rayleigh scattering provides a measure of the dissociation fraction, and multi-wavelength line imaging enables the separation of Thomson scattering from Rayleigh scattering. Radar REMPI takes advantage of high-frequency microwave scattering from the region of laser-selected species ionization to extend REMPI to atmospheric pressures and implement it as a stand-off detection method for atomic and molecular species in combusting environments. Femtosecond laser electronic excitation tagging (FLEET) generates highly excited molecular species and dissociation through the focal zone of the laser. The prompt fluorescence from excited molecular species yields temperature profiles, and the delayed fluorescence from recombining atomic fragments yields velocity profiles. PMID:26170432

  12. Modeling complex workflow in molecular diagnostics: design specifications of laboratory software for support of personalized medicine.

    PubMed

    Gomah, Mohamed E; Turley, James P; Lu, Huimin; Jones, Dan

    2010-01-01

    One of the hurdles to achieving personalized medicine has been implementing the laboratory processes for performing and reporting complex molecular tests. The rapidly changing test rosters and complex analysis platforms in molecular diagnostics have meant that many clinical laboratories still use labor-intensive manual processing and testing without the level of automation seen in high-volume chemistry and hematology testing. We provide here a discussion of design requirements and the results of implementation of a suite of lab management tools that incorporate the many elements required for use of molecular diagnostics in personalized medicine, particularly in cancer. These applications provide the functionality required for sample accessioning and tracking, material generation, and testing that are particular to the evolving needs of individualized molecular diagnostics. On implementation, the applications described here resulted in improvements in the turn-around time for reporting of more complex molecular test sets, and significant changes in the workflow. Therefore, careful mapping of workflow can permit design of software applications that simplify even the complex demands of specialized molecular testing. By incorporating design features for order review, software tools can permit a more personalized approach to sample handling and test selection without compromising efficiency.

  13. Highlights of the Third Annual Biomarker World Congress: biomarkers for molecular diagnostics.

    PubMed

    Burczynski, Michael E

    2007-09-01

    With the proliferation of high-content profiling technologies available for analyzing genetic, transcriptomic, proteomic and metabolomic markers in tissues, both novel analytes and increasingly complex signatures are emerging as biomarkers supporting drug development. If prospective studies during the course of clinical development support the clinical utility of a biomarker, consideration may eventually be given to converting such research-use only biomarker assays into medical diagnostics. The present report briefly summarizes a selected set of presentations geared towards the issues and principles involved in the validation of biomarkers for use as molecular diagnostics, as presented at the Third Annual Biomarker World Congress held in Philadelphia, Pennsylvania on 15 - 18 May 2007. More than 400 delegates attended the Third Annual Biomarker World Congress to discuss the role of biomarkers in all phases of drug discovery and development. The main conference consisted of four tracks addressing issues involving: i) biomarkers in early drug development; ii) biomarkers in clinical development; iii) biomarkers for molecular diagnostics; and iv) biomarker assay development. The present review focuses on selected presentations of relevance to the third track. Topics covered by the speakers included biomarker assays that seem to have diagnostic and/or theranostic potential in a variety of therapeutic settings and disease indications. Themes included both the general and specific issues that can be encountered when attempting to convert a biomarker assay into a molecular diagnostic for use in the clinical setting.

  14. [Will the new molecular karyotyping BACs-on-Beads technique replace the traditional cytogenetic prenatal diagnostics? Preliminary reports].

    PubMed

    Piotrowski, Krzysztof; Henkelman, Małgorzata; Zajaczek, Stanisław

    2012-04-01

    Recently several attempts have been made to introduce molecular karyotyping techniques into prenatal diagnosis. These methods can be used not only for the diagnosis of classical aneuploidies, but first of all they should be employed in the diagnostics of microaberrations, which are not revealed by low resolution methods of classical cytogenetics. The new method BACs-on-Beads is designed for quick detection of broad panel of aneuploidies and microdeletions, by the specified detection of deletions and duplications in the examined fetal DNA acquired from amniocytes. Prenatal diagnostics was performed with the use of BACs-on-Beads and classical amniocyte karyotyping simultaneously in a group of 54 pregnancies. This new method proved to be fully compatible with typical karyotyping in cultures of amniocytes in 98.2%. It was confirmed that the main advantage of this method is the possibility of quick diagnosis, within 48 hours, with much wider spectrum of detected anomalies when compared to classical methods. Contrary to other molecular karyotyping methods, the BACs-on-Beads technique is more economical, less time consuming and less complex equipment is needed than in case of other methods. We suppose that this technique can replace classical karyotyping methods in the near future.

  15. Nonparametric Methods in Molecular Biology

    PubMed Central

    Wittkowski, Knut M.; Song, Tingting

    2010-01-01

    In 2003, the completion of the Human Genome Project[1] together with advances in computational resources[2] were expected to launch an era where the genetic and genomic contributions to many common diseases would be found. In the years following, however, researchers became increasingly frustrated as most reported ‘findings’ could not be replicated in independent studies[3]. To improve the signal/noise ratio, it was suggested to increase the number of cases to be included to tens of thousands[4], a requirement that would dramatically restrict the scope of personalized medicine. Similarly, there was little success in elucidating the gene–gene interactions involved in complex diseases or even in developing criteria for assessing their phenotypes. As a partial solution to these enigmata, we here introduce a class of statistical methods as the ‘missing link’ between advances in genetics and informatics. As a first step, we provide a unifying view of a plethora of non-parametric tests developed mainly in the 1940s, all of which can be expressed as u-statistics. Then, we will extend this approach to reflect categorical and ordinal relationships between variables, resulting in a flexible and powerful approach to deal with the impact of (1) multi-allelic genetic loci, (2) poly-locus genetic regions, and (3) oligo-genetic and oligo-genomic collaborative interactions on complex phenotypes. PMID:20652502

  16. Molecular Diagnostics of the Internal Motions of Massive Cores

    NASA Astrophysics Data System (ADS)

    Pineda, Jorge; Velusamy, T.; Goldsmith, P.; Li, D.; Peng, R.; Langer, W.

    2009-12-01

    We present models of the internal kinematics of massive cores in the Orion molecular cloud. We use a sample of cores studied by Velusamy et al. (2008) that show red, blue, and no asymmetry in their HCO+ line profiles in equal proportion, and which therefore may represent a sample of cores in different kinematic states. We use the radiative transfer code RATRAN (Hogerheijde & van der Tak 2000) to model several transitions of HCO+ and H13CO+ as well as the dust continuum emission, of a spherical model cloud with radial density, temperature, and velocity gradients. We find that an excitation and velocity gradients are prerequisites to reproduce the observed line profiles. We use the dust continuum emission to constrain the density and temperature gradients. This allows us to narrow down the functional forms of the velocity gradient giving us the opportunity to test several theoretical predictions of velocity gradients produced by the effect of magnetic fields (e.g. Tassis et. al. 2007) and turbulence (e.g. Vasquez-Semanedi et al 2007).

  17. Digital diffraction analysis enables low-cost molecular diagnostics on a smartphone.

    PubMed

    Im, Hyungsoon; Castro, Cesar M; Shao, Huilin; Liong, Monty; Song, Jun; Pathania, Divya; Fexon, Lioubov; Min, Changwook; Avila-Wallace, Maria; Zurkiya, Omar; Rho, Junsung; Magaoay, Brady; Tambouret, Rosemary H; Pivovarov, Misha; Weissleder, Ralph; Lee, Hakho

    2015-05-05

    The widespread distribution of smartphones, with their integrated sensors and communication capabilities, makes them an ideal platform for point-of-care (POC) diagnosis, especially in resource-limited settings. Molecular diagnostics, however, have been difficult to implement in smartphones. We herein report a diffraction-based approach that enables molecular and cellular diagnostics. The D3 (digital diffraction diagnosis) system uses microbeads to generate unique diffraction patterns which can be acquired by smartphones and processed by a remote server. We applied the D3 platform to screen for precancerous or cancerous cells in cervical specimens and to detect human papillomavirus (HPV) DNA. The D3 assay generated readouts within 45 min and showed excellent agreement with gold-standard pathology or HPV testing, respectively. This approach could have favorable global health applications where medical access is limited or when pathology bottlenecks challenge prompt diagnostic readouts.

  18. Integrated residency training pathways of the future: diagnostic radiology, nuclear radiology, nuclear medicine, and molecular imaging.

    PubMed

    Oates, M Elizabeth

    2012-04-01

    Following up on the recommendations of the ACR/SNM Task Force on Nuclear Medicine Training, the respective leaderships convened Task Force II. Its charge is to develop realistic residency training pathways integrating diagnostic radiology, nuclear radiology, nuclear medicine, and molecular imaging. The diagnostic radiology participants offer these "pathways of the future" that are built on a foundation of training in diagnostic radiology. It is hoped that these pathways will ensure that the traditional and emerging clinical, educational, and research domains of nuclear radiology, nuclear medicine, and molecular imaging will be sustained and will indeed flourish in the decades to come. Copyright © 2012 American College of Radiology. Published by Elsevier Inc. All rights reserved.

  19. Chasing down the triple-negative myeloproliferative neoplasms: Implications for molecular diagnostics.

    PubMed

    Langabeer, Stephen E

    2016-01-01

    The majority of patients with classical myeloproliferative neoplasms (MPN) of polycythemia vera, essential thrombocythemia, and primary myelofibrosis harbor distinct disease-driving mutations within the JAK2, CALR, or MPL genes. The term triple-negative has been recently applied to those MPN without evidence of these consistent mutations, prompting whole or targeted exome sequencing approaches to determine the driver mutational status of this subgroup. These strategies have identified numerous novel mutations that occur in alternative exons of both JAK2 and MPL, the majority of which result in functional activation. Current molecular diagnostic approaches may possess insufficient coverage to detect these alternative mutations, prompting further consideration of targeted exon sequencing into routine diagnostic practice. How to incorporate these illuminating findings into the expanding molecular diagnostic algorithm for MPN requires continual attention.

  20. Updates on Immunohistochemical and Molecular Markers in Selected Head and Neck Diagnostic Problems.

    PubMed

    Yi, Chun-Hui; Jim Zhai, Qihui; Wang, Beverly Y

    2017-09-01

    - The head and neck regions have complex anatomic structures. They are not exempted from the rare occurrences of highly unusual, diagnostically challenging malignant neoplasms and mimickers. - To review and update the utility of immunohistochemistry and molecular biomarkers and to pursue diagnostic accuracy on selected rare neoplasms, especially some poorly differentiated malignancies. - Personal experience and information from the literature. - Head and neck tumors include neoplasms originating from heterogeneous tissue. Using the selected clinical cases, this review illustrates a continuous development of emerging molecular-genetic techniques to assist in the interpretation of uncommon, often poorly differentiated, highly malignant neoplasms. The diagnostic results are appropriately transmitted to the oncologists, radiation oncologists, and surgeons to create a coordinated plan of care for patients with these unusual disorders affecting the head and neck.

  1. Digital diffraction analysis enables low-cost molecular diagnostics on a smartphone

    PubMed Central

    Im, Hyungsoon; Castro, Cesar M.; Shao, Huilin; Liong, Monty; Song, Jun; Pathania, Divya; Fexon, Lioubov; Min, Changwook; Avila-Wallace, Maria; Zurkiya, Omar; Rho, Junsung; Magaoay, Brady; Tambouret, Rosemary H.; Pivovarov, Misha; Weissleder, Ralph; Lee, Hakho

    2015-01-01

    The widespread distribution of smartphones, with their integrated sensors and communication capabilities, makes them an ideal platform for point-of-care (POC) diagnosis, especially in resource-limited settings. Molecular diagnostics, however, have been difficult to implement in smartphones. We herein report a diffraction-based approach that enables molecular and cellular diagnostics. The D3 (digital diffraction diagnosis) system uses microbeads to generate unique diffraction patterns which can be acquired by smartphones and processed by a remote server. We applied the D3 platform to screen for precancerous or cancerous cells in cervical specimens and to detect human papillomavirus (HPV) DNA. The D3 assay generated readouts within 45 min and showed excellent agreement with gold-standard pathology or HPV testing, respectively. This approach could have favorable global health applications where medical access is limited or when pathology bottlenecks challenge prompt diagnostic readouts. PMID:25870273

  2. Pathogen Inactivating Properties and Increased Sensitivity in Molecular Diagnostics by PAXgene, a Novel Non-Crosslinking Tissue Fixative

    PubMed Central

    Loibner, Martina; Buzina, Walter; Viertler, Christian; Groelz, Daniel; Hausleitner, Anja; Siaulyte, Gintare; Kufferath, Iris; Kölli, Bettina; Zatloukal, Kurt

    2016-01-01

    Background Requirements on tissue fixatives are getting more demanding as molecular analysis becomes increasingly relevant for routine diagnostics. Buffered formaldehyde in pathology laboratories for tissue fixation is known to cause chemical modifications of biomolecules which affect molecular testing. A novel non-crosslinking tissue preservation technology, PAXgene Tissue (PAXgene), was developed to preserve the integrity of nucleic acids in a comparable way to cryopreservation and also to preserve morphological features comparable to those of formalin fixed samples. Methods Because of the excellent preservation of biomolecules by PAXgene we investigated its pathogen inactivation ability and biosafety in comparison to formalin by in-vitro testing of bacteria, human relevant fungi and human cytomegalovirus (CMV). Guidelines for testing disinfectants served as reference for inactivation assays. Furthermore, we tested the properties of PAXgene for detection of pathogens by PCR based assays. Results All microorganisms tested were similarly inactivated by PAXgene and formalin except Clostridium sporogenes, which remained viable in seven out of ten assays after PAXgene treatment and in three out of ten assays after formalin fixation. The findings suggest that similar biosafety measures can be applied for PAXgene and formalin fixed samples. Detection of pathogens in PCR-based diagnostics using two CMV assays resulted in a reduction of four to ten quantification cycles of PAXgene treated samples which is a remarkable increase of sensitivity. Conclusion PAXgene fixation might be superior to formalin fixation when molecular diagnostics and highly sensitive detection of pathogens is required in parallel to morphology assessment. PMID:26974150

  3. Molecular Diagnostics for the Study of Hypersonic Flows

    DTIC Science & Technology

    2000-04-01

    kiloelectron volts, which can induce many orders of magnitude stronger than that from fluorescence in the visible, ultraviolet and X ray the...sparks are sometimes utilized.Thehig eerg eectonsinucebradbnd X - ray emission, which results from aIle high energy electrons induce broadband...Combustion Institute, pp 1677-1691, 1986. [20] Voronel E.S, Kuznetsov L.I., Parfenov M.V., Yarygin V.N., "Electron X ray method for [9] Kychakoff G

  4. Application of Molecular Diagnostic Techniques for Viral Testing

    PubMed Central

    Cobo, Fernando

    2012-01-01

    Nucleic acid amplification techniques are commonly used currently to diagnose viral diseases and manage patients with this kind of illnesses. These techniques have had a rapid but unconventional route of development during the last 30 years, with the discovery and introduction of several assays in clinical diagnosis. The increase in the number of commercially available methods has facilitated the use of this technology in the majority of laboratories worldwide. This technology has reduced the use of some other techniques such as viral culture based methods and serological assays in the clinical virology laboratory. Moreover, nucleic acid amplification techniques are now the methods of reference and also the most useful assays for the diagnosis in several diseases. The introduction of these techniques and their automation provides new opportunities for the clinical laboratory to affect patient care. The main objectives in performing nucleic acid tests in this field are to provide timely results useful for high-quality patient care at a reasonable cost, because rapid results are associated with improvements in patients care. The use of amplification techniques such as polymerase chain reaction, real-time polymerase chain reaction or nucleic acid sequence-based amplification for virus detection, genotyping and quantification have some advantages like high sensitivity and reproducibility, as well as a broad dynamic range. This review is an up-to-date of the main nucleic acid techniques and their clinical applications, and special challenges and opportunities that these techniques currently provide for the clinical virology laboratory. PMID:23248732

  5. Influenza subtype identification with molecular methods

    USDA-ARS?s Scientific Manuscript database

    Gene sequencing and RT-PCR based methods are the molecular alternative to serology for the identification of influenza virus hemagglutinin and neuraminidase antigenic subtypes. Compared to serology both RT-PCR and sequencing are preferred subtyping methods because of the number of reference reagents...

  6. A review on the molecular diagnostics of Lynch syndrome: a central role for the pathology laboratory.

    PubMed

    van Lier, Margot G F; Wagner, Anja; van Leerdam, Monique E; Biermann, Katharina; Kuipers, Ernst J; Steyerberg, Ewout W; Dubbink, Hendrikus Jan; Dinjens, Winand N M

    2010-01-01

    Lynch syndrome (LS) is caused by mutations in mismatch repair genes and is characterized by a high cumulative risk for the development of mainly colorectal carcinoma and endometrial carcinoma. Early detection of LS is important since surveillance can reduce morbidity and mortality. However, the diagnosis of LS is complicated by the absence of a pre-morbid phenotype and germline mutation analysis is expensive and time consuming. Therefore it is standard practice to precede germline mutation analysis by a molecular diagnostic work-up of tumours, guided by clinical and pathological criteria, to select patients for germline mutation analysis. In this review we address these molecular analyses, the central role for the pathologist in the selection of patients for germline diagnostics of LS, as well as the molecular basis of LS.

  7. New Methods and Transducer Designs for Ultrasonic Diagnostics and Therapy

    NASA Astrophysics Data System (ADS)

    Rybyanets, A. N.; Naumenko, A. A.; Sapozhnikov, O. A.; Khokhlova, V. A.

    Recent advances in the field of physical acoustics, imaging technologies, piezoelectric materials, and ultrasonic transducer design have led to emerging of novel methods and apparatus for ultrasonic diagnostics, therapy and body aesthetics. The paper presents the results on development and experimental study of different high intensity focused ultrasound (HIFU) transducers. Technological peculiarities of the HIFU transducer design as well as theoretical and numerical models of such transducers and the corresponding HIFU fields are discussed. Several HIFU transducers of different design have been fabricated using different advanced piezoelectric materials. Acoustic field measurements for those transducers have been performed using a calibrated fiber optic hydrophone and an ultrasonic measurement system (UMS). The results of ex vivo experiments with different tissues as well as in vivo experiments with blood vessels are presented that prove the efficacy, safety and selectivity of the developed HIFU transducers and methods.

  8. Vaccines and diagnostic methods for bovine mastitis: fact and fiction.

    PubMed

    Yancey, R J

    1999-01-01

    A number of problems are uniquely associated with vaccination of dairy cows for mastitis. One of these is that the number of mastitis pathogens is numerous and heterogeneous. Vaccine efforts have concentrated mainly on the major mastitis pathogens. While at least one S. aureus bacterin has been commercially available for a number of years, no large-scale, independent field trials have been published in refereed journals which support the efficacy of this vaccine. Experimental vaccines for S. aureus composed of pseudocapsule-enriched bacterins supplemented with alpha- and/or beta-toxoids appear promising, but none of these has been commercialized. With S. uberis, some protection against homologous strain challenges was reported recently with a live strain and a bacterin, but other data from the same laboratory showed this vaccine would not protect against heterologous challenge strains. At this time there is only one highly effective vaccine for mastitis, the core-antigen vaccine for coliform mastitis. All of the commercially available vaccines for this indication are bacterins of rough mutants of E. coli strain J5 or Salmonella spp. Preliminary success with an experimental vaccine based on the plasminogen activator of S. uberis is a very different approach for a mastitis vaccine. Little success has been reported with vaccination against other mastitis pathogens. For diagnostic methods, the high somatic cell count, as measured by direct count or indirect assays, remains the cornerstone of mastitis diagnosis. However, for subclinical mastitis, bacterial cell culture is a reliable diagnostic method. Pathogen identification may rely on older biochemical testing methods or newer commercial identification systems, depending on the laboratory budget. ELISA assays also have been used to assess herd infection status. Epidemiologic studies have used DNA fingerprinting and ribotyping, but none of these methods has yet produced an easily utilized commercial format. Within the

  9. A comprehensive electrocardiographic, molecular, and echocardiographic study of Brugada syndrome: validation of the 2013 diagnostic criteria.

    PubMed

    Savastano, Simone; Rordorf, Roberto; Vicentini, Alessandro; Petracci, Barbara; Taravelli, Erika; Castelletti, Silvia; D'Errico, Alessandra; Torchio, Margherita; Dossena, Cinzia; Novara, Paola; Dagradi, Federica; Landolina, Maurizio; Spazzolini, Carla; Crotti, Lia; Schwartz, Peter J

    2014-07-01

    The debate on the diagnostic value of high intercostal spaces (ICSs) and of the number of diagnostic leads in Brugada syndrome (BrS) has been settled by a recent expert consensus statement. To test the validity, and the underlying anatomy, of the new electrocardiographic (ECG) diagnostic criteria using echocardiographic, molecular, and clinical evidence in 1 clinical study population with BrS. We analyzed 114 patients with BrS and with a spontaneous or drug-induced type 1 ECG pattern recorded in 1 or more right precordial leads in fourth, third, and second ICSs. The right ventricular outflow tract (RVOT) was localized by using echocardiography. All probands were screened on the SCN5A gene. The percentage of mutation carriers (MCs) and the event rate were similar regardless of the diagnostic ICS (fourth vs high ICSs: MCs 23% vs 19%; event rate 22% vs 28%) and the number of diagnostic leads (1 vs ≥2: MCs 20% vs 22%; event rate 22% vs 27%). The concordance between RVOT anatomical location and the diagnostic ICSs was 86%. The percentage of the diagnostic ECG pattern recorded was significantly increased by the exploration of the ICSs showing RVOT by echocardiography (echocardiography-guided approach vs conventional approach 100% vs 43%; P < .001). The high ICSs are not inferior to the standard fourth ICS for the ECG diagnosis of BrS, and the interindividual variability depends on the anatomical location of the RVOT as assessed by using echocardiography. This approach significantly increases diagnostic sensitivity without decreasing specificity and fully supports the recently published new diagnostic criteria. Copyright © 2014 Heart Rhythm Society. Published by Elsevier Inc. All rights reserved.

  10. The Changing Landscape of Molecular Diagnostic Testing: Implications for Academic Medical Centers

    PubMed Central

    Rehm, Heidi L.; Hynes, Elizabeth; Funke, Birgit H.

    2016-01-01

    Over the last decade, the field of molecular diagnostics has undergone tremendous transformation, catalyzed by the clinical implementation of next generation sequencing (NGS). As technical capabilities are enhanced and current limitations are addressed, NGS is increasingly capable of detecting most variant types and will therefore continue to consolidate and simplify diagnostic testing. It is likely that genome sequencing will eventually serve as a universal first line test for disorders with a suspected genetic origin. Academic Medical Centers (AMCs), which have been at the forefront of this paradigm shift are now presented with challenges to keep up with increasing technical, bioinformatic and interpretive complexity of NGS-based tests in a highly competitive market. Additional complexity may arise from altered regulatory oversight, also triggered by the unprecedented scope of NGS-based testing, which requires new approaches. However, these challenges are balanced by unique opportunities, particularly at the interface between clinical and research operations, where AMCs can capitalize on access to cutting edge research environments and establish collaborations to facilitate rapid diagnostic innovation. This article reviews present and future challenges and opportunities for AMC associated molecular diagnostic laboratories from the perspective of the Partners HealthCare Laboratory for Molecular Medicine (LMM). PMID:26828522

  11. Assessing value of innovative molecular diagnostic tests in the concept of predictive, preventive, and personalized medicine.

    PubMed

    Akhmetov, Ildar; Bubnov, Rostyslav V

    2015-01-01

    Molecular diagnostic tests drive the scientific and technological uplift in the field of predictive, preventive, and personalized medicine offering invaluable clinical and socioeconomic benefits to the key stakeholders. Although the results of diagnostic tests are immensely influential, molecular diagnostic tests (MDx) are still grudgingly reimbursed by payers and amount for less than 5 % of the overall healthcare costs. This paper aims at defining the value of molecular diagnostic test and outlining the most important components of "value" from miscellaneous assessment frameworks, which go beyond accuracy and feasibility and impact the clinical adoption, informing healthcare resource allocation decisions. The authors suggest that the industry should facilitate discussions with various stakeholders throughout the entire assessment process in order to arrive at a consensus about the depth of evidence required for positive marketing authorization or reimbursement decisions. In light of the evolving "value-based healthcare" delivery practices, it is also recommended to account for social and ethical parameters of value, since these are anticipated to become as critical for reimbursement decisions and test acceptance as economic and clinical criteria.

  12. Current and future molecular diagnostics in non-small-cell lung cancer.

    PubMed

    Li, Chun Man; Chu, Wing Ying; Wong, Di Lun; Tsang, Hin Fung; Tsui, Nancy Bo Yin; Chan, Charles Ming Lok; Xue, Vivian Wei Wen; Siu, Parco Ming Fai; Yung, Benjamin Yat Ming; Chan, Lawrence Wing Chi; Wong, Sze Chuen Cesar

    2015-01-01

    The molecular investigation of lung cancer has opened up an advanced area for the diagnosis and therapeutic management of lung cancer patients. Gene alterations in cancer initiation and progression provide not only information on molecular changes in lung cancer but also opportunities in advanced therapeutic regime by personalized targeted therapy. EGFR mutations and ALK rearrangement are important predictive biomarkers for the efficiency of tyrosine kinase inhibitor treatment in lung cancer patients. Moreover, epigenetic aberration and microRNA dysregulation are recent advances in the early detection and monitoring of lung cancer. Although a wide range of molecular tests are available, standardization and validation of assay protocols are essential for the quality of the test outcome. In this review, current and new advancements of molecular biomarkers for non-small-cell lung cancer will be discussed. Recommendations on future development of molecular diagnostic services will also be explored.

  13. [Beta-thalassemias: molecular, epidemiological, diagnostical and clinical aspects].

    PubMed

    Joly, Philippe; Pondarre, Corinne; Badens, Catherine

    2014-01-01

    Beta-thalassemia is one of most common autosomal recessive disorders worldwide. In France, 5 to 10 new major or intermedia forms are diagnosed annually and the global prevalence is about 500 cases. Since 20 years and thanks to the generalization of iron chelator treatments, the life expectancy has dramatically increased. Nearly 90% of the β-thalassemic alleles are point mutations easily identified by Sanger sequencing or dedicated methods. The remaining 10% are deletions detectable by MLPA or CGH Array. The alpha-globin genotype is also essential in the exploration of beta-thalassemia because an alpha-thalassemia improves the clinical state whereas an alpha triplication worsens it. The additional genotyping of a few HbF inducer polymorphisms allows to predict the age of the first transfusion, thanks to a recent dedicated algorithm, making beta-thalassemia one of the first potential application of predictive medicine. Gene therapy, pre-implantatory diagnosis and new drugs (Sotatercept®, hepcidin-like molecules) have also recently contributed to make beta-thalassemia a main scientific topic again.

  14. Comparison of diagnostic methods for onychomycosis, and proposal of a diagnostic algorithm.

    PubMed

    Jung, M Y; Shim, J H; Lee, J H; Lee, J H; Yang, J M; Lee, D-Y; Jang, K-T; Lee, N Y; Lee, J-H; Park, J-H; Park, K K

    2015-07-01

    Traditionally, the gold standard for diagnosis of onychomycosis has been the combination of direct microscopy with potassium hydroxide (KOH) staining and fungal culture. However, several studies have suggested that periodic-acid-Schiff (PAS) staining of nail-plate clippings may be a very sensitive method for the diagnosis of onychomycosis. To compare the sensitivities of direct microscopy with KOH, fungal culture and PAS staining of nail-plate clippings, and to define an efficient, high-yield and cost-effective diagnostic strategy for the diagnosis of onychomycosis in the clinical setting. We evaluated a total of 493 patients with clinically suspected onychomycosis. Group A comprised 400 patient samples, evaluated using fungal culture and PAS stain, while group B comprised 93 patient samples evaluated using KOH, fungal culture and PAS. Diagnosis of onychomycosis was defined as clinical morphology plus at least one positive test result. In group A, sensitivities of fungal culture and PAS were 49.5% and 93.1% (P < 0.005), respectively. In group B, the most sensitive single test was PAS (88.2%) followed by KOH (55.9%) and fungal culture (29.4%). The combination of fungal culture and PAS (94.1%) was significantly (P < 0.001) more sensitive than that of KOH and culture (72.1%). PAS staining of nail clippings is much more sensitive than KOH and fungal culture for the diagnosis of onychomycosis. Based on our results, we propose a diagnostic algorithm for onychomycosis that takes into consideration the sensitivity, cost-effectiveness and necessary time for each test. © 2015 British Association of Dermatologists.

  15. Molecular diagnostic testing for Klinefelter syndrome and other male sex chromosome aneuploidies

    PubMed Central

    2012-01-01

    Background Male sex chromosome aneuploidies are underdiagnosed despite concomitant physical and behavioral manifestations. Objective To develop a non-invasive, rapid and high-throughput molecular diagnostic assay for detection of male sex chromosome aneuploidies, including 47,XXY (Klinefelter), 47,XYY, 48,XXYY and 48,XXXY syndromes. Methods The assay utilizes three XYM and four XA markers to interrogate Y:X and X:autosome ratios, respectively. The seven markers were PCR amplified using genomic DNA isolated from a cohort of 323 males with aneuploid (n = 117) and 46,XY (n = 206) karyotypes. The resulting PCR products were subjected to Pyrosequencing, a quantitative DNA sequencing method. Results Receiver operator characteristic (ROC) curves were used to establish thresholds for the discrimination of aneuploid from normal samples. The XYM markers permitted the identification of 47,XXY, 48,XXXY and 47,XYY syndromes with 100% sensitivity and specificity in both purified DNA and buccal swab samples. The 48,XXYY karyotype was delineated by XA marker data from 46,XY; an X allele threshold of 43% also permitted detection of 48,XXYY with 100% sensitivity and specificity. Analysis of X chromosome-specific biallelic SNPs demonstrated that 43 of 45 individuals (96%) with 48,XXYY karyotype had two distinct X chromosomes, while 2 (4%) had a duplicate X, providing evidence that 48,XXYY may result from nondisjunction during early mitotic divisions of a 46,XY embryo. Conclusions Quantitative Pyrosequencing, with high-throughput potential, can detect male sex chromosome aneuploidies with 100% sensitivity. PMID:22524164

  16. A composite likelihood method for bivariate meta-analysis in diagnostic systematic reviews

    PubMed Central

    Liu, Yulun; Ning, Jing; Nie, Lei; Zhu, Hongjian; Chu, Haitao

    2014-01-01

    Diagnostic systematic review is a vital step in the evaluation of diagnostic technologies. In many applications, it involves pooling pairs of sensitivity and specificity of a dichotomized diagnostic test from multiple studies. We propose a composite likelihood method for bivariate meta-analysis in diagnostic systematic reviews. This method provides an alternative way to make inference on diagnostic measures such as sensitivity, specificity, likelihood ratios and diagnostic odds ratio. Its main advantages over the standard likelihood method are the avoidance of the non-convergence problem, which is non-trivial when the number of studies are relatively small, the computational simplicity and some robustness to model mis-specifications. Simulation studies show that the composite likelihood method maintains high relative efficiency compared to that of the standard likelihood method. We illustrate our method in a diagnostic review of the performance of contemporary diagnostic imaging technologies for detecting metastases in patients with melanoma. PMID:25512146

  17. Accurate methods for large molecular systems.

    PubMed

    Gordon, Mark S; Mullin, Jonathan M; Pruitt, Spencer R; Roskop, Luke B; Slipchenko, Lyudmila V; Boatz, Jerry A

    2009-07-23

    Three exciting new methods that address the accurate prediction of processes and properties of large molecular systems are discussed. The systematic fragmentation method (SFM) and the fragment molecular orbital (FMO) method both decompose a large molecular system (e.g., protein, liquid, zeolite) into small subunits (fragments) in very different ways that are designed to both retain the high accuracy of the chosen quantum mechanical level of theory while greatly reducing the demands on computational time and resources. Each of these methods is inherently scalable and is therefore eminently capable of taking advantage of massively parallel computer hardware while retaining the accuracy of the corresponding electronic structure method from which it is derived. The effective fragment potential (EFP) method is a sophisticated approach for the prediction of nonbonded and intermolecular interactions. Therefore, the EFP method provides a way to further reduce the computational effort while retaining accuracy by treating the far-field interactions in place of the full electronic structure method. The performance of the methods is demonstrated using applications to several systems, including benzene dimer, small organic species, pieces of the alpha helix, water, and ionic liquids.

  18. Influence of Molecular Size on the Retention of Polymeric Nanocarrier Diagnostic Agents in Breast Ducts

    PubMed Central

    Singh, Yashveer; Gao, Dayuan; Gu, Zichao; Li, Shike; Rivera, Kristia A.; Stein, Stanley; Love, Susan

    2012-01-01

    Purpose To investigate the influence of nanocarrier molecular size and shape on breast duct retention in normal rats using a non-invasive optical imaging method. Methods Fluorescein-labeled PEG nanocarriers of different molecular weights and shapes (linear, two-arm, four-arm, and eight-arm) were intraductally administered (50 nmol) to female Sprague-Dawley rats. Whole body images were obtained non-invasively. Fluorescence intensities (i.e., amount remaining in duct) were plotted against time to estimate the nanocarrier ductal retention half-lives (t1/2). Plasma samples were taken and the pharmacokinetics (Tmax, Cmax) of absorbed nanocarriers was also assessed. Results The t1/2 of linear 12, 20, 30, 40, and two-arm 60 kDa nanocarriers were 6.7 ± 0.9, 16.1 ± 4.1, 16.6 ± 3.4, 21.5 ± 2.7, and 19.5 ± 6.1 h, whereas the four-arm 20, 40, and eight-arm 20 kDa had t1/2 of 9.0 ± 0.5, 11.5 ± 1.9, and 12.6 ± 3.0 h. The t1/2 of unconjugated fluorescein was significantly lower (14.5 ± 1.4 min). The Tmax for 12, 40, 60 kDa nanocarriers were 1, 24, and 32 h, respectively, and only 30 min for fluorescein. Conclusions Since normal breast ducts are highly permeable, the use of nanocarriers may be helpful in prolonging ductal retention of diagnostic and/or therapeutic agents. PMID:22569800

  19. Array-on-a-disk? How Blu-ray technology can be applied to molecular diagnostics.

    PubMed

    Morais, Sergi; Tortajada-Genaro, Luis; Maquieira, Angel

    2014-09-01

    This editorial comments on the balance and perspectives of compact disk technology applied to molecular diagnostics. The development of sensitive, rapid and multiplex assays using Blu-ray technology for the determination of biomarkers, drug allergens, pathogens and detection of infections would have a direct impact on diagnostics. Effective tests for use in clinical, environmental and food applications require versatile and low-cost platforms as well as cost-effective detectors. Blu-ray technology accomplishes those requirements and advances on the concept of high density arrays for massive screening to achieve the demands of point of care or in situ analysis.

  20. CT-guided transthoracic core needle biopsy for small pulmonary lesions: diagnostic performance and adequacy for molecular testing

    PubMed Central

    Tian, Panwen; Wang, Ye; Li, Lei; Zhou, Yongzhao; Luo, Wenxin

    2017-01-01

    Background Computed tomography (CT)-guided transthoracic needle biopsy is a well-established, minimally invasive diagnostic tool for pulmonary lesions. Few large studies have been conducted on the diagnostic performance and adequacy for molecular testing of transthoracic core needle biopsy (TCNB) for small pulmonary lesions. Methods This study included CT-guided TCNB with 18-gauge cutting needles in 560 consecutive patients with small (≤3 cm) pulmonary lesions from January 2012 to January 2015. There were 323 males and 237 females, aged 51.8±12.7 years. The size of the pulmonary lesions was 1.8±0.6 cm. The sensitivity, specificity, accuracy and complications of the biopsies were investigated. The risk factors of diagnostic failure were assessed using univariate and multivariate analyses. The sample’s adequacy for molecular testing of non-small cell lung cancer (NSCLC) was analyzed. Results The overall sensitivity, specificity, and accuracy for diagnosis of malignancy were 92.0% (311/338), 98.6% (219/222), and 94.6% (530/560), respectively. The incidence of bleeding complications was 22.9% (128/560), and the incidence of pneumothorax was 10.4% (58/560). Logistic multivariate regression analysis showed that the independent risk factors for diagnostic failure were a lesion size ≤1 cm [odds ratio (OR), 3.95; P=0.007], lower lobe lesions (OR, 2.83; P=0.001), and pneumothorax (OR, 1.98; P=0.004). Genetic analysis was successfully performed on 95.45% (168/176) of specimens diagnosed as NSCLC. At least 96.8% of samples with two or more passes from a lesion were sufficient for molecular testing. Conclusions The diagnostic yield of small pulmonary lesions by CT-guided TCNB is high, and the procedure is relatively safe. A lesion size ≤1 cm, lower lobe lesions, and pneumothorax are independent risk factors for biopsy diagnostic failure. TCNB specimens could provide adequate tissues for molecular testing. PMID:28275482

  1. Current and proposed molecular diagnostics in a genitourinary service line laboratory at a tertiary clinical institution.

