Sample records for keskkonnakeemia labori juhataja

  1. [Comparison of new portable home electronic uroflowmeter with Laborie uroflowmeter].

    PubMed

    Guan, Zhi-chen; Deng, Xiao-lin; Zhang, Qian

    2011-08-18

    To design a new portable home electronic uroflowmeter and compare it with traditional methods. The system consists of collectors, urine conducting apparatus, intelligent cell phone, wireless network communication technology, computer analysis and drawing, and data storage technology, etc., and can automatically collect voiding information from patients with lower urinary tract symptoms(LUTS) Through Bluetooth, the voiding information was sent to the patient's intelligent cell phone from the collector, then stored directly by intelligent cell phone and wirelessly transmitted to the workstation in hospital. The system was primarily tested with regard to accuracy of measurement of the voided volume. Multiple doses with known volume were introduced in the system and Laborie uroflowmeter. Furthermore, 38 outpatients who had LUTS were tested simultaneously with the system and Laborie uroflowmeter. The statistical method for assessing agreement between the two methods of clinical measurement was Bland-Altman analysis. Among the subjects, there were 22 male patients and 16 female patients, ranging from 21 to 37 years old, with an average age of 25.5 years, of whom, 19 were tested once and 19 patients twice, equaling to 57 tests. The system could accurately collect and analyze voiding time, uroflowmetry, voided volume, and automatically provide uroflowmetry parameters. The measurement error of 100, 200, 300, 500 and 800 mL is less than 5%. 12.28%, 5.26% and 3.51% of the Qmax, Qave and voided volume points were beyond the 95% limits of agreement. The maximum absolute values of the Qmax, Qave and voided volume difference were 0.38 mL/s, 0.70 mL/s and 2.90 mL, respectively.They agreed with the recommendation of Standardization International Continence Society. The new portable home electronic uroflowmeter has good agreement with Laborie uroflowmeter,and is a new LUTS monitoring system integrated with correct, reliable, real-time, convenient and easy-managing advantages. It is

  2. [Compensable occupational disease and cancer: how to improve the recognition rate? "Cursus Laboris" Project in Midi-Pyrenees: feasibility study].

    PubMed

    Rougé-Bugat, Marie-Eve; Hérin, Fabrice; Julien, Sylvie; Oustric, Stéphane; Forichon, Emmanuel; Delaperche, Florence; Bauvin, Eric; Delord, Jean-Pierre; Grosclaude, Pascale

    2012-10-01

    Five to ten percent of cancers are of occupational origin but only 0.5% of cancers are compensable occupational diseases recognized in 2001. The project "Curriculum Laboris" was launched in Midi-Pyrenees with the objective to establish an organization to improve the identification, reporting and recognition of occupational cancers. The project consisted firstly in creating an online training module for professionals. Furthermore, a pilot has identified patients with lung, bladder, head and neck or hematologic cancer. Afterwards, four investigators realized an interview with the patients "marked" to define their careers. Finally, a group of experts produced advice, providing the general practitioner, the aid element in drafting the initial medical certificate (CMI) as part of the recognition process. Twenty-three patients were identified, 21 surveys were carried out. Six returns were filed and actually recognized. The generalization of our device measures meet the Cancer Plan II 2009 to 2013 and may improve the number of cancers recognized as compensable occupational diseases.

  3. Yoga – a laborious way to well-being: patients’ experiences of yoga as a treatment for hypertension in primary care

    PubMed Central

    Wolff, Moa; Brorsson, Annika; Midlöv, Patrik; Sundquist, Kristina; Strandberg, Eva Lena

    2017-01-01

    Objective The aim of the study was to describe patients’ experience of yoga as a treatment for hypertension, as well as their experience of living with hypertension. Design Qualitative interview study Method and materials In 2013–2014, in southern Sweden, patients with hypertension from three health care centres were invited to participate in a randomised controlled trial on yoga for hypertension. After completion of the study, eight women and five men (aged 35–79), who had practiced the yoga intervention, were interviewed about their experiences. We used a semi-structured interview guide according to Kvale. Qualitative analysis was conducted by systematic text condensation inspired by Malterud. Results Two main themes emerged during the analysis process: Yoga – a laborious way to well-being and hypertension – a silent disease. The positive experiences of doing yoga were described in terms of tranquillity and increased agility. The drawbacks were mainly linked to the time required to perform the exercises. Living with high blood pressure and having to take medication can imply a stigma and cause concerns for future cardiovascular events. Most patients that we interviewed expressed a wish to find alternative ways to treat their high blood pressure. Participating in the yoga study was seen as a good possibility to try such an alternative way. Conclusions Many patients with hypertension in Swedish primary care seem to be interested in trying alternative treatments to control blood pressure. The patients in our study experienced several benefits from doing yoga, but they also pointed out difficulties in implementing yoga as a regular and permanent lifestyle change. PMID:29124990

  4. Laborious and perilous adventures: the triumphant return of Francois Arago to France

    NASA Astrophysics Data System (ADS)

    Murdin, P.

    2005-08-01

    As a young man, while measuring the Paris Meridian in the Balearic Islands, the French astronomer Francois Arago was caught up in events of the Peninsular and Napoleonic Wars and found himself under arrest in Algiers. Released from custody and returning from Algiers to Marseille in 1809, he was detained again, this time by the British Royal Navy warship HMS Minstrel, but let go. The Algerian ships with which he was traveling were captured and taken to Gibraltar. The incident caused an abrupt deterioration in Anglo-Algerian relations, which however recovered when Napoleon declared war on Algiers. A comparison of the account in his autobiography with the logs of Royal Navy ships confirms the outline and many details of his account of his arrest but also sheds light on the reliability of his autobiography.

  5. Data and Tools | Research Site Name | NREL

    Science.gov Websites

    aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo laboris nisi ut aliquip ex ea commodo consequat. Research Topic 1 Lorem Ipsum Tool 1 Lorem Ipsum Facility

  6. Research Topic | Research Site Name | NREL

    Science.gov Websites

    exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Capabilities Width of 1746px - Height can , quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Subtopic Heading 2 ex ea commodo consequat. Publications Article Title, Journal Name (Year) Conference Paper Title

  7. Impacts | Research Site Name | NREL

    Science.gov Websites

    laboris nisi ut aliquip ex ea commodo consequat. Width of 1746px - Height can vary Read more Success nisi ut aliquip ex ea commodo consequat. Title 2 Lorem ipsum dolor sit amet, consectetur adipiscing nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Title 3 Lorem ipsum dolor

  8. Development of DNA-Free Sediment for Ecological Assays with Genomic Endpoints (NAC SETAC)

    EPA Science Inventory

    Recent advances in genomics are currently being exploited to discern ecological changes that have conventionally been measured using laborious counting techniques. For example, next generation sequencing technologies can be used to create DNA libraries from benthic community ass...

  9. Development of DNA-Free Sediment for Ecological Assays with Genomic Endpoints

    EPA Science Inventory

    Recent advances in genomics are currently being exploited to discern ecological changes that have conventionally been measured using laborious counting techniques. For example, next generation sequencing technologies can be used to create DNA libraries from benthic community ass...

  10. Reusable three-dimensional nanostructured substrates for surface-enhanced Raman scattering.

    PubMed

    Zhu, Zhendong; Li, Qunqing; Bai, Benfeng; Fan, Shoushan

    2014-01-13

    To date, fabricating three-dimensional (3D) nanostructured substrate with small nanogap was a laborious challenge by conventional fabrication techniques. In this article, we address a simple, low-cost, large-area, and spatially controllable method to fabricate 3D nanostructures, involving hemisphere, hemiellipsoid, and pyramidal pits based on nanosphere lithography (NSL). These 3D nanostructures were used as surface-enhanced Raman scattering (SERS) substrates of single Rhodamine 6G (R6G) molecule. The average SERS enhancement factor achieved up to 1011. The inevitably negative influence of the adhesion-promoting intermediate layer of Cr or Ti was resolved by using such kind of 3D nanostructures. The nanostructured quartz substrate is a free platform as a SERS substrate and is nondestructive when altering with different metal films and is recyclable, which avoids the laborious and complicated fabricating procedures.

  11. Reusable three-dimensional nanostructured substrates for surface-enhanced Raman scattering

    PubMed Central

    2014-01-01

    To date, fabricating three-dimensional (3D) nanostructured substrate with small nanogap was a laborious challenge by conventional fabrication techniques. In this article, we address a simple, low-cost, large-area, and spatially controllable method to fabricate 3D nanostructures, involving hemisphere, hemiellipsoid, and pyramidal pits based on nanosphere lithography (NSL). These 3D nanostructures were used as surface-enhanced Raman scattering (SERS) substrates of single Rhodamine 6G (R6G) molecule. The average SERS enhancement factor achieved up to 1011. The inevitably negative influence of the adhesion-promoting intermediate layer of Cr or Ti was resolved by using such kind of 3D nanostructures. The nanostructured quartz substrate is a free platform as a SERS substrate and is nondestructive when altering with different metal films and is recyclable, which avoids the laborious and complicated fabricating procedures. PMID:24417892

  12. A MEMBRANE FILTER PROCEDURE FOR ASSAYING CYTOTOXIC ACTIVITY IN HETEROTROPHIC BACTERIA ISOLATED FROM DRINKING WATER

    EPA Science Inventory

    Cytotoxic activity assays of Gram-negative, heterotrophic bacteria are often laborious and time consuming. The objective of this study was to develop in situ procedures for testing potential cytotoxic activities of heterotrophic bacteria isolated from drinking water systems. Wate...

  13. Gene Expression Changes in Developing Zebrafish as Potential Markers for Rapid Developmental Neurotoxicity Screening

    EPA Science Inventory

    Sparse information exists on many chemicals to guide developmental neurotoxicity (DNT) risk assessments. As DNT testing using rodents is laborious and expensive, alternative species such as zebrafish are being adapted for toxicity screening. Assessing the DNT potential of chem...

  14. Investigation of high-strength bolt-tightening verification techniques.

    DOT National Transportation Integrated Search

    2016-03-01

    The current means and methods of verifying that high-strength bolts have been properly tightened are very laborious and time : consuming. In some cases, the techniques require special equipment and, in other cases, the verification itself may be some...

  15. Gene action analysis by inheritance and QTL mapping of resistance to root-knot nematodes in cotton.

    USDA-ARS?s Scientific Manuscript database

    Host-plant resistance is highly effective in controlling crop loss from nematode infection. In addition, molecular markers can be powerful tools for marker-assisted selection (MAS), where they reduce laborious greenhouse phenotype evaluation to identify root-knot nematode (RKN) Meloidogyne incognita...

  16. Laboratory microwave measurement of the moisture content in seed cotton and ginned cotton fiber

    USDA-ARS?s Scientific Manuscript database

    The timely and accurate measurement of cotton fiber moisture content is important, but the measurement is often performed by laborious, time-consuming laboratory oven drying methods. Microwave technology for measuring fiber moisture content directly (not for drying only) offers potential advantages...

  17. Automatic recognition of lactating sow behaviors through depth image processing

    USDA-ARS?s Scientific Manuscript database

    Manual observation and classification of animal behaviors is laborious, time-consuming, and of limited ability to process large amount of data. A computer vision-based system was developed that automatically recognizes sow behaviors (lying, sitting, standing, kneeling, feeding, drinking, and shiftin...

  18. Meiotic homoeologous recombination-based alien gene introgression in the genomics era of wheat

    USDA-ARS?s Scientific Manuscript database

    Wheat (Triticum spp.) has a narrow genetic basis due to its allopolyploid origin. However, wheat has numerous wild relatives usable for expanding genetic variability of its genome through meiotic homoeologous recombination. Traditionally, laborious cytological analyses have been employed to detect h...

  19. Comparison of an automated Most Probable Number (MPN) technique to traditional plating methods for estimating populations of total aerobes, coliforms and E. coli associated with freshly processed broiler chickens

    USDA-ARS?s Scientific Manuscript database

    Traditional microbiological techniques for estimating populations of viable bacteria can be laborious and time consuming. The Most Probable Number (MPN) technique is especially tedious as multiple series of tubes must be inoculated at several different dilutions. Recently, an instrument (TEMPOTM) ...

  20. Quantification of soil water evaporation using TDR-microlysimetry

    USDA-ARS?s Scientific Manuscript database

    Soil water evaporation is conventionally measured using microlysimeters by evaluating the daily change in mass. Daily removal is laborious and replacement immediately after irrigation events is impractical because of field wetness which leads to delays and an underestimation of evaporation. Irrigati...

  1. Characterization of Aspergillus section Nigri species populations in vineyard soil using droplet digital PCR

    USDA-ARS?s Scientific Manuscript database

    Identification of populations of Aspergillus section Nigri species in environmental samples using traditional methods is laborious and impractical for large numbers of samples. We developed species-specific primers and probes for quantitative droplet digital PCR (ddPCR) to improve sample throughput ...

  2. Relationship between population estimates of cotton fleahoppers (Hemiptera: Miridae) obtained by terminal and whole plant examinations

    USDA-ARS?s Scientific Manuscript database

    The standard sampling technique used to quantify cotton fleahopper, Pseudatomoscelis seriatus (Reuter), abundance in cotton, Gossypium hirsutum L., involves direct counts of adults and nymphs on plants. This method, however, becomes increasingly laborious and time consuming as plants increase in si...

  3. Acetone Enhances the Direct Analysis of Total Condensed Tannins in Forage Legumes by the Butanol-HCl Assay

    USDA-ARS?s Scientific Manuscript database

    Depending on concentration, condensed tannins (CT) in forages have no effect, enhance, or impede protein utilization and performance of ruminants. Defining optimal forage CT levels has been elusive, partly because current methods for estimating total soluble plus insoluble CT are laborious or inaccu...

  4. Fireflies in the Coalmine: Luciferase Technologies in Next-Generation Toxicity Testing

    EPA Science Inventory

    Whole-animal studies have been the mainstay of toxicity testing for decades. These approaches are too expensive and laborious to effectively characterize all of the chemicals currently in commercial use. In addition, there are social and ethical pressures to reduce, refine and re...

  5. A Post-Intentional Exploration of Agnostic College Students' Experiences

    ERIC Educational Resources Information Center

    Armstrong, Amanda

    2017-01-01

    Scholars have adapted college student identity development models to examine and highlight the unique, laborious, and varied experiences of marginalized populations. However, researchers have minimally explored the perspectives of nontheistic and nonreligious college students using poststructural methodologies. I followed a post-intentional…

  6. [Trial to stimulate learning motivation of medical students in the dissection practice "teaching assistant system"].

    PubMed

    Kawashiro, Yukiko; Kadota, Tomoko; Matsuno, Yoshiharu; Miyaso, Hidenobu; Komiyama, Masatoshi; Mori, Chisato

    2008-06-01

    At the Medical School of Chiba University, educational dissection tours have been conducted for intra- and extramural students in other programs, such as students of nursing. In the 2006 school year there were more than 1,500 students. As presented in a previous report, we tested an educational program in which our medical students teach other students parts of splanchnology, neurology, and myology to promote student understanding of human physiology through their own teaching. Since this system, termed the "teaching assistant system," was fairly laborious for many medical students, we attempted to improve it by decreasing the students' load and reducing the frequency of teaching from several times to once during the one-term dissection practice. We assessed the improved method with questionnaires for medical students who had studied at the school in 2006 and 2007 (n = 206) before and after teaching other students. The response rate for the questionnaires was 91.3% (n = 188). The results were as follows. (1) Most medical students (69.7%) realized that the task of teaching had stimulating effects on their own learning motivation. (2) According to most of their evaluations (80.4%), the duties of teaching involved in the previous assistant system were laborious. In contrast, the ratio of medical students who considered teaching to be laborious decreased by about half (55.3%) in the present improved system. (3) Most students (79.8%) were satisfied with the teaching assistant system. We concluded that the improved teaching assistant system was effective for the dissection practice.

  7. The Perceptions and Experiences of Students in a Paperless Accounting Class

    ERIC Educational Resources Information Center

    Teeter, Steve; Madsen, Susan R.; Hughes, Jason; Eagar, Brent

    2007-01-01

    Although financial accounting practices in business have capitalized on the use of technology, this technology has not been fully integrated in higher education for accounting students. While traditional accounting courses laboriously involve rote transcription of debits and credits, educational technology in accounting courses may prove…

  8. Combining Language Corpora with Experimental and Computational Approaches for Language Acquisition Research

    ERIC Educational Resources Information Center

    Monaghan, Padraic; Rowland, Caroline F.

    2017-01-01

    Historically, first language acquisition research was a painstaking process of observation, requiring the laborious hand coding of children's linguistic productions, followed by the generation of abstract theoretical proposals for how the developmental process unfolds. Recently, the ability to collect large-scale corpora of children's language…

  9. Challenges Confronting Beginning Researchers in Conducting Literature Reviews

    ERIC Educational Resources Information Center

    Chen, Der-Thanq; Wang, Yu-Mei; Lee, Wei Ching

    2016-01-01

    Conducting literature review is a complicated, sometimes confusing and laborious process that beginning educational researchers, especially graduate students, often find challenging. However, in the past these challenges were hardly considered, but in more recent times they have been increasingly considered by various faculties and graduate…

  10. Variation in density and diversity of species of Phytophthora in two forest stream networks

    Treesearch

    Jaesoon Hwang; Steven N. Jeffers; Steven W. Oak

    2010-01-01

    Monitoring occurrence and distribution of Phytophthora species, including Phytophthora ramorum, in forest ecosystems can be achieved in several ways including sampling symptomatic plants, infested soils, and infested streams. Collecting plant and soil samples can be laborious and time consuming due to the distance surveyors...

  11. Overview of the international workshop on emerging approaches for typing, detection, and characterization of Escherichia coli

    USDA-ARS?s Scientific Manuscript database

    Determination of the O:H antigens in E. coli has been the gold standard for ascertaining the serotype of E. coli strains and identifying pathogenic clones. However, conventional serotyping is laborious, time-consuming, often gives equivocal results, and there are technical difficulties with antiser...

  12. 21ST CENTURY MOLD ANALYSIS IN FOOD

    EPA Science Inventory

    Traditionally, the indoor air community has relied on mold analysis performed by either microscopic observations or the culturing of molds on various media to assess indoor air quality. These techniques were developed in the 19th century and are very laborious and time consumin...

  13. Real-time detection and quantification of Rhizoctonia and Pythium species on the Cook Agronomy Farm.

    USDA-ARS?s Scientific Manuscript database

    Populations of Rhizoctonia and Pythium are diverse in eastern Washington, with multiple species/anastomosis groups present throughout the region and within individual fields. The process of identifying the pathogen present in a sample is laborious and the high diversity increases the difficulty in a...

  14. Biolistic transformation of cotton zygotic embryo meristem

    USDA-ARS?s Scientific Manuscript database

    Biolistic transformation of cotton meristems, isolated from mature seed is detailed in this book chapter. This method is simple and avoids the necessity to use genotype-dependent regenerable cell cultures. However, identification of germ line transformation using this method is laborious and time-c...

  15. Microwave moisture measurement of cotton fiber moisture content in the laboratory

    USDA-ARS?s Scientific Manuscript database

    The moisture content of cotton fiber is an important fiber property, but it is often measured by a laborious, time-consuming laboratory oven drying method. A program was implemented to establish the capabilities of a laboratory microwave moisture measurement instrument to perform rapid, precise and...

  16. Acoustic detection of Melolonthine larvae in Australian sugarcane

    USDA-ARS?s Scientific Manuscript database

    Decision support systems have been developed for risk analysis and control of root-feeding white grub pests in Queensland sugarcane, based partly on manual inspection of cane soil samples. Acoustic technology was considered as a potential alternative to this laborious procedure. Field surveys were...

  17. Mannosylated Lipoarabinomannan in serum as a biomarker candidate for subclinical bovine tuberculosis

    USDA-ARS?s Scientific Manuscript database

    Background: Early and unambiguous detection of bovine tuberculosis (bTB), a significant disease of cattle worldwide, is necessary to control the spread of infection to other animals and humans. Current testing strategies are laborious, time consuming and heavily reliant on host responses that do n...

  18. The gene CmACS-7 provides sequence variation for the development of DNA markers associated with monoecious sex expresion in melon (Cucumis melo L.)

    USDA-ARS?s Scientific Manuscript database

    Most melon (Cucumis melo L.) breeding lines in South Korea display andromonoecious sex expression (i.e., possessing both bisexual and male flowers on the same plant), which, in turn, necessitates laborious hand emasculation during F1 hybrid seed production. Thus, there is a need to develop monoecio...

  19. Predicting Stored Grain Insect Population Densities Using an Electronic Probe Trap

    USDA-ARS?s Scientific Manuscript database

    Manual sampling of insects in stored grain is a laborious and time consuming process. Automation of grain sampling should help to increase the adoption of stored-grain integrated pest management. A new commercial electronic grain probe trap (OPI Insector™) has recently been marketed. We field tested...

  20. BAC Libraries from Wheat Chromosome 7D – Efficient Tool for Positional Cloning of Aphid Resistance Genes

    USDA-ARS?s Scientific Manuscript database

    Positional cloning in bread wheat is a tedious task due to its huge genome size (~17 Gbp) and polyploid character. BAC libraries represent an essential tool for positional cloning. However, wheat BAC libraries comprise more than million clones, which make their screening very laborious. Here we pres...

  1. Resolving Struggling Learners' Homework Difficulties: Working with Elementary School Learners and Parents

    ERIC Educational Resources Information Center

    Margolis, Howard

    2005-01-01

    Struggling learners and their parents often are exasperated by homework. They find it difficult, frustrating, and laborious, producing resistance, slipshod work, stress at home, and conflicts between struggling learners, parents, and school personnel. The author (1) identifies several causes of struggling learners' homework difficulties, (2)…

  2. The optimization of iloprost inhalation under moderate flow of oxygen therapy in severe pulmonary arterial hypertension.

    PubMed

    Nakayama, Kazuhiko; Emoto, Noriaki; Tamada, Naoki; Okano, Mitsumasa; Shinkura, Yuto; Yanaka, Kenichi; Onishi, Hiroyuki; Hiraishi, Mana; Yamada, Shinichiro; Tanaka, Hidekazu; Shinke, Toshiro; Hirata, Ken-Ichi

    2018-01-01

    Inhaled iloprost efficiently improves pulmonary hemodynamics, exercise capacity, and quality of life in patients with pulmonary arterial hypertension (PAH). However, the process of inhalation is laborious for patients suffering from resting dyspnea. We describe a 75-year-old man with idiopathic PAH and a low gas transfer. Investigations excluded significant parenchymal lung disease and airflow obstruction (presuming FEV1/FVC ration > 70%). The patient struggled to complete iloprost inhalation due to severe dyspnea and hypoxemia. As such, we optimized the methods of oxygen supply from the nasal cannula to the trans-inhalator during the inhalation. We successfully shortened the inhalation duration that effectively reduced the laborious efforts required of patients. We also recorded pulmonary hemodynamics during inhalation of nebulized iloprost. This revealed significant hemodynamic improvement immediately following inhalation but hemodynamics returned to baseline within 2 hours. We hope that this optimization will enable patients with severe PAH to undergo iloprost inhalation.

  3. Generation and development of RNA ligase ribozymes with modular architecture through "design and selection".

    PubMed

    Fujita, Yuki; Ishikawa, Junya; Furuta, Hiroyuki; Ikawa, Yoshiya

    2010-08-26

    In vitro selection with long random RNA libraries has been used as a powerful method to generate novel functional RNAs, although it often requires laborious structural analysis of isolated RNA molecules. Rational RNA design is an attractive alternative to avoid this laborious step, but rational design of catalytic modules is still a challenging task. A hybrid strategy of in vitro selection and rational design has been proposed. With this strategy termed "design and selection," new ribozymes can be generated through installation of catalytic modules onto RNA scaffolds with defined 3D structures. This approach, the concept of which was inspired by the modular architecture of naturally occurring ribozymes, allows prediction of the overall architectures of the resulting ribozymes, and the structural modularity of the resulting ribozymes allows modification of their structures and functions. In this review, we summarize the design, generation, properties, and engineering of four classes of ligase ribozyme generated by design and selection.

  4. The use of PacBio and Hi-C data in denovo assembly of the goat genome

    USDA-ARS?s Scientific Manuscript database

    Generating de novo reference genome assemblies for non-model organisms is a laborious task that often requires a large amount of data from several sequencing platforms and cytogenetic surveys. By using PacBio sequence data and new library creation techniques, we present a de novo, high quality refer...

  5. Open Experimentation on Phenomena of Chemical Reactions via the Learning Company Approach in Early Secondary Chemistry Education

    ERIC Educational Resources Information Center

    Beck, Katharina; Witteck, Torsten; Eilks, Ingo

    2010-01-01

    Presented is a case study on the implementation of open and inquiry-type experimentation in early German secondary chemistry education. The teaching strategy discussed follows the learning company approach. Originally adopted from vocational education, the learning company method is used to redirect lab-oriented classroom practice towards a more…

  6. Mapping soil moisture across an irrigated field using electromagnetic conductivity imaging

    USDA-ARS?s Scientific Manuscript database

    The ability to measure and map volumetric soil water theta quickly and accurately is important in irrigated agriculture. However, the traditional approach of using thermogravimetric moisture (w) and converting this to theta using measurements of bulk density (theta – cm3/cm3) is laborious and time c...

  7. A Constrained Bayesian Approach for Testing TTBT Compliance

    DTIC Science & Technology

    1992-03-06

    These figures show that the treatment of the covariance matrix is very im- portant. In many of the previous figures the power curves of all four...Drawer 719 Richland, WA 99352 Santa Barbara, CA 93102 Prof Stale Fla. Dr. James Hannon AplidSceces Bilding Lawrence Uivermare National Labory Uveity

  8. Why Professors Don't Do More To Stop Students Who Cheat.

    ERIC Educational Resources Information Center

    Schneider, Alison

    1999-01-01

    While college faculty complain about student cheating and plagiarism, many do little or nothing about it. Few lodge formal complaints against individual students, finding the campus judicial process laborious, and punishments often unrelated to the offense. At institutions with honor codes, the issues can be different, with reporting of…

  9. A Case for Community-Run Pre-Schools and Daycare Centres.

    ERIC Educational Resources Information Center

    Renard, Rosamunde

    This booklet advocates and describes the establishment of community run preschool and day care centers. The type described is based on the Laborie Community Education Centre in Saint Lucia, West Indies. Chapter 1 advocates establishing small, local institutions that are community managed, community owned, concerned with quality, and sustainable.…

  10. CPS-Rater: Automated Sequential Annotation for Conversations in Collaborative Problem-Solving Activities. Research Report. ETS RR-17-58

    ERIC Educational Resources Information Center

    Hao, Jiangang; Chen, Lei; Flor, Michael; Liu, Lei; von Davier, Alina A.

    2017-01-01

    Conversations in collaborative problem-solving activities can be used to probe the collaboration skills of the team members. Annotating the conversations into different collaboration skills by human raters is laborious and time consuming. In this report, we report our work on developing an automated annotation system, CPS-rater, for conversational…

  11. Neural Correlates of High Performance in Foreign Language Vocabulary Learning

    ERIC Educational Resources Information Center

    Macedonia, Manuela; Muller, Karsten; Friederici, Angela D.

    2010-01-01

    Learning vocabulary in a foreign language is a laborious task which people perform with varying levels of success. Here, we investigated the neural underpinning of high performance on this task. In a within-subjects paradigm, participants learned 92 vocabulary items under two multimodal conditions: one condition paired novel words with iconic…

  12. Finger-Writing Intervention Impacts the Spelling and Handwriting Skills of Children with Developmental Language Disorder: A Multiple Single-Case Study

    ERIC Educational Resources Information Center

    Van Reybroeck, Marie; Michiels, Nathalie

    2018-01-01

    Learning to use grapheme to phoneme correspondences (GPCs) provides a powerful mechanism for the foundation of reading skills in children. However, for some children, such as those with Developmental Language Disorder (DLD), the GPC learning process takes time, is laborious, and impacts the entire reading and spelling processes. The present study…

  13. User Centric Policy Management

    ERIC Educational Resources Information Center

    Cheek, Gorrell P.

    2013-01-01

    Internet use, in general, and online social networking sites, in particular, are experiencing tremendous growth with hundreds of millions of active users. As a result, there is a tremendous amount of privacy information and content online. Protecting this information is a challenge. Access control policy composition is complex, laborious and…

  14. The integrated business information system: using automation to monitor cost-effectiveness of park operations

    Treesearch

    Dick Stanley; Bruce Jackson

    1995-01-01

    The cost-effectiveness of park operations is often neglected because information is laborious to compile. The information, however, is critical if we are to derive maximum benefit from scarce resources. This paper describes an automated system for calculating cost-effectiveness ratios with minimum effort using data from existing data bases.

  15. Prototype Expert System for Climate Classification.

    ERIC Educational Resources Information Center

    Harris, Clay

    Many students find climate classification laborious and time-consuming, and through their lack of repetition fail to grasp the details of classification. This paper describes an expert system for climate classification that is being developed at Middle Tennessee State University. Topics include: (1) an introduction to the nature of classification,…

  16. Data assimilation in optimizing and integrating soil and water quality water model predictions at different scales

    USDA-ARS?s Scientific Manuscript database

    Relevant data about subsurface water flow and solute transport at relatively large scales that are of interest to the public are inherently laborious and in most cases simply impossible to obtain. Upscaling in which fine-scale models and data are used to predict changes at the coarser scales is the...

  17. Work with Us | Research Site Name | NREL

    Science.gov Websites

    ullamco laboris nisi ut aliquip ex ea commodo consequat. Hero Image - Width of 1746px - Height can vary ex ea commodo consequat. Learn about our technology partnership agreements. Use our cutting-edge commercialization programs. Join Our Team Find an opportunity: Job | Internship | Post Doc | Director's Postdoctoral

  18. Searches for Randomized Controlled Trials of Drugs in MEDLINE and EMBASE Using Only Generic Drug Names Compared with Searches Applied in Current Practice in Systematic Reviews

    ERIC Educational Resources Information Center

    Waffenschmidt, Siw; Guddat, Charlotte

    2015-01-01

    Background: It is unclear which terms should be included in bibliographic searches for randomized controlled trials (RCTs) of drugs, and identifying relevant drug terms can be extremely laborious. The aim of our analysis was to determine whether a bibliographic search using only the generic drug name produces sufficient results for the generation…

  19. When Work Experience Is Not Enough

    ERIC Educational Resources Information Center

    Lum, Lydia

    2009-01-01

    Legal practitioners find the leap into academia difficult. A much bigger deterrent for lawyers interested in teaching is a laborious, oft-vexing application process that places little value on work experience and interests. They also chide law school hiring committees for a lack of outreach to Asian Pacific Islanders. Law educators emphasize that…

  20. Tree height and tropical forest biomass estimation

    Treesearch

    M.O. Hunter; M. Keller; D. Vitoria; D.C. Morton

    2013-01-01

    Tropical forests account for approximately half of above-ground carbon stored in global vegetation. However, uncertainties in tropical forest carbon stocks remain high because it is costly and laborious to quantify standing carbon stocks. Carbon stocks of tropical forests are determined using allometric relations between tree stem diameter and height and biomass....

  1. Non-Native Chinese Language Learners' Attitudes towards Online Vision-Based Motion Games

    ERIC Educational Resources Information Center

    Hao, Yungwei; Hong, Jon-Chao; Jong, Jyh-Tsorng; Hwang, Ming-Yueh; Su, Chao-Ya; Yang, Jin-Shin

    2010-01-01

    Learning to write Chinese characters is often thought to be a very challenging and laborious task. However, new learning tools are being designed that might reduce learners' tedium. This study explores one such tool, an online program in which learners can learn Chinese characters through vision-based motion games. The learner's gestures are…

  2. Using Multimodal Learning Analytics to Model Student Behaviour: A Systematic Analysis of Behavioural Framing

    ERIC Educational Resources Information Center

    Andrade, Alejandro; Delandshere, Ginette; Danish, Joshua A.

    2016-01-01

    One of the challenges many learning scientists face is the laborious task of coding large amounts of video data and consistently identifying social actions, which is time consuming and difficult to accomplish in a systematic and consistent manner. It is easier to catalog observable behaviours (e.g., body motions or gaze) without explicitly…

  3. LiDAR-derived site index in the U.S. Pacihic Northwest--challenges and opportunities

    Treesearch

    Demetrios Gatziolis

    2007-01-01

    Site Index (SI), a key inventory parameter, is traditionally estimated by using costly and laborious field assessments of tree height and age. The increasing availability of reliable information on stand initiation timing and extent of planted, even-aged stands maintained in digital databases suggests that information on the height of dominant trees suffices for...

  4. Innovative Second Language Speaking Practice with Interactive Videos in a Rich Internet Application Environment

    ERIC Educational Resources Information Center

    Pereira, Juan A.; Sanz-Santamaría, Silvia; Montero, Raúl; Gutiérrez, Julián

    2012-01-01

    Attaining a satisfactory level of oral communication in a second language is a laborious process. In this action research paper we describe a new method applied through the use of interactive videos and the Babelium Project Rich Internet Application (RIA), which allows students to practice speaking skills through a variety of exercises. We present…

  5. Classification of shiga toxin-producing escherichia coli (STEC) serotypes with hyperspectral microscope imagery

    USDA-ARS?s Scientific Manuscript database

    Non-O157:H7 Shiga toxin-producing Escherichia coli (STEC) strains such as O26, O45, O103, O111, O121 and O145 are recognized as serious outbreak to cause human illness due to their toxicity. Since a conventional microbiological method for cell counting is laborious and time-consuming process, optica...

  6. Classification of non-O157 shiga toxin-producing escherichia coli(STEC) serotypes with hyperspectral microscope imaging

    USDA-ARS?s Scientific Manuscript database

    Non-O157 Shiga toxin-producing Escherichia coli (STEC) strains such as O26, O45, O103, O111, O121 and O145 are recognized as serious outbreak to cause human illness due to their toxicity. A conventional microbiological method for cell counting is laborious and needs long time for the results. Since ...

  7. Not Only Size Matters: Early-Talker and Late-Talker Vocabularies Support Different Word-Learning Biases in Babies and Networks

    ERIC Educational Resources Information Center

    Colunga, Eliana; Sims, Clare E.

    2017-01-01

    In typical development, word learning goes from slow and laborious to fast and seemingly effortless. Typically developing 2-year-olds seem to intuit the whole range of things in a category from hearing a single instance named--they have word-learning biases. This is not the case for children with relatively small vocabularies ("late…

  8. Characterization of (CA)n microsatellite repeats from large-insert clones.

    PubMed

    Litt, M; Browne, D

    2001-05-01

    The most laborious part of developing (CA)n microsatellite repeats as genetic markers is constructing DNA clones to permit determination of sequences flanking the microsatellites. When cosmids or large-insert phage clones are used as primary sources of (CA)n repeat markers, they have traditionally been subcloned into plasmid vectors such as pUC18 or M13 mp 18/19 cloning vectors to obtain fragments of suitable size for DNA sequencing. This unit presents an alternative approach whereby a set of degenerate sequencing primers that anneal directly to (CA)n microsatellites can be used to determine sequences that are inaccessible with vector-derived primers. Because the primers anneal to the repeat and not to the vector, they can be used with subclones containing inserts of several kilobases and should, in theory, always give sequence in the regions directly flanking the repeat. Degeneracy at the 3 end of each of these primers prevents elongation of primers that have annealed out-of-register. The most laborious part of developing (CA)n microsatellite repeats as genetic markers is constructing DNA clones to permit.

  9. E-health in Switzerland: The laborious adoption of the federal law on electronic health records (EHR) and health information exchange (HIE) networks.

    PubMed

    De Pietro, Carlo; Francetic, Igor

    2018-02-01

    Within the framework of a broader e-health strategy launched a decade ago, in 2015 Switzerland passed a new federal law on patients' electronic health records (EHR). The reform requires hospitals to adopt interoperable EHRs to facilitate data sharing and cooperation among healthcare providers, ultimately contributing to improvements in quality of care and efficiency in the health system. Adoption is voluntary for ambulatories and private practices, that may however be pushed towards EHRs by patients. The latter have complete discretion in the choice of the health information to share. Moreover, careful attention is given to data security issues. Despite good intentions, the high institutional and organisational fragmentation of the Swiss healthcare system, as well as the lack of full agreement with stakeholders on some critical points of the reform, slowed the process of adoption of the law. In particular, pilot projects made clear that the participation of ambulatories is doomed to be low unless appropriate incentives are put in place. Moreover, most stakeholders point at the strategy proposed to finance technical implementation and management of EHRs as a major drawback. After two years of intense preparatory work, the law entered into force in April 2017. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

  10. Assessment of in-place wood floor systems

    Treesearch

    Michael O. Hunt; Robert J. Ross; Xiping Wang; Lawrence Andrew Soltis; R. R. Leavitt; Zhiyong Cai

    2007-01-01

    Structural assessment of in-place wood floors is currently limited to inspection of individual members. This is costly and laborious. Consequently, the continued use or adaptive reuse of old/historic buildings is often in jeopardy because of the lack of an efficient and economical assessment method. A systems approach of assessment is the subject of this research....

  11. Bootstrap evaluation of a young Douglas-fir height growth model for the Pacific Northwest

    Treesearch

    Nicholas R. Vaughn; Eric C. Turnblom; Martin W. Ritchie

    2010-01-01

    We evaluated the stability of a complex regression model developed to predict the annual height growth of young Douglas-fir. This model is highly nonlinear and is fit in an iterative manner for annual growth coefficients from data with multiple periodic remeasurement intervals. The traditional methods for such a sensitivity analysis either involve laborious math or...

  12. Repeated Reading for Developing Reading Fluency and Reading Comprehension: The Case of EFL Learners in Vietnam

    ERIC Educational Resources Information Center

    Gorsuch, Greta; Taguchi, Etsuo

    2008-01-01

    Reading in a foreign or second language is often a laborious process, often caused by underdeveloped word recognition skills, among other things, of second and foreign language readers. Developing fluency in L2/FL reading has become an important pedagogical issue in L2 settings and one major component of reading fluency is fast and accurate word…

  13. Army Strong: Equipped, Trained and Ready. Final Report of the 2010 Army Acquisition Review

    DTIC Science & Technology

    2011-01-01

    program execution. Why is there such enduring dissatisfaction with DoD acquisition by leaders, workforce, customers and taxpayers? Succinctly...documentation; counterproductive, costly government and industry overhead; and increasingly dissatisfied customers . Even with a laborious requirements...retired, operating and generating force, customers and suppliers. The panel is grateful to all those interviewed for their time, insight, and service

  14. What Mothers Have To Say. Evaluation: Parents as Teachers. Programme: Part One.

    ERIC Educational Resources Information Center

    Renard, Rosamunde

    A survey was administered to families in St. Lucia during home visits between November 1993 and July 1995, after the local Parents As Teachers Programme had been affiliated with the Parents As Teachers Program in St. Louis, Missouri (affiliation took place in 1991). In all, 2000 home visits were conducted in the communities of Laborie, Banse,…

  15. Technology Tips: Simulation with the TI-Nspire

    ERIC Educational Resources Information Center

    Rudolph, Heidi J.

    2009-01-01

    Simulation is an important learning tool that allows students to grasp probability concepts, especially when the actual scenario does not need to be replicated entirely. In the cases of tossing coins and rolling dice, gathering the data before analyzing them can be laborious and might be a waste of precious class time--time that might be better…

  16. Use of Novel Surfaces to Reduce Bioadhesion on Infrastructure

    DTIC Science & Technology

    2010-06-01

    Research and Development Center Model species selection • Terrestrial gastropod  Danger to crops  Intermediate host to pathogens  Nocturnal...TBT  Non-target species, legacy contamination  Laborious • Bio-inspiration: leverage biological surfaces that have adapted unique properties... Adapted over 1000s of years • Hypothesis: microstructured pattern tessellations, hydrophobicity, surface properties or hybridizations will reduce

  17. New graphic methods for determining the depth and thickness of strata and the projection of dip

    USGS Publications Warehouse

    Palmer, Harold S.

    1919-01-01

    Geologists, both in the field and in the office, frequently encounter trigonometric problems the solution of which, though simple enough, is somewhat laborious by the use of trigonometric and logarithmic tables. Charts, tables, and diagrams of various types for facilitating the computations have been published, and a new method may seem to be a superfluous addition to the literature.

  18. Comparison of pre-processing techniques for fluorescence microscopy images of cells labeled for actin.

    PubMed

    Muralidhar, Gautam S; Channappayya, Sumohana S; Slater, John H; Blinka, Ellen M; Bovik, Alan C; Frey, Wolfgang; Markey, Mia K

    2008-11-06

    Automated analysis of fluorescence microscopy images of endothelial cells labeled for actin is important for quantifying changes in the actin cytoskeleton. The current manual approach is laborious and inefficient. The goal of our work is to develop automated image analysis methods, thereby increasing cell analysis throughput. In this study, we present preliminary results on comparing different algorithms for cell segmentation and image denoising.

  19. Creating a Culture of General Education Assessment

    ERIC Educational Resources Information Center

    Wong, Erwin J.; Campos, Francisca C.; Buxton, Ralph W.

    2008-01-01

    Many people know the myth of Sisyphus, the ancient king who committed an offense against the gods and was condemned for an eternity to roll a boulder unsuccessfully to the top of a steep hill. Each time he reached the summit, the boulder, of its own weight, would roll back to the bottom, whereupon Sisyphus would have to begin laboriously rolling…

  20. Computer assisted generation of the matrix elements between contracted wavefunctions in a Complete Active Space scheme

    NASA Astrophysics Data System (ADS)

    Angeli, C.; Cimiraglia, R.

    2005-02-01

    Starting from a CAS-SCF calculation a sequence of contracted functions can be generated by applying strings of spin-traced replacement operators to the CAS-SCF solution. The laborious task of producing the Hamiltonian matrix elements between such functions can be substantially reduced making use of a computer algebra system. An implementation employing the MuPAD system is presented and illustrated.

  1. Research | Research Site Name | NREL

    Science.gov Websites

    laboris nisi ut aliquip ex ea commodo consequat. Research Topic Images should have a width of 768 - height can vary. Lorem Ipsum Images should have a width of 768 - height can vary. Lorem Ipsum dolor sit amet consectetur Images should have a width of 768 - height can vary. Lorem Ipsum Lorem ipsum dolor sit amet

  2. Artificial Intelligence Methods: Challenge in Computer Based Polymer Design

    NASA Astrophysics Data System (ADS)

    Rusu, Teodora; Pinteala, Mariana; Cartwright, Hugh

    2009-08-01

    This paper deals with the use of Artificial Intelligence Methods (AI) in the design of new molecules possessing desired physical, chemical and biological properties. This is an important and difficult problem in the chemical, material and pharmaceutical industries. Traditional methods involve a laborious and expensive trial-and-error procedure, but computer-assisted approaches offer many advantages in the automation of molecular design.

  3. Contrasting Views of Complexity and Their Implications For Network-Centric Infrastructures

    DTIC Science & Technology

    2010-07-04

    problem) can be undecidable. While two gravitationally interacting bodies yield simple orbits, Poincare showed that the motion of even three...statistical me- chanics are valid only when the [billiard] balls are distributed, in their positions and motions , in a helter-skelter, i.e., a disorga- nized...Rube Goldberg, whose famous cartoons depict “ comically involved complicated invention[s], laboriously contrived to perform a simple operation” [68

  4. A Method for Isolation of Pasteuria penetrans Endospores for Bioassay and Genomic Studies

    PubMed Central

    Waterman, Jenora T.; Bird, David McK.; Opperman, Charles H.

    2006-01-01

    A rapid method for collection of Pasteuria penetrans endospores was developed. Roots containing P. penetrans-infected root-knot nematode females were softened by pectinase digestion, mechanically processed, and filtered to collect large numbers of viable endospores. This method obviates laborious handpicking of Pasteuria-infected females and yields endospores competent to attach to and infect nematodes. Endospores are suitable for morphology studies and DNA preparations. PMID:19259442

  5. A Method for Isolation of Pasteuria penetrans Endospores for Bioassay and Genomic Studies.

    PubMed

    Waterman, Jenora T; Bird, David McK; Opperman, Charles H

    2006-03-01

    A rapid method for collection of Pasteuria penetrans endospores was developed. Roots containing P. penetrans-infected root-knot nematode females were softened by pectinase digestion, mechanically processed, and filtered to collect large numbers of viable endospores. This method obviates laborious handpicking of Pasteuria-infected females and yields endospores competent to attach to and infect nematodes. Endospores are suitable for morphology studies and DNA preparations.

  6. A Bibliography of Shift Work Research: 1950-1982

    DTIC Science & Technology

    1983-09-01

    Opladen: Westdeutscher Verlag, pp. 103-112, 1975. :%i 630. Kojima, A., and Y. Niiyama: Diurnal Variations of 17- Ketogenic Steroid and Catecholamine...Experimental Food and Drinking Diet . Studia Laboris et Salutis, 11:42-45, 1972. 813. Miura, K.: Industrial Fatigue Survey on Three Shift Workers, Part 1... Ketogenic Steriod Excretion and the Adaptation to Changes of the Activity-Sleep Routine. Journal of Endocrinology, 22:377-385, 1961. 1083. Shephard, R

  7. Lymphogranuloma venereum variant L2b-specific polymerase chain reaction: insertion used to close an epidemiological gap.

    PubMed

    Verweij, S P; Catsburg, A; Ouburg, S; Lombardi, A; Heijmans, R; Dutly, F; Frei, R; Morré, S A; Goldenberger, D

    2011-11-01

    The management of the ongoing lymphogranuloma venereum epidemic in industrialized Western countries caused by Chlamydia trachomatis variant L2b still needs improvements in diagnosis, therapy and prevention. We therefore developed the first rapid C. trachomatis variant L2b-specific polymerase chain reaction to circumvent laborious ompA gene sequencing. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.

  8. Spindled and hollow spars

    NASA Technical Reports Server (NTRS)

    Blyth, J D

    1926-01-01

    The most usual method of arriving at the maximum amount of spindling or hollowing out permissible in the case of any particular spar section is by trial and error, a process which is apt to become laborious in the absence of good guessing - or luck. The following tables have been got out with the object of making it possible to arrive with certainty at a suitable section at the first attempt.

  9. Automated generation of a World Wide Web-based data entry and check program for medical applications.

    PubMed

    Kiuchi, T; Kaihara, S

    1997-02-01

    The World Wide Web-based form is a promising method for the construction of an on-line data collection system for clinical and epidemiological research. It is, however, laborious to prepare a common gateway interface (CGI) program for each project, which the World Wide Web server needs to handle the submitted data. In medicine, it is even more laborious because the CGI program must check deficits, type, ranges, and logical errors (bad combination of data) of entered data for quality assurance as well as data length and meta-characters of the entered data to enhance the security of the server. We have extended the specification of the hypertext markup language (HTML) form to accommodate information necessary for such data checking and we have developed software named AUTOFORM for this purpose. The software automatically analyzes the extended HTML form and generates the corresponding ordinary HTML form, 'Makefile', and C source of CGI programs. The resultant CGI program checks the entered data through the HTML form, records them in a computer, and returns them to the end-user. AUTOFORM drastically reduces the burden of development of the World Wide Web-based data entry system and allows the CGI programs to be more securely and reliably prepared than had they been written from scratch.

  10. Valence-bond theory of compounds of transition metals

    PubMed Central

    Pauling, Linus

    1975-01-01

    An equation relating the strength (bondforming power) of an spd hybrid bond orbital to the angles it makes with other bond orbitals is formulated and applied in the discussion of the structures of transition-metal carbonyls and other substances by the valence-bond method. The rather simple theory gives results that agree well with those obtained by the complicated and laborious calculation of sets of orthogonal hybrid bond orbitals with maximum strength. PMID:16592279

  11. Design and Construction of the Aerobot Robotic Manipulator (ARM)

    DTIC Science & Technology

    1993-12-01

    operation, position data was collected from an 8 Optotrak noncontact, position sensing device. This data was compared to the model and analyzed. (Chapter V...Moving the ARM and taking a measurement would have been a laborious task indeed. Instead, a device known as the Optotrak was used. The Optotrak is a...the position. To record the motor angles the data acquisition unit on the Optotrak had to be used. It had the capability of collecting information in

  12. A simple and novel modification of comet assay for determination of bacteriophage mediated bacterial cell lysis.

    PubMed

    Khairnar, Krishna; Sanmukh, Swapnil; Chandekar, Rajshree; Paunikar, Waman

    2014-07-01

    The comet assay is the widely used method for in vitro toxicity testing which is also an alternative to the use of animal models for in vivo testing. Since, its inception in 1984 by Ostling and Johansson, it is being modified frequently for a wide range of application. In spite of its wide applicability, unfortunately there is no report of its application in bacteriophages research. In this study, a novel application of comet assay for the detection of bacteriophage mediated bacterial cell lysis was described. The conventional methods in bacteriophage research for studying bacterial lysis by bacteriophages are plaque assay method. It is time consuming, laborious and costly. The lytic activity of bacteriophage devours the bacterial cell which results in the release of bacterial genomic material that gets detected by ethidium bromide staining method by the comet assay protocol. The objective of this study was to compare efficacy of comet assay with different assay used to study phage mediated bacterial lysis. The assay was performed on culture isolates (N=80 studies), modified comet assay appear to have relatively higher sensitivity and specificity than other assay. The results of the study showed that the application of comet assay can be an economical, time saving and less laborious alternative to conventional plaque assay for the detection of bacteriophage mediated bacterial cell lysis. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. A new design approach to MMI-based (de)multiplexers

    NASA Astrophysics Data System (ADS)

    Yueyu, Xiao; Sailing, He

    2004-09-01

    A novel design method of the wavelength (de)multiplexer is presented. The output spectral response of a (de)multiplexer is designed from the view of FIR filters. Avoiding laborious mathematic analysis, the (de)multiplexer is analyzed and designed in this explicit and simple method. A four channel (de)multiplexer based on multimode interference (MMI) is designed as an example. The result obtained agrees with that of the commonly used method, and is verified by a finite difference beam propagation method (FDBPM) simulation.

  14. Development of the System on the Internet for Pre-Assessment of Child Abuse Prevention

    NASA Astrophysics Data System (ADS)

    Honma, Satoru; Wakamatsu, Hidetoshi; Ueda, Reiko

    Some assessments have been applied to find possible factors that might lead to child abuse. PACAP is a new method proposed by Ueda and others as a pre-assessment of the concerning child abuse, which reduces its false-positive misclassification. The Internet PACAP is developed to reduce the laborious work of nurses and health care workers for the necessary processing and classifying the scores of the pre-assessment. The present system is expected to prevent the child abuse more effectively.

  15. Flow-through polymerase chain reaction inside a seamless 3D helical microreactor fabricated utilizing a silicone tube and a paraffin mold.

    PubMed

    Wu, Wenming; Trinh, Kieu The Loan; Lee, Nae Yoon

    2015-03-07

    We introduce a new strategy for fabricating a seamless three-dimensional (3D) helical microreactor utilizing a silicone tube and a paraffin mold. With this method, various shapes and sizes of 3D helical microreactors were fabricated, and a complicated and laborious photolithographic process, or 3D printing, was eliminated. With dramatically enhanced portability at a significantly reduced fabrication cost, such a device can be considered to be the simplest microreactor, developed to date, for performing the flow-through polymerase chain reaction (PCR).