    PubMed

    Udager, Aaron M; Alva, Ajjai; Mehra, Rohit

    2014-01-01

    The idea that detailed knowledge of molecular oncogenesis will drive diagnostic, prognostic, and therapeutic clinical decision making in an increasingly multidisciplinary practice of oncologic care has been anticipated for many years. With the recent rapid advancement in our understanding of the molecular underpinnings of genitourinary malignancies, this concept is now starting to take shape in the fields of prostate, kidney, bladder, testicular, and penile cancer. Such breakthroughs necessitate the development of robust clinical-grade assays that can be quickly made available for patients to facilitate diagnosis in challenging cases, risk-stratify patients for subsequent clinical management, select the appropriate targeted therapy from among increasingly diverse and numerous options, and enroll patients in advanced clinical trials. This rapid translation of basic and clinical cancer research requires a streamlined, multidisciplinary approach to clinical assay development, termed here the molecular diagnostics service line laboratory. In this review, we summarize the current state and explore the future of molecular diagnostics in genitourinary oncology to conceptualize a genitourinary service line laboratory at a tertiary clinical institution.

  2. Development of a curriculum in molecular diagnostics, genomics and personalized medicine for dermatology trainees.

    PubMed

    Murphy, Michael J; Shahriari, Neda; Payette, Michael; Mnayer, Laila; Elaba, Zendee

    2016-10-01

    Results of molecular studies are redefining the diagnosis and management of a wide range of skin disorders. Dermatology training programs maintain a relative gap in relevant teaching. To develop a curriculum in molecular diagnostics, genomics and personalized medicine for dermatology trainees at our institution. The aim is to provide trainees with a specialty-appropriate, working knowledge in clinical molecular dermatology. The Departments of Dermatology and Pathology and Laboratory Medicine collaborated on the design and implementation of educational objectives and teaching modalities for the new curriculum. A multidisciplinary curriculum was developed. It comprises: (i) assigned reading from the medical literature and reference textbook; (ii) review of teaching sets; (iii) two 1 hour lectures; (iv) trainee presentations; (v) 1-week rotation in a clinical molecular pathology and cytogenetics laboratory; and (vi) assessments and feedback. Residents who participated in the curriculum to date have found the experience to be of value. Our curriculum provides a framework for other dermatology residency programs to develop their own specific approach to molecular diagnostics education. Such training will provide a foundation for lifelong learning as molecular testing evolves and becomes integral to the practice of dermatology. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  3. Molecular energies from an incremental fragmentation method

    NASA Astrophysics Data System (ADS)

    Meitei, Oinam Romesh; Heßelmann, Andreas

    2016-02-01

    The systematic molecular fragmentation method by Collins and Deev [J. Chem. Phys. 125, 104104 (2006)] has been used to calculate total energies and relative conformational energies for a number of small and extended molecular systems. In contrast to the original approach by Collins, we have tested the accuracy of the fragmentation method by utilising an incremental scheme in which the energies at the lowest level of the fragmentation are calculated on an accurate quantum chemistry level while lower-cost methods are used to correct the low-level energies through a high-level fragmentation. In this work, the fragment energies at the lowest level of fragmentation were calculated using the random-phase approximation (RPA) and two recently developed extensions to the RPA while the incremental corrections at higher levels of the fragmentation were calculated using standard density functional theory (DFT) methods. The complete incremental fragmentation method has been shown to reproduce the supermolecule results with a very good accuracy, almost independent on the molecular type, size, or type of decomposition. The fragmentation method has also been used in conjunction with the DFT-SAPT (symmetry-adapted perturbation theory) method which enables a breakdown of the total nonbonding energy contributions into individual interaction energy terms. Finally, the potential problems of the method connected with the use of capping hydrogen atoms are analysed and two possible solutions are supplied.

  4. Molecular energies from an incremental fragmentation method.

    PubMed

    Meitei, Oinam Romesh; Heßelmann, Andreas

    2016-02-28

    The systematic molecular fragmentation method by Collins and Deev [J. Chem. Phys. 125, 104104 (2006)] has been used to calculate total energies and relative conformational energies for a number of small and extended molecular systems. In contrast to the original approach by Collins, we have tested the accuracy of the fragmentation method by utilising an incremental scheme in which the energies at the lowest level of the fragmentation are calculated on an accurate quantum chemistry level while lower-cost methods are used to correct the low-level energies through a high-level fragmentation. In this work, the fragment energies at the lowest level of fragmentation were calculated using the random-phase approximation (RPA) and two recently developed extensions to the RPA while the incremental corrections at higher levels of the fragmentation were calculated using standard density functional theory (DFT) methods. The complete incremental fragmentation method has been shown to reproduce the supermolecule results with a very good accuracy, almost independent on the molecular type, size, or type of decomposition. The fragmentation method has also been used in conjunction with the DFT-SAPT (symmetry-adapted perturbation theory) method which enables a breakdown of the total nonbonding energy contributions into individual interaction energy terms. Finally, the potential problems of the method connected with the use of capping hydrogen atoms are analysed and two possible solutions are supplied.

  5. Emerging molecular methods for male infertility investigation.

    PubMed

    Benkhalifa, Moncef; Montjean, Debbie; Belloc, Stephanie; Dalleac, Alain; Ducasse, Michel; Boyer, Pierre; Merviel, Philippe; Copin, Henri

    2014-01-01

    Male factors account for approximately 50% of reproductive pathology. Different disorders, including urogenital and endocrine system development abnormalities, lead to testicular and gametogenesis defects. Parallely, studies have reported that somatic and germ cell genome decay are a major cause of male infertility. It has been shown that in somatic karyotype, there is a higher incidence of chromosomal aberrations in infertile men than neonatal population and significant chromosome Y microdeletion or specific gene alterations in affected spermatogenesis. Karyotyping and FISH application at somatic and germ cell levels are no longer sufficient to investigate the potential contribution of genome disorders on male infertility. A wide range of molecular methods are required for better understanding of male infertility causes. Molecular omes and omics techniques have become a great tool to investigate male infertility from chromosome to protein. This review reports different molecular tests and methods that can be offered for male infertility investigation.

  6. Comparison of Machine Learning Methods for the Arterial Hypertension Diagnostics

    PubMed Central

    Belo, David; Gamboa, Hugo

    2017-01-01

    The paper presents results of machine learning approach accuracy applied analysis of cardiac activity. The study evaluates the diagnostics possibilities of the arterial hypertension by means of the short-term heart rate variability signals. Two groups were studied: 30 relatively healthy volunteers and 40 patients suffering from the arterial hypertension of II-III degree. The following machine learning approaches were studied: linear and quadratic discriminant analysis, k-nearest neighbors, support vector machine with radial basis, decision trees, and naive Bayes classifier. Moreover, in the study, different methods of feature extraction are analyzed: statistical, spectral, wavelet, and multifractal. All in all, 53 features were investigated. Investigation results show that discriminant analysis achieves the highest classification accuracy. The suggested approach of noncorrelated feature set search achieved higher results than data set based on the principal components. PMID:28831239

  7. Helicobacter pylori identification: a diagnostic/confirmatory method for evaluation.

    PubMed

    Mesquita, B; Gonçalves, M J; Pacheco, P; Lopes, J; Salazar, F; Relvas, M; Coelho, C; Pacheco, J J; Velazco, C

    2014-09-01

    The Helicobacter pylori extra gastric reservoir is probably the oral cavity. In order to evaluate the presence of this bacterium in patients with periodontitis and suspicious microbial cultures, saliva was collected from these and non-periodontitis subjects. PCRs targeting 16S rRNA gene and a 860 bp specific region were performed, and digested with the restriction enzyme DdeI. We observed that the PCR-RFLP approach augments the accuracy from 26.2 % (16/61), found in the PCR-based results, to 42.6 % (26/61), which is an excellent indicator for the establishment of this low-cost procedure as a diagnostic/confirmatory method for H. pylori evaluation.

  8. Pedophilia: an evaluation of diagnostic and risk prediction methods.

    PubMed

    Wilson, Robin J; Abracen, Jeffrey; Looman, Jan; Picheca, Janice E; Ferguson, Meaghan

    2011-06-01

    One hundred thirty child sexual abusers were diagnosed using each of following four methods: (a) phallometric testing, (b) strict application of Diagnostic and Statistical Manual of Mental Disorders (4th ed., text revision [DSM-IV-TR]) criteria, (c) Rapid Risk Assessment of Sex Offender Recidivism (RRASOR) scores, and (d) "expert" diagnoses rendered by a seasoned clinician. Comparative utility and intermethod consistency of these methods are reported, along with recidivism data indicating predictive validity for risk management. Results suggest that inconsistency exists in diagnosing pedophilia, leading to diminished accuracy in risk assessment. Although the RRASOR and DSM-IV-TR methods were significantly correlated with expert ratings, RRASOR and DSM-IV-TR were unrelated to each other. Deviant arousal was not associated with any of the other methods. Only the expert ratings and RRASOR scores were predictive of sexual recidivism. Logistic regression analyses showed that expert diagnosis did not add to prediction of sexual offence recidivism over and above RRASOR alone. Findings are discussed within a context of encouragement of clinical consistency and evidence-based practice regarding treatment and risk management of those who sexually abuse children.

  9. [Imputation methods for missing data in educational diagnostic evaluation].

    PubMed

    Fernández-Alonso, Rubén; Suárez-Álvarez, Javier; Muñiz, José

    2012-02-01

    In the diagnostic evaluation of educational systems, self-reports are commonly used to collect data, both cognitive and orectic. For various reasons, in these self-reports, some of the students' data are frequently missing. The main goal of this research is to compare the performance of different imputation methods for missing data in the context of the evaluation of educational systems. On an empirical database of 5,000 subjects, 72 conditions were simulated: three levels of missing data, three types of loss mechanisms, and eight methods of imputation. The levels of missing data were 5%, 10%, and 20%. The loss mechanisms were set at: Missing completely at random, moderately conditioned, and strongly conditioned. The eight imputation methods used were: listwise deletion, replacement by the mean of the scale, by the item mean, the subject mean, the corrected subject mean, multiple regression, and Expectation-Maximization (EM) algorithm, with and without auxiliary variables. The results indicate that the recovery of the data is more accurate when using an appropriate combination of different methods of recovering lost data. When a case is incomplete, the mean of the subject works very well, whereas for completely lost data, multiple imputation with the EM algorithm is recommended. The use of this combination is especially recommended when data loss is greater and its loss mechanism is more conditioned. Lastly, the results are discussed, and some future lines of research are analyzed.

  10. Sialoendoscopy, sialography, and ultrasound: a comparison of diagnostic methods

    PubMed Central

    Pniak, Tomáš; Štrympl, Pavel; Staníková, Lucia; Zeleník, Karol; Matoušek, Petr

    2016-01-01

    Abstract Objective To compare the accuracy of ultrasound, sialography, and sialendoscopy for examining benign salivary gland obstructions. Methods In this prospective study, patients with symptoms of obstruction of the major salivary gland duct system presenting at the ENT Clinic University Hospital, Ostrava, from June 2010 to December 2013 were included. All patients (n=76) underwent ultrasound, sialography, and sialoendoscopy. The signs of sialolithiasis, ductal stenosis, or normal findings were recorded after the examinations. Statistical analysis of the sensitivity and specificity of all the methods was performed, as well as a comparison of the accuracy of each method for different kinds of pathology (sialolithiasis or stenosis). Results The sensitivity of ultrasound, sialography, and sialoendoscopy for sialolithiasis findings were 71.9%, 86.7 %, and 100%, respectively. The sensitivity of sialography and sialoendoscopy for stenosis of the duct was 69.0%, and 100%, respectively. The study showed impossibility of ultrasonic diagnostics of ductal stenosis. The sensitivity of sialoendoscopy for both pathologies was significantly higher than that from ultrasound or sialography (p<0.05). The specificity of sialoendoscopy was significantly higher than that from by ultrasound or sialography (p<0.05). Conclusion Sialoendoscopy was the most accurate method for examination ductal pathology, with significantly higher sensitivity and specificity than by ultrasound or sialography. PMID:28352836

  11. A Large Cohort of Hemoglobin Variants in Thailand: Molecular Epidemiological Study and Diagnostic Consideration

    PubMed Central

    Srivorakun, Hataichanok; Singha, Kritsada; Fucharoen, Goonnapa; Sanchaisuriya, Kanokwan; Fucharoen, Supan

    2014-01-01

    Background Hemoglobin (Hb) variants are structurally inherited changes of globin chains. Accurate diagnoses of these variants are important for planning of appropriate management and genetic counseling. Since no epidemiological study has been conducted before, we have investigated frequencies, molecular and hematological features of Hb variants found in a large cohort of Thai subjects. Materials and Methods Study was conducted on 26,013 unrelated subjects, inhabiting in all geographical parts of Thailand over a period of 11 years from January 2002-December 2012. Hb analysis was done on high performance liquid chromatography (HPLC) or capillary electrophoresis (CE). Mutations causing Hb variants were identified using PCR and related techniques. Results Among 26,013 subjects investigated, 636 (2.4%) were found to carry Hb variants. Of these 636 subjects, 142 (22.4%) carried α-chain variants with 13 different mutations. The remaining included 451 (70.9%) cases with 16 β-chain variants, 37 (5.8%) cases with Hb Lepore (δβ-hybrid Hb) and 6 (0.9%) cases with a single δ-chain variant. The most common α-globin chain variant was the Hb Q-Thailand (α74GAC-CAC, Asp-His) which was found in 101 cases (15.8%). For β-globin chain variants, Hb Hope (β136GGT-GAT, Gly-Asp) and Hb Tak (β146+AC, Ter-Thr) are the two most common ones, found in 121 (19.0%) and 90 (14.2%) cases, respectively. Seven Hb variants have never been found in Thai population. Hb analysis profiles on HPLC or CE of these variants were illustrated to guide presumptive diagnostics. Conclusions Hb variants are common and heterogeneous in Thai population. With varieties of thalassemias and hemoglobinopathies in the population, interactions between them leading to complex syndromes are common and render their diagnoses difficult in routine practices. Knowledge of the spectrum, molecular basis, genotype-phenotype correlation and diagnostic features should prove useful for prevention and control of the diseases

  12. A WAO - ARIA - GA²LEN consensus document on molecular-based allergy diagnostics.

    PubMed

    Canonica, Giorgio Walter; Ansotegui, Ignacio J; Pawankar, Ruby; Schmid-Grendelmeier, Peter; van Hage, Marianne; Baena-Cagnani, Carlos E; Melioli, Giovanni; Nunes, Carlos; Passalacqua, Giovanni; Rosenwasser, Lanny; Sampson, Hugh; Sastre, Joaquin; Bousquet, Jean; Zuberbier, Torsten

    2013-10-03

    Molecular-based allergy (MA) diagnostics is an approach used to map the allergen sensitization of a patient at a molecular level, using purified natural or recombinant allergenic molecules (allergen components) instead of allergen extracts. Since its introduction, MA diagnostics has increasingly entered routine care, with currently more than 130 allergenic molecules commercially available for in vitro specific IgE (sIgE) testing.MA diagnostics allows for an increased accuracy in allergy diagnosis and prognosis and plays an important role in three key aspects of allergy diagnosis: (1) resolving genuine versus cross-reactive sensitization in poly-sensitized patients, thereby improving the understanding of triggering allergens; (2) assessing, in selected cases, the risk of severe, systemic versus mild, local reactions in food allergy, thereby reducing unnecessary anxiety for the patient and the need for food challenge testing; and (3) identifying patients and triggering allergens for specific immunotherapy (SIT).Singleplex and multiplex measurement platforms are available for MA diagnostics. The Immuno-Solid phase Allergen Chip (ISAC) is the most comprehensive platform currently available, which involves a biochip technology to measure sIgE antibodies against more than one hundred allergenic molecules in a single assay. As the field of MA diagnostics advances, future work needs to focus on large-scale, population-based studies involving practical applications, elucidation and expansion of additional allergenic molecules, and support for appropriate test interpretation. With the rapidly expanding evidence-base for MA diagnosis, there is a need for allergists to keep abreast of the latest information. The aim of this consensus document is to provide a practical guide for the indications, determination, and interpretation of MA diagnostics for clinicians trained in allergology.

  13. A WAO - ARIA - GA²LEN consensus document on molecular-based allergy diagnostics

    PubMed Central

    2013-01-01

    Molecular-based allergy (MA) diagnostics is an approach used to map the allergen sensitization of a patient at a molecular level, using purified natural or recombinant allergenic molecules (allergen components) instead of allergen extracts. Since its introduction, MA diagnostics has increasingly entered routine care, with currently more than 130 allergenic molecules commercially available for in vitro specific IgE (sIgE) testing. MA diagnostics allows for an increased accuracy in allergy diagnosis and prognosis and plays an important role in three key aspects of allergy diagnosis: (1) resolving genuine versus cross-reactive sensitization in poly-sensitized patients, thereby improving the understanding of triggering allergens; (2) assessing, in selected cases, the risk of severe, systemic versus mild, local reactions in food allergy, thereby reducing unnecessary anxiety for the patient and the need for food challenge testing; and (3) identifying patients and triggering allergens for specific immunotherapy (SIT). Singleplex and multiplex measurement platforms are available for MA diagnostics. The Immuno-Solid phase Allergen Chip (ISAC) is the most comprehensive platform currently available, which involves a biochip technology to measure sIgE antibodies against more than one hundred allergenic molecules in a single assay. As the field of MA diagnostics advances, future work needs to focus on large-scale, population-based studies involving practical applications, elucidation and expansion of additional allergenic molecules, and support for appropriate test interpretation. With the rapidly expanding evidence-base for MA diagnosis, there is a need for allergists to keep abreast of the latest information. The aim of this consensus document is to provide a practical guide for the indications, determination, and interpretation of MA diagnostics for clinicians trained in allergology. PMID:24090398

  14. Emerging technologies in point-of-care molecular diagnostics for resource-limited settings.

    PubMed

    Peeling, Rosanna W; McNerney, Ruth

    2014-06-01

    Emerging molecular technologies to diagnose infectious diseases at the point at which care is delivered have the potential to save many lives in developing countries where access to laboratories is poor. Molecular tests are needed to improve the specificity of syndromic management, monitor progress towards disease elimination and screen for asymptomatic infections with the goal of interrupting disease transmission and preventing long-term sequelae. In simplifying laboratory-based molecular assays for use at point-of-care, there are inevitable compromises between cost, ease of use and test performance. Despite significant technological advances, many challenges remain for the development of molecular diagnostics for resource-limited settings. There needs to be more advocacy for these technologies to be applied to infectious diseases, increased efforts to lower the barriers to market entry through streamlined and harmonized regulatory approaches, faster policy development for adoption of new technologies and novel financing mechanisms to enable countries to scale up implementation.

  15. Plasma DNA integrity index as a potential molecular diagnostic marker for breast cancer.

    PubMed

    Kamel, Azza M; Teama, Salwa; Fawzy, Amal; El Deftar, Mervat

    2016-06-01

    Plasma DNA integrity index is increased in various malignancies including breast cancer, the most common cancer in women worldwide; early detection is crucial for successful treatment. Current screening methods fail to detect many cases of breast cancer at an early stage. In this study, we evaluated the level of plasma DNA integrity index in 260 females (95 with breast cancer, 95 with benign breast lesions, and 70 healthy controls) to verify its potential value in discriminating malignant from benign breast lesions. The criteria of the American Joint Committee on Cancer were used for staging of breast cancer patients. DNA integrity index was measured by real-time PCR. DNA integrity index was significantly higher in breast cancer than in benign breast patients and healthy subjects (P = <0.001). DNA integrity index is correlated with TNM stage. Given 100 % specificity, the highest sensitivity achieved in detecting cancer group was 85.3 % at 0.55 DNA integrity index cutoff. In conclusion, the plasma DNA integrity index may be a promising molecular diagnostic marker of malignancy in breast lesions.

  16. Advantages and limitations of Raman spectroscopy for molecular diagnostics: an update.

    PubMed

    Eberhardt, Katharina; Stiebing, Clara; Matthäus, Christian; Schmitt, Michael; Popp, Jürgen

    2015-06-01

    Over the last decade, Raman spectroscopy has gained more and more interest in research as well as in clinical laboratories. As a vibrational spectroscopy technique, it is complementary to the also well-established infrared spectroscopy. Through specific spectral patterns, substances can be identified and molecular changes can be observed with high specificity. Because of a high spatial resolution due to an excitation wavelength in the visible and near-infrared range, Raman spectroscopy combined with microscopy is very powerful for imaging biological samples. Individual cells can be imaged on the subcellular level. In vivo tissue examinations are becoming increasingly important for clinical applications. In this review, we present currently ongoing research in different fields of medical diagnostics involving linear Raman spectroscopy and imaging. We give a wide overview over applications for the detection of atherosclerosis, cancer, inflammatory diseases and pharmacology, with a focus on developments over the past 5 years. Conclusions drawn from Raman spectroscopy are often validated by standard methods, for example, histopathology or PCR. The future potential of Raman spectroscopy and its limitations are discussed in consideration of other non-linear Raman techniques.

  17. Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories.

    PubMed

    Luo, C; Bueno, M; Kant, J; Randhawa, P

    2008-10-01

    Data on polyomavirus genomic diversity has greatly expanded in the past few years. The implications of viral DNA sequence variation on the performance of molecular diagnostic assays have not been systematically examined. 716 BK, 1626 JC, and 73 SV40 virus sequences available in GenBank were aligned using Clustal-X. Five different published BKV PCR assays currently in use at major medical centers were evaluated for primer and probe mismatches with available GenBank sequences. Coverage of naturally occurring BKV strains varied amongst different assay methods. Targeted viral sequences showed major mismatch with primer or probe sequence in up to 30.7% of known BKV strains. BKV subtypes IVa, IVb, and IVc were more prone to this problem, reflecting common use of Type I Dun sequence for assay design. Despite the known polymorphism of this gene, 484 VP-1 sequences with conserved areas potentially suitable for PCR assay design are available. Assay targets in the Large T-antigen and agnogene are less subject to genetic variation, but sequence information corresponding to the latter two genes is available only for 164 and 174 published strains, respectively. Cross reactivity of appropriately selected BKV primers with JCV and SV40 sequences available in current databases was not a significant problem.

  18. Diagnostic methods to assess inspiratory and expiratory muscle strength*

    PubMed Central

    Caruso, Pedro; de Albuquerque, André Luis Pereira; Santana, Pauliane Vieira; Cardenas, Leticia Zumpano; Ferreira, Jeferson George; Prina, Elena; Trevizan, Patrícia Fernandes; Pereira, Mayra Caleffi; Iamonti, Vinicius; Pletsch, Renata; Macchione, Marcelo Ceneviva; Carvalho, Carlos Roberto Ribeiro

    2015-01-01

    Impairment of (inspiratory and expiratory) respiratory muscles is a common clinical finding, not only in patients with neuromuscular disease but also in patients with primary disease of the lung parenchyma or airways. Although such impairment is common, its recognition is usually delayed because its signs and symptoms are nonspecific and late. This delayed recognition, or even the lack thereof, occurs because the diagnostic tests used in the assessment of respiratory muscle strength are not widely known and available. There are various methods of assessing respiratory muscle strength during the inspiratory and expiratory phases. These methods are divided into two categories: volitional tests (which require patient understanding and cooperation); and non-volitional tests. Volitional tests, such as those that measure maximal inspiratory and expiratory pressures, are the most commonly used because they are readily available. Non-volitional tests depend on magnetic stimulation of the phrenic nerve accompanied by the measurement of inspiratory mouth pressure, inspiratory esophageal pressure, or inspiratory transdiaphragmatic pressure. Another method that has come to be widely used is ultrasound imaging of the diaphragm. We believe that pulmonologists involved in the care of patients with respiratory diseases should be familiar with the tests used in order to assess respiratory muscle function.Therefore, the aim of the present article is to describe the advantages, disadvantages, procedures, and clinical applicability of the main tests used in the assessment of respiratory muscle strength. PMID:25972965

  19. Diagnostic methods to assess inspiratory and expiratory muscle strength.

    PubMed

    Caruso, Pedro; Albuquerque, André Luis Pereira de; Santana, Pauliane Vieira; Cardenas, Leticia Zumpano; Ferreira, Jeferson George; Prina, Elena; Trevizan, Patrícia Fernandes; Pereira, Mayra Caleffi; Iamonti, Vinicius; Pletsch, Renata; Macchione, Marcelo Ceneviva; Carvalho, Carlos Roberto Ribeiro

    2015-01-01

    Impairment of (inspiratory and expiratory) respiratory muscles is a common clinical finding, not only in patients with neuromuscular disease but also in patients with primary disease of the lung parenchyma or airways. Although such impairment is common, its recognition is usually delayed because its signs and symptoms are nonspecific and late. This delayed recognition, or even the lack thereof, occurs because the diagnostic tests used in the assessment of respiratory muscle strength are not widely known and available. There are various methods of assessing respiratory muscle strength during the inspiratory and expiratory phases. These methods are divided into two categories: volitional tests (which require patient understanding and cooperation); and non-volitional tests. Volitional tests, such as those that measure maximal inspiratory and expiratory pressures, are the most commonly used because they are readily available. Non-volitional tests depend on magnetic stimulation of the phrenic nerve accompanied by the measurement of inspiratory mouth pressure, inspiratory esophageal pressure, or inspiratory transdiaphragmatic pressure. Another method that has come to be widely used is ultrasound imaging of the diaphragm. We believe that pulmonologists involved in the care of patients with respiratory diseases should be familiar with the tests used in order to assess respiratory muscle function.Therefore, the aim of the present article is to describe the advantages, disadvantages, procedures, and clinical applicability of the main tests used in the assessment of respiratory muscle strength.

  20. Different diagnostic methods for detection of influenza epidemics.

    PubMed Central

    Rebelo-de-Andrade, H.; Zambon, M. C.

    2000-01-01

    Linking continuous community-based morbidity recording of influenza-like illness (ILI) with virological sampling has consistently proved its value as one of the earliest indicators of circulating influenza activity. The clinical morbidity recording in the Portuguese national surveillance network, during a 7-year period, and the contribution of different diagnostic techniques, including virus isolation, multiplex RT-PCR, immunocapture enzyme linked immunoassay (EIA) and complement fixation tests (CFTs) for the detection of influenza in such a community-based setting is described and evaluated in this study. There was good correlation between the increase of morbidity, total samples taken and the detection of influenza virus by all the methods although this was less evident for virus isolation and EIA than for RT-PCR or serology. From a total of 1685 throat swabs collected from cases of ILI, 43.6% were RT-PCR positive, 17.5% were positive by capture EIA and in 5% virus isolates were made. The detection of influenza by RT-PCR occurred earlier than by any other method and showed the best correlation with epidemic patterns of morbidity registration. We conclude that in surveillance systems where virus culture is sub-optimal, RT-PCR provides a rapid, sensitive, specific method for detecting influenza viruses from community-based sampling. PMID:10982076

  1. Practical molecular diagnostics in neuropathology: making a tough job a little easier.

    PubMed

    Horbinski, Craig

    2010-05-01

    Neuropathology is a challenging field, in large part because of the consequential decisions that must be made with small biopsy material. This is especially true concerning the most common primary brain tumor, the infiltrative glioma. Fortunately, abundant research has identified specific molecular alterations that are characteristic of gliomas, according to diagnostic class and tumor grade. Such alterations include 1p19q codeletion, EGFR amplification, p16 deletion, and IDH1/2 mutations. Using specific cases as examples, this review illustrates how molecular testing is of great help in avoiding misdiagnoses and enhancing the quality of information provided to clinicians.

  2. Molecular diagnostics for Chagas disease: up to date and novel methodologies.

    PubMed

    Alonso-Padilla, Julio; Gallego, Montserrat; Schijman, Alejandro G; Gascon, Joaquim

    2017-07-01

    Chagas disease is caused by the parasite Trypanosoma cruzi. It affects 7 million people, mainly in Latin America. Diagnosis is usually made serologically, but at some clinical scenarios serology cannot be used. Then, molecular detection is required for early detection of congenital transmission, treatment response follow up, and diagnosis of immune-suppression reactivation. However, present tests are technically demanding and require well-equipped laboratories which make them unfeasible in low-resources endemic regions. Areas covered: Available molecular tools for detection of T. cruzi DNA, paying particular attention to quantitative PCR protocols, and to the latest developments of user-friendly molecular diagnostic methodologies. Expert commentary: In the absence of appropriate biomarkers, molecular diagnosis is the only option for the assessment of treatment response. Besides, it is very useful for the early detection of acute infections, like congenital cases. Since current Chagas disease molecular tests are restricted to referential labs, research efforts must focus in the implementation of easy-to-use diagnostic tools in order to overcome the access to diagnosis gap.

  3. Current and future molecular diagnostics in colorectal cancer and colorectal adenoma.

    PubMed

    Tsang, Andy Hin-Fung; Cheng, Ka-Ho; Wong, Apple Siu-Ping; Ng, Simon Siu-Man; Ma, Brigette Buig-Yue; Chan, Charles Ming-Lok; Tsui, Nancy Bo-Yin; Chan, Lawrence Wing-Chi; Yung, Benjamin Yat-Ming; Wong, Sze-Chuen Cesar

    2014-04-14

    Colorectal cancer (CRC) is one of the most prevalent cancers in developed countries. On the other hand, CRC is also one of the most curable cancers if it is detected in early stages through regular colonoscopy or sigmoidoscopy. Since CRC develops slowly from precancerous lesions, early detection can reduce both the incidence and mortality of the disease. Fecal occult blood test is a widely used non-invasive screening tool for CRC. Although fecal occult blood test is simple and cost-effective in screening CRC, there is room for improvement in terms of the accuracy of the test. Genetic dysregulations have been found to play an important role in CRC development. With better understanding of the molecular basis of CRC, there is a growing expectation on the development of diagnostic tests based on more sensitive and specific molecular markers and those tests may provide a breakthrough to the limitations of current screening tests for CRC. In this review, the molecular basis of CRC development, the characteristics and applications of different non-invasive molecular biomarkers, as well as the technologies available for the detection were discussed. This review intended to provide a summary on the current and future molecular diagnostics in CRC and its pre-malignant state, colorectal adenoma.

  4. Juvenile retinoschisis: a model for molecular diagnostic testing of X-linked ophthalmic disease.

    PubMed

    Sieving, P A; Yashar, B M; Ayyagari, R

    1999-01-01

    X-linked juvenile retinoschisis (RS) provides a starting point to define clinical paradigms and understand the limitations of diagnostic molecular testing. The RS phenotype is specific, but the broad severity range is clinically confusing. Molecular diagnostic testing obviates unnecessary examinations for boys at-risk and identifies carrier females who otherwise show no clinical signs. The XLRS1 gene has 6 exons of 26-196 base-pair size. Each exon is amplified by a single polymerase chain reaction and then sequenced, starting with exons 4 through 6, which contain mutation "hot spots." The 6 XLRS1 exons are sequenced serially. If alterations are found, they are compared with mutations in our > 120 XLRS families and with the > 300 mutations reported worldwide. Point mutations, small deletions, or rearrangements are identified in nearly 90% of males with a clinical diagnosis of RS. XLRS1 has very few sequence polymorphisms. Carrier-state testing produces 1 of 3 results: (1) positive, in which the woman has the same mutation as an affected male relative or known in other RS families; (2) negative, in which she lacks the mutation of her affected male relative; and (3) uninformative, in which no known mutation is identified or no information exists about the familial mutation. Molecular RS screening is an effective diagnostic tool that complements the clinician's skills for early detection of at-risk males. Useful outcomes of carrier testing depend on several factors: (1) a male relative with a clear clinical diagnosis; (2) a well-defined inheritance pattern; (3) high disease penetrance; (4) size and organization of the gene; and (5) the types of disease-associated mutations. Ethical questions include molecular diagnostic testing of young at-risk females before the age of consent, the impact of this information on the emotional health of the patient and family, and issues of employability and insurance coverage.

  5. Multi-method automated diagnostics of rotating machines

    NASA Astrophysics Data System (ADS)

    Kostyukov, A. V.; Boychenko, S. N.; Shchelkanov, A. V.; Burda, E. A.

    2017-08-01

    The automated machinery diagnostics and monitoring systems utilized within the petrochemical plants are an integral part of the measures taken to ensure safety and, as a consequence, the efficiency of these industrial facilities. Such systems are often limited in their functionality due to the specifics of the diagnostic techniques adopted. As the diagnostic techniques applied in each system are limited, and machinery defects can have different physical nature, it becomes necessary to combine several diagnostics and monitoring systems to control various machinery components. Such an approach is inconvenient, since it requires additional measures to bring the diagnostic results in a single view of the technical condition of production assets. In this case, we mean by a production facility a bonded complex of a process unit, a drive, a power source and lines. A failure of any of these components will cause an outage of the production asset, which is unacceptable. The purpose of the study is to test a combined use of vibration diagnostics and partial discharge techniques within the diagnostic systems of enterprises for automated control of the technical condition of rotating machinery during maintenance and at production facilities. The described solutions allow you to control the condition of mechanical and electrical components of rotating machines. It is shown that the functionality of the diagnostics systems can be expanded with minimal changes in technological chains of repair and operation of rotating machinery. Automation of such systems reduces the influence of the human factor on the quality of repair and diagnostics of the machinery.

  6. Molecular Biological Methods in Environmental Engineering.

    PubMed

    Zhang, Guocai; Wei, Li; Chang, Chein-Chi; Zhang, Yuhua; Wei, Dong

    2016-10-01

    Bacteria, acting as catalysts, perform the function of degrading pollutants. Molecular biological techniques play an important role in research on the community analysis, the composition and the functions of complex microbial communities. The development of secondary high-throughput pyrosequencing techiniques enhances the understanding of the composition of the microbial community. The literatures of 2015 indicated that 16S rDNA gene as genetic tag is still the important method for bacteria identification and classification. 454 high throughput sequencing and Illumina MiSeq sequencing have been the primary and widely recognized methods to analyze the microbial. This review will provide environmental engineers and microbiologists an overview of important advancements in molecular techniques and highlight the application of these methods in diverse environments.

  7. Molecular diagnostics for sleeping sickness: what is the benefit for the patient?

    PubMed

    Deborggraeve, Stijn; Büscher, Philippe

    2010-06-01

    Sleeping sickness, or human African trypanosomiasis, is a vector-borne disease caused by two subspecies of the protozoan parasite Trypanosoma brucei, and is geographically restricted to sub-Saharan Africa. Although the disease causes major public-health and socioeconomic problems among affected populations, sleeping sickness is one of the world's most neglected diseases. Within the rapidly evolving field of biotechnology, many molecular diagnostics have been developed to detect the parasite. These range from conventional, high-tech, and low-tech PCR formats (eg, isothermal nucleic-acid-amplification techniques), to direct visualisation of the parasite's nucleic acids by fluorescent probes. Besides reviewing the most important molecular diagnostics available, we discuss their current role in diagnosis and disease control. Although powerful, molecular diagnostics are confined to research settings and do not reach the patient or national control programmes. The current formats are not applicable to field conditions, and simplification, standardisation, and proper test evaluation in the target setting should be the main focus for future development.

  8. Diagnostic Applications of Next Generation Sequencing in Immunogenetics and Molecular Oncology

    PubMed Central

    Grumbt, Barbara; Eck, Sebastian H.; Hinrichsen, Tanja; Hirv, Kaimo

    2013-01-01

    Summary With the introduction of the next generation sequencing (NGS) technologies, remarkable new diagnostic applications have been established in daily routine. Implementation of NGS is challenging in clinical diagnostics, but definite advantages and new diagnostic possibilities make the switch to the technology inevitable. In addition to the higher sequencing capacity, clonal sequencing of single molecules, multiplexing of samples, higher diagnostic sensitivity, workflow miniaturization, and cost benefits are some of the valuable features of the technology. After the recent advances, NGS emerged as a proven alternative for classical Sanger sequencing in the typing of human leukocyte antigens (HLA). By virtue of the clonal amplification of single DNA molecules ambiguous typing results can be avoided. Simultaneously, a higher sample throughput can be achieved by tagging of DNA molecules with multiplex identifiers and pooling of PCR products before sequencing. In our experience, up to 380 samples can be typed for HLA-A, -B, and -DRB1 in high-resolution during every sequencing run. In molecular oncology, NGS shows a markedly increased sensitivity in comparison to the conventional Sanger sequencing and is developing to the standard diagnostic tool in detection of somatic mutations in cancer cells with great impact on personalized treatment of patients. PMID:23922545

  9. Nailfold capillaroscopy as a diagnostic and prognostic method in rosacea.

    PubMed

    Fonseca, Gabriela Poglia; Brenner, Fabiane Mulinari; Muller, Carolina de Souza; Wojcik, Adma Lima

    2011-01-01

    There is no appropriate and reliable method of evaluating and monitoring severity in rosacea. To determine the importance of nailfold capillaroscopy as a diagnostic and prognostic method for patients with rosacea. A cross-sectional study where eight patients with rosacea and 8 control subjects were submitted to nailfold capillaroscopy from May to July 2009. We collected clinical data related to gender, age, skin phototype, and rosacea stage according to Plewig and Kligman classification and the classification of the National Rosacea Society. Additionally, we evaluated the progression of the disease and treatment therapies previously used. The majority of the patients evaluated (6 out of 8 patients) had rosacea subtype I (vascular) or erythematotelangiectatic rosacea. The mean duration of the disorder was 5.96 years, and 87.5% of the patients were under treatment with topical metronidazole. Nailfold cappilaroscopy showed that evidence of devascularization was absent in both groups. Nailfold capillaroscopy presents a nonspecific pattern and does not seem to help in the diagnosis or prognosis of rosacea.