  16. [The use of micromycetes for cleaning parts of aircraft].

    PubMed

    Dotsenko, G N; Feofilova, E P; Tereshina, V M; Memorskaia, A S

    2001-01-01

    The mycelial Fungi Penicillium funiculosum, P. citrinum, P. expansum, P. chrysogenum, Aspergillus ochraceus, A. alliaceus, A. luchaensis, A. flavus, and A. niger were isolated from enrichment cultures. These fungi actively destruct carbon deposits formed during exploitation of aircraft. A biotechnological method for removing fouling from parts of aircraft engines (PAE) was developed. This method is less laborious, more rapid and ecologically clean than contemporary chemical methods. Scanning microscopy was suggested to use for estimating the degree of decarbonization of PAE surfaces.

  17. Radio Frequency Identification for Space Habitat Inventory and Stowage Allocation Management

    NASA Technical Reports Server (NTRS)

    Wagner, Carole Y.

    2015-01-01

    To date, the most extensive space-based inventory management operation has been the International Space Station (ISS). Approximately 20,000 items are tracked with the Inventory Management System (IMS) software application that requires both flight and ground crews to update the database daily. This audit process is manually intensive and laborious, requiring the crew to open cargo transfer bags (CTBs), then Ziplock bags therein, to retrieve individual items. This inventory process contributes greatly to the time allocated for general crew tasks.

  18. A test of the 'one-point method' for estimating maximum carboxylation capacity from field-measured, light-saturated photosynthesis

    DOE PAGES

    Martin G. De Kauwe; Serbin, Shawn P.; Lin, Yan -Shih; ...

    2015-12-31

    Here, simulations of photosynthesis by terrestrial biosphere models typically need a specification of the maximum carboxylation rate (V cmax). Estimating this parameter using A–C i curves (net photosynthesis, A, vs intercellular CO 2 concentration, C i) is laborious, which limits availability of V cmax data. However, many multispecies field datasets include net photosynthetic rate at saturating irradiance and at ambient atmospheric CO 2 concentration (A sat) measurements, from which V cmax can be extracted using a ‘one-point method’.

  19. 2,2'-Biphenols via protecting group-free thermal or microwave-accelerated Suzuki-Miyaura coupling in water.

    PubMed

    Schmidt, Bernd; Riemer, Martin; Karras, Manfred

    2013-09-06

    User-friendly protocols for the protecting group-free synthesis of 2,2'-biphenols via Suzuki-Miyaura coupling of o-halophenols and o-boronophenol are presented. The reactions proceed in water in the presence of simple additives such as K2CO3, KOH, KF, or TBAF and with commercially available Pd/C as precatalyst. Expensive or laboriously synthesized ligands or other additives are not required. In the case of bromophenols, efficient rate acceleration and short reaction times were accomplished by microwave irradiation.

  20. Holdup measurement for nuclear fuel manufacturing plants

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zucker, M.S.; Degen, M.; Cohen, I.

    1981-07-13

    The assay of nuclear material holdup in fuel manufacturing plants is a laborious but often necessary part of completing the material balance. A range of instruments, standards, and a methodology for assaying holdup has been developed. The objectives of holdup measurement are ascertaining the amount, distribution, and how firmly fixed the SNM is. The purposes are reconciliation of material unbalance during or after a manufacturing campaign or plant decommissioning, to decide security requirements, or whether further recovery efforts are justified.

  1. British media attacks on homeopathy: are they justified?

    PubMed

    Vithoulkas, George

    2008-04-01

    Homeopathy is being attacked by the British media. These attacks draw support from irresponsible and unjustified claims by certain teachers of homeopathy. Such claims include the use of 'dream' and 'imaginative' methods for provings. For prescribing some such teachers attempt to replace the laborious process of matching symptom picture and remedy with spurious theories based on 'signatures', sensations and other methods. Other irresponsible claims have also been made. These "new ideas" risk destroying the principles, theory, and practice of homeopathy.

  2. Life's Still Lifes

    NASA Astrophysics Data System (ADS)

    McIntosh, Harold V.

    The de Bruijn diagram describing those decompositions of the neighborhoods of a one dimensional cellular automaton which conform to predetermined requirements of periodicity and translational symmetry shows how to construct extended configurations satisfying the same requirements. Similar diagrams, formed by stages, describe higher dimensional automata, although they become more laborious to compute with increasing neighborhood size. The procedure is illustrated by computing some still lifes for Conway's game of Life, a widely known two dimensional cellular automaton. This paper is written in September 10, 1988.

  3. A New Method with General Diagnostic Utility for the Calculation of Immunoglobulin G Avidity

    PubMed Central

    Korhonen, Maria H.; Brunstein, John; Haario, Heikki; Katnikov, Alexei; Rescaldani, Roberto; Hedman, Klaus

    1999-01-01

    The reference method for immunoglobulin G (IgG) avidity determination includes reagent-consuming serum titration. Aiming at better IgG avidity diagnostics, we applied a logistic model for the reproduction of antibody titration curves. This method was tested with well-characterized serum panels for cytomegalovirus, Epstein-Barr virus, rubella virus, parvovirus B19, and Toxoplasma gondii. This approach for IgG avidity calculation is generally applicable and attains the diagnostic performance of the reference method while being less laborious and twice as cost-effective. PMID:10473525

  4. Formic Acid-Based Direct, On-Plate Testing of Yeast and Corynebacterium Species by Bruker Biotyper Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry

    PubMed Central

    Theel, Elitza S.; Schmitt, Bryan H.; Hall, Leslie; Cunningham, Scott A.; Walchak, Robert C.; Patel, Robin

    2012-01-01

    An on-plate testing method using formic acid was evaluated on the Bruker Biotyper matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry system using 90 yeast and 78 Corynebacterium species isolates, and 95.6 and 81.1% of yeast and 96.1 and 92.3% of Corynebacterium isolates were correctly identified to the genus and species levels, respectively. The on-plate method using formic acid yielded identification percentages similar to those for the conventional but more laborious tube-based extraction. PMID:22760034

  5. A size-adjustable radiofrequency coil for investigating plants in a Halbach magnet

    NASA Astrophysics Data System (ADS)

    Oligschläger, Dirk; Rehorn, Christian; Lehmkuhl, Sören; Adams, Michael; Adams, Alina; Blümich, Bernhard

    2017-05-01

    A radio-frequency coil with adjustable distance has been developed and tested for in-situ examination of growing plants. The Helmholtz-based coil design reduces laborious tuning and matching efforts encountered with solenoids wound around a growing stem or branch. Relaxation experiments were performed on tomato plants and winter wheat under controlled light irradiation. Changes in signal amplitude and in relaxation times T2 were recorded over day and night cycles. Peaks in distributions of relaxation times were attributed to different tissue components of two different plants.

  6. Auxiliary Library Explorer (ALEX) Development

    DTIC Science & Technology

    2016-02-01

    non-empty cells. This is a laborious manual task and could probably have been avoided by using Java code to read the data directly from Excel. In fact...it might be even easier to leave the data as a comma separated variables (CSV) file and read the data in with Java , although this could create other...This is first implemented using the MakeFullDatabaseapp Java project, which performs an SQL query on the DSpace data to return a list of items for which

  7. Symmetry dependence of holograms for optical trapping

    NASA Astrophysics Data System (ADS)

    Curtis, Jennifer E.; Schmitz, Christian H. J.; Spatz, Joachim P.

    2005-08-01

    No iterative algorithm is necessary to calculate holograms for most holographic optical trapping patterns. Instead, holograms may be produced by a simple extension of the prisms-and-lenses method. This formulaic approach yields the same diffraction efficiency as iterative algorithms for any asymmetric or symmetric but nonperiodic pattern of points while requiring less calculation time. A slight spatial disordering of periodic patterns significantly reduces intensity variations between the different traps without extra calculation costs. Eliminating laborious hologram calculations should greatly facilitate interactive holographic trapping.

  8. Reducing maintenance costs in agreement with CNC machine tools reliability

    NASA Astrophysics Data System (ADS)

    Ungureanu, A. L.; Stan, G.; Butunoi, P. A.

    2016-08-01

    Aligning maintenance strategy with reliability is a challenge due to the need to find an optimal balance between them. Because the various methods described in the relevant literature involve laborious calculations or use of software that can be costly, this paper proposes a method that is easier to implement on CNC machine tools. The new method, called the Consequence of Failure Analysis (CFA) is based on technical and economic optimization, aimed at obtaining a level of required performance with minimum investment and maintenance costs.

  9. The Connectivity Map: a new tool for biomedical research.

    PubMed

    Lamb, Justin

    2007-01-01

    The ultimate objective of biomedical research is to connect human diseases with the genes that underlie them and drugs that treat them. But this remains a daunting task, and even the most inspired researchers still have to resort to laborious screens of genetic or chemical libraries. What if at least some parts of this screening process could be systematized and centralized? And hits found and hypotheses generated with something resembling an internet search engine? These are the questions the Connectivity Map project set out to answer.

  10. Application of Theodorsen's Theory to Propeller Design

    NASA Technical Reports Server (NTRS)

    Crigler, John L

    1948-01-01

    A theoretical analysis is presented for obtaining by use of Theodorsen's propeller theory the load distribution along a propeller radius to give the optimum propeller efficiency for any design condition.The efficiencies realized by designing for the optimum load distribution are given in graphs, and the optimum efficiency for any design condition may be read directly from the graph without any laborious calculations. Examples are included to illustrate the method of obtaining the optimum load distributions for both single-rotating and dual-rotating propellers.

  11. Application of Theodorsen's theory to propeller design

    NASA Technical Reports Server (NTRS)

    Crigler, John L

    1949-01-01

    A theoretical analysis is presented for obtaining, by use of Theodorsen's propeller theory, the load distribution along a propeller radius to give the optimum propeller efficiency for any design condition. The efficiencies realized by designing for the optimum load distribution are given in graphs, and the optimum efficiency for any design condition may be read directly from the graph without any laborious calculations. Examples are included to illustrate the method of obtaining the optimum load distributions for both single-rotating and dual-rotating propellers.

  12. Extending the Query Language of a Data Warehouse for Patient Recruitment.

    PubMed

    Dietrich, Georg; Ertl, Maximilian; Fette, Georg; Kaspar, Mathias; Krebs, Jonathan; Mackenrodt, Daniel; Störk, Stefan; Puppe, Frank

    2017-01-01

    Patient recruitment for clinical trials is a laborious task, as many texts have to be screened. Usually, this work is done manually and takes a lot of time. We have developed a system that automates the screening process. Besides standard keyword queries, the query language supports extraction of numbers, time-spans and negations. In a feasibility study for patient recruitment from a stroke unit with 40 patients, we achieved encouraging extraction rates above 95% for numbers and negations and ca. 86% for time spans.

  13. Formic acid-based direct, on-plate testing of yeast and Corynebacterium species by Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry.

    PubMed

    Theel, Elitza S; Schmitt, Bryan H; Hall, Leslie; Cunningham, Scott A; Walchak, Robert C; Patel, Robin; Wengenack, Nancy L

    2012-09-01

    An on-plate testing method using formic acid was evaluated on the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system using 90 yeast and 78 Corynebacterium species isolates, and 95.6 and 81.1% of yeast and 96.1 and 92.3% of Corynebacterium isolates were correctly identified to the genus and species levels, respectively. The on-plate method using formic acid yielded identification percentages similar to those for the conventional but more laborious tube-based extraction.

  14. Bacteriophage PRD1 batch experiments to study attachment, detachment and inactivation processes

    NASA Astrophysics Data System (ADS)

    Sadeghi, Gholamreza; Schijven, Jack F.; Behrends, Thilo; Hassanizadeh, S. Majid; van Genuchten, Martinus Th.

    2013-09-01

    Knowledge of virus removal in subsurface environments is pivotal for assessing the risk of viral contamination of water resources and developing appropriate protection measures. Columns packed with sand are frequently used to quantify attachment, detachment and inactivation rates of viruses. Since column transport experiments are very laborious, a common alternative is to perform batch experiments where usually one or two measurements are done assuming equilibrium is reached. It is also possible to perform kinetic batch experiments. In that case, however, it is necessary to monitor changes in the concentration with time. This means that kinetic batch experiments will be almost as laborious as column experiments. Moreover, attachment and detachment rate coefficients derived from batch experiments may differ from those determined using column experiments. The aim of this study was to determine the utility of kinetic batch experiments and investigate the effects of different designs of the batch experiments on estimated attachment, detachment and inactivation rate coefficients. The experiments involved various combinations of container size, sand-water ratio, and mixing method (i.e., rolling or tumbling by pivoting the tubes around their horizontal or vertical axes, respectively). Batch experiments were conducted with clean quartz sand, water at pH 7 and ionic strength of 20 mM, and using the bacteriophage PRD1 as a model virus. Values of attachment, detachment and inactivation rate coefficients were found by fitting an analytical solution of the kinetic model equations to the data. Attachment rate coefficients were found to be systematically higher under tumbling than under rolling conditions because of better mixing and more efficient contact of phages with the surfaces of the sand grains. In both mixing methods, more sand in the container yielded higher attachment rate coefficients. A linear increase in the detachment rate coefficient was observed with increased

  15. Bacteriophage PRD1 batch experiments to study attachment, detachment and inactivation processes.

    PubMed

    Sadeghi, Gholamreza; Schijven, Jack F; Behrends, Thilo; Hassanizadeh, S Majid; van Genuchten, Martinus Th

    2013-09-01

    Knowledge of virus removal in subsurface environments is pivotal for assessing the risk of viral contamination of water resources and developing appropriate protection measures. Columns packed with sand are frequently used to quantify attachment, detachment and inactivation rates of viruses. Since column transport experiments are very laborious, a common alternative is to perform batch experiments where usually one or two measurements are done assuming equilibrium is reached. It is also possible to perform kinetic batch experiments. In that case, however, it is necessary to monitor changes in the concentration with time. This means that kinetic batch experiments will be almost as laborious as column experiments. Moreover, attachment and detachment rate coefficients derived from batch experiments may differ from those determined using column experiments. The aim of this study was to determine the utility of kinetic batch experiments and investigate the effects of different designs of the batch experiments on estimated attachment, detachment and inactivation rate coefficients. The experiments involved various combinations of container size, sand-water ratio, and mixing method (i.e., rolling or tumbling by pivoting the tubes around their horizontal or vertical axes, respectively). Batch experiments were conducted with clean quartz sand, water at pH 7 and ionic strength of 20 mM, and using the bacteriophage PRD1 as a model virus. Values of attachment, detachment and inactivation rate coefficients were found by fitting an analytical solution of the kinetic model equations to the data. Attachment rate coefficients were found to be systematically higher under tumbling than under rolling conditions because of better mixing and more efficient contact of phages with the surfaces of the sand grains. In both mixing methods, more sand in the container yielded higher attachment rate coefficients. A linear increase in the detachment rate coefficient was observed with increased

  16. Diagnosis of autosomal dominant polycystic kidney disease using efficient PKD1 and PKD2 targeted next-generation sequencing.

    PubMed

    Trujillano, Daniel; Bullich, Gemma; Ossowski, Stephan; Ballarín, José; Torra, Roser; Estivill, Xavier; Ars, Elisabet

    2014-09-01

    Molecular diagnostics of autosomal dominant polycystic kidney disease (ADPKD) relies on mutation screening of PKD1 and PKD2, which is complicated by extensive allelic heterogeneity and the presence of six highly homologous sequences of PKD1. To date, specific sequencing of PKD1 requires laborious long-range amplifications. The high cost and long turnaround time of PKD1 and PKD2 mutation analysis using conventional techniques limits its widespread application in clinical settings. We performed targeted next-generation sequencing (NGS) of PKD1 and PKD2. Pooled barcoded DNA patient libraries were enriched by in-solution hybridization with PKD1 and PKD2 capture probes. Bioinformatics analysis was performed using an in-house developed pipeline. We validated the assay in a cohort of 36 patients with previously known PKD1 and PKD2 mutations and five control individuals. Then, we used the same assay and bioinformatics analysis in a discovery cohort of 12 uncharacterized patients. We detected 35 out of 36 known definitely, highly likely, and likely pathogenic mutations in the validation cohort, including two large deletions. In the discovery cohort, we detected 11 different pathogenic mutations in 10 out of 12 patients. This study demonstrates that laborious long-range PCRs of the repeated PKD1 region can be avoided by in-solution enrichment of PKD1 and PKD2 and NGS. This strategy significantly reduces the cost and time for simultaneous PKD1 and PKD2 sequence analysis, facilitating routine genetic diagnostics of ADPKD.

  17. The cost and quality of hospitalists.

    PubMed

    Gipe, B T

    2000-03-01

    The Hospitalist concept is becoming the standard of practice as managed care penetration grows. It is increasingly difficult to do a good job in the outpatient arena and this makes the old "double threat" model in which the physician speeds through inpatient rounds in the morning before clinic, during lunch, and again at night after his office closes, obsolete. There is simply too much at stake in the inpatient arena to have large periods of time in which physician coverage is minimal. Controversy exists as to whether or not the services should be "outsourced" to a Hospitalist management company or developed internally, using physicians who historically have had a significant presence in the hospital. If the services are outsourced, then it is essential that they be built around a strong local physician leader who remains active in patient care. The French author, Anais Nin wrote: "There are very few human beings who receive the truth, complete and staggering, by instant illumination. Most of them acquire it fragment by fragment, on a small scale, by successive developments, cellularly, like a laborious mosaic." Inpatient care in the United States is adequately described as a laborious mosaic in which providers of many different services surround patients with many different problems. Hospitalist programs can help to bring order to the mosaic by consistently combining the correct physician talent with the system's sickest and most expensive patients in order to achieve the best possible outcomes.

  18. Applying high resolution remote sensing image and DEM to falling boulder hazard assessment

    NASA Astrophysics Data System (ADS)

    Huang, Changqing; Shi, Wenzhong; Ng, K. C.

    2005-10-01

    Boulder fall hazard assessing generally requires gaining the boulder information. The extensive mapping and surveying fieldwork is a time-consuming, laborious and dangerous conventional method. So this paper proposes an applying image processing technology to extract boulder and assess boulder fall hazard from high resolution remote sensing image. The method can replace the conventional method and extract the boulder information in high accuracy, include boulder size, shape, height and the slope and aspect of its position. With above boulder information, it can be satisfied for assessing, prevention and cure boulder fall hazard.

  19. A noninvasive, direct real-time PCR method for sex determination in multiple avian species

    USGS Publications Warehouse

    Brubaker, Jessica L.; Karouna-Renier, Natalie K.; Chen, Yu; Jenko, Kathryn; Sprague, Daniel T.; Henry, Paula F.P.

    2011-01-01

    Polymerase chain reaction (PCR)-based methods to determine the sex of birds are well established and have seen few modifications since they were first introduced in the 1990s. Although these methods allowed for sex determination in species that were previously difficult to analyse, they were not conducive to high-throughput analysis because of the laboriousness of DNA extraction and gel electrophoresis. We developed a high-throughput real-time PCR-based method for analysis of sex in birds, which uses noninvasive sample collection and avoids DNA extraction and gel electrophoresis.

  20. Isolation of genomic DNA using magnetic cobalt ferrite and silica particles.

    PubMed

    Prodelalová, Jana; Rittich, Bohuslav; Spanová, Alena; Petrová, Katerina; Benes, Milan J

    2004-11-12

    Adsorption separation techniques as an alternative to laborious traditional methods (e.g., based on phenol extraction procedure) have been applied for DNA purification. In this work we used two types of particles: silica and cobalt ferrite (unmodified or modified with a reagent containing weakly basic aminoethyl groups, aminophenyl groups, or alginic acid). DNA from chicken erythrocytes and DNA isolated from bacteria Lactococcus lactis were used for testing of adsorption/desorption properties of particles. The cobalt ferrite particles modified with different reagents were used for isolation of PCR-ready bacterial DNA from different dairy products.

  1. A practical method to rapidly dissolve metallic stents.

    PubMed

    Bradshaw, Scott H; Kennedy, Lloyd; Dexter, David F; Veinot, John P

    2009-01-01

    Metallic stents are commonly used in many clinical applications including peripheral vascular disease intervention, biliary obstruction, endovascular repair of aneurysms, and percutaneous coronary interventions. In the examination of vascular stent placement, it is important to determine if the stent is open or has become obstructed. This is increasingly important in the era of drug-eluting stent usage in coronary arteries. We describe a practical, rapid and cost-effective method to dissolve most metallic stents leaving the vascular and luminal tissues intact. This practical method may replace the laborious and expensive plastic embedding methods currently utilized.

  2. Consistent Correlations for Parameterised Boolean Equation Systems with Applications in Correctness Proofs for Manipulations

    NASA Astrophysics Data System (ADS)

    Willemse, Tim A. C.

    We introduce the concept of consistent correlations for parameterised Boolean equation systems (PBESs), motivated largely by the laborious proofs of correctness required for most manipulations in this setting. Consistent correlations focus on relating the equations that occur in PBESs, rather than their solutions. For a fragment of PBESs, consistent correlations are shown to coincide with a recently introduced form of bisimulation. Finally, we show that bisimilarity on processes induces consistent correlations on PBESs encoding model checking problems. We apply our theory to two example manipulations from the literature.

  3. Laboratory Information Management System Chain of Custody: Reliability and Security

    PubMed Central

    Tomlinson, J. J.; Elliott-Smith, W.; Radosta, T.

    2006-01-01

    A chain of custody (COC) is required in many laboratories that handle forensics, drugs of abuse, environmental, clinical, and DNA testing, as well as other laboratories that want to assure reliability of reported results. Maintaining a dependable COC can be laborious, but with the recent establishment of the criteria for electronic records and signatures by US regulatory agencies, laboratory information management systems (LIMSs) are now being developed to fully automate COCs. The extent of automation and of data reliability can vary, and FDA- and EPA-compliant electronic signatures and system security are rare. PMID:17671623

  4. Microrheology with optical tweezers: measuring the relative viscosity of solutions 'at a glance'.

    PubMed

    Tassieri, Manlio; Del Giudice, Francesco; Robertson, Emma J; Jain, Neena; Fries, Bettina; Wilson, Rab; Glidle, Andrew; Greco, Francesco; Netti, Paolo Antonio; Maffettone, Pier Luca; Bicanic, Tihana; Cooper, Jonathan M

    2015-03-06

    We present a straightforward method for measuring the relative viscosity of fluids via a simple graphical analysis of the normalised position autocorrelation function of an optically trapped bead, without the need of embarking on laborious calculations. The advantages of the proposed microrheology method are evident when it is adopted for measurements of materials whose availability is limited, such as those involved in biological studies. The method has been validated by direct comparison with conventional bulk rheology methods, and has been applied both to characterise synthetic linear polyelectrolytes solutions and to study biomedical samples.

  5. Microrheology with Optical Tweezers: Measuring the relative viscosity of solutions ‘at a glance'

    PubMed Central

    Tassieri, Manlio; Giudice, Francesco Del; Robertson, Emma J.; Jain, Neena; Fries, Bettina; Wilson, Rab; Glidle, Andrew; Greco, Francesco; Netti, Paolo Antonio; Maffettone, Pier Luca; Bicanic, Tihana; Cooper, Jonathan M.

    2015-01-01

    We present a straightforward method for measuring the relative viscosity of fluids via a simple graphical analysis of the normalised position autocorrelation function of an optically trapped bead, without the need of embarking on laborious calculations. The advantages of the proposed microrheology method are evident when it is adopted for measurements of materials whose availability is limited, such as those involved in biological studies. The method has been validated by direct comparison with conventional bulk rheology methods, and has been applied both to characterise synthetic linear polyelectrolytes solutions and to study biomedical samples. PMID:25743468

  6. Nanoscale Label-free Bioprobes to Detect Intracellular Proteins in Single Living Cells

    PubMed Central

    Hong, Wooyoung; Liang, Feng; Schaak, Diane; Loncar, Marko; Quan, Qimin

    2014-01-01

    Fluorescent labeling techniques have been widely used in live cell studies; however, the labeling processes can be laborious and challenging for use in non-transfectable cells, and labels can interfere with protein functions. While label-free biosensors have been realized by nanofabrication, a method to track intracellular protein dynamics in real-time, in situ and in living cells has not been found. Here we present the first demonstration of label-free detection of intracellular p53 protein dynamics through a nanoscale surface plasmon-polariton fiber-tip-probe (FTP). PMID:25154394

  7. Development of an automated processing and screening system for the space shuttle orbiter flight test data

    NASA Technical Reports Server (NTRS)

    Mccutchen, D. K.; Brose, J. F.; Palm, W. E.

    1982-01-01

    One nemesis of the structural dynamist is the tedious task of reviewing large quantities of data. This data, obtained from various types of instrumentation, may be represented by oscillogram records, root-mean-squared (rms) time histories, power spectral densities, shock spectra, 1/3 octave band analyses, and various statistical distributions. In an attempt to reduce the laborious task of manually reviewing all of the space shuttle orbiter wideband frequency-modulated (FM) analog data, an automated processing system was developed to perform the screening process based upon predefined or predicted threshold criteria.

  8. DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rogers, Jameson K.; Church, George M.

    Here, engineering cells to produce valuable metabolic products is hindered by the slow and laborious methods available for evaluating product concentration. Consequently, many designs go unevaluated, and the dynamics of product formation over time go unobserved. In this work, we develop a framework for observing product formation in real time without the need for sample preparation or laborious analytical methods. We use genetically encoded biosensors derived from small-molecule responsive transcription factors to provide a fluorescent readout that is proportional to the intracellular concentration of a target metabolite. Combining an appropriate biosensor with cells designed to produce a metabolic product allowsmore » us to track product formation by observing fluorescence. With individual cells exhibiting fluorescent intensities proportional to the amount of metabolite they produce, high-throughput methods can be used to rank the quality of genetic variants or production conditions. We observe production of several renewable plastic precursors with fluorescent readouts and demonstrate that higher fluorescence is indeed an indicator of higher product titer. Using fluorescence as a guide, we identify process parameters that produce 3-hydroxypropionate at 4.2 g/L, 23-fold higher than previously reported. We also report, to our knowledge, the first engineered route from glucose to acrylate, a plastic precursor with global sales of 14 billion. Finally, we monitor the production of glucarate, a replacement for environmentally damaging detergents, and muconate, a renewable precursor to polyethylene terephthalate and nylon with combined markets of 51 billion, in real time, demonstrating that our method is applicable to a wide range of molecules.« less

  9. Genetically encoded sensors enable real-time observation of metabolite production

    PubMed Central

    Rogers, Jameson K.; Church, George M.

    2016-01-01

    Engineering cells to produce valuable metabolic products is hindered by the slow and laborious methods available for evaluating product concentration. Consequently, many designs go unevaluated, and the dynamics of product formation over time go unobserved. In this work, we develop a framework for observing product formation in real time without the need for sample preparation or laborious analytical methods. We use genetically encoded biosensors derived from small-molecule responsive transcription factors to provide a fluorescent readout that is proportional to the intracellular concentration of a target metabolite. Combining an appropriate biosensor with cells designed to produce a metabolic product allows us to track product formation by observing fluorescence. With individual cells exhibiting fluorescent intensities proportional to the amount of metabolite they produce, high-throughput methods can be used to rank the quality of genetic variants or production conditions. We observe production of several renewable plastic precursors with fluorescent readouts and demonstrate that higher fluorescence is indeed an indicator of higher product titer. Using fluorescence as a guide, we identify process parameters that produce 3-hydroxypropionate at 4.2 g/L, 23-fold higher than previously reported. We also report, to our knowledge, the first engineered route from glucose to acrylate, a plastic precursor with global sales of $14 billion. Finally, we monitor the production of glucarate, a replacement for environmentally damaging detergents, and muconate, a renewable precursor to polyethylene terephthalate and nylon with combined markets of $51 billion, in real time, demonstrating that our method is applicable to a wide range of molecules. PMID:26858408

  10. Genetically encoded sensors enable real-time observation of metabolite production

    DOE PAGES

    Rogers, Jameson K.; Church, George M.

    2016-02-08

    Here, engineering cells to produce valuable metabolic products is hindered by the slow and laborious methods available for evaluating product concentration. Consequently, many designs go unevaluated, and the dynamics of product formation over time go unobserved. In this work, we develop a framework for observing product formation in real time without the need for sample preparation or laborious analytical methods. We use genetically encoded biosensors derived from small-molecule responsive transcription factors to provide a fluorescent readout that is proportional to the intracellular concentration of a target metabolite. Combining an appropriate biosensor with cells designed to produce a metabolic product allowsmore » us to track product formation by observing fluorescence. With individual cells exhibiting fluorescent intensities proportional to the amount of metabolite they produce, high-throughput methods can be used to rank the quality of genetic variants or production conditions. We observe production of several renewable plastic precursors with fluorescent readouts and demonstrate that higher fluorescence is indeed an indicator of higher product titer. Using fluorescence as a guide, we identify process parameters that produce 3-hydroxypropionate at 4.2 g/L, 23-fold higher than previously reported. We also report, to our knowledge, the first engineered route from glucose to acrylate, a plastic precursor with global sales of 14 billion. Finally, we monitor the production of glucarate, a replacement for environmentally damaging detergents, and muconate, a renewable precursor to polyethylene terephthalate and nylon with combined markets of 51 billion, in real time, demonstrating that our method is applicable to a wide range of molecules.« less

  11. Multibody dynamics model building using graphical interfaces

    NASA Technical Reports Server (NTRS)

    Macala, Glenn A.

    1989-01-01

    In recent years, the extremely laborious task of manually deriving equations of motion for the simulation of multibody spacecraft dynamics has largely been eliminated. Instead, the dynamicist now works with commonly available general purpose dynamics simulation programs which generate the equations of motion either explicitly or implicitly via computer codes. The user interface to these programs has predominantly been via input data files, each with its own required format and peculiarities, causing errors and frustrations during program setup. Recent progress in a more natural method of data input for dynamics programs: the graphical interface, is described.

  12. Implementation of Arithmetic and Nonarithmetic Functions on a Label-free and DNA-based Platform

    NASA Astrophysics Data System (ADS)

    Wang, Kun; He, Mengqi; Wang, Jin; He, Ronghuan; Wang, Jianhua

    2016-10-01

    A series of complex logic gates were constructed based on graphene oxide and DNA-templated silver nanoclusters to perform both arithmetic and nonarithmetic functions. For the purpose of satisfying the requirements of progressive computational complexity and cost-effectiveness, a label-free and universal platform was developed by integration of various functions, including half adder, half subtractor, multiplexer and demultiplexer. The label-free system avoided laborious modification of biomolecules. The designed DNA-based logic gates can be implemented with readout of near-infrared fluorescence, and exhibit great potential applications in the field of bioimaging as well as disease diagnosis.

  13. Design and Implementation of Harmful Algal Bloom Diagnosis System Based on J2EE Platform

    NASA Astrophysics Data System (ADS)

    Guo, Chunfeng; Zheng, Haiyong; Ji, Guangrong; Lv, Liang

    According to the shortcomings which are time consuming and laborious of the traditional HAB (Harmful Algal Bloom) diagnosis by the experienced experts using microscope, all kinds of methods and technologies to identify HAB emerged such as microscopic images, molecular biology, characteristics of pigments analysis, fluorescence spectra, inherent optical properties, etc. This paper proposes the design and implementation of a web-based diagnosis system integrating the popular methods for HAB identification. This system is designed with J2EE platform based on MVC (Model-View-Controller) model as well as technologies such as JSP, Servlets, EJB and JDBC.

  14. Free-living amoebae: Health concerns in the indoor environment

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tyndall, R.L.; Ironside, K.S.

    1990-01-01

    Free-living amoebae are the most likely protozoa implicated in health concerns of the indoor environment. These amoebae can be the source of allergic reactions, eye infections or, on rare occasions, encephalitis. While too large to be effectively aerosolized, free- living amoebae can support the multiplication of pathogens such as Legionella which are easily aerosolized and infectious via the pulmonary route. Traditional detection methods for free-living amoebae are laborious and time consuming. Newer techniques for rapidly detecting and quantitating free-living amoebae such as monoclonal antibodies, flow cytometry, gene probes, and laser optics have or could be employed. 25 refs.

  15. [Proteomics in infectious diseases].

    PubMed

    Quero, Sara; Párraga-Niño, Noemí; García-Núñez, Marian; Sabrià, Miquel

    2016-04-01

    Infectious diseases have a high incidence in the population, causing a major impact on global health. In vitro culture of microorganisms is the first technique applied for infection diagnosis which is laborious and time consuming. In recent decades, efforts have been focused on the applicability of "Omics" sciences, highlighting the progress provided by proteomic techniques in the field of infectious diseases. This review describes the management, processing and analysis of biological samples for proteomic research. Copyright © 2014 Elsevier España, S.L.U. y Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

  16. [Delayed (tension) pneumothorax after placement of a central venous catheter].

    PubMed

    Tan, E C; van der Vliet, J A

    1999-09-11

    Laborious attempts at introducing a central venous catheter for parenteral nutrition in two women, aged 36 and 62 years, were followed by shortness of breath after 32 and 10 hours, respectively. This symptom was due to a (tension) pneumothorax not visible on earlier roentgenograms. Thoracic drainage led to recovery. In all patients with a central venous catheter an undetected delayed pneumothorax can be present. Urgent chest X-ray examination should be performed in all patients with acute respiratory symptoms. Patients undergoing elective intubation with positive pressure breathing should be examined carefully, since they are at risk of developing a late (tension) pneumothorax.

  17. A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms.

    PubMed

    Leakey, Tatiana I; Zielinski, Jerzy; Siegfried, Rachel N; Siegel, Eric R; Fan, Chun-Yang; Cooney, Craig A

    2008-06-01

    DNA methylation at cytosines is a widely studied epigenetic modification. Methylation is commonly detected using bisulfite modification of DNA followed by PCR and additional techniques such as restriction digestion or sequencing. These additional techniques are either laborious, require specialized equipment, or are not quantitative. Here we describe a simple algorithm that yields quantitative results from analysis of conventional four-dye-trace sequencing. We call this method Mquant and we compare it with the established laboratory method of combined bisulfite restriction assay (COBRA). This analysis of sequencing electropherograms provides a simple, easily applied method to quantify DNA methylation at specific CpG sites.

  18. Poly(ethylene oxide) functionalization

    DOEpatents

    Pratt, Russell Clayton

    2014-04-08

    A simple procedure is provided by which the hydroxyl termini of poly(ethylene oxide) can be appended with functional groups to a useful extent by reaction and precipitation. The polymer is dissolved in warmed toluene, treated with an excess of organic base and somewhat less of an excess of a reactive acylating reagent, reacted for several hours, then precipitated in isopropanol so that the product can be isolated as a solid, and salt byproducts are washed away. This procedure enables functionalization of the polymer while not requiring laborious purification steps such as solvent-solvent extraction or dialysis to remove undesirable side products.

  19. Automatic generation of the index of productive syntax for child language transcripts.

    PubMed

    Hassanali, Khairun-nisa; Liu, Yang; Iglesias, Aquiles; Solorio, Thamar; Dollaghan, Christine

    2014-03-01

    The index of productive syntax (IPSyn; Scarborough (Applied Psycholinguistics 11:1-22, 1990) is a measure of syntactic development in child language that has been used in research and clinical settings to investigate the grammatical development of various groups of children. However, IPSyn is mostly calculated manually, which is an extremely laborious process. In this article, we describe the AC-IPSyn system, which automatically calculates the IPSyn score for child language transcripts using natural language processing techniques. Our results show that the AC-IPSyn system performs at levels comparable to scores computed manually. The AC-IPSyn system can be downloaded from www.hlt.utdallas.edu/~nisa/ipsyn.html .

  20. Nanotechnology in vascular tissue engineering: from nanoscaffolding towards rapid vessel biofabrication.

    PubMed

    Mironov, Vladimir; Kasyanov, Vladimir; Markwald, Roger R

    2008-06-01

    The existing methods of biofabrication for vascular tissue engineering are still bioreactor-based, extremely expensive, laborious and time consuming and, furthermore, not automated, which would be essential for an economically successful large-scale commercialization. The advances in nanotechnology can bring additional functionality to vascular scaffolds, optimize internal vascular graft surface and even help to direct the differentiation of stem cells into the vascular cell phenotype. The development of rapid nanotechnology-based methods of vascular tissue biofabrication represents one of most important recent technological breakthroughs in vascular tissue engineering because it dramatically accelerates vascular tissue assembly and, importantly, also eliminates the need for a bioreactor-based scaffold cellularization process.

  1. High-performance liquid chromatography purification of homogenous-length RNA produced by trans cleavage with a hammerhead ribozyme.

    PubMed Central

    Shields, T P; Mollova, E; Ste Marie, L; Hansen, M R; Pardi, A

    1999-01-01

    An improved method is presented for the preparation of milligram quantities of homogenous-length RNAs suitable for nuclear magnetic resonance or X-ray crystallographic structural studies. Heterogeneous-length RNA transcripts are processed with a hammerhead ribozyme to yield homogenous-length products that are then readily purified by anion exchange high-performance liquid chromatography. This procedure eliminates the need for denaturing polyacrylamide gel electrophoresis, which is the most laborious step in the standard procedure for large-scale production of RNA by in vitro transcription. The hammerhead processing of the heterogeneous-length RNA transcripts also substantially improves the overall yield and purity of the desired RNA product. PMID:10496226

  2. Medical Device for Automated Prick Test Reading.

    PubMed

    Justo, Xabier; Diaz, Inaki; Gil, Jorge Juan; Gastaminza, Gabriel

    2018-05-01

    Allergy tests are routinely performed in most hospitals everyday. However, measuring the outcomes of these tests is still a very laborious manual task. Current methods and systems lack of precision and repeatability. This paper presents a novel mechatronic system that is able to scan a patient's entire arm and provide allergists with precise measures of wheals for diagnosis. The device is based on 3-D laser technology and specific algorithms have been developed to process the information gathered. This system aims to automate the reading of skin prick tests and make gains in speed, accuracy, and reliability. Several experiments have been performed to evaluate the performance of the system.

  3. An integrated workflow for analysis of ChIP-chip data.

    PubMed

    Weigelt, Karin; Moehle, Christoph; Stempfl, Thomas; Weber, Bernhard; Langmann, Thomas

    2008-08-01

    Although ChIP-chip is a powerful tool for genome-wide discovery of transcription factor target genes, the steps involving raw data analysis, identification of promoters, and correlation with binding sites are still laborious processes. Therefore, we report an integrated workflow for the analysis of promoter tiling arrays with the Genomatix ChipInspector system. We compare this tool with open-source software packages to identify PU.1 regulated genes in mouse macrophages. Our results suggest that ChipInspector data analysis, comparative genomics for binding site prediction, and pathway/network modeling significantly facilitate and enhance whole-genome promoter profiling to reveal in vivo sites of transcription factor-DNA interactions.

  4. Multislice imaging of integrated circuits by precession X-ray ptychography.

    PubMed

    Shimomura, Kei; Hirose, Makoto; Takahashi, Yukio

    2018-01-01

    A method for nondestructively visualizing multisection nanostructures of integrated circuits by X-ray ptychography with a multislice approach is proposed. In this study, tilt-series ptychographic diffraction data sets of a two-layered circuit with a ∼1.4 µm gap at nine incident angles are collected in a wide Q range and then artifact-reduced phase images of each layer are successfully reconstructed at ∼10 nm resolution. The present method has great potential for the three-dimensional observation of flat specimens with thickness on the order of 100 µm, such as three-dimensional stacked integrated circuits based on through-silicon vias, without laborious sample preparation.

  5. A video-based system for hand-driven stop-motion animation.

    PubMed

    Han, Xiaoguang; Fu, Hongbo; Zheng, Hanlin; Liu, Ligang; Wang, Jue

    2013-01-01

    Stop-motion is a well-established animation technique but is often laborious and requires craft skills. A new video-based system can animate the vast majority of everyday objects in stop-motion style, more flexibly and intuitively. Animators can perform and capture motions continuously instead of breaking them into increments and shooting one still picture per increment. More important, the system permits direct hand manipulation without resorting to rigs, achieving more natural object control for beginners. The system's key component is two-phase keyframe-based capturing and processing, assisted by computer vision techniques. With this system, even amateurs can generate high-quality stop-motion animations.

  6. Laser interferometry for the determination of thickness distributions of low absorbing films and their spatial and thickness resolutions.

    PubMed

    Mishima, T; Kao, K C

    1982-03-15

    New laser interferometry has been developed, based on the principle that a 2-D fringe pattern can be produced by interference of spatially coherent light beams. To avoid the effect of reflection from the back surface of the substrate, the Brewster angle of incidence is adopted; to suppress the effect of diffraction, a lens or a lens system is used. This laser interferometry is an efficient nondestructive technique for the determination of thickness distributions or uniformities of low absorbing films on transparent substrates over a large area without involving laborious computations. The limitation of spatial resolution, thickness resolution, and visibility of fringes is fully analyzed.

  7. A comparison study on microwave-assisted extraction of Artemisia sphaerocephala polysaccharides with conventional method: Molecule structure and antioxidant activities evaluation.

    PubMed

    Wang, Junlong; Zhang, Ji; Wang, Xiaofang; Zhao, Baotang; Wu, Yiqian; Yao, Jian

    2009-12-01

    The conventional extraction methods for polysaccharides were time-consuming, laborious and energy-consuming. Microwave-assisted extraction (MAE) technique was employed for the extraction of Artemisia sphaerocephala polysaccharides (ASP), which is a traditional Chinese food. The extracting parameters were optimized by Box-Behnken design. In microwave heating process, a decrease in molecular weight (M(w)) was detected in SEC-LLS measurement. A d(f) value of 2.85 indicated ASP using MAE exhibited as a sphere conformation of branched clusters in aqueous solution. Furthermore, it showed stronger antioxidant activities compared with hot water extraction. The data obtained showed that the molecular weights played a more important role in antioxidant activities.

  8. Strong, light, multifunctional fibers of carbon nanotubes with ultrahigh conductivity.

    PubMed

    Behabtu, Natnael; Young, Colin C; Tsentalovich, Dmitri E; Kleinerman, Olga; Wang, Xuan; Ma, Anson W K; Bengio, E Amram; ter Waarbeek, Ron F; de Jong, Jorrit J; Hoogerwerf, Ron E; Fairchild, Steven B; Ferguson, John B; Maruyama, Benji; Kono, Junichiro; Talmon, Yeshayahu; Cohen, Yachin; Otto, Marcin J; Pasquali, Matteo

    2013-01-11

    Broader applications of carbon nanotubes to real-world problems have largely gone unfulfilled because of difficult material synthesis and laborious processing. We report high-performance multifunctional carbon nanotube (CNT) fibers that combine the specific strength, stiffness, and thermal conductivity of carbon fibers with the specific electrical conductivity of metals. These fibers consist of bulk-grown CNTs and are produced by high-throughput wet spinning, the same process used to produce high-performance industrial fibers. These scalable CNT fibers are positioned for high-value applications, such as aerospace electronics and field emission, and can evolve into engineered materials with broad long-term impact, from consumer electronics to long-range power transmission.

  9. New drug candidates and therapeutic targets for tuberculosis therapy.

    PubMed

    Zhang, Ying; Post-Martens, Katrin; Denkin, Steven

    2006-01-01

    Despite advances in chemotherapy and the BCG (Bacillus Calmette-Guérin) vaccine, tuberculosis remains a significant infectious disease. Although it can be cured, the therapy takes at least 6-9 months, and the laborious and lengthy treatment brings with it dangers of noncompliance, significant toxicity and drug resistance. The increasing emergence of drug resistance and the problem of mycobacterial persistence highlight the need to develop novel TB drugs that are active against drug resistant bacteria but, more importantly, kill persistent bacteria and shorten the length of treatment. Recent new and exciting developments in tuberculosis drug discovery show good promise of a possible revolution in the chemotherapy of tuberculosis.

  10. Decision support system for outage management and automated crew dispatch

    DOEpatents

    Kang, Ning; Mousavi, Mirrasoul

    2018-01-23

    A decision support system is provided for utility operations to assist with crew dispatch and restoration activities following the occurrence of a disturbance in a multiphase power distribution network, by providing a real-time visualization of possible location(s). The system covers faults that occur on fuse-protected laterals. The system uses real-time data from intelligent electronics devices coupled with other data sources such as static feeder maps to provide a complete picture of the disturbance event, guiding the utility crew to the most probable location(s). This information is provided in real-time, reducing restoration time and avoiding more costly and laborious fault location finding practices.

  11. Automatic Registration of GF4 Pms: a High Resolution Multi-Spectral Sensor on Board a Satellite on Geostationary Orbit

    NASA Astrophysics Data System (ADS)

    Gao, M.; Li, J.

    2018-04-01

    Geometric correction is an important preprocessing process in the application of GF4 PMS image. The method of geometric correction that is based on the manual selection of geometric control points is time-consuming and laborious. The more common method, based on a reference image, is automatic image registration. This method involves several steps and parameters. For the multi-spectral sensor GF4 PMS, it is necessary for us to identify the best combination of parameters and steps. This study mainly focuses on the following issues: necessity of Rational Polynomial Coefficients (RPC) correction before automatic registration, base band in the automatic registration and configuration of GF4 PMS spatial resolution.

  12. Preliminary Method for Direct Quantification of Colistin Methanesulfonate by Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy

    PubMed Central

    Niece, Krista L.

    2015-01-01

    Colistin use has increased in response to the advent of infections caused by multidrug-resistant organisms. It is administered parenterally as an inactive prodrug, colistin methanesulfonate (CMS). Various formulations of CMS and labeling conventions can lead to confusion about colistin dosing, and questions remain about the pharmacokinetics of CMS. Since CMS does not have strong UV absorbance, current methods employ a laborious process of chemical conversion to colistin followed by precolumn derivatization to detect formed colistin by high-performance liquid chromatography. Here, we report a method for direct quantification of colistin methanesulfonate by attenuated total reflectance Fourier transform infrared spectroscopy (ATR FTIR). PMID:26124160

  13. Conducting pilot and feasibility studies.

    PubMed

    Cope, Diane G

    2015-03-01

    Planning a well-designed research study can be tedious and laborious work. However, this process is critical and ultimately can produce valid, reliable study findings. Designing a large-scale randomized, controlled trial (RCT)-the gold standard in quantitative research-can be even more challenging. Even the most well-planned study potentially can result in issues with research procedures and design, such as recruitment, retention, or methodology. One strategy that may facilitate sound study design is the completion of a pilot or feasibility study prior to the initiation of a larger-scale trial. This article will discuss pilot and feasibility studies, their advantages and disadvantages, and implications for oncology nursing research. 
.

  14. Multi-spectral brain tissue segmentation using automatically trained k-Nearest-Neighbor classification.

    PubMed

    Vrooman, Henri A; Cocosco, Chris A; van der Lijn, Fedde; Stokking, Rik; Ikram, M Arfan; Vernooij, Meike W; Breteler, Monique M B; Niessen, Wiro J

    2007-08-01

    Conventional k-Nearest-Neighbor (kNN) classification, which has been successfully applied to classify brain tissue in MR data, requires training on manually labeled subjects. This manual labeling is a laborious and time-consuming procedure. In this work, a new fully automated brain tissue classification procedure is presented, in which kNN training is automated. This is achieved by non-rigidly registering the MR data with a tissue probability atlas to automatically select training samples, followed by a post-processing step to keep the most reliable samples. The accuracy of the new method was compared to rigid registration-based training and to conventional kNN-based segmentation using training on manually labeled subjects for segmenting gray matter (GM), white matter (WM) and cerebrospinal fluid (CSF) in 12 data sets. Furthermore, for all classification methods, the performance was assessed when varying the free parameters. Finally, the robustness of the fully automated procedure was evaluated on 59 subjects. The automated training method using non-rigid registration with a tissue probability atlas was significantly more accurate than rigid registration. For both automated training using non-rigid registration and for the manually trained kNN classifier, the difference with the manual labeling by observers was not significantly larger than inter-observer variability for all tissue types. From the robustness study, it was clear that, given an appropriate brain atlas and optimal parameters, our new fully automated, non-rigid registration-based method gives accurate and robust segmentation results. A similarity index was used for comparison with manually trained kNN. The similarity indices were 0.93, 0.92 and 0.92, for CSF, GM and WM, respectively. It can be concluded that our fully automated method using non-rigid registration may replace manual segmentation, and thus that automated brain tissue segmentation without laborious manual training is feasible.

  15. Droplet-based magnetic bead immunoassay using microchannel-connected multiwell plates (μCHAMPs) for the detection of amyloid beta oligomers.

    PubMed

    Park, Min Cheol; Kim, Moojong; Lim, Gun Taek; Kang, Sung Min; An, Seong Soo A; Kim, Tae Song; Kang, Ji Yoon

    2016-06-21

    Multiwell plates are regularly used in analytical research and clinical diagnosis but often require laborious washing steps and large sample or reagent volumes (typically, 100 μL per well). To overcome such drawbacks in the conventional multiwell plate, we present a novel microchannel-connected multiwell plate (μCHAMP) that can be used for automated disease biomarker detection in a small sample volume by performing droplet-based magnetic bead immunoassay inside the plate. In this μCHAMP-based immunoassay platform, small volumes (30-50 μL) of aqueous-phase working droplets are stably confined within each well by the simple microchannel structure (200-300 μm in height and 0.5-1 mm in width), and magnetic beads are exclusively transported into an adjacent droplet through the oil-filled microchannels assisted by a magnet array aligned beneath and controlled by a XY-motorized stage. Using this μCHAMP-based platform, we were able to perform parallel detection of synthetic amyloid beta (Aβ) oligomers as a model analyte for the early diagnosis of Alzheimer's disease (AD). This platform easily simplified the laborious and consumptive immunoassay procedure by achieving automated parallel immunoassay (32 assays per operation in 3-well connected 96-well plate) within 1 hour and at low sample consumption (less than 10 μL per assay) with no cumbersome manual washing step. Moreover, it could detect synthetic Aβ oligomers even below 10 pg mL(-1) concentration with a calculated detection limit of ∼3 pg mL(-1). Therefore, the μCHAMP and droplet-based magnetic bead immunoassay, with the combination of XY-motorized magnet array, would be a useful platform in the diagnosis of human disease, including AD, which requires low consumption of the patient's body fluid sample and automation of the entire immunoassay procedure for high processing capacity.

  16. A base-modified PNA-graphene oxide platform as a turn-on fluorescence sensor for the detection of human telomeric repeats

    NASA Astrophysics Data System (ADS)

    Sabale, Pramod M.; George, Jerrin Thomas; Srivatsan, Seergazhi G.

    2014-08-01

    Given the biological and therapeutic significance of telomeres and other G-quadruplex forming sequences in human genome, it is highly desirable to develop simple methods to study these structures, which can also be implemented in screening formats for the discovery of G-quadruplex binders. The majority of telomere detection methods developed so far are laborious and use elaborate assay and instrumental setups, and hence, are not amenable to discovery platforms. Here, we describe the development of a simple homogeneous fluorescence turn-on method, which uses a unique combination of an environment-sensitive fluorescent nucleobase analogue, the superior base pairing property of PNA, and DNA-binding and fluorescence quenching properties of graphene oxide, to detect human telomeric DNA repeats of varying lengths. Our results demonstrate that this method, which does not involve a rigorous assay setup, would provide new opportunities to study G-quadruplex structures.Given the biological and therapeutic significance of telomeres and other G-quadruplex forming sequences in human genome, it is highly desirable to develop simple methods to study these structures, which can also be implemented in screening formats for the discovery of G-quadruplex binders. The majority of telomere detection methods developed so far are laborious and use elaborate assay and instrumental setups, and hence, are not amenable to discovery platforms. Here, we describe the development of a simple homogeneous fluorescence turn-on method, which uses a unique combination of an environment-sensitive fluorescent nucleobase analogue, the superior base pairing property of PNA, and DNA-binding and fluorescence quenching properties of graphene oxide, to detect human telomeric DNA repeats of varying lengths. Our results demonstrate that this method, which does not involve a rigorous assay setup, would provide new opportunities to study G-quadruplex structures. Electronic supplementary information (ESI

  17. NOTE: Solving the ECG forward problem by means of a meshless finite element method

    NASA Astrophysics Data System (ADS)

    Li, Z. S.; Zhu, S. A.; He, Bin

    2007-07-01

    The conventional numerical computational techniques such as the finite element method (FEM) and the boundary element method (BEM) require laborious and time-consuming model meshing. The new meshless FEM only uses the boundary description and the node distribution and no meshing of the model is required. This paper presents the fundamentals and implementation of meshless FEM and the meshless FEM method is adapted to solve the electrocardiography (ECG) forward problem. The method is evaluated on a single-layer torso model, in which the analytical solution exists, and tested in a realistic geometry homogeneous torso model, with satisfactory results being obtained. The present results suggest that the meshless FEM may provide an alternative for ECG forward solutions.

  18. Image processing in biodosimetry: A proposal of a generic free software platform.

    PubMed

    Dumpelmann, Matthias; Cadena da Matta, Mariel; Pereira de Lemos Pinto, Marcela Maria; de Salazar E Fernandes, Thiago; Borges da Silva, Edvane; Amaral, Ademir

    2015-08-01

    The scoring of chromosome aberrations is the most reliable biological method for evaluating individual exposure to ionizing radiation. However, microscopic analyses of chromosome human metaphases, generally employed to identify aberrations mainly dicentrics (chromosome with two centromeres), is a laborious task. This method is time consuming and its application in biological dosimetry would be almost impossible in case of a large scale radiation incidents. In this project, a generic software was enhanced for automatic chromosome image processing from a framework originally developed for the Framework V project Simbio, of the European Union for applications in the area of source localization from electroencephalographic signals. The platforms capability is demonstrated by a study comparing automatic segmentation strategies of chromosomes from microscopic images.

  19. ASCOT: a text mining-based web-service for efficient search and assisted creation of clinical trials

    PubMed Central

    2012-01-01

    Clinical trials are mandatory protocols describing medical research on humans and among the most valuable sources of medical practice evidence. Searching for trials relevant to some query is laborious due to the immense number of existing protocols. Apart from search, writing new trials includes composing detailed eligibility criteria, which might be time-consuming, especially for new researchers. In this paper we present ASCOT, an efficient search application customised for clinical trials. ASCOT uses text mining and data mining methods to enrich clinical trials with metadata, that in turn serve as effective tools to narrow down search. In addition, ASCOT integrates a component for recommending eligibility criteria based on a set of selected protocols. PMID:22595088

  20. Another procedure for the preliminary ordering of loci based on two point lod scores.

    PubMed

    Curtis, D

    1994-01-01

    Because of the difficulty of performing full likelihood analysis over multiple loci and the large numbers of possible orders, a number of methods have been proposed for quickly evaluating orders and, to a lesser extent, for generating good orders. A new method is proposed which uses a function which is moderately laborious to compute, the sum of lod scores between all pairs of loci. This function can be smoothly minimized by initially allowing the loci to be placed anywhere in space, and only subsequently constraining them to lie along a one-dimensional map. Application of this approach to sample data suggests that it has promise and might usefully be combined with other methods when loci need to be ordered.

  1. Modification of gDNA extraction from soil for PCR designed for the routine examination of soil samples contaminated with Toxocara spp. eggs.

    PubMed

    Borecka, A; Gawor, J

    2008-06-01

    A modification of gDNA extraction was developed for the polymerase chain reaction (PCR) technique, intended for the detection and differentiation of Toxocara spp. eggs in soil or sediments. Sand samples from sandpits confirmed as being contaminated with Toxocara spp. eggs by the flotation technique were analysed by PCR. The use of proteinase K made it possible to obtain genomic DNA from the sample without needing to isolate eggs using flotation or to inactivate PCR inhibitors present in the sand. Specific primers in the PCR reaction allowed discrimination between T. canis and T. cati eggs. The modification simplified the procedure, thanks to eliminating the step of gDNA isolation from eggs, which is both laborious and difficult.

  2. Real-time tracking and fast retrieval of persons in multiple surveillance cameras of a shopping mall

    NASA Astrophysics Data System (ADS)

    Bouma, Henri; Baan, Jan; Landsmeer, Sander; Kruszynski, Chris; van Antwerpen, Gert; Dijk, Judith

    2013-05-01

    The capability to track individuals in CCTV cameras is important for e.g. surveillance applications at large areas such as train stations, airports and shopping centers. However, it is laborious to track and trace people over multiple cameras. In this paper, we present a system for real-time tracking and fast interactive retrieval of persons in video streams from multiple static surveillance cameras. This system is demonstrated in a shopping mall, where the cameras are positioned without overlapping fields-of-view and have different lighting conditions. The results show that the system allows an operator to find the origin or destination of a person more efficiently. The misses are reduced with 37%, which is a significant improvement.

  3. Assembling the Streptococcus thermophilus clustered regularly interspaced short palindromic repeats (CRISPR) array for multiplex DNA targeting.

    PubMed

    Guo, Lijun; Xu, Kun; Liu, Zhiyuan; Zhang, Cunfang; Xin, Ying; Zhang, Zhiying

    2015-06-01

    In addition to the advantages of scalable, affordable, and easy to engineer, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) technology is superior for multiplex targeting, which is laborious and inconvenient when achieved by cloning multiple gRNA expressing cassettes. Here, we report a simple CRISPR array assembling method which will facilitate multiplex targeting usage. First, the Streptococcus thermophilus CRISPR3/Cas locus was cloned. Second, different CRISPR arrays were assembled with different crRNA spacers. Transformation assays using different Escherichia coli strains demonstrated efficient plasmid DNA targeting, and we achieved targeting efficiency up to 95% with an assembled CRISPR array with three crRNA spacers. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Urban mosquitoes, situational publics, and the pursuit of interspecies separation in Dar es Salaam

    PubMed Central

    KELLY, ANN H.; LEZAUN, JAVIER

    2014-01-01

    Recent work in anthropology points to the recognition of multispecies entanglements as the grounds for a more ethical politics. In this article, we examine efforts to control mosquitoes in Dar es Salaam, Tanzania, as an example of the laborious tasks of disentanglement that characterize public health interventions. The mosquito surveillance and larval elimination practices of an urban malaria control program offer an opportunity to observe how efforts to create distance between species relate to the physical and civic textures of the city. Seen in the particular context of the contemporary African metropolis, the work of public health appears less a matter of control than a commitment to constant urban maintenance and political mobilization. PMID:25429167

  5. ASCOT: a text mining-based web-service for efficient search and assisted creation of clinical trials.

    PubMed

    Korkontzelos, Ioannis; Mu, Tingting; Ananiadou, Sophia

    2012-04-30

    Clinical trials are mandatory protocols describing medical research on humans and among the most valuable sources of medical practice evidence. Searching for trials relevant to some query is laborious due to the immense number of existing protocols. Apart from search, writing new trials includes composing detailed eligibility criteria, which might be time-consuming, especially for new researchers. In this paper we present ASCOT, an efficient search application customised for clinical trials. ASCOT uses text mining and data mining methods to enrich clinical trials with metadata, that in turn serve as effective tools to narrow down search. In addition, ASCOT integrates a component for recommending eligibility criteria based on a set of selected protocols.

  6. Lessons for HIV from Tuskegee.

    PubMed

    Stebbing, Justin; Bower, Mark

    2004-09-01

    We are fortunate to live in an era in which research allows significant progress in the therapy of the major diseases that affect us. However, evaluating their efficacy and safety is expensive, laborious and involves the study of human subjects in an appropriate manner. The principles of such trials have a heterogeneous basis encompassing the principles of utilitarianism, distributive justice, the protection of individual rights and the investigators' commitment to patients. The Tuskegee study of untreated syphilis is the longest non-therapeutic experiment on human beings in medical history. It continues to cast its shadow on the relationship between black Americans and the broader biomedical community. Parallels and the relationship with the HIV pandemic are discussed.

  7. A successful strategy for the recovering of active P21, an insoluble recombinant protein of Trypanosoma cruzi

    NASA Astrophysics Data System (ADS)

    Santos, Marlus Alves Dos; Teixeira, Francesco Brugnera; Moreira, Heline Hellen Teixeira; Rodrigues, Adele Aud; Machado, Fabrício Castro; Clemente, Tatiana Mordente; Brigido, Paula Cristina; Silva, Rebecca Tavares E.; Purcino, Cecílio; Gomes, Rafael Gonçalves Barbosa; Bahia, Diana; Mortara, Renato Arruda; Munte, Claudia Elisabeth; Horjales, Eduardo; da Silva, Claudio Vieira

    2014-03-01

    Structural studies of proteins normally require large quantities of pure material that can only be obtained through heterologous expression systems and recombinant technique. In these procedures, large amounts of expressed protein are often found in the insoluble fraction, making protein purification from the soluble fraction inefficient, laborious, and costly. Usually, protein refolding is avoided due to a lack of experimental assays that can validate correct folding and that can compare the conformational population to that of the soluble fraction. Herein, we propose a validation method using simple and rapid 1D 1H nuclear magnetic resonance (NMR) spectra that can efficiently compare protein samples, including individual information of the environment of each proton in the structure.

  8. Gene cassette knock-in in mammalian cells and zygotes by enhanced MMEJ.

    PubMed

    Aida, Tomomi; Nakade, Shota; Sakuma, Tetsushi; Izu, Yayoi; Oishi, Ayu; Mochida, Keiji; Ishikubo, Harumi; Usami, Takako; Aizawa, Hidenori; Yamamoto, Takashi; Tanaka, Kohichi

    2016-11-28

    Although CRISPR/Cas enables one-step gene cassette knock-in, assembling targeting vectors containing long homology arms is a laborious process for high-throughput knock-in. We recently developed the CRISPR/Cas-based precise integration into the target chromosome (PITCh) system for a gene cassette knock-in without long homology arms mediated by microhomology-mediated end-joining. Here, we identified exonuclease 1 (Exo1) as an enhancer for PITCh in human cells. By combining the Exo1 and PITCh-directed donor vectors, we achieved convenient one-step knock-in of gene cassettes and floxed allele both in human cells and mouse zygotes. Our results provide a technical platform for high-throughput knock-in.

  9. FlowCam: Quantification and Classification of Phytoplankton by Imaging Flow Cytometry.

    PubMed

    Poulton, Nicole J

    2016-01-01

    The ability to enumerate, classify, and determine biomass of phytoplankton from environmental samples is essential for determining ecosystem function and their role in the aquatic community and microbial food web. Traditional micro-phytoplankton quantification methods using microscopic techniques require preservation and are slow, tedious and very laborious. The availability of more automated imaging microscopy platforms has revolutionized the way particles and cells are detected within their natural environment. The ability to examine cells unaltered and without preservation is key to providing more accurate cell concentration estimates and overall phytoplankton biomass. The FlowCam(®) is an imaging cytometry tool that was originally developed for use in aquatic sciences and provides a more rapid and unbiased method for enumerating and classifying phytoplankton within diverse aquatic environments.

  10. Magnetic bead purification of labeled DNA fragments forhigh-throughput capillary electrophoresis sequencing

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Elkin, Christopher; Kapur, Hitesh; Smith, Troy

    2001-09-15

    We have developed an automated purification method for terminator sequencing products based on a magnetic bead technology. This 384-well protocol generates labeled DNA fragments that are essentially free of contaminates for less than $0.005 per reaction. In comparison to laborious ethanol precipitation protocols, this method increases the phred20 read length by forty bases with various DNA templates such as PCR fragments, Plasmids, Cosmids and RCA products. Our method eliminates centrifugation and is compatible with both the MegaBACE 1000 and ABIPrism 3700 capillary instruments. As of September 2001, this method has produced over 1.6 million samples with 93 percent averaging 620more » phred20 bases as part of Joint Genome Institutes Production Process.« less

  11. Universal fragment descriptors for predicting properties of inorganic crystals

    NASA Astrophysics Data System (ADS)

    Isayev, Olexandr; Oses, Corey; Toher, Cormac; Gossett, Eric; Curtarolo, Stefano; Tropsha, Alexander

    2017-06-01

    Although historically materials discovery has been driven by a laborious trial-and-error process, knowledge-driven materials design can now be enabled by the rational combination of Machine Learning methods and materials databases. Here, data from the AFLOW repository for ab initio calculations is combined with Quantitative Materials Structure-Property Relationship models to predict important properties: metal/insulator classification, band gap energy, bulk/shear moduli, Debye temperature and heat capacities. The prediction's accuracy compares well with the quality of the training data for virtually any stoichiometric inorganic crystalline material, reciprocating the available thermomechanical experimental data. The universality of the approach is attributed to the construction of the descriptors: Property-Labelled Materials Fragments. The representations require only minimal structural input allowing straightforward implementations of simple heuristic design rules.

  12. Bounding the Resource Availability of Partially Ordered Events with Constant Resource Impact

    NASA Technical Reports Server (NTRS)

    Frank, Jeremy

    2004-01-01

    We compare existing techniques to bound the resource availability of partially ordered events. We first show that, contrary to intuition, two existing techniques, one due to Laborie and one due to Muscettola, are not strictly comparable in terms of the size of the search trees generated under chronological search with a fixed heuristic. We describe a generalization of these techniques called the Flow Balance Constraint to tightly bound the amount of available resource for a set of partially ordered events with piecewise constant resource impact We prove that the new technique generates smaller proof trees under chronological search with a fixed heuristic, at little increase in computational expense. We then show how to construct tighter resource bounds but at increased computational cost.

  13. Emerging applications of fluorescence spectroscopy in medical microbiology field.

    PubMed

    Shahzad, Aamir; Köhler, Gottfried; Knapp, Martin; Gaubitzer, Erwin; Puchinger, Martin; Edetsberger, Michael

    2009-11-26

    There are many diagnostic techniques and methods available for diagnosis of medically important microorganisms like bacteria, viruses, fungi and parasites. But, almost all these techniques and methods have some limitations or inconvenience. Most of these techniques are laborious, time consuming and with chances of false positive or false negative results. It warrants the need of a diagnostic technique which can overcome these limitations and problems. At present, there is emerging trend to use Fluorescence spectroscopy as a diagnostic as well as research tool in many fields of medical sciences. Here, we will critically discuss research studies which propose that Fluorescence spectroscopy may be an excellent diagnostic as well as excellent research tool in medical microbiology field with high sensitivity and specificity.

  14. Universal fragment descriptors for predicting properties of inorganic crystals.

    PubMed

    Isayev, Olexandr; Oses, Corey; Toher, Cormac; Gossett, Eric; Curtarolo, Stefano; Tropsha, Alexander

    2017-06-05

    Although historically materials discovery has been driven by a laborious trial-and-error process, knowledge-driven materials design can now be enabled by the rational combination of Machine Learning methods and materials databases. Here, data from the AFLOW repository for ab initio calculations is combined with Quantitative Materials Structure-Property Relationship models to predict important properties: metal/insulator classification, band gap energy, bulk/shear moduli, Debye temperature and heat capacities. The prediction's accuracy compares well with the quality of the training data for virtually any stoichiometric inorganic crystalline material, reciprocating the available thermomechanical experimental data. The universality of the approach is attributed to the construction of the descriptors: Property-Labelled Materials Fragments. The representations require only minimal structural input allowing straightforward implementations of simple heuristic design rules.

  15. Rule-based interface generation on mobile devices for structured documentation.

    PubMed

    Kock, Ann-Kristin; Andersen, Björn; Handels, Heinz; Ingenerf, Josef

    2014-01-01

    In many software systems to date, interactive graphical user interfaces (GUIs) are represented implicitly in the source code, together with the application logic. Hence, the re-use, development, and modification of these interfaces is often very laborious. Flexible adjustments of GUIs for various platforms and devices as well as individual user preferences are furthermore difficult to realize. These problems motivate a software-based separation of content and GUI models on the one hand, and application logic on the other. In this project, a software solution for structured reporting on mobile devices is developed. Clinical content archetypes developed in a previous project serve as the content model while the Android SDK provides the GUI model. The necessary bindings between the models are specified using the Jess Rule Language.

  16. In situ synthesis of protein arrays.

    PubMed

    He, Mingyue; Stoevesandt, Oda; Taussig, Michael J

    2008-02-01

    In situ or on-chip protein array methods use cell free expression systems to produce proteins directly onto an immobilising surface from co-distributed or pre-arrayed DNA or RNA, enabling protein arrays to be created on demand. These methods address three issues in protein array technology: (i) efficient protein expression and availability, (ii) functional protein immobilisation and purification in a single step and (iii) protein on-chip stability over time. By simultaneously expressing and immobilising many proteins in parallel on the chip surface, the laborious and often costly processes of DNA cloning, expression and separate protein purification are avoided. Recently employed methods reviewed are PISA (protein in situ array) and NAPPA (nucleic acid programmable protein array) from DNA and puromycin-mediated immobilisation from mRNA.

  17. New developments in electron microscopy for serial image acquisition of neuronal profiles.

    PubMed

    Kubota, Yoshiyuki

    2015-02-01

    Recent developments in electron microscopy largely automate the continuous acquisition of serial electron micrographs (EMGs), previously achieved by laborious manual serial ultrathin sectioning using an ultramicrotome and ultrastructural image capture process with transmission electron microscopy. The new systems cut thin sections and capture serial EMGs automatically, allowing for acquisition of large data sets in a reasonably short time. The new methods are focused ion beam/scanning electron microscopy, ultramicrotome/serial block-face scanning electron microscopy, automated tape-collection ultramicrotome/scanning electron microscopy and transmission electron microscope camera array. In this review, their positive and negative aspects are discussed. © The Author 2015. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  18. Load Carrying Capacity of Metal Dowel Type Connections of Timber Structures

    NASA Astrophysics Data System (ADS)

    Gocál, Jozef

    2014-12-01

    This paper deals with the load-carrying capacity calculation of laterally loaded metal dowel type connections according to Eurocode 5. It is based on analytically derived, relatively complicated mathematical relationships, and thus it can be quite laborious for practical use. The aim is to propose a possible simplification of the calculation. Due to quite a great variability of fasteners' types and the connection arrangements, the attention is paid to the most commonly used nailed connections. There was performed quite an extensive parametric study focused on the calculation of load-carrying capacity of the simple shear and double shear plane nail connections, joining two or three timber parts of softwood or hardwood. Based on the study results, in conclusion there are presented simplifying recommendations for practical design.

  19. An Alu-based, MGB Eclipse real-time PCR method for quantitation of human DNA in forensic samples.

    PubMed

    Nicklas, Janice A; Buel, Eric

    2005-09-01

    The forensic community needs quick, reliable methods to quantitate human DNA in crime scene samples to replace the laborious and imprecise slot blot method. A real-time PCR based method has the possibility of allowing development of a faster and more quantitative assay. Alu sequences are primate-specific and are found in many copies in the human genome, making these sequences an excellent target or marker for human DNA. This paper describes the development of a real-time Alu sequence-based assay using MGB Eclipse primers and probes. The advantages of this assay are simplicity, speed, less hands-on-time and automated quantitation, as well as a large dynamic range (128 ng/microL to 0.5 pg/microL).

  20. Graphene-enabled electron microscopy and correlated super-resolution microscopy of wet cells.

    PubMed

    Wojcik, Michal; Hauser, Margaret; Li, Wan; Moon, Seonah; Xu, Ke

    2015-06-11

    The application of electron microscopy to hydrated biological samples has been limited by high-vacuum operating conditions. Traditional methods utilize harsh and laborious sample dehydration procedures, often leading to structural artefacts and creating difficulties for correlating results with high-resolution fluorescence microscopy. Here, we utilize graphene, a single-atom-thick carbon meshwork, as the thinnest possible impermeable and conductive membrane to protect animal cells from vacuum, thus enabling high-resolution electron microscopy of wet and untreated whole cells with exceptional ease. Our approach further allows for facile correlative super-resolution and electron microscopy of wet cells directly on the culturing substrate. In particular, individual cytoskeletal actin filaments are resolved in hydrated samples through electron microscopy and well correlated with super-resolution results.

  1. A Sensitive and Effective Proteomic Approach to Identify She-Donkey’s and Goat’s Milk Adulterations by MALDI-TOF MS Fingerprinting

    PubMed Central

    Di Girolamo, Francesco; Masotti, Andrea; Salvatori, Guglielmo; Scapaticci, Margherita; Muraca, Maurizio; Putignani, Lorenza

    2014-01-01

    She-donkey’s milk (DM) and goat’s milk (GM) are commonly used in newborn and infant feeding because they are less allergenic than other milk types. It is, therefore, mandatory to avoid adulteration and contamination by other milk allergens, developing fast and efficient analytical methods to assess the authenticity of these precious nutrients. In this experimental work, a sensitive and robust matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling was designed to assess the genuineness of DM and GM milks. This workflow allows the identification of DM and GM adulteration at levels of 0.5%, thus, representing a sensitive tool for milk adulteration analysis, if compared with other laborious and time-consuming analytical procedures. PMID:25110863

  2. Optimization of the intravenous glucose tolerance test in T2DM patients using optimal experimental design.

    PubMed

    Silber, Hanna E; Nyberg, Joakim; Hooker, Andrew C; Karlsson, Mats O

    2009-06-01

    Intravenous glucose tolerance test (IVGTT) provocations are informative, but complex and laborious, for studying the glucose-insulin system. The objective of this study was to evaluate, through optimal design methodology, the possibilities of more informative and/or less laborious study design of the insulin modified IVGTT in type 2 diabetic patients. A previously developed model for glucose and insulin regulation was implemented in the optimal design software PopED 2.0. The following aspects of the study design of the insulin modified IVGTT were evaluated; (1) glucose dose, (2) insulin infusion, (3) combination of (1) and (2), (4) sampling times, (5) exclusion of labeled glucose. Constraints were incorporated to avoid prolonged hyper- and/or hypoglycemia and a reduced design was used to decrease run times. Design efficiency was calculated as a measure of the improvement with an optimal design compared to the basic design. The results showed that the design of the insulin modified IVGTT could be substantially improved by the use of an optimized design compared to the standard design and that it was possible to use a reduced number of samples. Optimization of sample times gave the largest improvement followed by insulin dose. The results further showed that it was possible to reduce the total sample time with only a minor loss in efficiency. Simulations confirmed the predictions from PopED. The predicted uncertainty of parameter estimates (CV) was low in all tested cases, despite the reduction in the number of samples/subject. The best design had a predicted average CV of parameter estimates of 19.5%. We conclude that improvement can be made to the design of the insulin modified IVGTT and that the most important design factor was the placement of sample times followed by the use of an optimal insulin dose. This paper illustrates how complex provocation experiments can be improved by sequential modeling and optimal design.

  3. Optimisation of decontamination method and influence of culture media on the recovery of Mycobacterium avium subspecies paratuberculosis from spiked water sediments.

    PubMed

    Aboagye, G; Rowe, M T

    2018-07-01

    The recovery of Mycobacterium avium subspecies paratuberculosis (Map) from the environment can be a laborious process - owing to Map being fastidious, its low number, and also high numbers of other microbial populations in such settings. Protocols i.e. filtration, decontamination and modified elution were devised to recover Map from spiked water sediments. Three culture media: Herrold's Egg Yolk Media (HEYM), Middlebrook 7H10 (M-7H10) and Bactec 12B were then employed to grow the organism following its elution. In the sterile sediment samples the recovery of Map was significant between the time of exposure for each of HEYM and M-7H10, and insignificant between both media (P < 0.05). However, in the non-sterile sediment samples, the HEYM grew other background microflora including moulds at all the times of exposure whilst 4 h followed by M-7H10 culture yielded Map colonies without any background microflora. Using sterile samples only for the Bactec 12B, the recovery of Map decreased as time of exposure increased. Based on these findings, M-7H10 should be considered for the recovery of Map from the natural environment including water sediments where the recovery of diverse microbial species remains a challenge. Map is a robust pathogen that abides in the environment. In water treatment operations, Map associates with floccules and other particulate matter including sediments. It is also a fastidious organism, and its detection and recovery from the water environment is a laborious process and can be misleading within the abundance of other mycobacterial species owing to their close resemblance in phylogenetic traits. In the absence of a reliable recovery method, Map continues to pose public health risks through biofilm in household water tanks, hence the need for the development of a reliable recovery protocol to monitor the presence of Map in water systems in order to curtail its public health risks. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. Saccharomyces cerevisiae as a platform for assessing sphingolipid lipid kinase inhibitors

    PubMed Central

    Agah, Sayeh; Mendelson, Anna J.; Eletu, Oluwafunmilayo T.; Barkey-Bircann, Peter; Gesualdi, James

    2018-01-01

    Successful medicinal chemistry campaigns to discover and optimize sphingosine kinase inhibitors require a robust assay for screening chemical libraries and for determining rank order potencies. Existing assays for these enzymes are laborious, expensive and/or low throughput. The toxicity of excessive levels of phosphorylated sphingoid bases for the budding yeast, Saccharomyces cerevisiae, affords an assay wherein inhibitors added to the culture media rescue growth in a dose-dependent fashion. Herein, we describe our adaptation of a simple, inexpensive, and high throughput assay for assessing inhibitors of sphingosine kinase types 1 and 2 as well as ceramide kinase and for testing enzymatic activity of sphingosine kinase type 2 mutants. The assay was validated using recombinant enzymes and generally agrees with the rank order of potencies of existing inhibitors. PMID:29672528

  5. Distinguishing friends, foes, and freeloaders in giant genomes.

    PubMed

    Bennetzen, Jeffrey L; Park, Minkyu

    2018-04-01

    Most annotations of large eukaryotic genomes initially find transposable elements (TEs) and other repeats, then mask them so that subsequent efforts can be concentrated on the annotation and study of non-TE genes. However, TEs often contribute to host biology, and their community biologies are of intrinsic interest. This review discusses the challenges, rationale and technologies for comprehensive TE annotation in the commonly giant genomes of animals and plants. Complete discovery of the TEs in a fully sequenced genome is laborious, but feasible, with current strategies in the hands of a careful researcher. These deep TE studies have begun to provide important perspectives on how genomes evolve and the degree to which genome changes do and do not affect eukaryotic biology. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  6. Simplified methods for the construction of RNA and DNA virus infectious clones.

    PubMed

    Nagata, Tatsuya; Inoue-Nagata, Alice Kazuko

    2015-01-01

    Infectious virus clones are one of the most powerful tools in plant pathology, molecular biology, and biotechnology. The construction of infectious clones of RNA and DNA viruses, however, usually requires laborious cloning and subcloning steps. In addition, instability of the RNA virus genome is frequently reported after its introduction into the vector and transference to Escherichia coli. These difficulties hamper the cloning procedures, making it tedious and cumbersome. This chapter describes two protocols for a simple construction of infectious viruses, an RNA virus, the tobamovirus Pepper mild mottle virus, and a DNA virus, a bipartite begomovirus. For this purpose, the strategy of overlap-extension PCR was used for the construction of infectious tobamovirus clone and of rolling circle amplification (RCA) for the construction of a dimeric form of the begomovirus clone.

  7. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants.

    PubMed

    Taheri, Sima; Lee Abdullah, Thohirah; Yusop, Mohd Rafii; Hanafi, Mohamed Musa; Sahebi, Mahbod; Azizi, Parisa; Shamshiri, Redmond Ramin

    2018-02-13

    Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.

  8. The temporolimbic system theory of paranoid schizophrenia.

    PubMed

    Casanova, M F

    1997-01-01

    The hippocampus serves as a funnel for heavily processed sensory information that has converged at the entorhinal cortex. Lesions of the hippocampus do not alter incoming sensory or motor information but, rather, alter their integration with our baggage of emotional experiences and social values. According to Bogerts, such a lesion would be ideally situated to result in laboriously processed sensory information that is out of context to our outside environment. In this regard, Bogerts describes the pathological findings of a patient with a gross delusional disorder. The salient finding at autopsy was a developmental lesion in the left posterior parahippocampal gyrus. Although a number of lesions have been described in the brains of patients with schizophrenia, Bogerts believes that those in the limbic system appear critical to the expression of paranoid symptoms.

  9. Genomics and metagenomics in medical microbiology.

    PubMed

    Padmanabhan, Roshan; Mishra, Ajay Kumar; Raoult, Didier; Fournier, Pierre-Edouard

    2013-12-01

    Over the last two decades, sequencing tools have evolved from laborious time-consuming methodologies to real-time detection and deciphering of genomic DNA. Genome sequencing, especially using next generation sequencing (NGS) has revolutionized the landscape of microbiology and infectious disease. This deluge of sequencing data has not only enabled advances in fundamental biology but also helped improve diagnosis, typing of pathogen, virulence and antibiotic resistance detection, and development of new vaccines and culture media. In addition, NGS also enabled efficient analysis of complex human micro-floras, both commensal, and pathological, through metagenomic methods, thus helping the comprehension and management of human diseases such as obesity. This review summarizes technological advances in genomics and metagenomics relevant to the field of medical microbiology. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Check-off logs for routine equipment maintenance.

    PubMed

    Brewster, M A; Carver, P H; Randolph, B

    1995-12-01

    The regulatory requirement for appropriate routine instrument maintenance documentation is approached by laboratories in numerous ways. Standard operating procedures (SOPs) may refer to maintenance listed in instrument manuals, may indicate "periodic" performance of an action, or may indicate specific tasks to be performed at certain frequencies. The Quality Assurance Unit (QAU) task of assuring the performance of these indicated maintenance tasks can be extremely laborious if these records are merged with other analysis records. Further, the lack of written maintenance schedules often leads to omission of infrequently performed tasks. We recommend creation of routine maintenance check-off logs for instruments with tasks grouped by frequency of expected performance. Usage of such logs should result in better laboratory compliance with SOPs and the compliance can be readily monitored by QAU or by regulatory agencies.

  11. Integrated two-cylinder liquid piston Stirling engine

    NASA Astrophysics Data System (ADS)

    Yang, Ning; Rickard, Robert; Pluckter, Kevin; Sulchek, Todd

    2014-10-01

    Heat engines utilizing the Stirling cycle may run on low temperature differentials with the capacity to function at high efficiency due to their near-reversible operation. However, current approaches to building Stirling engines are laborious and costly. Typically the components are assembled by hand and additional components require a corresponding increase in manufacturing complexity, akin to electronics before the integrated circuit. We present a simple and integrated approach to fabricating Stirling engines with precisely designed cylinders. We utilize computer aided design and one-step, planar machining to form all components of the engine. The engine utilizes liquid pistons and displacers to harness useful work from heat absorption and rejection. As a proof of principle of the integrated design, a two-cylinder engine is produced and characterized and liquid pumping is demonstrated.

  12. A simple and efficient method for poly-3-hydroxybutyrate quantification in diazotrophic bacteria within 5 minutes using flow cytometry.

    PubMed

    Alves, L P S; Almeida, A T; Cruz, L M; Pedrosa, F O; de Souza, E M; Chubatsu, L S; Müller-Santos, M; Valdameri, G

    2017-01-16

    The conventional method for quantification of polyhydroxyalkanoates based on whole-cell methanolysis and gas chromatography (GC) is laborious and time-consuming. In this work, a method based on flow cytometry of Nile red stained bacterial cells was established to quantify poly-3-hydroxybutyrate (PHB) production by the diazotrophic and plant-associated bacteria, Herbaspirillum seropedicae and Azospirillum brasilense. The method consists of three steps: i) cell permeabilization, ii) Nile red staining, and iii) analysis by flow cytometry. The method was optimized step-by-step and can be carried out in less than 5 min. The final results indicated a high correlation coefficient (R2=0.99) compared to a standard method based on methanolysis and GC. This method was successfully applied to the quantification of PHB in epiphytic bacteria isolated from rice roots.

  13. A simple and efficient method for poly-3-hydroxybutyrate quantification in diazotrophic bacteria within 5 minutes using flow cytometry

    PubMed Central

    Alves, L.P.S.; Almeida, A.T.; Cruz, L.M.; Pedrosa, F.O.; de Souza, E.M.; Chubatsu, L.S.; Müller-Santos, M.; Valdameri, G.

    2017-01-01

    The conventional method for quantification of polyhydroxyalkanoates based on whole-cell methanolysis and gas chromatography (GC) is laborious and time-consuming. In this work, a method based on flow cytometry of Nile red stained bacterial cells was established to quantify poly-3-hydroxybutyrate (PHB) production by the diazotrophic and plant-associated bacteria, Herbaspirillum seropedicae and Azospirillum brasilense. The method consists of three steps: i) cell permeabilization, ii) Nile red staining, and iii) analysis by flow cytometry. The method was optimized step-by-step and can be carried out in less than 5 min. The final results indicated a high correlation coefficient (R2=0.99) compared to a standard method based on methanolysis and GC. This method was successfully applied to the quantification of PHB in epiphytic bacteria isolated from rice roots. PMID:28099582

  14. Modified cleaning method for biomineralized components

    NASA Astrophysics Data System (ADS)

    Tsutsui, Hideto; Jordan, Richard W.

    2018-02-01

    The extraction and concentration of biomineralized components from sediment or living materials is time consuming and laborious and often involves steps that remove either the calcareous or siliceous part, in addition to organic matter. However, a relatively quick and easy method using a commercial cleaning fluid for kitchen drains, sometimes combined with a kerosene soaking step, can produce remarkable results. In this study, the method is applied to sediments and living materials bearing calcareous (e.g., coccoliths, foraminiferal tests, holothurian ossicles, ichthyoliths, and fish otoliths) and siliceous (e.g., diatom valves, silicoflagellate skeletons, and sponge spicules) components. The method preserves both components in the same sample, without etching or partial dissolution, but is not applicable to unmineralized components such as dinoflagellate thecae, tintinnid loricae, pollen, or plant fragments.

  15. Extractive procedure for uranium determination in water samples by liquid scintillation counting.

    PubMed

    Gomez Escobar, V; Vera Tomé, F; Lozano, J C; Martín Sánchez, A

    1998-07-01

    An extractive procedure for uranium determination using liquid scintillation counting with the URAEX cocktail is described. Interference from radon and a strong influence of nitrate ion were detected in this procedure. Interference from radium, thorium and polonium emissions were very low when optimal operating conditions were reached. Quenching effects were considered and the minimum detectable activity was evaluated for different sample volumes. Isotopic analysis of samples can be performed using the proposed method. Comparisons with the results obtained with the general procedure used in alpha spectrometry with passivated implanted planar silicon detectors showed good agreement. The proposed procedure is thus suitable for uranium determination in water samples and can be considered as an alternative to the laborious conventional chemical preparations needed for alpha spectrometry methods using semiconductor detectors.

  16. Bioinspired Synthesis of Monolithic and Layered Aerogels.

    PubMed

    Han, Xiao; Hassan, Khalil T; Harvey, Alan; Kulijer, Dejan; Oila, Adrian; Hunt, Michael R C; Šiller, Lidija

    2018-06-01

    Aerogels are the least dense and most porous materials known to man, with potential applications from lightweight superinsulators to smart energy materials. To date their use has been seriously hampered by their synthesis methods, which are laborious and expensive. Taking inspiration from the life cycle of the damselfly, a novel ambient pressure-drying approach is demonstrated in which instead of employing low-surface-tension organic solvents to prevent pore collapse during drying, sodium bicarbonate solution is used to generate pore-supporting carbon dioxide in situ, significantly reducing energy, time, and cost in aerogel production. The generic applicability of this readily scalable new approach is demonstrated through the production of granules, monoliths, and layered solids with a number of precursor materials. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. OutKnocker: a web tool for rapid and simple genotyping of designer nuclease edited cell lines.

    PubMed

    Schmid-Burgk, Jonathan L; Schmidt, Tobias; Gaidt, Moritz M; Pelka, Karin; Latz, Eicke; Ebert, Thomas S; Hornung, Veit

    2014-10-01

    The application of designer nucleases allows the induction of DNA double-strand breaks (DSBs) at user-defined genomic loci. Due to imperfect DNA repair mechanisms, DSBs can lead to alterations in the genomic architecture, such as the disruption of the reading frame of a critical exon. This can be exploited to generate somatic knockout cell lines. While high genome editing activities can be achieved in various cellular systems, obtaining cell clones that contain all-allelic frameshift mutations at the target locus of interest remains a laborious task. To this end, we have developed an easy-to-follow deep sequencing workflow and the evaluation tool OutKnocker (www.OutKnocker.org), which allows convenient, reliable, and cost-effective identification of knockout cell lines. © 2014 Schmid-Burgk et al.; Published by Cold Spring Harbor Laboratory Press.

  18. Collagen Quantification in Tissue Specimens.

    PubMed

    Coentro, João Quintas; Capella-Monsonís, Héctor; Graceffa, Valeria; Wu, Zhuning; Mullen, Anne Maria; Raghunath, Michael; Zeugolis, Dimitrios I

    2017-01-01

    Collagen is the major extracellular protein in mammals. Accurate quantification of collagen is essential in the biomaterials (e.g., reproducible collagen scaffold fabrication), drug discovery (e.g., assessment of collagen in pathophysiologies, such as fibrosis), and tissue engineering (e.g., quantification of cell-synthesized collagen) fields. Although measuring hydroxyproline content is the most widely used method to quantify collagen in biological specimens, the process is very laborious. To this end, the Sircol™ Collagen Assay is widely used due to its inherent simplicity and convenience. However, this method leads to overestimation of collagen content due to the interaction of Sirius red with basic amino acids of non-collagenous proteins. Herein, we describe the addition of an ultrafiltration purification step in the process to accurately determine collagen content in tissues.

  19. Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays.

    PubMed

    Nielsen, Henrik Bjørn; Wernersson, Rasmus; Knudsen, Steen

    2003-07-01

    Optimal design of oligonucleotides for microarrays involves tedious and laborious work evaluating potential oligonucleotides relative to a series of parameters. The currently available tools for this purpose are limited in their flexibility and do not present the oligonucleotide designer with an overview of these parameters. We present here a flexible tool named OligoWiz for designing oligonucleotides for multiple purposes. OligoWiz presents a set of parameter scores in a graphical interface to facilitate an overview for the user. Additional custom parameter scores can easily be added to the program to extend the default parameters: homology, DeltaTm, low-complexity, position and GATC-only. Furthermore we present an analysis of the limitations in designing oligonucleotide sets that can detect transcripts from multiple organisms. OligoWiz is available at www.cbs.dtu.dk/services/OligoWiz/.

  20. Comparison of two eukaryotic systems for the expression of VP6 protein of rotavirus specie A: transient gene expression in HEK293-T cells and insect cell-baculovirus system.

    PubMed

    da Silva Junior, Haroldo Cid; da Silva E Mouta Junior, Sérgio; de Mendonça, Marcos César Lima; de Souza Pereira, Mirian Claudia; da Rocha Nogueira, Alanderson; de Azevedo, Maria Luiza Borges; Leite, José Paulo Gagliardi; de Moraes, Márcia Terezinha Baroni

    2012-09-01

    The VP6 protein of rotavirus A (RVA) is a target antigen used for diagnostic assays and also for the development of new RVA vaccines. We have compared the expression of VP6 protein in human embryonic kidney (HEK293-T) cells with results obtained using a well-established insect cell-baculovirus system. The recombinant VP6 (rVP6) expressed in HEK293-T cells did not present degradation and also retained the ability to form trimers. In the insect cell-baculovirus system, rVP6 was expressed at higher levels and with protein degradation as well as partial loss of ability to form trimers was observed. Therefore, HEK293-T cells represent a less laborious alternative system than insect cells for expression of rVP6 from human RVA.

  1. Fingerprints of Modified RNA Bases from Deep Sequencing Profiles.

    PubMed

    Kietrys, Anna M; Velema, Willem A; Kool, Eric T

    2017-11-29

    Posttranscriptional modifications of RNA bases are not only found in many noncoding RNAs but have also recently been identified in coding (messenger) RNAs as well. They require complex and laborious methods to locate, and many still lack methods for localized detection. Here we test the ability of next-generation sequencing (NGS) to detect and distinguish between ten modified bases in synthetic RNAs. We compare ultradeep sequencing patterns of modified bases, including miscoding, insertions and deletions (indels), and truncations, to unmodified bases in the same contexts. The data show widely varied responses to modification, ranging from no response, to high levels of mutations, insertions, deletions, and truncations. The patterns are distinct for several of the modifications, and suggest the future use of ultradeep sequencing as a fingerprinting strategy for locating and identifying modifications in cellular RNAs.

  2. Time- and Cost-Efficient Identification of T-DNA Insertion Sites through Targeted Genomic Sequencing

    PubMed Central

    Lepage, Étienne; Zampini, Éric; Boyle, Brian; Brisson, Normand

    2013-01-01

    Forward genetic screens enable the unbiased identification of genes involved in biological processes. In Arabidopsis, several mutant collections are publicly available, which greatly facilitates such practice. Most of these collections were generated by agrotransformation of a T-DNA at random sites in the plant genome. However, precise mapping of T-DNA insertion sites in mutants isolated from such screens is a laborious and time-consuming task. Here we report a simple, low-cost and time efficient approach to precisely map T-DNA insertions simultaneously in many different mutants. By combining sequence capture, next-generation sequencing and 2D-PCR pooling, we developed a new method that allowed the rapid localization of T-DNA insertion sites in 55 out of 64 mutant plants isolated in a screen for gyrase inhibition hypersensitivity. PMID:23951038

  3. Mississippi Company Using NASA Software Program to Provide Unique Imaging Service: DATASTAR Success Story

    NASA Technical Reports Server (NTRS)

    2001-01-01

    DATASTAR, Inc., of Picayune, Miss., has taken NASA's award-winning Earth Resources Laboratory Applications (ELAS) software program and evolved it to the point that the company is now providing a unique, spatial imagery service over the Internet. ELAS was developed in the early 80's to process satellite and airborne sensor imagery data of the Earth's surface into readable and useable information. While there are several software packages on the market that allow the manipulation of spatial data into useable products, this is usually a laborious task. The new program, called the DATASTAR Image Processing Exploitation, or DIPX, Delivery Service, is a subscription service available over the Internet that takes the work out of the equation and provides normalized geo-spatial data in the form of decision products.

  4. Visual Computing Environment Workshop

    NASA Technical Reports Server (NTRS)

    Lawrence, Charles (Compiler)

    1998-01-01

    The Visual Computing Environment (VCE) is a framework for intercomponent and multidisciplinary computational simulations. Many current engineering analysis codes simulate various aspects of aircraft engine operation. For example, existing computational fluid dynamics (CFD) codes can model the airflow through individual engine components such as the inlet, compressor, combustor, turbine, or nozzle. Currently, these codes are run in isolation, making intercomponent and complete system simulations very difficult to perform. In addition, management and utilization of these engineering codes for coupled component simulations is a complex, laborious task, requiring substantial experience and effort. To facilitate multicomponent aircraft engine analysis, the CFD Research Corporation (CFDRC) is developing the VCE system. This system, which is part of NASA's Numerical Propulsion Simulation System (NPSS) program, can couple various engineering disciplines, such as CFD, structural analysis, and thermal analysis.

  5. Successful Treatment of Endometriosis-Related Hemorrhagic Ascites: A Report of Three Cases.

    PubMed

    Mendes, Sofia; Carvalho, Catarina; Rodrigues, GonÇalo; Barata, Sónia; Calhaz-Jorge, Carlos; Osório, Filipa

    2018-06-01

    Endometriosis-related ascites is rare and is frequently confused with an ovarian malignancy. Since it affects women in reproductive age, its diagnosis and therapy are even more challenging. These patients usually present with abdominal distension, pelvic pain, and weight loss, but a careful questioning usually reveals the typical endometriosis symptoms-such as dysmenorrhea and dyspareunia. We present three cases of endometriosis-related ascites, one of them with pleural effusion. All cases were associated with extensive disease and required laborious laparoscopic surgery, medical therapy with gonadotropin releasing hormone analogs, and long-term follow-up. One of the patients delivered twins following an in vitro fertilization (IVF) cycle without recurrence of ascites. We aim to raise awareness toward the importance of considering endometriosis in a patient with ascites of unknown origin.

  6. The Rationale for Growth Hormone Therapy in Children with Short Stature

    PubMed Central

    Deodati, Annalisa; Cianfarani, Stefano

    2017-01-01

    Growth hormone (GH) was first isolated from cadaver pituitary glands, requiring laborious and expensive collection of glands, followed by extraction and purification of the hormone. This limited supply restricted its use to children with severe GH deficiency who were treated with low dosages and suboptimal schedules. The development of recombinant DNA-derived GH, allowed the production of virtually unlimited amounts of GH, leading to the approval for therapy for a large number of childhood conditions characterized by non-GH deficient short stature. The aim of this review is to provide a critical overview on the daily use of GH in two paradigmatic conditions of non-GH deficient short stature which are children born small for gestational age and with idiopathic short stature, highlighting the available strength of evidence for efficacy and safety. PMID:29280742

  7. Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation.

    PubMed

    Klee, Kathrin; Ernst, Rebecca; Spannagl, Manuel; Mayer, Klaus F X

    2007-08-30

    Apollo, a genome annotation viewer and editor, has become a widely used genome annotation and visualization tool for distributed genome annotation projects. When using Apollo for annotation, database updates are carried out by uploading intermediate annotation files into the respective database. This non-direct database upload is laborious and evokes problems of data synchronicity. To overcome these limitations we extended the Apollo data adapter with a generic, configurable web service client that is able to retrieve annotation data in a GAME-XML-formatted string and pass it on to Apollo's internal input routine. This Apollo web service adapter, Apollo2Go, simplifies the data exchange in distributed projects and aims to render the annotation process more comfortable. The Apollo2Go software is freely available from ftp://ftpmips.gsf.de/plants/apollo_webservice.

  8. Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation

    PubMed Central

    Klee, Kathrin; Ernst, Rebecca; Spannagl, Manuel; Mayer, Klaus FX

    2007-01-01

    Background Apollo, a genome annotation viewer and editor, has become a widely used genome annotation and visualization tool for distributed genome annotation projects. When using Apollo for annotation, database updates are carried out by uploading intermediate annotation files into the respective database. This non-direct database upload is laborious and evokes problems of data synchronicity. Results To overcome these limitations we extended the Apollo data adapter with a generic, configurable web service client that is able to retrieve annotation data in a GAME-XML-formatted string and pass it on to Apollo's internal input routine. Conclusion This Apollo web service adapter, Apollo2Go, simplifies the data exchange in distributed projects and aims to render the annotation process more comfortable. The Apollo2Go software is freely available from . PMID:17760972

  9. Isolation of Mitochondrial DNA from Single, Short Hairs without Roots Using Pressure Cycling Technology.

    PubMed

    Harper, Kathryn A; Meiklejohn, Kelly A; Merritt, Richard T; Walker, Jessica; Fisher, Constance L; Robertson, James M

    2018-02-01

    Hairs are commonly submitted as evidence to forensic laboratories, but standard nuclear DNA analysis is not always possible. Mitochondria (mt) provide another source of genetic material; however, manual isolation is laborious. In a proof-of-concept study, we assessed pressure cycling technology (PCT; an automated approach that subjects samples to varying cycles of high and low pressure) for extracting mtDNA from single, short hairs without roots. Using three microscopically similar donors, we determined the ideal PCT conditions and compared those yields to those obtained using the traditional manual micro-tissue grinder method. Higher yields were recovered from grinder extracts, but yields from PCT extracts exceeded the requirements for forensic analysis, with the DNA quality confirmed through sequencing. Automated extraction of mtDNA from hairs without roots using PCT could be useful for forensic laboratories processing numerous samples.

  10. A Novel Algorithm for the Generation of Distinct Kinematic Chain

    NASA Astrophysics Data System (ADS)

    Medapati, Sreenivasa Reddy; Kuchibhotla, Mallikarjuna Rao; Annambhotla, Balaji Srinivasa Rao

    2016-07-01

    Generation of distinct kinematic chains is an important topic in the design of mechanisms for various industrial applications i.e., robotic manipulator, tractor, crane etc. Many researchers have intently focused on this area and explained various processes of generating distinct kinematic chains which are laborious and complex. It is desirable to enumerate the kinematic chains systematically to know the inherent characteristics of a chain related to its structure so that all the distinct chains can be analyzed in depth, prior to the selection of a chain for a purpose. This paper proposes a novel and simple method with set of rules defined to eliminate isomorphic kinematic chains generating distinct kinematic chains. Also, this method simplifies the process of generating distinct kinematic chains even at higher levels i.e., 10-link, 11-link with single and multiple degree of freedom.

  11. Notes on aerodynamic forces 1 : rectilinear motion

    NASA Technical Reports Server (NTRS)

    Munk, Max M

    1922-01-01

    The study of the motion of perfect fluids is of paramount importance for the understanding of the chief phenomena occurring in the air surrounding an aircraft, and for the numerical determination of their effects. The author recently successfully employed some simple methods for the investigation of the flow of a perfect fluid that have never been mentioned in connection with aeronautical problems. These methods appeal particularly to the engineer who is untrained in performing laborious mathematical computations, as they do away with these and allow one to obtain many interesting results by the mere application of some general and well-known principles of mechanics. Discussed here are the kinetic energy of moving fluids, the momentum of a body in a perfect fluid, two dimensional flow, three dimensional flow, and the distribution of the transverse forces of very elongated surfaces of revolution.

  12. A Sensitive and Versatile Fluorescent Activity Assay for ABHD6.

    PubMed

    Savinainen, Juha R; Navia-Paldanius, Dina; Laitinen, Jarmo T

    2016-01-01

    The α/β-hydrolase domain-containing 6 (ABHD6) enzyme is a newly found serine hydrolase whose substrate profile resembles that of monoacylglycerol lipase (MAGL), the major 2-arachidonoyl glycerol (2-AG) hydrolase in the brain. Here, we describe a sensitive fluorescent assay of ABHD6 activity in a 96-well-plate format that allows parallel testing of inhibitor activities of up to 40 compounds in a single assay. The method utilizes lysates of HEK293 cells transiently overexpressing human ABHD6 as the enzymatic source, and kinetically monitors glycerol liberated in the hydrolysis of 1(3)-AG, the preferred arachidonoyl glycerol isomer. Glycerol output is coupled to an enzymatic cascade generating the fluorescent end-product resorufin. The approach has major benefits compared to laborious traditional mass spectrometric methods and liquid scintillation-based assays, or approaches using unnatural substrates.