  10. Computer methods for ITER-like materials LIBS diagnostics

    NASA Astrophysics Data System (ADS)

    Łepek, Michał; Gąsior, Paweł

    2014-11-01

    Recent development of Laser-Induced Breakdown Spectroscopy (LIBS) caused that this method is considered as the most promising for future diagnostic applications for characterization of the deposited materials in the International Thermonuclear Experimental Reactor (ITER), which is currently under construction. In this article the basics of LIBS are shortly discussed and the software for spectra analyzing is presented. The main software function is to analyze measured spectra with respect to the certain element lines presence. Some program operation results are presented. Correct results for graphite and aluminum are obtained although identification of tungsten lines is a problem. The reason for this is low tungsten lines intensity, and thus low signal to noise ratio of the measured signal. In the second part artificial neural networks (ANNs) as the next step for LIBS spectra analyzing are proposed. The idea is focused on multilayer perceptron network (MLP) with backpropagation learning method. The potential of ANNs for data processing was proved through application in several LIBS-related domains, e.g. differentiating ancient Greek ceramics (discussed). The idea is to apply an ANN for determination of W, Al, C presence on ITER-like plasma-facing materials.

  11. Scrambled eggs: A highly sensitive molecular diagnostic workflow for Fasciola species specific detection from faecal samples

    PubMed Central

    Calvani, Nichola Eliza Davies; Windsor, Peter Andrew; Bush, Russell David

    2017-01-01

    Background Fasciolosis, due to Fasciola hepatica and Fasciola gigantica, is a re-emerging zoonotic parasitic disease of worldwide importance. Human and animal infections are commonly diagnosed by the traditional sedimentation and faecal egg-counting technique. However, this technique is time-consuming and prone to sensitivity errors when a large number of samples must be processed or if the operator lacks sufficient experience. Additionally, diagnosis can only be made once the 12-week pre-patent period has passed. Recently, a commercially available coprological antigen ELISA has enabled detection of F. hepatica prior to the completion of the pre-patent period, providing earlier diagnosis and increased throughput, although species differentiation is not possible in areas of parasite sympatry. Real-time PCR offers the combined benefits of highly sensitive species differentiation for medium to large sample sizes. However, no molecular diagnostic workflow currently exists for the identification of Fasciola spp. in faecal samples. Methodology/Principal findings A new molecular diagnostic workflow for the highly-sensitive detection and quantification of Fasciola spp. in faecal samples was developed. The technique involves sedimenting and pelleting the samples prior to DNA isolation in order to concentrate the eggs, followed by disruption by bead-beating in a benchtop homogeniser to ensure access to DNA. Although both the new molecular workflow and the traditional sedimentation technique were sensitive and specific, the new molecular workflow enabled faster sample throughput in medium to large epidemiological studies, and provided the additional benefit of speciation. Further, good correlation (R2 = 0.74–0.76) was observed between the real-time PCR values and the faecal egg count (FEC) using the new molecular workflow for all herds and sampling periods. Finally, no effect of storage in 70% ethanol was detected on sedimentation and DNA isolation outcomes; enabling

  12. [Evaluation of the diagnostic power of 3 methods for assaying free T4. Results in the diagnostic strategy of hyperthyroidism].

    PubMed

    Fragu, P; Noel, M; Patois, E; Delarue, J C; Paugam-Capelle, J; Parmentier, C

    1985-01-01

    The free thyroxin (FT4) tests of Amersham, Clinical Assay and Corning Medical were evaluated in 240 patients who were suspected of hyperthyroidism. The diagnostic performances of the Corning method were of less value while those of the other methods were equivalent to that obtained with the free thyroxin index for an average cost reduced. Furthermore our results show that T3 determination is better than T4 determination in patients who remained doubtful after FT4. However the development of ultra-short methods of measurement of total thyroid hormone blood levels using fluorescence polarization could lead to reconsider the diagnostic strategy of hyperthyroidism.

  13. Turbulence in molecular clouds - A new diagnostic tool to probe their origin

    NASA Technical Reports Server (NTRS)

    Canuto, V. M.; Battaglia, A.

    1985-01-01

    A method is presented to uncover the instability responsible for the type of turbulence observed in molecular clouds and the value of the physical parameters of the 'placental medium' from which turbulence originated. The method utilizes the observational relation between velocities and sizes of molecular clouds, together with a recent model for large-scale turbulence (constructed by Canuto and Goldman, 1985).

  14. A guide for clinicians in the evaluation of emerging molecular diagnostics for newly diagnosed prostate cancer.

    PubMed

    Canfield, Steven E; Kibel, Adam S; Kemeter, Michael J; Febbo, Phillip G; Lawrence, H Jeffrey; Moul, Judd W

    2014-01-01

    Prostate-specific antigen (PSA) screening is associated with a decline in prostate cancer-related mortality. However, screening has also led to overdiagnosis and overtreatment of clinically insignificant tumors. Recently, certain national guidelines (eg, US Preventive Services Task Force) have recommended against PSA screening, which may lead to a reverse-stage migration. Although many prostate tumors are indolent at presentation, others are aggressive and are appropriate targets for treatment interventions. Utilization of molecular markers may improve our ability to measure tumor biology and allow better discrimination of indolent and aggressive tumors at diagnosis. Many emerging commercial molecular diagnostic assays have been designed to provide more accurate risk stratification for newly diagnosed prostate cancer. Unfamiliarity with molecular diagnostics may make it challenging for some clinicians to navigate and interpret the medical literature to ascertain whether particular assays are appropriately developed and validated for clinical use. Herein, the authors provide a framework for practitioners to use when assessing new tissue-based molecular assays. This review outlines aspects of assay development, clinical and analytic validation and clinical utility studies, and regulatory issues, which collectively determine whether tests (1) are actionable for specific clinical indications, (2) measurably influence treatment decisions, and (3) are sufficiently validated to warrant incorporation into clinical practice.

  15. Decentralized molecular diagnostic testing plan for pandemic influenza in the Ontario Public Health Laboratory system.

    PubMed

    Drews, Steven J; Majury, Anna; Jamieson, Frances; Riley, Garth; Mazzulli, Tony; Low, Donald E

    2008-01-01

    The Ontario Public Health Laboratories system (OPHL) is in the midst of a six-year plan to implement molecular tools for pandemic influenza diagnostics in one central and three regional public health laboratories. This plan has been formulated as a consequence of: (1) experiences gained through severe acute respiratory syndrome (SARS), and comments of the members of the Expert Panel on SARS and Infectious Disease Control (i.e., the Walker report); (2) a review of pandemic preparedness literature; (3) historical and epidemiologic discussions about previous pandemics; and (4) suggestions made by various pandemic working committees. The OPHL plan includes: (1) an aggressive restructuring of the overall molecular microbiology testing capacity of the OPHL; (2) the ability to shift influenza testing of samples between designated OPHL laboratories; and (3) the development of screening tools for pandemic influenza diagnostic tests. The authors believe that investing in increased molecular testing capacity for regional laboratories outside the greater Toronto area will be beneficial to the OPHL system whether or not an influenza pandemic occurs. Well-trained technologists and microbiologists, and the introduction of new technologies, will facilitate the development of a wide variety of molecular tests for other infectious diseases at public health laboratories geographically distant from Toronto, thus enhancing overall laboratory testing capacity in the province of Ontario.

  16. Optical biosensor technologies for molecular diagnostics at the point-of-care

    NASA Astrophysics Data System (ADS)

    Schotter, Joerg; Schrittwieser, Stefan; Muellner, Paul; Melnik, Eva; Hainberger, Rainer; Koppitsch, Guenther; Schrank, Franz; Soulantika, Katerina; Lentijo-Mozo, Sergio; Pelaz, Beatriz; Parak, Wolfgang; Ludwig, Frank; Dieckhoff, Jan

    2015-05-01

    Label-free optical schemes for molecular biosensing hold a strong promise for point-of-care applications in medical research and diagnostics. Apart from diagnostic requirements in terms of sensitivity, specificity, and multiplexing capability, also other aspects such as ease of use and manufacturability have to be considered in order to pave the way to a practical implementation. We present integrated optical waveguide as well as magnetic nanoparticle based molecular biosensor concepts that address these aspects. The integrated optical waveguide devices are based on low-loss photonic wires made of silicon nitride deposited by a CMOS compatible plasma-enhanced chemical vapor deposition (PECVD) process that allows for backend integration of waveguides on optoelectronic CMOS chips. The molecular detection principle relies on evanescent wave sensing in the 0.85 μm wavelength regime by means of Mach-Zehnder interferometers, which enables on-chip integration of silicon photodiodes and, thus, the realization of system-on-chip solutions. Our nanoparticle-based approach is based on optical observation of the dynamic response of functionalized magneticcore/ noble-metal-shell nanorods (`nanoprobes') to an externally applied time-varying magnetic field. As target molecules specifically bind to the surface of the nanoprobes, the observed dynamics of the nanoprobes changes, and the concentration of target molecules in the sample solution can be quantified. This approach is suitable for dynamic real-time measurements and only requires minimal sample preparation, thus presenting a highly promising point-of-care diagnostic system. In this paper, we present a prototype of a diagnostic device suitable for highly automated sample analysis by our nanoparticle-based approach.

  17. Diagnostic Methods for Bile Acid Malabsorption in Clinical Practice

    PubMed Central

    Vijayvargiya, Priya; Camilleri, Michael; Shin, Andrea; Saenger, Amy

    2013-01-01

    Altered bile acid (BA) concentrations in the colon may cause diarrhea or constipation. BA malabsorption (BAM) accounts for >25% of patients with irritable bowel syndrome (IBS) with diarrhea and chronic diarrhea in Western countries. As BAM is increasingly recognized, proper diagnostic methods are desired in clinical practice to help direct the most effective treatment course for the chronic bowel dysfunction. This review appraises the methodology, advantages and disadvantages of 4 tools that directly measure BAM: 14C-glycocholate breath and stool test, 75Selenium HomotauroCholic Acid Test (SeHCAT), 7 α-hydroxy-4-cholesten-3-one (C4) and fecal BAs. 14C-glycocholate is a laborious test no longer widely utilized. 75SeHCAT is validated, but not available in the United States. Serum C4 is a simple, accurate method that is applicable to a majority of patients, but requires further clinical validation. Fecal measurements to quantify total and individual fecal BAs are technically cumbersome and not widely available. Regrettably, none of these tests are routinely available in the U.S., and a therapeutic trial with a BA binder is used as a surrogate for diagnosis of BAM. Recent data suggest there is an advantage to studying fecal excretion of the individual BAs and their role in BAM; this may constitute a significant advantage of the fecal BA method over the other tests. Fecal BA test could become a routine addition to fecal fat measurement in patients with unexplained diarrhea. In summary, availability determines the choice of test among C4, SeHCAT and fecal BA; more widespread availability of such tests would enhance clinical management of these patients. PMID:23644387

  18. A Review of the Diagnostic Methods Reported in the Journal of Autism and Developmental Disorders.

    ERIC Educational Resources Information Center

    Waller, Stacey A.; Armstrong, Kevin J.; McGrath, Ann M.; Sullivan, Cristin L.

    1999-01-01

    This review summarizes subject selection and diagnostic procedures documented in 142 empirical articles published between 1993 and 1997. Although most researchers reported use of standard diagnostic criteria in classifying subjects, numerous studies did not report diagnostic methods and there was often a lack of specification of inclusion and…

  19. Image processing methods and architectures in diagnostic pathology.

    PubMed

    Bueno, Gloria; Déniz, Oscar; Salido, Jesús; Rojo, Marcial García

    2009-01-01

    Grid technology has enabled the clustering and the efficient and secure access to and interaction among a wide variety of geographically distributed resources such as: supercomputers, storage systems, data sources, instruments and special devices and services. Their main applications include large-scale computational and data intensive problems in science and engineering. General grid structures and methodologies for both software and hardware in image analysis for virtual tissue-based diagnosis has been considered in this paper. This methods are focus on the user level middleware. The article describes the distributed programming system developed by the authors for virtual slide analysis in diagnostic pathology. The system supports different image analysis operations commonly done in anatomical pathology and it takes into account secured aspects and specialized infrastructures with high level services designed to meet application requirements. Grids are likely to have a deep impact on health related applications, and therefore they seem to be suitable for tissue-based diagnosis too. The implemented system is a joint application that mixes both Web and Grid Service Architecture around a distributed architecture for image processing. It has shown to be a successful solution to analyze a big and heterogeneous group of histological images under architecture of massively parallel processors using message passing and non-shared memory.

  20. Interrater reliability of diagnostic methods in traditional Indian ayurvedic medicine.

    PubMed

    Kurande, Vrinda; Bilgrau, Anders Ellern; Waagepetersen, Rasmus; Toft, Egon; Prasad, Ramjee

    2013-01-01

    This study assesses the interrater reliability of Ayurvedic pulse (nadi), tongue (jivha), and body constitution (prakriti) assessments. Fifteen registered Ayurvedic doctors with 3-15 years of experience independently examined twenty healthy subjects. Subjects completed self-assessment questionnaires and software analyses for prakriti assessment. Weighted kappa statistics for all 105 pairs of doctors were computed for the pulse, tongue, and prakriti data sets. According to the Landis-Koch scale, the pairwise kappas ranged from poor to slight, slight to fair, and fair to moderate for pulse, tongue, and prakriti assessments, respectively. The average pairwise kappa for pulse, tongue, and prakriti was 0.07, 0.17, and 0.28, respectively. For each data set and pair of doctors, the null hypothesis of random rating was rejected for just twelve pairs of doctors for prakriti, one pair of doctors for pulse examination, and no pairs of doctors for tongue assessment. Thus, the results demonstrate a low level of reliability for all types of assessment made by doctors. There was significant evidence against random rating by software and questionnaire use and by the diagnosis preferred by the majority of doctors. Prakriti assessment appears reliable when questionnaire and software assessment are used, while other diagnostic methods have room for improvement.

  1. Diagnostic Methods for Detection of Blood-Borne Candidiasis.

    PubMed

    Clancy, Cornelius J; Nguyen, M Hong

    2016-01-01

    β-D-glucan (Fungitell) and polymerase chain reaction-based (T2Candida) assays of blood samples are FDA-approved adjuncts to cultures for diagnosing candidemia and other types of invasive candidiasis, but their clinical roles are unclear. In this chapter, we describe laboratory protocols for performing Fungitell and T2Candida assays. We then discuss step-by-step methods for interpreting test results at the bedside using a Bayesian framework, and for incorporating assays into rational patient management strategies. Prior to interpreting results, clinicians must recognize that test performance varies based on the type of invasive candidiasis being diagnosed. In general, the type of invasive candidiasis that is most likely in a given patient can be identified, and the pretest likelihood of disease estimated. From there, positive and negative predictive values (PPV, NPV) for an assay can be calculated. At a population level, tests can be incorporated into screening strategies for antifungal treatment. NPV and PPV thresholds can be defined for discontinuing antifungal prophylaxis or initiating preemptive treatment, respectively. Using the thresholds, it is possible to assign windows of pretest likelihood for invasive candidiasis (and corresponding patient populations) in which tests are most likely to valuable. At the individual patient level, tests may be useful outside of the windows proposed for screening populations. The interpretive and clinical decision-making processes we discuss will be applicable to other diagnostic assays as they enter the clinic, and to existing assays as more data emerge from various populations.

  2. Molecular and biological diagnostic tests for monitoring benzimidazole resistance in human soil-transmitted helminths.

    PubMed

    Diawara, Aïssatou; Schwenkenbecher, Jan M; Kaplan, Ray M; Prichard, Roger K

    2013-06-01

    In endemic countries with soil-transmitted helminths mass drug administration with albendazole or mebendazole are being implemented as a control strategy. However, it is well known in veterinary helminths that the use of the same benzimidazole drugs can place selection on the β-tubulin gene, leading to resistance. Given the concern that resistance could arise in human soil-transmitted helminths, there is an urgent need to develop accurate diagnostic tools for monitoring resistance. In this study, we developed molecular assays to detect putative resistance genetic changes in Ascaris lumbricoides, Trichuris trichiura, and hookworms, and we optimized an egg hatch assay for the canine hookworm Ancylostoma caninum and applied it to Necator americanus. Both assays were tested on field samples. The molecular assays demonstrated their reproducibility and capacity to detect the presence of worms carrying putative resistance-associated genetic changes. However, further investigations are needed to validate our molecular and biological tests on additional field isolates.

  3. Optical caries diagnostics: comparison of laser spectroscopic PNC method with method of laser integral fluorescence

    NASA Astrophysics Data System (ADS)

    Masychev, Victor I.

    2000-11-01

    In this research we present the results of approbation of two methods of optical caries diagnostics: PNC-spectral diagnostics and caries detection by laser integral fluorescence. The research was conducted in a dental clinic. PNC-method analyses parameters of probing laser radiation and PNC-spectrums of stimulated secondary radiations: backscattering and endogenous fluorescence of caries-involved bacterias. He-Ne-laser ((lambda) =632,8 nm, 1-2mW) was used as a source of probing (stimulated) radiation. For registration of signals, received from intact and pathological teeth PDA-detector was applied. PNC-spectrums were processed by special algorithms, and were displayed on PC monitor. The method of laser integral fluorescence was used for comparison. In this case integral power of fluorescence of human teeth was measured. As a source of probing (stimulated) radiation diode lasers ((lambda) =655 nm, 0.1 mW and 630nm, 1mW) and He-Ne laser were applied. For registration of signals Si-photodetector was used. Integral power was shown in a digital indicator. Advantages and disadvantages of these methods are described in this research. It is disclosed that the method of laser integral power of fluorescence has the following characteristics: simplicity of construction and schema-technical decisions. However the method of PNC-spectral diagnostics are characterized by considerably more sensitivity in diagnostics of initial caries and capability to differentiate pathologies of various stages (for example, calculus/initial caries). Estimation of spectral characteristics of PNC-signals allows eliminating a number of drawbacks, which are character for detection by method of laser integral fluorescence (for instance, detection of fluorescent fillings, plagues, calculus, discolorations generally, amalgam, gold fillings as if it were caries.

  4. [Application of chromatography methods for the diagnostics of systemic inflammation].

    PubMed

    Pastukhova, N K; Starkov, G E

    2010-01-01

    Specific manifestations of systemic inflammation in patients with acute destructive cholecystitis in the postoperative period were studied by the methods of high-precision exclusive liquid chromatography with chromatograph "Trirotar" (Japan) with columns "Polysep G-5", "Toyopearl-Sw - 2000-2500". It was found that systemic inflammation was accompanied by active accumulation of middle- and low-molecular mass. Later their spectrum was found to change when going over to unfavorable clinical course. In patients with septic shock there occurred enrichment of the chromatographic picture spectrum with new peaks (substances which can be considered as endotoxins), decrease of the albumin concentration, as well as increase of dispersity of the biochemical composition of blood.

  5. Keeping up with the times: revising the dermatology residency curriculum in the era of molecular diagnostics and personalized medicine.

    PubMed

    LaChance, Avery; Murphy, Michael J

    2014-11-01

    The clinical use of molecular diagnostics, genomics, and personalized medicine is increasing and improving rapidly over time. However, medical education incorporating the practical application of these techniques is lagging behind. Although instruction in these areas should be expanded upon and improved at all levels of training, residency provides a concentrated period of time in which to hone in on skills that are practically applicable to a trainee's specialty of choice. Although residencies in some fields, such as pathology, have begun to incorporate practical molecular diagnostics training, this area remains a relative gap in dermatology residency programs. Herein, we advocate for the incorporation of training in molecular diagnostics and personalized medicine into dermatology residency programs and propose a basic curriculum template for how to begin approaching these topics. By incorporating molecular diagnostics into dermatology residency training, dermatologists have the opportunity to lead the way and actively shape the specialty's transition into the era of personalized medicine. © 2014 The International Society of Dermatology.

  6. The development, evaluation and performance of molecular diagnostics for detection of Mycobacterium tuberculosis.

    PubMed

    Bates, Matthew; Zumla, Alimuddin

    2016-01-01

    The unique pathogenesis of tuberculosis (TB) poses several barriers to the development of accurate diagnostics: a) the establishment of life-long latency by Mycobacterium tuberculosis (M.tb) after primary infection confounds the development of classical antibody or antigen based assays; b) our poor understanding of the molecular pathways that influence progression from latent to active disease; c) the intracellular nature of M.tb infection in tissues means that M.tb and/or its components, are not readily detectable in peripheral specimens; and d) the variable presence of M.tb bacilli in specimens from patients with extrapulmonary TB or children. The literature on the current portfolio of molecular diagnostics tests for TB is reviewed here and the developmental pipeline is summarized. Also reviewed are data from recently published operational research on the GeneXpert MTB/RIF assay and discussed are the lessons that can be taken forward for the design of studies to evaluate the impact of TB diagnostics.

  7. Mass spectrometry-based serum proteome pattern analysis in molecular diagnostics of early stage breast cancer

    PubMed Central

    Pietrowska, Monika; Marczak, Lukasz; Polanska, Joanna; Behrendt, Katarzyna; Nowicka, Elzbieta; Walaszczyk, Anna; Chmura, Aleksandra; Deja, Regina; Stobiecki, Maciej; Polanski, Andrzej; Tarnawski, Rafal; Widlak, Piotr

    2009-01-01

    Background Mass spectrometric analysis of the blood proteome is an emerging method of clinical proteomics. The approach exploiting multi-protein/peptide sets (fingerprints) detected by mass spectrometry that reflect overall features of a specimen's proteome, termed proteome pattern analysis, have been already shown in several studies to have applicability in cancer diagnostics. We aimed to identify serum proteome patterns specific for early stage breast cancer patients using MALDI-ToF mass spectrometry. Methods Blood samples were collected before the start of therapy in a group of 92 patients diagnosed at stages I and II of the disease, and in a group of age-matched healthy controls (104 women). Serum specimens were purified and the low-molecular-weight proteome fraction was examined using MALDI-ToF mass spectrometry after removal of albumin and other high-molecular-weight serum proteins. Protein ions registered in a mass range between 2,000 and 10,000 Da were analyzed using a new bioinformatic tool created in our group, which included modeling spectra as a sum of Gaussian bell-shaped curves. Results We have identified features of serum proteome patterns that were significantly different between blood samples of healthy individuals and early stage breast cancer patients. The classifier built of three spectral components that differentiated controls and cancer patients had 83% sensitivity and 85% specificity. Spectral components (i.e., protein ions) that were the most frequent in such classifiers had approximate m/z values of 2303, 2866 and 3579 Da (a biomarker built from these three components showed 88% sensitivity and 78% specificity). Of note, we did not find a significant correlation between features of serum proteome patterns and established prognostic or predictive factors like tumor size, nodal involvement, histopathological grade, estrogen and progesterone receptor expression. In addition, we observed a significantly (p = 0.0003) increased level of

  8. Dental and dental hygiene students' diagnostic accuracy in oral radiology: effect of diagnostic strategy and instructional method.

    PubMed

    Baghdady, Mariam T; Carnahan, Heather; Lam, Ernest W N; Woods, Nicole N

    2014-09-01

    There has been much debate surrounding diagnostic strategies and the most appropriate training models for novices in oral radiology. It has been argued that an analytic approach, using a step-by-step analysis of the radiographic features of an abnormality, is ideal. Alternative research suggests that novices can successfully employ non-analytic reasoning. Many of these studies do not take instructional methodology into account. This study evaluated the effectiveness of non-analytic and analytic strategies in radiographic interpretation and explored the relationship between instructional methodology and diagnostic strategy. Second-year dental and dental hygiene students were taught four radiographic abnormalities using basic science instructions or a step-by-step algorithm. The students were tested on diagnostic accuracy and memory immediately after learning and one week later. A total of seventy-three students completed both immediate and delayed sessions and were included in the analysis. Students were randomly divided into two instructional conditions: one group provided a diagnostic hypothesis for the image and then identified specific features to support it, while the other group first identified features and then provided a diagnosis. Participants in the diagnosis-first condition (non-analytic reasoning) had higher diagnostic accuracy then those in the features-first condition (analytic reasoning), regardless of their learning condition. No main effect of learning condition or interaction with diagnostic strategy was observed. Educators should be mindful of the potential influence of analytic and non-analytic approaches on the effectiveness of the instructional method.

  9. A study of diagnostic methods for Marteilioides chungmuensis infections in the Pacific oyster Crassostrea gigas.

    PubMed

    Choi, Hee Jung; Hwang, Jee Youn; Choi, Dong Lim; Huh, Min Do; Park, Myoung Ae

    2012-09-15

    The eggs of the Pacific oyster, Crassostraea gigas, become infertile when infected by the parasite Marteilioides chungmuensis. Histologically, M. chungmuensis infects the oyster oocyte cytoplasm, and the ovaries take on a "lumpy" appearance once infected, which lowers commercial value of the oyster. This has a negative economic impact on oyster farms in South Korea and Japan. In this study, we compared traditional diagnostic methods (histology) with two molecular-based methods (polymerase chain reaction [PCR] amplification and in situ hybridization [ISH]) to identify M. chungmuensis-infected oysters. The efficacy of PCR and ISH to identify M. chungmuensis-infected oysters was compared to that of routine histology in 100 oysters. Thirty infections were identified using PCR and 16 using histology, whereas 31 infections were identified using ISH. The ISH and PCR assays were more sensitive compared to using histology with standard epidemiological methods. We strongly recommend that early parasitic invasion should be monitored with PCR/ISH methodologies as a basis for developing effective diagnostic techniques to identify M. chungmuensis-infected oysters.

  10. Leveling the Playing Field: Bringing Development of Biomarkers and Molecular Diagnostics up to the Standards for Drug Development

    PubMed Central

    Poste, George; Carbone, David P.; Parkinson, David R.; Verweij, Jaap; Hewitt, Stephen; Jessup, J. Milburn

    2012-01-01

    Molecular diagnostics are increasingly important in clinical research to stratify or identify molecularly profiled patient cohorts for targeted therapies, to modify the dose of a therapeutic, or to assess early response to therapy or monitor patients. Molecular diagnostics can also be used to identify pharmocogenetic risk of adverse drug reactions. The articles of this CCR Focus section on Molecular Diagnosis describe the development and use of markers for medical decision-making in the cancer patient. They define the sources of preanalytic variability to minimize as well as the regulatory and financial challenges in diagnostic development and integration into clinical practice. They also outline an NCI program to assist diagnostic development. Molecular diagnostic clinical tests require rigor in their development and clinical validation with sufficient sensitivity, specificity and validity that is comparable to that used for development of therapeutics. These diagnostics must be offered at a realistic cost that reflects both their clinical value and the costs associated with their development. When genome sequencing technologies move into the clinic, they must be integrated with and traceable to current technology because they may identify more efficient and accurate approaches to drug development. In addition, regulators may define progressive drug approval for companion diagnostics that requires further evidence regarding efficacy and safety before full approval. A way to accomplish this is to emphasize Phase IV post-marketing hypothesis driven clinical trials with biological characterization that permits accurate definition of the association of low prevalence gene alterations with toxicity or response in large cohorts. PMID:22422403

  11. Modified PAS stain: A new diagnostic method for onychomycosis.

    PubMed

    Hajar, Tamar; Fernández-Martínez, Ramon; Moreno-Coutiño, Gabriela; Vásquez Del Mercado, Elsa; Arenas, Roberto

    2016-01-01

    Onychomycosis is the most common nail disease and represents around 50% of nail disorders. Accurate diagnosis with adequate evidence is ideal before starting any treatment. Current diagnostic methods offer low specificity and sensitivity. To create a new method for the diagnosis of onychomycosis, and to compare its sensitivity and specificity with the existing methods. One hundred and ninety-two samples with clinical suspicion of onychomycosis were included and underwent modified PAS stain (M-PAS), KOH/chlorazol black (KOH/CB) and culture testing. Sensitivity, specificity, positive and negative predictive values were calculated. In 152 out of 192 samples (79.2%) fungi structures were found in at least one of the three tests performed, and the patients were diagnosed with onychomycosis; 40 samples out of 192 (20.8%) were negative. Using M-PAS, filaments and/or spores were seen in 143 samples from the 152 positive (94%); 39 of them were negative to KOH/CB and positive to M-PAS (25.6%). With KOH/CB, filaments and/or spores were seen in 113 cases from the 152 positive samples (73.8% of the onychomycosis cases). Thirty-five cultures were positive, of which 77% were identified as Trichophyton rubrum; 117 onychomycosis cases were diagnosed despite the negative culture (76.9%). M-PAS showed 92.5% sensitivity and 55.55% specificity, a 67.5% positive predictive value and a 81.6% negative productive value. This procedure, a combination of the existing methods to diagnose onychomycosis, KOH/CB together with a nail clipping biopsy, proved to have high sensitivity, as well as being rapid, easy, inexpensive and readily available in most hospital settings. M-PAS allowed us to diagnose 39 cases (25.6% of the cases of onychomycosis) that were false negative using only KOH/CB and culture. Copyright © 2014 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

  12. Astrovirus Diagnostics

    PubMed Central

    Pérot, Philippe; Lecuit, Marc; Eloit, Marc

    2017-01-01

    Various methods exist to detect an astrovirus infection. Current methods include electron microscopy (EM), cell culture, immunoassays, polymerase chain reaction (PCR) and various other molecular approaches that can be applied in the context of diagnostic or in surveillance studies. With the advent of metagenomics, novel human astrovirus (HAstV) strains have been found in immunocompromised individuals in association with central nervous system (CNS) infections. This work reviews the past and current methods for astrovirus detection and their uses in both research laboratories and for medical diagnostic purposes. PMID:28085120

  13. Molecular methods for the detection of mutations.

    PubMed

    Monteiro, C; Marcelino, L A; Conde, A R; Saraiva, C; Giphart-Gassler, M; De Nooij-van Dalen, A G; Van Buuren-van Seggelen, V; Van der Keur, M; May, C A; Cole, J; Lehmann, A R; Steinsgrimsdottir, H; Beare, D; Capulas, E; Armour, J A

    2000-01-01

    We report the results of a collaborative study aimed at developing reliable, direct assays for mutation in human cells. The project used common lymphoblastoid cell lines, both with and without mutagen treatment, as a shared resource to validate the development of new molecular methods for the detection of low-level mutations in the presence of a large excess of normal alleles. As the "gold standard, " hprt mutation frequencies were also measured on the same samples. The methods under development included i) the restriction site mutation (RSM) assay, in which mutations lead to the destruction of a restriction site; ii) minisatellite length-change mutation, in which mutations lead to alleles containing new numbers of tandem repeat units; iii) loss of heterozygosity for HLA epitopes, in which antibodies can be used to direct selection for mutant cells; iv) multiple fluorescence-based long linker arm nucleotides assay (mf-LLA) technology, for the detection of substitutional mutations; v) detection of alterations in the TP53 locus using a (CA) array as the target for the screening; and vi) PCR analysis of lymphocytes for the presence of the BCL2 t(14:18) translocation. The relative merits of these molecular methods are discussed, and a comparison made with more "traditional" methods.

  14. Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification

    PubMed Central

    2016-01-01

    For many complex diseases, an earlier and more reliable diagnosis is considered a key prerequisite for developing more effective therapies to prevent or delay disease progression. Classical statistical learning approaches for specimen classification using omics data, however, often cannot provide diagnostic models with sufficient accuracy and robustness for heterogeneous diseases like cancers or neurodegenerative disorders. In recent years, new approaches for building multivariate biomarker models on omics data have been proposed, which exploit prior biological knowledge from molecular networks and cellular pathways to address these limitations. This survey provides an overview of these recent developments and compares pathway- and network-based specimen classification approaches in terms of their utility for improving model robustness, accuracy and biological interpretability. Different routes to translate omics-based multifactorial biomarker models into clinical diagnostic tests are discussed, and a previous study is presented as example. PMID:26141830

  15. Advancing the education in molecular diagnostics: the IFCC-Initiative "Clinical Molecular Biology Curriculum" (C-CMBC); a ten-year experience.

    PubMed

    Lianidou, Evi; Ahmad-Nejad, Parviz; Ferreira-Gonzalez, Andrea; Izuhara, Kenji; Cremonesi, Laura; Schroeder, Maria-Eugenia; Richter, Karin; Ferrari, Maurizio; Neumaier, Michael

    2014-09-25

    Molecular techniques are becoming commonplace in the diagnostic laboratory. Their applications influence all major phases of laboratory medicine including predisposition/genetic risk, primary diagnosis, therapy stratification and prognosis. Readily available laboratory hardware and wetware (i.e. consumables and reagents) foster rapid dissemination to countries that are just establishing molecular testing programs. Appropriate skill levels extending beyond the technical procedure are required for analytical and diagnostic proficiency that is mandatory in molecular genetic testing. An international committee (C-CMBC) of the International Federation for Clinical Chemistry (IFCC) was established to disseminate skills in molecular genetic testing in member countries embarking on the respective techniques. We report the ten-year experience with different teaching and workshop formats for beginners in molecular diagnostics.

  16. [Application of molecular diagnostic techniques in precision medicine of personalized treatment for colorectal cancer].

    PubMed

    Fu, Ji; Lin, Guole

    2016-01-01

    Precision medicine is to customize the treatment options for individual patient based on the personal genome information. Colorectal cancer (CRC) is one of the most common cancer worldwide. Molecular heterogeneity of CRC, which includes the MSI phenotype, hypermutation phenotype, and their relationship with clinical preferences, is believed to be one of the main factors responsible for the considerable variability in treatment response. The development of powerful next-generation sequencing (NGS) technologies allows us to further understand the biological behavior of colorectal cancer, and to analyze the prognosis and chemotherapeutic drug reactions by molecular diagnostic techniques, which can guide the clinical treatment. This paper will introduce the new findings in this field. Meanwhile we integrate the new progress of key pathways including EGFR, RAS, PI3K/AKT and VEGF, and the experience in selective patients through associated molecular diagnostic screening who gain better efficacy after target therapy. The technique for detecting circulating tumor DNA (ctDNA) is introduced here as well, which can identify patients with high risk for recurrence, and demonstrate the risk of chemotherapy resistance. Mechanism of tumor drug resistance may be revealed by dynamic observation of gene alteration during treatment.

  17. Potential of molecular based diagnostics and its impact on allergen immunotherapy.

    PubMed

    Melioli, Giovanni; Savi, Eleonora; Crivellaro, Maria Angiola; Passalacqua, Giovanni

    2016-01-01

    Molecular based in vitro technologies greatly changed the diagnostic approaches in allergy. At present, sensitization profiles can be dissected according to IgE subsets, which are specific for genuine or cross-reacting components and potentially dangerous or virtually harmless components. The identification of IgE in components with specific characteristics has a direct impact on the accuracy of the diagnosis (indeed, it is possible at present to not only identify the allergen derived from a given allergen source but also the family of molecules to which the patient is sensitized), on the prognosis of the patient's allergy, and on the prevention activities to be implemented. More interestingly, during the last few years, and thanks to the tools of molecular diagnostics, the indications for Allergen Immunotherapy (AIT) have also be modified, and novel strategies for the selection of the allergens to be administered have been better defined. Indeed, protocols indicating how Molecular Based Diagnosis (MBD) can be used to identify the best AIT approach have been recently published. In this review, the rationale for the use of MBD tools is discussed, and the recent strategies for the choice of allergens to be used in AIT are reported.

  18. Diagnostic Tests for Quantitative Measurements of Singlet Molecular Oxygen on Ice

    NASA Astrophysics Data System (ADS)

    Bower, J.; McKellar, S.; Anastasio, C.

    2006-12-01

    Singlet molecular oxygen (^1O_2^*) can rapidly react with atmospheric pollutants such as furans, phenols, polycyclic aromatic hydrocarbons (PAHs), and reduced sulfur species. Furthermore, ^1O_2^* might be an important oxidant of atmospheric trace species on frozen atmospheric particles and drops. Thus, a quantitative understanding of ^1O_2^* activity on ice is essential in assessing its importance to the chemistry of the troposphere of cold regions. In aqueous samples, the loss of furfuryl alcohol (FFA) can be measured to determine ^1O_2^* concentrations. Using this method, samples are illuminated and the photoformed ^1O_2^* reacts with FFA, decreasing its concentration over time. This process, however, is confounded by the fact that the decay of FFA can occur via other pathways, such as direct photolysis or reaction with other oxidants, including OH. The goal of this work is to investigate the behavior of ^1O_2^* on ice so that its concentrations can be determined using the decay of FFA. To achieve this, we are working through a series of diagnostic tests, taking into account complications presented by direct photolysis, reactions with other oxidants, and changes in quasi-liquid layer volume and composition. To examine effects of specific oxidants, sources of ^1O_2^* and OH (rose bengal and HOOH, respectively) are added to simulated snow solutions with and without methionine, an efficient ^1O_2^* quencher and OH scavenger. With these laboratory liquid and ice samples we hope to understand the photochemical behavior of ^1O_2^* on ice and use methionine, or other scavengers, to discriminate between decay due to ^1O_2^* and other loss mechanisms for FFA. We will discuss results from these tests, as well as preliminary measurements of ^1O_2^* concentrations on snow from Greenland.

  19. Rheonix CARD(®) Technology: An Innovative and Fully Automated Molecular Diagnostic Device.

    PubMed

    Spizz, Gwendolyn; Young, Lincoln; Yasmin, Rubina; Chen, Zongyuan; Lee, Travis; Mahoney, Deborah; Zhang, Xun; Mouchka, Greg; Thomas, Benjamin; Honey, Whitney; Roswech, Todd; McGuire, Cristina; Montagna, Richard; Zhou, Peng

    2012-03-01

    A versatile microfluidic platform for the evolving molecular diagnostics industry is described. It incorporates low cost Rheonix CARD(®) (Chemistry and Reagent Device) technology to analyze a variety of clinical specimens. A patented lamination process incorporates all pumps, valves, microchannels and reaction compartments into an inexpensive disposable plastic device. Once an untreated clinical specimen is introduced, all assay steps, including cell lysis, nucleic acid purification, multiplex PCR, and end-point analysis, are automatically performed. Three distinct CARD assays are described which utilize either a low density microarray for multiplex detection of amplicons or an integrated primer extension assay to detect single nucleotide polymorphisms of interest. The STI (Sexually Transmitted Infections) CARD(®) is able to simultaneously detect four sexually transmitted infectious agents (N. gonorrhoeae, C.trachomatis, T. pallidum and T. vaginalis). Human C33A cervical epithelial cells were spiked with different levels of genomic DNA from the four species of interest, singly or in combination, and applied to the CARD device. Using multiplex PCR amplification of the targets followed by microarray detection, the CARD device was able to correctly detect a minimum of 10 copies of each of the four pathogens. The HPV (Human Papillomavirus) CARD(®) was able to detect and distinguish 20 different clinically relevant HPV types using cloned HPV DNA. In addition, the HPV CARD could identify HPV types in vaginal specimens previously demonstrated to contain high or low risk HPV using a currently commercially available testing method. Finally, the detection of specific single nucleotide polymorphisms (SNP) associated with warfarin dosing sensitivity was achieved on the Warfarin Genotyping CARD(®) by analyzing human buccal swabs. Once multiplex PCR was completed, the SNPs were detected using a primer extension assay.

  20. Computational methods for optical molecular imaging

    PubMed Central

    Chen, Duan; Wei, Guo-Wei; Cong, Wen-Xiang; Wang, Ge

    2010-01-01

    Summary A new computational technique, the matched interface and boundary (MIB) method, is presented to model the photon propagation in biological tissue for the optical molecular imaging. Optical properties have significant differences in different organs of small animals, resulting in discontinuous coefficients in the diffusion equation model. Complex organ shape of small animal induces singularities of the geometric model as well. The MIB method is designed as a dimension splitting approach to decompose a multidimensional interface problem into one-dimensional ones. The methodology simplifies the topological relation near an interface and is able to handle discontinuous coefficients and complex interfaces with geometric singularities. In the present MIB method, both the interface jump condition and the photon flux jump conditions are rigorously enforced at the interface location by using only the lowest-order jump conditions. This solution near the interface is smoothly extended across the interface so that central finite difference schemes can be employed without the loss of accuracy. A wide range of numerical experiments are carried out to validate the proposed MIB method. The second-order convergence is maintained in all benchmark problems. The fourth-order convergence is also demonstrated for some three-dimensional problems. The robustness of the proposed method over the variable strength of the linear term of the diffusion equation is also examined. The performance of the present approach is compared with that of the standard finite element method. The numerical study indicates that the proposed method is a potentially efficient and robust approach for the optical molecular imaging. PMID:20485461

  1. Advanced Optical Diagnostic Methods for Describing Fuel Injection and Combustion Flowfield Phenomena

    NASA Technical Reports Server (NTRS)

    Locke, Randy J.; Hicks, Yolanda R.; Anderson, Robert C.

    2004-01-01

    Over the past decade advanced optical diagnostic techniques have evolved and matured to a point where they are now widely applied in the interrogation of high pressure combusting flows. At NASA Glenn Research Center (GRC), imaging techniques have been used successfully in on-going work to develop the next generation of commercial aircraft gas turbine combustors. This work has centered on providing a means by which researchers and designers can obtain direct visual observation and measurements of the fuel injection/mixing/combustion processes and combustor flowfield in two- and three-dimensional views at actual operational conditions. Obtaining a thorough understanding of the chemical and physical processes at the extreme operating conditions of the next generation of combustors is critical to reducing emissions and increasing fuel efficiency. To accomplish this and other tasks, the diagnostic team at GRC has designed and constructed optically accessible, high pressurer high temperature flame tubes and sectar rigs capable of optically probing the 20-60 atm flowfields of these aero-combustors. Among the techniques employed at GRC are planar laser-induced fluorescence (PLIF) for imaging molecular species as well as liquid and gaseous fuel; planar light scattering (PLS) for imaging fuel sprays and droplets; and spontaneous Raman scattering for species and temperature measurement. Using these techniques, optical measurements never before possible have been made in the actual environments of liquid fueled gas turbines. 2-D mapping of such parameters as species (e.g. OH-, NO and kerosene-based jet fuel) distribution, injector spray angle, and fuel/air distribution are just some of the measurements that are now routinely made. Optical imaging has also provided prompt feedback to researchers regarding the effects of changes in the fuel injector configuration on both combustor performance and flowfield character. Several injector design modifications and improvements have

  2. Advanced Optical Diagnostic Methods for Describing Fuel Injection and Combustion Flowfield Phenomena

    NASA Technical Reports Server (NTRS)

    Locke, Randy J.; Hicks, Yolanda R.; Anderson, Robert C.

    2004-01-01

    Over the past decade advanced optical diagnostic techniques have evolved and matured to a point where they are now widely applied in the interrogation of high pressure combusting flows. At NASA Glenn Research Center (GRC), imaging techniques have been used successfully in on-going work to develop the next generation of commercial aircraft gas turbine combustors. This work has centered on providing a means by which researchers and designers can obtain direct visual observation and measurements of the fuel injection/mixing/combustion processes and combustor flowfield in two- and three-dimensional views at actual operational conditions. Obtaining a thorough understanding of the chemical and physical processes at the extreme operating conditions of the next generation of combustors is critical to reducing emissions and increasing fuel efficiency. To accomplish this and other tasks, the diagnostic team at GRC has designed and constructed optically accessible, high pressurer high temperature flame tubes and sectar rigs capable of optically probing the 20-60 atm flowfields of these aero-combustors. Among the techniques employed at GRC are planar laser-induced fluorescence (PLIF) for imaging molecular species as well as liquid and gaseous fuel; planar light scattering (PLS) for imaging fuel sprays and droplets; and spontaneous Raman scattering for species and temperature measurement. Using these techniques, optical measurements never before possible have been made in the actual environments of liquid fueled gas turbines. 2-D mapping of such parameters as species (e.g. OH-, NO and kerosene-based jet fuel) distribution, injector spray angle, and fuel/air distribution are just some of the measurements that are now routinely made. Optical imaging has also provided prompt feedback to researchers regarding the effects of changes in the fuel injector configuration on both combustor performance and flowfield character. Several injector design modifications and improvements have

  3. Studying the Impact of Spaceflight Environment on Immune Functions Using New Molecular Diagnostics System

    NASA Astrophysics Data System (ADS)

    Cohen, Luchino

    Immune functions are altered during space flights. Latent virus reactivation, reduction in the number of immune cells, decreased cell activation and increased sensitivity of astronauts to infections following their return on Earth demonstrate that the immune system is less efficient during space flight. The causes of this immune deficiency are not fully understood and this dysfunction during long-term missions could result in the appearance of opportunistic infections or a decrease in the immuno-surveillance mechanisms that eradicate cancer cells. Therefore, the immune functions of astronauts will have to be monitored continuously during long-term missions in space, using miniature and semi-automated diagnostic systems. The objectives of this project are to study the causes of space-related immunodeficiency, to develop countermeasures to maintain an optimal immune function and to improve our capacity to detect infectious diseases during space missions through the monitoring of astronauts' immune system. In order to achieve these objectives, an Immune Function Diagnostic System (IFDS) will be designed to perform a set of immunological assays on board spacecrafts or on planet-bound bases. Through flow cytometric assays and molecular biology analyses, this diagnostic system could improve medical surveillance of astronauts and could be used to test countermeasures aimed at preventing immune deficiency during space missions. The capacity of the instrument to assess cellular fluorescence and to quantify the presence of soluble molecules in biological samples would support advanced molecular studies in space life sciences. Finally, such diagnostic system could also be used on Earth in remote areas or in mobile hospitals following natural disasters to fight against infectious diseases and other pathologies.

  4. Franciszek Neugebauer's Ichnograms as a Pioneering Diagnostic Method in Orthopedics in the 19th Century.

    PubMed

    Nowakowska-Zamachowska, Monika

    2015-01-01

    The aim of this paper is to present an original orthopedic diagnostic method from the late 19th century developed by Franciszek Neugebauer, a distinguished Polish physician. His technique of detecting skeletal abnormalities was an excellent coping method in the time before the first diagnostic imaging method - x-ray imaging - had been invented.

  5. Nanomechanical transduction of molecular interactions on microcantilevers for biochemical detection and diagnostics

    NASA Astrophysics Data System (ADS)

    Tark, Soo-Hyun

    There is a strong demand for a reliable detection platform that can provide the benefits of enhanced sensitivity and selectivity with greater simplicity and cost-effectiveness. The new generations of biosensors also require microfabricated platforms with integrated biologically sensitive components for specific and quantitative detection of analytes in a miniaturized format as well as capabilities for label-free detection and massive parallelization. It has been unambiguously demonstrated that the molecular binding-induced surface stress can be used to monitor specific biochemical binding events and kinetics in real-time with high sensitivity, representing the promising potential for nanomechanical sensors. The fundamental validation of the receptor immobilization and target binding as well as the transduction and quantitative detection of such molecular recognition events taking place on microcantilevers are demonstrated utilizing the optical approach for monitoring the cantilever deflection. The label-free detection of cholera toxin using microcantilevers functionalized with ganglioside-Nanodiscs is demonstrated as a new strategy for immobilizing receptors on microcantilevers. The microcantilever-based sensors, however, require a new paradigm for signal transduction and detection beyond the optical method that supports the unique multiplexing capability by operating a large array of cantilevers with means for simple and accurate readout. Hence, a new electrical readout mechanism comprising a microcantilever array with MOSFETs embedded in the high stress region of the microcantilevers is developed, which provides label- and optics-free signal transduction mechanism. In this work, significant strides have been made towards the MOSFET-microcantilever detection approach. The process and device simulations for embedded-MOSFETs are performed to optimize process parameters and establish guidelines for device design and fabrication. Various designs of MOSFET

  6. Molecular Diagnostics of Gliomas Using Next Generation Sequencing of a Glioma-Tailored Gene Panel.

    PubMed

    Zacher, Angela; Kaulich, Kerstin; Stepanow, Stefanie; Wolter, Marietta; Köhrer, Karl; Felsberg, Jörg; Malzkorn, Bastian; Reifenberger, Guido

    2017-03-01

    Current classification of gliomas is based on histological criteria according to the World Health Organization (WHO) classification of tumors of the central nervous system. Over the past years, characteristic genetic profiles have been identified in various glioma types. These can refine tumor diagnostics and provide important prognostic and predictive information. We report on the establishment and validation of gene panel next generation sequencing (NGS) for the molecular diagnostics of gliomas. We designed a glioma-tailored gene panel covering 660 amplicons derived from 20 genes frequently aberrant in different glioma types. Sensitivity and specificity of glioma gene panel NGS for detection of DNA sequence variants and copy number changes were validated by single gene analyses. NGS-based mutation detection was optimized for application on formalin-fixed paraffin-embedded tissue specimens including small stereotactic biopsy samples. NGS data obtained in a retrospective analysis of 121 gliomas allowed for their molecular classification into distinct biological groups, including (i) isocitrate dehydrogenase gene (IDH) 1 or 2 mutant astrocytic gliomas with frequent α-thalassemia/mental retardation syndrome X-linked (ATRX) and tumor protein p53 (TP53) gene mutations, (ii) IDH mutant oligodendroglial tumors with 1p/19q codeletion, telomerase reverse transcriptase (TERT) promoter mutation and frequent Drosophila homolog of capicua (CIC) gene mutation, as well as (iii) IDH wildtype glioblastomas with frequent TERT promoter mutation, phosphatase and tensin homolog (PTEN) mutation and/or epidermal growth factor receptor (EGFR) amplification. Oligoastrocytic gliomas were genetically assigned to either of these groups. Our findings implicate gene panel NGS as a promising diagnostic technique that may facilitate integrated histological and molecular glioma classification.

  7. Molecular Pathology and Personalized Medicine: The Dawn of a New Era in Companion Diagnostics-Practical Considerations about Companion Diagnostics for Non-Small-Cell-Lung-Cancer.

    PubMed

    Plönes, Till; Engel-Riedel, Walburga; Stoelben, Erich; Limmroth, Christina; Schildgen, Oliver; Schildgen, Verena

    2016-01-15

    Companion diagnostics (CDx) have become a major tool in molecular pathology and assist in therapy decisions in an increasing number of various cancers. Particularly, the developments in lung cancer have been most impressing in the last decade and consequently lung cancer mutation testing and molecular profiling has become a major business of diagnostic laboratories. However, it has become difficult to decide which biomarkers are currently relevant for therapy decisions, as many of the new biomarkers are not yet approved as therapy targets, remain in the status of clinical studies, or still have not left the experimental phase. The current review is focussed on those markers that do have current therapy implications, practical implications arising from the respective companion diagnostics, and thus is focused on daily practice.

  8. Numerical methods for molecular dynamics. Progress report

    SciTech Connect

    Skeel, R.D.

    1991-12-31

    This report summarizes our research progress to date on the use of multigrid methods for three-dimensional elliptic partial differential equations, with particular emphasis on application to the Poisson-Boltzmann equation of molecular biophysics. This research is motivated by the need for fast and accurate numerical solution techniques for three-dimensional problems arising in physics and engineering. In many applications these problems must be solved repeatedly, and the extremely large number of discrete unknowns required to accurately approximate solutions to partial differential equations in three-dimensional regions necessitates the use of efficient solution methods. This situation makes clear the importance of developing methods which are of optimal order (or nearly so), meaning that the number of operations required to solve the discrete problem is on the order of the number of discrete unknowns. Multigrid methods are generally regarded as being in this class of methods, and are in fact provably optimal order for an increasingly large class of problems. The fundamental goal of this research is to develop a fast and accurate numerical technique, based on multi-level principles, for the solutions of the Poisson-Boltzmann equation of molecular biophysics and similar equations occurring in other applications. An outline of the report is as follows. We first present some background material, followed by a survey of the literature on the use of multigrid methods for solving problems similar to the Poisson-Boltzmann equation. A short description of the software we have developed so far is then given, and numerical results are discussed. Finally, our research plans for the coming year are presented.

  9. Bench-to-bedside review: Rapid molecular diagnostics for bloodstream infection - a new frontier?

    PubMed Central

    2012-01-01

    Among critically ill patients, the diagnosis of bloodstream infection poses a major challenge. Current standard bacterial identification based on blood culture platforms is intrinsically time-consuming and slow. The continuous evolvement of molecular techniques has the potential of providing a faster, more sensitive and direct identification of causative pathogens without prior need for cultivation. This may ultimately impact clinical decision-making and antimicrobial treatment. This review summarises the currently available technologies, their strengths and limitations and the obstacles that have to be overcome in order to develop a satisfactory bedside point-of-care diagnostic tool for detection of bloodstream infection. PMID:22647543

  10. A new genotype of border disease virus with implications for molecular diagnostics.

    PubMed

    Peletto, Simone; Caruso, Claudio; Cerutti, Francesco; Modesto, Paola; Zoppi, Simona; Dondo, Alessandro; Acutis, Pier Luigi; Masoero, Loretta

    2016-02-01

    Border disease virus (BDV) is a (+) single-stranded RNA pestivirus affecting mainly sheep and goats worldwide. Genetic typing of BDV has led to the identification of at least seven major genotypes. This study reports the detection of a BDV strain from a goat in northwestern Italy during routine investigations. Sequence analysis revealed mutations in the 5'-UTR of the virus with implications for BDV molecular diagnostics. Moreover, subsequent phylogenetic analysis based on the combined 5'-UTR and Npro/partial C genes, showed divergence from known BDV genotypes, revealing the detection of a novel pestivirus group, for which we propose the name BDV genotype 8.

  11. Multiplexed Molecular Diagnostics for Respiratory, Gastrointestinal, and Central Nervous System Infections.

    PubMed

    Hanson, Kimberly E; Couturier, Marc Roger

    2016-11-15

    The development and implementation of highly multiplexed molecular diagnostic tests have allowed clinical microbiology laboratories to more rapidly and sensitively detect a variety of pathogens directly in clinical specimens. Current US Food and Drug Administration-approved multiplex panels target multiple different organisms simultaneously and can identify the most common pathogens implicated in respiratory viral, gastrointestinal, or central nervous system infections. This review summarizes the test characteristics of available assays, highlights the advantages and limitations of multiplex technology for infectious diseases, and discusses potential utilization of these new tests in clinical practice.

  12. Stationary microfluidics: molecular diagnostic assays by moving magnetic beads through non-moving liquids

    NASA Astrophysics Data System (ADS)

    Becker, Holger; Carstens, Cornelia; Kuhlmeier, Dirk; Sandetskaya, Natalia; Schröter, Nicole; Zilch, Christian; Gärtner, Claudia

    2013-03-01

    Commonly, microfluidic devices are based on the movement of fluids. For molecular diagnostics assays which often include steps like PCR, this practically always involves a more or less complicated set of external pumps, valves and liquid controls. In the presented paper, we follow a different approach in which the fluid after sample introduction remains stationary and the main bioactive sample molecules are moved through a chain of reaction compartments which contain the different reagents necessary for the assay. The big advantage of this concept is the lack of any external fluid actuation/control. Results on sample carry-over experiments and complete assays will be given.

  13. CMOS Time-Resolved, Contact, and Multispectral Fluorescence Imaging for DNA Molecular Diagnostics

    PubMed Central

    Guo, Nan; Cheung, Ka Wai; Wong, Hiu Tung; Ho, Derek

    2014-01-01

    Instrumental limitations such as bulkiness and high cost prevent the fluorescence technique from becoming ubiquitous for point-of-care deoxyribonucleic acid (DNA) detection and other in-field molecular diagnostics applications. The complimentary metal-oxide-semiconductor (CMOS) technology, as benefited from process scaling, provides several advanced capabilities such as high integration density, high-resolution signal processing, and low power consumption, enabling sensitive, integrated, and low-cost fluorescence analytical platforms. In this paper, CMOS time-resolved, contact, and multispectral imaging are reviewed. Recently reported CMOS fluorescence analysis microsystem prototypes are surveyed to highlight the present state of the art. PMID:25365460

  14. [Cognitive functions, their development and modern diagnostic methods].

    PubMed

    Klasik, Adam; Janas-Kozik, Małgorzata; Krupka-Matuszczyk, Irena; Augustyniak, Ewa

    2006-01-01

    provided a theory. The psychometric approach concentrates on studying the differences in intelligence. The aim of this approach is to test intelligence by means of standardized tests (e.g. WISC-R, WAIS-R) used to show the individual differences among humans. Human cognitive functions determine individuals' adaptation capabilities and disturbances in this area indicate a number of psychopathological changes and are a symptom enabling to differentiate or diagnose one with a disorder. That is why the psychological assessment of cognitive functions is an important part of patients' diagnosis. Contemporary neuropsychological studies are to a great extent based computer tests. The use of computer methods has a number of measurement-related advantages. It allows for standardized testing environment, increasing therefore its reliability and standardizes the patient assessment process. Special attention should be paid to the neuropsychological tests included in the Vienna Test System (Cognitron, SIGNAL, RT, VIGIL, DAUF), which are used to assess the operational memory span, learning processes, reaction time, attention selective function, attention continuity as well as attention interference resistance. It also seems justified to present the CPT id test (Continuous Performance Test) as well as Free Recall. CPT is a diagnostic tool used to assess the attention selective function, attention continuity of attention, attention interference resistance as well as attention alertness. The Free Recall test is used in the memory processes diagnostics to assess patients' operational memory as well as the information organization degree in operational memory. The above mentioned neuropsychological tests are tools used in clinical assessment of cognitive function disorders.

  15. The Molecular Revolution in Cutaneous Biology: Era of Molecular Diagnostics for Inherited Skin Diseases.

    PubMed

    McGrath, John A

    2017-05-01

    The discovery of pathogenic mutations in inherited skin diseases represents one of the major landmarks of late 20th century molecular genetics. Mutation data can provide accurate diagnoses, improve genetic counseling, help define disease mechanisms, establish disease models, and provide a basis for translational research and testing of novel therapeutics. The process of detecting disease mutations, however, has not always been straightforward. Traditional approaches using genetic linkage or candidate gene analysis have often been limited, costly, and slow to yield new insights, but the advent of next-generation sequencing (NGS) technologies has altered the landscape of current gene discovery and mutation detection approaches. Copyright © 2017 The Author. Published by Elsevier Inc. All rights reserved.

  16. [Positron emission tomography in neuroscience. An integrative part of clinical diagnostic methods and experimental research].

    PubMed

    Schaller, B

    2005-02-01

    The role of molecular neuroimaging techniques is increasing in the understanding of pathophysiological mechanism of diseases. To date, positron emission tomography is the most powerful tool for the non-invasive study of biochemical and molecular processes in humans and animals in vivo. With the development in radiochemistry and tracer technology, a variety of endogenously expressed and exogenously introduced genes can be analyzed by PET. This opens up the exciting and rapidly field of molecular imaging, aiming at the non-invasive localisation of a biological process of interest in normal and diseased cells in animal models and humans in vivo. Besides its usefulness for basic research positron emission tomography has been proven to be superior to conventional diagnostic methods in several clinical indications. This is illustrated by detection of biological or anatomic changes that cannot be demonstrated by computed tomography or magnetic resonance imaging, as well as even before symptoms are expressed. The present review summarizes the clinical use of positron emission tomography in neuroscience that has helped elucidate the pathophysiology of a number of diseases and has suggested strategies in the treatment of these patients. Special reference is given to the neurovascular, neurodegenerative and neurooncological disease.

  17. Conventional, molecular methods and biomarkers molecules in detection of septicemia

    PubMed Central

    Arabestani, Mohammad Reza; Rastiany, Sahar; Kazemi, Sima; Mousavi, Seyed Masoud

    2015-01-01

    Sepsis is a leading cause of morbidity and mortality in hospitalized patients worldwide and based on studies, 30–40% of all cases of severe sepsis and septic shock results from the blood stream infections (BSIs). Identifying of the disease, performing laboratory tests, and consequently treatment are factors that required for optimum management of BSIs. In addition, applying precise and immediate identification of the etiologic agent is a prerequisite for specific antibiotic therapy of pathogen and thereby decreasing mortality rates. The diagnosis of sepsis is difficult because clinical signs of sepsis often overlap with other noninfectious cases of systemic inflammation. BSIs are usually diagnosed by performing a series of techniques such as blood cultures, polymerase chain reaction-based methods, and biomarkers of sepsis. Extremely time-consuming even to take up to several days is a major limitation of conventional methods. In addition, yielding false-negative results due to fastidious and slow-growing microorganisms and also in case of antibiotic pretreated samples are other limitations. In comparison, molecular methods are capable of examining a blood sample obtained from suspicious patient with BSI and gave the all required information to prescribing antimicrobial therapy for detected bacterial or fungal infections immediately. Because of an emergency of sepsis, new methods are being developed. In this review, we discussed about the most important sepsis diagnostic methods and numbered the advantage and disadvantage of the methods in detail. PMID:26261822

  18. Direct anharmonic correction method by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Liu, Zhong-Li; Li, Rui; Zhang, Xiu-Lu; Qu, Nuo; Cai, Ling-Cang

    2017-04-01

    The quick calculation of accurate anharmonic effects of lattice vibrations is crucial to the calculations of thermodynamic properties, the construction of the multi-phase diagram and equation of states of materials, and the theoretical designs of new materials. In this paper, we proposed a direct free energy interpolation (DFEI) method based on the temperature dependent phonon density of states (TD-PDOS) reduced from molecular dynamics simulations. Using the DFEI method, after anharmonic free energy corrections we reproduced the thermal expansion coefficients, the specific heat, the thermal pressure, the isothermal bulk modulus, and the Hugoniot P- V- T relationships of Cu easily and accurately. The extensive tests on other materials including metal, alloy, semiconductor and insulator also manifest that the DFEI method can easily uncover the rest anharmonicity that the quasi-harmonic approximation (QHA) omits. It is thus evidenced that the DFEI method is indeed a very efficient method used to conduct anharmonic effect corrections beyond QHA. More importantly it is much more straightforward and easier compared to previous anharmonic methods.

  19. Ruling in or ruling out thyroid malignancy by molecular diagnostics of thyroid nodules.

    PubMed

    Eszlinger, Markus; Hegedüs, László; Paschke, Ralf

    2014-08-01

    Routine morphologic cytology is the basis for any kind of (integrated) molecular FNA diagnostics. The rule out (gene expression classifier) approach requires confirmation by independent studies, whereas the rule in approach (detection of BRAF, NRAS, HRAS, and KRAS and PAX8/PPARG- and RET/PTC rearrangements) has been investigated by several groups with overall reproducible results. Moreover, molecular screening for point mutations and rearrangements is feasible in routine air-dried FNA smears, offering several advantages over obtaining additional fresh FNA material. The current panel of somatic mutations (rule in approach) for indeterminate FNAs clarifies only a subgroup of indeterminate FNAs. Therefore, further markers are urgently needed that can reliably identify the malignant, but mutation negative and especially the many benign nodules, among the indeterminate FNAs. miRNA markers and the targeted next generation sequencing (NGS) technology do have the potential to identify those nodules that are mutation negative by current approaches.

  20. [Development of Standards for Baseline Quality in Quality Management of Molecular-Diagnostic Testing].

    PubMed

    Miyachi, Hayato

    2015-07-01

    As molecular-diagnostic testing is expanding in clinical use, the demand for its quality assurance is increasing. To this end, efforts towards quality management have been made regionally and globally. An entire testing procedure needs to be properly performed from the preanalytic, analytic, and postanalytic processes. Particularly, the preanalytic process largely affects the measurement and, thus, the result. The Japanese Committee for Clinical Laboratory and Standard developed the standard documents, such as that for the quality management of clinical specimens and best-practice guideline for quality assurance of molecular-genetic testing. These standard documents would provide not only the requirements as the best practice for testing, but also the basis of baseline quality and reliability. They can be used as the basis for assessment of the quality of practice in reimbursement coverage by payers and in certification or accreditation by a third party.

  1. Systemic mast cell activation disease: the role of molecular genetic alterations in pathogenesis, heritability and diagnostics.

    PubMed

    Haenisch, Britta; Nöthen, Markus M; Molderings, Gerhard J

    2012-11-01

    Despite increasing understanding of its pathophysiology, the aetiology of systemic mast cell activation disease (MCAD) remains largely unknown. Research has shown that somatic mutations in kinases are necessary for the establishment of a clonal mast cell population, in particular mutations in the tyrosine kinase Kit and in enzymes and receptors with crucial involvement in the regulation of mast cell activity. However, other, as yet undetermined, abnormalities are necessary for the manifestation of clinical disease. The present article reviews molecular genetic research into the identification of disease-associated genes and their mutational alterations. The authors also present novel data on familial systemic MCAD and review the associated literature. Finally, the importance of understanding the molecular basis of inherited mutations in terms of diagnostics and therapy is emphasized.

  2. Electrically heated particulate filter diagnostic systems and methods

    SciTech Connect

    Gonze, Eugene V

    2009-09-29

    A system that diagnoses regeneration of an electrically heated particulate filter is provided. The system generally includes a grid module that diagnoses a fault of the grid based on at least one of a current signal and a voltage signal. A diagnostic module at least one of sets a fault status and generates a warning signal based on the fault of the grid.

  3. Sherlock Holmes's Methods of Deductive Reasoning Applied to Medical Diagnostics

    PubMed Central

    Miller, Larry

    1985-01-01

    Having patterned the character of Sherlock Holmes after one of his professors, Sir Arthur Conan Doyle, himself a physician, incorporated many of the didactic qualities of the 19th century medical diagnostician into the character of Holmes. In this paper I explore Holmes's techniques of deductive reasoning and their basis in 19th and 20th century medical diagnostics. PMID:3887762

  4. Sherlock Holmes' methods of deductive reasoning applied to medical diagnostics.

    PubMed

    Miller, L

    1985-03-01

    Having patterned the character of Sherlock Holmes after one of his professors, Sir Arthur Conan Doyle, himself a physician, incorporated many of the didactic qualities of the 19th century medical diagnostician into the character of Holmes. In this paper I explore Holmes's techniques of deductive reasoning and their basis in 19th and 20th century medical diagnostics.

  5. Immersed molecular electrokinetic finite element method

    NASA Astrophysics Data System (ADS)

    Kopacz, Adrian M.; Liu, Wing K.

    2013-07-01

    A unique simulation technique has been developed capable of modeling electric field induced detection of biomolecules such as viruses, at room temperatures where thermal fluctuations must be considered. The proposed immersed molecular electrokinetic finite element method couples electrokinetics with fluctuating hydrodynamics to study the motion and deformation of flexible objects immersed in a suspending medium under an applied electric field. The force induced on an arbitrary object due to an electric field is calculated based on the continuum electromechanics and the Maxwell stress tensor. The thermal fluctuations are included in the Navier-Stokes fluid equations via the stochastic stress tensor. Dielectrophoretic and fluctuating forces acting on the particle are coupled through the fluid-structure interaction force calculated within the surrounding environment. This method was used to perform concentration and retention efficacy analysis of nanoscale biosensors using gold particles of various sizes. The analysis was also applied to a human papillomavirus.

  6. Monocyte-Targeting Supramolecular Micellar Assemblies: A Molecular Diagnostic Tool for Atherosclerosis

    PubMed Central

    Chung, E. J.; Nord, K.; Sugimoto, M. J.; Wonder, E.; Tirrell, M.; Mlinar, L. B.; Alenghat, F. J.; Fang, Y.

    2014-01-01

    Atherosclerosis is a multifactorial inflammatory disease that can progress silently for decades and result in myocardial infarction, stroke, and death. Diagnostic imaging technologies have made great strides to define the degree of atherosclerotic plaque burden through the severity of arterial stenosis. However, current technologies cannot differentiate more lethal “vulnerable plaques,” and are not sensitive enough for preventive medicine. Imaging early molecular markers and quantifying the extent of disease progression continues to be a major challenge in the field. To this end, monocyte-targeting, peptide amphiphile micelles (PAMs) are engineered through the incorporation of the chemokine receptor CCR2-binding motif of monocyte chemoattractant protein-1 (MCP-1) and MCP-1 PAMs are evaluated preclinically as diagnostic tools for atherosclerosis. Monocyte-targeting is desirable as the influx of monocytes is a marker of early lesions, accumulation of monocytes is linked to atherosclerosis progression, and rupture-prone plaques have higher numbers of monocytes. MCP-1 PAMs bind to monocytes in vitro, and MCP-1 PAMs detect and discriminate between early- and late-stage atherosclerotic aortas. Moreover, MCP-1 PAMs are found to be eliminated via renal clearance and the mononuclear phagocyte system (MPS) without adverse side effects. Thus, MCP-1 PAMs are a promising new class of diagnostic agents capable of monitoring the progression of atherosclerosis. PMID:25156590

  7. Monocyte-targeting supramolecular micellar assemblies: a molecular diagnostic tool for atherosclerosis.

    PubMed

    Chung, Eun Ji; Mlinar, Laurie B; Nord, Kathryn; Sugimoto, Matthew J; Wonder, Emily; Alenghat, Francis J; Fang, Yun; Tirrell, Matthew

    2015-02-18

    Atherosclerosis is a multifactorial inflammatory disease that can progress silently for decades and result in myocardial infarction, stroke, and death. Diagnostic imaging technologies have made great strides to define the degree of atherosclerotic plaque burden through the severity of arterial stenosis. However, current technologies cannot differentiate more lethal "vulnerable plaques," and are not sensitive enough for preventive medicine. Imaging early molecular markers and quantifying the extent of disease progression continues to be a major challenge in the field. To this end, monocyte-targeting, peptide amphiphile micelles (PAMs) are engineered through the incorporation of the chemokine receptor CCR2-binding motif of monocyte chemoattractant protein-1 (MCP-1) and MCP-1 PAMs are evaluated preclinically as diagnostic tools for atherosclerosis. Monocyte-targeting is desirable as the influx of monocytes is a marker of early lesions, accumulation of monocytes is linked to atherosclerosis progression, and rupture-prone plaques have higher numbers of monocytes. MCP-1 PAMs bind to monocytes in vitro, and MCP-1 PAMs detect and discriminate between early- and late-stage atherosclerotic aortas. Moreover, MCP-1 PAMs are found to be eliminated via renal clearance and the mononuclear phagocyte system (MPS) without adverse side effects. Thus, MCP-1 PAMs are a promising new class of diagnostic agents capable of monitoring the progression of atherosclerosis.

  8. Hereditary hemorrhagic telangiectasia: genetics and molecular diagnostics in a new era

    PubMed Central

    McDonald, Jamie; Wooderchak-Donahue, Whitney; VanSant Webb, Chad; Whitehead, Kevin; Stevenson, David A.; Bayrak-Toydemir, Pinar

    2015-01-01

    Hereditary hemorrhagic telangiectasia (HHT) is a vascular dysplasia characterized by telangiectases and arteriovenous malformations (AVMs) in particular locations described in consensus clinical diagnostic criteria published in 2000. Two genes in the transforming growth factor-beta (TGF-β) signaling pathway, ENG and ACVRL1, were discovered almost two decades ago, and mutations in these genes have been reported to cause up to 85% of HHT. In our experience, approximately 96% of individuals with HHT have a mutation in these two genes, when published (Curaçao) diagnostic criteria for HHT are strictly applied. More recently, two additional genes in the same pathway, SMAD4 and GDF2, have been identified in a much smaller number of patients with a similar or overlapping phenotype to HHT. Yet families still exist with compelling evidence of a hereditary telangiectasia disorder, but no identifiable mutation in a known gene. Recent availability of whole exome and genome testing has created new opportunities to facilitate gene discovery, identify genetic modifiers to explain clinical variability, and potentially define an increased spectrum of hereditary telangiectasia disorders. An expanded approach to molecular diagnostics for inherited telangiectasia disorders that incorporates a multi-gene next generation sequencing (NGS) HHT panel is proposed. PMID:25674101

  9. Hereditary hemorrhagic telangiectasia: genetics and molecular diagnostics in a new era.

    PubMed

    McDonald, Jamie; Wooderchak-Donahue, Whitney; VanSant Webb, Chad; Whitehead, Kevin; Stevenson, David A; Bayrak-Toydemir, Pinar

    2015-01-01

    Hereditary hemorrhagic telangiectasia (HHT) is a vascular dysplasia characterized by telangiectases and arteriovenous malformations (AVMs) in particular locations described in consensus clinical diagnostic criteria published in 2000. Two genes in the transforming growth factor-beta (TGF-β) signaling pathway, ENG and ACVRL1, were discovered almost two decades ago, and mutations in these genes have been reported to cause up to 85% of HHT. In our experience, approximately 96% of individuals with HHT have a mutation in these two genes, when published (Curaçao) diagnostic criteria for HHT are strictly applied. More recently, two additional genes in the same pathway, SMAD4 and GDF2, have been identified in a much smaller number of patients with a similar or overlapping phenotype to HHT. Yet families still exist with compelling evidence of a hereditary telangiectasia disorder, but no identifiable mutation in a known gene. Recent availability of whole exome and genome testing has created new opportunities to facilitate gene discovery, identify genetic modifiers to explain clinical variability, and potentially define an increased spectrum of hereditary telangiectasia disorders. An expanded approach to molecular diagnostics for inherited telangiectasia disorders that incorporates a multi-gene next generation sequencing (NGS) HHT panel is proposed.