  13. Automatic design and manufacture of robotic lifeforms.

    PubMed

    Lipson, H; Pollack, J B

    2000-08-31

    Biological life is in control of its own means of reproduction, which generally involves complex, autocatalysing chemical reactions. But this autonomy of design and manufacture has not yet been realized artificially. Robots are still laboriously designed and constructed by teams of human engineers, usually at considerable expense. Few robots are available because these costs must be absorbed through mass production, which is justified only for toys, weapons and industrial systems such as automatic teller machines. Here we report the results of a combined computational and experimental approach in which simple electromechanical systems are evolved through simulations from basic building blocks (bars, actuators and artificial neurons); the 'fittest' machines (defined by their locomotive ability) are then fabricated robotically using rapid manufacturing technology. We thus achieve autonomy of design and construction using evolution in a 'limited universe' physical simulation coupled to automatic fabrication.

  14. A potential drop strain sensor for in-situ power station creep monitoring

    NASA Astrophysics Data System (ADS)

    Corcoran, Joseph; Cawley, Peter; Nagy, Peter B.

    2014-02-01

    Creep is a high temperature damage mechanism of interest to the power industry and at present lacks a satisfactory inspection technique. Existing material inspection techniques are extremely laborious while strain measurements rely on often infrequent off-load measurements. A quasi-DC directional potential drop technique has been suggested that is able to suppress the effects of permeability and is primarily sensitive to changes in resistivity and also the geometry that will develop through strain. The change in creep related resistivity is shown by an equivalent effective resistivity approach to be small at <2% change when compared to the >100% change in transfer resistance that occurs due to strain as observed in laboratory tests. A biaxial inversion is then presented and demonstrated on in-lab samples showing good performance. The result is a sensor that performs as a very robust high temperature strain gauge.

  15. Two cases of occupational allergic contact dermatitis from a cycloaliphatic epoxy resin in a neat oil: Case Report

    PubMed Central

    Jensen, Charlotte D; Andersen, Klaus E

    2003-01-01

    Background Metal-working fluids contain complex mixtures of chemicals and metal workers constitute a potential risk group for the development of allergic contact dermatitis. Case presentation Two metal workers developed allergic contact dermatitis on the hands and lower arms from exposure to a neat oil used in metal processing. Patch testing revealed that the relevant contact allergen was a cycloaliphatic epoxy resin, 1,2-cyclohexanedicarboxylic acid, bis(oxiranylmethyl) ester, added to the oil as a stabilizer. None of the patients had positive reactions to the bisphenol A-based epoxy resin in the standard series. Conclusions These cases emphasize that well-known contact allergens may show up from unexpected sources of exposure. Further, it can be a long-lasting, laborious process to detect an occupational contact allergen and cooperation from the patient and the manufacturer of the sensitizing product is essential. PMID:12685935

  16. Microfluidic-Mass Spectrometry Interfaces for Translational Proteomics.

    PubMed

    Pedde, R Daniel; Li, Huiyan; Borchers, Christoph H; Akbari, Mohsen

    2017-10-01

    Interfacing mass spectrometry (MS) with microfluidic chips (μchip-MS) holds considerable potential to transform a clinician's toolbox, providing translatable methods for the early detection, diagnosis, monitoring, and treatment of noncommunicable diseases by streamlining and integrating laborious sample preparation workflows on high-throughput, user-friendly platforms. Overcoming the limitations of competitive immunoassays - currently the gold standard in clinical proteomics - μchip-MS can provide unprecedented access to complex proteomic assays having high sensitivity and specificity, but without the labor, costs, and complexities associated with conventional MS sample processing. This review surveys recent μchip-MS systems for clinical applications and examines their emerging role in streamlining the development and translation of MS-based proteomic assays by alleviating many of the challenges that currently inhibit widespread clinical adoption. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

  17. Visualizing tumor evolution with the fishplot package for R.

    PubMed

    Miller, Christopher A; McMichael, Joshua; Dang, Ha X; Maher, Christopher A; Ding, Li; Ley, Timothy J; Mardis, Elaine R; Wilson, Richard K

    2016-11-07

    Massively-parallel sequencing at depth is now enabling tumor heterogeneity and evolution to be characterized in unprecedented detail. Tracking these changes in clonal architecture often provides insight into therapeutic response and resistance. In complex cases involving multiple timepoints, standard visualizations, such as scatterplots, can be difficult to interpret. Current data visualization methods are also typically manual and laborious, and often only approximate subclonal fractions. We have developed an R package that accurately and intuitively displays changes in clonal structure over time. It requires simple input data and produces illustrative and easy-to-interpret graphs suitable for diagnosis, presentation, and publication. The simplicity, power, and flexibility of this tool make it valuable for visualizing tumor evolution, and it has potential utility in both research and clinical settings. The fishplot package is available at https://github.com/chrisamiller/fishplot .

  18. Tensorial dynamic time warping with articulation index representation for efficient audio-template learning.

    PubMed

    Le, Long N; Jones, Douglas L

    2018-03-01

    Audio classification techniques often depend on the availability of a large labeled training dataset for successful performance. However, in many application domains of audio classification (e.g., wildlife monitoring), obtaining labeled data is still a costly and laborious process. Motivated by this observation, a technique is proposed to efficiently learn a clean template from a few labeled, but likely corrupted (by noise and interferences), data samples. This learning can be done efficiently via tensorial dynamic time warping on the articulation index-based time-frequency representations of audio data. The learned template can then be used in audio classification following the standard template-based approach. Experimental results show that the proposed approach outperforms both (1) the recurrent neural network approach and (2) the state-of-the-art in the template-based approach on a wildlife detection application with few training samples.

  19. Integrated two-cylinder liquid piston Stirling engine

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yang, Ning; Rickard, Robert; Pluckter, Kevin

    2014-10-06

    Heat engines utilizing the Stirling cycle may run on low temperature differentials with the capacity to function at high efficiency due to their near-reversible operation. However, current approaches to building Stirling engines are laborious and costly. Typically the components are assembled by hand and additional components require a corresponding increase in manufacturing complexity, akin to electronics before the integrated circuit. We present a simple and integrated approach to fabricating Stirling engines with precisely designed cylinders. We utilize computer aided design and one-step, planar machining to form all components of the engine. The engine utilizes liquid pistons and displacers to harnessmore » useful work from heat absorption and rejection. As a proof of principle of the integrated design, a two-cylinder engine is produced and characterized and liquid pumping is demonstrated.« less

  20. A PCR technique to detect enterotoxigenic and verotoxigenic Escherichia coli in boar semen samples.

    PubMed

    Bussalleu, E; Pinart, E; Yeste, M; Briz, M; Sancho, S; Torner, E; Bonet, S

    2012-08-01

    In semen, bacteria's isolation from a pure culture is complex, laborious and easily alterable by the presence of antibiotics and inhibitors. We developed a PCR technique to detect the presence of the enterotoxigenic (ETEC) and verotoxigenic Escherichia coli (VTEC) (strains with high prevalence in the swine industry) in semen by adapting the protocols developed by Zhang et al. (2007) and Yilmaz et al. (2006). We artificially inoculated extended semen samples at different infective concentrations of bacteria (from 10(2) to 10(8) bacteria ml(-1)) with two enterotoxigenic and verotoxigenic strains, and performed two multiplex and one conventional PCR. This technique proved to be a quick, useful and reliable tool to detect the presence of ETEC and VTEC up to an infective dose of 10(5) bacteria ml(-1) in semen. Copyright © 2011 Elsevier Ltd. All rights reserved.

  1. Governmental oversight of prescribing medications: history of the US Food and Drug Administration and prescriptive authority.

    PubMed

    Plank, Linda S

    2011-01-01

    The evolution of drug regulation and awarding of prescriptive authority is a complex and sometimes convoluted process that can be confusing for health care providers. A review of the history of how drugs have been manufactured and dispensed helps explain why this process has been so laborious and complicated. Because the federal and state governments have the responsibility for protecting the public, most regulations have been passed with the intentions of ensuring consumer safety. The current system of laws and regulations is the result of many years of using the legal system to correct drug marketing that had adverse health consequences. Government oversight will continue as prescribing medications transitions to an electronic form and as health care professionals in addition to physicians seek to gain prescriptive authority. © 2011 by the American College of Nurse-Midwives.

  2. 3D reconstruction based on light field images

    NASA Astrophysics Data System (ADS)

    Zhu, Dong; Wu, Chunhong; Liu, Yunluo; Fu, Dongmei

    2018-04-01

    This paper proposed a method of reconstructing three-dimensional (3D) scene from two light field images capture by Lytro illium. The work was carried out by first extracting the sub-aperture images from light field images and using the scale-invariant feature transform (SIFT) for feature registration on the selected sub-aperture images. Structure from motion (SFM) algorithm is further used on the registration completed sub-aperture images to reconstruct the three-dimensional scene. 3D sparse point cloud was obtained in the end. The method shows that the 3D reconstruction can be implemented by only two light field camera captures, rather than at least a dozen times captures by traditional cameras. This can effectively solve the time-consuming, laborious issues for 3D reconstruction based on traditional digital cameras, to achieve a more rapid, convenient and accurate reconstruction.

  3. Comparison of soil pollution concentrations determined using AAS and portable XRF techniques.

    PubMed

    Radu, Tanja; Diamond, Dermot

    2009-11-15

    Past mining activities in the area of Silvermines, Ireland, have resulted in heavily polluted soils. The possibility of spreading pollution to the surrounding areas through dust blow-offs poses a potential threat for the local communities. Conventional environmental soil and dust analysis techniques are very slow and laborious and consequently there is a need for fast and accurate analytical methods, which can provide real-time in situ pollution mapping. Laboratory-based aqua regia acid digestion of the soil samples collected in the area followed by the atomic absorption spectrophotometry (AAS) analysis confirmed very high pollution, especially by Pb, As, Cu, and Zn. In parallel, samples were analyzed using portable X-ray fluorescence radioisotope and miniature tube powered (XRF) NITON instruments and their performance was compared. Overall, the portable XRF instrument gave excellent correlation with the laboratory-based reference AAS method.

  4. Automated Monitoring and Analysis of Social Behavior in Drosophila

    PubMed Central

    Dankert, Heiko; Wang, Liming; Hoopfer, Eric D.; Anderson, David J.; Perona, Pietro

    2009-01-01

    We introduce a method based on machine vision for automatically measuring aggression and courtship in Drosophila melanogaster. The genetic and neural circuit bases of these innate social behaviors are poorly understood. High-throughput behavioral screening in this genetically tractable model organism is a potentially powerful approach, but it is currently very laborious. Our system monitors interacting pairs of flies, and computes their location, orientation and wing posture. These features are used for detecting behaviors exhibited during aggression and courtship. Among these, wing threat, lunging and tussling are specific to aggression; circling, wing extension (courtship “song”) and copulation are specific to courtship; locomotion and chasing are common to both. Ethograms may be constructed automatically from these measurements, saving considerable time and effort. This technology should enable large-scale screens for genes and neural circuits controlling courtship and aggression. PMID:19270697

  5. Brownmillerite-type Ca2 FeCoO5 as a Practicable Oxygen Evolution Reaction Catalyst.

    PubMed

    Tsuji, Etsushi; Motohashi, Teruki; Noda, Hiroyuki; Kowalski, Damian; Aoki, Yoshitaka; Tanida, Hajime; Niikura, Junji; Koyama, Yukinori; Mori, Masahiro; Arai, Hajime; Ioroi, Tsutomu; Fujiwara, Naoko; Uchimoto, Yoshiharu; Ogumi, Zempachi; Habazaki, Hiroki

    2017-07-21

    Here, we report remarkable oxygen evolution reaction (OER) catalytic activity of brownmillerite (BM)-type Ca 2 FeCoO 5 . The OER activity of this oxide is comparable to or beyond those of the state-of-the-art perovskite (PV)-catalyst Ba 0.5 Sr 0.5 Co 0.8 Fe 0.2 O 3-δ (BSCF) and a precious-metal catalyst RuO 2 , emphasizing the importance of the characteristic BM structure with multiple coordination environments of transition metal (TM) species. Also, Ca 2 FeCoO 5 is clearly advantageous in terms of expense/laboriousness of the material synthesis. These facts make this oxide a promising OER catalyst used in many energy conversion technologies such as metal-air secondary batteries and hydrogen production from electrochemical/photocatalytic water splitting. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. A Rotifer-Based Technique to Rear Zebrafish Larvae in Small Academic Settings.

    PubMed

    Allen, Raymond L; Wallace, Robert L; Sisson, Barbara E

    2016-08-01

    Raising zebrafish from larvae to juveniles can be laborious, requiring frequent water exchanges and continuous culturing of live feed. This task becomes even more difficult for small institutions that do not have access to the necessary funding, equipment, or personnel to maintain large-scale systems usually employed in zebrafish husbandry. To open this opportunity to smaller institutions, a cost-efficient protocol was developed to culture Nannochloropsis to feed the halophilic, planktonic rotifer Brachionus plicatilis; the rotifers were then used to raise larval zebrafish to juveniles. By using these methods, small institutions can easily raise zebrafish embryos in a cost-efficient manner without the need to establish an extensive fish-raising facility. In addition, culturing rotifers provides a micrometazoan that serves as a model organism for teaching and undergraduate research studies for a variety of topics, including aging, toxicology, and predator-prey dynamics.

  7. Comparative evaluation of two methods of enumerating enterococci in foods: collaborative study.

    PubMed

    Peterz, M; Steneryd, A C

    1993-05-01

    Two methods of enumerating enterococci in foods were compared in a collaborative study. Thirteen laboratories tested four blind duplicate samples containing different levels of enterococci and two negative control samples. Freeze-dried mixtures of bacteria were used as simulated food samples. The freeze-dried samples were reconstituted and either spread directly on the surface of Slanetz and Bartley medium (SB) and incubated at 44 degrees C for 48 h or preincubated in tryptone soya agar at 37 degrees C for 2 h before being overlaid by SB and incubated at 37 degrees C for a further 46 h. The numbers CFU of enterococci recovered by the two methods were not significantly different except for one sample where the 37 degrees C method gave a somewhat higher recovery. The 44 degrees C method was less time-consuming and less laborious.

  8. INfORM: Inference of NetwOrk Response Modules.

    PubMed

    Marwah, Veer Singh; Kinaret, Pia Anneli Sofia; Serra, Angela; Scala, Giovanni; Lauerma, Antti; Fortino, Vittorio; Greco, Dario

    2018-06-15

    Detecting and interpreting responsive modules from gene expression data by using network-based approaches is a common but laborious task. It often requires the application of several computational methods implemented in different software packages, forcing biologists to compile complex analytical pipelines. Here we introduce INfORM (Inference of NetwOrk Response Modules), an R shiny application that enables non-expert users to detect, evaluate and select gene modules with high statistical and biological significance. INfORM is a comprehensive tool for the identification of biologically meaningful response modules from consensus gene networks inferred by using multiple algorithms. It is accessible through an intuitive graphical user interface allowing for a level of abstraction from the computational steps. INfORM is freely available for academic use at https://github.com/Greco-Lab/INfORM. Supplementary data are available at Bioinformatics online.

  9. Simplified Deployment of Health Informatics Applications by Providing Docker Images.

    PubMed

    Löbe, Matthias; Ganslandt, Thomas; Lotzmann, Lydia; Mate, Sebastian; Christoph, Jan; Baum, Benjamin; Sariyar, Murat; Wu, Jie; Stäubert, Sebastian

    2016-01-01

    Due to the specific needs of biomedical researchers, in-house development of software is widespread. A common problem is to maintain and enhance software after the funded project has ended. Even if many tools are made open source, only a couple of projects manage to attract a user basis large enough to ensure sustainability. Reasons for this include complex installation and configuration of biomedical software as well as an ambiguous terminology of the features provided; all of which make evaluation of software laborious. Docker is a para-virtualization technology based on Linux containers that eases deployment of applications and facilitates evaluation. We investigated a suite of software developments funded by a large umbrella organization for networked medical research within the last 10 years and created Docker containers for a number of applications to support utilization and dissemination.

  10. Fractal Properties of Some Machined Surfaces

    NASA Astrophysics Data System (ADS)

    Thomas, T. R.; Rosén, B.-G.

    Many surface profiles are self-affine fractals defined by fractal dimension D and topothesy Λ. Traditionally these parameters are derived laboriously from the slope and intercept of the profile's structure function. Recently a quicker and more convenient derivation from standard roughness parameters has been suggested. Based on this derivation, it is shown that D and Λ depend on two dimensionless numbers: the ratio of the mean peak spacing to the rms roughness, and the ratio of the mean local peak spacing to the sampling interval. Using this approach, values of D and Λ are calculated for 125 profiles produced by polishing, plateau honing and various single-point machining processes. Different processes are shown to occupy different regions in D-Λ space, and polished surfaces show a relationship between D and Λ which is independent of the surface material.

  11. Isolation of bioactive allelochemicals from sunflower (variety Suncross-42) through fractionation-guided bioassays.

    PubMed

    Anjum, Tehmina; Bajwa, Rukhsana

    2010-11-01

    Plants are rich source of biologically active allelochemicals. However, natural product discovery is not an easy task. Many problems encountered during this laborious practice can be overcome through the modification of preliminary trials. Bioassay-directed isolation of active plant compounds can increase efficiency by eliminating many of the problems encountered. This strategy avoids unnecessary compounds, concentrating on potential components and thus reducing the cost and time required. In this study, a crude aqueous extract of sunflower leaves was fractionated through high performance liquid chromatography. The isolated fractions were checked against Chenopodium album and Rumex dentatus. The fraction found active against two selected weeds was re-fractionated, and the active components were checked for their composition. Thin layer chromatography isolated a range of phenolics, whereas the presence of bioactive terpenoids was confirmed through mass spectroscopy and nuclear magnetic resonance spectroscopy.

  12. Design of Multilayer Insulation for the Multipurpose Hydrogen Test Bed

    NASA Technical Reports Server (NTRS)

    Marlow, Weston A.

    2011-01-01

    Multilayer insulation (MLI) is a critical component for future, long term space missions. These missions will require the storage of cryogenic fuels for extended periods of time with little to no boil-off and MLI is vital due to its exceptional radiation shielding properties. Several MLI test articles were designed and fabricated which explored methods of assembling and connecting blankets, yielding results for evaluation. Insight gained, along with previous design experience, will be used in the design of the replacement blanket for the Multipurpose Hydrogen Test Bed (MHTB), which is slated for upcoming tests. Future design considerations are discussed which include mechanical testing to determine robustness of such a system, as well as cryostat testing of samples to give insight to the loss of thermal performance of sewn panels in comparison to the highly efficient, albeit laborious application of the original MHTB blanket.

  13. Simultaneous digital quantification and fluorescence-based size characterization of massively parallel sequencing libraries.

    PubMed

    Laurie, Matthew T; Bertout, Jessica A; Taylor, Sean D; Burton, Joshua N; Shendure, Jay A; Bielas, Jason H

    2013-08-01

    Due to the high cost of failed runs and suboptimal data yields, quantification and determination of fragment size range are crucial steps in the library preparation process for massively parallel sequencing (or next-generation sequencing). Current library quality control methods commonly involve quantification using real-time quantitative PCR and size determination using gel or capillary electrophoresis. These methods are laborious and subject to a number of significant limitations that can make library calibration unreliable. Herein, we propose and test an alternative method for quality control of sequencing libraries using droplet digital PCR (ddPCR). By exploiting a correlation we have discovered between droplet fluorescence and amplicon size, we achieve the joint quantification and size determination of target DNA with a single ddPCR assay. We demonstrate the accuracy and precision of applying this method to the preparation of sequencing libraries.

  14. Damage estimation of sewer pipe using subtitles of CCTV inspection video

    NASA Astrophysics Data System (ADS)

    Park, Kitae; Kim, Byeongcheol; Kim, Taeheon; Seo, Dongwoo

    2017-04-01

    Recent frequent occurrence of urban sinkhole serves as a momentum of the periodic inspection of sewer pipelines. Sewer inspection using a CCTV device needs a lot of time and efforts. Many of previous studies which reduce the laborious tasks are mainly interested in the developments of image processing S/W and exploring H/W. And there has been no attempt to find meaningful information from the existing CCTV images stored by the sewer maintenance manager. This study adopts a cross-correlation based image processing method and extracts sewer inspection device's location data from CCTV images. As a result of the analysis of location-time relation, it show strong correlation between device stand time and the sewer damages. In case of using this method to investigate sewer inspection CCTV images, it will save the investigator's efforts and improve sewer maintenance efficiency and reliability.

  15. Concerted application of LC-MS and ligand binding assays to better understand exposure of a large molecule drug.

    PubMed

    Xu, Weifeng; Jiang, Hao; Titsch, Craig; Gadkari, Snaehal; Batog, Alicja; Wang, Bonnie; Hippeli, Lauren; Yamamoto, Brent; Chadwick, Kristina; Wheeler, Jennifer; Thompson, Chris; Stahl, James; Willett, Scott; DeSilva, Binodh S; Myler, Heather; Dodge, Robert W; Pillutla, Renuka C

    2018-06-20

    A ligand-binding assay (LBA) was used to measure exposure of PRM-151, the recombinant form of human pentraxin-2 (PTX-2), a complex pentamer with multiple binding partners. However, the assay showed a lack of dose-dependent exposure in select preclinical species and it could not differentiate the infused PRM-151 from the endogenous PTX-2 in nonhuman primates. Instead of assessing interference from its multiple binding partners, which could be time consuming and laborious, a LC-MS assay avoid of these interference was implemented to measure 'total' drug without the use of immunoaffinity capture reagents. The resultant LC-MS data confirmed the original data and the lack of dose-dependent exposure is now understood to be due to the multiple and diverse targets and functions and resultant complex biodistribution rather than an assay artifact.

  16. Plasmids for increased efficiency of vector construction and genetic engineering in filamentous fungi.

    PubMed

    Schoberle, Taylor J; Nguyen-Coleman, C Kim; May, Gregory S

    2013-01-01

    Fungal species are continuously being studied to not only understand disease in humans and plants but also to identify novel antibiotics and other metabolites of industrial importance. Genetic manipulations, such as gene deletion, gene complementation, and gene over-expression, are common techniques to investigate fungal gene functions. Although advances in transformation efficiency and promoter usage have improved genetic studies, some basic steps in vector construction are still laborious and time-consuming. Gateway cloning technology solves this problem by increasing the efficiency of vector construction through the use of λ phage integrase proteins and att recombination sites. We developed a series of Gateway-compatible vectors for use in genetic studies in a range of fungal species. They contain nutritional and drug-resistance markers and can be utilized to manipulate different filamentous fungal genomes. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. A Novel Algorithm for the Generation of Distinct Kinematic Chain

    NASA Astrophysics Data System (ADS)

    Medapati, Sreenivasa Reddy; Kuchibhotla, Mallikarjuna Rao; Annambhotla, Balaji Srinivasa Rao

    2018-06-01

    Generation of distinct kinematic chains is an important topic in the design of mechanisms for various industrial applications i.e., robotic manipulator, tractor, crane etc. Many researchers have intently focused on this area and explained various processes of generating distinct kinematic chains which are laborious and complex. It is desirable to enumerate the kinematic chains systematically to know the inherent characteristics of a chain related to its structure so that all the distinct chains can be analyzed in depth, prior to the selection of a chain for a purpose. This paper proposes a novel and simple method with set of rules defined to eliminate isomorphic kinematic chains generating distinct kinematic chains. Also, this method simplifies the process of generating distinct kinematic chains even at higher levels i.e., 10-link, 11-link with single and multiple degree of freedom.

  18. CodeSlinger: a case study in domain-driven interactive tool design for biomedical coding scheme exploration and use.

    PubMed

    Flowers, Natalie L

    2010-01-01

    CodeSlinger is a desktop application that was developed to aid medical professionals in the intertranslation, exploration, and use of biomedical coding schemes. The application was designed to provide a highly intuitive, easy-to-use interface that simplifies a complex business problem: a set of time-consuming, laborious tasks that were regularly performed by a group of medical professionals involving manually searching coding books, searching the Internet, and checking documentation references. A workplace observation session with a target user revealed the details of the current process and a clear understanding of the business goals of the target user group. These goals drove the design of the application's interface, which centers on searches for medical conditions and displays the codes found in the application's database that represent those conditions. The interface also allows the exploration of complex conceptual relationships across multiple coding schemes.

  19. Multiple sclerosis lesion segmentation using dictionary learning and sparse coding.

    PubMed

    Weiss, Nick; Rueckert, Daniel; Rao, Anil

    2013-01-01

    The segmentation of lesions in the brain during the development of Multiple Sclerosis is part of the diagnostic assessment for this disease and gives information on its current severity. This laborious process is still carried out in a manual or semiautomatic fashion by clinicians because published automatic approaches have not been universal enough to be widely employed in clinical practice. Thus Multiple Sclerosis lesion segmentation remains an open problem. In this paper we present a new unsupervised approach addressing this problem with dictionary learning and sparse coding methods. We show its general applicability to the problem of lesion segmentation by evaluating our approach on synthetic and clinical image data and comparing it to state-of-the-art methods. Furthermore the potential of using dictionary learning and sparse coding for such segmentation tasks is investigated and various possibilities for further experiments are discussed.

  20. Predicting Essential Genes and Proteins Based on Machine Learning and Network Topological Features: A Comprehensive Review

    PubMed Central

    Zhang, Xue; Acencio, Marcio Luis; Lemke, Ney

    2016-01-01

    Essential proteins/genes are indispensable to the survival or reproduction of an organism, and the deletion of such essential proteins will result in lethality or infertility. The identification of essential genes is very important not only for understanding the minimal requirements for survival of an organism, but also for finding human disease genes and new drug targets. Experimental methods for identifying essential genes are costly, time-consuming, and laborious. With the accumulation of sequenced genomes data and high-throughput experimental data, many computational methods for identifying essential proteins are proposed, which are useful complements to experimental methods. In this review, we show the state-of-the-art methods for identifying essential genes and proteins based on machine learning and network topological features, point out the progress and limitations of current methods, and discuss the challenges and directions for further research. PMID:27014079

  1. Bioterrorism web site resources for infectious disease clinicians and epidemiologists.

    PubMed

    Ferguson, Natalie E; Steele, Lynn; Crawford, Carol Y; Huebner, Nathan L; Fonseka, Jamila C; Bonander, Jason C; Kuehnert, Matthew J

    2003-06-01

    Finding bioterrorism-related information on the World Wide Web can be laborious. We hope to help readers find such information more easily by summarizing essential information in a consistent framework. A panel of 7 Centers for Disease Control and Prevention reviewers identified Web sites and evaluated them for sponsorship, mission, content usefulness, online ease of use, and adherence to commonly accepted quality criteria. Of >100 potential sites identified, 81 were chosen for target content of interest, and 43 were selected for inclusion. The results were classified into general purpose/portal sites; biological agent information; laboratory, infection control, epidemiology, and mental health information; and emergency contact sources, news and updates, event preparedness resources, information for first-responder settings, clinical and public education materials, and research resources. Agents covered included anthrax, smallpox, plague, botulism, tularemia, and viral hemorrhagic fever.

  2. Prediction of novel pre-microRNAs with high accuracy through boosting and SVM.

    PubMed

    Zhang, Yuanwei; Yang, Yifan; Zhang, Huan; Jiang, Xiaohua; Xu, Bo; Xue, Yu; Cao, Yunxia; Zhai, Qian; Zhai, Yong; Xu, Mingqing; Cooke, Howard J; Shi, Qinghua

    2011-05-15

    High-throughput deep-sequencing technology has generated an unprecedented number of expressed short sequence reads, presenting not only an opportunity but also a challenge for prediction of novel microRNAs. To verify the existence of candidate microRNAs, we have to show that these short sequences can be processed from candidate pre-microRNAs. However, it is laborious and time consuming to verify these using existing experimental techniques. Therefore, here, we describe a new method, miRD, which is constructed using two feature selection strategies based on support vector machines (SVMs) and boosting method. It is a high-efficiency tool for novel pre-microRNA prediction with accuracy up to 94.0% among different species. miRD is implemented in PHP/PERL+MySQL+R and can be freely accessed at http://mcg.ustc.edu.cn/rpg/mird/mird.php.

  3. Ultra-fast stem cell labelling using cationised magnetoferritin

    NASA Astrophysics Data System (ADS)

    Correia Carreira, S.; Armstrong, J. P. K.; Seddon, A. M.; Perriman, A. W.; Hartley-Davies, R.; Schwarzacher, W.

    2016-03-01

    Magnetic cell labelling with superparamagnetic iron oxide nanoparticles (SPIONs) facilitates many important biotechnological applications, such as cell imaging and remote manipulation. However, to achieve adequate cellular loading of SPIONs, long incubation times (24 hours and more) or laborious surface functionalisation are often employed, which can adversely affect cell function. Here, we demonstrate that chemical cationisation of magnetoferritin produces a highly membrane-active nanoparticle that can magnetise human mesenchymal stem cells (hMSCs) using incubation times as short as one minute. Magnetisation persisted for several weeks in culture and provided significant T2* contrast enhancement during magnetic resonance imaging. Exposure to cationised magnetoferritin did not adversely affect the membrane integrity, proliferation and multi-lineage differentiation capacity of hMSCs, which provides the first detailed evidence for the biocompatibility of magnetoferritin. The combination of synthetic ease and flexibility, the rapidity of labelling and absence of cytotoxicity make this novel nanoparticle system an easily accessible and versatile platform for a range of cell-based therapies in regenerative medicine.Magnetic cell labelling with superparamagnetic iron oxide nanoparticles (SPIONs) facilitates many important biotechnological applications, such as cell imaging and remote manipulation. However, to achieve adequate cellular loading of SPIONs, long incubation times (24 hours and more) or laborious surface functionalisation are often employed, which can adversely affect cell function. Here, we demonstrate that chemical cationisation of magnetoferritin produces a highly membrane-active nanoparticle that can magnetise human mesenchymal stem cells (hMSCs) using incubation times as short as one minute. Magnetisation persisted for several weeks in culture and provided significant T2* contrast enhancement during magnetic resonance imaging. Exposure to cationised

  4. High-resolution time series of Pseudomonas aeruginosa gene expression and rhamnolipid secretion through growth curve synchronization.

    PubMed

    van Ditmarsch, Dave; Xavier, João B

    2011-06-17

    Online spectrophotometric measurements allow monitoring dynamic biological processes with high-time resolution. Contrastingly, numerous other methods require laborious treatment of samples and can only be carried out offline. Integrating both types of measurement would allow analyzing biological processes more comprehensively. A typical example of this problem is acquiring quantitative data on rhamnolipid secretion by the opportunistic pathogen Pseudomonas aeruginosa. P. aeruginosa cell growth can be measured by optical density (OD600) and gene expression can be measured using reporter fusions with a fluorescent protein, allowing high time resolution monitoring. However, measuring the secreted rhamnolipid biosurfactants requires laborious sample processing, which makes this an offline measurement. Here, we propose a method to integrate growth curve data with endpoint measurements of secreted metabolites that is inspired by a model of exponential cell growth. If serial diluting an inoculum gives reproducible time series shifted in time, then time series of endpoint measurements can be reconstructed using calculated time shifts between dilutions. We illustrate the method using measured rhamnolipid secretion by P. aeruginosa as endpoint measurements and we integrate these measurements with high-resolution growth curves measured by OD600 and expression of rhamnolipid synthesis genes monitored using a reporter fusion. Two-fold serial dilution allowed integrating rhamnolipid measurements at a ~0.4 h-1 frequency with high-time resolved data measured at a 6 h-1 frequency. We show how this simple method can be used in combination with mutants lacking specific genes in the rhamnolipid synthesis or quorum sensing regulation to acquire rich dynamic data on P. aeruginosa virulence regulation. Additionally, the linear relation between the ratio of inocula and the time-shift between curves produces high-precision measurements of maximum specific growth rates, which were

  5. Computer Spectrometers

    NASA Astrophysics Data System (ADS)

    Dattani, Nikesh S.

    2017-06-01

    Ideally, the cataloguing of spectroscopic linelists would not demand laborious and expensive experiments. Whatever an experiment might achieve, the same information would be attainable by running a calculation on a computer. Kolos and Wolniewicz were the first to demonstrate that calculations on a computer can outperform even the most sophisticated molecular spectroscopic experiments of the time, when their 1964 calculations of the dissociation energies of H_2 and D_{2} were found to be more than 1 cm^{-1} larger than the best experiments by Gerhard Herzberg, suggesting the experiment violated a strict variational principle. As explained in his Nobel Lecture, it took 5 more years for Herzberg to perform an experiment which caught up to the accuracy of the 1964 calculations. Today, numerical solutions to the Schrödinger equation, supplemented with relativistic and higher-order quantum electrodynamics (QED) corrections can provide ro-vibrational spectra for molecules that we strongly believe to be correct, even in the absence of experimental data. Why do we believe these calculated spectra are correct if we do not have experiments against which to test them? All evidence seen so far suggests that corrections due to gravity or other forces are not needed for a computer simulated QED spectrum of ro-vibrational energy transitions to be correct at the precision of typical spectrometers. Therefore a computer-generated spectrum can be considered to be as good as one coming from a more conventional spectrometer, and this has been shown to be true not just for the H_2 energies back in 1964, but now also for several other molecules. So are we at the stage where we can launch an array of calculations, each with just the atomic number changed in the input file, to reproduce the NIST energy level databases? Not quite. But I will show that for the 6e^- molecule Li_2, we have reproduced the vibrational spacings to within 0.001 cm^{-1} of the experimental spectrum, and I will

  6. High-resolution mapping of bifurcations in nonlinear biochemical circuits

    NASA Astrophysics Data System (ADS)

    Genot, A. J.; Baccouche, A.; Sieskind, R.; Aubert-Kato, N.; Bredeche, N.; Bartolo, J. F.; Taly, V.; Fujii, T.; Rondelez, Y.

    2016-08-01

    Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate. Here, using droplet-based microfluidics, we map with high resolution and dimensionality the bifurcation diagrams of two synthetic, out-of-equilibrium and nonlinear programs: a bistable DNA switch and a predator-prey DNA oscillator. The diagrams delineate where function is optimal, dynamics bifurcates and models fail. Inverse problem solving on these large-scale data sets indicates interference from enzymatic coupling. Additionally, data mining exposes the presence of rare, stochastically bursting oscillators near deterministic bifurcations.

  7. Neuroscience and Psychoanalysis

    PubMed Central

    2007-01-01

    There exists an enormous amount of biological and scientific data in the field of neuroscience, which are daunting and laborious to those who are not directly engaged in these specialized areas. The intricacies and complexities of the role of the central nervous system (CNS) in psychiatric disorders and human behavior are, of course, acknowledged. In this article, observations and speculations of some prominent workers in the field of neuroscience are described with focus on their conclusions, rather than specific findings as they pertain to the mind-body relationship. The mind-brain/body issue has not been resolved insofar as clarifying the connections between CNS activity and thinking is concerned. Currently, it is useful to accept the concept of parallelism between CNS activity and thought. An argument will be made for the inclusion of the psychoanalytic method as an essential component of the scientific effort to elucidate consciousness and thinking. PMID:20711329

  8. Digital dream analysis: a revised method.

    PubMed

    Bulkeley, Kelly

    2014-10-01

    This article demonstrates the use of a digital word search method designed to provide greater accuracy, objectivity, and speed in the study of dreams. A revised template of 40 word search categories, built into the website of the Sleep and Dream Database (SDDb), is applied to four "classic" sets of dreams: The male and female "Norm" dreams of Hall and Van de Castle (1966), the "Engine Man" dreams discussed by Hobson (1988), and the "Barb Sanders Baseline 250" dreams examined by Domhoff (2003). A word search analysis of these original dream reports shows that a digital approach can accurately identify many of the same distinctive patterns of content found by previous investigators using much more laborious and time-consuming methods. The results of this study emphasize the compatibility of word search technologies with traditional approaches to dream content analysis. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Lysine acetylation sites prediction using an ensemble of support vector machine classifiers.

    PubMed

    Xu, Yan; Wang, Xiao-Bo; Ding, Jun; Wu, Ling-Yun; Deng, Nai-Yang

    2010-05-07

    Lysine acetylation is an essentially reversible and high regulated post-translational modification which regulates diverse protein properties. Experimental identification of acetylation sites is laborious and expensive. Hence, there is significant interest in the development of computational methods for reliable prediction of acetylation sites from amino acid sequences. In this paper we use an ensemble of support vector machine classifiers to perform this work. The experimentally determined acetylation lysine sites are extracted from Swiss-Prot database and scientific literatures. Experiment results show that an ensemble of support vector machine classifiers outperforms single support vector machine classifier and other computational methods such as PAIL and LysAcet on the problem of predicting acetylation lysine sites. The resulting method has been implemented in EnsemblePail, a web server for lysine acetylation sites prediction available at http://www.aporc.org/EnsemblePail/. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  10. Antibody biosensors for spoilage yeast detection based on impedance spectroscopy.

    PubMed

    Tubía, I; Paredes, J; Pérez-Lorenzo, E; Arana, S

    2018-04-15

    Brettanomyces is a yeast species responsible for wine and cider spoilage, producing volatile phenols that result in off-odors and loss of fruity sensorial qualities. Current commercial detection methods for these spoilage species are liable to frequent false positives, long culture times and fungal contamination. In this work, an interdigitated (IDE) biosensor was created to detect Brettanomyces using immunological reactions and impedance spectroscopy analysis. To promote efficient antibody immobilization on the electrodes' surface and to decrease non-specific adsorption, a Self-Assembled Monolayer (SAM) was developed. An impedance spectroscopy analysis, over four yeast strains, confirmed our device's increased efficacy. Compared to label-free sensors, antibody biosensors showed a higher relative impedance. The results also suggested that these biosensors could be a promising method to monitor some spoilage yeasts, offering an efficient alternative to the laborious and expensive traditional methods. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Evaluating conflation methods using uncertainty modeling

    NASA Astrophysics Data System (ADS)

    Doucette, Peter; Dolloff, John; Canavosio-Zuzelski, Roberto; Lenihan, Michael; Motsko, Dennis

    2013-05-01

    The classic problem of computer-assisted conflation involves the matching of individual features (e.g., point, polyline, or polygon vectors) as stored in a geographic information system (GIS), between two different sets (layers) of features. The classical goal of conflation is the transfer of feature metadata (attributes) from one layer to another. The age of free public and open source geospatial feature data has significantly increased the opportunity to conflate such data to create enhanced products. There are currently several spatial conflation tools in the marketplace with varying degrees of automation. An ability to evaluate conflation tool performance quantitatively is of operational value, although manual truthing of matched features is laborious and costly. In this paper, we present a novel methodology that uses spatial uncertainty modeling to simulate realistic feature layers to streamline evaluation of feature matching performance for conflation methods. Performance results are compiled for DCGIS street centerline features.

  12. Direct characterization of commercial lecithins by easy ambient sonic-spray ionization mass spectrometry.

    PubMed

    Fernandes, Gabriel D; Alberici, Rosana M; Pereira, Gustavo G; Cabral, Elaine C; Eberlin, Marcos N; Barrera-Arellano, Daniel

    2012-12-01

    Commercial lecithins are composed mainly of phospholipids and triacylglycerols. The analysis of the commercial lecithins, including their fraction of phospholipids, normally involves laborious and expensive protocols. Easy ambient sonic-spray ionization mass spectrometry (EASI-MS) is shown to be an efficient technique for the analysis of lipids. Samples of commercial lecithins including standards, refined, deoiled and modified soy lecithin were tested. Characteristic profiles of phosphatidylcholines and triacylglycerols are detected by EASI(+)-MS, whereas EASI(-)-MS provided phosphatidylethanolamines, glycophospholipids and free fatty acids profiles. Acetylated lecithins also displayed characteristic acetylated derivatives. EASI-MS data was also compared to MALDI-MS, and found to display richer compositional information. The industrial process applied to lecithin fabrication was also characterised via typical EASI-MS profiles. EASI-MS both in its positive and negative ion modes offers a direct, fast and efficient technique able to characterise commercial lecithin. Copyright © 2012 Elsevier Ltd. All rights reserved.

  13. Quantifying and predicting Drosophila larvae crawling phenotypes

    NASA Astrophysics Data System (ADS)

    Günther, Maximilian N.; Nettesheim, Guilherme; Shubeita, George T.

    2016-06-01

    The fruit fly Drosophila melanogaster is a widely used model for cell biology, development, disease, and neuroscience. The fly’s power as a genetic model for disease and neuroscience can be augmented by a quantitative description of its behavior. Here we show that we can accurately account for the complex and unique crawling patterns exhibited by individual Drosophila larvae using a small set of four parameters obtained from the trajectories of a few crawling larvae. The values of these parameters change for larvae from different genetic mutants, as we demonstrate for fly models of Alzheimer’s disease and the Fragile X syndrome, allowing applications such as genetic or drug screens. Using the quantitative model of larval crawling developed here we use the mutant-specific parameters to robustly simulate larval crawling, which allows estimating the feasibility of laborious experimental assays and aids in their design.

  14. Pelvic confined idiopathic retroperitoneal fibrosis mimicking a large tumor.

    PubMed

    Salemis, N S; Tsiambas, E; Tsohataridis, E

    2009-01-01

    Idiopathic retroperitoneal fibrosis (IRF) entirely confined to the pelvic cavity is an extremely rare clinical entity. Herein, is described the case of a 36- year old male who presented with clinical and imaging manifestations of a large pelvic tumor. Exploratory laparotomy revealed a large mass in the right pelvis originating from the retroperitoneal space, displacing the right iliac vessels, the right ureter and the urinary bladder completely to the left. A laborious resection of the mass measuring 14 x 10cm was performed. Histopathological examination and detailed immunohistochemistry analysis were suggestive of idiopathic retroperitoneal fibrosis with no evidence of malignancy. This is a very rare case regarding localization and clinical presentation of idiopathic retroperitoneal fibrosis. We conclude that IRF should be included in the differential diagnosis of patients presenting with a pelvic mass even if there is no involvement of the typical para aortic area.

  15. FireProt: web server for automated design of thermostable proteins

    PubMed Central

    Musil, Milos; Stourac, Jan; Brezovsky, Jan; Prokop, Zbynek; Zendulka, Jaroslav; Martinek, Tomas

    2017-01-01

    Abstract There is a continuous interest in increasing proteins stability to enhance their usability in numerous biomedical and biotechnological applications. A number of in silico tools for the prediction of the effect of mutations on protein stability have been developed recently. However, only single-point mutations with a small effect on protein stability are typically predicted with the existing tools and have to be followed by laborious protein expression, purification, and characterization. Here, we present FireProt, a web server for the automated design of multiple-point thermostable mutant proteins that combines structural and evolutionary information in its calculation core. FireProt utilizes sixteen tools and three protein engineering strategies for making reliable protein designs. The server is complemented with interactive, easy-to-use interface that allows users to directly analyze and optionally modify designed thermostable mutants. FireProt is freely available at http://loschmidt.chemi.muni.cz/fireprot. PMID:28449074

  16. Development of an interactive data base management system for capturing large volumes of data.

    PubMed

    Moritz, T E; Ellis, N K; VillaNueva, C B; Steeger, J E; Ludwig, S T; Deegan, N I; Shroyer, A L; Henderson, W G; Sethi, G K; Grover, F L

    1995-10-01

    Accurate collection and successful management of data are problems common to all scientific studies. For studies in which large quantities of data are collected by means of questionnaires and/or forms, data base management becomes quite laborious and time consuming. Data base management comprises data collection, data entry, data editing, and data base maintenance. In this article, the authors describe the development of an interactive data base management (IDM) system for the collection of more than 1,400 variables from a targeted population of 6,000 patients undergoing heart surgery requiring cardiopulmonary bypass. The goals of the IDM system are to increase the accuracy and efficiency with which this large amount of data is collected and processed, to reduce research nurse work load through automation of certain administrative and clerical activities, and to improve the process for implementing a uniform study protocol, standardized forms, and definitions across sites.

  17. Optimization of a Viability PCR Method for the Detection of Listeria monocytogenes in Food Samples.

    PubMed

    Agustí, Gemma; Fittipaldi, Mariana; Codony, Francesc

    2018-06-01

    Rapid detection of Listeria and other microbial pathogens in food is an essential part of quality control and it is critical for ensuring the safety of consumers. Culture-based methods for detecting foodborne pathogens are time-consuming, laborious and cannot detect viable but non-culturable microorganism, whereas viability PCR methodology provides quick results; it is able to detect viable but non-culturable cells, and allows for easier handling of large amount of samples. Although the most critical point to use viability PCR technique is achieving the complete exclusion of dead cell amplification signals, many improvements are being introduced to overcome this. In the present work, the yield of dead cell DNA neutralization was enhanced by incorporating two new sample treatment strategies: tube change combined with a double light treatment. This procedure was successfully tested using artificially contaminated food samples, showing improved neutralization of dead cell DNA.

  18. Using UMLS to construct a generalized hierarchical concept-based dictionary of brain functions for information extraction from the fMRI literature.

    PubMed

    Hsiao, Mei-Yu; Chen, Chien-Chung; Chen, Jyh-Horng

    2009-10-01

    With a rapid progress in the field, a great many fMRI studies are published every year, to the extent that it is now becoming difficult for researchers to keep up with the literature, since reading papers is extremely time-consuming and labor-intensive. Thus, automatic information extraction has become an important issue. In this study, we used the Unified Medical Language System (UMLS) to construct a hierarchical concept-based dictionary of brain functions. To the best of our knowledge, this is the first generalized dictionary of this kind. We also developed an information extraction system for recognizing, mapping and classifying terms relevant to human brain study. The precision and recall of our system was on a par with that of human experts in term recognition, term mapping and term classification. Our approach presented in this paper presents an alternative to the more laborious, manual entry approach to information extraction.

  19. Automatic repositioning of jaw segments for three-dimensional virtual treatment planning of orthognathic surgery.

    PubMed

    Santos, Rodrigo Mologni Gonçalves Dos; De Martino, José Mario; Passeri, Luis Augusto; Attux, Romis Ribeiro de Faissol; Haiter Neto, Francisco

    2017-09-01

    To develop a computer-based method for automating the repositioning of jaw segments in the skull during three-dimensional virtual treatment planning of orthognathic surgery. The method speeds up the planning phase of the orthognathic procedure, releasing surgeons from laborious and time-consuming tasks. The method finds the optimal positions for the maxilla, mandibular body, and bony chin in the skull. Minimization of cephalometric differences between measured and standard values is considered. Cone-beam computed tomographic images acquired from four preoperative patients with skeletal malocclusion were used for evaluating the method. Dentofacial problems of the four patients were rectified, including skeletal malocclusion, facial asymmetry, and jaw discrepancies. The results show that the method is potentially able to be used in routine clinical practice as support for treatment-planning decisions in orthognathic surgery. Copyright © 2017 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

  20. A novel technique based on in vitro oocyte injection to improve CRISPR/Cas9 gene editing in zebrafish

    PubMed Central

    Xie, Shao-Lin; Bian, Wan-Ping; Wang, Chao; Junaid, Muhammad; Zou, Ji-Xing; Pei, De-Sheng

    2016-01-01

    Contemporary improvements in the type II clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system offer a convenient way for genome editing in zebrafish. However, the low efficiencies of genome editing and germline transmission require a time-intensive and laborious screening work. Here, we reported a method based on in vitro oocyte storage by injecting oocytes in advance and incubating them in oocyte storage medium to significantly improve the efficiencies of genome editing and germline transmission by in vitro fertilization (IVF) in zebrafish. Compared to conventional methods, the prior micro-injection of zebrafish oocytes improved the efficiency of genome editing, especially for the sgRNAs with low targeting efficiency. Due to high throughputs, simplicity and flexible design, this novel strategy will provide an efficient alternative to increase the speed of generating heritable mutants in zebrafish by using CRISPR/Cas9 system. PMID:27680290

  1. Preparation, characterization and dissolution of passive oxide film on the 400 series stainless steel surfaces

    NASA Astrophysics Data System (ADS)

    Sathyaseelan, V. S.; Rufus, A. L.; Chandramohan, P.; Subramanian, H.; Velmurugan, S.

    2015-12-01

    Full system decontamination of Primary Heat Transport (PHT) system of Pressurised Heavy Water Reactors (PHWRs) resulted in low decontamination factors (DF) on stainless steel (SS) surfaces. Hence, studies were carried out with 403 SS and 410 SS that are the material of construction of "End-Fitting body" and "End-Fitting Liner tubes". Three formulations were evaluated for the dissolution of passive films formed over these alloys viz., i) Two-step process consisting of oxidation and reduction reactions, ii) Dilute Chemical Decontamination (DCD) and iii) High Temperature Process. The two-step and high temperature processes could dissolve the oxide completely while the DCD process could remove only 60%. Various techniques like XRD, Raman spectroscopy and SEM-EDX were used for assessing the dissolution process. The two-step process is time consuming, laborious while the high temperature process is less time consuming and is recommended for SS decontamination.

  2. LiDAR: Providing structure

    USGS Publications Warehouse

    Vierling, Lee A.; Martinuzzi, Sebastián; Asner, Gregory P.; Stoker, Jason M.; Johnson, Brian R.

    2011-01-01

    Since the days of MacArthur, three-dimensional (3-D) structural information on the environment has fundamentally transformed scientific understanding of ecological phenomena (MacArthur and MacArthur 1961). Early data on ecosystem structure were painstakingly laborious to collect. However, as reviewed and reported in recent volumes of Frontiers(eg Vierling et al. 2008; Asner et al.2011), advances in light detection and ranging (LiDAR) remote-sensing technology provide quantitative and repeatable measurements of 3-D ecosystem structure that enable novel ecological insights at scales ranging from the plot, to the landscape, to the globe. Indeed, annual publication of studies using LiDAR to interpret ecological phenomena increased 17-fold during the past decade, with over 180 new studies appearing in 2010 (ISI Web of Science search conducted on 23 Mar 2011: [{lidar AND ecol*} OR {lidar AND fores*} OR {lidar AND plant*}]).

  3. Intraabdominal pressure in women during CrossFit exercises and the effect of age and parity.

    PubMed

    Gephart, Laura Faye; Doersch, Karen M; Reyes, Michelle; Kuehl, Thomas J; Danford, Jill M

    2018-07-01

    To determine intraabdominal pressure (IAP) in women during CrossFit and to determine whether parity, age, or CrossFit experience affects IAP during CrossFit exercises, we evaluated 10 women: 5 experienced and active CrossFitters and 5 who were not regularly engaged in CrossFit. A Laborie urodynamics abdominal pressure probe with the Goby wireless system measured IAP during 10 repetitions of 13 different CrossFit exercises. Women had a mean age of 36 years. A significant difference was found between mean peak IAP of the 5 parous vs the 5 nulliparous women ( P = 0.009). Experience with CrossFit did not affect mean peak IAP achieved with exercise. In some exercises, there was a significant change in IAP as participants progressed through repetitions ( P = 0.003 for back squats and 0.04 for sit-ups). Participants achieved IAP values that were markedly higher than those previously published.