  10. Infectious Disease Management through Point-of-Care Personalized Medicine Molecular Diagnostic Technologies.

    PubMed

    Bissonnette, Luc; Bergeron, Michel G

    2012-05-02

    Infectious disease management essentially consists in identifying the microbial cause(s) of an infection, initiating if necessary antimicrobial therapy against microbes, and controlling host reactions to infection. In clinical microbiology, the turnaround time of the diagnostic cycle (>24 hours) often leads to unnecessary suffering and deaths; approaches to relieve this burden include rapid diagnostic procedures and more efficient transmission or interpretation of molecular microbiology results. Although rapid nucleic acid-based diagnostic testing has demonstrated that it can impact on the transmission of hospital-acquired infections, we believe that such life-saving procedures should be performed closer to the patient, in dedicated 24/7 laboratories of healthcare institutions, or ideally at point of care. While personalized medicine generally aims at interrogating the genomic information of a patient, drug metabolism polymorphisms, for example, to guide drug choice and dosage, personalized medicine concepts are applicable in infectious diseases for the (rapid) identification of a disease-causing microbe and determination of its antimicrobial resistance profile, to guide an appropriate antimicrobial treatment for the proper management of the patient. The implementation of point-of-care testing for infectious diseases will require acceptance by medical authorities, new technological and communication platforms, as well as reimbursement practices such that time- and life-saving procedures become available to the largest number of patients.

  11. Infectious Disease Management through Point-of-Care Personalized Medicine Molecular Diagnostic Technologies

    PubMed Central

    Bissonnette, Luc; Bergeron, Michel G.

    2012-01-01

    Infectious disease management essentially consists in identifying the microbial cause(s) of an infection, initiating if necessary antimicrobial therapy against microbes, and controlling host reactions to infection. In clinical microbiology, the turnaround time of the diagnostic cycle (>24 hours) often leads to unnecessary suffering and deaths; approaches to relieve this burden include rapid diagnostic procedures and more efficient transmission or interpretation of molecular microbiology results. Although rapid nucleic acid-based diagnostic testing has demonstrated that it can impact on the transmission of hospital-acquired infections, we believe that such life-saving procedures should be performed closer to the patient, in dedicated 24/7 laboratories of healthcare institutions, or ideally at point of care. While personalized medicine generally aims at interrogating the genomic information of a patient, drug metabolism polymorphisms, for example, to guide drug choice and dosage, personalized medicine concepts are applicable in infectious diseases for the (rapid) identification of a disease-causing microbe and determination of its antimicrobial resistance profile, to guide an appropriate antimicrobial treatment for the proper management of the patient. The implementation of point-of-care testing for infectious diseases will require acceptance by medical authorities, new technological and communication platforms, as well as reimbursement practices such that time- and life-saving procedures become available to the largest number of patients. PMID:25562799

  12. Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology.

    PubMed

    Schrijver, Iris; Aziz, Nazneen; Farkas, Daniel H; Furtado, Manohar; Gonzalez, Andrea Ferreira; Greiner, Timothy C; Grody, Wayne W; Hambuch, Tina; Kalman, Lisa; Kant, Jeffrey A; Klein, Roger D; Leonard, Debra G B; Lubin, Ira M; Mao, Rong; Nagan, Narasimhan; Pratt, Victoria M; Sobel, Mark E; Voelkerding, Karl V; Gibson, Jane S

    2012-11-01

    This report of the Whole Genome Analysis group of the Association for Molecular Pathology illuminates the opportunities and challenges associated with clinical diagnostic genome sequencing. With the reality of clinical application of next-generation sequencing, technical aspects of molecular testing can be accomplished at greater speed and with higher volume, while much information is obtained. Although this testing is a next logical step for molecular pathology laboratories, the potential impact on the diagnostic process and clinical correlations is extraordinary and clinical interpretation will be challenging. We review the rapidly evolving technologies; provide application examples; discuss aspects of clinical utility, ethics, and consent; and address the analytic, postanalytic, and professional implications.

  13. Economic evaluation of diagnostic methods used in dentistry. A systematic review.

    PubMed

    Christell, Helena; Birch, Stephen; Horner, Keith; Lindh, Christina; Rohlin, Madeleine

    2014-11-01

    To review the literature of economic evaluations regarding diagnostic methods used in dentistry. Four databases (MEDLINE, Web of Science, The Cochrane library, the NHS Economic Evaluation Database) were searched for studies, complemented by hand search, until February 2013. Two authors independently screened all titles or abstracts and then applied inclusion and exclusion criteria to select full-text publications published in English, which reported an economic evaluation comparing at least two alternative methods. Studies of diagnostic methods were assessed by four reviewers using a protocol based on the QUADAS tool regarding diagnostic methods and a check-list for economic evaluations. The results of the data extraction were summarized in a structured table and as a narrative description. From 476 identified full-text publications, 160 were considered to be economic evaluations. Only 12 studies (7%) were on diagnostic methods, whilst 78 studies (49%) were on prevention and 70 (40%) on treatment. Among studies on diagnostic methods, there was between-study heterogeneity methodologically, regarding the diagnostic method analysed and type of economic evaluation addressed. Generally, the choice of economic evaluation method was not justified and the perspective of the study not stated. Costing of diagnostic methods varied. A small body of literature addresses economic evaluation of diagnostic methods in dentistry. Thus, there is a need for studies from various perspectives with well defined research questions and measures of the cost and effectiveness. Economic resources in healthcare are finite. For diagnostic methods, an understanding of efficacy provides only part of the information needed for evidence-based practice. This study highlighted a paucity of economic evaluations of diagnostic methods used in dentistry, indicating that much of what we practise lacks sufficient evidence.

  14. Molecular Diagnostics for Precision Medicine in Colorectal Cancer: Current Status and Future Perspective.

    PubMed

    Chen, Guoli; Yang, Zhaohai; Eshleman, James R; Netto, George J; Lin, Ming-Tseh

    2016-01-01

    Precision medicine, a concept that has recently emerged and has been widely discussed, emphasizes tailoring medical care to individuals largely based on information acquired from molecular diagnostic testing. As a vital aspect of precision cancer medicine, targeted therapy has been proven to be efficacious and less toxic for cancer treatment. Colorectal cancer (CRC) is one of the most common cancers and among the leading causes for cancer related deaths in the United States and worldwide. By far, CRC has been one of the most successful examples in the field of precision cancer medicine, applying molecular tests to guide targeted therapy. In this review, we summarize the current guidelines for anti-EGFR therapy, revisit the roles of pathologists in an era of precision cancer medicine, demonstrate the transition from traditional "one test-one drug" assays to multiplex assays, especially by using next-generation sequencing platforms in the clinical diagnostic laboratories, and discuss the future perspectives of tumor heterogeneity associated with anti-EGFR resistance and immune checkpoint blockage therapy in CRC.

  15. Molecular Diagnostics for Precision Medicine in Colorectal Cancer: Current Status and Future Perspective

    PubMed Central

    Chen, Guoli; Yang, Zhaohai; Eshleman, James R.; Netto, George J.

    2016-01-01

    Precision medicine, a concept that has recently emerged and has been widely discussed, emphasizes tailoring medical care to individuals largely based on information acquired from molecular diagnostic testing. As a vital aspect of precision cancer medicine, targeted therapy has been proven to be efficacious and less toxic for cancer treatment. Colorectal cancer (CRC) is one of the most common cancers and among the leading causes for cancer related deaths in the United States and worldwide. By far, CRC has been one of the most successful examples in the field of precision cancer medicine, applying molecular tests to guide targeted therapy. In this review, we summarize the current guidelines for anti-EGFR therapy, revisit the roles of pathologists in an era of precision cancer medicine, demonstrate the transition from traditional “one test-one drug” assays to multiplex assays, especially by using next-generation sequencing platforms in the clinical diagnostic laboratories, and discuss the future perspectives of tumor heterogeneity associated with anti-EGFR resistance and immune checkpoint blockage therapy in CRC. PMID:27699178

  16. Optimized acoustic biochip integrated with microfluidics for biomarkers detection in molecular diagnostics.

    PubMed

    Papadakis, G; Friedt, J M; Eck, M; Rabus, D; Jobst, G; Gizeli, E

    2017-09-01

    The development of integrated platforms incorporating an acoustic device as the detection element requires addressing simultaneously several challenges of technological and scientific nature. The present work was focused on the design of a microfluidic module, which, combined with a dual or array type Love wave acoustic chip could be applied to biomedical applications and molecular diagnostics. Based on a systematic study we optimized the mechanics of the flow cell attachment and the sealing material so that fluidic interfacing/encapsulation would impose minimal losses to the acoustic wave. We have also investigated combinations of operating frequencies with waveguide materials and thicknesses for maximum sensitivity during the detection of protein and DNA biomarkers. Within our investigations neutravidin was used as a model protein biomarker and unpurified PCR amplified Salmonella DNA as the model genetic target. Our results clearly indicate the need for experimental verification of the optimum engineering and analytical parameters, in order to develop commercially viable systems for integrated analysis. The good reproducibility of the signal together with the ability of the array biochip to detect multiple samples hold promise for the future use of the integrated system in a Lab-on-a-Chip platform for application to molecular diagnostics.

  17. Hidden mutations in Cornelia de Lange syndrome limitations of sanger sequencing in molecular diagnostics.

    PubMed

    Braunholz, Diana; Obieglo, Carolin; Parenti, Ilaria; Pozojevic, Jelena; Eckhold, Juliane; Reiz, Benedikt; Braenne, Ingrid; Wendt, Kerstin S; Watrin, Erwan; Vodopiutz, Julia; Rieder, Harald; Gillessen-Kaesbach, Gabriele; Kaiser, Frank J

    2015-01-01

    Cornelia de Lange syndrome (CdLS) is a well-characterized developmental disorder. The genetic cause of CdLS is a mutation in one of five associated genes (NIPBL, SMC1A, SMC3, RAD21, and HDAC8) accounting for about 70% of cases. To improve our current molecular diagnostic and to analyze some of CdLS candidate genes, we developed and established a gene panel approach. Because recent data indicate a high frequency of mosaic NIPBL mutations that were not detected by conventional sequencing approaches of blood DNA, we started to collect buccal mucosa (BM) samples of our patients that were negative for mutations in the known CdLS genes. Here, we report the identification of three mosaic NIPBL mutations by our high-coverage gene panel sequencing approach that were undetected by classical Sanger sequencing analysis of BM DNA. All mutations were confirmed by the use of highly sensitive SNaPshot fragment analysis using DNA from BM, urine, and fibroblast samples. In blood samples, we could not detect the respective mutation. Finally, in fibroblast samples from all three patients, Sanger sequencing could identify all the mutations. Thus, our study highlights the need for highly sensitive technologies in molecular diagnostic of CdLS to improve genetic diagnosis and counseling of patients and their families. © 2014 WILEY PERIODICALS, INC.

  18. Genetic predisposition to β-thalassemia and sickle cell anemia in Turkey: a molecular diagnostic approach.

    PubMed

    Basak, A Nazli; Tuzmen, Sukru

    2011-01-01

    The thalassemia syndromes are a diverse group of inherited disorders that can be characterized according to their insufficient synthesis or absent production of one or more of the globin chains. They are classified in to α, β, γ, δβ, δ, and εγδβ thalassemias depending on the globin chain(s) affected. The β-thalassemias refer to that group of inherited hemoglobin disorders, which are characterized by a reduced synthesis (β(+)-thalassemia) or absence (β(0)-thalassemia) of beta globin (β-globin) chain production (1). Though known as single-gene disorders, hemoglobinopathies such as β-thalassemia and sickle cell anemia are far from being fully resolved in terms of cure, considering the less complex nature of the beta globin (β-globin) gene family compared to more complex multifactorial genetic disorders such as cancer. Currently, there are no definitive therapeutic options for patients with β-thalassemia and sickle cell anemia, and new insights into the pathogenesis of these devastating diseases are urgently needed. Here we address in detail the overall picture utilizing molecular diagnostic approaches that contribute to unraveling the population-specific mutational analysis of β-globin gene. We also present approaches for molecular diagnostic strategies that are applicable to β-thalassemia, sickle cell anemia, and other genetic disorders.

  19. Scratching the surface of tomorrow's diagnostics: the Editor-in-Chief's opinion at the 15th year of Expert Review of Molecular Diagnostics.

    PubMed

    Lorincz, Attila; Raison, Claire

    2015-01-01

    Interview with Attila Lorincz by Claire Raison (Commissioning Editor) To mark the beginning of the 15th year of Expert Review of Molecular Diagnostics, the journal's Editor-in-Chief shares his expert knowledge on translational diagnostics, his opinion on recent controversies and his predictions for molecular diagnostics in 2015 and beyond. Attila Lorincz received his doctorate from Trinity College, Dublin, Republic of Ireland, and went on to become a research fellow at the University of California, Santa Barbara, CA, USA. During Professor Lorincz's research on human papillomavirus (HPV), he found several important and novel carcinogenic HPV types and pioneered the use of HPV DNA testing for clinical diagnostics. In 1988, Professor Lorincz's team produced the first HPV test to be FDA-approved for patients and in 2003, for general population cervical precancer screening. Now Professor of Molecular Epidemiology at the Centre for Cancer Prevention, Queen Mary University of London, UK, he and his team are furthering translational research into DNA methylation assays for cancer risk prediction.

  20. Molecular detection methods of human papillomavirus (HPV).

    PubMed

    Zaravinos, Apostolos; Mammas, Ioannis N; Sourvinos, George; Spandidos, Demetrios A

    2009-01-01

    Human papillomavirus (HPV) testing can identify women at risk of cervical cancer. Currently, molecular detection methods are the gold standard for identification of HPV. The three categories of molecular assays that are available are based on the detection of HPV DNA and include (1) non-amplified hybridization assays, such as Southern transfer hybridization (STH), dot blot hybridization (DB) and in situ hybridization (ISH); (2) signal amplified hybridization assays, such as hybrid capture assays (HC2); (3) target amplification assays, such as polymerase chain reaction (PCR) and in situ PCR. STH requires large amounts of DNA, is laborious and not reproducible, while ISH has only moderate sensitivity for HPV. The sensitivity of the HC2 assay is similar to that of PCR-based assays, with high sensitivity being achieved by signal rather than target amplification. PCR-based detection is both highly sensitive and specific. Since PCR can be performed on very small amounts of DNA, it is ideal for use on specimens with low DNA content. In the future, with the advance of technology, viral DNA extraction and amplification systems will become more rapid, more sensitive, and more automated.

  1. Detection of Respiratory Viruses by Molecular Methods

    PubMed Central

    Mahony, James B.

    2008-01-01

    Summary: Clinical laboratories historically diagnose seven or eight respiratory virus infections using a combination of techniques including enzyme immunoassay, direct fluorescent antibody staining, cell culture, and nucleic acid amplification tests. With the discovery of six new respiratory viruses since 2000, laboratories are faced with the challenge of detecting up to 19 different viruses that cause acute respiratory disease of both the upper and lower respiratory tracts. The application of nucleic acid amplification technology, particularly multiplex PCR coupled with fluidic or fixed microarrays, provides an important new approach for the detection of multiple respiratory viruses in a single test. These multiplex amplification tests provide a sensitive and comprehensive approach for the diagnosis of respiratory tract infections in individual hospitalized patients and the identification of the etiological agent in outbreaks of respiratory tract infection in the community. This review describes the molecular methods used to detect respiratory viruses and discusses the contribution that molecular testing, especially multiplex PCR, has made to our ability to detect respiratory viruses and to increase our understanding of the roles of various viral agents in acute respiratory disease. PMID:18854489

  2. Speckle methods for diagnostics of the human oral cavity

    NASA Astrophysics Data System (ADS)

    Kharish, Natalia A.; Sedykh, Alexey V.; Ulyanov, Sergey S.; Lepilin, Alexander V.; Tuchin, Valery V.

    1999-11-01

    Possibility of application of speckle interferometry for diagnostics in dentistry has been analyzed. Problem of standardization of the measuring procedure has been studied. Deviation of output characteristics of Doppler system for blood microcirculation measurements has been investigated. Dependence of form of Doppler spectrum on the degree of seriousness of diseases has been studied in experiments in vivo. Behavior of spectral moments of measuring signal during the treatment of parodontitis has been analyzed.

  3. Multiple biomarkers in molecular oncology. II. Molecular diagnostics applications in breast cancer management.

    PubMed

    Malinowski, Douglas P

    2007-05-01

    In recent years, the application of genomic and proteomic technologies to the problem of breast cancer prognosis and the prediction of therapy response have begun to yield encouraging results. Independent studies employing transcriptional profiling of primary breast cancer specimens using DNA microarrays have identified gene expression profiles that correlate with clinical outcome in primary breast biopsy specimens. Recent advances in microarray technology have demonstrated reproducibility, making clinical applications more achievable. In this regard, one such DNA microarray device based upon a 70-gene expression signature was recently cleared by the US FDA for application to breast cancer prognosis. These DNA microarrays often employ at least 70 gene targets for transcriptional profiling and prognostic assessment in breast cancer. The use of PCR-based methods utilizing a small subset of genes has recently demonstrated the ability to predict the clinical outcome in early-stage breast cancer. Furthermore, protein-based immunohistochemistry methods have progressed from using gene clusters and gene expression profiling to smaller subsets of expressed proteins to predict prognosis in early-stage breast cancer. Beyond prognostic applications, DNA microarray-based transcriptional profiling has demonstrated the ability to predict response to chemotherapy in early-stage breast cancer patients. In this review, recent advances in the use of multiple markers for prognosis of disease recurrence in early-stage breast cancer and the prediction of therapy response will be discussed.

  4. Jet Noise Diagnostics Supporting Statistical Noise Prediction Methods

    NASA Technical Reports Server (NTRS)

    Bridges, James E.

    2006-01-01

    The primary focus of my presentation is the development of the jet noise prediction code JeNo with most examples coming from the experimental work that drove the theoretical development and validation. JeNo is a statistical jet noise prediction code, based upon the Lilley acoustic analogy. Our approach uses time-average 2-D or 3-D mean and turbulent statistics of the flow as input. The output is source distributions and spectral directivity. NASA has been investing in development of statistical jet noise prediction tools because these seem to fit the middle ground that allows enough flexibility and fidelity for jet noise source diagnostics while having reasonable computational requirements. These tools rely on Reynolds-averaged Navier-Stokes (RANS) computational fluid dynamics (CFD) solutions as input for computing far-field spectral directivity using an acoustic analogy. There are many ways acoustic analogies can be created, each with a series of assumptions and models, many often taken unknowingly. And the resulting prediction can be easily reverse-engineered by altering the models contained within. However, only an approach which is mathematically sound, with assumptions validated and modeled quantities checked against direct measurement will give consistently correct answers. Many quantities are modeled in acoustic analogies precisely because they have been impossible to measure or calculate, making this requirement a difficult task. The NASA team has spent considerable effort identifying all the assumptions and models used to take the Navier-Stokes equations to the point of a statistical calculation via an acoustic analogy very similar to that proposed by Lilley. Assumptions have been identified and experiments have been developed to test these assumptions. In some cases this has resulted in assumptions being changed. Beginning with the CFD used as input to the acoustic analogy, models for turbulence closure used in RANS CFD codes have been explored and

  5. Use of Molecular Diagnostic Tools for the Identification of Species Responsible for Snakebite in Nepal: A Pilot Study

    PubMed Central

    Sharma, Sanjib Kumar; Kuch, Ulrich; Höde, Patrick; Bruhse, Laura; Pandey, Deb P.; Ghimire, Anup; Chappuis, François; Alirol, Emilie

    2016-01-01

    Snakebite is an important medical emergency in rural Nepal. Correct identification of the biting species is crucial for clinicians to choose appropriate treatment and anticipate complications. This is particularly important for neurotoxic envenoming which, depending on the snake species involved, may not respond to available antivenoms. Adequate species identification tools are lacking. This study used a combination of morphological and molecular approaches (PCR-aided DNA sequencing from swabs of bite sites) to determine the contribution of venomous and non-venomous species to the snakebite burden in southern Nepal. Out of 749 patients admitted with a history of snakebite to one of three study centres, the biting species could be identified in 194 (25.9%). Out of these, 87 had been bitten by a venomous snake, most commonly the Indian spectacled cobra (Naja naja; n = 42) and the common krait (Bungarus caeruleus; n = 22). When both morphological identification and PCR/sequencing results were available, a 100% agreement was noted. The probability of a positive PCR result was significantly lower among patients who had used inadequate “first aid” measures (e.g. tourniquets or local application of remedies). This study is the first to report the use of forensic genetics methods for snake species identification in a prospective clinical study. If high diagnostic accuracy is confirmed in larger cohorts, this method will be a very useful reference diagnostic tool for epidemiological investigations and clinical studies. PMID:27105074

  6. Method of making molecularly doped composite polymer material

    DOEpatents

    Affinito, John D [Tucson, AZ; Martin, Peter M [Kennewick, WA; Graff, Gordon L [West Richland, WA; Burrows, Paul E [Kennewick, WA; Gross, Mark E. , Sapochak, Linda S.

    2005-06-21

    A method of making a composite polymer of a molecularly doped polymer. The method includes mixing a liquid polymer precursor with molecular dopant forming a molecularly doped polymer precursor mixture. The molecularly doped polymer precursor mixture is flash evaporated forming a composite vapor. The composite vapor is cryocondensed on a cool substrate forming a composite molecularly doped polymer precursor layer, and the cryocondensed composite molecularly doped polymer precursor layer is cross linked thereby forming a layer of the composite polymer layer of the molecularly doped polymer.

  7. A Novel Fully Automated Molecular Diagnostic System (AMDS) for Colorectal Cancer Mutation Detection

    PubMed Central

    Kitano, Shiro; Myers, Jamie; Nakamura, Junko; Yamane, Akio; Yamashita, Mami; Nakayama, Masato; Tsukahara, Yusuke; Ushida, Hiroshi; Liu, Wanqing; Ratain, Mark J.; Amano, Masahiko

    2013-01-01

    Background KRAS, BRAF and PIK3CA mutations are frequently observed in colorectal cancer (CRC). In particular, KRAS mutations are strong predictors for clinical outcomes of EGFR-targeted treatments such as cetuximab and panitumumab in metastatic colorectal cancer (mCRC). For mutation analysis, the current methods are time-consuming, and not readily available to all oncologists and pathologists. We have developed a novel, simple, sensitive and fully automated molecular diagnostic system (AMDS) for point of care testing (POCT). Here we report the results of a comparison study between AMDS and direct sequencing (DS) in the detection of KRAS, BRAF and PI3KCA somatic mutations. Methodology/Principal Finding DNA was extracted from a slice of either frozen (n = 89) or formalin-fixed and paraffin-embedded (FFPE) CRC tissue (n = 70), and then used for mutation analysis by AMDS and DS. All mutations (n = 41 among frozen and 27 among FFPE samples) detected by DS were also successfully (100%) detected by the AMDS. However, 8 frozen and 6 FFPE samples detected as wild-type in the DS analysis were shown as mutants in the AMDS analysis. By cloning-sequencing assays, these discordant samples were confirmed as true mutants. One sample had simultaneous “hot spot” mutations of KRAS and PIK3CA, and cloning assay comfirmed that E542K and E545K were not on the same allele. Genotyping call rates for DS were 100.0% (89/89) and 74.3% (52/70) in frozen and FFPE samples, respectively, for the first attempt; whereas that of AMDS was 100.0% for both sample sets. For automated DNA extraction and mutation detection by AMDS, frozen tissues (n = 41) were successfully detected all mutations within 70 minutes. Conclusions/Significance AMDS has superior sensitivity and accuracy over DS, and is much easier to execute than conventional labor intensive manual mutation analysis. AMDS has great potential for POCT equipment for mutation analysis. PMID:23671647

  8. Kinetic and Diagnostic Studies of Molecular Plasmas Using Laser Absorption Techniques

    NASA Astrophysics Data System (ADS)

    Welzel, S.; Rousseau, A.; Davies, P. B.; Röpcke, J.

    2007-10-01

    Within the last decade mid infrared absorption spectroscopy between 3 and 20 μm, known as Infrared Laser Absorption Spectroscopy (IRLAS) and based on tuneable semiconductor lasers, namely lead salt diode lasers, often called tuneable diode lasers (TDL), and quantum cascade lasers (QCL) has progressed considerably as a powerful diagnostic technique for in situ studies of the fundamental physics and chemistry of molecular plasmas. The increasing interest in processing plasmas containing hydrocarbons, fluorocarbons, organo-silicon and boron compounds has lead to further applications of IRLAS because most of these compounds and their decomposition products are infrared active. IRLAS provides a means of determining the absolute concentrations of the ground states of stable and transient molecular species, which is of particular importance for the investigation of reaction kinetics. Information about gas temperature and population densities can also be derived from IRLAS measurements. A variety of free radicals and molecular ions have been detected, especially using TDLs. Since plasmas with molecular feed gases are used in many applications such as thin film deposition, semiconductor processing, surface activation and cleaning, and materials and waste treatment, this has stimulated the adaptation of infrared spectroscopic techniques to industrial requirements. The recent development of QCLs offers an attractive new option for the monitoring and control of industrial plasma processes as well as for highly time-resolved studies on the kinetics of plasma processes. The aim of the present article is threefold: (i) to review recent achievements in our understanding of molecular phenomena in plasmas, (ii) to report on selected studies of the spectroscopic properties and kinetic behaviour of radicals, and (iii) to describe the current status of advanced instrumentation for TDLAS in the mid infrared.

  9. Kinetic and Diagnostic Studies of Molecular Plasmas Using Laser Absorption Techniques

    NASA Astrophysics Data System (ADS)

    Röpcke, Jürgen; Engeln, Richard; Schram, Daan; Rousseau, Antoine; Davies, Paul B.

    Within the last decade, mid-infrared absorption spectroscopy between 3 and 20 μm - known as infrared laser absorption spectroscopy (IRLAS) and based on tunable semiconductor lasers, namely lead salt diode lasers, often called tunable diode lasers (TDLs), and quantum cascade lasers (QCLs) - has progressed considerably as a powerful diagnostic technique for in situ studies of the fundamental physics and chemistry of molecular plasmas. The increasing interest in processing plasmas containing hydrocarbons, fluorocarbons, and organosilicon compounds has led to further applications of IRLAS because most of these compounds and their decomposition products are infrared active. IRLAS provides a means of determining the absolute concentrations of the ground states of stable and transient molecular species, which is of particular importance for the investigation of reaction kinetics. Information about gas temperature and population densities can also be derived from IRLAS measurements. A variety of free radicals and molecular ions have been detected, especially using TDLs. Since plasmas with molecular feed gases are used in many applications such as thin film deposition, semiconductor processing, surface activation and cleaning, and materials and waste treatment, this has stimulated the adaptation of infrared spectroscopic techniques to industrial requirements. The recent development of QCLs offers an attractive new option for the monitoring and control of industrial plasma processes as well as for highly time-resolved studies on the kinetics of plasma processes. The aim of the present contribution is threefold (1) to review recent achievements in our understanding of molecular phenomena in plasmas including interactions with solid surfaces, (2) to report on selected studies of the spectroscopic properties and kinetic behavior of radicals, and (3) to review new applications of QCLs and to describe the current status of advanced instrumentation for QCLAS in the midinfrared.

  10. An objective method and measuring equipment for noise control and acoustic diagnostics of motorcars. [acoustic diagnostics on automobile engines

    NASA Technical Reports Server (NTRS)

    Kacprowski, J.; Motylewski, J.; Miazga, J.

    1974-01-01

    An objective method and apparatus for noise control and acoustic diagnostics of motorcar engines are reported. The method and apparatus let us know whether the noisiness of the vehicle under test exceeds the admissible threshold levels given by appropriate standards and if so what is the main source of the excessive noise. The method consists in measuring both the overall noise level and the sound pressure levels in definite frequency bands while the engine speed is controlled as well and may be fixed at prescribed values. Whenever the individually adjusted threshold level has been exceeded in any frequency band, a self-sustaining control signal is sent.

  11. Method matters: Understanding diagnostic reliability in DSM-IV and DSM-5.

    PubMed

    Chmielewski, Michael; Clark, Lee Anna; Bagby, R Michael; Watson, David

    2015-08-01

    Diagnostic reliability is essential for the science and practice of psychology, in part because reliability is necessary for validity. Recently, the DSM-5 field trials documented lower diagnostic reliability than past field trials and the general research literature, resulting in substantial criticism of the DSM-5 diagnostic criteria. Rather than indicating specific problems with DSM-5, however, the field trials may have revealed long-standing diagnostic issues that have been hidden due to a reliance on audio/video recordings for estimating reliability. We estimated the reliability of DSM-IV diagnoses using both the standard audio-recording method and the test-retest method used in the DSM-5 field trials, in which different clinicians conduct separate interviews. Psychiatric patients (N = 339) were diagnosed using the SCID-I/P; 218 were diagnosed a second time by an independent interviewer. Diagnostic reliability using the audio-recording method (N = 49) was "good" to "excellent" (M κ = .80) and comparable to the DSM-IV field trials estimates. Reliability using the test-retest method (N = 218) was "poor" to "fair" (M κ = .47) and similar to DSM-5 field-trials' estimates. Despite low test-retest diagnostic reliability, self-reported symptoms were highly stable. Moreover, there was no association between change in self-report and change in diagnostic status. These results demonstrate the influence of method on estimates of diagnostic reliability. (c) 2015 APA, all rights reserved).

  12. Method Matters: Understanding Diagnostic Reliability in DSM-IV and DSM-5

    PubMed Central

    Chmielewski, Michael; Clark, Lee Anna; Bagby, R. Michael; Watson, David

    2015-01-01

    Diagnostic reliability is essential for the science and practice of psychology, in part because reliability is necessary for validity. Recently, the DSM-5 Field Trials documented lower diagnostic reliability than past field trials and the general research literature, resulting in substantial criticism of the DSM-5 diagnostic criteria. Rather than indicating specific problems with DSM-5, however, the Field Trials may have revealed long-standing diagnostic issues that have been hidden due to a reliance on audio/video-recordings for estimating reliability. We estimated the reliability of DSM-IV diagnoses using both the standard audio-recording method and the test-retest method used in the DSM-5 Field Trials, in which different clinicians conduct separate interviews. Psychiatric patients (N = 339) were diagnosed using the SCID-I/P; 218 were diagnosed a second time by an independent interviewer. Diagnostic reliability using the audio-recording method (N = 49) was “good” to “excellent” (M kappa = .80) and comparable to the DSM-IV Field Trials estimates. Reliability using the test-retest method (N = 218) was “poor” to “fair” (M kappa = .47) and similar to DSM-5 Field-Trials’ estimates. Despite low test-retest diagnostic reliability, self-reported symptoms were highly stable. Moreover, there was no association between change in self-report and change in diagnostic status. These results demonstrate the influence of method on estimates of diagnostic reliability. PMID:26098046

  13. From plasticity to complexity: a new diagnostic method for psychiatry.

    PubMed

    Peled, Avi

    2004-01-01

    There is growing dissatisfaction regarding the available diagnostic systems for psychiatric disorders (DSM, ICD). Psychiatrists acknowledge that though mental disease reflects brain disorders, the descriptive and symptom based nature of psychiatric diagnosis bears no relation to brain functions. According to Helmut's article published in the October 2003 issue of Science, in the coming decade researchers and psychiatrists will be called upon to propose a basis for the psychiatric diagnostic system of the future. I propose a new etiology-oriented diagnostic system for psychiatry by integrating two recently emerging bodies of knowledge, one regarding plasticity and the other involving complex systems. Plasticity refers to all brain processes involved in dynamic alterations within communicating neuronal ensembles or networks, in the brain. Complexity refers to certain formulations from system theories relevant to brain dynamics and plasticity. It is proposed to divide plasticity processes into three types based on time domains: (1) "developmental plasticity", (2) "tuning plasticity" and (3) "fast stabilizing plasticity". Each type of plasticity is related to different complexity models achieved by the brain, developmental plasticity is life-long brain organization, it is related to state-space configurations molded into brain representations internalized via processes such as Hebbian learning. Tuning plasticity is related to "matching complexity" a measure of adaptability between internal configurations in the brain-system and externally originating event stimuli. Fast stabilizing plasticity is related to "neural complexity" a measure of neural network integration in the brain. Neural complexity meets the mental requirement to extract important features from different sensory inputs and to simultaneously generate coherent perceptual and cognitive states, thus balancing specialized segregated brain processes with coherent globally integrated whole brain activity

  14. [Concepts, evaluation methods, diagnostic and prognostic values of implant stability].

    PubMed

    Grognard, Nicolas; Vande Vannet, Bart

    2010-01-01

    The outcome of oral implant treatment is in part focused on the obtained implant stability as outlined in the success criteria as propose by Albrektsson T. & Albrektsson B. (1987) and by Buser et al. (1997). In those criteria, clinical diagnostic testing of implant stability is a rather crude and subjective procedure. Quantitative measurement technology, such as the Periotest and the Osstell Mentor devices do provide more refined and objective tools to diagnose and monitor the state of osseointegration. On the other hand, their power to predict treatment outcome is rather low.

  15. Raman spectroscopy of saliva as a perspective method for periodontitis diagnostics Raman spectroscopy of saliva

    NASA Astrophysics Data System (ADS)

    Gonchukov, S.; Sukhinina, A.; Bakhmutov, D.; Minaeva, S.

    2012-01-01

    In view of its potential for biological tissues analyses at a molecular level, Raman spectroscopy in optical range has been the object of biomedical research for the last years. The main aim of this work is the development of Raman spectroscopy for organic content identifying and determination of biomarkers of saliva at a molecular level for periodontitis diagnostics. Four spectral regions were determined: 1155 and 1525 cm-1, 1033 and 1611 cm-1, which can be used as biomarkers of this widespread disease.

  16. Enterovirus infections in England and Wales, 2000-2011: the impact of increased molecular diagnostics.

    PubMed

    Kadambari, S; Bukasa, A; Okike, I O; Pebody, R; Brown, D; Gallimore, C; Xerry, J; Sharland, M; Ladhani, S N

    2014-12-01

    There have recently been significant changes in diagnostic practices for detecting enterovirus (EV) infections across England and Wales. Reports of laboratory-confirmed EV infections submitted by National Health Service (NHS) hospital laboratories to Public Health England (PHE) over a 12-year period (2000-2011) were analysed. Additionally, the PHE Virus Reference Department (VRD) electronic database containing molecular typing data from 2004 onwards was interrogated. Of the 13,901 reports, there was a decline from a peak of 2254 in 2001 to 589 in 2006, and then an increase year-on-year to 1634 in 2011. This increase coincided with increasing PCR-based laboratory diagnosis, which accounted for 36% of reported cases in 2000 and 92% in 2011. The estimated annual incidence in 2011 was 3.9/100,000 overall and 238/100,000 in those aged <3 months, who accounted for almost one-quarter of reported cases (n = 2993, 23%). During 2004-2011, 2770 strains were submitted for molecular typing to the VRD, who found no evidence for a predominance of any particular strain. Thus, the recent increase in reported cases closely reflects the increase in PCR testing by NHS hospitals, but is associated with a lower proportion of samples being submitted for molecular typing. The high EV rate in young infants merits further investigation to inform evidence-based management guidance. © 2014 The Authors Clinical Microbiology and Infection © 2014 European Society of Clinical Microbiology and Infectious Diseases.

  17. Methods in molecular cardiology: microarray technology

    PubMed Central

    van den Bosch, B.; Doevendans, P.A.; Lips, D.; Smeets, H.J.M.

    2003-01-01

    It has become more and more evident that changes in expression levels of genes can play an important role in cardiovascular diseases. Specific gene expression profiles may explain, for example, the pathophysiology of myocardial hypertrophy and pump failure and may provide clues for therapeutic interventions. Knowledge of gene expression patterns can also be applied for diagnostic and prognostic purposes, in which differences in gene activity can be used for classification. DNA microarray technology has become the method of choice to simultaneously study the expression of many different genes in a single assay. Each microarray contains many thousands of different DNA sequences attached to a glass slide. The amount of messenger RNA, which is a measure of gene activity, is compared for each gene on the microarray by labelling the mRNA with different fluorescently labelled nucleotides (Cy3 or Cy5) for the test and reference samples. After hybridisation to the microarray the relative amounts of a particular gene transcript in the two samples can be determined by measuring the signal intensities for the fluorescent groups (Cy3 and Cy5) and calculating signal ratios. This paper describes the development of in-house microarray technology, using commercially available cDNA collections. Several technical approaches will be compared and an overview of the pitfalls and possibilities will be presented. The technology will be explained in the context of our project to determine gene expression differences between normal, hypertrophic and failing heart. ImagesFigure 1Figure 2Figure 3Figure 4Figure 5Figure 6Figure 7Figure 9 PMID:25696214

  18. Molecular method for determining sex of walruses

    USGS Publications Warehouse

    Fischbach, A.S.; Jay, C.V.; Jackson, J.V.; Andersen, L.W.; Sage, G.K.; Talbot, S.L.

    2008-01-01

    We evaluated the ability of a set of published trans-species molecular sexing primers and a set of walrus-specific primers, which we developed, to accurately identify sex of 235 Pacific walruses (Odobenus rosmarus divergens). The trans-species primers were developed for mammals and targeted the X- and Y-gametologs of the zinc finger protein genes (ZFX, ZFY). We extended this method by using these primers to obtain sequence from Pacific and Atlantic walrus (0. r. rosmarus) ZFX and ZFY genes to develop new walrus-specific primers, which yield polymerase chain reaction products of distinct lengths (327 and 288 base pairs from the X- and Y-chromosome, respectively), allowing them to be used for sex determination. Both methods yielded a determination of sex in all but 1-2% of samples with an accuracy of 99.6-100%. Our walrus-specific primers offer the advantage of small fragment size and facile application to automated electrophoresis and visualization.

  19. DEVELOPMENT OF MOLECULAR METHODS TO DETECT ...

    EPA Pesticide Factsheets

    A large number of human enteric viruses are known to cause gastrointestinal illness and waterborne outbreaks. Many of these are emerging viruses that do not grow or grow poorly in cell culture and so molecular detectoin methods based on the polymerase chain reaction (PCR) are being developed. Current studies focus on detecting two virus groups, the caliciviruses and the hepatitis E virus strains, both of which have been found to cause significant outbraks via contaminated drinking water. Once developed, these methods will be used to collect occurrence data for risk assessment studies. Develop sensitive techniques to detect and identify emerging human waterborne pathogenic viruses and viruses on the CCL.Determine effectiveness of viral indicators to measure microbial quality in water matrices.Support activities: (a) culture and distribution of mammalian cells for Agency and scientific community research needs, (b) provide operator expertise for research requiring confocal and electron microscopy, (c) glassware cleaning, sterilization and biological waste disposal for the Cincinnati EPA facility, (d) operation of infectious pathogenic suite, (e) maintenance of walk-in constant temperature rooms and (f) provide Giardia cysts.

  20. Current Nucleic Acid Extraction Methods and Their Implications to Point-of-Care Diagnostics

    PubMed Central

    Ali, Nasir; Rampazzo, Rita de Cássia Pontello; Krieger, Marco Aurelio

    2017-01-01

    Nucleic acid extraction (NAE) plays a vital role in molecular biology as the primary step for many downstream applications. Many modifications have been introduced to the original 1869 method. Modern processes are categorized into chemical or mechanical, each with peculiarities that influence their use, especially in point-of-care diagnostics (POC-Dx). POC-Dx is a new approach aiming to replace sophisticated analytical machinery with microanalytical systems, able to be used near the patient, at the point of care or point of need. Although notable efforts have been made, a simple and effective extraction method is still a major challenge for widespread use of POC-Dx. In this review, we dissected the working principle of each of the most common NAE methods, overviewing their advantages and disadvantages, as well their potential for integration in POC-Dx systems. At present, it seems difficult, if not impossible, to establish a procedure which can be universally applied to POC-Dx. We also discuss the effects of the NAE chemicals upon the main plastic polymers used to mass produce POC-Dx systems. We end our review discussing the limitations and challenges that should guide the quest for an efficient extraction method that can be integrated in a POC-Dx system. PMID:28785592

  1. Development of wide area environment accelerator operation and diagnostics method

    NASA Astrophysics Data System (ADS)

    Uchiyama, Akito; Furukawa, Kazuro

    2015-08-01

    Remote operation and diagnostic systems for particle accelerators have been developed for beam operation and maintenance in various situations. Even though fully remote experiments are not necessary, the remote diagnosis and maintenance of the accelerator is required. Considering remote-operation operator interfaces (OPIs), the use of standard protocols such as the hypertext transfer protocol (HTTP) is advantageous, because system-dependent protocols are unnecessary between the remote client and the on-site server. Here, we have developed a client system based on WebSocket, which is a new protocol provided by the Internet Engineering Task Force for Web-based systems, as a next-generation Web-based OPI using the Experimental Physics and Industrial Control System Channel Access protocol. As a result of this implementation, WebSocket-based client systems have become available for remote operation. Also, as regards practical application, the remote operation of an accelerator via a wide area network (WAN) faces a number of challenges, e.g., the accelerator has both experimental device and radiation generator characteristics. Any error in remote control system operation could result in an immediate breakdown. Therefore, we propose the implementation of an operator intervention system for remote accelerator diagnostics and support that can obviate any differences between the local control room and remote locations. Here, remote-operation Web-based OPIs, which resolve security issues, are developed.

  2. Benchmarking Gas Path Diagnostic Methods: A Public Approach

    NASA Technical Reports Server (NTRS)

    Simon, Donald L.; Bird, Jeff; Davison, Craig; Volponi, Al; Iverson, R. Eugene

    2008-01-01

    Recent technology reviews have identified the need for objective assessments of engine health management (EHM) technology. The need is two-fold: technology developers require relevant data and problems to design and validate new algorithms and techniques while engine system integrators and operators need practical tools to direct development and then evaluate the effectiveness of proposed solutions. This paper presents a publicly available gas path diagnostic benchmark problem that has been developed by the Propulsion and Power Systems Panel of The Technical Cooperation Program (TTCP) to help address these needs. The problem is coded in MATLAB (The MathWorks, Inc.) and coupled with a non-linear turbofan engine simulation to produce "snap-shot" measurements, with relevant noise levels, as if collected from a fleet of engines over their lifetime of use. Each engine within the fleet will experience unique operating and deterioration profiles, and may encounter randomly occurring relevant gas path faults including sensor, actuator and component faults. The challenge to the EHM community is to develop gas path diagnostic algorithms to reliably perform fault detection and isolation. An example solution to the benchmark problem is provided along with associated evaluation metrics. A plan is presented to disseminate this benchmark problem to the engine health management technical community and invite technology solutions.

  3. The Revised Research Diagnostic Criteria for Temporomandibular Disorders: Methods used to Establish and Validate Revised Axis I Diagnostic Algorithms

    PubMed Central

    Schiffman, Eric L.; Ohrbach, Richard; Truelove, Edmond L.; Feng, Tai; Anderson, Gary C.; Pan, Wei; Gonzalez, Yoly M.; John, Mike T.; Sommers, Earl; List, Thomas; Velly, Ana M.; Kang, Wenjun; Look, John O.

    2011-01-01

    AIMS To derive reliable and valid revised Research Diagnostic Criteria for Temporomandibular Disorders (RDC/TMD) Axis I diagnostic algorithms for clinical TMD diagnoses. METHODS The multi-site RDC/TMD Validation Project’s dataset (614 TMD community and clinic cases, and 91 controls) was used to derive revised algorithms for Axis I TMD diagnoses. Validity of diagnostic algorithms was assessed relative to reference standards, the latter based on consensus diagnoses rendered by 2 TMD experts using criterion examination data, including temporomandibular joint imaging. Cut-offs for target validity were sensitivity ≥ 0.70 and specificity ≥ 0.95. Reliability of revised algorithms was assessed in 27 study participants. RESULTS Revised algorithm sensitivity and specificity exceeded the target levels for myofascial pain (0.82, 0.99, respectively) and myofascial pain with limited opening (0.93, 0.97). Combining diagnoses for any myofascial pain showed sensitivity of 0.91 and specificity of 1.00. For joint pain, target sensitivity and specificity were observed (0.92, 0.96) when arthralgia and osteoarthritis were combined as “any joint pain.” Disc displacement without reduction with limited opening demonstrated target sensitivity and specificity (0.80, 0.97). For the other Group II disc displacements and Group III osteoarthritis and osteoarthrosis, sensitivity was below target (0.35 to 0.53), and specificity ranged from 0.80 to meeting target. Kappa for revised algorithm diagnostic reliability was ≥ 0.63. CONCLUSION Revised RDC/TMD Axis I TMD diagnostic algorithms are recommended for myofascial pain and joint pain as reliable and valid. However, revised clinical criteria alone, without recourse to imaging, are inadequate for valid diagnosis of two of the three disc displacements and osteoarthritis/osteoarthrosis. PMID:20213032

  4. [The hepatitis A virus: structural and functional organization of the genome, its molecular diagnostic value and cultivation].

    PubMed

    Bondarenko, T Iu; Ternovoĭ, V A; Netesov, S V

    2013-01-01

    The analysis of recently published data on hepatitis A virus (HAV) genome clinical features, molecular diagnostic value and cell culture propagation are reviewed. The growing need in the study of the genetic diversity of HAV isolates and the search of its possible new antigenic variants are underlined. The results of the cultivation of different HAV strains are analyzed for possible application in vaccine and diagnostic kit production.

  5. Leveling the playing field: bringing development of biomarkers and molecular diagnostics up to the standards for drug development.

    PubMed

    Poste, George; Carbone, David P; Parkinson, David R; Verweij, Jaap; Hewitt, Stephen M; Jessup, J Milburn

    2012-03-15

    Molecular diagnostics are becoming increasingly important in clinical research to stratify or identify molecularly profiled patient cohorts for targeted therapies, to modify the dose of a therapeutic, and to assess early response to therapy or monitor patients. Molecular diagnostics can also be used to identify the pharmacogenetic risk of adverse drug reactions. The articles in this CCR Focus section on molecular diagnosis describe the development and use of markers to guide medical decisions regarding cancer patients. They define sources of preanalytic variability that need to be minimized, as well as the regulatory and financial challenges involved in developing diagnostics and integrating them into clinical practice. They also outline a National Cancer Institute program to assist diagnostic development. Molecular diagnostic clinical tests require rigor in their development and clinical validation, with sensitivity, specificity, and validity comparable to those required for the development of therapeutics. These diagnostics must be offered at a realistic cost that reflects both their clinical value and the costs associated with their development. When genome-sequencing technologies move into the clinic, they must be integrated with and traceable to current technology because they may identify more efficient and accurate approaches to drug development. In addition, regulators may define progressive drug approval for companion diagnostics that requires further evidence regarding efficacy and safety before full approval can be achieved. One way to accomplish this is to emphasize phase IV postmarketing, hypothesis-driven clinical trials with biological characterization that would permit an accurate definition of the association of low-prevalence gene alterations with toxicity or response in large cohorts.

  6. Introduction to methods in molecular cardiology.

    PubMed

    Sun, Zhongjie

    2005-01-01

    Molecular cardiology is a new area of cardiovascular medicine that aims to apply molecular biological techniques for the mechanistic investigation, diagnosis, prevention, and treatment of cardiovascular disease. As an emerging discipline, it has changed our conceptual thinking of cardiovascular development, disease etiology, and pathophysiology. Although molecular cardiology is still at a very early stage, it has opened a promising avenue for understanding and controlling cardiovascular disease. With the rapid development and application of molecular biological techniques, scientists and clinicians are closer to curing heart diseases that were thought to be incurable 20 yr ago. There clearly is a need for a more thorough understanding of the molecular mechanisms of cardiovascular diseases to promote the advancement of cell and gene therapy for heart diseases. This chapter briefly reviews state-of-the-art techniques in the area of molecular cardiology.

  7. Recommendations for reporting results of diagnostic genetic testing (biochemical, cytogenetic and molecular genetic).

    PubMed

    Claustres, Mireille; Kožich, Viktor; Dequeker, Els; Fowler, Brain; Hehir-Kwa, Jayne Y; Miller, Konstantin; Oosterwijk, Cor; Peterlin, Borut; van Ravenswaaij-Arts, Conny; Zimmermann, Uwe; Zuffardi, Orsetta; Hastings, Ros J; Barton, David E

    2014-02-01

    Genetic test results can have considerable importance for patients, their parents and more remote family members. Clinical therapy and surveillance, reproductive decisions and genetic diagnostics in family members, including prenatal diagnosis, are based on these results. The genetic test report should therefore provide a clear, concise, accurate, fully interpretative and authoritative answer to the clinical question. The need for harmonizing reporting practice of genetic tests has been recognised by the External Quality Assessment (EQA), providers and laboratories. The ESHG Genetic Services Quality Committee has produced reporting guidelines for the genetic disciplines (biochemical, cytogenetic and molecular genetic). These guidelines give assistance on report content, including the interpretation of results. Selected examples of genetic test reports for all three disciplines are provided in an annexe.

  8. Fluorescence-Raman Dual Modal Endoscopic System for Multiplexed Molecular Diagnostics

    NASA Astrophysics Data System (ADS)

    Jeong, Sinyoung; Kim, Yong-Il; Kang, Homan; Kim, Gunsung; Cha, Myeong Geun; Chang, Hyejin; Jung, Kyung Oh; Kim, Young-Hwa; Jun, Bong-Hyun; Hwang, Do Won; Lee, Yun-Sang; Youn, Hyewon; Lee, Yoon-Sik; Kang, Keon Wook; Lee, Dong Soo; Jeong, Dae Hong

    2015-03-01

    Optical endoscopic imaging, which was recently equipped with bioluminescence, fluorescence, and Raman scattering, allows minimally invasive real-time detection of pathologies on the surface of hollow organs. To characterize pathologic lesions in a multiplexed way, we developed a dual modal fluorescence-Raman endomicroscopic system (FRES), which used fluorescence and surface-enhanced Raman scattering nanoprobes (F-SERS dots). Real-time, in vivo, and multiple target detection of a specific cancer was successful, based on the fast imaging capability of fluorescence signals and the multiplex capability of simultaneously detected SERS signals using an optical fiber bundle for intraoperative endoscopic system. Human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor (EGFR) on the breast cancer xenografts in a mouse orthotopic model were successfully detected in a multiplexed way, illustrating the potential of FRES as a molecular diagnostic instrument that enables real-time tumor characterization of receptors during routine endoscopic procedures.

  9. Carbon Nanotube Biosensors for Space Molecule Detection and Clinical Molecular Diagnostics

    NASA Technical Reports Server (NTRS)

    Han, Jie

    2001-01-01

    Both space molecule detection and clinical molecule diagnostics need to develop ultra sensitive biosensors for detection of less than attomole molecules such as amino acids for DNA. However all the electrode sensor systems including those fabricated from the existing carbon nanotubes, have a background level of nA (nanoAmp). This has limited DNA or other molecule detection to nA level or molecules whose concentration is, much higher than attomole level. A program has been created by NASA and NCI (National Cancer Institute) to exploit the possibility of carbon nanotube based biosensors to solve this problem for both's interest. In this talk, I will present our effort on the evaluation and novel design of carbon nanotubes as electrode biosensors with strategies to minimize background currents while maximizing signal intensity.The fabrication of nanotube electrode arrays, immobilization of molecular probes on nanotube electrodes and in vitro biosensor testing will also be discussed.

  10. Applications of molecular diagnostics for personalized treatment of head and neck cancer: state of the art.

    PubMed

    Mes, Steven W; Leemans, C René; Brakenhoff, Ruud H

    2016-01-01

    Squamous cell carcinomas of the head and neck are the sixth most frequent tumors worldwide. Risk factors are carcinogenic exposure, infection with the human papillomavirus (HPV) and genetic predisposition. Lymph node metastasis in the neck and HPV status are major prognostic factors. There are several important clinical challenges that determine the research agenda in head and neck cancer. The first is more accurate staging, particularly of occult metastatic lymph nodes in the neck. A second challenge is the lack of biomarkers for personalized therapy. There are a number of treatment modalities that can be employed both single and in combination, but at present only site and stage of the tumor are used for treatment planning. Provided here is an overview of the successes and failures of molecular diagnostic approaches that have been and are being evaluated to address these clinical challenges.

  11. Fluorescence-Raman Dual Modal Endoscopic System for Multiplexed Molecular Diagnostics

    PubMed Central

    Jeong, Sinyoung; Kim, Yong-il; Kang, Homan; Kim, Gunsung; Cha, Myeong Geun; Chang, Hyejin; Jung, Kyung Oh; Kim, Young-Hwa; Jun, Bong-Hyun; Hwang, Do Won; Lee, Yun-Sang; Youn, Hyewon; Lee, Yoon-Sik; Kang, Keon Wook; Lee, Dong Soo; Jeong, Dae Hong

    2015-01-01

    Optical endoscopic imaging, which was recently equipped with bioluminescence, fluorescence, and Raman scattering, allows minimally invasive real-time detection of pathologies on the surface of hollow organs. To characterize pathologic lesions in a multiplexed way, we developed a dual modal fluorescence-Raman endomicroscopic system (FRES), which used fluorescence and surface-enhanced Raman scattering nanoprobes (F-SERS dots). Real-time, in vivo, and multiple target detection of a specific cancer was successful, based on the fast imaging capability of fluorescence signals and the multiplex capability of simultaneously detected SERS signals using an optical fiber bundle for intraoperative endoscopic system. Human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor (EGFR) on the breast cancer xenografts in a mouse orthotopic model were successfully detected in a multiplexed way, illustrating the potential of FRES as a molecular diagnostic instrument that enables real-time tumor characterization of receptors during routine endoscopic procedures. PMID:25820115

  12. Fluorescence-Raman dual modal endoscopic system for multiplexed molecular diagnostics.

    PubMed

    Jeong, Sinyoung; Kim, Yong-il; Kang, Homan; Kim, Gunsung; Cha, Myeong Geun; Chang, Hyejin; Jung, Kyung Oh; Kim, Young-Hwa; Jun, Bong-Hyun; Hwang, Do Won; Lee, Yun-Sang; Youn, Hyewon; Lee, Yoon-Sik; Kang, Keon Wook; Lee, Dong Soo; Jeong, Dae Hong

    2015-03-30

    Optical endoscopic imaging, which was recently equipped with bioluminescence, fluorescence, and Raman scattering, allows minimally invasive real-time detection of pathologies on the surface of hollow organs. To characterize pathologic lesions in a multiplexed way, we developed a dual modal fluorescence-Raman endomicroscopic system (FRES), which used fluorescence and surface-enhanced Raman scattering nanoprobes (F-SERS dots). Real-time, in vivo, and multiple target detection of a specific cancer was successful, based on the fast imaging capability of fluorescence signals and the multiplex capability of simultaneously detected SERS signals using an optical fiber bundle for intraoperative endoscopic system. Human epidermal growth factor receptor 2 (HER2) and epidermal growth factor receptor (EGFR) on the breast cancer xenografts in a mouse orthotopic model were successfully detected in a multiplexed way, illustrating the potential of FRES as a molecular diagnostic instrument that enables real-time tumor characterization of receptors during routine endoscopic procedures.

  13. Carbon Nanotube Biosensors for Space Molecule Detection and Clinical Molecular Diagnostics

    NASA Technical Reports Server (NTRS)

    Han, Jie

    2001-01-01

    Both space molecule detection and clinical molecule diagnostics need to develop ultra sensitive biosensors for detection of less than attomole molecules such as amino acids for DNA. However all the electrode sensor systems including those fabricated from the existing carbon nanotubes, have a background level of nA (nanoAmp). This has limited DNA or other molecule detection to nA level or molecules whose concentration is, much higher than attomole level. A program has been created by NASA and NCI (National Cancer Institute) to exploit the possibility of carbon nanotube based biosensors to solve this problem for both's interest. In this talk, I will present our effort on the evaluation and novel design of carbon nanotubes as electrode biosensors with strategies to minimize background currents while maximizing signal intensity.The fabrication of nanotube electrode arrays, immobilization of molecular probes on nanotube electrodes and in vitro biosensor testing will also be discussed.

  14. State of the art and new developments in molecular diagnostics for hemoglobinopathies in multiethnic societies.

    PubMed

    Harteveld, C L

    2014-02-01

    For detecting carriers of thalassemia traits, the basic part of diagnostics consists of measurement of the hematological indices followed by mostly automatic separation and measurement of the Hb fractions, while direct Hb separation either on high pressure liquid chromatography or capillary electrophoresis is sufficient to putatively identify carriers of the common Hb variants like HbS, C, E, D, and O-Arab. A putative positive result is reported together with an advice for parents, partner, or family analysis. For couples, presumed at-risk confirmation at the DNA level is essential. In general, this part of diagnostics is done in specialized centers provided with sufficient experience and the technical tools needed to combine hematological and biochemical interpretation with identification of the mutations at the molecular level. State-of-the-art tools are usually available in centers that also provide prenatal diagnosis and should consist of gap-PCR for the common deletions, direct DNA sequencing for all kind of point-mutations and the capacity to uncover novel or rare mutations or disease mechanisms. New developments are MLPA for large and eventually unknown deletion defects and microarray technology for fine mapping and primer design for breakpoint analysis. Gap-PCR primers designed in the region flanking the deletion breakpoints can subsequently be used to facilitate carrier detection of uncommon deletions in family members or isolated populations in laboratories where no microarray technology or MLPA is available.

  15. Diagnostic efficacy of in vitro methods vs. skin testing in patients with inhalant allergies

    SciTech Connect

    Corey, J.P.; Liudahl, J.J.; Young, S.A.; Rodman, S.M. )

    1991-03-01

    The purpose of our study was to investigate the diagnostic efficacy of two selected methods of in vitro allergy testing. Specifically, the PRIST/modified RAST I125 isotope systems and the Quantizyme/modified EAST alkaline phosphatase method were compared. The time, expense, convenience, and diagnostic efficacy of the two procedures are discussed. Special attention is given to the practicality of each method for the practicing physician.

  16. The Rapid-Heat LAMPellet Method: A Potential Diagnostic Method for Human Urogenital Schistosomiasis

    PubMed Central

    Carranza-Rodríguez, Cristina; Pérez-Arellano, José Luis; Vicente, Belén; López-Abán, Julio; Muro, Antonio

    2015-01-01

    Background Urogenital schistosomiasis due to Schistosoma haematobium is a serious underestimated public health problem affecting 112 million people - particularly in sub-Saharan Africa. Microscopic examination of urine samples to detect parasite eggs still remains as definitive diagnosis. This work was focussed on developing a novel loop-mediated isothermal amplification (LAMP) assay for detection of S. haematobium DNA in human urine samples as a high-throughput, simple, accurate and affordable diagnostic tool to use in diagnosis of urogenital schistosomiasis. Methodology/Principal Findings A LAMP assay targeting a species specific sequence of S. haematobium ribosomal intergenic spacer was designed. The effectiveness of our LAMP was assessed in a number of patients´ urine samples with microscopy confirmed S. haematobium infection. For potentially large-scale application in field conditions, different DNA extraction methods, including a commercial kit, a modified NaOH extraction method and a rapid heating method were tested using small volumes of urine fractions (whole urine, supernatants and pellets). The heating of pellets from clinical samples was the most efficient method to obtain good-quality DNA detectable by LAMP. The detection limit of our LAMP was 1 fg/µL of S. haematobium DNA in urine samples. When testing all patients´ urine samples included in our study, diagnostic parameters for sensitivity and specificity were calculated for LAMP assay, 100% sensitivity (95% CI: 81.32%-100%) and 86.67% specificity (95% CI: 75.40%-94.05%), and also for microscopy detection of eggs in urine samples, 69.23% sensitivity (95% CI: 48.21% -85.63%) and 100% specificity (95% CI: 93.08%-100%). Conclusions/Significance We have developed and evaluated, for the first time, a LAMP assay for detection of S. haematobium DNA in heated pellets from patients´ urine samples using no complicated requirement procedure for DNA extraction. The procedure has been named the Rapid

  17. Molecular diagnostics of Meckel-Gruber syndrome highlights phenotypic differences between MKS1 and MKS3.

    PubMed

    Consugar, Mark B; Kubly, Vickie J; Lager, Donna J; Hommerding, Cynthia J; Wong, Wai Chong; Bakker, Egbert; Gattone, Vincent H; Torres, Vicente E; Breuning, Martijn H; Harris, Peter C

    2007-06-01

    Meckel-Gruber syndrome (MKS) is a recessively inherited, lethal disorder characterized by renal cystic dysplasia, occipital encephalocele, polydactyly and biliary dysgenesis. MKS is genetically heterogeneous with three loci mapped and two identified; MKS1 (17q23) and MKS3 (8q22.1). MKS1 is part of the Finnish disease heritage, while MKS3 has been described exclusively in consanguineous Asian families. Here we aimed to establish molecular diagnostics for MKS, determine the importance of MKS1 and MKS3 in non-consanguineous populations, and study genotype/phenotype correlations. The coding regions of MKS1 and MKS3 were screened for mutations by direct sequencing in 17 families clinically diagnosed with MKS in the US or The Netherlands. The clinical phenotype was compared to genic and allelic effects. Both mutations were identified in ten families; five MKS1 and five MKS3. All but two were compound heterozygotes, consistent with their non-consanguineous nature. The MKS1-Fin(major) mutation accounted for 7/10 MKS1 mutations; two novel changes were additionally detected. Seven novel mutations were found in MKS3, including three missense changes. We concluded that MKS1 and MKS3 account for the majority of MKS in non-consanguineous populations of European origin. Polydactyly is usually found in MKS1 but rare in MKS3. Cases with no, or milder, CNS phenotypes were only found in MKS3; hypomorphic missense mutations may be associated with less severe CNS outcomes. This study is consistent with further genetic heterogeneity of MKS, but underlines the value of molecular diagnostics of the known genes to aid family planning decisions.

  18. Hepatocellular Carcinoma, Fibrolamellar Variant: Diagnostic Pathologic Criteria and Molecular Pathology Update. A Primer

    PubMed Central

    Sergi, Consolato M.

    2015-01-01

    Fibrolamellar hepatocellular carcinoma (FL-HCC) is generally a fairly rare event in routine pathology practice. This variant of hepatocellular carcinoma (HCC) is peculiarly intriguing and,in addition, poorly understood. Young people or children are often the target individuals with this type of cancer. Previously, I highlighted some pathology aspects of FL-HCC, but in this review, the distinctive clinico-pathologic features of FL-HCC and the diagnostic pathologic criteria of FL-HCC are fractionally reviewed and expanded upon. Further, molecular genetics update data with reference to this specific tumor are particularly highlighted as a primer for general pathologists and pediatric histopathologists. FL-HCC may present with metastases, and regional lymph nodes may be sites of metastatic spread. However, peritoneal and pulmonary metastatic foci have also been reported. To the best of our knowledge, FL-HCC was initially considered having an indolent course, but survival outcomes have recently been updated reconsidering the prognosis of this tumor. Patients seem to respond well to surgical resection, but recurrences are common. Thus, alternative therapies, such as chemotherapy and radiation, are ongoing. Overall, it seems that this aspect has not been well-studied for this variant of HCC and should be considered as target for future clinical trials. Remarkably, FL-HCC data seem to point to a liver neoplasm of uncertain origin and unveiled outcome. A functional chimeric transcript incorporating DNAJB1 and PRKACA was recently added to FL-HCC. This sensational result may give remarkable insights into the understanding of this rare disease and potentially provide the basis for its specific diagnostic marker. Detection of DNAJB1-PRKACA seems to be, indeed, a very sensitive and specific finding in supporting the diagnosis of FL-HCC. In a quite diffuse opinion, prognosis of this tumor should be reconsidered following the potentially mandatory application of new molecular

  19. Hepatocellular Carcinoma, Fibrolamellar Variant: Diagnostic Pathologic Criteria and Molecular Pathology Update. A Primer.

    PubMed

    Sergi, Consolato M

    2015-12-30

    Fibrolamellar hepatocellular carcinoma (FL-HCC) is generally a fairly rare event in routine pathology practice. This variant of hepatocellular carcinoma (HCC) is peculiarly intriguing and,in addition, poorly understood. Young people or children are often the target individuals with this type of cancer. Previously, I highlighted some pathology aspects of FL-HCC, but in this review, the distinctive clinico-pathologic features of FL-HCC and the diagnostic pathologic criteria of FL-HCC are fractionally reviewed and expanded upon. Further, molecular genetics update data with reference to this specific tumor are particularly highlighted as a primer for general pathologists and pediatric histopathologists. FL-HCC may present with metastases, and regional lymph nodes may be sites of metastatic spread. However, peritoneal and pulmonary metastatic foci have also been reported. To the best of our knowledge, FL-HCC was initially considered having an indolent course, but survival outcomes have recently been updated reconsidering the prognosis of this tumor. Patients seem to respond well to surgical resection, but recurrences are common. Thus, alternative therapies, such as chemotherapy and radiation, are ongoing. Overall, it seems that this aspect has not been well-studied for this variant of HCC and should be considered as target for future clinical trials. Remarkably, FL-HCC data seem to point to a liver neoplasm of uncertain origin and unveiled outcome. A functional chimeric transcript incorporating DNAJB1 and PRKACA was recently added to FL-HCC. This sensational result may give remarkable insights into the understanding of this rare disease and potentially provide the basis for its specific diagnostic marker. Detection of DNAJB1-PRKACA seems to be, indeed, a very sensitive and specific finding in supporting the diagnosis of FL-HCC. In a quite diffuse opinion, prognosis of this tumor should be reconsidered following the potentially mandatory application of new molecular

  20. C3H2 observations as a diagnostic probe for molecular clouds

    NASA Technical Reports Server (NTRS)

    Avery, L. W.

    1986-01-01

    Recently the three-membered ring molecule, cyclopropenylidene, C3H2, has been identified in the laboratory and detected in molecular clouds by Thaddeus, Vrtilek and Gottlieb (1985). This molecule is wide-spread throughout the Galaxy and has been detected in 25 separate sources including cold dust clouds, circumstellar envelopes, HII regions, and the spiral arms observed against the Cas supernova remnant. In order to evaluate the potential of C3H2 as a diagnostic probe for molecular clouds, and to attempt to identify the most useful transitions, statistical equilibrium calculations were carried out for the lowest 24 levels of the ortho species and the lowest 10 levels of the para species. Many of the sources observed by Matthews and Irvine (1985) show evidence of being optically thick in the 1(10)-1(01) line. Consequently, the effects of radiative trapping should be incorporated into the equilibrium calculations. This was done using the Large Velocity Gradient approximation for a spherical cloud of uniform density. Some results of the calculations for T(K)=10K are given. Figures are presented which show contours of the logarithm of the ratio of peak line brightness temperatures for ortho-para pairs of lines at similar frequencies. It appears that the widespread nature of C3H2, the relatively large strength of its spectral lines, and their sensitivity to density and molecular abundance combine to make this a useful molecule for probing physical conditions in molecular clouds. The 1(10)-1(01) and 2(20)-2(11) K-band lines may be especially useful in this regard because of the ease with which they are observed and their unusual density-dependent emission/absorption properties.

  1. [Radiological methods in the diagnostics of extrinsic allergic alveolitis].

    PubMed

    Makhmudova, S

    2005-09-01

    There were 77 patients with EAA under our observation with the following X-ray symptom groups: emphysematous-interstitial; parenchymatous-interstitial; pneumonic. The emphysematous-interstitial X-ray symptom group is the most non-specific for the X-ray diagnostics. The changes indicate to symptoms of impaired bronchial conductance of different expression and are relevant to clinical EAA options characteristic for the obstructive syndrome. The parenchymatous-interstitial X-ray symptom group is more characteristic for occupational EAA. In such cases the most important are changes in the lung parenchyma that have a diffusive character and are accompanied by general symptoms indicating to bronchial impairments of different severity. In pneumatic X-ray symptom group, the major X-ray symptom is presence of local sites of lung tissue consolidation of hypoventilation-infiltrative character that can be bilateral, multiple with a trend to migration.

  2. Non-Intrusive Optical Diagnostic Methods for Flowfield Characterization

    NASA Technical Reports Server (NTRS)

    Tabibi, Bagher M.; Terrell, Charles A.; Spraggins, Darrell; Lee, Ja. H.; Weinstein, Leonard M.

    1997-01-01

    Non-intrusive optical diagnostic techniques such as Electron Beam Fluorescence (EBF), Laser-Induced Fluorescence (LIF), and Focusing Schlieren (FS) have been setup for high-speed flow characterization and large flowfield visualization, respectively. Fluorescence emission from the First Negative band of N2(+) with the (0,0) vibration transition (at lambda =391.44 nm) was obtained using the EBF technique and a quenching rate of N2(+)* molecules by argon gas was reported. A very high sensitivity FS system was built and applied in the High-Speed Flow Generator (HFG) at NASA LaRC. A LIF system is available at the Advanced Propulsion Laboratory (APL) on campus and a plume exhaust velocity measurement, measuring the Doppler shift from lambda = 728.7 nm of argon gas, is under way.

  3. Diagnostic methods and recommendations for the cerebral creatine deficiency syndromes.

    PubMed

    Clark, Joseph F; Cecil, Kim M

    2015-03-01

    Primary care pediatricians and a variety of specialist physicians strive to define an accurate diagnosis for children presenting with impairment of expressive speech and delay in achieving developmental milestones. Within the past two decades, a group of disorders featuring this presentation have been identified as cerebral creatine deficiency syndromes (CCDS). Patients with these disorders were initially discerned using proton magnetic resonance spectroscopy of the brain within a magnetic resonance imaging (MRI) examination. The objective of this review is to provide the clinician with an overview of the current information available on identifying and treating these conditions. We explain the salient features of creatine metabolism, synthesis, and transport required for normal development. We propose diagnostic approaches for confirming a CCDS diagnosis. Finally, we describe treatment approaches for managing patients with these conditions.

  4. [Rapid methods for the diagnostic of food-borne infections determined by bacteria pertaining to genus Salmonella].

    PubMed

    Năşcuţiu, Alexandra-Maria

    2011-01-01

    For a long period of time, microbiological analysis of samples gathered from individuals, food and environment was based on culture techniques which were considered "gold standard". These conventional methods are yet time-consuming (with respect to germ identification and characterization), cumulative costs are huge, which made research focus on obtaining methods with a rapidity / cost ratio higher than that of classical methods. Rapid diagnostic became as well a priority in the case of food-borne diseases determined by Salmonella spp. These methods of rapid diagnostic are based on phenotypic or molecular techniques for identification and typing, as well as on tests using biosensors and DNA chips, which are under development, and which use the capacity of real-time monitoring of the presence of multiple pathogens in food. With the continuous development of new molecular technologies allowing the rapid detection of food pathogens, the future of conventional microbiological methods looks rather insecure, the more so as there is continuous interest in improving the performances of genotypic methods regarding easy handling, reliability and low costs. The work reviews the panoply of Salmonella identification and typing tests available in the present.

  5. Bayesian analysis of two diagnostic methods for paediatric ringworm infections in a teaching hospital.

    PubMed

    Rath, S; Panda, M; Sahu, M C; Padhy, R N

    2015-09-01

    Quantitatively, conventional methods of diagnosis of tinea capitis or paediatric ringworm, microscopic and culture tests were evaluated with Bayes rule. This analysis would help in quantifying the pervasive errors in each diagnostic method, particularly the microscopic method, as a long-term treatment would be involved to eradicate the infection by the use of a particular antifungal chemotherapy. Secondly, the analysis of clinical data would help in obtaining digitally the fallible standard of the microscopic test method, as the culture test method is taken as gold standard. Test results of 51 paediatric patients were of 4 categories: 21 samples were true positive (both tests positive), and 13 were true negative; the rest samples comprised both 14 false positive (microscopic test positivity with culture test negativity) and 3 false negative (microscopic test negativity with culture test positivity) samples. The prevalence of tinea infection was 47.01% in the population of 51 children. The microscopic test of a sample was efficient by 87.5%, in arriving at a positive result on diagnosis, when its culture test was positive; and, this test was efficient by 76.4%, in arriving at a negative result, when its culture test was negative. But, the post-test probability value of a sample with both microscopic and culture tests would be correct in distinguishing a sample from a sick or a healthy child with a chance of 71.5%. However, since the sensitivity of the analysis is 87.5%, the microscopic test positivity would be easier to detect in the presence of infection. In conclusion, it could be stated that Trychophyton rubrum was the most prevalent species; sensitivity and specificity of treating the infection, by antifungal therapy before ascertaining by the culture method remain as 0.8751 and 0.7642, respectively. A correct/coveted diagnostic method of fungal infection would be could be achieved by modern molecular methods (matrix-assisted laser desorption ionisation

  6. Application of modern diagnostic methods to environmental improvement. Annual progress report, October 1994--September 1995

    SciTech Connect

    Shepard, W.S.