  4. Relationships among condition indices, feeding and growth of walleye in Lake Erie

    USGS Publications Warehouse

    Hartman, K.J.; Margraf, F.J.

    2006-01-01

    Condition indices are often used as surrogates of fish health, growth, and feeding and to compare ecological well-being among fish populations. In an effort to identify easily measured indices, growth and food consumption were compared with gonadal-somatic index, liver-somatic index (LSI), fat-somatic index and relative weight (Wr) for ages 1-3 walleye, Sander vitreus (Mitchill), in Lake Erie from 1986 to 1988. The LSI and Wr were significantly correlated with growth rate or food consumption, but correlations were too small to be considered biologically meaningful. Furthermore, no consistent relationships between condition indices and growth or consumption were found among combinations of fish age and season. None of the indices are considered reliable surrogates for more laborious estimates of growth and food consumption for Lake Erie walleye. Significant relationships between Wr and relative abundance of key prey species warrant further investigation. ?? 2006 Blackwell Publishing Ltd.

  5. Detection of heavy metal by paper-based microfluidics.

    PubMed

    Lin, Yang; Gritsenko, Dmitry; Feng, Shaolong; Teh, Yi Chen; Lu, Xiaonan; Xu, Jie

    2016-09-15

    Heavy metal pollution has shown great threat to the environment and public health worldwide. Current methods for the detection of heavy metals require expensive instrumentation and laborious operation, which can only be accomplished in centralized laboratories. Various microfluidic paper-based analytical devices have been developed recently as simple, cheap and disposable alternatives to conventional ones for on-site detection of heavy metals. In this review, we first summarize current development of paper-based analytical devices and discuss the selection of paper substrates, methods of device fabrication, and relevant theories in these devices. We then compare and categorize recent reports on detection of heavy metals using paper-based microfluidic devices on the basis of various detection mechanisms, such as colorimetric, fluorescent, and electrochemical methods. To finalize, the future development and trend in this field are discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. High-throughput automatic defect review for 300mm blank wafers with atomic force microscope

    NASA Astrophysics Data System (ADS)

    Zandiatashbar, Ardavan; Kim, Byong; Yoo, Young-kook; Lee, Keibock; Jo, Ahjin; Lee, Ju Suk; Cho, Sang-Joon; Park, Sang-il

    2015-03-01

    While feature size in lithography process continuously becomes smaller, defect sizes on blank wafers become more comparable to device sizes. Defects with nm-scale characteristic size could be misclassified by automated optical inspection (AOI) and require post-processing for proper classification. Atomic force microscope (AFM) is known to provide high lateral and the highest vertical resolution by mechanical probing among all techniques. However, its low throughput and tip life in addition to the laborious efforts for finding the defects have been the major limitations of this technique. In this paper we introduce automatic defect review (ADR) AFM as a post-inspection metrology tool for defect study and classification for 300 mm blank wafers and to overcome the limitations stated above. The ADR AFM provides high throughput, high resolution, and non-destructive means for obtaining 3D information for nm-scale defect review and classification.

  7. Bio-Intelligence: A Research Program Facilitating the Development of New Paradigms for Tomorrow's Patient Care

    NASA Astrophysics Data System (ADS)

    Phan, Sieu; Famili, Fazel; Liu, Ziying; Peña-Castillo, Lourdes

    The advancement of omics technologies in concert with the enabling information technology development has accelerated biological research to a new realm in a blazing speed and sophistication. The limited single gene assay to the high throughput microarray assay and the laborious manual count of base-pairs to the robotic assisted machinery in genome sequencing are two examples to name. Yet even more sophisticated, the recent development in literature mining and artificial intelligence has allowed researchers to construct complex gene networks unraveling many formidable biological puzzles. To harness these emerging technologies to their full potential to medical applications, the Bio-intelligence program at the Institute for Information Technology, National Research Council Canada, aims to develop and exploit artificial intelligence and bioinformatics technologies to facilitate the development of intelligent decision support tools and systems to improve patient care - for early detection, accurate diagnosis/prognosis of disease, and better personalized therapeutic management.

  8. Translating human genetics into mouse: the impact of ultra-rapid in vivo genome editing.

    PubMed

    Aida, Tomomi; Imahashi, Risa; Tanaka, Kohichi

    2014-01-01

    Gene-targeted mutant animals, such as knockout or knockin mice, have dramatically improved our understanding of the functions of genes in vivo and the genetic diversity that characterizes health and disease. However, the generation of targeted mice relies on gene targeting in embryonic stem (ES) cells, which is a time-consuming, laborious, and expensive process. The recent groundbreaking development of several genome editing technologies has enabled the targeted alteration of almost any sequence in any cell or organism. These technologies have now been applied to mouse zygotes (in vivo genome editing), thereby providing new avenues for simple, convenient, and ultra-rapid production of knockout or knockin mice without the need for ES cells. Here, we review recent achievements in the production of gene-targeted mice by in vivo genome editing. © 2013 The Authors Development, Growth & Differentiation © 2013 Japanese Society of Developmental Biologists.

  9. Bridging experiment and theory: A template for unifying NMR data and electronic structure calculations

    DOE PAGES

    Brown, David M. L.; Cho, Herman; de Jong, Wibe A.

    2016-02-09

    Here, the testing of theoretical models with experimental data is an integral part of the scientific method, and a logical place to search for new ways of stimulating scientific productivity. Often experiment/theory comparisons may be viewed as a workflow comprised of well-defined, rote operations distributed over several distinct computers, as exemplified by the way in which predictions from electronic structure theories are evaluated with results from spectroscopic experiments. For workflows such as this, which may be laborious and time consuming to perform manually, software that could orchestrate the operations and transfer results between computers in a seamless and automated fashionmore » would offer major efficiency gains. Such tools also promise to alter how researchers interact with data outside their field of specialization by, e.g., making raw experimental results more accessible to theorists, and the outputs of theoretical calculations more readily comprehended by experimentalists.« less

  10. One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy.

    PubMed

    Yofe, Ido; Weill, Uri; Meurer, Matthias; Chuartzman, Silvia; Zalckvar, Einat; Goldman, Omer; Ben-Dor, Shifra; Schütze, Conny; Wiedemann, Nils; Knop, Michael; Khmelinskii, Anton; Schuldiner, Maya

    2016-04-01

    The yeast Saccharomyces cerevisiae is ideal for systematic studies relying on collections of modified strains (libraries). Despite the significance of yeast libraries and the immense variety of available tags and regulatory elements, only a few such libraries exist, as their construction is extremely expensive and laborious. To overcome these limitations, we developed a SWAp-Tag (SWAT) method that enables one parental library to be modified easily and efficiently to give rise to an endless variety of libraries of choice. To showcase the versatility of the SWAT approach, we constructed and investigated a library of ∼1,800 strains carrying SWAT-GFP modules at the amino termini of endomembrane proteins and then used it to create two new libraries (mCherry and seamless GFP). Our work demonstrates how the SWAT method allows fast and effortless creation of yeast libraries, opening the door to new ways of systematically studying cell biology.

  11. High-throughput tetrad analysis.

    PubMed

    Ludlow, Catherine L; Scott, Adrian C; Cromie, Gareth A; Jeffery, Eric W; Sirr, Amy; May, Patrick; Lin, Jake; Gilbert, Teresa L; Hays, Michelle; Dudley, Aimée M

    2013-07-01

    Tetrad analysis has been a gold-standard genetic technique for several decades. Unfortunately, the need to manually isolate, disrupt and space tetrads has relegated its application to small-scale studies and limited its integration with high-throughput DNA sequencing technologies. We have developed a rapid, high-throughput method, called barcode-enabled sequencing of tetrads (BEST), that uses (i) a meiosis-specific GFP fusion protein to isolate tetrads by FACS and (ii) molecular barcodes that are read during genotyping to identify spores derived from the same tetrad. Maintaining tetrad information allows accurate inference of missing genetic markers and full genotypes of missing (and presumably nonviable) individuals. An individual researcher was able to isolate over 3,000 yeast tetrads in 3 h, an output equivalent to that of almost 1 month of manual dissection. BEST is transferable to other microorganisms for which meiotic mapping is significantly more laborious.

  12. The Linear Bias in the Zeldovich Approximation and a Relation between the Number Density and the Linear Bias of Dark Halos

    NASA Astrophysics Data System (ADS)

    Fan, Zuhui

    2000-01-01

    The linear bias of the dark halos from a model under the Zeldovich approximation is derived and compared with the fitting formula of simulation results. While qualitatively similar to the Press-Schechter formula, this model gives a better description for the linear bias around the turnaround point. This advantage, however, may be compromised by the large uncertainty of the actual behavior of the linear bias near the turnaround point. For a broad class of structure formation models in the cold dark matter framework, a general relation exists between the number density and the linear bias of dark halos. This relation can be readily tested by numerical simulations. Thus, instead of laboriously checking these models one by one, numerical simulation studies can falsify a whole category of models. The general validity of this relation is important in identifying key physical processes responsible for the large-scale structure formation in the universe.

  13. Cryptic intragenic deletion of the SHOX gene in a family with Léri-Weill dyschondrosteosis detected by Multiplex Ligation-Dependent Probe Amplification (MLPA).

    PubMed

    Funari, Mariana F A; Jorge, Alexander A L; Pinto, Emilia M; Arnhold, Ivo J P; Mendonca, Berenice B; Nishi, Mirian Y

    2008-11-01

    LWD is associated to SHOX haploinsufficiency, in most cases, due to gene deletion. Generally FISH and microsatellite analysis are used to identify SHOX deletion. MLPA is a new method of detecting gene copy variation, allowing simultaneous analysis of several regions. Here we describe the presence of a SHOX intragenic deletion in a family with LWD, analyzed through different methodologies. Genomic DNA of 11 subjects from one family were studied by microsatellite analysis, direct sequencing and MLPA. FISH was performed in two affected individuals. Microsatellite analysis showed that all affected members shared the same haplotype suggesting the involvement of SHOX. MLPA detected an intragenic deletion involving exons IV-VIa, which was not detected by FISH and microsatellite analysis. In conclusion, the MLPA technique was proved to be the best solution on detecting this small deletion, it has the advantage of being less laborious also allowing the analysis of several regions simultaneously.

  14. Barcode extension for analysis and reconstruction of structures

    NASA Astrophysics Data System (ADS)

    Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L.; Gootenberg, Jonathan S.; Yin, Peng

    2017-03-01

    Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures.

  15. Barcode extension for analysis and reconstruction of structures.

    PubMed

    Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L; Gootenberg, Jonathan S; Yin, Peng

    2017-03-13

    Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures.

  16. Evaluation of the SeedCounter, A Mobile Application for Grain Phenotyping.

    PubMed

    Komyshev, Evgenii; Genaev, Mikhail; Afonnikov, Dmitry

    2016-01-01

    Grain morphometry in cereals is an important step in selecting new high-yielding plants. Manual assessment of parameters such as the number of grains per ear and grain size is laborious. One solution to this problem is image-based analysis that can be performed using a desktop PC. Furthermore, the effectiveness of analysis performed in the field can be improved through the use of mobile devices. In this paper, we propose a method for the automated evaluation of phenotypic parameters of grains using mobile devices running the Android operational system. The experimental results show that this approach is efficient and sufficiently accurate for the large-scale analysis of phenotypic characteristics in wheat grains. Evaluation of our application under six different lighting conditions and three mobile devices demonstrated that the lighting of the paper has significant influence on the accuracy of our method, unlike the smartphone type.

  17. Development Study of Cartridge/Crucible Tube Materials

    NASA Technical Reports Server (NTRS)

    McKechnie, Timothy N.; ODell, Scott J.

    1998-01-01

    The limitations of traditional alloys and the desire for improved performance for components is driving the increased utilization of refractory metals in tile space industry. From advanced propulsion systems to high temperature furnace components for microgravity processing, refractory metals are being used for their high melting temperatures and inherent chemical stability. Techniques have been developed to produce near net shape refractory metal components utilizing vacuum plasma spraying. Material utilization is very high, and laborious machining can be avoided. As-spray formed components have been tested and found to perform adequately. However, increased mechanical and thermal properties are needed. To improve these properties, post processing thermal treatments such as hydrogen sintering and vacuum annealing have been performed. Components formed from alloys of tungsten, rhenium, tantalum, niobium, and molybdenum are discussed and a metallurgical analyses detailing the results are presented. A qualitative comparison of mechanical properties is also included.

  18. Applicability of discovery science approach to determine biological effects of mobile phone radiation.

    PubMed

    Leszczynski, Dariusz; Nylund, Reetta; Joenväärä, Sakari; Reivinen, Jukka

    2004-02-01

    We argue that the use of high-throughput screening techniques, although expensive and laborious, is justified and necessary in studies that examine biological effects of mobile phone radiation. The "case of hsp27 protein" presented here suggests that even proteins with only modestly altered (by exposure to mobile phone radiation) expression and activity might have an impact on cell physiology. However, this short communication does not attempt to present the full scientific evidence that is far too large to be presented in a single article and that is being prepared for publication in three separate research articles. Examples of the experimental evidence presented here were designed to show the flow of experimental process demonstrating that the use of high-throughput screening techniques might help in rapid identification of the responding proteins. This, in turn, can help in speeding up of the process of determining whether these changes might affect human health.*

  19. Alterations of the occipital lobe in schizophrenia

    PubMed Central

    Tohid, Hassaan; Faizan, Muhammad; Faizan, Uzma

    2015-01-01

    The relationship of the occipital lobe of the brain with schizophrenia is not commonly studied; however, this topic is considered an essential subject matter among clinicians and scientists. We conducted this systematic review to elaborate the relationship in depth. We found that most schizophrenic patients show normal occipital anatomy and physiology, a minority showed dwindled values, and some demonstrated augmented function and structure. The findings are laborious to incorporate within single disease models that present the involvement of the occipital lobe in schizophrenia. Schizophrenia progresses clinically in the mid-twenties and thirties and its prognosis is inadequate. Changes in the volume, the gray matter, and the white matter in the occipital lobe are quite evident; however, the mechanism behind this involvement is not yet fully understood. Therefore, we recommend further research to explore the occipital lobe functions and volumes across the different stages of schizophrenia. PMID:26166588

  20. Barcode extension for analysis and reconstruction of structures

    PubMed Central

    Myhrvold, Cameron; Baym, Michael; Hanikel, Nikita; Ong, Luvena L; Gootenberg, Jonathan S; Yin, Peng

    2017-01-01

    Collections of DNA sequences can be rationally designed to self-assemble into predictable three-dimensional structures. The geometric and functional diversity of DNA nanostructures created to date has been enhanced by improvements in DNA synthesis and computational design. However, existing methods for structure characterization typically image the final product or laboriously determine the presence of individual, labelled strands using gel electrophoresis. Here we introduce a new method of structure characterization that uses barcode extension and next-generation DNA sequencing to quantitatively measure the incorporation of every strand into a DNA nanostructure. By quantifying the relative abundances of distinct DNA species in product and monomer bands, we can study the influence of geometry and sequence on assembly. We have tested our method using 2D and 3D DNA brick and DNA origami structures. Our method is general and should be extensible to a wide variety of DNA nanostructures. PMID:28287117

  1. Transfection of embryonated Muscovy duck eggs with a recombinant plasmid is suitable for rescue of infectious Muscovy duck parvovirus.

    PubMed

    Wang, Jianye; Huang, Yu; Ling, Jueyi; Wang, Zhixiang; Zhu, Guoqiang

    2017-12-01

    For members of the family Parvoviridae, rescue of infectious virus from recombinant plasmid is usually done in cultured cells. In this study, the whole genome of the pathogenic Muscovy duck parvovirus (MDPV) strain YY was cloned into the pBluescript II (SK) vector, generating recombinant plasmid pYY. With the aid of a transfection reagent, pYY plasmid was inoculated into 11-day-old embryonated Muscovy duck eggs via the chorioallantoic membrane route, resulting in the successful rescue of infectious virus and death of the embryos. The rescued virus exhibited pathogenicity in Muscovy ducklings similar to that of its parental strain, as evaluated based on the mortality rate. The results demonstrate that plasmid transfection in embryonated Muscovy duck eggs is a convenient and efficacious method for rescue of infectious MDPV in comparison to transfection of primary cells, which is somewhat time-consuming and laborious.

  2. Bridging experiment and theory: A template for unifying NMR data and electronic structure calculations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Brown, David M. L.; Cho, Herman; de Jong, Wibe A.

    Here, the testing of theoretical models with experimental data is an integral part of the scientific method, and a logical place to search for new ways of stimulating scientific productivity. Often experiment/theory comparisons may be viewed as a workflow comprised of well-defined, rote operations distributed over several distinct computers, as exemplified by the way in which predictions from electronic structure theories are evaluated with results from spectroscopic experiments. For workflows such as this, which may be laborious and time consuming to perform manually, software that could orchestrate the operations and transfer results between computers in a seamless and automated fashionmore » would offer major efficiency gains. Such tools also promise to alter how researchers interact with data outside their field of specialization by, e.g., making raw experimental results more accessible to theorists, and the outputs of theoretical calculations more readily comprehended by experimentalists.« less

  3. Fabrication of micropatterned alginate-gelatin and k-carrageenan hydrogels of defined shapes using simple wax mould method as a platform for stem cell/induced Pluripotent Stem Cells (iPSC) culture.

    PubMed

    Vignesh, S; Gopalakrishnan, Aswathi; M R, Poorna; Nair, Shantikumar V; Jayakumar, R; Mony, Ullas

    2018-06-01

    Micropatterning techniques involve soft lithography, which is laborious, expensive and restricted to a narrow spectrum of biomaterials. In this work we report, first time employment of patterned wax moulds for generation of micropatterned alginate-gelatin and κ-carrageenan (κ-CRG) hydrogel systems by a novel, simple and cost effective method. We generated and characterized uniform and reproducible micropatterned hydrogels of varying sizes and shapes such as square projections, square grooves, and circular grids and crisscrossed hillocks. The rheological analysis showed that κ-carrageenan hydrogels had higher gel strength when compared to alginate-gelatin hydrogels. Human Mesenchymal stem cells (hMSCs) and Human Induced Pluripotent Stem Cells (hiPSCs) were found to be cytocompatible with these hydrogels. This micropatterned hydrogel system may have potential application in tissue engineering and also in understanding the basic biology behind the stem cell/iPSC fate. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. Microwave platform as a valuable tool for characterization of nanophotonic devices

    PubMed Central

    Shishkin, Ivan; Baranov, Dmitry; Slobozhanyuk, Alexey; Filonov, Dmitry; Lukashenko, Stanislav; Samusev, Anton; Belov, Pavel

    2016-01-01

    The rich potential of the microwave experiments for characterization and optimization of optical devices is discussed. While the control of the light fields together with their spatial mapping at the nanoscale is still laborious and not always clear, the microwave setup allows to measure both amplitude and phase of initially determined magnetic and electric field components without significant perturbation of the near-field. As an example, the electromagnetic properties of an add-drop filter, which became a well-known workhorse of the photonics, is experimentally studied with the aid of transmission spectroscopy measurements in optical and microwave ranges and through direct mapping of the near fields at microwave frequencies. We demonstrate that the microwave experiments provide a unique platform for the comprehensive studies of electromagnetic properties of micro- and nanophotonic devices, and allow to obtain data which are hardly acquirable by conventional optical methods. PMID:27759058

  5. Cloud Properties Derived from Surface-Based Near-Infrared Spectral Transmission

    NASA Technical Reports Server (NTRS)

    Pilewskie, Peter; Twomey, S.; Gore, Warren J. Y. (Technical Monitor)

    1996-01-01

    Surface based near-infrared cloud spectral transmission measurements from a recent precipitation/cloud physics field study are used to determine cloud physical properties and relate them to other remote sensing and in situ measurements. Asymptotic formulae provide an effective means of closely approximating the qualitative and quantitative behavior of transmission computed by more laborious detailed methods. Relationships derived from asymptotic formulae are applied to measured transmission spectra to test objectively the internal consistency of data sets acquired during the field program and they confirmed the quality of the measurements. These relationships appear to be very useful in themselves, not merely as a quality control measure, but also a potentially valuable remote-sensing technique in its own right. Additional benefits from this analysis have been the separation of condensed water (cloud) transmission and water vapor transmission and the development of a method to derive cloud liquid water content.

  6. Characterization of neutrophils and macrophages from ex vivo cultured murine bone marrow for morphologic maturation and functional responses by imaging flow cytometry

    PubMed Central

    Pelletier, Margery G. H.; Szymczak, Klaudia; Barbeau, Anna M.; Prata, Gianna N.; O’Fallon, Kevin S.; Gaines, Peter

    2016-01-01

    Neutrophils and macrophages differentiate from common myeloid progenitors in the bone marrow, where they undergo nuclear morphologic changes during maturation. During this process, both cell types acquire critical innate immune functions that include phagocytosis of pathogens, and for neutrophils the release of nuclear material called nuclear extracellular traps (NETs). Primary cells used to study these functions are typically purified from mature mouse tissues, but bone marrow-derived ex vivo cultures provide more abundant numbers of progenitors and functionally mature cells. Routine analyses of these cells use conventional microscopy and flow cytometry, which present limitations; microscopy is laborious and subjective, whereas flow cytometry lacks spatial resolution. Here we describe methods to generate enriched populations of neutrophils or macrophages from cryopreserved mouse bone marrow cultured ex vivo, and to use imaging flow cytometry that combines the resolution of microscopy with flow cytometry to analyze cells for morphologic features, phagocytosis, and NETosis. PMID:27663441

  7. Interruption of vector transmission by native vectors and “the art of the possible”

    PubMed Central

    Salvatella, Roberto; Irabedra, Pilar; Castellanos, Luis G

    2013-01-01

    In a recent article in the Reader’s Opinion, advantages and disadvantages of the certification processes of interrupted Chagas disease transmission (American trypanosomiasis) by native vector were discussed. Such concept, accepted by those authors for the case of endemic situations with introduced vectors, has been built on a long and laborious process by endemic countries and Subregional Initiatives for Prevention, Control and Treatment of Chagas, with Technical Secretariat of the Pan American Health Organization/World Health Organization, to create a horizon target and goal to concentrate priorities and resource allocation and actions. With varying degrees of sucess, which are not replaceable for a certificate of good practice, has allowed during 23 years to safeguard the effective control of transmission of Trypanosoma cruzi not to hundreds of thousands, but millions of people at risk conditions, truly “the art of the possible.” PMID:24626310

  8. Re-identification of persons in multi-camera surveillance under varying viewpoints and illumination

    NASA Astrophysics Data System (ADS)

    Bouma, Henri; Borsboom, Sander; den Hollander, Richard J. M.; Landsmeer, Sander H.; Worring, Marcel

    2012-06-01

    The capability to track individuals in CCTV cameras is important for surveillance and forensics alike. However, it is laborious to do over multiple cameras. Therefore, an automated system is desirable. In literature several methods have been proposed, but their robustness against varying viewpoints and illumination is limited. Hence performance in realistic settings is also limited. In this paper, we present a novel method for the automatic re-identification of persons in video from surveillance cameras in a realistic setting. The method is computationally efficient, robust to a wide variety of viewpoints and illumination, simple to implement and it requires no training. We compare the performance of our method to several state-of-the-art methods on a publically available dataset that contains the variety of viewpoints and illumination to allow benchmarking. The results indicate that our method shows good performance and enables a human operator to track persons five times faster.

  9. Novel Technology for Enrichment of Biomolecules from Cell-Free Body Fluids and Subsequent DNA Sizing.

    PubMed

    Patel, Vipulkumar; Celec, Peter; Grunt, Magdalena; Schwarzenbach, Heidi; Jenneckens, Ingo; Hillebrand, Timo

    2016-01-01

    Circulating cell-free DNA (ccfDNA) is a promising diagnostic tool and its size fractionation is of interest. However, kits for isolation of ccfDNA available on the market are designed for small volumes hence processing large sample volumes is laborious. We have tested a new method that enables enrichment of ccfDNA from large volumes of plasma and subsequently allows size-fractionation of isolated ccfDNA into two fractions with individually established cut-off levels of ccfDNA length. This method allows isolation of low-abundant DNA as well as separation of long and short DNA molecules. This procedure may be important e.g., in prenatal diagnostics and cancer research that have been already confirmed by our primary experiments. Here, we report the results of selective separation of 200- and 500-bp long synthetic DNA fragments spiked in plasma samples. Furthermore, we size-fractionated ccfDNA from the plasma of pregnant women and verified the prevalence of fetal ccfDNA in all fractions.

  10. Disposable attenuated total reflection-infrared crystals from silicon wafer: a versatile approach to surface infrared spectroscopy.

    PubMed

    Karabudak, Engin; Kas, Recep; Ogieglo, Wojciech; Rafieian, Damon; Schlautmann, Stefan; Lammertink, R G H; Gardeniers, Han J G E; Mul, Guido

    2013-01-02

    Attenuated total reflection-infrared (ATR-IR) spectroscopy is increasingly used to characterize solids and liquids as well as (catalytic) chemical conversion. Here we demonstrate that a piece of silicon wafer cut by a dicing machine or cleaved manually can be used as disposable internal reflection element (IRE) without the need for polishing and laborious edge preparation. Technical aspects, fundamental differences, and pros and cons of these novel disposable IREs and commercial IREs are discussed. The use of a crystal (the Si wafer) in a disposable manner enables simultaneous preparation and analysis of substrates and application of ATR spectroscopy in high temperature processes that may lead to irreversible interaction between the crystal and the substrate. As representative application examples, the disposable IREs were used to study high temperature thermal decomposition and chemical changes of polyvinyl alcohol (PVA) in a titania (TiO(2)) matrix and assemblies of 65-450 nm thick polystyrene (PS) films.

  11. Towards symbiosis in knowledge representation and natural language processing for structuring clinical practice guidelines.

    PubMed

    Weng, Chunhua; Payne, Philip R O; Velez, Mark; Johnson, Stephen B; Bakken, Suzanne

    2014-01-01

    The successful adoption by clinicians of evidence-based clinical practice guidelines (CPGs) contained in clinical information systems requires efficient translation of free-text guidelines into computable formats. Natural language processing (NLP) has the potential to improve the efficiency of such translation. However, it is laborious to develop NLP to structure free-text CPGs using existing formal knowledge representations (KR). In response to this challenge, this vision paper discusses the value and feasibility of supporting symbiosis in text-based knowledge acquisition (KA) and KR. We compare two ontologies: (1) an ontology manually created by domain experts for CPG eligibility criteria and (2) an upper-level ontology derived from a semantic pattern-based approach for automatic KA from CPG eligibility criteria text. Then we discuss the strengths and limitations of interweaving KA and NLP for KR purposes and important considerations for achieving the symbiosis of KR and NLP for structuring CPGs to achieve evidence-based clinical practice.

  12. Construction of a System for the Strawberry Nursery Production towards Elimination of Latent Infection of Anthracnose Fungi by a Combination of PCR and Microtube Hybridization

    PubMed Central

    Furuta, Kazuyoshi; Nagashima, Saki; Inukai, Tsuyoshi; Masuta, Chikara

    2017-01-01

    One of the major problems in strawberry production is difficulty in diagnosis of anthracnose caused by Colletotrichum acutatum or Glomerella cingulata in latent infection stage. We here developed a diagnostic tool for the latent infection consisting of initial culturing of fungi, DNA extraction, synthesis of PCR-amplified probes and microtube hybridization (MTH) using a macroarray. The initial culturing step is convenient to lure the fungi out of the plant tissues, and to extract PCR-inhibitor-free DNA directly from fungal hyphae. For specific detection of the fungi, PCR primers were designed to amplify the fungal MAT1-2 gene. The subsequent MTH step using the PCR products as probes can replace the laborious electrophoresis step providing us sequence information and high-throughput screening. Using this method, we have conducted a survey for a few thousands nursery plants every year for three consecutive years, and finally succeeded in eliminating latent infection in the third year of challenge. PMID:28167891

  13. A biosensor generated via high throughput screening quantifies cell edge Src dynamics

    PubMed Central

    Gulyani, Akash; Vitriol, Eric; Allen, Richard; Wu, Jianrong; Gremyachinskiy, Dmitriy; Lewis, Steven; Dewar, Brian; Graves, Lee M.; Kay, Brian K.; Kuhlman, Brian; Elston, Tim; Hahn, Klaus M.

    2011-01-01

    Fluorescent biosensors for living cells currently require laborious optimization and a unique design for each target. They are limited by the availability of naturally occurring ligands with appropriate target specificity. Here we describe a biosensor based on an engineered fibronectin monobody scaffold that can be tailored to bind different targets via high throughput screening. This Src family kinase (SFK) biosensor was made by derivatizing a monobody specific for activated SFK with a bright dye whose fluorescence increases upon target binding. We identified sites for dye attachment and alterations to eliminate vesiculation in living cells, providing a generalizable scaffold for biosensor production. This approach minimizes cell perturbation because it senses endogenous, unmodified target, and because sensitivity is enhanced by direct dye excitation. Automated correlation of cell velocities and SFK activity revealed that SFK are activated specifically during protrusion. Activity correlates with velocity, and peaks 1–2 microns from the leading edge. PMID:21666688

  14. Cloning of Plasmodium falciparum by single-cell sorting

    PubMed Central

    Miao, Jun; Li, Xiaolian; Cui, Liwang

    2010-01-01

    Malaria parasite cloning is traditionally carried out mainly by using the limiting dilution method, which is laborious, imprecise, and unable to distinguish multiply-infected RBCs. In this study, we used a parasite engineered to express green fluorescent protein (GFP) to evaluate a single-cell sorting method for rapidly cloning Plasmodium falciparum. By dividing a two dimensional scattergram from a cell sorter into 17 gates, we determined the parameters for isolating singly-infected erythrocytes and sorted them into individual cultures. Pre-gating of the engineered parasites for GFP allowed the isolation of almost 100% GFP-positive clones. Compared with the limiting dilution method, the number of parasite clones obtained by single-cell sorting was much higher. Molecular analyses showed that parasite isolates obtained by single-cell sorting were highly homogenous. This highly efficient single-cell sorting method should prove very useful for cloning both P. falciparum laboratory populations from genetic manipulation experiments and clinical samples. PMID:20435038

  15. Filtering of windborne particles by a natural windbreak

    NASA Astrophysics Data System (ADS)

    Bouvet, Thomas; Loubet, Benjamin; Wilson, John D.; Tuzet, Andree

    2007-06-01

    New measurements of the transport and deposition of artificial heavy particles (glass beads) to a thick ‘shelterbelt’ of maize (width/height ratio W/ H ≈ 1.6) are used to test numerical simulations with a Lagrangian stochastic trajectory model driven by the flow field from a RANS (Reynolds-averaged, Navier-Stokes) wind and turbulence model. We illustrate the ambiguity inherent in applying to such a thick windbreak the pre-existing (Raupach et al. 2001; Atmos. Environ. 35, 3373-3383) ‘thin windbreak’ theory of particle filtering by vegetation, and show that the present description, while much more laborious, provides a reasonably satisfactory account of what was measured. A sizeable fraction of the particle flux entering the shelterbelt across its upstream face is lifted out of its volume by the mean updraft induced by the deceleration of the flow in the near-upstream and entry region, and these particles thereby escape deposition in the windbreak.

  16. Experimental method of in-vivo dosimetry without build-up device on the skin for external beam radiotherapy

    NASA Astrophysics Data System (ADS)

    Jeon, Hosang; Nam, Jiho; Lee, Jayoung; Park, Dahl; Baek, Cheol-Ha; Kim, Wontaek; Ki, Yongkan; Kim, Dongwon

    2015-06-01

    Accurate dose delivery is crucial to the success of modern radiotherapy. To evaluate the dose actually delivered to patients, in-vivo dosimetry (IVD) is generally performed during radiotherapy to measure the entrance doses. In IVD, a build-up device should be placed on top of an in-vivo dosimeter to satisfy the electron equilibrium condition. However, a build-up device made of tissue-equivalent material or metal may perturb dose delivery to a patient, and requires an additional laborious and time-consuming process. We developed a novel IVD method using a look-up table of conversion ratios instead of a build-up device. We validated this method through a monte-carlo simulation and 31 clinical trials. The mean error of clinical IVD is 3.17% (standard deviation: 2.58%), which is comparable to that of conventional IVD methods. Moreover, the required time was greatly reduced so that the efficiency of IVD could be improved for both patients and therapists.

  17. Cloning of Plasmodium falciparum by single-cell sorting.

    PubMed

    Miao, Jun; Li, Xiaolian; Cui, Liwang

    2010-10-01

    Malaria parasite cloning is traditionally carried out mainly by using the limiting dilution method, which is laborious, imprecise, and unable to distinguish multiply-infected RBCs. In this study, we used a parasite engineered to express green fluorescent protein (GFP) to evaluate a single-cell sorting method for rapidly cloning Plasmodium falciparum. By dividing a two-dimensional scattergram from a cell sorter into 17 gates, we determined the parameters for isolating singly-infected erythrocytes and sorted them into individual cultures. Pre-gating of the engineered parasites for GFP allowed the isolation of almost 100% GFP-positive clones. Compared with the limiting dilution method, the number of parasite clones obtained by single-cell sorting was much higher. Molecular analyses showed that parasite isolates obtained by single-cell sorting were highly homogenous. This highly efficient single-cell sorting method should prove very useful for cloning both P. falciparum laboratory populations from genetic manipulation experiments and clinical samples. Copyright 2010 Elsevier Inc. All rights reserved.

  18. Cloning-free template DNA preparation for cell-free protein synthesis via two-step PCR using versatile primer designs with short 3'-UTR.

    PubMed

    Nomoto, Mika; Tada, Yasuomi

    2018-01-01

    Cell-free protein synthesis (CFPS) systems largely retain the endogenous translation machinery of the host organism, making them highly applicable for proteomics analysis of diverse biological processes. However, laborious and time-consuming cloning procedures hinder progress with CFPS systems. Herein, we report the development of a rapid and efficient two-step polymerase chain reaction (PCR) method to prepare linear DNA templates for a wheat germ CFPS system. We developed a novel, effective short 3'-untranslated region (3'-UTR) sequence that facilitates translation. Application of the short 3'-UTR to two-step PCR enabled the generation of various transcription templates from the same plasmid, including fusion proteins with N- or C-terminal tags, and truncated proteins. Our method supports the cloning-free expression of target proteins using an mRNA pool from biological material. The established system is a highly versatile platform for in vitro protein synthesis using wheat germ CFPS. © 2017 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

  19. FASOR - A second generation shell of revolution code

    NASA Technical Reports Server (NTRS)

    Cohen, G. A.

    1978-01-01

    An integrated computer program entitled Field Analysis of Shells of Revolution (FASOR) currently under development for NASA is described. When completed, this code will treat prebuckling, buckling, initial postbuckling and vibrations under axisymmetric static loads as well as linear response and bifurcation under asymmetric static loads. Although these modes of response are treated by existing programs, FASOR extends the class of problems treated to include general anisotropy and transverse shear deformations of stiffened laminated shells. At the same time, a primary goal is to develop a program which is free of the usual problems of modeling, numerical convergence and ill-conditioning, laborious problem setup, limitations on problem size and interpretation of output. The field method is briefly described, the shell differential equations are cast in a suitable form for solution by this method and essential aspects of the input format are presented. Numerical results are given for both unstiffened and stiffened anisotropic cylindrical shells and compared with previously published analytical solutions.

  20. Universal Fragment Descriptors for Predicting Electronic and Mechanical Properties of Inorganic Crystals

    NASA Astrophysics Data System (ADS)

    Oses, Corey; Isayev, Olexandr; Toher, Cormac; Curtarolo, Stefano; Tropsha, Alexander

    Historically, materials discovery is driven by a laborious trial-and-error process. The growth of materials databases and emerging informatics approaches finally offer the opportunity to transform this practice into data- and knowledge-driven rational design-accelerating discovery of novel materials exhibiting desired properties. By using data from the AFLOW repository for high-throughput, ab-initio calculations, we have generated Quantitative Materials Structure-Property Relationship (QMSPR) models to predict critical materials properties, including the metal/insulator classification, band gap energy, and bulk modulus. The prediction accuracy obtained with these QMSPR models approaches training data for virtually any stoichiometric inorganic crystalline material. We attribute the success and universality of these models to the construction of new materials descriptors-referred to as the universal Property-Labeled Material Fragments (PLMF). This representation affords straightforward model interpretation in terms of simple heuristic design rules that could guide rational materials design. This proof-of-concept study demonstrates the power of materials informatics to dramatically accelerate the search for new materials.

  1. Disease Heritability Inferred from Familial Relationships Reported in Medical Records.

    PubMed

    Polubriaginof, Fernanda C G; Vanguri, Rami; Quinnies, Kayla; Belbin, Gillian M; Yahi, Alexandre; Salmasian, Hojjat; Lorberbaum, Tal; Nwankwo, Victor; Li, Li; Shervey, Mark M; Glowe, Patricia; Ionita-Laza, Iuliana; Simmerling, Mary; Hripcsak, George; Bakken, Suzanne; Goldstein, David; Kiryluk, Krzysztof; Kenny, Eimear E; Dudley, Joel; Vawdrey, David K; Tatonetti, Nicholas P

    2018-05-15

    Heritability is essential for understanding the biological causes of disease but requires laborious patient recruitment and phenotype ascertainment. Electronic health records (EHRs) passively capture a wide range of clinically relevant data and provide a resource for studying the heritability of traits that are not typically accessible. EHRs contain next-of-kin information collected via patient emergency contact forms, but until now, these data have gone unused in research. We mined emergency contact data at three academic medical centers and identified 7.4 million familial relationships while maintaining patient privacy. Identified relationships were consistent with genetically derived relatedness. We used EHR data to compute heritability estimates for 500 disease phenotypes. Overall, estimates were consistent with the literature and between sites. Inconsistencies were indicative of limitations and opportunities unique to EHR research. These analyses provide a validation of the use of EHRs for genetics and disease research. Copyright © 2018 Elsevier Inc. All rights reserved.

  2. Beyond regulation: A social compact' for gas and electricity

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Stram, B.; Thorn, T.

    The public utility covenant, granting franchise protection to firms in return for just and reasonable rate regulation, has come under increasing scrutiny as socially inefficient for several reasons. First, cost-based regulation fails to adequately incite cost-minimization and new product development. Second, public utility regulation has turned into a micro-management exercise where prospective strategies are laboriously scrutinized and past performance is penalized from 20-20 hind-sight. Third, traditional regulation has provided a forum for nontraditional special interest regulation that may not be in the ratepayer's interest. An alternative to the regulatory covenant is the social compact where long-term contracts among the affectedmore » parties set price and service terms. The advantages of such contracting would be to reduce the administrative costs of regulation, better incite the market's entrepreneurial discovery process, deregulate upstream production and transportation, and eliminate extraneous regulation of electric and gas distribution. The winners would be gas consumers and the most efficient industry suppliers.« less

  3. Not Only Size Matters: Early-Talker and Late-Talker Vocabularies Support Different Word-Learning Biases in Babies and Networks.

    PubMed

    Colunga, Eliana; Sims, Clare E

    2017-02-01

    In typical development, word learning goes from slow and laborious to fast and seemingly effortless. Typically developing 2-year-olds seem to intuit the whole range of things in a category from hearing a single instance named-they have word-learning biases. This is not the case for children with relatively small vocabularies (late talkers). We present a computational model that accounts for the emergence of word-learning biases in children at both ends of the vocabulary spectrum based solely on vocabulary structure. The results of Experiment 1 show that late-talkers' and early-talkers' noun vocabularies have different structures and that neural networks trained on the vocabularies of individual late talkers acquire different word-learning biases than those trained on early-talker vocabularies. These models make novel predictions about the word-learning biases in these two populations. Experiment 2 tests these predictions on late- and early-talking toddlers in a novel noun generalization task. Copyright © 2016 Cognitive Science Society, Inc.

  4. Spin wave Feynman diagram vertex computation package

    NASA Astrophysics Data System (ADS)

    Price, Alexander; Javernick, Philip; Datta, Trinanjan

    Spin wave theory is a well-established theoretical technique that can correctly predict the physical behavior of ordered magnetic states. However, computing the effects of an interacting spin wave theory incorporating magnons involve a laborious by hand derivation of Feynman diagram vertices. The process is tedious and time consuming. Hence, to improve productivity and have another means to check the analytical calculations, we have devised a Feynman Diagram Vertex Computation package. In this talk, we will describe our research group's effort to implement a Mathematica based symbolic Feynman diagram vertex computation package that computes spin wave vertices. Utilizing the non-commutative algebra package NCAlgebra as an add-on to Mathematica, symbolic expressions for the Feynman diagram vertices of a Heisenberg quantum antiferromagnet are obtained. Our existing code reproduces the well-known expressions of a nearest neighbor square lattice Heisenberg model. We also discuss the case of a triangular lattice Heisenberg model where non collinear terms contribute to the vertex interactions.

  5. Use of dyes in cariology.

    PubMed

    van de Rijke, J W

    1991-04-01

    The property of dyes to enhance contrast by their colour can be used in clinical dentistry and in investigations in vitro or in vivo. They have been used for indication of affected dental tissues, improvement of diagnostic methods, enhancement of patient awareness and information about specific processes. The development of particular dye systems, aimed at clinical application, is often laborious because of toxic effects, lack of specificity, irreversible staining or difficulties with removal of the dye. Clinically used dyes are often visually observed, which means a qualitative assessment of the staining, while quantification of the staining, if performed at all, is confined mostly to laboratory experiments. In this paper the application of dyes, arranged according to their specific purpose in cariology, is discussed, and a brief historical overview is given of the development of two particular dye applications for which commercial dye systems are now available. If certain requirements are met, dyes can be of great help in detection and quantification when used with several diagnostic methods.

  6. Replication-Competent Influenza A Viruses Expressing Reporter Genes.

    PubMed

    Breen, Michael; Nogales, Aitor; Baker, Steven F; Martínez-Sobrido, Luis

    2016-06-23

    Influenza A viruses (IAV) cause annual seasonal human respiratory disease epidemics. In addition, IAV have been implicated in occasional pandemics with inordinate health and economic consequences. Studying IAV, in vitro or in vivo, requires the use of laborious secondary methodologies to identify virus-infected cells. To circumvent this requirement, replication-competent IAV expressing an easily traceable reporter protein can be used. Here we discuss the development and applications of recombinant replication-competent IAV harboring diverse fluorescent or bioluminescent reporter genes in different locations of the viral genome. These viruses have been employed for in vitro and in vivo studies, such as the screening of neutralizing antibodies or antiviral compounds, the identification of host factors involved in viral replication, cell tropism, the development of vaccines, or the assessment of viral infection dynamics. In summary, reporter-expressing, replicating-competent IAV represent a powerful tool for the study of IAV both in vitro and in vivo.

  7. Automating Phase Change Lines and Their Labels Using Microsoft Excel(R).

    PubMed

    Deochand, Neil

    2017-09-01

    Many researchers have rallied against drawn in graphical elements and offered ways to avoid them, especially regarding the insertion of phase change lines (Deochand, Costello, & Fuqua, 2015; Dubuque, 2015; Vanselow & Bourret, 2012). However, few have offered a solution to automating the phase labels, which are often utilized in behavior analytic graphical displays (Deochand et al., 2015). Despite the fact that Microsoft Excel® is extensively utilized by behavior analysts, solutions to resolve issues in our graphing practices are not always apparent or user-friendly. Considering the insertion of phase change lines and their labels constitute a repetitious and laborious endeavor, any minimization in the steps to accomplish these graphical elements could offer substantial time-savings to the field. The purpose of this report is to provide an updated way (and templates in the supplemental materials) to add phase change lines with their respective labels, which stay embedded to the graph when they are moved or updated.

  8. Multiplex High-Throughput Targeted Proteomic Assay To Identify Induced Pluripotent Stem Cells.

    PubMed

    Baud, Anna; Wessely, Frank; Mazzacuva, Francesca; McCormick, James; Camuzeaux, Stephane; Heywood, Wendy E; Little, Daniel; Vowles, Jane; Tuefferd, Marianne; Mosaku, Olukunbi; Lako, Majlinda; Armstrong, Lyle; Webber, Caleb; Cader, M Zameel; Peeters, Pieter; Gissen, Paul; Cowley, Sally A; Mills, Kevin

    2017-02-21

    Induced pluripotent stem cells have great potential as a human model system in regenerative medicine, disease modeling, and drug screening. However, their use in medical research is hampered by laborious reprogramming procedures that yield low numbers of induced pluripotent stem cells. For further applications in research, only the best, competent clones should be used. The standard assays for pluripotency are based on genomic approaches, which take up to 1 week to perform and incur significant cost. Therefore, there is a need for a rapid and cost-effective assay able to distinguish between pluripotent and nonpluripotent cells. Here, we describe a novel multiplexed, high-throughput, and sensitive peptide-based multiple reaction monitoring mass spectrometry assay, allowing for the identification and absolute quantitation of multiple core transcription factors and pluripotency markers. This assay provides simpler and high-throughput classification into either pluripotent or nonpluripotent cells in 7 min analysis while being more cost-effective than conventional genomic tests.

  9. Theory for plasticity of face-centered cubic metals.

    PubMed

    Jo, Minho; Koo, Yang Mo; Lee, Byeong-Joo; Johansson, Börje; Vitos, Levente; Kwon, Se Kyun

    2014-05-06

    The activation of plastic deformation mechanisms determines the mechanical behavior of crystalline materials. However, the complexity of plastic deformation and the lack of a unified theory of plasticity have seriously limited the exploration of the full capacity of metals. Current efforts to design high-strength structural materials in terms of stacking fault energy have not significantly reduced the laborious trial and error works on basic deformation properties. To remedy this situation, here we put forward a comprehensive and transparent theory for plastic deformation of face-centered cubic metals. This is based on a microscopic analysis that, without ambiguity, reveals the various deformation phenomena and elucidates the physical fundaments of the currently used phenomenological correlations. We identify an easily accessible single parameter derived from the intrinsic energy barriers, which fully specifies the potential diversity of metals. Based entirely on this parameter, a simple deformation mode diagram is shown to delineate a series of convenient design criteria, which clarifies a wide area of material functionality by texture control.

  10. Detection of free and covalently bound microcystins in animal tissues by liquid chromatography-tandem mass spectrometry.

    PubMed

    Neffling, Milla-Riina; Lance, Emilie; Meriluoto, Jussi

    2010-03-01

    Microcystins are cyanobacterial hepatotoxins capable of accumulation into animal tissues. The toxins act by inhibiting specific protein phosphatases and both non-covalent and covalent interactions occur. The 2-methyl-3-methoxy-4-phenylbutyric acid (MMPB) method determines the total, i.e. the sum of free and protein-bound microcystin in tissues. The aim of the method development in this paper was to tackle the problems with the MMPB methodology: the rather laborious workflow and the loss of material during different steps of the method. In the optimised workflow the oxidation recovery was of acceptable level (29-40%), the extraction efficiency good (62-97%), but the signal suppression effect from the matrix remained severe in our system (16-37% signal left). The extraction efficiency for the determination of the free, extractable microcystins, was found to be good, 52-100%, depending on the sample and the toxin variant and concentration. Copyright (c) 2009 Elsevier Ltd. All rights reserved.

  11. A simple approach for human recombinant apolipoprotein E4 expression and purification.

    PubMed

    Argyri, Letta; Skamnaki, Vassiliki; Stratikos, Efstratios; Chroni, Angeliki

    2011-10-01

    We report a simple expression and purification procedure for the production of recombinant apolipoprotein E4 (apoE4), an important protein for the lipid homeostasis in humans that plays critical roles in the pathogenesis of cardiovascular and neurodegenerative diseases. Our approach is based on the expression of a thioredoxin-apoE4 fusion construct in bacterial cells and subsequent removal of the fused thioredoxin using the highly specific 3C protease, avoiding costly and laborious lipidation-delipidation steps used before. Our approach results in rapid, high-yield production of structurally and functionally competent apoE4 as evidenced by secondary structure measurements, thermal and chemical melting profiles and the kinetic profile of solubilization of dimyristoyl-phosphatidylcholine (DMPC) vesicles. This protocol is appropriate for laboratories with little experience in apolipoprotein biochemistry and will facilitate future studies on the role of apoE4 in the pathogenesis of cardiovascular disease and neurodegenerative diseases, including Alzheimer's disease. Copyright © 2011 Elsevier Inc. All rights reserved.

  12. Mechanisation and automation technologies development in work at construction sites

    NASA Astrophysics Data System (ADS)

    Sobotka, A.; Pacewicz, K.

    2017-10-01

    Implementing construction work that creates buildings is a very complicated and laborious task and requires the use of various types of machines and equipment. For years there has been a desire for designers and technologists to introduce devices that replace people’s work on machine construction, automation and even robots. Technologies for building construction are still being developed and implemented to limit people’s hard work and improve work efficiency and quality in innovative architectonical and construction solutions. New opportunities for improving work on the construction site include computerisation of technological processes and construction management for projects and processes. The aim of the paper was to analyse the development of mechanisation, automation and computerisation of construction processes and selected building technologies, with special attention paid to 3D printing technology. The state of mechanisation of construction works in Poland and trends in its development in construction technologies are presented. These studies were conducted on the basis of the available literature and a survey of Polish construction companies.

  13. High-throughput sequencing enhanced phage display enables the identification of patient-specific epitope motifs in serum.

    PubMed

    Christiansen, Anders; Kringelum, Jens V; Hansen, Christian S; Bøgh, Katrine L; Sullivan, Eric; Patel, Jigar; Rigby, Neil M; Eiwegger, Thomas; Szépfalusi, Zsolt; de Masi, Federico; Nielsen, Morten; Lund, Ole; Dufva, Martin

    2015-08-06

    Phage display is a prominent screening technique with a multitude of applications including therapeutic antibody development and mapping of antigen epitopes. In this study, phages were selected based on their interaction with patient serum and exhaustively characterised by high-throughput sequencing. A bioinformatics approach was developed in order to identify peptide motifs of interest based on clustering and contrasting to control samples. Comparison of patient and control samples confirmed a major issue in phage display, namely the selection of unspecific peptides. The potential of the bioinformatic approach was demonstrated by identifying epitopes of a prominent peanut allergen, Ara h 1, in sera from patients with severe peanut allergy. The identified epitopes were confirmed by high-density peptide micro-arrays. The present study demonstrates that high-throughput sequencing can empower phage display by (i) enabling the analysis of complex biological samples, (ii) circumventing the traditional laborious picking and functional testing of individual phage clones and (iii) reducing the number of selection rounds.