    1995-12-01

    The Diagnostic Instrumentation and Analysis Laboratory (DIAL), an interdisciplinary research department in the College of Engineering at Mississippi State University (MSU), is under contract with the US Department of Energy (DOE) to develop and apply advanced diagnostic instrumentation and analysis techniques to aid in solving DOE`s nuclear waste problem. The program is a comprehensive effort which includes five focus areas: advanced diagnostic systems; development/application; torch operation and test facilities; process development; on-site field measurement and analysis; technology transfer/commercialization. As part of this program, diagnostic methods will be developed and evaluated for characterization, monitoring and process control. Also, the measured parameters, will be employed to improve, optimize and control the operation of the plasma torch and the overall plasma treatment process. Moreover, on-site field measurements at various DOE facilities are carried out to aid in the rapid demonstration and implementation of modern fieldable diagnostic methods. Such efforts also provide a basis for technology transfer.

  7. Multiplex molecular testing for management of infectious gastroenteritis in a hospital setting: a comparative diagnostic and clinical utility study.

    PubMed

    Halligan, E; Edgeworth, J; Bisnauthsing, K; Bible, J; Cliff, P; Aarons, E; Klein, J; Patel, A; Goldenberg, S

    2014-08-01

    Laboratory diagnosis and clinical management of inpatients with diarrhoea is complex and time consuming. Tests are often requested sequentially and undertaken in different laboratories. This causes prolonged unnecessary presumptive isolation of patients, because most cases are non-infectious. A molecular multiplex test (Luminex(®) Gastrointestinal Pathogen Panel (GPP)) was compared with conventional testing over 8 months to determine diagnostic accuracy, turnaround times, laboratory costs, use of isolation facilities and user acceptability. A total of 262 (12%) patients had a pathogen detected by conventional methods compared with 483 (22.1%) by GPP. Most additional cases were detected in patients developing symptoms in the first 4 days of admission. Additional cases were detected because of presumed improved diagnostic sensitivity but also because clinicians had not requested the correct pathogen. Turnaround time (41.8 h) was faster than bacterial culture (66.5 h) and parasite investigation (66.5 h) but slower than conventional testing for Clostridium difficile (17.3 h) and viruses (27 h). The test could allow simplified requesting by clinicians and a consolidated laboratory workflow, reducing the overall number of specimens received by the laboratory. A total of 154 isolation days were saved at an estimated cost of £30 800. Consumables and labour were estimated at £150 641 compared with £63 431 for conventional testing. Multiplex molecular testing using a panel of targets allowed enhanced detection and a consolidated laboratory workflow. This is likely to be of greater benefit to cases that present within the first 4 days of hospital admission.

  8. [Comparison of calculation methods for diagnostic trials under different sample size].

    PubMed

    Wang, Yang; Hu, Bo; Chen, Tao; Li, Wei

    2010-12-01

    To discuss the calculation methods under different sample size, used for diagnostic trials. The purpose of the diagnostic trial was to demonstrate the sensitivity and specificity of the new method. Equations and results were directly compared. Monte Carlo random simulation was used to validate the results. Sample size obtained from the sampling method was always smaller than from the target value method. Results from simulation showed that the target value method could offer more and larger power. The two sample size determination method showed essential differences of the results, suggesting that the investigator should choose appropriate method in accordance with the study design. If the hypothesis of study was to demonstrate the new diagnostic method which could meet the clinical requirements, only if the target value method provides enough statistical power.

  9. [The analysis of the low and medium molecular weight substances for differential diagnostics of deaths from acute small-focal myocardial infarction and other forms of cardiac pathology].

    PubMed

    Edelev, N S; Obuhova, L M; Edelev, I S; Katirkina, A A

    The objective of the present study was to analyze the possibilities for the use of the low and medium molecular weight substances for differential diagnostics of deaths from acute small-focal myocardial infarction and other forms of cardiac pathology. We determined the amount of the low and medium molecular weight substances in the urine obtained from the subjects who had died as a result of chronic coronary heart disease, acute myocardial infarction, and alcoholic cardiomyopathy. The levels of the low and medium molecular weight substances in the urine were measured by the method of N.Ya. Malakhov in the modification of T.V. Kopytova [5]. The study has demonstrated the appearance of the products of cardiomyocyte degradation (giving rise to a peak at a wavelength of 278 nm) in the fraction of the low and medium molecular weight substances of the urine from the patients suffering from acute small-focal myocardial infarction and some other forms of cardiac pathology.

  10. Frequency-Domain Methods for Characterization of Pulsed Power Diagnostics

    SciTech Connect

    White, A D; Anderson, R A; Ferriera, T J; Goerz, D A

    2009-07-27

    This paper discusses methods of frequency-domain characterization of pulsed power sensors using vector network analyzer and spectrum analyzer techniques that offer significant simplification over time-domain methods, while mitigating or minimizing the effect of the difficulties present in time domain characterization. These methods are applicable to characterization of a wide variety of sensors.

  11. Standardised molecular diagnostic tool for the identification of cryptic species within the Bemisia tabaci complex.

    PubMed

    Elfekih, S; Tay, W T; Gordon, K; Court, L; De Barro, P

    2017-07-23

    The whitefly Bemisia tabaci complex harbours over 40 cryptic species that have been placed in 11 phylogenetically distinct clades based on the molecular characterisation of partial mitochondrial DNA COI (mtCOI) gene region. Four cryptic species are currently within the invasive clade i.e. 'MED', 'MEAM1', 'MEAM2' and IO'. Correct identification of these species is a critical step towards implementing reliable measures for plant biosecurity and border protection, however no standardised B. tabaci-specific primers are currently available which has caused inconsistencies in the species identification processes. We report three sets of PCR primers developed to amplify the mtCOI region which can be used for genotyping 'MED', 'MEAM1', and 'IO' species and tested these primers on 91 MED, 35 MEAM1 and five IO individuals. PCR and sequencing of amplicons identified a total of 21, six and one haplotypes in MED, MEAM1 and IO respectively, of which six haplotypes were new to the B. tabaci database. These primer pairs enabled standardisation and robust molecular species identification via mtCOI screening of the targeted invasive cryptic species and will improve quarantine decisions. The use of this diagnostic tool could be extended to other species within the complex. This article is protected by copyright. All rights reserved.

  12. Aptamers as promising molecular recognition elements for diagnostics and therapeutics in the central nervous system.

    PubMed

    McConnell, Erin M; Holahan, Matthew R; DeRosa, Maria C

    2014-12-01

    Oligonucleotide aptamers are short, synthetic, single-stranded DNA or RNA able to recognize and bind to a multitude of targets ranging from small molecules to cells. Aptamers have emerged as valuable tools for fundamental research, clinical diagnosis, and therapy. Due to their small size, strong target affinity, lack of immunogenicity, and ease of chemical modification, aptamers are an attractive alternative to other molecular recognition elements, such as antibodies. Although it is a challenging environment, the central nervous system and related molecular targets present an exciting potential area for aptamer research. Aptamers hold promise for targeted drug delivery, diagnostics, and therapeutics. Here we review recent advances in aptamer research for neurotransmitter and neurotoxin targets, demyelinating disease and spinal cord injury, cerebrovascular disorders, pathologies related to protein aggregation (Alzheimer's, Parkinson's, and prions), brain cancer (glioblastomas and gliomas), and regulation of receptor function. Challenges and limitations posed by the blood brain barrier are described. Future perspectives for the application of aptamers to the central nervous system are also discussed.

  13. Express diagnostic of anaerobic infection and disbacteriosis by optical PNC method in clinical dentistry

    NASA Astrophysics Data System (ADS)

    Alexandrov, Michail T.; Koz'ma, Sergey U.; Taubinsky, Ilia M.; Masychev, Victor I.

    2000-11-01

    In this research a new way of express (real time) diagnostics of anaerobic infection and disbacteriosis is suggested. The express diagnostics of anaerobic infection allows to perform quick assessment of the injury microbiocenosis, the state of gastroenteric tract, the disbacteriosis presence and the degree of its development, to follow up dynamics of microflora variations in the process of medication treatment. The research were performed with optical PNC-method. The basic of the method is in registration of stimulated (secondary) radiations and registration of their space fields, which occur in the process of probing radiation interaction with biological tissues and their active elements. The process is called Photon- undulatory Nonlinear Conversion or in short PNC-process (PNC- method, PNC-diagnostic). The optimal diagnostic PNC-method developed here allows detecting the presence of anaerobic microflora directly at the bed of a patient. It makes possible to control the dynamic of patient rehabilitation process, providing strictly individual assessments.

  14. Hydroxymethyl phosphine compounds for use as diagnostic and therapeutic pharmaceuticals and method of making same

    DOEpatents

    Katti, Kattesh V.; Karra, Srinivasa Rao; Berning, Douglas E.; Smith, C. Jeffrey; Volkert, Wynn A.; Ketring, Alan R.

    2000-01-01

    A compound and method of making a compound for use as a diagnostic or therapeutic pharmaceutical comprises at least one functionalized hydroxyalkyl phosphine donor group and one or more sulfur or nitrogen donor and a metal combined with the ligand.

  15. Hydroxymethyl phosphine compounds for use as diagnostic and therapeutic pharmaceuticals and method of making same

    DOEpatents

    Katti, Kattesh V.; Karra, Srinivasa Rao; Berning, Douglas E.; Smith, C. Jeffrey; Volkert, Wynn A.; Ketring, Alan R.

    1999-01-01

    A compound and method of making a compound for use as a diagnostic or therapeutic pharmaceutical comprises at least one functionalized hydroxyalkyl phosphine donor group and one or more sulfur or nitrogen donor and a metal combined with the ligand.

  16. The agony of choice in dermatophyte diagnostics-performance of different molecular tests and culture in the detection of Trichophyton rubrum and Trichophyton interdigitale.

    PubMed

    Kupsch, C; Ohst, T; Pankewitz, F; Nenoff, P; Uhrlaß, S; Winter, I; Gräser, Y

    2016-08-01

    Dermatophytosis caused by dermatophytes of the genera Trichophyton and Microsporum belong to the most frequent mycoses worldwide. Molecular detection methods proved to be highly sensitive and enable rapid and accurate detection of dermatophyte species from clinical specimens. For the first time, we compare the performance of different molecular methods with each other and with conventional diagnostics in the detection of dermatophytoses caused by Trichophyton rubrum and Trichophyton interdigitale in clinical specimens (nail, skin and hair). The compared molecular methods comprise two already published PCR-ELISAs, a published quantitative RT-PCR as well as a newly developed PCR-ELISA targeting the internal transcribed spacer region. We investigated the sensitivity of the assays by analysing 375 clinical samples. In 148 specimens (39.5%) a positive result was gained in at least one of the four molecular tests or by culture, but the number of detected agents differed significantly between some of the assays. The most sensitive assay, a PCR-ELISA targeting a microsatellite region, detected 81 T. rubrum infections followed by an internal transcribed spacer PCR-ELISA (60), quantitative RT-PCR (52) and a topoisomerase II PCR-ELISA (51), whereas cultivation resulted in T. rubrum identification in 37 samples. The pros and cons of all four tests in routine diagnostics are discussed.

  17. The fate and future of patents on human genes and genetic diagnostic methods.

    PubMed

    Huys, Isabelle; Matthijs, Gert; Van Overwalle, Geertrui

    2012-05-18

    Since the 1970s, patents on human genes and genetic diagnostic methods have been granted under the assumption that they stimulate the development of diagnostic methods and therapeutic products. However, the principles and practices of patenting vary between jurisdictions. Do patent holders, researchers, clinicians and patients really benefit from this heterogeneous patent system? We discuss the problems that result from the current system and suggest how they might be solved by altering the way in which patents are granted and/or licensed.

  18. Gene dosage methods as diagnostic tools for the identification of chromosome abnormalities.

    PubMed

    Gouas, L; Goumy, C; Véronèse, L; Tchirkov, A; Vago, P

    2008-09-01

    Cytogenetics is the part of genetics that deals with chromosomes, particularly with numerical and structural chromosome abnormalities, and their implications in congenital or acquired genetic disorders. Standard karyotyping, successfully used for the last 50 years in investigating the chromosome etiology in patients with infertility, fetal abnormalities and congenital disorders, is constrained by the limits of microscopic resolution and is not suited for the detection of subtle chromosome abnormalities. The ability to detect submicroscopic chromosomal rearrangements that lead to copy-number changes has escalated progressively in recent years with the advent of molecular cytogenetic techniques. Here, we review various gene dosage methods such as FISH, PCR-based approaches (MLPA, QF-PCR, QMPSF and real time PCR), CGH and array-CGH, that can be used for the identification and delineation of copy-number changes for diagnostic purposes. Besides comparing their relative strength and weakness, we will discuss the impact that these detection methods have on our understanding of copy number variations in the human genome and their implications in genetic counseling.

  19. A promising diagnostic method: Terahertz pulsed imaging and spectroscopy

    PubMed Central

    Sun, Yiwen; Sy, Ming Yiu; Wang, Yi-Xiang J; Ahuja, Anil T; Zhang, Yuan-Ting; Pickwell-MacPherson, Emma

    2011-01-01

    The terahertz band lies between the microwave and infrared regions of the electromagnetic spectrum. This radiation has very low photon energy and thus it does not pose any ionization hazard for biological tissues. It is strongly attenuated by water and very sensitive to water content. Unique absorption spectra due to intermolecular vibrations in this region have been found in different biological materials. These unique features make terahertz imaging very attractive for medical applications in order to provide complimentary information to existing imaging techniques. There has been an increasing interest in terahertz imaging and spectroscopy of biologically related applications within the last few years and more and more terahertz spectra are being reported. This paper introduces terahertz technology and provides a short review of recent advances in terahertz imaging and spectroscopy techniques, and a number of applications such as molecular spectroscopy, tissue characterization and skin imaging are discussed. PMID:21512652

  20. Diagnostic methods and treatment modalities of dry eye conditions.

    PubMed

    Holly, F J

    1993-06-01

    One may view dry eye conditions as a group of diseases in which the ocular surface is adversely affected. Tear film instability invariably leads to some degree of cellular surface damage over the cornea and conjunctiva. In turn, ocular epitheliopathy may adversely affect tear film stability. The clinical presentation of the disease may not yield a clue as to its etiology. In recent years considerable progress was made both in the diagnosis and the treatment of the disease and promising studies are planned or are underway. The diagnostic techniques can be divided into four groups. The first is concerned with the clinical presentation. The second is concerned with the bulk properties of the aqueous tears including dynamic characteristics, composition, and colligative properties. The third is tear-film related and includes the film break-up time, evaporation rate, and lipid abnormality. The fourth is concerned with the ocular surface and includes vital staining, impression cytology, and surface microscopy. The most promising attempts are being made in the second group by attempting to elucidate the role of enzyme and enzyme activator activity and inhibitor contents as well as the tear protein profiles and correlating them with the specific disease states. The treatment modalities belong to three major groups aside from surgical intervention; the supplementation, preservation, and the stimulation of tears. The modern version of tear supplementation is expected to include the topical use of efficacious aqueous formulations that typically contain film stabilizing polymers, nutrients, and/or--in the future--biochemically active ingredients such as enzyme activators and inhibitors.

  1. Tokamak physics studies using x-ray diagnostic methods

    SciTech Connect

    Hill, K.W.; Bitter, M.; von Goeler, S.; Beiersdorfer, P.; Fredrickson, E.; Hsuan, H.; McGuire, K.; Sauthoff, N.R.; Sesnic, S.; Stevens, J.E.

    1987-03-01

    X-ray diagnostic measurements have been used in a number of experiments to improve our understanding of important tokamak physics issues. The impurity content in TFTR plasmas, its sources and control have been clarified through soft x-ray pulse-height analysis (PHA) measurements. The dependence of intrinsic impurity concentrations and Z/sub eff/ on electron density, plasma current, limiter material and conditioning, and neutral-beam power have shown that the limiter is an important source of metal impurities. Neoclassical-like impurity peaking following hydrogen pellet injection into Alcator C and a strong effect of impurities on sawtooth behavior were demonstrated by x-ray imaging (XIS) measurements. Rapid inward motion of impurities and continuation of m = 1 activity following an internal disruption were demonstrated with XIS measurements on PLT using injected aluminum to enhance the signals. Ion temperatures up to 12 keV and a toroidal plasma rotation velocity up to 6 x 10/sup 5/ m/s have been measured by an x-ray crystal spectrometer (XCS) with up to 13 MW of 85-keV neutral-beam injection in TFTR. Precise wavelengths and relative intensities of x-ray lines in several helium-like ions and neon-like ions of silver have been measured in TFTR and PLT by the XCS. The data help to identify the important excitation processes predicted in atomic physics. Wavelengths of n = 3 to 2 silver lines of interest for x-ray lasers were measured, and precise instrument calibration techniques were developed. Electron thermal conductivity and sawtooth dynamics have been studied through XIS measurements on TFTR of heat-pulse propagation and compound sawteeth. A non-Maxwellian electron distribution function has been measured, and evidence of the Parail-Pogutse instability identified by hard x-ray PHA measurements on PLT during lower-hybrid current-drive experiments.

  2. A novel diagnostic method for malaria using loop-mediated isothermal amplification (LAMP) and MinION™ nanopore sequencer.

    PubMed

    Imai, Kazuo; Tarumoto, Norihito; Misawa, Kazuhisa; Runtuwene, Lucky Ronald; Sakai, Jun; Hayashida, Kyoko; Eshita, Yuki; Maeda, Ryuichiro; Tuda, Josef; Murakami, Takashi; Maesaki, Shigefumi; Suzuki, Yutaka; Yamagishi, Junya; Maeda, Takuya

    2017-09-13

    A simple and accurate molecular diagnostic method for malaria is urgently needed due to the limitations of conventional microscopic examination. In this study, we demonstrate a new diagnostic procedure for human malaria using loop mediated isothermal amplification (LAMP) and the MinION™ nanopore sequencer. We generated specific LAMP primers targeting the 18S-rRNA gene of all five human Plasmodium species including two P. ovale subspecies (P. falciparum, P. vivax, P. ovale wallikeri, P. ovale curtisi, P. knowlesi and P. malariae) and examined human blood samples collected from 63 malaria patients in Indonesia. Additionally, we performed amplicon sequencing of our LAMP products using MinION™ nanopore sequencer to identify each Plasmodium species. Our LAMP method allowed amplification of all targeted 18S-rRNA genes of the reference plasmids with detection limits of 10-100 copies per reaction. Among the 63 clinical samples, 54 and 55 samples were positive by nested PCR and our LAMP method, respectively. Identification of the Plasmodium species by LAMP amplicon sequencing analysis using the MinION™ was consistent with the reference plasmid sequences and the results of nested PCR. Our diagnostic method combined with LAMP and MinION™ could become a simple and accurate tool for the identification of human Plasmodium species, even in resource-limited situations.

  3. Analizing Student Biology Education Misconception And Scientific Argumentation Ability Using Diagnostic Question Clusters (Dqcs) Of Molecular Genetic Concept

    NASA Astrophysics Data System (ADS)

    Nurlaila, L.; Sriyati, S.; Riandi

    2017-02-01

    The purpose of this research is to describe the profile of misconceptions and scientific argumentation ability using Diagnostic Question Cluster (DQCs) of molecular genetics concept. This research use descriptive research method and biology education students as a research subject. The Instrument that used in this research are DQCs, sheets interviews, observations, and field notes. The DQCs tested by writing and oral that used to analyze misconceptions and scientific argumentation ability. Sheets interviews, observations and field notes, are used to analyze the possible factors causing misconceptions and scientific argumentation ability. The results showed that misconception of molecular genetics are: DNA (23.75%), genes (18.75%) of chromosomes (15%) and protein synthesis (5.5%). The pattern of the highest misconceptions owned Misconception-Understand Partial. The average scientific argumentation ability is 55% and still categorized warrant (W). The pattern of the scientific argumentation abilities formed is level 2 to level 2 that consists of the arguments in the form of a claim with a counter claim that accompanied by data, collateral (warrant) or support (backing) but does not contain a disclaimer (rebutal).

  4. A Simplified Diagnostic Method for Elastomer Bond Durability

    NASA Technical Reports Server (NTRS)

    White, Paul

    2009-01-01

    A simplified method has been developed for determining bond durability under exposure to water or high humidity conditions. It uses a small number of test specimens with relatively short times of water exposure at elevated temperature. The method is also gravimetric; the only equipment being required is an oven, specimen jars, and a conventional laboratory balance.

  5. Laboratory methods for diagnostics of HIV infection and HIV-associated neuroinfections.

    PubMed

    Beno, Pavol; Kaiglova, Alzbeta; Samohyl, Martin

    2017-01-01

    HIV Infection resulting in AIDS remains serious global public health problem. In the fight with the global health problem plays a key role a simple, reliable and fast diagnostics. An important method in diagnostics is the identification and detection of viral capside p24 antigen levels. Fourth generation tests for the diagnostics of HIV infection simultaneously detect the presence of HIV antibodies and p24 antigen. Based on the monitoring of CD4 count, we can estimate the stage in which the infection is, and we can also suggest a therapeutic approach. Cerebral toxoplasmosis is the most common neurological opportunistic disease manifested in HIV infected patients. Cryptococcal meningitis is the second most common cause of the opportunistic neuroinfections. Despite of significant advances in the diagnostics and treatment of HIV infection, this disease is still unable to get completely under control. The future perspective in HIV diagnostics are biosensors.

  6. Acanthamoeba keratitis: improving the Scottish diagnostic service for the rapid molecular detection of Acanthamoeba species.

    PubMed

    Alexander, Claire Low; Coyne, Michael; Jones, Brian; Anijeet, Deepa

    2015-07-01

    Acanthamoeba species are responsible for causing the potentially sight-threatening condition, Acanthamoeba keratitis, which is commonly associated with contact lens use. In this report, we highlight the challenges faced using conventional laboratory identification methods to identify this often under-reported pathogen, and discuss the reasons for introducing the first national service in Scotland for the rapid and sensitive molecular identification of Acanthamoeba species. By comparing culture and molecular testing data from a total of 63 patients (n = 80 samples) throughout Scotland presenting with ocular eye disease, we describe the improvement in detection rates where an additional four positive cases were identified using a molecular assay versus culture. The testing of a further ten patients by confocal imaging is also presented. This report emphasizes the importance of continuing to improve clinical laboratory services to ensure a prompt, correct diagnosis and better prognosis, in addition to raising awareness of this potentially debilitating opportunistic pathogen.

  7. Mapping the different methods adopted for diagnostic imaging instruction at medical schools in Brazil

    PubMed Central

    Chojniak, Rubens; Carneiro, Dominique Piacenti; Moterani, Gustavo Simonetto Peres; Duarte, Ivone da Silva; Bitencourt, Almir Galvão Vieira; Muglia, Valdair Francisco; D'Ippolito, Giuseppe

    2017-01-01

    Objective To map the different methods for diagnostic imaging instruction at medical schools in Brazil. Materials and Methods In this cross-sectional study, a questionnaire was sent to each of the coordinators of 178 Brazilian medical schools. The following characteristics were assessed: teaching model; total course hours; infrastructure; numbers of students and professionals involved; themes addressed; diagnostic imaging modalities covered; and education policies related to diagnostic imaging. Results Of the 178 questionnaires sent, 45 (25.3%) were completed and returned. Of those 45 responses, 17 (37.8%) were from public medical schools, whereas 28 (62.2%) were from private medical schools. Among the 45 medical schools evaluated, the method of diagnostic imaging instruction was modular at 21 (46.7%), classic (independent discipline) at 13 (28.9%), hybrid (classical and modular) at 9 (20.0%), and none of the preceding at 3 (6.7%). Diagnostic imaging is part of the formal curriculum at 36 (80.0%) of the schools, an elective course at 3 (6.7%), and included within another modality at 6 (13.3%). Professors involved in diagnostic imaging teaching are radiologists at 43 (95.5%) of the institutions. Conclusion The survey showed that medical courses in Brazil tend to offer diagnostic imaging instruction in courses that include other content and at different time points during the course. Radiologists are extensively involved in undergraduate medical education, regardless of the teaching methodology employed at the institution. PMID:28298730

  8. Propulsion Diagnostic Method Evaluation Strategy (ProDiMES) User's Guide

    NASA Technical Reports Server (NTRS)

    Simon, Donald L.

    2010-01-01

    This report is a User's Guide for the Propulsion Diagnostic Method Evaluation Strategy (ProDiMES). ProDiMES is a standard benchmarking problem and a set of evaluation metrics to enable the comparison of candidate aircraft engine gas path diagnostic methods. This Matlab (The Mathworks, Inc.) based software tool enables users to independently develop and evaluate diagnostic methods. Additionally, a set of blind test case data is also distributed as part of the software. This will enable the side-by-side comparison of diagnostic approaches developed by multiple users. The Users Guide describes the various components of ProDiMES, and provides instructions for the installation and operation of the tool.

  9. Solving the molecular diagnostic testing conundrum for Mendelian disorders in the era of next-generation sequencing: single-gene, gene panel, or exome/genome sequencing.

    PubMed

    Xue, Yuan; Ankala, Arunkanth; Wilcox, William R; Hegde, Madhuri R

    2015-06-01

    Next-generation sequencing is changing the paradigm of clinical genetic testing. Today there are numerous molecular tests available, including single-gene tests, gene panels, and exome sequencing or genome sequencing. As a result, ordering physicians face the conundrum of selecting the best diagnostic tool for their patients with genetic conditions. Single-gene testing is often most appropriate for conditions with distinctive clinical features and minimal locus heterogeneity. Next-generation sequencing-based gene panel testing, which can be complemented with array comparative genomic hybridization and other ancillary methods, provides a comprehensive and feasible approach for heterogeneous disorders. Exome sequencing and genome sequencing have the advantage of being unbiased regarding what set of genes is analyzed, enabling parallel interrogation of most of the genes in the human genome. However, current limitations of next-generation sequencing technology and our variant interpretation capabilities caution us against offering exome sequencing or genome sequencing as either stand-alone or first-choice diagnostic approaches. A growing interest in personalized medicine calls for the application of genome sequencing in clinical diagnostics, but major challenges must be addressed before its full potential can be realized. Here, we propose a testing algorithm to help clinicians opt for the most appropriate molecular diagnostic tool for each scenario.

  10. Using comparative genomics to develop a molecular diagnostic for the identification of an emerging pest Drosophila suzukii.

    PubMed

    Murphy, K A; Unruh, T R; Zhou, L M; Zalom, F G; Shearer, P W; Beers, E H; Walton, V M; Miller, B; Chiu, J C

    2015-06-01

    Drosophila suzukii (Spotted Wing Drosophila) has recently become a serious invasive pest of fruit crops in the USA, Canada, and Europe, leading to substantial economic losses. D. suzukii is a direct pest, ovipositing directly into ripe or ripening fruits; in contrast, other Drosophilids utilize decaying or blemished fruits and are nuisance pests at worst. Immature stages of D. suzukii are difficult to differentiate from other Drosophilids, posing problems for research and for meeting quarantine restrictions designed to prevent the spread of this pest in fruit exports. Here we used a combined phylogenetic and bioinformatic approach to discover genetic markers suitable for a species diagnostic protocol of this agricultural pest. We describe a molecular diagnostic for rapid identification of single D. suzukii larva using multiplex polymerase chain reaction. Our molecular diagnostic was validated using nine different species of Drosophila for specificity and 19 populations of D. suzukii from different geographical regions to ensure utility within species.

  11. Combat-Related Pythium aphanidermatum Invasive Wound Infection: Case Report and Discussion of Utility of Molecular Diagnostics

    PubMed Central

    Murray, Clinton K.; Driscoll, Ian R.; Wickes, Brian L.; Wiederhold, Nathan; Sutton, Deanna A.; Sanders, Carmita; Mende, Katrin; Enniss, Brent; Feig, James; Ganesan, Anuradha; Rini, Elizabeth A.; Vento, Todd J.

    2015-01-01

    We describe a 22-year-old soldier with 19% total body surface area burns, polytrauma, and sequence- and culture-confirmed Pythium aphanidermatum wound infection. Antemortem histopathology suggested disseminated Pythium infection, including brain involvement; however, postmortem PCR revealed Cunninghamella elegans, Lichtheimia corymbifera, and Saksenaea vasiformis coinfection. The utility of molecular diagnostics in invasive fungal infections is discussed. PMID:25832301

  12. Using next-generation sequencing to develop molecular diagnostics for Pseudoperonospora cubensis, the cucurbit downy mildew pathogen

    USDA-ARS?s Scientific Manuscript database

    Advances in Next Generation Sequencing (NGS) allow for rapid development of genomics resources needed to generate molecular diagnostics assays for infectious agents. NGS approaches are particularly helpful for organisms that cannot be cultured, such as the downy mildew pathogens, a group of biotrop...

  13. DNA barcodes and molecular diagnostics to distinguish an introduced and native Laricobius (Coleoptera: Derodontidae) species in eastern North America

    Treesearch

    G.A. Davis; N.P. Havill; Z.N. Adelman; A. Caccone; L.T. Kok; S.M. Salom

    2011-01-01

    Molecular diagnostics based on DNA barcodes can be powerful identification tools in the absence of distinctive morphological characters for distinguishing between closely related species. A specific example is distinguishing the endemic species Laricobius rubidus from Laricobius nigrinus, a biological control agent of hemlock...

  14. Molecular phylogenetic analysis of Enterobius vermicularis and development of an 18S ribosomal DNA-targeted diagnostic PCR.

    PubMed

    Zelck, Ulrike E; Bialek, Ralf; Weiss, Michael

    2011-04-01

    We genetically characterized pinworms obtained from 37 children from different regions of Germany and established new species-specific molecular diagnostic tools. No ribosomal DNA diversity was found; the phylogenetic position of Enterobius vermicularis within the Oxyurida order and its close relationship to the Ascaridida and Spirurida orders was confirmed.

  15. Molecular Phylogenetic Analysis of Enterobius vermicularis and Development of an 18S Ribosomal DNA-Targeted Diagnostic PCR▿

    PubMed Central

    Zelck, Ulrike E.; Bialek, Ralf; Weiß, Michael

    2011-01-01

    We genetically characterized pinworms obtained from 37 children from different regions of Germany and established new species-specific molecular diagnostic tools. No ribosomal DNA diversity was found; the phylogenetic position of Enterobius vermicularis within the Oxyurida order and its close relationship to the Ascaridida and Spirurida orders was confirmed. PMID:21248085

  16. Combat-Related Pythium aphanidermatum Invasive Wound Infection: Case Report and Discussion of Utility of Molecular Diagnostics.

    PubMed

    Farmer, Aaron R; Murray, Clinton K; Driscoll, Ian R; Wickes, Brian L; Wiederhold, Nathan; Sutton, Deanna A; Sanders, Carmita; Mende, Katrin; Enniss, Brent; Feig, James; Ganesan, Anuradha; Rini, Elizabeth A; Vento, Todd J

    2015-06-01

    We describe a 22-year-old soldier with 19% total body surface area burns, polytrauma, and sequence- and culture-confirmed Pythium aphanidermatum wound infection. Antemortem histopathology suggested disseminated Pythium infection, including brain involvement; however, postmortem PCR revealed Cunninghamella elegans, Lichtheimia corymbifera, and Saksenaea vasiformis coinfection. The utility of molecular diagnostics in invasive fungal infections is discussed.

  17. Analysis method for Thomson scattering diagnostics in GAMMA 10/PDX

    NASA Astrophysics Data System (ADS)

    Ohta, K.; Yoshikawa, M.; Yasuhara, R.; Chikatsu, M.; Shima, Y.; Kohagura, J.; Sakamoto, M.; Nakasima, Y.; Imai, T.; Ichimura, M.; Yamada, I.; Funaba, H.; Minami, T.

    2016-11-01

    We have developed an analysis method to improve the accuracies of electron temperature measurement by employing a fitting technique for the raw Thomson scattering (TS) signals. Least square fitting of the raw TS signals enabled reduction of the error in the electron temperature measurement. We applied the analysis method to a multi-pass (MP) TS system. Because the interval between the MPTS signals is very short, it is difficult to separately analyze each Thomson scattering signal intensity by using the raw signals. We used the fitting method to obtain the original TS scattering signals from the measured raw MPTS signals to obtain the electron temperatures in each pass.

  18. Molecular signature of salivary gland tumors: potential use as diagnostic and prognostic marker.

    PubMed

    Fonseca, Felipe Paiva; Sena Filho, Marcondes; Altemani, Albina; Speight, Paul M; Vargas, Pablo Agustin

    2016-02-01

    Salivary gland tumors are a highly heterogeneous group of lesions with diverse microscopic appearances and variable clinical behavior. The use of clinical and histological parameters to predict patient prognosis and survival rates has been of limited utility, and the search for new biomarkers that could not only aid in a better understanding of their pathogenesis but also be reliable auxiliaries for prognostic determination and useful diagnostic tools has been performed in the last decades with very exciting results. Hence, gene rearrangements such as CRTC1-MAML2 in mucoepidermoid carcinomas have shown excellent specificity, and more than that, it has been strongly correlated with low-grade tumors and consequently with an increased survival rate and better prognosis of patients affected by neoplasms carrying this translocation. Moreover, MYB-NFIB and EWSR1-ATF1 gene fusions were shown to be specifically found in cases of adenoid cystic carcinomas and hyalinizing clear cell carcinomas, respectively, in the context of salivary gland tumors, becoming reliable diagnostic tools for these entities and potential therapeutic targets for future therapeutic protocols. Finally, the identification of ETV6-NTRK3 in cases previously diagnosed as uncommon acinic cell carcinomas, cystadenocarcinomas, and adenocarcinomas not otherwise specified led to the characterization of a completely new and now widely accepted entity, including, therefore, mammary analogue secretory carcinoma in the list of well-recognized salivary gland carcinomas. Thus, further molecular investigations of salivary gland tumors are warranted, and the recognition of other genetic abnormalities can lead to the acknowledgment of new entities and the acquirement of reliable biomarkers.

  19. Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing

    PubMed Central

    Yu, Stephanie C. Y.; Chan, K. C. Allen; Zheng, Yama W. L.; Jiang, Peiyong; Liao, Gary J. W.; Sun, Hao; Akolekar, Ranjit; Leung, Tak Y.; Go, Attie T. J. I.; van Vugt, John M. G.; Minekawa, Ryoko; Oudejans, Cees B. M.; Nicolaides, Kypros H.; Chiu, Rossa W. K.; Lo, Y. M. Dennis

    2014-01-01

    Noninvasive prenatal testing using fetal DNA in maternal plasma is an actively researched area. The current generation of tests using massively parallel sequencing is based on counting plasma DNA sequences originating from different genomic regions. In this study, we explored a different approach that is based on the use of DNA fragment size as a diagnostic parameter. This approach is dependent on the fact that circulating fetal DNA molecules are generally shorter than the corresponding maternal DNA molecules. First, we performed plasma DNA size analysis using paired-end massively parallel sequencing and microchip-based capillary electrophoresis. We demonstrated that the fetal DNA fraction in maternal plasma could be deduced from the overall size distribution of maternal plasma DNA. The fetal DNA fraction is a critical parameter affecting the accuracy of noninvasive prenatal testing using maternal plasma DNA. Second, we showed that fetal chromosomal aneuploidy could be detected by observing an aberrant proportion of short fragments from an aneuploid chromosome in the paired-end sequencing data. Using this approach, we detected fetal trisomy 21 and trisomy 18 with 100% sensitivity (T21: 36/36; T18: 27/27) and 100% specificity (non-T21: 88/88; non-T18: 97/97). For trisomy 13, the sensitivity and specificity were 95.2% (20/21) and 99% (102/103), respectively. For monosomy X, the sensitivity and specificity were both 100% (10/10 and 8/8). Thus, this study establishes the principle of size-based molecular diagnostics using plasma DNA. This approach has potential applications beyond noninvasive prenatal testing to areas such as oncology and transplantation monitoring. PMID:24843150

  20. Molecular diagnostic for boll weevil (Coleoptera: Curculionidae) based on amplification of three species-specific microsatellites.

    PubMed

    Kim, Kyung Seok; Szendrei, Zsofia; Rodriguez-Saona, Cesar; Mulder, Phillip G; Sappington, Thomas W

    2009-04-01

    The boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), is a serious pest of cultivated cotton, Gossypium hirsutum L., in the Americas, and reinfestation of zones from which they have been eradicated is of perpetual concern. Extensive arrays of pheromone traps monitor for reintroductions, but occasionally the traps collect nontarget weevils that can be misidentified by scouts. For example, the congeneric pepper weevil, Anthonomus eugenii Cano, and other superficially similar weevils are attracted to components of the boll weevil lure or trap color. Although morphologically distinguishable by trained personnel, the potential for misidentification is compounded when captured weevils are dismembered or partially consumed by ants or ground beetles that sometimes feed on them in the traps. Because misidentification can have expensive consequences, a molecular diagnostic tool would be of great value to eradication managers. We demonstrate that a cocktail of three primer pairs in a single polymerase chain reaction (PCR) amplify species-specific microsatellites that unambiguously distinguish the boll weevil from three other weevil species tested, including pepper weevil; cranberry weevil, Anthonomus eugenii musculus Say; and pecan weevil, Curculio caryae Horn. However, it does not distinguish the boll weevil from the subspecific "thurberia" weevil. A universal internal transcribed spacer primer pair included in the cocktail cross-amplifies DNA from all species, serving as a positive control. Furthermore, the diagnostic primers amplified the target microsatellites from various boll weevil adult body parts, indicating that the PCR technology using the primer cocktail is sensitive enough to positively identify a boll weevil even when the body is partly degraded.