  14. Convenient Detection of the Citrus Greening (Huanglongbing) Bacterium ‘Candidatus Liberibacter asiaticus’ by Direct PCR from the Midrib Extract

    PubMed Central

    Fujikawa, Takashi; Miyata, Shin-Ichi; Iwanami, Toru

    2013-01-01

    A phloem-limited bacterium, ‘Candidatus Liberibacter asiaticus’ (Las) is a major pathogen of citrus greening (huanglongbing), one of the most destructive citrus diseases worldwide. The rapid identification and culling of infected trees and budwoods in quarantine are the most important control measures. DNA amplification including conventional polymerase chain reaction (PCR) has commonly been used for rapid detection and identification. However, long and laborious procedures for DNA extraction have greatly reduced the applicability of this method. In this study, we found that the Las bacterial cells in the midribs of infected leaves were extracted rapidly and easily by pulverization and centrifugation with mini homogenization tubes. We also found that the Las bacterial cells in the midrib extract were suitable for highly sensitive direct PCR. The performance of direct PCR using this extraction method was not inferior to that of conventional PCR. Thus, the direct PCR method described herein is characterized by its simplicity, sensitivity, and robustness, and is applicable to quarantine testing. PMID:23437295

  15. Template-directed covalent conjugation of DNA to native antibodies, transferrin and other metal-binding proteins

    NASA Astrophysics Data System (ADS)

    Rosen, Christian B.; Kodal, Anne L. B.; Nielsen, Jesper S.; Schaffert, David H.; Scavenius, Carsten; Okholm, Anders H.; Voigt, Niels V.; Enghild, Jan J.; Kjems, Jørgen; Tørring, Thomas; Gothelf, Kurt V.

    2014-09-01

    DNA-protein conjugates are important in bioanalytical chemistry, molecular diagnostics and bionanotechnology, as the DNA provides a unique handle to identify, functionalize or otherwise manipulate proteins. To maintain protein activity, conjugation of a single DNA handle to a specific location on the protein is often needed. However, preparing such high-quality site-specific conjugates often requires genetically engineered proteins, which is a laborious and technically challenging approach. Here we demonstrate a simpler method to create site-selective DNA-protein conjugates. Using a guiding DNA strand modified with a metal-binding functionality, we directed a second DNA strand to the vicinity of a metal-binding site of His6-tagged or wild-type metal-binding proteins, such as serotransferrin, where it subsequently reacted with lysine residues at that site. This method, DNA-templated protein conjugation, facilitates the production of site-selective protein conjugates, and also conjugation to IgG1 antibodies via a histidine cluster in the constant domain.

  16. Mapping the miRNA interactome by crosslinking ligation and sequencing of hybrids (CLASH)

    PubMed Central

    Helwak, Aleksandra; Tollervey, David

    2014-01-01

    RNA-RNA interactions play critical roles in many cellular processes but studying them is difficult and laborious. Here, we describe an experimental procedure, termed crosslinking ligation and sequencing of hybrids (CLASH), which allows high-throughput identification of sites of RNA-RNA interaction. During CLASH, a tagged bait protein is UV crosslinked in vivo to stabilise RNA interactions and purified under denaturing conditions. RNAs associated with the bait protein are partially truncated, and the ends of RNA-duplexes are ligated together. Following linker addition, cDNA library preparation and high-throughput sequencing, the ligated duplexes give rise to chimeric cDNAs, which unambiguously identify RNA-RNA interaction sites independent of bioinformatic predictions. This protocol is optimized for studying miRNA targets bound by Argonaute proteins, but should be easily adapted for other RNA-binding proteins and classes of RNA. The protocol requires around 5 days to complete, excluding the time required for high-throughput sequencing and bioinformatic analyses. PMID:24577361

  17. Development of a method for the quantitation of chloro-, bromo-, and iodoacetic acids in alcoholic beverages.

    PubMed

    Cardador, Maria Jose; Gallego, Mercedes

    2012-01-25

    Chloroacetic, bromoacetic, and iodoacetic acids can be found in alcoholic beverages when they are used as preservatives/stabilizers or as disinfectants. As they are toxic components, their addition is not permitted under European Union and U.S. regulations. To date, no sensitive methods are available, and those proposed are very laborious. This paper describes a sensitive and straightforward method for the determination of the three monohalogenated acetic acids (m-HAAs) in wines and beers using static headspace extraction coupled with gas chromatography-mass spectrometry. Prior to extraction, the target analytes were esterified to increase their volatility, and all parameters related to the extraction/methylation process were optimized to achieve high efficiency (>90%). The study examined the influence both of the ethanol concentration on the headspace partitioning and of the primary acids present in wine on the derivatization reaction of the m-HAAs. The proposed method allows the determination of these compounds at microgram per liter levels in alcoholic beverages.

  18. The interactive electrode localization utility: software for automatic sorting and labeling of intracranial subdural electrodes

    PubMed Central

    Tang, Wei; Peled, Noam; Vallejo, Deborah I.; Borzello, Mia; Dougherty, Darin D.; Eskandar, Emad N.; Widge, Alik S.; Cash, Sydney S.; Stufflebeam, Steven M.

    2018-01-01

    Purpose Existing methods for sorting, labeling, registering, and across-subject localization of electrodes in intracranial encephalography (iEEG) may involve laborious work requiring manual inspection of radiological images. Methods We describe a new open-source software package, the interactive electrode localization utility which presents a full pipeline for the registration, localization, and labeling of iEEG electrodes from CT and MR images. In addition, we describe a method to automatically sort and label electrodes from subdural grids of known geometry. Results We validated our software against manual inspection methods in twelve subjects undergoing iEEG for medically intractable epilepsy. Our algorithm for sorting and labeling performed correct identification on 96% of the electrodes. Conclusions The sorting and labeling methods we describe offer nearly perfect performance and the software package we have distributed may simplify the process of registering, sorting, labeling, and localizing subdural iEEG grid electrodes by manual inspection. PMID:27915398

  19. Differentiation of arterioles from venules in mouse histology images using machine learning

    NASA Astrophysics Data System (ADS)

    Elkerton, J. S.; Xu, Yiwen; Pickering, J. G.; Ward, Aaron D.

    2016-03-01

    Analysis and morphological comparison of arteriolar and venular networks are essential to our understanding of multiple diseases affecting every organ system. We have developed and evaluated the first fully automatic software system for differentiation of arterioles from venules on high-resolution digital histology images of the mouse hind limb immunostained for smooth muscle α-actin. Classifiers trained on texture and morphologic features by supervised machine learning provided excellent classification accuracy for differentiation of arterioles and venules, achieving an area under the receiver operating characteristic curve of 0.90 and balanced false-positive and false-negative rates. Feature selection was consistent across cross-validation iterations, and a small set of three features was required to achieve the reported performance, suggesting potential generalizability of the system. This system eliminates the need for laborious manual classification of the hundreds of microvessels occurring in a typical sample, and paves the way for high-throughput analysis the arteriolar and venular networks in the mouse.

  20. Using PAFEC as a preprocessor for COSMIC/NASTRAN

    NASA Technical Reports Server (NTRS)

    Gray, W. H.; Baudry, T. V.

    1983-01-01

    Programs for Automatic Finite Element Calculations (PAFEC) is a general purpose, three dimensional linear and nonlinear finite element program (ref. 1). PAFEC's features include free format input utilizing engineering keywords, powerful mesh generating facilities, sophisticated data base management procedures, and extensive data validation checks. Presented here is a description of a software interface that permits PAFEC to be used as a preprocessor for COSMIC/NASTRAN. This user friendly software, called PAFCOS, frees the stress analyst from the laborious and error prone procedure of creating and debugging a rigid format COSMIC/NASTRAN bulk data deck. By interactively creating and debugging a finite element model with PAFEC, thus taking full advantage of the free format engineering keyword oriented data structure of PAFEC, the amount of time spent during model generation can be drastically reduced. The PAFCOS software will automatically convert a PAFEC data structure into a COSMIC/NASTRAN bulk data deck. The capabilities and limitations of the PAFCOS software are fully discussed in the following report.

  1. Quantitative neuroanatomy for connectomics in Drosophila

    PubMed Central

    Schneider-Mizell, Casey M; Gerhard, Stephan; Longair, Mark; Kazimiers, Tom; Li, Feng; Zwart, Maarten F; Champion, Andrew; Midgley, Frank M; Fetter, Richard D; Saalfeld, Stephan; Cardona, Albert

    2016-01-01

    Neuronal circuit mapping using electron microscopy demands laborious proofreading or reconciliation of multiple independent reconstructions. Here, we describe new methods to apply quantitative arbor and network context to iteratively proofread and reconstruct circuits and create anatomically enriched wiring diagrams. We measured the morphological underpinnings of connectivity in new and existing reconstructions of Drosophila sensorimotor (larva) and visual (adult) systems. Synaptic inputs were preferentially located on numerous small, microtubule-free 'twigs' which branch off a single microtubule-containing 'backbone'. Omission of individual twigs accounted for 96% of errors. However, the synapses of highly connected neurons were distributed across multiple twigs. Thus, the robustness of a strong connection to detailed twig anatomy was associated with robustness to reconstruction error. By comparing iterative reconstruction to the consensus of multiple reconstructions, we show that our method overcomes the need for redundant effort through the discovery and application of relationships between cellular neuroanatomy and synaptic connectivity. DOI: http://dx.doi.org/10.7554/eLife.12059.001 PMID:26990779

  2. iPhysioMeter: a new approach for measuring heart rate and normalized pulse volume using only a smartphone.

    PubMed

    Matsumura, Kenta; Yamakoshi, Takehiro

    2013-12-01

    Heart rate (HR) and normalized pulse volume (NPV) are physiological indices that have been used in a diversity of psychological studies. However, measuring these indices often requires laborious processes. We therefore developed a new smartphone program, named iPhysioMeter, that makes it possible to measure beat-by-beat HR and ln NPV using only a smartphone. We examined its accuracy against conventional laboratory measures. Mental stress tasks were used to alter HR and ln NPV in 12 participants. Bland-Altman analyses revealed negligible proportional bias for HR and ln NPV or for their change values, expressed as ΔHR and Δln NPV. However, a relatively large fixed bias did emerge for ln NPV, as well as a small one for Δln NPV, although both were within the limits of agreement. These findings suggest that iPhysioMeter can yield valid measures of the absolute level of HR and of relative changes in ln NPV.

  3. Intraabdominal pressure in women during CrossFit exercises and the effect of age and parity

    PubMed Central

    Gephart, Laura Faye; Doersch, Karen M.; Reyes, Michelle; Kuehl, Thomas J.; Danford, Jill M.

    2018-01-01

    ABSTRACT To determine intraabdominal pressure (IAP) in women during CrossFit and to determine whether parity, age, or CrossFit experience affects IAP during CrossFit exercises, we evaluated 10 women: 5 experienced and active CrossFitters and 5 who were not regularly engaged in CrossFit. A Laborie urodynamics abdominal pressure probe with the Goby wireless system measured IAP during 10 repetitions of 13 different CrossFit exercises. Women had a mean age of 36 years. A significant difference was found between mean peak IAP of the 5 parous vs the 5 nulliparous women (P = 0.009). Experience with CrossFit did not affect mean peak IAP achieved with exercise. In some exercises, there was a significant change in IAP as participants progressed through repetitions (P = 0.003 for back squats and 0.04 for sit-ups). Participants achieved IAP values that were markedly higher than those previously published. PMID:29904290

  4. From organized high throughput data to phenomenological theory: The example of dielectric breakdown

    NASA Astrophysics Data System (ADS)

    Kim, Chiho; Pilania, Ghanshyam; Ramprasad, Rampi

    Understanding the behavior (and failure) of dielectric insulators experiencing extreme electric fields is critical to the operation of present and emerging electrical and electronic devices. Despite its importance, the development of a predictive theory of dielectric breakdown has remained a challenge, owing to the complex multiscale nature of this process. Here, we focus on the intrinsic dielectric breakdown field of insulators--the theoretical limit of breakdown determined purely by the chemistry of the material, i.e., the elements the material is composed of, the atomic-level structure, and the bonding. Starting from a benchmark dataset (generated from laborious first principles computations) of the intrinsic dielectric breakdown field of a variety of model insulators, simple predictive phenomenological models of dielectric breakdown are distilled using advanced statistical or machine learning schemes, revealing key correlations and analytical relationships between the breakdown field and easily accessible material properties. The models are shown to be general, and can hence guide the screening and systematic identification of high electric field tolerant materials.

  5. Laser-assisted metal spinning for an efficient and flexible processing of challenging materials

    NASA Astrophysics Data System (ADS)

    Brummer, C.; Eck, S.; Marsoner, S.; Arntz, K.; Klocke, F.

    2016-03-01

    The demand for components made from high performance materials like titanium or nickel-based alloys as well as strain-hardening stainless steel is steadily increasing. However, conventional forming operations conducted on these materials are generally very laborious and time-consuming. This is where the limitations of metal spinning also become apparent. Using a laser to apply heat localized to the forming zone during metal spinning facilitates to enhance the formability of a material. In order to analyse the potential of the new manufacturing process, experimental investigations on laser-assisted shear forming and multi-pass metal spinning have been performed with austenitic stainless steel X5CrNi18-10, nickel-based alloy Inconel 718 and titanium grade 2. It could be demonstrated that the formability of these materials can be enhanced by laser-assistance. Besides the resulting enhancement of forming limits for metal spinning of challenging materials, the forming forces were reduced and the product quality was improved significantly.

  6. Microwave-assisted Derivatization of Fatty Acids for Its Measurement in Milk Using High-Performance Liquid Chromatography.

    PubMed

    Shrestha, Rojeet; Miura, Yusuke; Hirano, Ken-Ichi; Chen, Zhen; Okabe, Hiroaki; Chiba, Hitoshi; Hui, Shu-Ping

    2018-01-01

    Fatty acid (FA) profiling of milk has important applications in human health and nutrition. Conventional methods for the saponification and derivatization of FA are time-consuming and laborious. We aimed to develop a simple, rapid, and economical method for the determination of FA in milk. We applied a beneficial approach of microwave-assisted saponification (MAS) of milk fats and microwave-assisted derivatization (MAD) of FA to its hydrazides, integrated with HPLC-based analysis. The optimal conditions for MAS and MAD were determined. Microwave irradiation significantly reduced the sample preparation time from 80 min in the conventional method to less than 3 min. We used three internal standards for the measurement of short-, medium- and long-chain FA. The proposed method showed satisfactory analytical sensitivity, recovery and reproducibility. There was a significant correlation in the milk FA concentrations between the proposed and conventional methods. Being quick, economic, and convenient, the proposed method for the milk FA measurement can be substitute for the convention method.

  7. Replication-Competent Influenza A Viruses Expressing Reporter Genes

    PubMed Central

    Breen, Michael; Nogales, Aitor; Baker, Steven F.; Martínez-Sobrido, Luis

    2016-01-01

    Influenza A viruses (IAV) cause annual seasonal human respiratory disease epidemics. In addition, IAV have been implicated in occasional pandemics with inordinate health and economic consequences. Studying IAV, in vitro or in vivo, requires the use of laborious secondary methodologies to identify virus-infected cells. To circumvent this requirement, replication-competent IAV expressing an easily traceable reporter protein can be used. Here we discuss the development and applications of recombinant replication-competent IAV harboring diverse fluorescent or bioluminescent reporter genes in different locations of the viral genome. These viruses have been employed for in vitro and in vivo studies, such as the screening of neutralizing antibodies or antiviral compounds, the identification of host factors involved in viral replication, cell tropism, the development of vaccines, or the assessment of viral infection dynamics. In summary, reporter-expressing, replicating-competent IAV represent a powerful tool for the study of IAV both in vitro and in vivo. PMID:27347991

  8. Tag SNP selection via a genetic algorithm.

    PubMed

    Mahdevar, Ghasem; Zahiri, Javad; Sadeghi, Mehdi; Nowzari-Dalini, Abbas; Ahrabian, Hayedeh

    2010-10-01

    Single Nucleotide Polymorphisms (SNPs) provide valuable information on human evolutionary history and may lead us to identify genetic variants responsible for human complex diseases. Unfortunately, molecular haplotyping methods are costly, laborious, and time consuming; therefore, algorithms for constructing full haplotype patterns from small available data through computational methods, Tag SNP selection problem, are convenient and attractive. This problem is proved to be an NP-hard problem, so heuristic methods may be useful. In this paper we present a heuristic method based on genetic algorithm to find reasonable solution within acceptable time. The algorithm was tested on a variety of simulated and experimental data. In comparison with the exact algorithm, based on brute force approach, results show that our method can obtain optimal solutions in almost all cases and runs much faster than exact algorithm when the number of SNP sites is large. Our software is available upon request to the corresponding author.

  9. Charge transport in organic molecular semiconductors from first principles: The bandlike hole mobility in a naphthalene crystal

    NASA Astrophysics Data System (ADS)

    Lee, Nien-En; Zhou, Jin-Jian; Agapito, Luis A.; Bernardi, Marco

    2018-03-01

    Predicting charge transport in organic molecular crystals is notoriously challenging. Carrier mobility calculations in organic semiconductors are dominated by quantum chemistry methods based on charge hopping, which are laborious and only moderately accurate. We compute from first principles the electron-phonon scattering and the phonon-limited hole mobility of naphthalene crystal in the framework of ab initio band theory. Our calculations combine GW electronic bandstructures, ab initio electron-phonon scattering, and the Boltzmann transport equation. The calculated hole mobility is in very good agreement with experiment between 100 -300 K , and we can predict its temperature dependence with high accuracy. We show that scattering between intermolecular phonons and holes regulates the mobility, though intramolecular phonons possess the strongest coupling with holes. We revisit the common belief that only rigid molecular motions affect carrier dynamics in organic molecular crystals. Our paper provides a quantitative and rigorous framework to compute charge transport in organic crystals and is a first step toward reconciling band theory and carrier hopping computational methods.

  10. Optimization of a yeast RNA interference system for controlling gene expression and enabling rapid metabolic engineering.

    PubMed

    Crook, Nathan C; Schmitz, Alexander C; Alper, Hal S

    2014-05-16

    Reduction of endogenous gene expression is a fundamental operation of metabolic engineering, yet current methods for gene knockdown (i.e., genome editing) remain laborious and slow, especially in yeast. In contrast, RNA interference allows facile and tunable gene knockdown via a simple plasmid transformation step, enabling metabolic engineers to rapidly prototype knockdown strategies in multiple strains before expending significant cost to undertake genome editing. Although RNAi is naturally present in a myriad of eukaryotes, it has only been recently implemented in Saccharomyces cerevisiae as a heterologous pathway and so has not yet been optimized as a metabolic engineering tool. In this study, we elucidate a set of design principles for the construction of hairpin RNA expression cassettes in yeast and implement RNA interference to quickly identify routes for improvement of itaconic acid production in this organism. The approach developed here enables rapid prototyping of knockdown strategies and thus accelerates and reduces the cost of the design-build-test cycle in yeast.

  11. SYRIAC: The systematic review information automated collection system a data warehouse for facilitating automated biomedical text classification.

    PubMed

    Yang, Jianji J; Cohen, Aaron M; Cohen, Aaron; McDonagh, Marian S

    2008-11-06

    Automatic document classification can be valuable in increasing the efficiency in updating systematic reviews (SR). In order for the machine learning process to work well, it is critical to create and maintain high-quality training datasets consisting of expert SR inclusion/exclusion decisions. This task can be laborious, especially when the number of topics is large and source data format is inconsistent.To approach this problem, we build an automated system to streamline the required steps, from initial notification of update in source annotation files to loading the data warehouse, along with a web interface to monitor the status of each topic. In our current collection of 26 SR topics, we were able to standardize almost all of the relevance judgments and recovered PMIDs for over 80% of all articles. Of those PMIDs, over 99% were correct in a manual random sample study. Our system performs an essential function in creating training and evaluation data sets for SR text mining research.

  12. SYRIAC: The SYstematic Review Information Automated Collection System A Data Warehouse for Facilitating Automated Biomedical Text Classification

    PubMed Central

    Yang, Jianji J.; Cohen, Aaron M.; McDonagh, Marian S.

    2008-01-01

    Automatic document classification can be valuable in increasing the efficiency in updating systematic reviews (SR). In order for the machine learning process to work well, it is critical to create and maintain high-quality training datasets consisting of expert SR inclusion/exclusion decisions. This task can be laborious, especially when the number of topics is large and source data format is inconsistent. To approach this problem, we build an automated system to streamline the required steps, from initial notification of update in source annotation files to loading the data warehouse, along with a web interface to monitor the status of each topic. In our current collection of 26 SR topics, we were able to standardize almost all of the relevance judgments and recovered PMIDs for over 80% of all articles. Of those PMIDs, over 99% were correct in a manual random sample study. Our system performs an essential function in creating training and evaluation datasets for SR text mining research. PMID:18999194

  13. Preliminary study of soil permeability properties using principal component analysis

    NASA Astrophysics Data System (ADS)

    Yulianti, M.; Sudriani, Y.; Rustini, H. A.

    2018-02-01

    Soil permeability measurement is undoubtedly important in carrying out soil-water research such as rainfall-runoff modelling, irrigation water distribution systems, etc. It is also known that acquiring reliable soil permeability data is rather laborious, time-consuming, and costly. Therefore, it is desirable to develop the prediction model. Several studies of empirical equations for predicting permeability have been undertaken by many researchers. These studies derived the models from areas which soil characteristics are different from Indonesian soil, which suggest a possibility that these permeability models are site-specific. The purpose of this study is to identify which soil parameters correspond strongly to soil permeability and propose a preliminary model for permeability prediction. Principal component analysis (PCA) was applied to 16 parameters analysed from 37 sites consist of 91 samples obtained from Batanghari Watershed. Findings indicated five variables that have strong correlation with soil permeability, and we recommend a preliminary permeability model, which is potential for further development.

  14. Dynamic longitudinal investigation of individual nerve endings in the skin of anesthetized mice using in vivo two-photon microscopy

    NASA Astrophysics Data System (ADS)

    Yuryev, Mikhail; Khiroug, Leonard

    2012-04-01

    Visualization of individual cutaneous nerve endings has previously relied on laborious procedures of tissue excision, fixation, sectioning and staining for light or electron microscopy. We present a method for non-invasive, longitudinal two-photon microscopy of single nerve endings within the skin of anesthetized transgenic mice. Besides excellent signal-to-background ratio and nanometer-scale spatial resolution, this method offers time-lapse ``movies'' of pathophysiological changes in nerve fine structure over minutes, hours, days or weeks. Structure of keratinocytes and dermal matrix is visualized simultaneously with nerve endings, providing clear landmarks for longitudinal analysis. We further demonstrate feasibility of dissecting individual nerve fibers with infra-red laser and monitoring their degradation and regeneration. In summary, our excision-free optical biopsy technique is ideal for longitudinal microscopic analysis of animal skin and skin innervations in vivo and can be applied widely in preclinical models of chronic pain, allergies, skin cancers and a variety of dermatological disorders.

  15. Sensitive Detection of Norovirus Using Phage Nanoparticle Reporters in Lateral-Flow Assay

    PubMed Central

    Hagström, Anna E. V.; Garvey, Gavin; Paterson, Andrew S.; Dhamane, Sagar; Adhikari, Meena; Estes, Mary K.; Strych, Ulrich; Kourentzi, Katerina; Atmar, Robert L.; Willson, Richard C.

    2015-01-01

    Noroviruses are recognized worldwide as the principal cause of acute, non-bacterial gastroenteritis, resulting in 19-21 million cases of disease every year in the United States. Noroviruses have a very low infectious dose, a short incubation period, high resistance to traditional disinfection techniques and multiple modes of transmission, making early, point-of-care detection essential for controlling the spread of the disease. The traditional diagnostic tools, electron microscopy, RT-PCR and ELISA require sophisticated and expensive instrumentation, and are considered too laborious and slow to be useful during severe outbreaks. In this paper we describe the development of a new, rapid and sensitive lateral-flow assay using labeled phage particles for the detection of the prototypical norovirus GI.1 (Norwalk), with a limit of detection of 107 virus-like particles per mL, one hundred-fold lower than a conventional gold nanoparticle lateral-flow assay using the same antibody pair. PMID:25978622

  16. Automated segmentation of knee and ankle regions of rats from CT images to quantify bone mineral density for monitoring treatments of rheumatoid arthritis

    NASA Astrophysics Data System (ADS)

    Cruz, Francisco; Sevilla, Raquel; Zhu, Joe; Vanko, Amy; Lee, Jung Hoon; Dogdas, Belma; Zhang, Weisheng

    2014-03-01

    Bone mineral density (BMD) obtained from a CT image is an imaging biomarker used pre-clinically for characterizing the Rheumatoid arthritis (RA) phenotype. We use this biomarker in animal studies for evaluating disease progression and for testing various compounds. In the current setting, BMD measurements are obtained manually by selecting the regions of interest from three-dimensional (3-D) CT images of rat legs, which results in a laborious and low-throughput process. Combining image processing techniques, such as intensity thresholding and skeletonization, with mathematical techniques in curve fitting and curvature calculations, we developed an algorithm for quick, consistent, and automatic detection of joints in large CT data sets. The implemented algorithm has reduced analysis time for a study with 200 CT images from 10 days to 3 days and has improved the robust detection of the obtained regions of interest compared with manual segmentation. This algorithm has been used successfully in over 40 studies.

  17. Simultaneous imaging of fat crystallinity and crystal polymorphic types by Raman microspectroscopy.

    PubMed

    Motoyama, Michiyo; Ando, Masahiro; Sasaki, Keisuke; Nakajima, Ikuyo; Chikuni, Koichi; Aikawa, Katsuhiro; Hamaguchi, Hiro-O

    2016-04-01

    The crystalline states of fats, i.e., the crystallinity and crystal polymorphic types, strongly influence their physical properties in fat-based foods. Imaging of fat crystalline states has thus been a subject of abiding interest, but conventional techniques cannot image crystallinity and polymorphic types all at once. This article demonstrates a new technique using Raman microspectroscopy for simultaneously imaging the crystallinity and polymorphic types of fats. The crystallinity and β' crystal polymorph, which contribute to the hardness of fat-based food products, were quantitatively visualized in a model fat (porcine adipose tissue) by analyzing several key Raman bands. The emergence of the β crystal polymorph, which generally results in food product deterioration, was successfully imaged by analyzing the whole fingerprint regions of Raman spectra using multivariate curve resolution alternating least squares analysis. The results demonstrate that the crystalline states of fats can be nondestructively visualized and analyzed at the molecular level, in situ, without laborious sample pretreatments. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system.

    PubMed

    Belhaj, Khaoula; Chaparro-Garcia, Angela; Kamoun, Sophien; Nekrasov, Vladimir

    2013-10-11

    Targeted genome engineering (also known as genome editing) has emerged as an alternative to classical plant breeding and transgenic (GMO) methods to improve crop plants. Until recently, available tools for introducing site-specific double strand DNA breaks were restricted to zinc finger nucleases (ZFNs) and TAL effector nucleases (TALENs). However, these technologies have not been widely adopted by the plant research community due to complicated design and laborious assembly of specific DNA binding proteins for each target gene. Recently, an easier method has emerged based on the bacterial type II CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) immune system. The CRISPR/Cas system allows targeted cleavage of genomic DNA guided by a customizable small noncoding RNA, resulting in gene modifications by both non-homologous end joining (NHEJ) and homology-directed repair (HDR) mechanisms. In this review we summarize and discuss recent applications of the CRISPR/Cas technology in plants.

  19. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: a new possibility for the identification and typing of anaerobic bacteria.

    PubMed

    Nagy, Elizabeth

    2014-01-01

    Anaerobic bacteria predominate in the normal flora of humans and are important, often life-threatening pathogens in mixed infections originating from the indigenous microbiota. The isolation and identification of anaerobes by phenotypic and DNA-based molecular methods at a species level is time-consuming and laborious. Following the successful adaptation of the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the routine laboratory identification of bacteria, the extensive development of a database has been initiated to use this method for the identification of anaerobic bacteria. Not only frequently isolated anaerobic species, but also newly recognized and taxonomically rearranged genera and species can be identified using direct smear samples or whole-cell protein extraction, and even phylogenetically closely related species can be identified correctly by means of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Typing of anaerobic bacteria on a subspecies level, determination of antibiotic resistance and direct identification of blood culture isolates will revolutionize anaerobe bacteriology in the near future.

  20. A Method for the Automatic Detection of Insect Clutter in Doppler-Radar Returns.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Luke,E.; Kollias, P.; Johnson, K.

    2006-06-12

    The accurate detection and removal of insect clutter from millimeter wavelength cloud radar (MMCR) returns is of high importance to boundary layer cloud research (e.g., Geerts et al., 2005). When only radar Doppler moments are available, it is difficult to produce a reliable screening of insect clutter from cloud returns because their distributions overlap. Hence, screening of MMCR insect clutter has historically involved a laborious manual process of cross-referencing radar moments against measurements from other collocated instruments, such as lidar. Our study looks beyond traditional radar moments to ask whether analysis of recorded Doppler spectra can serve as the basismore » for reliable, automatic insect clutter screening. We focus on the MMCR operated by the Department of Energy's (DOE) Atmospheric Radiation Measurement (ARM) program at its Southern Great Plains (SGP) facility in Oklahoma. Here, archiving of full Doppler spectra began in September 2003, and during the warmer months, a pronounced insect presence regularly introduces clutter into boundary layer returns.« less

  1. Experience of targeted Usher exome sequencing as a clinical test

    PubMed Central

    Besnard, Thomas; García-García, Gema; Baux, David; Vaché, Christel; Faugère, Valérie; Larrieu, Lise; Léonard, Susana; Millan, Jose M; Malcolm, Sue; Claustres, Mireille; Roux, Anne-Françoise

    2014-01-01

    We show that massively parallel targeted sequencing of 19 genes provides a new and reliable strategy for molecular diagnosis of Usher syndrome (USH) and nonsyndromic deafness, particularly appropriate for these disorders characterized by a high clinical and genetic heterogeneity and a complex structure of several of the genes involved. A series of 71 patients including Usher patients previously screened by Sanger sequencing plus newly referred patients was studied. Ninety-eight percent of the variants previously identified by Sanger sequencing were found by next-generation sequencing (NGS). NGS proved to be efficient as it offers analysis of all relevant genes which is laborious to reach with Sanger sequencing. Among the 13 newly referred Usher patients, both mutations in the same gene were identified in 77% of cases (10 patients) and one candidate pathogenic variant in two additional patients. This work can be considered as pilot for implementing NGS for genetically heterogeneous diseases in clinical service. PMID:24498627

  2. 3D-Printed Detector Band for Magnetic Off-Plane Flux Measurements in Laminated Machine Cores.

    PubMed

    Shilyashki, Georgi; Pfützner, Helmut; Palkovits, Martin; Windischhofer, Andreas; Giefing, Markus

    2017-12-19

    Laminated soft magnetic cores of transformers, rotating machines etc. may exhibit complex 3D flux distributions with pronounced normal fluxes (off-plane fluxes), perpendicular to the plane of magnetization. As recent research activities have shown, detections of off-plane fluxes tend to be essential for the optimization of core performances aiming at a reduction of core losses and of audible noise. Conventional sensors for off-plane flux measurements tend to be either of high thickness, influencing the measured fluxes significantly, or require laborious preparations. In the current work, thin novel detector bands for effective and simple off-plane flux detections in laminated machine cores were manufactured. They are printed in an automatic way by an in-house developed 3D/2D assembler. The latter enables a unique combination of conductive and non-conductive materials. The detector bands were effectively tested in the interior of a two-package, three-phase model transformer core. They proved to be mechanically resilient, even for strong clamping of the core.

  3. Using a Scoring Rubric to Assess the Writing of Bioethics Students.

    PubMed

    Stoddard, Hugh A; Labrecque, Cory A; Schonfeld, Toby

    2016-04-01

    Educators in bioethics have struggled to find valid and reliable assessments that transcend the "reproduction of knowledge" to target more important skill sets. This manuscript reports on the process of developing and grading a minimal-competence comprehensive examination in a bioethics master's degree program. We describe educational theory and practice for the creation and deployment of scoring rubrics for high-stakes performance assessments that reduce scoring inconsistencies. The rubric development process can also benefit the program by building consensus among stakeholders regarding program goals and student outcomes. We describe the Structure of the Observed Learning Outcome taxonomy as a mechanism for rubric design and provide an example of how we applied that taxonomy to define pass/fail cut scores. Details about domains of assessment and writing descriptors of performance are also presented. Despite the laborious work required to create a scoring rubric, we found the effort to be worthwhile for our program.

  4. Output ordering and prioritisation system (OOPS): ranking biosynthetic gene clusters to enhance bioactive metabolite discovery.

    PubMed

    Peña, Alejandro; Del Carratore, Francesco; Cummings, Matthew; Takano, Eriko; Breitling, Rainer

    2017-12-18

    The rapid increase of publicly available microbial genome sequences has highlighted the presence of hundreds of thousands of biosynthetic gene clusters (BGCs) encoding valuable secondary metabolites. The experimental characterization of new BGCs is extremely laborious and struggles to keep pace with the in silico identification of potential BGCs. Therefore, the prioritisation of promising candidates among computationally predicted BGCs represents a pressing need. Here, we propose an output ordering and prioritisation system (OOPS) which helps sorting identified BGCs by a wide variety of custom-weighted biological and biochemical criteria in a flexible and user-friendly interface. OOPS facilitates a judicious prioritisation of BGCs using G+C content, coding sequence length, gene number, cluster self-similarity and codon bias parameters, as well as enabling the user to rank BGCs based upon BGC type, novelty, and taxonomic distribution. Effective prioritisation of BGCs will help to reduce experimental attrition rates and improve the breadth of bioactive metabolites characterized.

  5. A Common Platform for Antibiotic Dereplication and Adjuvant Discovery.

    PubMed

    Cox, Georgina; Sieron, Arthur; King, Andrew M; De Pascale, Gianfranco; Pawlowski, Andrew C; Koteva, Kalinka; Wright, Gerard D

    2017-01-19

    Solving the antibiotic resistance crisis requires the discovery of new antimicrobial drugs and the preservation of existing ones. The discovery of inhibitors of antibiotic resistance, antibiotic adjuvants, is a proven example of the latter. A major difficulty in identifying new antibiotics is the frequent rediscovery of known compounds, necessitating laborious "dereplication" to identify novel chemical entities. We have developed an antibiotic resistance platform (ARP) that can be used for both the identification of antibiotic adjuvants and for antibiotic dereplication. The ARP is a cell-based array of mechanistically distinct individual resistance elements in an identical genetic background. In dereplication mode, we demonstrate the rapid identification, and thus discrimination, of common antibiotics. In adjuvant discovery mode, we show that the ARP can be harnessed in screens to identify inhibitors of resistance. The ARP is therefore a powerful tool that has broad application in confronting the resistance crisis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Food adulteration analysis without laboratory prepared or determined reference food adulterant values.

    PubMed

    Kalivas, John H; Georgiou, Constantinos A; Moira, Marianna; Tsafaras, Ilias; Petrakis, Eleftherios A; Mousdis, George A

    2014-04-01

    Quantitative analysis of food adulterants is an important health and economic issue that needs to be fast and simple. Spectroscopy has significantly reduced analysis time. However, still needed are preparations of analyte calibration samples matrix matched to prediction samples which can be laborious and costly. Reported in this paper is the application of a newly developed pure component Tikhonov regularization (PCTR) process that does not require laboratory prepared or reference analysis methods, and hence, is a greener calibration method. The PCTR method requires an analyte pure component spectrum and non-analyte spectra. As a food analysis example, synchronous fluorescence spectra of extra virgin olive oil samples adulterated with sunflower oil is used. Results are shown to be better than those obtained using ridge regression with reference calibration samples. The flexibility of PCTR allows including reference samples and is generic for use with other instrumental methods and food products. Copyright © 2013 Elsevier Ltd. All rights reserved.

  7. Environmental and human monitoring of Americium-241 utilizing extraction chromatography and alpha-spectrometry.

    PubMed

    Goldstein, S J; Hensley, C A; Armenta, C E; Peters, R J

    1997-03-01

    Recent developments in extraction chromatography have simplified the separation of americium from complex matrices in preparation for alpha-spectroscopy relative to traditional methods. Here we present results of procedures developed/adapted for water, air, and bioassay samples with less than 1 g of inorganic residue. Prior analytical methods required the use of a complex, multistage procedure for separation of americium from these matrices. The newer, simplified procedure requires only a single 2 mL extraction chromatographic separation for isolation of Am and lanthanides from other components of the sample. This method has been implemented on an extensive variety of "real" environmental and bioassay samples from the Los Alamos area, and consistently reliable and accurate results with appropriate detection limits have been obtained. The new method increases analytical throughput by a factor of approximately 2 and decreases environmental hazards from acid and mixed-waste generation relative to the prior technique. Analytical accuracy, reproducibility, and reliability are also significantly improved over the more complex and laborious method used previously.

  8. Sampling Host-Seeking Anthropophilic Mosquito Vectors in West Africa: Comparisons of An Active Human-Baited Tent-Trap against Gold Standard Methods

    PubMed Central

    Krajacich, Benjamin J.; Slade, Jeremiah R.; Mulligan, Robert F.; LaBrecque, Brendan; Alout, Haoues; Grubaugh, Nathan D.; Meyers, Jacob I.; Fakoli, Lawrence S.; Bolay, Fatorma K.; Brackney, Doug E.; Burton, Timothy A.; Seaman, Jonathan A.; Diclaro, Joseph W.; Dabiré, Roch K.; Foy, Brian D.

    2015-01-01

    In this study, we characterize the ability of the previously described Infoscitex tent (IST) to capture mosquitoes in comparison to either the Centers for Disease Control Light Trap hung next to individuals under a bed net (LTC) or to human landing catches (HLC). In Senegal, the IST caught 6.14 times the number of Anopheles gambiae sensu lato (s.l.), and 8.78 times the Culex group V mosquitoes as LTC. In one of two locations in Burkina Faso, the IST caught An. gambiae at a rate not significantly different than HLC. Of importance, 9.1–36.1% of HLC caught An. gambiae were blood fed, mostly with fresh blood, suggesting they fed upon the collector, whereas only 0.5–5.0% from the IST had partial or old blood. The IST also caught outdoor biting species in proportions comparable to HLC. The results show this tent provides a safer and effective alternative to the skill-dependent, risky, and laborious HLC method. PMID:25422393

  9. Automation, parallelism, and robotics for proteomics.

    PubMed

    Alterovitz, Gil; Liu, Jonathan; Chow, Jijun; Ramoni, Marco F

    2006-07-01

    The speed of the human genome project (Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C. et al., Nature 2001, 409, 860-921) was made possible, in part, by developments in automation of sequencing technologies. Before these technologies, sequencing was a laborious, expensive, and personnel-intensive task. Similarly, automation and robotics are changing the field of proteomics today. Proteomics is defined as the effort to understand and characterize proteins in the categories of structure, function and interaction (Englbrecht, C. C., Facius, A., Comb. Chem. High Throughput Screen. 2005, 8, 705-715). As such, this field nicely lends itself to automation technologies since these methods often require large economies of scale in order to achieve cost and time-saving benefits. This article describes some of the technologies and methods being applied in proteomics in order to facilitate automation within the field as well as in linking proteomics-based information with other related research areas.

  10. Distribution and visualisation of chlorhexidine within the skin using ToF-SIMS: a potential platform for the design of more efficacious skin antiseptic formulations.

    PubMed

    Judd, Amy M; Scurr, David J; Heylings, Jon R; Wan, Ka-Wai; Moss, Gary P

    2013-07-01

    In order to increase the efficacy of a topically applied antimicrobial compound the permeation profile, localisation and mechanism of action within the skin must first be investigated. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to visualise the distribution of a conventional antimicrobial compound, chlorhexidine digluconate, within porcine skin without the need for laborious preparation, radio-labels or fluorescent tags. High mass resolution and high spatial resolution mass spectra and chemical images were achieved when analysing chlorhexidine digluconate treated cryo-sectioned porcine skin sections by ToF-SIMS. The distribution of chlorhexidine digluconate was mapped throughout the skin sections and our studies indicate that the compound appears to be localised within the stratum corneum. In parallel, tape strips taken from chlorhexidine digluconate treated porcine skin were analysed by ToF-SIMS to support the distribution profile obtained from the skin sections. ToF-SIMS can act as a powerful complementary technique to map the distribution of topically applied compounds within the skin.

  11. Money Cues Increase Agency and Decrease Prosociality Among Children: Early Signs of Market-Mode Behaviors.

    PubMed

    Gasiorowska, Agata; Chaplin, Lan Nguyen; Zaleskiewicz, Tomasz; Wygrab, Sandra; Vohs, Kathleen D

    2016-03-01

    People can get most of their needs broadly satisfied in two ways: by close communal ties and by dealings with people in the marketplace. These modes of relating-termed communal and market-often necessitate qualitatively different motives, behaviors, and mind-sets. We reasoned that activating market mode would produce behaviors consistent with it and impair behaviors consistent with communal mode. In a series of experiments, money-the market-mode cue-was presented to Polish children ages 3 to 6. We measured communal behavior by prosocial helpfulness and generosity and measured market behavior by performance and effort. Results showed that handling money (compared with other objects) increased laborious effort and reduced helpfulness and generosity. The effects of money primes were not due to the children's mood, liking for money, or task engagement. This work is the first to demonstrate that young children tacitly understand market mode and also understand that money is a cue to shift into it. © The Author(s) 2016.

  12. Innovative electrochemical approach for an early detection of microRNAs.

    PubMed

    Lusi, E A; Passamano, M; Guarascio, P; Scarpa, A; Schiavo, L

    2009-04-01

    The recent findings of circulating cell-free tissue specific microRNAs in the systemic circulation and the potential of their use as specific markers of disease highlight the need to make microRNAs testing a routine part of medical care. At the present time, microRNAs are detected by long and laborious techniques such as Northern blot, RT-PCR, and microarrays. The originality of our work consists in performing microRNAs detection through an electrochemical genosensor using a label-free method. We were able to directly detect microRNAs without the need of PCR and a labeling reaction. The test is simple, very fast and ultrasensitive, with a detection limit of 0.1 pmol. Particularly feasible for a routine microRNAs detection in serum and other biological samples, our technical approach would be of great scientific value and become a common method for simple miRNAs routine detection in both clinical and research settings.

  13. Realtime Multichannel System for Beat to Beat QT Interval Variability

    NASA Technical Reports Server (NTRS)

    Starc, Vito; Schlegel, Todd T.

    2006-01-01

    The measurement of beat-to-beat QT interval variability (QTV) shows clinical promise for identifying several types of cardiac pathology. However, until now, there has been no device capable of displaying, in real time on a beattobeat basis, changes in QTV in all 12 conventional leads in a continuously monitored patient. While several software programs have been designed to analyze QTV, heretofore, such programs have all involved only a few channels (at most) and/or have required laborious user interaction or offline calculations and postprocessing, limiting their clinical utility. This paper describes a PC-based ECG software program that in real time, acquires, analyzes and displays QTV and also PQ interval variability (PQV) in each of the eight independent channels that constitute the 12lead conventional ECG. The system also processes certain related signals that are derived from singular value decomposition and that help to reduce the overall effects of noise on the realtime QTV and PQV results.

  14. A combined method for correlative 3D imaging of biological samples from macro to nano scale

    NASA Astrophysics Data System (ADS)

    Kellner, Manuela; Heidrich, Marko; Lorbeer, Raoul-Amadeus; Antonopoulos, Georgios C.; Knudsen, Lars; Wrede, Christoph; Izykowski, Nicole; Grothausmann, Roman; Jonigk, Danny; Ochs, Matthias; Ripken, Tammo; Kühnel, Mark P.; Meyer, Heiko

    2016-10-01

    Correlative analysis requires examination of a specimen from macro to nano scale as well as applicability of analytical methods ranging from morphological to molecular. Accomplishing this with one and the same sample is laborious at best, due to deformation and biodegradation during measurements or intermediary preparation steps. Furthermore, data alignment using differing imaging techniques turns out to be a complex task, which considerably complicates the interconnection of results. We present correlative imaging of the accessory rat lung lobe by combining a modified Scanning Laser Optical Tomography (SLOT) setup with a specially developed sample preparation method (CRISTAL). CRISTAL is a resin-based embedding method that optically clears the specimen while allowing sectioning and preventing degradation. We applied and correlated SLOT with Multi Photon Microscopy, histological and immunofluorescence analysis as well as Transmission Electron Microscopy, all in the same sample. Thus, combining CRISTAL with SLOT enables the correlative utilization of a vast variety of imaging techniques.

  15. A light-controlled cell lysis system in bacteria.

    PubMed

    Wang, Geyi; Lu, Xin; Zhu, Yisha; Zhang, Wei; Liu, Jiahui; Wu, Yankang; Yu, Liyang; Sun, Dongchang; Cheng, Feng

    2018-05-08

    Intracellular products (e.g., insulin), which are obtained through cell lysis, take up a big share of the biotech industry. It is often time-consuming, laborious, and environment-unfriendly to disrupt bacterial cells with traditional methods. In this study, we developed a molecular device for controlling cell lysis with light. We showed that intracellular expression of a single lysin protein was sufficient for efficient bacterial cell lysis. By placing the lysin-encoding gene under the control of an improved light-controlled system, we successfully controlled cell lysis by switching on/off light: OD 600 of the Escherichia coli cell culture was decreased by twofold when the light-controlled system was activated under dark condition. We anticipate that our work would not only pave the way for cell lysis through a convenient biological way in fermentation industry, but also provide a paradigm for applying the light-controlled system in other fields of biotech industry.

  16. Standardized mappings--a framework to combine different semantic mappers into a standardized web-API.

    PubMed

    Neuhaus, Philipp; Doods, Justin; Dugas, Martin

    2015-01-01

    Automatic coding of medical terms is an important, but highly complicated and laborious task. To compare and evaluate different strategies a framework with a standardized web-interface was created. Two UMLS mapping strategies are compared to demonstrate the interface. The framework is a Java Spring application running on a Tomcat application server. It accepts different parameters and returns results in JSON format. To demonstrate the framework, a list of medical data items was mapped by two different methods: similarity search in a large table of terminology codes versus search in a manually curated repository. These mappings were reviewed by a specialist. The evaluation shows that the framework is flexible (due to standardized interfaces like HTTP and JSON), performant and reliable. Accuracy of automatically assigned codes is limited (up to 40%). Combining different semantic mappers into a standardized Web-API is feasible. This framework can be easily enhanced due to its modular design.

  17. Determination of Phosphorus in Cola Drinks

    NASA Astrophysics Data System (ADS)

    Lozano-Calero, Diego; Martìn-Palomeque, Pilar; Madueño-Lorguillo, Silvia

    1996-12-01

    Laboratory experiments can improve student interest in science. However, the contrary effect could occur if they are not well designed and seem tedious, too laborious, and disconnected from daily life. Cola beverages are one of the most widely consumed drinks and are most popular among students. Much attention is being paid to possible consequences of excessive consumption for human health. Intensive efforts are being made to assess the erosive potential for teeth because of the beverages' acidity (1, 2); adverse effects secondary to high caffeine intake (e.g., hypertension, allergic reactions, gastrointestinal disturbances) (3 - 5); and adverse effects on calcium metabolism due to their high phosphoric acid content, which combined with low dietary calcium intake could increase the risk of suffering from bone diseases (6 - 9). We propose here the quantification of the phosphorus content in this kind of drinks by a different procedure from that previously described by Murphy in this Journal (10). We think this laboratory experiment will seem very interesting to students.

  18. Continent cecostomy. An account of 30 patients.

    PubMed

    Kock, N G; Myrvold, H E; Philipson, B M; Svaninger, G; Ojerskog, B

    1985-10-01

    In this paper, an account is given of our experience with continent colostomy in man. In five patients, the end-sigmoidostomy was provided with an intussusception valve. Evacuation of the bowel by irrigation through a catheter was laborious and time-consuming and this method was abandoned. In another group of 30 patients, the cecum was isolated from the rest of the colon and its distal end was provided with an intussusception valve. Of the 30 patients, eight were later given continent ileostomies, two were converted to conventional sigmoidostomies, and one patient with fecal incontinence preferred to have intestinal continuity reestablished. Thus, 19 patients still have continent cecostomies and are satisfied with their function. When comparing the function of the continent cecostomy with that of the continent ileostomy, however, it is obvious that the ileostomy function is superior. The experience obtained with this group of patients has resulted in a widening of the indications for constructing a continent ileostomy, including selected patients with various anorectal disorders.

  19. Direct screening for chromatin status on DNA barcodes in yeast delineates the regulome of H3K79 methylation by Dot1.

    PubMed

    Vlaming, Hanneke; Molenaar, Thom M; van Welsem, Tibor; Poramba-Liyanage, Deepani W; Smith, Desiree E; Velds, Arno; Hoekman, Liesbeth; Korthout, Tessy; Hendriks, Sjoerd; Altelaar, A F Maarten; van Leeuwen, Fred

    2016-12-06

    Given the frequent misregulation of chromatin in cancer, it is important to understand the cellular mechanisms that regulate chromatin structure. However, systematic screening for epigenetic regulators is challenging and often relies on laborious assays or indirect reporter read-outs. Here we describe a strategy, Epi-ID, to directly assess chromatin status in thousands of mutants. In Epi-ID, chromatin status on DNA barcodes is interrogated by chromatin immunoprecipitation followed by deep sequencing, allowing for quantitative comparison of many mutants in parallel. Screening of a barcoded yeast knock-out collection for regulators of histone H3K79 methylation by Dot1 identified all known regulators as well as novel players and processes. These include histone deposition, homologous recombination, and adenosine kinase, which influences the methionine cycle. Gcn5, the acetyltransferase within the SAGA complex, was found to regulate histone methylation and H2B ubiquitination. The concept of Epi-ID is widely applicable and can be readily applied to other chromatin features.

  20. BEST: barcode enabled sequencing of tetrads.

    PubMed

    Scott, Adrian C; Ludlow, Catherine L; Cromie, Gareth A; Dudley, Aimée M

    2014-05-01

    Tetrad analysis is a valuable tool for yeast genetics, but the laborious manual nature of the process has hindered its application on large scales. Barcode Enabled Sequencing of Tetrads (BEST)1 replaces the manual processes of isolating, disrupting and spacing tetrads. BEST isolates tetrads by virtue of a sporulation-specific GFP fusion protein that permits fluorescence-activated cell sorting of tetrads directly onto agar plates, where the ascus is enzymatically digested and the spores are disrupted and randomly arrayed by glass bead plating. The haploid colonies are then assigned sister spore relationships, i.e. information about which spores originated from the same tetrad, using molecular barcodes read during genotyping. By removing the bottleneck of manual dissection, hundreds or even thousands of tetrads can be isolated in minutes. Here we present a detailed description of the experimental procedures required to perform BEST in the yeast Saccharomyces cerevisiae, starting with a heterozygous diploid strain through the isolation of colonies derived from the haploid meiotic progeny.

  1. Genotyping of Listeria monocytogenes isolates from poultry carcasses using high resolution melting (HRM) analysis.

    PubMed

    Sakaridis, Ioannis; Ganopoulos, Ioannis; Madesis, Panagiotis; Tsaftaris, Athanasios; Argiriou, Anagnostis

    2014-01-02

    An outbreak situation of human listeriosis requires a fast and accurate protocol for typing Listeria monocytogenes . Existing techniques are either characterized by low discriminatory power or are laborious and require several days to give a final result. Polymerase chain reaction (PCR) coupled with high resolution melting (HRM) analysis was investigated in this study as an alternative tool for a rapid and precise genotyping of L. monocytogenes isolates. Fifty-five isolates of L. monocytogenes isolated from poultry carcasses and the environment of four slaughterhouses were typed by HRM analysis using two specific markers, internalin B and ssrA genes. The analysis of genotype confidence percentage of L. monocytogenes isolates produced by HRM analysis generated dendrograms with two major groups and several subgroups. Furthermore, the analysis of the HRM curves revealed that all L. monocytogenes isolates could easily be distinguished. In conclusion, HRM was proven to be a fast and powerful tool for genotyping isolates of L. monocytogenes .

  2. Statistical framework for detection of genetically modified organisms based on Next Generation Sequencing.

    PubMed

    Willems, Sander; Fraiture, Marie-Alice; Deforce, Dieter; De Keersmaecker, Sigrid C J; De Loose, Marc; Ruttink, Tom; Herman, Philippe; Van Nieuwerburgh, Filip; Roosens, Nancy

    2016-02-01

    Because the number and diversity of genetically modified (GM) crops has significantly increased, their analysis based on real-time PCR (qPCR) methods is becoming increasingly complex and laborious. While several pioneers already investigated Next Generation Sequencing (NGS) as an alternative to qPCR, its practical use has not been assessed for routine analysis. In this study a statistical framework was developed to predict the number of NGS reads needed to detect transgene sequences, to prove their integration into the host genome and to identify the specific transgene event in a sample with known composition. This framework was validated by applying it to experimental data from food matrices composed of pure GM rice, processed GM rice (noodles) or a 10% GM/non-GM rice mixture, revealing some influential factors. Finally, feasibility of NGS for routine analysis of GM crops was investigated by applying the framework to samples commonly encountered in routine analysis of GM crops. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  3. Advances in Dendrobium molecular research: Applications in genetic variation, identification and breeding.

    PubMed

    Teixeira da Silva, Jaime A; Jin, Xiaohua; Dobránszki, Judit; Lu, Jiangjie; Wang, Huizhong; Zotz, Gerhard; Cardoso, Jean Carlos; Zeng, Songjun

    2016-02-01

    Orchids of the genus Dendrobium are of great economic importance in global horticultural trade and in Asian traditional medicine. For both areas, research yielding solid information on taxonomy, phylogeny, and breeding of this genus are essential. Traditional morphological and cytological characterization are used in combination with molecular results in classification and identification. Markers may be useful when used alone but are not always reliable in identification. The number of species studied and identified by molecular markers is small at present. Conventional breeding methods are time-consuming and laborious. In the past two decades, promising advances have been made in taxonomy, phylogeny and breeding of Dendrobium species due to the intensive use of molecular markers. In this review, we focus on the main molecular techniques used in 121 published studies and discuss their importance and possibilities in speeding up the breeding of new cultivars and hybrids. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. A study of navigation in virtual space

    NASA Technical Reports Server (NTRS)

    Darken, Rudy; Sibert, John L.; Shumaker, Randy

    1994-01-01

    In the physical world, man has developed efficient methods for navigation and orientation. These methods are dependent on the high-fidelity stimuli presented by the environment. When placed in a virtual world which cannot offer stimuli of the same quality due to computing constraints and immature technology, tasks requiring the maintenance of position and orientation knowledge become laborious. In this paper, we present a representative set of techniques based on principles of navigation derived from real world analogs including human and avian navigation behavior and cartography. A preliminary classification of virtual worlds is presented based on the size of the world, the density of objects in the world, and the level of activity taking place in the world. We also summarize an informal study we performed to determine how the tools influenced the subjects' navigation strategies and behavior. We conclude that principles extracted from real world navigation aids such as maps can be seen to apply in virtual environments.

  5. Magnetoencephalography in ellipsoidal geometry

    NASA Astrophysics Data System (ADS)

    Dassios, George; Kariotou, Fotini

    2003-01-01

    An exact analytic solution for the forward problem in the theory of biomagnetics of the human brain is known only for the (1D) case of a sphere and the (2D) case of a spheroid, where the excitation field is due to an electric dipole within the corresponding homogeneous conductor. In the present work the corresponding problem for the more realistic ellipsoidal brain model is solved and the leading quadrupole approximation for the exterior magnetic field is obtained in a form that exhibits the anisotropic character of the ellipsoidal geometry. The results are obtained in a straightforward manner through the evaluation of the interior electric potential and a subsequent calculation of the surface integral over the ellipsoid, using Lamé functions and ellipsoidal harmonics. The basic formulas are expressed in terms of the standard elliptic integrals that enter the expressions for the exterior Lamé functions. The laborious task of reducing the results to the spherical geometry is also included.

  6. Visible and near infrared spectroscopy coupled to random forest to quantify some soil quality parameters

    NASA Astrophysics Data System (ADS)

    de Santana, Felipe Bachion; de Souza, André Marcelo; Poppi, Ronei Jesus

    2018-02-01

    This study evaluates the use of visible and near infrared spectroscopy (Vis-NIRS) combined with multivariate regression based on random forest to quantify some quality soil parameters. The parameters analyzed were soil cation exchange capacity (CEC), sum of exchange bases (SB), organic matter (OM), clay and sand present in the soils of several regions of Brazil. Current methods for evaluating these parameters are laborious, timely and require various wet analytical methods that are not adequate for use in precision agriculture, where faster and automatic responses are required. The random forest regression models were statistically better than PLS regression models for CEC, OM, clay and sand, demonstrating resistance to overfitting, attenuating the effect of outlier samples and indicating the most important variables for the model. The methodology demonstrates the potential of the Vis-NIR as an alternative for determination of CEC, SB, OM, sand and clay, making possible to develop a fast and automatic analytical procedure.

  7. Comparing different methods for fast screening of microbiological quality of beach sand aimed at rapid-response remediation.

    PubMed

    Testolin, Renan C; Almeida, Tito C M; Polette, Marcus; Branco, Joaquim O; Fischer, Larissa L; Niero, Guilherme; Poyer-Radetski, Gabriel; Silva, Valéria C; Somensi, Cleder A; Corrêa, Albertina X R; Corrêa, Rogério; Rörig, Leonardo R; Itokazu, Ana Gabriela; Férard, Jean-François; Cotelle, Sylvie; Radetski, Claudemir M

    2017-05-15

    There is scientific evidence that beach sands are a significant contributor to the pathogen load to which visitors are exposed. To develop beach quality guidelines all beach zones must be included in microbiological evaluations, but monitoring methods for beach sand quality are relatively longstanding, expensive, laborious and require moderate laboratory infrastructure. This paper aimed to evaluate the microorganism activity in different beach zones applying and comparing a classical method of membrane filtration (MF) with two colorimetric screening methods based on fluorescein (FDA) and tetrazolium (TTC) salt biotransformation to evaluate a new rapid and low-cost method for beach sand microbiological contamination assessments. The colorimetric results can help beach managers to evaluate rapidly and at low cost the microbiological quality of different beach zones in order to decide whether remedial actions need to be adopted to prevent exposure of the public to microbes due to beach sand and/or water contamination. Copyright © 2017. Published by Elsevier Ltd.

  8. Development of a multivariate calibration model for the determination of dry extract content in Brazilian commercial bee propolis extracts through UV-Vis spectroscopy

    NASA Astrophysics Data System (ADS)

    Barbeira, Paulo J. S.; Paganotti, Rosilene S. N.; Ássimos, Ariane A.

    2013-10-01

    This study had the objective of determining the content of dry extract of commercial alcoholic extracts of bee propolis through Partial Least Squares (PLS) multivariate calibration and electronic spectroscopy. The PLS model provided a good prediction of dry extract content in commercial alcoholic extracts of bee propolis in the range of 2.7 a 16.8% (m/v), presenting the advantage of being less laborious and faster than the traditional gravimetric methodology. The PLS model was optimized with outlier detection tests according to the ASTM E 1655-05. In this study it was possible to verify that a centrifugation stage is extremely important in order to avoid the presence of waxes, resulting in a more accurate model. Around 50% of the analyzed samples presented content of dry extract lower than the value established by Brazilian legislation, in most cases, the values found were different from the values claimed in the product's label.

  9. Analysis of phosphorothionate pesticides using a chloroperoxidase pretreatment and acetylcholinesterase biosensor detection.

    PubMed

    Roepcke, Clarisse B S; Muench, Susanne B; Schulze, Holger; Bachmann, Till T; Bachmann, Till; Schmid, Rolf D; Hauer, Bernhard

    2010-08-11

    Acetylcholinesterase (AChE) is responsible for the hydrolysis of acetylcholine in the nervous system. It is inhibited by organophosphate and carbamate pesticides. However, this enzyme is only slightly inhibited by organophosphorothionates, which makes the detection of these pesticides analytically very difficult. A new enzymatic method for the activation and detection of phosphorothionates was developed with the capability to be used directly in food samples without the need of laborious solvent extraction steps. Chloroperoxidase (CPO) from Caldariomyces fumago was combined with tert-butyl hydroperoxide and two halides. Chlorpyrifos and triazophos were completely oxidized. Fenitrothion, methidathion and parathion methyl showed conversion rates between 54 and 61%. Furthermore, the oxidized solution was submitted to an AChE biosensor assay. Chlorpyrifos spiked in organic orange juice was oxidized, where its oxon product was detected in concentrations down to 5 microg/L (final concentration food sample: 25 microg/L). The complete duration of the method takes about 2 h.

  10. Properties of murine embryonic stem cells maintained on human foreskin fibroblasts without LIF.

    PubMed

    Meng, G L; Zur Nieden, N I; Liu, S Y; Cormier, J T; Kallos, M S; Rancourt, D E

    2008-04-01

    In embryonic stem (ES) cells, leukemia inhibitory factor (LIF)/STAT3, wnt and nodal/activin signaling are mainly active to control pluripotency during expansion. To maintain pluripotency, ES cells are typically cultured on feeder cells of varying origins. Murine ES cells are commonly cultured on murine embryonic fibroblasts (MEFs), which senesce early and must be frequently prepared. This process is laborious and leads to batch variation presenting a challenge for high-throughput ES cell expansion. Although some cell lines can be sustained by exogenous LIF, this method is costly. We present here a novel and inexpensive culture method for expanding murine ES cells on human foreskin fibroblast (HFF) feeders. After 20 passages on HFFs without LIF, ES cell lines showed normal expression levels of pluripotency markers, maintained a normal karyotype and retained the ability to contribute to the germline. As HFFs do not senesce for at least 62 passages, they present a vast supply of feeders. Copyright 2007 Wiley-Liss, Inc.

  11. Nanoscale surface characterization using laser interference microscopy

    NASA Astrophysics Data System (ADS)

    Ignatyev, Pavel S.; Skrynnik, Andrey A.; Melnik, Yury A.

    2018-03-01

    Nanoscale surface characterization is one of the most significant parts of modern materials development and application. The modern microscopes are expensive and complicated tools, and its use for industrial tasks is limited due to laborious sample preparation, measurement procedures, and low operation speed. The laser modulation interference microscopy method (MIM) for real-time quantitative and qualitative analysis of glass, metals, ceramics, and various coatings has a spatial resolution of 0.1 nm for vertical and up to 100 nm for lateral. It is proposed as an alternative to traditional scanning electron microscopy (SEM) and atomic force microscopy (AFM) methods. It is demonstrated that in the cases of roughness metrology for super smooth (Ra >1 nm) surfaces the application of a laser interference microscopy techniques is more optimal than conventional SEM and AFM. The comparison of semiconductor test structure for lateral dimensions measurements obtained with SEM and AFM and white light interferometer also demonstrates the advantages of MIM technique.

  12. Visualization of early influenza A virus trafficking in human dendritic cells using STED microscopy.

    PubMed

    Baharom, Faezzah; Thomas, Oliver S; Lepzien, Rico; Mellman, Ira; Chalouni, Cécile; Smed-Sörensen, Anna

    2017-01-01

    Influenza A viruses (IAV) primarily target respiratory epithelial cells, but can also replicate in immune cells, including human dendritic cells (DCs). Super-resolution microscopy provides a novel method of visualizing viral trafficking by overcoming the resolution limit imposed by conventional light microscopy, without the laborious sample preparation of electron microscopy. Using three-color Stimulated Emission Depletion (STED) microscopy, we visualized input IAV nucleoprotein (NP), early and late endosomal compartments (EEA1 and LAMP1 respectively), and HLA-DR (DC membrane/cytosol) by immunofluorescence in human DCs. Surface bound IAV were internalized within 5 min of infection. The association of virus particles with early endosomes peaked at 5 min when 50% of NP+ signals were also EEA1+. Peak association with late endosomes occurred at 15 min when 60% of NP+ signals were LAMP1+. At 30 min of infection, the majority of NP signals were in the nucleus. Our findings illustrate that early IAV trafficking in human DCs proceeds via the classical endocytic pathway.

  13. Detection of antibody to Purpureocillium lilacinum by immunofluorescent assay and flow cytometry in serum of infected C57BL/6 mice.

    PubMed

    de Sequeira, Danielly C M; Peixoto, Mariana L P; De Luca, Paula M; Oliveira-Ferreira, Joseli; Antas, Paulo R Z; Borba, Cintia M

    2013-10-31

    Purpureocillium lilacinum is an emerging pathogenic fungus that can cause different clinical manifestations ranging from cutaneous and sub-cutaneous infections to severe oculomycosis. In this study, using both conventional indirect immunofluorescence and non-conventional flow cytometry approaches, IgG antibodies were readily detected in both C57BL/6 immunocompetent and immunosuppressed mice after i.v. infection with P. lilacinum. The humoral immune response was specific, since virtually no antibodies were detected in the serum of control mice. Flow cytometry assays also showed both quantitative and qualitative differences in total IgG and its isotypes in sera of immunocompetent and immunosupressed infected mice. Although a good starting point, it is clear that the effectiveness of serological assays for P. lilacinum hyalohyphomycosis identification in clinical studies still requires further standardization. Upon further validation in humans, these techniques have the potential to be suitable to detect P. lilacinum infection in patients, thereby avoiding current laborious and time-consuming culture techniques. © 2013.

  14. Integrative strategies to identify candidate genes in rodent models of human alcoholism.

    PubMed

    Treadwell, Julie A

    2006-01-01

    The search for genes underlying alcohol-related behaviours in rodent models of human alcoholism has been ongoing for many years with only limited success. Recently, new strategies that integrate several of the traditional approaches have provided new insights into the molecular mechanisms underlying ethanol's actions in the brain. We have used alcohol-preferring C57BL/6J (B6) and alcohol-avoiding DBA/2J (D2) genetic strains of mice in an integrative strategy combining high-throughput gene expression screening, genetic segregation analysis, and mapping to previously published quantitative trait loci to uncover candidate genes for the ethanol-preference phenotype. In our study, 2 genes, retinaldehyde binding protein 1 (Rlbp1) and syntaxin 12 (Stx12), were found to be strong candidates for ethanol preference. Such experimental approaches have the power and the potential to greatly speed up the laborious process of identifying candidate genes for the animal models of human alcoholism.

  15. Effortful echolalia.

    PubMed

    Hadano, K; Nakamura, H; Hamanaka, T

    1998-02-01

    We report three cases of effortful echolalia in patients with cerebral infarction. The clinical picture of speech disturbance is associated with Type 1 Transcortical Motor Aphasia (TCMA, Goldstein, 1915). The patients always spoke nonfluently with loss of speech initiative, dysarthria, dysprosody, agrammatism, and increased effort and were unable to repeat sentences longer than those containing four or six words. In conversation, they first repeated a few words spoken to them, and then produced self initiated speech. The initial repetition as well as the subsequent self initiated speech, which were realized equally laboriously, can be regarded as mitigated echolalia (Pick, 1924). They were always aware of their own echolalia and tried to control it without effect. These cases demonstrate that neither the ability to repeat nor fluent speech are always necessary for echolalia. The possibility that a lesion in the left medial frontal lobe, including the supplementary motor area, plays an important role in effortful echolalia is discussed.

  16. A fully automatable enzymatic method for DNA extraction from plant tissues

    PubMed Central

    Manen, Jean-François; Sinitsyna, Olga; Aeschbach, Lorène; Markov, Alexander V; Sinitsyn, Arkady

    2005-01-01

    Background DNA extraction from plant tissues, unlike DNA isolation from mammalian tissues, remains difficult due to the presence of a rigid cell wall around the plant cells. Currently used methods inevitably require a laborious mechanical grinding step, necessary to disrupt the cell wall for the release of DNA. Results Using a cocktail of different carbohydrases, a method was developed that enables a complete digestion of the plant cell walls and subsequent DNA release. Optimized conditions for the digestion reaction minimize DNA shearing and digestion, and maximize DNA release from the plant cell. The method gave good results in 125 of the 156 tested species. Conclusion In combination with conventional DNA isolation techniques, the new enzymatic method allows to obtain high-yield, high-molecular weight DNA, which can be used for many applications, including genome characterization by AFLP, RAPD and SSR. Automation of the protocol (from leaf disks to DNA) is possible with existing workstations. PMID:16269076

  17. Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons

    DOE PAGES

    Wetmore, Kelly M.; Price, Morgan N.; Waters, Robert J.; ...

    2015-05-12

    Transposon mutagenesis with next-generation sequencing (TnSeq) is a powerful approach to annotate gene function in bacteria, but existing protocols for TnSeq require laborious preparation of every sample before sequencing. Thus, the existing protocols are not amenable to the throughput necessary to identify phenotypes and functions for the majority of genes in diverse bacteria. Here, we present a method, random bar code transposon-site sequencing (RB-TnSeq), which increases the throughput of mutant fitness profiling by incorporating random DNA bar codes into Tn5 and mariner transposons and by using bar code sequencing (BarSeq) to assay mutant fitness. RB-TnSeq can be used with anymore » transposon, and TnSeq is performed once per organism instead of once per sample. Each BarSeq assay requires only a simple PCR, and 48 to 96 samples can be sequenced on one lane of an Illumina HiSeq system. We demonstrate the reproducibility and biological significance of RB-TnSeq with Escherichia coli, Phaeobacter inhibens, Pseudomonas stutzeri, Shewanella amazonensis, and Shewanella oneidensis. To demonstrate the increased throughput of RB-TnSeq, we performed 387 successful genome-wide mutant fitness assays representing 130 different bacterium-carbon source combinations and identified 5,196 genes with significant phenotypes across the five bacteria. In P. inhibens, we used our mutant fitness data to identify genes important for the utilization of diverse carbon substrates, including a putative D-mannose isomerase that is required for mannitol catabolism. RB-TnSeq will enable the cost-effective functional annotation of diverse bacteria using mutant fitness profiling. A large challenge in microbiology is the functional assessment of the millions of uncharacterized genes identified by genome sequencing. Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach to assign phenotypes and functions to genes. However, the current strategies for TnSeq are

  18. Rapid quantification of mutant fitness in diverse bacteria by sequencing randomly bar-coded transposons

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wetmore, Kelly M.; Price, Morgan N.; Waters, Robert J.

    Transposon mutagenesis with next-generation sequencing (TnSeq) is a powerful approach to annotate gene function in bacteria, but existing protocols for TnSeq require laborious preparation of every sample before sequencing. Thus, the existing protocols are not amenable to the throughput necessary to identify phenotypes and functions for the majority of genes in diverse bacteria. Here, we present a method, random bar code transposon-site sequencing (RB-TnSeq), which increases the throughput of mutant fitness profiling by incorporating random DNA bar codes into Tn5 and mariner transposons and by using bar code sequencing (BarSeq) to assay mutant fitness. RB-TnSeq can be used with anymore » transposon, and TnSeq is performed once per organism instead of once per sample. Each BarSeq assay requires only a simple PCR, and 48 to 96 samples can be sequenced on one lane of an Illumina HiSeq system. We demonstrate the reproducibility and biological significance of RB-TnSeq with Escherichia coli, Phaeobacter inhibens, Pseudomonas stutzeri, Shewanella amazonensis, and Shewanella oneidensis. To demonstrate the increased throughput of RB-TnSeq, we performed 387 successful genome-wide mutant fitness assays representing 130 different bacterium-carbon source combinations and identified 5,196 genes with significant phenotypes across the five bacteria. In P. inhibens, we used our mutant fitness data to identify genes important for the utilization of diverse carbon substrates, including a putative D-mannose isomerase that is required for mannitol catabolism. RB-TnSeq will enable the cost-effective functional annotation of diverse bacteria using mutant fitness profiling. A large challenge in microbiology is the functional assessment of the millions of uncharacterized genes identified by genome sequencing. Transposon mutagenesis coupled to next-generation sequencing (TnSeq) is a powerful approach to assign phenotypes and functions to genes. However, the current strategies for TnSeq are

  19. A non-isotopic assay uses bromouridine and RNA synthesis to detect DNA damage responses.

    PubMed

    Hasegawa, Mayu; Iwai, Shigenori; Kuraoka, Isao

    2010-06-17

    Individuals with inherited xeroderma pigmentosum (XP) disorder and Cockayne syndrome (CS) are deficient in nucleotide excision repair and experience hypersensitivity to sunlight. Although there are several diagnostic assays for these disorders, the recovery of RNA synthesis (RRS) assay that can discriminate between XP cells and CS cells is very laborious. Here, we report on a novel non-radioisotope RRS assay that uses bromouridine (a uridine analog) as an alternative to (3)H-uridine. This assay can easily detect RNA polymerase I transcription in nucleoli and RNA polymerase II transcription in nuclei. The non-RI RSS assay also can rapidly detect normal RRS activity in HeLa cells. Thus, this assay is useful as a novel and easy technique for CS diagnosis. Because RRS is thought to be related to transcription-coupled DNA repair, which is triggered by the blockage of transcriptional machinery by DNA lesions, this assay may be of use for analysis of DNA repair, transcription, and/or genetic toxicity. Copyright 2010 Elsevier B.V. All rights reserved.

  20. [Quantitative estimation of vegetation cover and management factor in USLE and RUSLE models by using remote sensing data: a review].

    PubMed

    Wu, Chang-Guang; Li, Sheng; Ren, Hua-Dong; Yao, Xiao-Hua; Huang, Zi-Jie

    2012-06-01

    Soil loss prediction models such as universal soil loss equation (USLE) and its revised universal soil loss equation (RUSLE) are the useful tools for risk assessment of soil erosion and planning of soil conservation at regional scale. To make a rational estimation of vegetation cover and management factor, the most important parameters in USLE or RUSLE, is particularly important for the accurate prediction of soil erosion. The traditional estimation based on field survey and measurement is time-consuming, laborious, and costly, and cannot rapidly extract the vegetation cover and management factor at macro-scale. In recent years, the development of remote sensing technology has provided both data and methods for the estimation of vegetation cover and management factor over broad geographic areas. This paper summarized the research findings on the quantitative estimation of vegetation cover and management factor by using remote sensing data, and analyzed the advantages and the disadvantages of various methods, aimed to provide reference for the further research and quantitative estimation of vegetation cover and management factor at large scale.

  1. Modeling the Biodegradability of Chemical Compounds Using the Online CHEmical Modeling Environment (OCHEM)

    PubMed Central

    Vorberg, Susann

    2013-01-01

    Abstract Biodegradability describes the capacity of substances to be mineralized by free‐living bacteria. It is a crucial property in estimating a compound’s long‐term impact on the environment. The ability to reliably predict biodegradability would reduce the need for laborious experimental testing. However, this endpoint is difficult to model due to unavailability or inconsistency of experimental data. Our approach makes use of the Online Chemical Modeling Environment (OCHEM) and its rich supply of machine learning methods and descriptor sets to build classification models for ready biodegradability. These models were analyzed to determine the relationship between characteristic structural properties and biodegradation activity. The distinguishing feature of the developed models is their ability to estimate the accuracy of prediction for each individual compound. The models developed using seven individual descriptor sets were combined in a consensus model, which provided the highest accuracy. The identified overrepresented structural fragments can be used by chemists to improve the biodegradability of new chemical compounds. The consensus model, the datasets used, and the calculated structural fragments are publicly available at http://ochem.eu/article/31660. PMID:27485201

  2. Mapping Neurodegenerative Disease Onset and Progression.

    PubMed

    Seeley, William W

    2017-08-01

    Brain networks have been of long-standing interest to neurodegeneration researchers, including but not limited to investigators focusing on conventional prion diseases, which are known to propagate along neural pathways. Tools for human network mapping, however, remained inadequate, limiting our understanding of human brain network architecture and preventing clinical research applications. Until recently, neuropathological studies were the only viable approach to mapping disease onset and progression in humans but required large autopsy cohorts and laborious methods for whole-brain sectioning and staining. Despite important advantages, postmortem studies cannot address in vivo, physiological, or longitudinal questions and have limited potential to explore early-stage disease except for the most common disorders. Emerging in vivo network-based neuroimaging strategies have begun to address these issues, providing data that complement the neuropathological tradition. Overall, findings to date highlight several fundamental principles of neurodegenerative disease anatomy and pathogenesis, as well as some enduring mysteries. These principles and mysteries provide a road map for future research. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

  3. Guidelines for Genome-Scale Analysis of Biological Rhythms.

    PubMed

    Hughes, Michael E; Abruzzi, Katherine C; Allada, Ravi; Anafi, Ron; Arpat, Alaaddin Bulak; Asher, Gad; Baldi, Pierre; de Bekker, Charissa; Bell-Pedersen, Deborah; Blau, Justin; Brown, Steve; Ceriani, M Fernanda; Chen, Zheng; Chiu, Joanna C; Cox, Juergen; Crowell, Alexander M; DeBruyne, Jason P; Dijk, Derk-Jan; DiTacchio, Luciano; Doyle, Francis J; Duffield, Giles E; Dunlap, Jay C; Eckel-Mahan, Kristin; Esser, Karyn A; FitzGerald, Garret A; Forger, Daniel B; Francey, Lauren J; Fu, Ying-Hui; Gachon, Frédéric; Gatfield, David; de Goede, Paul; Golden, Susan S; Green, Carla; Harer, John; Harmer, Stacey; Haspel, Jeff; Hastings, Michael H; Herzel, Hanspeter; Herzog, Erik D; Hoffmann, Christy; Hong, Christian; Hughey, Jacob J; Hurley, Jennifer M; de la Iglesia, Horacio O; Johnson, Carl; Kay, Steve A; Koike, Nobuya; Kornacker, Karl; Kramer, Achim; Lamia, Katja; Leise, Tanya; Lewis, Scott A; Li, Jiajia; Li, Xiaodong; Liu, Andrew C; Loros, Jennifer J; Martino, Tami A; Menet, Jerome S; Merrow, Martha; Millar, Andrew J; Mockler, Todd; Naef, Felix; Nagoshi, Emi; Nitabach, Michael N; Olmedo, Maria; Nusinow, Dmitri A; Ptáček, Louis J; Rand, David; Reddy, Akhilesh B; Robles, Maria S; Roenneberg, Till; Rosbash, Michael; Ruben, Marc D; Rund, Samuel S C; Sancar, Aziz; Sassone-Corsi, Paolo; Sehgal, Amita; Sherrill-Mix, Scott; Skene, Debra J; Storch, Kai-Florian; Takahashi, Joseph S; Ueda, Hiroki R; Wang, Han; Weitz, Charles; Westermark, Pål O; Wijnen, Herman; Xu, Ying; Wu, Gang; Yoo, Seung-Hee; Young, Michael; Zhang, Eric Erquan; Zielinski, Tomasz; Hogenesch, John B

    2017-10-01

    Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding "big data" that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them.

  4. Guidelines for Genome-Scale Analysis of Biological Rhythms

    PubMed Central

    Hughes, Michael E.; Abruzzi, Katherine C.; Allada, Ravi; Anafi, Ron; Arpat, Alaaddin Bulak; Asher, Gad; Baldi, Pierre; de Bekker, Charissa; Bell-Pedersen, Deborah; Blau, Justin; Brown, Steve; Ceriani, M. Fernanda; Chen, Zheng; Chiu, Joanna C.; Cox, Juergen; Crowell, Alexander M.; DeBruyne, Jason P.; Dijk, Derk-Jan; DiTacchio, Luciano; Doyle, Francis J.; Duffield, Giles E.; Dunlap, Jay C.; Eckel-Mahan, Kristin; Esser, Karyn A.; FitzGerald, Garret A.; Forger, Daniel B.; Francey, Lauren J.; Fu, Ying-Hui; Gachon, Frédéric; Gatfield, David; de Goede, Paul; Golden, Susan S.; Green, Carla; Harer, John; Harmer, Stacey; Haspel, Jeff; Hastings, Michael H.; Herzel, Hanspeter; Herzog, Erik D.; Hoffmann, Christy; Hong, Christian; Hughey, Jacob J.; Hurley, Jennifer M.; de la Iglesia, Horacio O.; Johnson, Carl; Kay, Steve A.; Koike, Nobuya; Kornacker, Karl; Kramer, Achim; Lamia, Katja; Leise, Tanya; Lewis, Scott A.; Li, Jiajia; Li, Xiaodong; Liu, Andrew C.; Loros, Jennifer J.; Martino, Tami A.; Menet, Jerome S.; Merrow, Martha; Millar, Andrew J.; Mockler, Todd; Naef, Felix; Nagoshi, Emi; Nitabach, Michael N.; Olmedo, Maria; Nusinow, Dmitri A.; Ptáček, Louis J.; Rand, David; Reddy, Akhilesh B.; Robles, Maria S.; Roenneberg, Till; Rosbash, Michael; Ruben, Marc D.; Rund, Samuel S.C.; Sancar, Aziz; Sassone-Corsi, Paolo; Sehgal, Amita; Sherrill-Mix, Scott; Skene, Debra J.; Storch, Kai-Florian; Takahashi, Joseph S.; Ueda, Hiroki R.; Wang, Han; Weitz, Charles; Westermark, Pål O.; Wijnen, Herman; Xu, Ying; Wu, Gang; Yoo, Seung-Hee; Young, Michael; Zhang, Eric Erquan; Zielinski, Tomasz; Hogenesch, John B.

    2017-01-01

    Genome biology approaches have made enormous contributions to our understanding of biological rhythms, particularly in identifying outputs of the clock, including RNAs, proteins, and metabolites, whose abundance oscillates throughout the day. These methods hold significant promise for future discovery, particularly when combined with computational modeling. However, genome-scale experiments are costly and laborious, yielding “big data” that are conceptually and statistically difficult to analyze. There is no obvious consensus regarding design or analysis. Here we discuss the relevant technical considerations to generate reproducible, statistically sound, and broadly useful genome-scale data. Rather than suggest a set of rigid rules, we aim to codify principles by which investigators, reviewers, and readers of the primary literature can evaluate the suitability of different experimental designs for measuring different aspects of biological rhythms. We introduce CircaInSilico, a web-based application for generating synthetic genome biology data to benchmark statistical methods for studying biological rhythms. Finally, we discuss several unmet analytical needs, including applications to clinical medicine, and suggest productive avenues to address them. PMID:29098954

  5. Recombination-assisted megaprimer (RAM) cloning

    PubMed Central

    Mathieu, Jacques; Alvarez, Emilia; Alvarez, Pedro J.J.

    2014-01-01

    No molecular cloning technique is considered universally reliable, and many suffer from being too laborious, complex, or expensive. Restriction-free cloning is among the simplest, most rapid, and cost-effective methods, but does not always provide successful results. We modified this method to enhance its success rate through the use of exponential amplification coupled with homologous end-joining. This new method, recombination-assisted megaprimer (RAM) cloning, significantly extends the application of restriction-free cloning, and allows efficient vector construction with much less time and effort when restriction-free cloning fails to provide satisfactory results. The following modifications were made to the protocol:•Limited number of PCR cycles for both megaprimer synthesis and the cloning reaction to reduce error propagation.•Elimination of phosphorylation and ligation steps previously reported for cloning methods that used exponential amplification, through the inclusion of a reverse primer in the cloning reaction with a 20 base pair region of homology to the forward primer.•The inclusion of 1 M betaine to enhance both reaction specificity and yield. PMID:26150930

  6. Phagocytosis: history's lessons.

    PubMed

    Garg, Manish; Chandawarkar, Rajiv Y

    2013-01-01

    The assimilation of lessons from the past is an essential component of education for scientists of tomorrow. These lessons are not easy to find. History books on science are few and usually highly dramatized and biographies of scientists tend to exaggerate the pomp of scientific discovery. Both underplay the hard and laborious work that is integral to any scientific pursuit. Here we illustrate one such example. A century ago, the Nobel Prize in Medicine was awarded to two scientists: Ilya Metchnikoff, a Russian zoologist, for the discovery ofphagocytosis-a cell-mediated ingestion ofmicrobes; and Paul Ehrlich, a distinguished physician-scientist, for discovering a highly antigen-specific serum-derived antibody-based immune defense. These two diametrically opposing views of the host-pathogen interaction set the stage for a strife that led to seminal advancements in immunology. Mirrored in this journey are important lessons for scientists today--ubiquitously as applicable to modern scientific life as they were a century ago. This commentaryhighlights these lessons--a fitting centenary to a well-deserved recognition.

  7. Quantitative Mapping of the Spatial Distribution of Nanoparticles in Endo-Lysosomes by Local pH.

    PubMed

    Wang, Jing; MacEwan, Sarah R; Chilkoti, Ashutosh

    2017-02-08

    Understanding the intracellular distribution and trafficking of nanoparticle drug carriers is necessary to elucidate their mechanisms of drug delivery and is helpful in the rational design of novel nanoparticle drug delivery systems. The traditional immunofluorescence method to study intracellular distribution of nanoparticles using organelle-specific antibodies is laborious and subject to artifacts. As an alternative, we developed a new method that exploits ratiometric fluorescence imaging of a pH-sensitive Lysosensor dye to visualize and quantify the spatial distribution of nanoparticles in the endosomes and lysosomes of live cells. Using this method, we compared the endolysosomal distribution of cell-penetrating peptide (CPP)-functionalized micelles to unfunctionalized micelles and found that CPP-functionalized micelles exhibited faster endosome-to-lysosome trafficking than unfunctionalized micelles. Ratiometric fluorescence imaging of pH-sensitive Lysosensor dye allows rapid quantitative mapping of nanoparticle distribution in endolysosomes in live cells while minimizing artifacts caused by extensive sample manipulation typical of alternative approaches. This new method can thus serve as an alternative to traditional immunofluorescence approaches to study the intracellular distribution and trafficking of nanoparticles within endosomes and lysosomes.

  8. Integrating mobile GIS, real-time D-GPS, and high-resolution satellite imagery for land use patrolling

    NASA Astrophysics Data System (ADS)

    Xu, Zhu; Chen, Xianwei; Liu, Guoxiang; Chen, Tao; Meng, Yanzi; Jiang, Lianjiang; Wang, Mei

    2009-06-01

    The illegal use of lands has come to impose a serious threat to land resources protection and land use plan implementation in China. Land use patrolling has long been proven to be an effective means for detection, investigation and prevention of illegal land use. However, land use patrolling performed in the traditional way is laborious and cumbersome. Central and regional government authorities are both seeking high-technology solution to enhance this job. In an effort to satisfy such requirements, we have designed and implemented an integrated system of mobile GIS, D-GPS and wireless Internet to assist land use patrolling and investigation. Details of this system are presented in this paper, including those of the system architecture, the field work-assisting subsystem, the Internet-based D-GPS subsystem ... etc. The main finding is that such technology is indispensable for land use patrolling and similar tasks. It can dramatically promote the patrolling or field work efficiency and tightly connect field and office staff to better perform the mission. Problems encountered in building the system are also discussed.

  9. Feeder-free reprogramming of human fibroblasts with messenger RNA.

    PubMed

    Warren, Luigi; Wang, Jiwu

    2013-11-13

    This unit describes a feeder-free protocol for deriving induced pluripotent stem cells (iPSCs) from human fibroblasts by transfection of synthetic mRNA. The reprogramming of somatic cells requires transient expression of a set of transcription factors that collectively activate an endogenous gene regulatory network specifying the pluripotent phenotype. The necessary ectopic factor expression was first effected using retroviruses; however, as viral integration into the genome is problematic for cell therapy applications, the use of footprint-free vectors such as mRNA is increasingly preferred. Strong points of the mRNA approach include high efficiency, rapid kinetics, and obviation of a clean-up phase to purge the vector. Still, the method is relatively laborious and has, up to now, involved the use of feeder cells, which brings drawbacks including poor applicability to clinically oriented iPSC derivation. Using the methods described here, mRNA reprogramming can be performed without feeders at much-reduced labor and material costs relative to established protocols. Copyright © 2013 John Wiley & Sons, Inc.

  10. Semantic photo synthesis

    NASA Astrophysics Data System (ADS)

    Johnson, Matthew; Brostow, G. J.; Shotton, J.; Kwatra, V.; Cipolla, R.

    2007-02-01

    Composite images are synthesized from existing photographs by artists who make concept art, e.g. storyboards for movies or architectural planning. Current techniques allow an artist to fabricate such an image by digitally splicing parts of stock photographs. While these images serve mainly to "quickly" convey how a scene should look, their production is laborious. We propose a technique that allows a person to design a new photograph with substantially less effort. This paper presents a method that generates a composite image when a user types in nouns, such as "boat" and "sand." The artist can optionally design an intended image by specifying other constraints. Our algorithm formulates the constraints as queries to search an automatically annotated image database. The desired photograph, not a collage, is then synthesized using graph-cut optimization, optionally allowing for further user interaction to edit or choose among alternative generated photos. Our results demonstrate our contributions of (1) a method of creating specific images with minimal human effort, and (2) a combined algorithm for automatically building an image library with semantic annotations from any photo collection.

  11. Semi-automatic recognition of marine debris on beaches

    PubMed Central

    Ge, Zhenpeng; Shi, Huahong; Mei, Xuefei; Dai, Zhijun; Li, Daoji

    2016-01-01

    An increasing amount of anthropogenic marine debris is pervading the earth’s environmental systems, resulting in an enormous threat to living organisms. Additionally, the large amount of marine debris around the world has been investigated mostly through tedious manual methods. Therefore, we propose the use of a new technique, light detection and ranging (LIDAR), for the semi-automatic recognition of marine debris on a beach because of its substantially more efficient role in comparison with other more laborious methods. Our results revealed that LIDAR should be used for the classification of marine debris into plastic, paper, cloth and metal. Additionally, we reconstructed a 3-dimensional model of different types of debris on a beach with a high validity of debris revivification using LIDAR-based individual separation. These findings demonstrate that the availability of this new technique enables detailed observations to be made of debris on a large beach that was previously not possible. It is strongly suggested that LIDAR could be implemented as an appropriate monitoring tool for marine debris by global researchers and governments. PMID:27156433

  12. Real-Time PCR for the Detection of Precise Transgene Copy Number in Wheat.

    PubMed

    Giancaspro, Angelica; Gadaleta, Agata; Blanco, Antonio

    2017-01-01

    Despite the unceasing advances in genetic transformation techniques, the success of common delivery methods still lies on the behavior of the integrated transgenes in the host genome. Stability and expression of the introduced genes are influenced by several factors such as chromosomal location, transgene copy number and interaction with the host genotype. Such factors are traditionally characterized by Southern blot analysis, which can be time-consuming, laborious, and often unable to detect the exact copy number of rearranged transgenes. Recent research in crop field suggests real-time PCR as an effective and reliable tool for the precise quantification and characterization of transgene loci. This technique overcomes most problems linked to phenotypic segregation analysis and can analyze hundreds of samples in a day, making it an efficient method for estimating a gene copy number integrated in a transgenic line. This protocol describes the use of real-time PCR for the detection of transgene copy number in durum wheat transgenic lines by means of two different chemistries (SYBR ® Green I dye and TaqMan ® probes).

  13. CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API.

    PubMed

    Ono, Keiichiro; Muetze, Tanja; Kolishovski, Georgi; Shannon, Paul; Demchak, Barry

    2015-01-01

    As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and publishing tasks, but it can be operated only manually via a point-and-click user interface. Consequently, Cytoscape-oriented tasks are laborious and often error prone, especially with multistep protocols involving many networks. In this paper, we present the new cyREST Cytoscape app and accompanying harmonization libraries. Together, they improve workflow reproducibility and researcher productivity by enabling popular languages (e.g., Python and R, JavaScript, and C#) and tools (e.g., IPython/Jupyter Notebook and RStudio) to directly define and query networks, and perform network analysis, layouts and renderings. We describe cyREST's API and overall construction, and present Python- and R-based examples that illustrate how Cytoscape can be integrated into large scale data analysis pipelines. cyREST is available in the Cytoscape app store (http://apps.cytoscape.org) where it has been downloaded over 1900 times since its release in late 2014.

  14. Automated Quantitative Characterization of Retinal Vascular Leakage and Microaneurysms in Ultra-widefield Fluorescein Angiography

    PubMed Central

    Ehlers, Justis P.; Wang, Kevin; Vasanji, Amit; Hu, Ming; Srivastava, Sunil K.

    2017-01-01

    Summary Ultra-widefield fluorescein angiography (UWFA) is an emerging imaging modality used to characterize pathology in the retinal vasculature such as microaneurysms (MA) and vascular leakage. Despites its potential value for diagnosis and disease surveillance, objective quantitative assessment of retinal pathology by UWFA is currently limited because it requires laborious manual segmentation by trained human graders. In this report, we describe a novel fully automated software platform, which segments MAs and leakage areas in native and dewarped UWFA images with retinal vascular disease. Comparison of the algorithm to human grader generated gold standards demonstrated significant strong correlations for MA and leakage areas (ICC=0.78-0.87 and ICC=0.70-0.86, respectively, p=2.1×10-7 to 3.5×10-10 and p=7.8×10-6 to 1.3×10-9, respectively). These results suggest the algorithm performs similarly to human graders in MA and leakage segmentation and may be of significant utility in clinical and research settings. PMID:28432113

  15. Development of a sensitive GC-C-IRMS method for the analysis of androgens.

    PubMed

    Polet, Michael; Van Gansbeke, Wim; Deventer, Koen; Van Eenoo, Peter

    2013-02-01

    The administration of anabolic steroids is one of the most important issues in doping control and is detectable through a change in the carbon isotopic composition of testosterone and/or its metabolites. Gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS), however, remains a very laborious and expensive technique and substantial amounts of urine are needed to meet the sensitivity requirements of the IRMS. This can be problematic because only a limited amount of urine is available for anti-doping analysis on a broad spectrum of substances. In this work we introduce a new type of injection that increases the sensitivity of GC-C-IRMS by a factor of 13 and reduces the limit of detection, simply by using solvent vent injections instead of splitless injection. This drastically reduces the amount of urine required. On top of that, by only changing the injection technique, the detection parameters of the IRMS are not affected and there is no loss in linearity. Copyright © 2012 John Wiley & Sons, Ltd.

  16. A plug-and-play pathway refactoring workflow for natural product research in Escherichia coli and Saccharomyces cerevisiae.

    PubMed

    Ren, Hengqian; Hu, Pingfan; Zhao, Huimin

    2017-08-01

    Pathway refactoring serves as an invaluable synthetic biology tool for natural product discovery, characterization, and engineering. However, the complicated and laborious molecular biology techniques largely hinder its application in natural product research, especially in a high-throughput manner. Here we report a plug-and-play pathway refactoring workflow for high-throughput, flexible pathway construction, and expression in both Escherichia coli and Saccharomyces cerevisiae. Biosynthetic genes were firstly cloned into pre-assembled helper plasmids with promoters and terminators, resulting in a series of expression cassettes. These expression cassettes were further assembled using Golden Gate reaction to generate fully refactored pathways. The inclusion of spacer plasmids in this system would not only increase the flexibility for refactoring pathways with different number of genes, but also facilitate gene deletion and replacement. As proof of concept, a total of 96 pathways for combinatorial carotenoid biosynthesis were built successfully. This workflow should be generally applicable to different classes of natural products produced by various organisms. Biotechnol. Bioeng. 2017;114: 1847-1854. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  17. [Automated procedures for microscopic analyses of blood smears: medical testing a MECOS-Ts2 complex].

    PubMed

    Pliasunova, S A; Balugian, R Sh; Khmel'nitskiĭ, K E; Medovyĭ, V S; Parpara, A A; Piatnitskiĭ, A M; Sokolinskiĭ, B Z; Dem'ianov, V L; Nikolaenko, D S

    2006-10-01

    The paper presents the results of medical tests of a group of computer-aided procedures for microscopic analysis by means of a MECOS-Ts2 complex (ZAO "MECOS", Russia), which have been conducted at the Republican Children's Clinical Hospital, the Research Institute of Emergency Pediatric Surgery and Traumatology, and Moscow City Clinical Hospital No. 23. Computer-aided procedures for calculating the differential count and for analyzing the morphology of red blood cells were tested on blood smears from a total of 443 patients and donors, computer-aided calculation of the count of reticulocytes was tested on 318 smears. The tests were carried out under the US standard NCCLS-H20A. Manual microscopy (443 smears) and flow blood analysis on a Coulter GEN*S (125 smears) were used as reference methods. The quality of collection of samples and laboriousness were additionally assessed. The certified MECOS-Ts2 subsystems were additionally used as reference tools. The tests indicated the advantage of computer-aided MECOS-Tsl2 complex microscopy over manual microscopy.

  18. Crystallization of FcpA from Leptospira, a novel flagellar protein that is essential for pathogenesis.

    PubMed

    San Martin, Fabiana; Mechaly, Ariel E; Larrieux, Nicole; Wunder, Elsio A; Ko, Albert I; Picardeau, Mathieu; Trajtenberg, Felipe; Buschiazzo, Alejandro

    2017-03-01

    The protein FcpA is a unique component of the flagellar filament of spirochete bacteria belonging to the genus Leptospira. Although it plays an essential role in translational motility and pathogenicity, no structures of FcpA homologues are currently available in the PDB. Its three-dimensional structure will unveil the novel motility mechanisms that render pathogenic Leptospira particularly efficient at invading and disseminating within their hosts, causing leptospirosis in humans and animals. FcpA from L. interrogans was purified and crystallized, but despite laborious attempts no useful X ray diffraction data could be obtained. This challenge was solved by expressing a close orthologue from the related saprophytic species L. biflexa. Three different crystal forms were obtained: a primitive and a centred monoclinic form, as well as a hexagonal variant. All forms diffracted X-rays to suitable resolutions for crystallographic analyses, with the hexagonal type typically reaching the highest limits of 2.0 Å and better. A variation of the quick-soaking procedure resulted in an iodide derivative that was instrumental for single-wavelength anomalous diffraction methods.

  19. Theory for plasticity of face-centered cubic metals

    PubMed Central

    Jo, Minho; Koo, Yang Mo; Lee, Byeong-Joo; Johansson, Börje; Vitos, Levente; Kwon, Se Kyun

    2014-01-01

    The activation of plastic deformation mechanisms determines the mechanical behavior of crystalline materials. However, the complexity of plastic deformation and the lack of a unified theory of plasticity have seriously limited the exploration of the full capacity of metals. Current efforts to design high-strength structural materials in terms of stacking fault energy have not significantly reduced the laborious trial and error works on basic deformation properties. To remedy this situation, here we put forward a comprehensive and transparent theory for plastic deformation of face-centered cubic metals. This is based on a microscopic analysis that, without ambiguity, reveals the various deformation phenomena and elucidates the physical fundaments of the currently used phenomenological correlations. We identify an easily accessible single parameter derived from the intrinsic energy barriers, which fully specifies the potential diversity of metals. Based entirely on this parameter, a simple deformation mode diagram is shown to delineate a series of convenient design criteria, which clarifies a wide area of material functionality by texture control. PMID:24753563

  20. Policy Considerations for Mobile Biosensors.

    PubMed

    Russell, Steven M; de la Rica, Roberto

    2018-06-22

    Meeting policy requirements is essential for advancing molecular diagnostic devices from the laboratory to real-world applications and commercialization. Considering policy as a starting point in the design of new technology is a winning strategy. Rapid developments have put mobile biosensors at the frontier of molecular diagnostics, at times outpacing policymakers, and therefore offering new opportunities for breakthroughs in global health. In this Perspective we survey influential global health policies and recent developments in mobile biosensing in order to gain a new perspective for the future of the field. We summarize the main requirements for mobile diagnostics outlined by policy makers such as the World Health Organization (WHO), the World Bank, the European Union (EU), and the Food and Drug Administration (FDA). We then classify current mobile diagnostic technologies according to the manner in which the biosensor interfaces with a smartphone. We observe a trend in reducing hardware components and substituting instruments and laborious data processing steps for user-friendly apps. From this perspective we see software application developers as key collaborators for bridging the gap between policy and practice.

  1. Application of an automatic thermal desorption-gas chromatography-mass spectrometry system for the analysis of polycyclic aromatic hydrocarbons in airborne particulate matter.

    PubMed

    Gil-Moltó, J; Varea, M; Galindo, N; Crespo, J

    2009-02-27

    The application of the thermal desorption (TD) method coupled with gas chromatography-mass spectrometry (GC-MS) to the analysis of aerosol organics has been the focus of many studies in recent years. This technique overcomes the main drawbacks of the solvent extraction approach such as the use of large amounts of toxic organic solvents and long and laborious extraction processes. In this work, the application of an automatic TD-GC-MS instrument for the determination of particle-bound polycyclic aromatic hydrocarbons (PAHs) is evaluated. This device offers the advantage of allowing the analysis of either gaseous or particulate organics without any modification. Once the thermal desorption conditions for PAH extraction were optimised, the method was verified on NIST standard reference material (SRM) 1649a urban dust, showing good linearity, reproducibility and accuracy for all target PAHs. The method has been applied to PM10 and PM2.5 samples collected on quartz fibre filters with low volume samplers, demonstrating its capability to quantify PAHs when only a small amount of sample is available.

  2. Strategies for identifying new prions in yeast

    PubMed Central

    MacLea, Kyle S

    2011-01-01

    The unexpected discovery of two prions, [URE3] and [PSI+], in Saccharomyces cerevisiae led to questions about how many other proteins could undergo similar prion-based structural conversions. However, [URE3] and [PSI+] were discovered by serendipity in genetic screens. Cataloging the full range of prions in yeast or in other organisms will therefore require more systematic search methods. Taking advantage of some of the unique features of prions, various researchers have developed bioinformatic and experimental methods for identifying novel prion proteins. These methods have generated long lists of prion candidates. The systematic testing of some of these prion candidates has led to notable successes; however, even in yeast, where rapid growth rate and ease of genetic manipulation aid in testing for prion activity, such candidate testing is laborious. Development of better methods to winnow the field of prion candidates will greatly aid in the discovery of new prions, both in yeast and in other organisms, and help us to better understand the role of prions in biology. PMID:22052351

  3. Improving Robotic Assembly of Planar High Energy Density Targets

    NASA Astrophysics Data System (ADS)

    Dudt, D.; Carlson, L.; Alexander, N.; Boehm, K.

    2016-10-01

    Increased quantities of planar assemblies for high energy density targets are needed with higher shot rates being implemented at facilities such as the National Ignition Facility and the Matter in Extreme Conditions station of the Linac Coherent Light Source. To meet this growing demand, robotics are used to reduce assembly time. This project studies how machine vision and force feedback systems can be used to improve the quantity and quality of planar target assemblies. Vision-guided robotics can identify and locate parts, reducing laborious manual loading of parts into precision pallets and associated teaching of locations. On-board automated inspection can measure part pickup offsets to correct part drop-off placement into target assemblies. Force feedback systems can detect pickup locations and apply consistent force to produce more uniform glue bond thickness, thus improving the performance of the targets. System designs and performance evaluations will be presented. Work supported in part by the US DOE under the Science Undergraduate Laboratory Internships Program (SULI) and ICF Target Fabrication DE-NA0001808.