  1. Size-based molecular diagnostics using plasma DNA for noninvasive prenatal testing.

    PubMed

    Yu, Stephanie C Y; Chan, K C Allen; Zheng, Yama W L; Jiang, Peiyong; Liao, Gary J W; Sun, Hao; Akolekar, Ranjit; Leung, Tak Y; Go, Attie T J I; van Vugt, John M G; Minekawa, Ryoko; Oudejans, Cees B M; Nicolaides, Kypros H; Chiu, Rossa W K; Lo, Y M Dennis

    2014-06-10

    Noninvasive prenatal testing using fetal DNA in maternal plasma is an actively researched area. The current generation of tests using massively parallel sequencing is based on counting plasma DNA sequences originating from different genomic regions. In this study, we explored a different approach that is based on the use of DNA fragment size as a diagnostic parameter. This approach is dependent on the fact that circulating fetal DNA molecules are generally shorter than the corresponding maternal DNA molecules. First, we performed plasma DNA size analysis using paired-end massively parallel sequencing and microchip-based capillary electrophoresis. We demonstrated that the fetal DNA fraction in maternal plasma could be deduced from the overall size distribution of maternal plasma DNA. The fetal DNA fraction is a critical parameter affecting the accuracy of noninvasive prenatal testing using maternal plasma DNA. Second, we showed that fetal chromosomal aneuploidy could be detected by observing an aberrant proportion of short fragments from an aneuploid chromosome in the paired-end sequencing data. Using this approach, we detected fetal trisomy 21 and trisomy 18 with 100% sensitivity (T21: 36/36; T18: 27/27) and 100% specificity (non-T21: 88/88; non-T18: 97/97). For trisomy 13, the sensitivity and specificity were 95.2% (20/21) and 99% (102/103), respectively. For monosomy X, the sensitivity and specificity were both 100% (10/10 and 8/8). Thus, this study establishes the principle of size-based molecular diagnostics using plasma DNA. This approach has potential applications beyond noninvasive prenatal testing to areas such as oncology and transplantation monitoring.

  2. CFTR mutations spectrum and the efficiency of molecular diagnostics in Polish cystic fibrosis patients.

    PubMed

    Ziętkiewicz, Ewa; Rutkiewicz, Ewa; Pogorzelski, Andrzej; Klimek, Barbara; Voelkel, Katarzyna; Witt, Michał

    2014-01-01

    Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane regulator gene (CFTR). In light of the strong allelic heterogeneity and regional specificity of the mutation spectrum, the strategy of molecular diagnostics and counseling in CF requires genetic tests to reflect the frequency profile characteristic for a given population. The goal of the study was to provide an updated comprehensive estimation of the distribution of CFTR mutations in Polish CF patients and to assess the effectiveness of INNOLiPA_CFTR tests in Polish population. The analyzed cohort consisted of 738 patients with the clinically confirmed CF diagnosis, prescreened for molecular defects using INNOLiPA_CFTR panels from Innogenetics. A combined efficiency of INNOLiPA CFTR_19 and CFTR_17_TnUpdate tests was 75.5%; both mutations were detected in 68.2%, and one mutation in 14.8% of the affected individuals. The group composed of all the patients with only one or with no mutation detected (109 and 126 individuals, respectively) was analyzed further using a mutation screening approach, i.e. SSCP/HD (single strand conformational polymorphism/heteroduplex) analysis of PCR products followed by sequencing of the coding sequence. As a result, 53 more mutations were found in 97 patients. The overall efficiency of the CF allele detection was 82.5% (7.0% increase compared to INNOLiPA tests alone). The distribution of the most frequent mutations in Poland was assessed. Most of the mutations repetitively found in Polish patients had been previously described in other European populations. The most frequent mutated allele, F508del, represented 54.5% of Polish CF chromosomes. Another eight mutations had frequencies over 1%, 24 had frequencies between 1 and 0.1%; c.2052-2053insA and c.3468+2_3468+3insT were the most frequent non-INNOLiPA mutations. Mutation distribution described herein is also relevant to the Polish diaspora. Our study also demonstrates that the reported efficiency of

  3. CFTR Mutations Spectrum and the Efficiency of Molecular Diagnostics in Polish Cystic Fibrosis Patients

    PubMed Central

    Ziętkiewicz, Ewa; Rutkiewicz, Ewa; Pogorzelski, Andrzej; Klimek, Barbara; Voelkel, Katarzyna; Witt, Michał

    2014-01-01

    Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane regulator gene (CFTR). In light of the strong allelic heterogeneity and regional specificity of the mutation spectrum, the strategy of molecular diagnostics and counseling in CF requires genetic tests to reflect the frequency profile characteristic for a given population. The goal of the study was to provide an updated comprehensive estimation of the distribution of CFTR mutations in Polish CF patients and to assess the effectiveness of INNOLiPA_CFTR tests in Polish population. The analyzed cohort consisted of 738 patients with the clinically confirmed CF diagnosis, prescreened for molecular defects using INNOLiPA_CFTR panels from Innogenetics. A combined efficiency of INNOLiPA CFTR_19 and CFTR_17_TnUpdate tests was 75.5%; both mutations were detected in 68.2%, and one mutation in 14.8% of the affected individuals. The group composed of all the patients with only one or with no mutation detected (109 and 126 individuals, respectively) was analyzed further using a mutation screening approach, i.e. SSCP/HD (single strand conformational polymorphism/heteroduplex) analysis of PCR products followed by sequencing of the coding sequence. As a result, 53 more mutations were found in 97 patients. The overall efficiency of the CF allele detection was 82.5% (7.0% increase compared to INNOLiPA tests alone). The distribution of the most frequent mutations in Poland was assessed. Most of the mutations repetitively found in Polish patients had been previously described in other European populations. The most frequent mutated allele, F508del, represented 54.5% of Polish CF chromosomes. Another eight mutations had frequencies over 1%, 24 had frequencies between 1 and 0.1%; c.2052-2053insA and c.3468+2_3468+3insT were the most frequent non-INNOLiPA mutations. Mutation distribution described herein is also relevant to the Polish diaspora. Our study also demonstrates that the reported efficiency of

  4. Biomarkers and molecular analysis to improve bloodstream infection diagnostics in an emergency care unit.

    PubMed

    Loonen, Anne J M; de Jager, Cornelis P C; Tosserams, Janna; Kusters, Ron; Hilbink, Mirrian; Wever, Peter C; van den Brule, Adriaan J C

    2014-01-01

    subsequent pathogen identification using molecular diagnostics.

  5. Biomarkers and Molecular Analysis to Improve Bloodstream Infection Diagnostics in an Emergency Care Unit

    PubMed Central

    Loonen, Anne J. M.; de Jager, Cornelis P. C.; Tosserams, Janna; Kusters, Ron; Hilbink, Mirrian; Wever, Peter C.; van den Brule, Adriaan J. C.

    2014-01-01

    subsequent pathogen identification using molecular diagnostics. PMID:24475269

  6. Mapping the different methods adopted for diagnostic imaging instruction at medical schools in Brazil.

    PubMed

    Chojniak, Rubens; Carneiro, Dominique Piacenti; Moterani, Gustavo Simonetto Peres; Duarte, Ivone da Silva; Bitencourt, Almir Galvão Vieira; Muglia, Valdair Francisco; D'Ippolito, Giuseppe

    2017-01-01

    To map the different methods for diagnostic imaging instruction at medical schools in Brazil. In this cross-sectional study, a questionnaire was sent to each of the coordinators of 178 Brazilian medical schools. The following characteristics were assessed: teaching model; total course hours; infrastructure; numbers of students and professionals involved; themes addressed; diagnostic imaging modalities covered; and education policies related to diagnostic imaging. Of the 178 questionnaires sent, 45 (25.3%) were completed and returned. Of those 45 responses, 17 (37.8%) were from public medical schools, whereas 28 (62.2%) were from private medical schools. Among the 45 medical schools evaluated, the method of diagnostic imaging instruction was modular at 21 (46.7%), classic (independent discipline) at 13 (28.9%), hybrid (classical and modular) at 9 (20.0%), and none of the preceding at 3 (6.7%). Diagnostic imaging is part of the formal curriculum at 36 (80.0%) of the schools, an elective course at 3 (6.7%), and included within another modality at 6 (13.3%). Professors involved in diagnostic imaging teaching are radiologists at 43 (95.5%) of the institutions. The survey showed that medical courses in Brazil tend to offer diagnostic imaging instruction in courses that include other content and at different time points during the course. Radiologists are extensively involved in undergraduate medical education, regardless of the teaching methodology employed at the institution.

  7. Evaluation of the Effect of Diagnostic Molecular Testing on the Surgical Decision-Making Process for Patients With Thyroid Nodules.

    PubMed

    Noureldine, Salem I; Najafian, Alireza; Aragon Han, Patricia; Olson, Matthew T; Genther, Dane J; Schneider, Eric B; Prescott, Jason D; Agrawal, Nishant; Mathur, Aarti; Zeiger, Martha A; Tufano, Ralph P

    2016-07-01

    Diagnostic molecular testing is used in the workup of thyroid nodules. While these tests appear to be promising in more definitively assigning a risk of malignancy, their effect on surgical decision making has yet to be demonstrated. To investigate the effect of diagnostic molecular profiling of thyroid nodules on the surgical decision-making process. A surgical management algorithm was developed and published after peer review that incorporated individual Bethesda System for Reporting Thyroid Cytopathology classifications with clinical, laboratory, and radiological results. This algorithm was created to formalize the decision-making process selected herein in managing patients with thyroid nodules. Between April 1, 2014, and March 31, 2015, a prospective study of patients who had undergone diagnostic molecular testing of a thyroid nodule before being seen for surgical consultation was performed. The recommended management undertaken by the surgeon was then prospectively compared with the corresponding one in the algorithm. Patients with thyroid nodules who did not undergo molecular testing and were seen for surgical consultation during the same period served as a control group. All pertinent treatment options were presented to each patient, and any deviation from the algorithm was recorded prospectively. To evaluate the appropriateness of any change (deviation) in management, the surgical histopathology diagnosis was correlated with the surgery performed. The study cohort comprised 140 patients who underwent molecular testing. Their mean (SD) age was 50.3 (14.6) years, and 75.0% (105 of 140) were female. Over a 1-year period, 20.3% (140 of 688) had undergone diagnostic molecular testing before surgical consultation, and 79.7% (548 of 688) had not undergone molecular testing. The surgical management deviated from the treatment algorithm in 12.9% (18 of 140) with molecular testing and in 10.2% (56 of 548) without molecular testing (P = .37). In the group with

  8. The SUCCESS model for laboratory performance and execution of rapid molecular diagnostics in patients with sepsis.

    PubMed

    Dekmezian, Mhair; Beal, Stacy G; Damashek, Mary Jane; Benavides, Raul; Dhiman, Neelam

    2015-04-01

    Successful performance and execution of rapid diagnostics in a clinical laboratory hinges heavily on careful validation, accurate and timely communication of results, and real-time quality monitoring. Laboratories must develop strategies to integrate diagnostics with stewardship and evidence-based clinical practice guidelines. We present a collaborative SUCCESS model for execution and monitoring of rapid sepsis diagnostics to facilitate timely treatment. Six months after execution of the Verigene Gram-Positive Blood Culture (BC-GP) and the AdvanDx PNA-FISH assays, data were collected on 579 and 28 episodes of bacteremia and fungemia, respectively. Clinical testing was executed using a SUCCESS model comprising the following components: stewardship, utilization of resources, core strategies, concierge services, education, support, and surveillance. Stewardship needs were identified by evaluating the specialty services benefiting from new testing. Utilization of resources was optimized by reviewing current treatment strategies and antibiogram and formulary options. Core strategies consisted of input from infectious disease leadership, pharmacy, and laboratory staff. Concierge services included automated Micro-eUpdate and physician-friendly actionable reports. Education modules were user-specific, and support was provided through a dedicated 24/7 microbiology hotline. Surveillance was performed by daily audit by the director. Using the SUCCESS model, the turnaround time for the detailed report with actionable guidelines to the physician was ∼3 hours from the time of culture positivity. The overall correlation between rapid methods and culture was 94% (546/579). Discrepant results were predominantly contaminants such as a coagulase-negative staphylococci or viridans streptococci in mixed cultures. SUCCESS is a cost-effective and easily adaptable model for clinical laboratories with limited stewardship resources.

  9. Optical methods for diagnostic of cell-tissue grafts

    NASA Astrophysics Data System (ADS)

    Timchenko, P. E.; Timchenko, E. V.; Volova, L. T.; Boltovskaya, V. V.; Zherdeva, L. A.; Belousov, N. V.; Pershutkina, S. V.

    2015-08-01

    In this work the results of cell-tissue grafts research with a complex of optical methods - confocal fluorescent microscopy and Raman spectroscopy are presented. It was established that coefficient M scatter is related to irregularity of demineralization process. It was microscopically shown that the quantity of integrated cells into these types of transplants amounts to 20% of its surface.

  10. Restrictive Stochastic Item Selection Methods in Cognitive Diagnostic Computerized Adaptive Testing

    ERIC Educational Resources Information Center

    Wang, Chun; Chang, Hua-Hua; Huebner, Alan

    2011-01-01

    This paper proposes two new item selection methods for cognitive diagnostic computerized adaptive testing: the restrictive progressive method and the restrictive threshold method. They are built upon the posterior weighted Kullback-Leibler (KL) information index but include additional stochastic components either in the item selection index or in…

  11. Simple fractal method of assessment of histological images for application in medical diagnostics

    PubMed Central

    2010-01-01

    We propose new method of assessment of histological images for medical diagnostics. 2-D image is preprocessed to form 1-D landscapes or 1-D signature of the image contour and then their complexity is analyzed using Higuchi's fractal dimension method. The method may have broad medical application, from choosing implant materials to differentiation between benign masses and malignant breast tumors. PMID:21134258

  12. Restrictive Stochastic Item Selection Methods in Cognitive Diagnostic Computerized Adaptive Testing

    ERIC Educational Resources Information Center

    Wang, Chun; Chang, Hua-Hua; Huebner, Alan

    2011-01-01

    This paper proposes two new item selection methods for cognitive diagnostic computerized adaptive testing: the restrictive progressive method and the restrictive threshold method. They are built upon the posterior weighted Kullback-Leibler (KL) information index but include additional stochastic components either in the item selection index or in…

  13. Calreticulin Mutations in Myeloproliferative Neoplasms: Comparison of Three Diagnostic Methods

    PubMed Central

    Park, Ji-Hye; Sevin, Margaux; Ramla, Selim; Truffot, Aurélie; Verrier, Tiffany; Bouchot, Dominique; Courtois, Martine; Bas, Mathilde; Benali, Sonia; Bailly, François; Favre, Bernardine; Guy, Julien; Martin, Laurent; Maynadié, Marc; Carillo, Serge; Girodon, François

    2015-01-01

    Calreticulin (CALR) mutations have recently been reported in 70–84% of JAK2V617F-negative myeloproliferative neoplasms (MPN), and this detection has become necessary to improve the diagnosis of MPN. In a large single-centre cohort of 298 patients suffering from Essential Thrombocythemia (ET), the JAK2V617F, CALR and MPL mutations were noted in 179 (60%), 56 (18.5%) and 13 (4.5%) respectively. For the detection of the CALR mutations, three methods were compared in parallel: high-resolution melting-curve analysis (HRM), product-sizing analysis and Sanger sequencing. The sensitivity for the HRM, product-sizing analysis and Sanger sequencing was 96.4%, 98.2% and 89.3% respectively, whereas the specificity was 96.3%, 100% and 100%. In our cohort, the product-sizing analysis was the most sensitive method and was the easiest to interpret, while the HRM was sometimes difficult to interpret. In contrast, when large series of samples were tested, HRM provided results more quickly than did the other methods, which required more time. Finally, the sequencing method, which is the reference method, had the lowest sensitivity but can be used to describe the type of mutation precisely. Altogether, our results suggest that in routine laboratory practice, product-sizing analysis is globally similar to HRM for the detection of CALR mutations, and that both may be used as first-line screening tests. If the results are positive, Sanger sequencing can be used to confirm the mutation and to determine its type. Product-sizing analysis provides sensitive and specific results, moreover, with the quantitative measurement of CALR, which might be useful to monitor specific treatments. PMID:26501981

  14. Rabies vaccine. Developments employing molecular biology methods.

    PubMed

    Paolazzi, C C; Pérez, O; De Filippo, J

    1999-04-01

    Rabies vaccines produced by means of molecular biology are described. Recombinant vaccines employing either viruses as vectors (vaccinia, adenovirus, poxvirus, baculovirus, plant viruses) or a plasmid vector carrying the rabies virus glycoprotein gene are discussed. Synthetic peptide technology directed to rabies vaccine production is also presented.

  15. Endorsing good quality assurance practices in molecular pathology: risks and recommendations for diagnostic laboratories and external quality assessment providers.

    PubMed

    Tembuyser, Lien; Dequeker, Elisabeth M C

    2016-01-01

    Quality assurance is an indispensable element in a molecular diagnostic laboratory. The ultimate goal is to warrant patient safety. Several risks that can compromise high quality procedures are at stake, from sample collection to the test performed by the laboratory, the reporting of test results to clinicians, and the organization of effective external quality assessment schemes. Quality assurance should therefore be safeguarded at each level and should imply a holistic multidisciplinary approach. This review aims to provide an overview of good quality assurance practices and discusses certain risks and recommendations to promote and improve quality assurance for both diagnostic laboratories and for external quality assessment providers. The number of molecular targets is continuously rising, and new technologies are evolving. As this poses challenges for clinical implementation and increases the demand for external quality assessment, the formation of an international association for improving quality assurance in molecular pathology is called for.

  16. Narrowing of the Diagnostic Gap of Acute Gastroenteritis in Children 0-6 Years of Age Using a Combination of Classical and Molecular Techniques, Delivers Challenges in Syndromic Approach Diagnostics.

    PubMed

    Steyer, Andrej; Jevšnik, Monika; Petrovec, Miroslav; Pokorn, Marko; Grosek, Štefan; Fratnik Steyer, Adela; Šoba, Barbara; Uršič, Tina; Cerar Kišek, Tjaša; Kolenc, Marko; Trkov, Marija; Šparl, Petra; Duraisamy, Raja; Lipkin, Ian W; Terzić, Sara; Kolnik, Mojca; Mrvič, Tatjana; Kapoor, Amit; Strle, Franc

    2016-09-01

    Twenty-five percent to 50% of acute gastroenteritis (AGE) cases remain etiologically undiagnosed. Our main aim was to determine the most appropriate list of enteric pathogens to be included in the daily diagnostics scheme of AGE, ensuring the lowest possible diagnostic gap. Two hundred ninety seven children ≤6 years of age, admitted to hospital in Slovenia, October 2011 to October 2012, with AGE, and 88 ≤6 years old healthy children were included in the study. A broad spectrum of enteric pathogens was targeted with molecular methods, including 8 viruses, 6 bacteria and 2 parasites. At least one enteric pathogen was detected in 91.2% of cases with AGE and 27.3% of controls. Viruses were the most prevalent (82.5% and 15.9%), followed by bacteria (27.3% and 10.2%) and parasites (3.0% and 1.1%) in cases and controls, respectively. A high proportion (41.8%) of mixed infections was observed in the cases. For cases with undetermined etiology (8.8%), stool samples were analyzed with next generation sequencing, and a potential viral pathogen was detected in 17 additional samples (5.8%). Our study suggests that tests for rotaviruses, noroviruses genogroup II, adenoviruses 40/41, astroviruses, Campylobacter spp. and Salmonella sp. should be included in the initial diagnostic algorithm, which revealed the etiology in 83.5% of children tested. The use of molecular methods in diagnostics of gastroenteritis is preferable because of their high sensitivity, specificity, fast performance and the possibility of establishing the concentration of the target. The latter may be valuable for assessing the clinical significance of the detected enteric, particularly viral pathogens.

  17. Molecular diagnostic development for begomovirus-betasatellite complexes undergoing diversification: A case study.

    PubMed

    Brown, Judith K; Ur-Rehman, Muhammad Zia; Avelar, Sofia; Chingandu, N; Hameed, Usman; Haider, Saleem; Ilyas, Muhammad

    2017-04-22

    At least five begomoviral species that cause leaf curl disease of cotton have emerged recently in Asia and Africa, reducing fiber quality and yield. The potential for the spread of these viruses to other cotton-vegetable growing regions throughout the world is extensive, owing to routine, global transport of alternative hosts of the leaf curl viruses, especially ornamentals. The research reported here describes the design and validation of polymerase chain reaction (PCR) primers undertaken to facilitate molecular detection of the two most-prevalent leaf curl-associated begomovirus-betasatellite complexes in the Indian Subcontinent and Africa, the Cotton leaf curl Kokhran virus-Burewala strain and Cotton leaf curl Gezira virus, endemic to Asia and Africa, respectively. Ongoing genomic diversification of these begomoviral-satellite complexes was evident based on nucleotide sequence alignments, and analysis of single nucleotide polymorphisms, both factors that created new challenges for primer design. The additional requirement for species and strain-specific, and betasatellite-specific primer design, imposes further constraints on primer design and validation due to the large number of related species and strains extant in 'core leaf curl virus complex', now with expanded distribution in south Asia, the Pacific region, and Africa-Arabian Peninsula that have relatively highly conserved coding and non-coding regions, which precludes much of the genome-betasatellite sequence when selecting primer 'targets'. Here, PCR primers were successfully designed and validated for detection of cloned viral genomes and betasatellites for representative 'core leaf curl' strains and species, distant relatives, and total DNA isolated from selected plant species. The application of molecular diagnostics to screen plant imports prior to export or release from ports of entry is expected to greatly reduce the likelihood of exotic leaf curl virus introductions that could dramatically affect

  18. Reevaluation of an Acanthamoeba Molecular Diagnostic Algorithm following an Atypical Case of Amoebic Keratitis.

    PubMed

    Lau, Rachel; Cunanan, Marlou; Jackson, Jonathan; Ali, Ibne Karim M; Chong-Kit, Ann; Gasgas, Jason; Tian, Jinfang; Ralevski, Filip; Boggild, Andrea K

    2015-10-01

    Amoebic keratitis (AK) is a potentially blinding infection, the prompt diagnosis of which is essential for limiting ocular morbidity. We undertook a quality improvement initiative with respect to the molecular detection of acanthamoebae in our laboratory because of an unusual case of discordance. Nine ATCC strains of Acanthamoeba and 40 delinked, biobanked, surplus corneal scraping specimens were analyzed for the presence of acanthamoebae with four separate real-time PCR assays. The assay used by the Free-Living and Intestinal Amebas Laboratory of the CDC was considered the reference standard, and the performance characteristics of each individual assay and pairs of assays were calculated. Outcome measures were sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Of 49 included specimens, 14 (28.6%) were positive by the gold standard assay, and 35 (71.4%) were negative. The sensitivities of the individual assays ranged from 64.3% to 92.9%, compared to the gold standard, while the specificities ranged from 88.6% to 91.4%. The PPVs and NPVs ranged from 69.2% to 78.6% and from 86.1% to 96.9%, respectively. Combinations of assay pairs led to improved performance, with sensitivities ranging from 92.9% to 100% and specificities ranging from 97.1% to 100%. ATCC and clinical strains of Acanthamoeba that failed to be detected by certain individual assays included Acanthamoeba castellanii, Acanthamoeba culbertsoni, and Acanthamoeba lenticulata. For three clinical specimens, false negativity of the gold standard assay could not be excluded. Molecular diagnostic approaches, especially combinations of highly sensitive and specific assays, offer a reasonably performing, operator-independent, rapid strategy for the detection of acanthamoebae in clinical specimens and are likely to be more practical than either culture or direct microscopic detection.

  19. Multiple light scattering methods for multiphase flow diagnostics

    NASA Astrophysics Data System (ADS)

    Estevadeordal, Jordi

    2015-11-01

    Multiphase flows of gases and liquids containing droplets, bubbles, or particulates present light scattering imaging challenges due to the interference from each phase, such as secondary reflections, extinctions, absorptions, and refractions. These factors often prevent the unambiguous detection of each phase and also produce undesired beam steering. The effects can be especially complex in presence of dense phases, multispecies flows, and high pressure environments. This investigation reports new methods for overcoming these effects for quantitative measurements of velocity, density, and temperature fields. The methods are based on light scattering techniques combining Mie and filtered Rayleigh scattering and light extinction analyses and measurements. The optical layout is designed to perform multiple property measurements with improved signal from each phase via laser spectral and polarization characterization, etalon decontamination, and use of multiple wavelengths and imaging detectors.

  20. Fraley's syndrome: case report and update on current diagnostic methods

    SciTech Connect

    Zuckier, L.S.; Patel, Y.D.; Fine, E.J.; Koenigsberg, M.

    1988-01-01

    A 38-year-old woman presented with fever, right flank pain, and a clinical diagnosis of pyelonephritis. Work-up revealed the presence of a crossing arterial branch causing obstruction of the superior infundibulum of the right kidney, which is an uncommon cause of nephralgia and urinary infection initially described by Fraley in 1966. Intravenous urography, retrograde pyelography, and angiography remain the mainstay of diagnosis, much as in the initial descriptions of this entity. (/sup 131/I)Hippuran imaging, with analysis of the upper and lower pole regions of interest, provides a simple yet powerful method of evaluating functional and excretory changes in the superior infundibulum, and has proved more efficacious than previously reported whole-kidney renograms. Renal scintigraphy represents a relatively noninvasive method of serial functional examination in this disorder. Ultrasound imaging, by monitoring upper-pole dilatation, may provide complementary morphologic information important for long-term follow-up.

  1. Apparatus and method for monitoring breath acetone and diabetic diagnostics

    DOEpatents

    Duan, Yixiang; Cao, Wenqing

    2008-08-26

    An apparatus and method for monitoring diabetes through breath acetone detection and quantitation employs a microplasma source in combination with a spectrometer. The microplasma source provides sufficient energy to produce excited acetone fragments from the breath gas that emit light. The emitted light is sent to the spectrometer, which generates an emission spectrum that is used to detect and quantify acetone in the breath gas.

  2. Development of Methods for Diagnostics of Discharges in Supersonic Flows

    DTIC Science & Technology

    2001-09-01

    channel and quartz combustor tube and for installation of plasma generators. The centering and fixation of quartz tube is provided by ribbon sealings ... unsteady parameters [1-3 ]. Under these conditions, the main advantage of the probe method (a possibility of local measurements with a high temporal...reactions (including ionization and recombination) in the air plasma. The unsteady character of plasma parameters suggests a necessity of development of

  3. Bearing diagnostics: A method based on differential geometry

    NASA Astrophysics Data System (ADS)

    Tian, Ye; Wang, Zili; Lu, Chen; Wang, Zhipeng

    2016-12-01

    The structures around bearings are complex, and the working environment is variable. These conditions cause the collected vibration signals to become nonlinear, non-stationary, and chaotic characteristics that make noise reduction, feature extraction, fault diagnosis, and health assessment significantly challenging. Thus, a set of differential geometry-based methods with superiorities in nonlinear analysis is presented in this study. For noise reduction, the Local Projection method is modified by both selecting the neighborhood radius based on empirical mode decomposition and determining noise subspace constrained by neighborhood distribution information. For feature extraction, Hessian locally linear embedding is introduced to acquire manifold features from the manifold topological structures, and singular values of eigenmatrices as well as several specific frequency amplitudes in spectrograms are extracted subsequently to reduce the complexity of the manifold features. For fault diagnosis, information geometry-based support vector machine is applied to classify the fault states. For health assessment, the manifold distance is employed to represent the health information; the Gaussian mixture model is utilized to calculate the confidence values, which directly reflect the health status. Case studies on Lorenz signals and vibration datasets of bearings demonstrate the effectiveness of the proposed methods.

  4. [Comparative study of different diagnostic methods in pulmonary alveolitis].

    PubMed

    Makhmudova, S Iu

    2009-05-01

    To evaluate and analyze, clinical and roentgenological manifestations of extrinsic allergic alveolitis (EAA) and idiopathic fibrosing alveolitis (IFA) 89 patients underwent bronchoscopy survey and functional test of lungs. Average age of patients was 38,3+/-5,8. Among examined 89 patients 31 (34,8%) patients were poultry farmers, 30 (33,7%) - millers, and 28 (31,5%) - tobacco-growers. EAA was found among 22 poultry farmers, 19 tobacco-growers, and 19 millers. IFA was found among 11 millers, 9 tobacco-growers and 9 poultry farmers. Acute respiratory disease (ARD) was found among 58 patients; 38 patients suffer from lung diseases. Control group consisted of 20 healthy people. Along with general blood analysis, all patients underwent - roentgenological analysis of thorax in two shifts. Recent studies show that CT lung screening is more sensitive than standard lung screening methods in detecting lung disease. Comparative analysis allowed concluding that Real-Time CT method is the most effective. CT lung screening is more sensitive than standard lung screening methods in detecting lung diseases.

  5. Applications of Replicating-Competent Reporter-Expressing Viruses in Diagnostic and Molecular Virology

    PubMed Central

    Li, Yongfeng; Li, Lian-Feng; Yu, Shaoxiong; Wang, Xiao; Zhang, Lingkai; Yu, Jiahui; Xie, Libao; Li, Weike; Ali, Razim; Qiu, Hua-Ji

    2016-01-01

    Commonly used tests based on wild-type viruses, such as immunostaining, cannot meet the demands for rapid detection of viral replication, high-throughput screening for antivirals, as well as for tracking viral proteins or virus transport in real time. Notably, the development of replicating-competent reporter-expressing viruses (RCREVs) has provided an excellent option to detect directly viral replication without the use of secondary labeling, which represents a significant advance in virology. This article reviews the applications of RCREVs in diagnostic and molecular virology, including rapid neutralization tests, high-throughput screening systems, identification of viral receptors and virus-host interactions, dynamics of viral infections in vitro and in vivo, vaccination approaches and others. However, there remain various challenges associated with RCREVs, including pathogenicity alterations due to the insertion of a reporter gene, instability or loss of the reporter gene expression, or attenuation of reporter signals in vivo. Despite all these limitations, RCREVs have become powerful tools for both basic and applied virology with the development of new technologies for generating RCREVs, the inventions of novel reporters and the better understanding of regulation of viral replication. PMID:27164126

  6. Applications of Replicating-Competent Reporter-Expressing Viruses in Diagnostic and Molecular Virology.

    PubMed

    Li, Yongfeng; Li, Lian-Feng; Yu, Shaoxiong; Wang, Xiao; Zhang, Lingkai; Yu, Jiahui; Xie, Libao; Li, Weike; Ali, Razim; Qiu, Hua-Ji

    2016-05-06

    Commonly used tests based on wild-type viruses, such as immunostaining, cannot meet the demands for rapid detection of viral replication, high-throughput screening for antivirals, as well as for tracking viral proteins or virus transport in real time. Notably, the development of replicating-competent reporter-expressing viruses (RCREVs) has provided an excellent option to detect directly viral replication without the use of secondary labeling, which represents a significant advance in virology. This article reviews the applications of RCREVs in diagnostic and molecular virology, including rapid neutralization tests, high-throughput screening systems, identification of viral receptors and virus-host interactions, dynamics of viral infections in vitro and in vivo, vaccination approaches and others. However, there remain various challenges associated with RCREVs, including pathogenicity alterations due to the insertion of a reporter gene, instability or loss of the reporter gene expression, or attenuation of reporter signals in vivo. Despite all these limitations, RCREVs have become powerful tools for both basic and applied virology with the development of new technologies for generating RCREVs, the inventions of novel reporters and the better understanding of regulation of viral replication.

  7. Polarization second harmonic generation microscopy provides quantitative enhanced molecular specificity for tissue diagnostics.

    PubMed

    Kumar, Rajesh; Grønhaug, Kirsten M; Romijn, Elisabeth I; Finnøy, Andreas; Davies, Catharina L; Drogset, Jon O; Lilledahl, Magnus B

    2015-09-01

    Due to specific structural organization at the molecular level, several biomolecules (e.g., collagen, myosin etc.) which are strong generators of second harmonic generation (SHG) signals, exhibit unique responses depending on the polarization of the excitation light. By using the polarization second harmonic generation (p-SHG) technique, the values of the second order susceptibility components can be used to differentiate the types of molecule, which cannot be done by the use of a standard SHG intensity image. In this report we discuss how to implement p-SHG on a commercial multiphoton microscope and overcome potential artifacts in susceptibility (χ) image. Furthermore we explore the potential of p-SHG microscopy by applying the technique to different types of tissue in order to determine corresponding reference values of the ratio of second-order χ tensor elements. These values may be used as a bio-marker to detect any structural alterations in pathological tissue for diagnostic purposes. The SHG intensity image (red) in (a) shows the distribution of collagen fibers in ovary tissue but cannot determine the type of collagen fiber. However, the histogram distribution (b) for the values of the χ tensor element ratio can be used to quantitatively identify the types of collagen fibers. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. The emerging role of the molecular diagnostics laboratory in breast cancer personalized medicine.

    PubMed

    De Abreu, Francine B; Wells, Wendy A; Tsongalis, Gregory J

    2013-10-01

    Breast cancer is a complex disease characterized by many morphological, clinical, and molecular features. For many years, breast cancer has been classified according to traditional parameters, such as histological type, grade, tumor size, lymph node involvement and vascular invasion, and biomarkers (eg, estrogen receptor, progesterone receptor, and epidermal growth factor receptor 2), which are used in patient management. With emerging imaging techniques (ie, digital mammography, tomosynthesis, ultrasonography, magnetic resonance imaging, nuclear medicine, and genomic techniques, such as real-time RT-PCR and microarrays), breast cancer diagnostics is going through a significant evolution. Imaging technologies have improved breast cancer diagnosis, survival, and treatment by early detection of primary or metastatic lesions, differentiating benign from malignant lesions and promoting intraoperative surgical guidance and postoperative specimen evaluation. Genomic and transcriptomic technologies make the analysis of gene expression signatures and mutation status possible so that tumors may be classified more accurately with respect to diagnosis and prognosis. The -omic era has also made possible the identification of new biomarkers involved in breast cancer development, survival, and invasion that can be gradually incorporated into clinical testing. These advances in both imaging and genomics contribute to more personalized and predictive patient management. We review the progress made in breast cancer diagnosis and management using these new tools. Copyright © 2013 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  9. Generating and evaluating evidence of the clinical utility of molecular diagnostic tests in oncology.

    PubMed

    Deverka, Patricia; Messner, Donna A; McCormack, Robert; Lyman, Gary H; Piper, Margaret; Bradley, Linda; Parkinson, David; Nelson, David; Smith, Mary Lou; Jacques, Louis; Dutta, Tania; Tunis, Sean R

    2016-08-01

    Enthusiasm for molecular diagnostic (MDx) testing in oncology is constrained by the gaps in required evidence regarding its impact on patient outcomes (clinical utility (CU)). This effectiveness guidance document proposes recommendations for the design and evaluation of studies intended to reflect the evidence expectations of payers, while also reflecting information needs of patients and clinicians. Our process included literature reviews and key informant interviews followed by iterative virtual and in-person consultation with an expert technical working group and an advisory group comprising life-sciences industry experts, public and private payers, patients, clinicians, regulators, researchers, and other stakeholders. Treatment decisions in oncology represent high-risk clinical decision making, and therefore the recommendations give preference to randomized controlled trials (RCTs) for demonstrating CU. The guidance also describes circumstances under which alternatives to RCTs could be considered, specifying conditions under which test developers could use prospective-retrospective studies with banked biospecimens, single-arm studies, prospective observational studies, or decision-analytic modeling techniques that make a reasonable case for CU. Using a process driven by multiple stakeholders, we developed a common framework for designing and evaluating studies of the clinical validity and CU of MDx tests, achieving a balance between internal validity of the studies and the relevance, feasibility, and timeliness of generating the desired evidence.Genet Med 18 8, 780-787.

  10. Automated nucleic acid isolation in viral molecular diagnostics: evaluation of the QIAsymphony SP.

    PubMed

    Parham, N J; Parmar, S A; Kumar, N; Aliyu, S; Curran, M D; Zhang, H

    2012-01-01

    The Qiagen QIAsymphony SP is a high-throughput (up to 96 samples per run), fully-automated nucleic acid isolation system. It was implemented in the authors' laboratory to cope with the high demand for pandemic H1N1 influenza testing in 2009. This study evaluated the QIAsymphony SP for viral nucleic acid isolation from quality control materials, pure cultures and various clinical specimens. The effect of varying sample volume on detection sensitivity was investigated using serial 10-fold dilutions of pure viral specimens and target nu