  4. Purification-Free, Target-Selective Immobilization of a Protein from Cell Lysates.

    PubMed

    Cha, Jaehyun; Kwon, Inchan

    2018-02-27

    Protein immobilization has been widely used for laboratory experiments and industrial processes. Preparation of a recombinant protein for immobilization usually requires laborious and expensive purification steps. Here, a novel purification-free, target-selective immobilization technique of a protein from cell lysates is reported. Purification steps are skipped by immobilizing a target protein containing a clickable non-natural amino acid (p-azidophenylalanine) in cell lysates onto alkyne-functionalized solid supports via bioorthogonal azide-alkyne cycloaddition. In order to achieve a target protein-selective immobilization, p-azidophenylalanine was introduced into an exogenous target protein, but not into endogenous non-target proteins using host cells with amber codon-free genomic DNAs. Immobilization of superfolder fluorescent protein (sfGFP) from cell lysates is as efficient as that of the purified sfGFP. Using two fluorescent proteins (sfGFP and mCherry), the authors also demonstrated that the target proteins are immobilized with a minimal immobilization of non-target proteins (target-selective immobilization). © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Southern Clusters for Standardizing CCD Photometry

    NASA Astrophysics Data System (ADS)

    Moon, T. T.

    2017-06-01

    Standardizing photometric measurements typically involves undertaking all-sky photometry. This can be laborious and time-consuming and, for CCD photometry, particularly challenging. Transforming photometry to a standard system is, however, a crucial step when routinely measuring variable stars, as it allows photoelectric measurements from different observers to be combined. For observers in the northern hemisphere, standardized UBVRI values of stars in open clusters such as M67 and NGC 7790 have been established, greatly facilitating quick and accurate transformation of CCD measurements. Recently the AAVSO added the cluster NGC 3532 for southern hemisphere observers to similarly standardize their photometry. The availability of NGC 3532 standards was announced on the AAVSO Variable Star Observing, Photometry forum on 27 October 2016. Published photometry, along with some new measurements by the author, provide a means of checking these NGC 3532 standards which were determined through the AAVSO's Bright Star Monitor (BSM) program (see: https://www.aavso.org/aavsonet-epoch-photometry-database). New measurements of selected stars in the open clusters M25 and NGC 6067 are also included.

  6. Tooth labeling in cone-beam CT using deep convolutional neural network for forensic identification

    NASA Astrophysics Data System (ADS)

    Miki, Yuma; Muramatsu, Chisako; Hayashi, Tatsuro; Zhou, Xiangrong; Hara, Takeshi; Katsumata, Akitoshi; Fujita, Hiroshi

    2017-03-01

    In large disasters, dental record plays an important role in forensic identification. However, filing dental charts for corpses is not an easy task for general dentists. Moreover, it is laborious and time-consuming work in cases of large scale disasters. We have been investigating a tooth labeling method on dental cone-beam CT images for the purpose of automatic filing of dental charts. In our method, individual tooth in CT images are detected and classified into seven tooth types using deep convolutional neural network. We employed the fully convolutional network using AlexNet architecture for detecting each tooth and applied our previous method using regular AlexNet for classifying the detected teeth into 7 tooth types. From 52 CT volumes obtained by two imaging systems, five images each were randomly selected as test data, and the remaining 42 cases were used as training data. The result showed the tooth detection accuracy of 77.4% with the average false detection of 5.8 per image. The result indicates the potential utility of the proposed method for automatic recording of dental information.

  7. From Organized High-Throughput Data to Phenomenological Theory using Machine Learning: The Example of Dielectric Breakdown

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kim, Chiho; Pilania, Ghanshyam; Ramprasad, Ramamurthy

    Understanding the behavior (and failure) of dielectric insulators experiencing extreme electric fields is critical to the operation of present and emerging electrical and electronic devices. Despite its importance, the development of a predictive theory of dielectric breakdown has remained a challenge, owing to the complex multiscale nature of this process. We focus on the intrinsic dielectric breakdown field of insulators—the theoretical limit of breakdown determined purely by the chemistry of the material, i.e., the elements the material is composed of, the atomic-level structure, and the bonding. Starting from a benchmark dataset (generated from laborious first principles computations) of the intrinsicmore » dielectric breakdown field of a variety of model insulators, simple predictive phenomenological models of dielectric breakdown are distilled using advanced statistical or machine learning schemes, revealing key correlations and analytical relationships between the breakdown field and easily accessible material properties. Lastly, the models are shown to be general, and can hence guide the screening and systematic identification of high electric field tolerant materials.« less

  8. A multiparametric assay for quantitative nerve regeneration evaluation.

    PubMed

    Weyn, B; van Remoortere, M; Nuydens, R; Meert, T; van de Wouwer, G

    2005-08-01

    We introduce an assay for the semi-automated quantification of nerve regeneration by image analysis. Digital images of histological sections of regenerated nerves are recorded using an automated inverted microscope and merged into high-resolution mosaic images representing the entire nerve. These are analysed by a dedicated image-processing package that computes nerve-specific features (e.g. nerve area, fibre count, myelinated area) and fibre-specific features (area, perimeter, myelin sheet thickness). The assay's performance and correlation of the automatically computed data with visually obtained data are determined on a set of 140 semithin sections from the distal part of a rat tibial nerve from four different experimental treatment groups (control, sham, sutured, cut) taken at seven different time points after surgery. Results show a high correlation between the manually and automatically derived data, and a high discriminative power towards treatment. Extra value is added by the large feature set. In conclusion, the assay is fast and offers data that currently can be obtained only by a combination of laborious and time-consuming tests.

  9. FTIR as an easy and fast analytical approach to follow up microbial growth during fungal pretreatment of poplar wood with Phanerochaete chrysosporium.

    PubMed

    Cornet, I; Wittner, N; Tofani, G; Tavernier, S

    2018-02-01

    Since the determination of the fermentation kinetics is one of the main challenges in solid state fermentation, the quantitative measurement of biomass growth during microbial pretreatment by FTIR spectroscopy in Attenuated Total Reflectance mode was evaluated. Peaks at wave numbers of 1651 cm -1 and 1593 cm -1 showed to be affected during pretreatment of poplar wood particles by Phanerochaete chrysosporium MUCL 19343. Samples with different microbial biomass fractions were obtained from two different experiments, i.e., shake flask and fixed-bed reactor experiments. The glucosamine concentration was compared to the normalized absorbance ratio of the 1651 cm -1 to 1593 cm -1 peak, measured by FTIR-ATR, and resulted in a linear relationship. The application of a normalized absorbance ratio in function of time provided a graph that was similar to the microbial growth curve. Application of FTIR in ATR mode to follow-up kinetics during solid state fermentation seems to be a fast and easy alternative to laborious measurement techniques, such as glucosamine determination. Copyright © 2018 Elsevier B.V. All rights reserved.

  10. Beyond informed consent.

    PubMed Central

    Bhutta, Zulfiqar A.

    2004-01-01

    Although a relatively recent phenomenon, the role of informed consent in human research is central to its ethical regulation and conduct. However, guidelines often recommend procedures for obtaining informed consent (usually written consent) that are difficult to implement in developing countries. This paper reviews the guidelines for obtaining informed consent and also discusses prevailing views on current controversies, ambiguities and problems with these guidelines and suggests potential solutions. The emphasis in most externally sponsored research projects in developing countries is on laborious documentation of several mechanical aspects of the research process rather than on assuring true comprehension and voluntary participation. The onus for the oversight of this process is often left to overworked and ill-equipped local ethics review committees. Current guidelines and processes for obtaining informed consent should be reviewed with the specific aim of developing culturally appropriate methods of sharing information about the research project and obtaining and documenting consent that is truly informed. Further research is needed to examine the validity and user friendliness of innovations in information sharing procedures for obtaining consent in different cultural settings. PMID:15643799

  11. Design and development of progressive tool for manufacturing washer

    NASA Astrophysics Data System (ADS)

    Annigeri, Ulhas K.; Raghavendra Ravi Kiran, K.; Deepthi, Y. P.

    2017-07-01

    In a progressive tool the raw material is worked at different station to finally fabricate the component. A progressive tool is a lucrative tool for mass production of components. A lot of automobile and other transport industries develop progressive tool for the production of components. The design of tool involves lot of planning and the same amount of skill of process planning is required in the fabrication of the tool. The design also involves use of thumb rules and standard elements as per experience gained in practice. Manufacturing the press tool is a laborious task as special jigs and fixtures have to be designed for the purpose. Assembly of all the press tool elements is another task where use of accurate measuring instruments for alignment of various tool elements is important. In the present study, design and fabrication of progressive press tool for production of washer has been developed and the press tool has been tried out on a mechanical type of press. The components produced are to dimensions.

  12. On Convergence Aspects of Spheroidal Monogenics

    NASA Astrophysics Data System (ADS)

    Georgiev, S.; Morais, J.

    2011-09-01

    Orthogonal polynomials have found wide applications in mathematical physics, numerical analysis, and other fields. Accordingly there is an enormous amount of variety of such polynomials and relations that describe their properties. The paper's main results are the discussion of approximation properties for monogenic functions over prolate spheroids in R3 in terms of orthogonal monogenic polynomials and their interdependences. Certain results are stated without proof for now. The motivation for the present study stems from the fact that these polynomials play an important role in the calculation of the Bergman kernel and Green's monogenic functions in a spheroid. Once these functions are known, it is possible to solve both basic boundary value and conformal mapping problems. Interestingly, most of the used methods have a n-dimensional counterpart and can be extended to arbitrary ellipsoids. But such a procedure would make the further study of the underlying ellipsoidal monogenics somewhat laborious, and for this reason we shall not discuss these general cases here. To the best of our knowledge, this does not appear to have been done in literature before.

  13. Determining Kinetic Parameters for Isothermal Crystallization of Glasses

    NASA Technical Reports Server (NTRS)

    Ray, C. S.; Zhang, T.; Reis, S. T.; Brow, R. K.

    2006-01-01

    Non-isothermal crystallization techniques are frequently used to determine the kinetic parameters for crystallization in glasses. These techniques are experimentally simple and quick compared to the isothermal techniques. However, the analytical models used for non-isothermal data analysis, originally developed for describing isothermal transformation kinetics, are fundamentally flawed. The present paper describes a technique for determining the kinetic parameters for isothermal crystallization in glasses, which eliminates most of the common problems that generally make the studies of isothermal crystallization laborious and time consuming. In this technique, the volume fraction of glass that is crystallized as a function of time during an isothermal hold was determined using differential thermal analysis (DTA). The crystallization parameters for the lithium-disilicate (Li2O.2SiO2) model glass were first determined and compared to the same parameters determined by other techniques to establish the accuracy and usefulness of the present technique. This technique was then used to describe the crystallization kinetics of a complex Ca-Sr-Zn-silicate glass developed for sealing solid oxide fuel cells.

  14. Constructing Benchmark Databases and Protocols for Medical Image Analysis: Diabetic Retinopathy

    PubMed Central

    Kauppi, Tomi; Kämäräinen, Joni-Kristian; Kalesnykiene, Valentina; Sorri, Iiris; Uusitalo, Hannu; Kälviäinen, Heikki

    2013-01-01

    We address the performance evaluation practices for developing medical image analysis methods, in particular, how to establish and share databases of medical images with verified ground truth and solid evaluation protocols. Such databases support the development of better algorithms, execution of profound method comparisons, and, consequently, technology transfer from research laboratories to clinical practice. For this purpose, we propose a framework consisting of reusable methods and tools for the laborious task of constructing a benchmark database. We provide a software tool for medical image annotation helping to collect class label, spatial span, and expert's confidence on lesions and a method to appropriately combine the manual segmentations from multiple experts. The tool and all necessary functionality for method evaluation are provided as public software packages. As a case study, we utilized the framework and tools to establish the DiaRetDB1 V2.1 database for benchmarking diabetic retinopathy detection algorithms. The database contains a set of retinal images, ground truth based on information from multiple experts, and a baseline algorithm for the detection of retinopathy lesions. PMID:23956787

  15. A Buoyancy-based Method of Determining Fat Levels in Drosophila.

    PubMed

    Hazegh, Kelsey E; Reis, Tânia

    2016-11-01

    Drosophila melanogaster is a key experimental system in the study of fat regulation. Numerous techniques currently exist to measure levels of stored fat in Drosophila, but most are expensive and/or laborious and have clear limitations. Here, we present a method to quickly and cheaply determine organismal fat levels in L3 Drosophila larvae. The technique relies on the differences in density between fat and lean tissues and allows for rapid detection of fat and lean phenotypes. We have verified the accuracy of this method by comparison to body fat percentage as determined by neutral lipid extraction and gas chromatography coupled with mass spectrometry (GCMS). We furthermore outline detailed protocols for the collection and synchronization of larvae as well as relevant experimental recipes. The technique presented below overcomes the major shortcomings in the most widely used lipid quantitation methods and provides a powerful way to quickly and sensitively screen L3 larvae for fat regulation phenotypes while maintaining the integrity of the larvae. This assay has wide applications for the study of metabolism and fat regulation using Drosophila.

  16. Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials

    NASA Astrophysics Data System (ADS)

    Cannon, William R.; Baker, Scott E.

    2017-10-01

    Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary states. The formulation uses chemical potentials instead of rate constants. When used to model deterministic systems, the method corresponds to a rescaling of the time dependent reactions in such a way that steady states can be reached on the same time scale but with significantly fewer computational steps. The relationships between reaction affinities, free energy changes and generalized detailed balance are central to the discussion. The significance for applications in systems biology are discussed as is the concept and assumption of maximum entropy production rate as a biological principle that links thermodynamics to natural selection.

  17. Translating bacterial detection by DNAzymes into a litmus test.

    PubMed

    Tram, Kha; Kanda, Pushpinder; Salena, Bruno J; Huan, Shuangyan; Li, Yingfu

    2014-11-17

    Microbial pathogens pose serious threats to public health and safety, and results in millions of illnesses and deaths as well as huge economic losses annually. Laborious and expensive pathogen tests often represent a significant hindrance to implementing effective front-line preventative care, particularly in resource-limited regions. Thus, there is a significant need to develop low-cost and easy-to-use methods for pathogen detection. Herein, we present a simple and inexpensive litmus test for bacterial detection. The method takes advantage of a bacteria-specific RNA-cleaving DNAzyme probe as the molecular recognition element and the ability of urease to hydrolyze urea and elevate the pH value of the test solution. By coupling urease to the DNAzyme on magnetic beads, the detection of bacteria is translated into a pH increase, which can be readily detected using a litmus dye or pH paper. The simplicity, low cost, and broad adaptability make this litmus test attractive for field applications, particularly in the developing world. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics.

    PubMed

    Röst, Hannes L; Liu, Yansheng; D'Agostino, Giuseppe; Zanella, Matteo; Navarro, Pedro; Rosenberger, George; Collins, Ben C; Gillet, Ludovic; Testa, Giuseppe; Malmström, Lars; Aebersold, Ruedi

    2016-09-01

    Next-generation mass spectrometric (MS) techniques such as SWATH-MS have substantially increased the throughput and reproducibility of proteomic analysis, but ensuring consistent quantification of thousands of peptide analytes across multiple liquid chromatography-tandem MS (LC-MS/MS) runs remains a challenging and laborious manual process. To produce highly consistent and quantitatively accurate proteomics data matrices in an automated fashion, we developed TRIC (http://proteomics.ethz.ch/tric/), a software tool that utilizes fragment-ion data to perform cross-run alignment, consistent peak-picking and quantification for high-throughput targeted proteomics. TRIC reduced the identification error compared to a state-of-the-art SWATH-MS analysis without alignment by more than threefold at constant recall while correcting for highly nonlinear chromatographic effects. On a pulsed-SILAC experiment performed on human induced pluripotent stem cells, TRIC was able to automatically align and quantify thousands of light and heavy isotopic peak groups. Thus, TRIC fills a gap in the pipeline for automated analysis of massively parallel targeted proteomics data sets.

  19. A simple method for imaging axonal transport in aging neurons using the adult Drosophila wing.

    PubMed

    Vagnoni, Alessio; Bullock, Simon L

    2016-09-01

    There is growing interest in the link between axonal cargo transport and age-associated neuronal dysfunction. The study of axonal transport in neurons of adult animals requires intravital or ex vivo imaging approaches, which are laborious and expensive in vertebrate models. We describe simple, noninvasive procedures for imaging cargo motility within axons using sensory neurons of the translucent Drosophila wing. A key aspect is a method for mounting the intact fly that allows detailed imaging of transport in wing neurons. Coupled with existing genetic tools in Drosophila, this is a tractable system for studying axonal transport over the life span of an animal and thus for characterization of the relationship between cargo dynamics, neuronal aging and disease. Preparation of a sample for imaging takes ∼5 min, with transport typically filmed for 2-3 min per wing. We also document procedures for the quantification of transport parameters from the acquired images and describe how the protocol can be adapted to study other cell biological processes in aging neurons.

  20. Visualization and Analysis of MiRNA-Targets Interactions Networks.

    PubMed

    León, Luis E; Calligaris, Sebastián D

    2017-01-01

    MicroRNAs are a class of small, noncoding RNA molecules of 21-25 nucleotides in length that regulate the gene expression by base-pairing with the target mRNAs, mainly leading to down-regulation or repression of the target genes. MicroRNAs are involved in diverse regulatory pathways in normal and pathological conditions. In this context, it is highly important to identify the targets of specific microRNA in order to understand the mechanism of its regulation and consequently its involvement in disease. However, the microRNA target identification is experimentally laborious and time-consuming. The in silico prediction of microRNA targets is an extremely useful approach because you can identify potential mRNA targets, reduce the number of possibilities and then, validate a few microRNA-mRNA interactions in an in vitro experimental model. In this chapter, we describe, in a simple way, bioinformatics guidelines to use miRWalk database and Cytoscape software for analyzing microRNA-mRNA interactions through their visualization as a network.

  1. High throughput screening of active pharmaceutical ingredients by UPLC.

    PubMed

    Al-Sayah, Mohammad A; Rizos, Panagiota; Antonucci, Vincent; Wu, Naijun

    2008-07-01

    Ultra performance LC (UPLC) was evaluated as an efficient screening approach to facilitate method development for drug candidates. Three stationary phases were screened: C-18, phenyl, and Shield RP 18 with column dimensions of 150 mm x 2.1 mm, 1.7 microm, which should theoretically generate 35,000 plates or 175% of the typical column plate count of a conventional 250 mm x 4.6 mm, 5 microm particle column. Thirteen different active pharmaceutical ingredients (APIs) were screened using this column set with a standardized mobile-phase gradient. The UPLC method selectivity results were compared to those obtained for these compounds via methods developed through laborious trial and error screening experiments using numerous conventional HPLC mobile and stationary phases. Peak capacity was compared for columns packed with 5 microm particles and columns packed with 1.7 microm particles. The impurities screened by UPLC were confirmed by LC/MS. The results demonstrate that simple, high efficiency UPLC gradients are a feasible and productive alternative to more conventional multiparametric chromatographic screening approaches for many compounds in the early stages of drug development.

  2. Beryllium10: a free and simple tool for creating and managing group safety data sheets

    PubMed Central

    2014-01-01

    Background Countless chemicals and mixtures are used in laboratories today, which all possess their own properties and dangers. Therefore, it is important to brief oneself about possible risks and hazards before doing any experiments. However, this task is laborious and time consuming. Summary Beryllium10 is a program, which supports users by carrying out a large part of the work such as collecting/importing data sets from different providers and compiling most of the information into a single group safety data sheet, which is suitable for having all necessary information at hand while an experiment is in progress. We present here the features of Beryllium10, their implementation, and their design and development criteria and ideas. Conclusion A program for creating and managing of group safety data sheets was developed and released as open source under GPL. The program provides a fast and clear user-interface, and well-conceived design for collecting and managing safety data. It is available for download from the web page http://beryllium.keksecks.de. PMID:24650446

  3. Functional toxicology: tools to advance the future of toxicity testing

    PubMed Central

    Gaytán, Brandon D.; Vulpe, Chris D.

    2014-01-01

    The increased presence of chemical contaminants in the environment is an undeniable concern to human health and ecosystems. Historically, by relying heavily upon costly and laborious animal-based toxicity assays, the field of toxicology has often neglected examinations of the cellular and molecular mechanisms of toxicity for the majority of compounds—information that, if available, would strengthen risk assessment analyses. Functional toxicology, where cells or organisms with gene deletions or depleted proteins are used to assess genetic requirements for chemical tolerance, can advance the field of toxicity testing by contributing data regarding chemical mechanisms of toxicity. Functional toxicology can be accomplished using available genetic tools in yeasts, other fungi and bacteria, and eukaryotes of increased complexity, including zebrafish, fruit flies, rodents, and human cell lines. Underscored is the value of using less complex systems such as yeasts to direct further studies in more complex systems such as human cell lines. Functional techniques can yield (1) novel insights into chemical toxicity; (2) pathways and mechanisms deserving of further study; and (3) candidate human toxicant susceptibility or resistance genes. PMID:24847352

  4. Further improvement of broad specificity hapten recognition with protein engineering.

    PubMed

    Korpimäki, Teemu; Rosenberg, Jaana; Virtanen, Pekka; Lamminmäki, Urpo; Tuomola, Mika; Saviranta, Petri

    2003-01-01

    Sulfa-antibiotics (sulfonamides) are widely used in veterinary medicine. Meat and milk from treated animals can be contaminated with sulfa residues. Current sulfonamide assays are unfit for screening of food, because they are either too laborious, insensitive or specific for a few sulfa compounds only. An immunoassay for detection of all sulfas in a single reaction would be useful for screening. Previously we have improved the broad specificity sulfa binding of antibody 27G3 with random mutagenesis and phage display. In order to improve the properties of this antibody further, mutants from the previous study were recombined and more mutations introduced. These new libraries were enriched with phage display and several different mutant antibodies were isolated. The cross-reaction profile of the best mutant was better than that of the wild-type antibody and the mutants of the previous study: it was capable of binding 10 of the tested 13 sulfonamides within a narrow concentration range and also bound the rest of the sulfas 5- to 11-fold better than the mutants of the previous study.

  5. Establishment of an efficient virus-induced gene silencing (VIGS) assay in Arabidopsis by Agrobacterium-mediated rubbing infection.

    PubMed

    Manhães, Ana Marcia E de A; de Oliveira, Marcos V V; Shan, Libo

    2015-01-01

    Several VIGS protocols have been established for high-throughput functional genomic screens as it bypasses the time-consuming and laborious process of generation of transgenic plants. The silencing efficiency in this approach is largely hindered by a technically demanding step in which the first pair of newly emerged true leaves at the 2-week-old stage are infiltrated with a needleless syringe. To further optimize VIGS efficiency and achieve rapid inoculation for a large-scale functional genomic study, here we describe a protocol of an efficient VIGS assay in Arabidopsis using Agrobacterium-mediated rubbing infection. The Agrobacterium inoculation is performed by simply rubbing the leaves with Filter Agent Celite(®) 545. The highly efficient and uniform silencing effect was indicated by the development of a visibly albino phenotype due to silencing of the Cloroplastos alterados 1 (CLA1) gene in the newly emerged leaves. In addition, the albino phenotype could be observed in stems and flowers, indicating its potential application for gene functional studies in the late vegetative development and flowering stages.

  6. 3D-Printed Detector Band for Magnetic Off-Plane Flux Measurements in Laminated Machine Cores

    PubMed Central

    Pfützner, Helmut; Palkovits, Martin; Windischhofer, Andreas; Giefing, Markus

    2017-01-01

    Laminated soft magnetic cores of transformers, rotating machines etc. may exhibit complex 3D flux distributions with pronounced normal fluxes (off-plane fluxes), perpendicular to the plane of magnetization. As recent research activities have shown, detections of off-plane fluxes tend to be essential for the optimization of core performances aiming at a reduction of core losses and of audible noise. Conventional sensors for off-plane flux measurements tend to be either of high thickness, influencing the measured fluxes significantly, or require laborious preparations. In the current work, thin novel detector bands for effective and simple off-plane flux detections in laminated machine cores were manufactured. They are printed in an automatic way by an in-house developed 3D/2D assembler. The latter enables a unique combination of conductive and non-conductive materials. The detector bands were effectively tested in the interior of a two-package, three-phase model transformer core. They proved to be mechanically resilient, even for strong clamping of the core. PMID:29257063

  7. Non-Destructive and rapid evaluation of staple foods quality by using spectroscopic techniques: A review.

    PubMed

    Su, Wen-Hao; He, Hong-Ju; Sun, Da-Wen

    2017-03-24

    Staple foods, including cereals, legumes, and root/tuber crops, dominate the daily diet of humans by providing valuable proteins, starch, oils, minerals, and vitamins. Quality evaluation of staple foods is primarily carried out on sensory (e.g. external defect, color), adulteration (e.g. species, origin), chemical (e.g. starch, proteins), mycotoxin (e.g. Fusarium toxin, aflatoxin), parasitic infection (e.g. weevil, beetle), and internal physiological (e.g. hollow heart, black heart) aspects. Conventional methods for the quality assessment of staple foods are always laborious, destructive, and time-consuming. Requirements for online monitoring of staple foods have been proposed to encourage the development of rapid, reagentless, and noninvasive techniques. Spectroscopic techniques, such as visible-infrared spectroscopy, Raman spectroscopy, nuclear magnetic resonance spectroscopy, and spectral imaging, have been introduced as promising analytical tools and applied for the quality evaluation of staple foods. This review summarizes the recent applications and progress of such spectroscopic techniques in determining various qualities of staple foods. Besides, challenges and future trends of these spectroscopic techniques are also presented.

  8. Efficient material decomposition method for dual-energy X-ray cargo inspection system

    NASA Astrophysics Data System (ADS)

    Lee, Donghyeon; Lee, Jiseoc; Min, Jonghwan; Lee, Byungcheol; Lee, Byeongno; Oh, Kyungmin; Kim, Jaehyun; Cho, Seungryong

    2018-03-01

    Dual-energy X-ray inspection systems are widely used today for it provides X-ray attenuation contrast of the imaged object and also its material information. Material decomposition capability allows a higher detection sensitivity of potential targets including purposely loaded impurities in agricultural product inspections and threats in security scans for example. Dual-energy X-ray transmission data can be transformed into two basis material thickness data, and its transformation accuracy heavily relies on a calibration of material decomposition process. The calibration process in general can be laborious and time consuming. Moreover, a conventional calibration method is often challenged by the nonuniform spectral characteristics of the X-ray beam in the entire field-of-view (FOV). In this work, we developed an efficient material decomposition calibration process for a linear accelerator (LINAC) based high-energy X-ray cargo inspection system. We also proposed a multi-spot calibration method to improve the decomposition performance throughout the entire FOV. Experimental validation of the proposed method has been demonstrated by use of a cargo inspection system that supports 6 MV and 9 MV dual-energy imaging.

  9. Temperature and strain registration by fibre-optic strain sensor in the polymer composite materials manufacturing

    NASA Astrophysics Data System (ADS)

    Matveenko, V. P.; Kosheleva, N. A.; Shardakov, I. N.; Voronkov, A. A.

    2018-04-01

    The presence of process-induced strains induced by various manufacturing and operational factors is one of the characteristics of polymer composite materials (PCM). Conventional methods of registration and evaluation of process-induced strains can be laborious, time-consuming and demanding in terms of technical applications. The employment of embedded fibre-optic strain sensors (FOSS) offers a real prospect of measuring residual strains. This paper demonstrates the potential for using embedded FOSS for recording technological strains in a PCM plate. The PCM plate is manufactured from prepreg, using the direct compression-moulding method. In this method, the prepared reinforcing package is placed inside a mould, heated, and then exposed to compaction pressure. The examined technology can be used for positioning FOSS between the layers of the composite material. Fibre-optic sensors, interacting with the material of the examined object, make it possible to register the evolution of the strain process during all stages of polymer-composite formation. FOSS data were recorded with interrogator ASTRO X 327. The obtained data were processed using specially developed algorithms.

  10. Force Evaluation in the Lattice Boltzmann Method Involving Curved Geometry

    NASA Technical Reports Server (NTRS)

    Mei, Renwei; Yu, Dazhi; Shyy, Wei; Luo, Li-Shi; Bushnell, Dennis M. (Technical Monitor)

    2002-01-01

    The present work investigates two approaches for force evaluation in the lattice Boltzmann equation: the momentum- exchange method and the stress-integration method on the surface of a body. The boundary condition for the particle distribution functions on curved geometries is handled with second order accuracy based on our recent works. The stress-integration method is computationally laborious for two-dimensional flows and in general difficult to implement for three-dimensional flows, while the momentum-exchange method is reliable, accurate, and easy to implement for both two-dimensional and three-dimensional flows. Several test cases are selected to evaluate the present methods, including: (i) two-dimensional pressure-driven channel flow; (ii) two-dimensional uniform flow past a column of cylinders; (iii) two-dimensional flow past a cylinder asymmetrically placed in a channel (with vortex shedding); (iv) three-dimensional pressure-driven flow in a circular pipe; and (v) three-dimensional flow past a sphere. The drag evaluated by using the momentum-exchange method agrees well with the exact or other published results.

  11. IntellEditS: intelligent learning-based editor of segmentations.

    PubMed

    Harrison, Adam P; Birkbeck, Neil; Sofka, Michal

    2013-01-01

    Automatic segmentation techniques, despite demonstrating excellent overall accuracy, can often produce inaccuracies in local regions. As a result, correcting segmentations remains an important task that is often laborious, especially when done manually for 3D datasets. This work presents a powerful tool called Intelligent Learning-Based Editor of Segmentations (IntellEditS) that minimizes user effort and further improves segmentation accuracy. The tool partners interactive learning with an energy-minimization approach to editing. Based on interactive user input, a discriminative classifier is trained and applied to the edited 3D region to produce soft voxel labeling. The labels are integrated into a novel energy functional along with the existing segmentation and image data. Unlike the state of the art, IntellEditS is designed to correct segmentation results represented not only as masks but also as meshes. In addition, IntellEditS accepts intuitive boundary-based user interactions. The versatility and performance of IntellEditS are demonstrated on both MRI and CT datasets consisting of varied anatomical structures and resolutions.

  12. Quantification of measles, mumps and rubella viruses using real-time quantitative TaqMan-based RT-PCR assay.

    PubMed

    Ammour, Y; Faizuloev, E; Borisova, T; Nikonova, A; Dmitriev, G; Lobodanov, S; Zverev, V

    2013-01-01

    In this study, a rapid quantitative method using TaqMan-based real-time reverse transcription-polymerase chain reaction (qPCR-RT) has been developed for estimating the titers of measles, mumps and rubella (MMR) viruses in infected cell culture supernatants. The qPCR-RT assay was demonstrated to be a specific, sensitive, efficient and reproducible method. For MMR viral samples obtained during MMR viral propagations in Vero cells at a different multiplicity of infection, titers determined by the qPCR-RT assay have been compared with estimates of infectious virus obtained by a traditional commonly used method for MMR viruses - 50% cell culture infective dose (CCID(50)) assay, in paired samples. Pearson analysis evidenced a significant correlation between both methods for a certain period after viral inoculation. Furthermore, the established qPCR-RT assay was faster and less-laborious. The developed method could be used as an alternative method or a supplementary tool for the routine titer estimation during MMR vaccine production. Copyright © 2012 Elsevier B.V. All rights reserved.

  13. Uncertainty estimates of purity measurements based on current information: toward a "live validation" of purity methods.

    PubMed

    Apostol, Izydor; Kelner, Drew; Jiang, Xinzhao Grace; Huang, Gang; Wypych, Jette; Zhang, Xin; Gastwirt, Jessica; Chen, Kenneth; Fodor, Szilan; Hapuarachchi, Suminda; Meriage, Dave; Ye, Frank; Poppe, Leszek; Szpankowski, Wojciech

    2012-12-01

    To predict precision and other performance characteristics of chromatographic purity methods, which represent the most widely used form of analysis in the biopharmaceutical industry. We have conducted a comprehensive survey of purity methods, and show that all performance characteristics fall within narrow measurement ranges. This observation was used to develop a model called Uncertainty Based on Current Information (UBCI), which expresses these performance characteristics as a function of the signal and noise levels, hardware specifications, and software settings. We applied the UCBI model to assess the uncertainty of purity measurements, and compared the results to those from conventional qualification. We demonstrated that the UBCI model is suitable to dynamically assess method performance characteristics, based on information extracted from individual chromatograms. The model provides an opportunity for streamlining qualification and validation studies by implementing a "live validation" of test results utilizing UBCI as a concurrent assessment of measurement uncertainty. Therefore, UBCI can potentially mitigate the challenges associated with laborious conventional method validation and facilitates the introduction of more advanced analytical technologies during the method lifecycle.

  14. A thermal extrapolation method for the effective temperatures and internal energies of activated ions

    NASA Astrophysics Data System (ADS)

    Meot-Ner (Mautner), Michael; Somogyi, Árpád

    2007-11-01

    The internal energies of dissociating ions, activated chemically or collisionally, can be estimated using the kinetics of thermal dissociation. The thermal Arrhenius parameters can be combined with the observed dissociation rate of the activated ions using kdiss = Athermalexp(-Ea,thermal/RTeff). This Arrhenius-type relation yields the effective temperature, Teff, at which the ions would dissociate thermally at the same rate, or yield the same product distributions, as the activated ions. In turn, Teff is used to calculate the internal energy of the ions and the energy deposited by the activation process. The method yields an energy deposition efficiency of 10% for a chemical ionization proton transfer reaction and 8-26% for the surface collisions of various peptide ions. Internal energies of ions activated by chemical ionization or by gas phase collisions, and of ions produced by desorption methods such as fast atom bombardment, can be also evaluated. Thermal extrapolation is especially useful for ion-molecule reaction products and for biological ions, where other methods to evaluate internal energies are laborious or unavailable.

  15. Environmental and human monitoring of Americium-241 utilizing extraction chromatography and {alpha}-Spectrometry

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Goldstein, S.J.; Hensley, C.A.; Armenta, C.E.

    1997-03-01

    Recent developments in extraction chromatography have simplified the separation of americium from complex matrices in preparation for {alpha}-spectroscopy relative to traditional methods. Here we present results of procedures developed/adapted for water, air, and bioassay samples with less than 1 g of inorganic residue. Prior analytical methods required the use of a complex, multistage procedure for separation of americium from these matrices. The newer, simplified procedure requires only a single 2 mL extraction chromatographic separation for isolation of Am and lanthanides from other components of the sample. This method has been implemented on an extensive variety of `real` environmental and bioassaymore » samples from the Los Alamos area, and consistently reliable and accurate results with appropriate detection limits have been obtained. The new method increases analytical throughput by a factor of {approx}2 and decreases environmental hazards from acid and mixed-waste generation relative to the prior technique. Analytical accuracy, reproducibility, and reliability are also significantly improved over the more complex and laborious method used previously. 24 refs., 2 figs., 2 tabs.« less

  16. Automatic classification of singular elements for the electrostatic analysis of microelectromechanical systems

    NASA Astrophysics Data System (ADS)

    Su, Y.; Ong, E. T.; Lee, K. H.

    2002-05-01

    The past decade has seen an accelerated growth of technology in the field of microelectromechanical systems (MEMS). The development of MEMS products has generated the need for efficient analytical and simulation methods for minimizing the requirement for actual prototyping. The boundary element method is widely used in the electrostatic analysis for MEMS devices. However, singular elements are needed to accurately capture the behavior at singular regions, such as sharp corners and edges, where standard elements fail to give an accurate result. The manual classification of boundary elements based on their singularity conditions is an immensely laborious task, especially when the boundary element model is large. This process can be automated by querying the geometric model of the MEMS device for convex edges based on geometric information of the model. The associated nodes of the boundary elements on these edges can then be retrieved. The whole process is implemented in the MSC/PATRAN platform using the Patran Command Language (the source code is available as supplementary data in the electronic version of this journal issue).

  17. Mass spectrometry compatible surfactant for optimized in-gel protein digestion.

    PubMed

    Saveliev, Sergei V; Woodroofe, Carolyn C; Sabat, Grzegorz; Adams, Christopher M; Klaubert, Dieter; Wood, Keith; Urh, Marjeta

    2013-01-15

    Identification of proteins resolved by SDS-PAGE depends on robust in-gel protein digestion and efficient peptide extraction, requirements that are often difficult to achieve. A lengthy and laborious procedure is an additional challenge of protein identification in gel. We show here that with the use of the mass spectrometry compatible surfactant sodium 3-((1-(furan-2-yl)undecyloxy)carbonylamino)propane-1-sulfonate, the challenges of in-gel protein digestion are effectively addressed. Peptide quantitation based on stable isotope labeling showed that the surfactant induced 1.5-2 fold increase in peptide recovery. Consequently, protein sequence coverage was increased by 20-30%, on average, and the number of identified proteins saw a substantial boost. The surfactant also accelerated the digestion process. Maximal in-gel digestion was achieved in as little as one hour, depending on incubation temperature, and peptides were readily recovered from gel eliminating the need for postdigestion extraction. This study shows that the surfactant provides an efficient means of improving protein identification in gel and streamlining the in-gel digestion procedure requiring no extra handling steps or special equipment.

  18. Recent advances in rapid and non-destructive assessment of meat quality using hyperspectral imaging

    NASA Astrophysics Data System (ADS)

    Tao, Feifei; Ngadi, Michael

    2016-05-01

    Meat is an important food item in human diet. Its production and consumption has greatly increased in the last decades with the development of economies and improvement of peoples' living standards. However, most of the traditional methods for evaluation of meat quality are time-consuming, laborious, inconsistent and destructive to samples, which make them not appropriate for a fast-paced production and processing environment. Development of innovative and non-destructive optical sensing techniques to facilitate simple, fast, and accurate evaluation of quality are attracting increasing attention in the food industry. Hyperspectral imaging is one of the promising techniques. It integrates the combined merits of imaging and spectroscopic techniques. This paper provides a comprehensive review on recent advances in evaluation of the important quality attributes of meat including color, marbling, tenderness, pH, water holding capacity, and also chemical composition attributes such as moisture content, protein content and fat content in pork, beef and lamb. In addition, the future potential applications and trends of hyperspectral imaging are also discussed in this paper.

  19. Practical Guide for Ascidian Microinjection: Phallusia mammillata.

    PubMed

    Yasuo, Hitoyoshi; McDougall, Alex

    2018-01-01

    Phallusia mammillata has recently emerged as a new ascidian model. Its unique characteristics, including the optical transparency of eggs and embryos and efficient translation of exogenously introduced mRNA in eggs, make the Phallusia system suitable for fluorescent protein (FP)-based imaging approaches. In addition, genomic and transcriptomic resources are readily available for this ascidian species, facilitating functional gene studies. Microinjection is probably the most versatile technique for introducing exogenous molecules such as plasmids, mRNAs, and proteins into ascidian eggs/embryos. However, it is not practiced widely within the community; presumably, because the system is rather laborious to set up and it requires practice. Here, we describe in as much detail as possible two microinjection methods that we use daily in the laboratory: one based on an inverted microscope and the other on a stereomicroscope. Along the stepwise description of system setup and injection procedure, we provide practical tips in the hope that this chapter might be a useful guide for introducing or improving a microinjection setup.

  20. UniPrime2: a web service providing easier Universal Primer design.

    PubMed

    Boutros, Robin; Stokes, Nicola; Bekaert, Michaël; Teeling, Emma C

    2009-07-01

    The UniPrime2 web server is a publicly available online resource which automatically designs large sets of universal primers when given a gene reference ID or Fasta sequence input by a user. UniPrime2 works by automatically retrieving and aligning homologous sequences from GenBank, identifying regions of conservation within the alignment, and generating suitable primers that can be used to amplify variable genomic regions. In essence, UniPrime2 is a suite of publicly available software packages (Blastn, T-Coffee, GramAlign, Primer3), which reduces the laborious process of primer design, by integrating these programs into a single software pipeline. Hence, UniPrime2 differs from previous primer design web services in that all steps are automated, linked, saved and phylogenetically delimited, only requiring a single user-defined gene reference ID or input sequence. We provide an overview of the web service and wet-laboratory validation of the primers generated. The system is freely accessible at: http://uniprime.batlab.eu. UniPrime2 is licenced under a Creative Commons Attribution Noncommercial-Share Alike 3.0 Licence.

  1. Expression and Purification of a Novel Computationally Designed Antigen for Simultaneously Detection of HTLV-1 and HBV Antibodies.

    PubMed

    Heydari Zarnagh, Hafez; Ravanshad, Mehrdad; Pourfatollah, Ali Akbar; Rasaee, Mohammad Javad

    2015-04-01

    Computational tools are reliable alternatives to laborious work in chimeric protein design. In this study, a chimeric antigen was designed using computational techniques for simultaneous detection of anti-HTLV-I and anti-HBV in infected sera. Databases were searched for amino acid sequences of HBV/HLV-I diagnostic antigens. The immunodominant fragments were selected based on propensity scales. The diagnostic antigen was designed using these fragments. Secondary and tertiary structures were predicted and the B-cell epitopes were mapped on the surface of built model. The synthetic DNA coding antigen was sub-cloned into pGS21a expression vector. SDS-PAGE analysis showed that glutathione fused antigen was highly expressed in E. coli BL21 (DE3) cells. The recombinant antigen was purified by nickel affinity chromatography. ELISA results showed that soluble antigen could specifically react with the HTLV-I and HBV infected sera. This specific antigen could be used as suitable agent for antibody-antigen based screening tests and can help clinicians in order to perform quick and precise screening of the HBV and HTLV-I infections.

  2. Scheduling-capable autonomic manager for policy-based IT change management system

    NASA Astrophysics Data System (ADS)

    AbdelSalam, Hady S.; Maly, Kurt; Mukkamala, Ravi; Zubair, Mohammad; Kaminsky, David

    2010-11-01

    Managing large IT environments is expensive and labour intensive. Maintaining and upgrading with minimal disruption and administrative support has always been a challenging task for system administrators. One challenge faced by IT administrators is arriving at schedules for applying one or more change requests to one of the system components. Most of the time, the impact analysis of the proposed changes is done by humans and is often laborious and error-prone. Although this methodology might be suitable to handle changes that are planned way ahead in time, it is completely inappropriate for changes that need to be done sooner. In addition, such manual handling does not scale well with the size of the IT infrastructure. In this article, the focus is on the problem of scheduling change requests in the presence of organisational policies governing the use of its resources. The authors propose two approaches for change management scheduling and present the implementation details of two prototypes that prove the feasibility of the proposed approaches. Their implementation is integrated with an autonomic manager which they had described in their earlier work.

  3. Building Cre Knockin Rat Lines Using CRISPR/Cas9.

    PubMed

    Ma, Yuanwu; Zhang, Lianfeng; Huang, Xingxu

    2017-01-01

    Conditional gene inactivation strategy helps researchers to study the gene functions that are critical in embryogenesis or in defined tissues of adulthood. The Cre/loxP system is widely used for conditional gene inactivation/activation in cells or organisms. Cre knockin animal lines are essential for gene expression or inactivation in a spatially and temporally restricted manner. However, to generate a Cre knockin line by traditional approach is laborious. Recently, the clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9) has been proven as a simple and efficient genome-editing tool. We have used CRISPR/Cas9 system to generate rat strains that carry Cre genes in different targeted gene loci by direct delivery of gRNAs/Cas9/donors into fertilized eggs. Here, we described a stepwise procedure for the generation of Cre knockin rat, including target site selection, RNA preparation, the construction of the template donor, pronuclear injection, and the genotyping of precise Cre insertion in F 0 rats. Taken together, the establishment of Cre knockin line can be achieved within 6 weeks.

  4. Engineering of a DNA Polymerase for Direct m6 A Sequencing.

    PubMed

    Aschenbrenner, Joos; Werner, Stephan; Marchand, Virginie; Adam, Martina; Motorin, Yuri; Helm, Mark; Marx, Andreas

    2018-01-08

    Methods for the detection of RNA modifications are of fundamental importance for advancing epitranscriptomics. N 6 -methyladenosine (m 6 A) is the most abundant RNA modification in mammalian mRNA and is involved in the regulation of gene expression. Current detection techniques are laborious and rely on antibody-based enrichment of m 6 A-containing RNA prior to sequencing, since m 6 A modifications are generally "erased" during reverse transcription (RT). To overcome the drawbacks associated with indirect detection, we aimed to generate novel DNA polymerase variants for direct m 6 A sequencing. Therefore, we developed a screen to evolve an RT-active KlenTaq DNA polymerase variant that sets a mark for N 6 -methylation. We identified a mutant that exhibits increased misincorporation opposite m 6 A compared to unmodified A. Application of the generated DNA polymerase in next-generation sequencing allowed the identification of m 6 A sites directly from the sequencing data of untreated RNA samples. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  5. Direct production of mouse disease models by embryo microinjection of TALENs and oligodeoxynucleotides

    PubMed Central

    Wefers, Benedikt; Meyer, Melanie; Ortiz, Oskar; Hrabé de Angelis, Martin; Hansen, Jens; Wurst, Wolfgang; Kühn, Ralf

    2013-01-01

    The study of genetic disease mechanisms relies mostly on targeted mouse mutants that are derived from engineered embryonic stem (ES) cells. Nevertheless, the establishment of mutant ES cells is laborious and time-consuming, restricting the study of the increasing number of human disease mutations discovered by high-throughput genomic analysis. Here, we present an advanced approach for the production of mouse disease models by microinjection of transcription activator-like effector nucleases (TALENs) and synthetic oligodeoxynucleotides into one-cell embryos. Within 2 d of embryo injection, we created and corrected chocolate missense mutations in the small GTPase RAB38; a regulator of intracellular vesicle trafficking and phenotypic model of Hermansky-Pudlak syndrome. Because ES cell cultures and targeting vectors are not required, this technology enables instant germline modifications, making heterozygous mutants available within 18 wk. The key features of direct mutagenesis by TALENs and oligodeoxynucleotides, minimal effort and high speed, catalyze the generation of future in vivo models for the study of human disease mechanisms and interventions. PMID:23426636

  6. DBS Programming: An Evolving Approach for Patients with Parkinson's Disease.

    PubMed

    Wagle Shukla, Aparna; Zeilman, Pam; Fernandez, Hubert; Bajwa, Jawad A; Mehanna, Raja

    2017-01-01

    Deep brain stimulation (DBS) surgery is a well-established therapy for control of motor symptoms in Parkinson's disease. Despite an appropriate targeting and an accurate placement of DBS lead, a thorough and efficient programming is critical for a successful clinical outcome. DBS programming is a time consuming and laborious manual process. The current approach involves use of general guidelines involving determination of the lead type, electrode configuration, impedance check, and battery check. However there are no validated and well-established programming protocols. In this review, we will discuss the current practice and the recent advances in DBS programming including the use of interleaving, fractionated current, directional steering of current, and the use of novel DBS pulses. These technological improvements are focused on achieving a more efficient control of clinical symptoms with the least possible side effects. Other promising advances include the introduction of computer guided programming which will likely impact the efficiency of programming for the clinicians and the possibility of remote Internet based programming which will improve access to DBS care for the patients.

  7. Text Classification for Organizational Researchers

    PubMed Central

    Kobayashi, Vladimer B.; Mol, Stefan T.; Berkers, Hannah A.; Kismihók, Gábor; Den Hartog, Deanne N.

    2017-01-01

    Organizations are increasingly interested in classifying texts or parts thereof into categories, as this enables more effective use of their information. Manual procedures for text classification work well for up to a few hundred documents. However, when the number of documents is larger, manual procedures become laborious, time-consuming, and potentially unreliable. Techniques from text mining facilitate the automatic assignment of text strings to categories, making classification expedient, fast, and reliable, which creates potential for its application in organizational research. The purpose of this article is to familiarize organizational researchers with text mining techniques from machine learning and statistics. We describe the text classification process in several roughly sequential steps, namely training data preparation, preprocessing, transformation, application of classification techniques, and validation, and provide concrete recommendations at each step. To help researchers develop their own text classifiers, the R code associated with each step is presented in a tutorial. The tutorial draws from our own work on job vacancy mining. We end the article by discussing how researchers can validate a text classification model and the associated output. PMID:29881249

  8. Direct screening for chromatin status on DNA barcodes in yeast delineates the regulome of H3K79 methylation by Dot1

    PubMed Central

    Vlaming, Hanneke; Molenaar, Thom M; van Welsem, Tibor; Poramba-Liyanage, Deepani W; Smith, Desiree E; Velds, Arno; Hoekman, Liesbeth; Korthout, Tessy; Hendriks, Sjoerd; Maarten Altelaar, AF; van Leeuwen, Fred

    2016-01-01

    Given the frequent misregulation of chromatin in cancer, it is important to understand the cellular mechanisms that regulate chromatin structure. However, systematic screening for epigenetic regulators is challenging and often relies on laborious assays or indirect reporter read-outs. Here we describe a strategy, Epi-ID, to directly assess chromatin status in thousands of mutants. In Epi-ID, chromatin status on DNA barcodes is interrogated by chromatin immunoprecipitation followed by deep sequencing, allowing for quantitative comparison of many mutants in parallel. Screening of a barcoded yeast knock-out collection for regulators of histone H3K79 methylation by Dot1 identified all known regulators as well as novel players and processes. These include histone deposition, homologous recombination, and adenosine kinase, which influences the methionine cycle. Gcn5, the acetyltransferase within the SAGA complex, was found to regulate histone methylation and H2B ubiquitination. The concept of Epi-ID is widely applicable and can be readily applied to other chromatin features. DOI: http://dx.doi.org/10.7554/eLife.18919.001 PMID:27922451

  9. FAST: a framework for simulation and analysis of large-scale protein-silicon biosensor circuits.

    PubMed

    Gu, Ming; Chakrabartty, Shantanu

    2013-08-01

    This paper presents a computer aided design (CAD) framework for verification and reliability analysis of protein-silicon hybrid circuits used in biosensors. It is envisioned that similar to integrated circuit (IC) CAD design tools, the proposed framework will be useful for system level optimization of biosensors and for discovery of new sensing modalities without resorting to laborious fabrication and experimental procedures. The framework referred to as FAST analyzes protein-based circuits by solving inverse problems involving stochastic functional elements that admit non-linear relationships between different circuit variables. In this regard, FAST uses a factor-graph netlist as a user interface and solving the inverse problem entails passing messages/signals between the internal nodes of the netlist. Stochastic analysis techniques like density evolution are used to understand the dynamics of the circuit and estimate the reliability of the solution. As an example, we present a complete design flow using FAST for synthesis, analysis and verification of our previously reported conductometric immunoassay that uses antibody-based circuits to implement forward error-correction (FEC).

  10. Freestanding films of crosslinked gold nanoparticles prepared via layer-by-layer spin-coating.

    PubMed

    Schlicke, Hendrik; Schröder, Jan H; Trebbin, Martin; Petrov, Alexey; Ijeh, Michael; Weller, Horst; Vossmeyer, Tobias

    2011-07-29

    A new, extremely efficient method for the fabrication of films comprised of gold nanoparticles (GNPs) crosslinked by organic dithiols is presented in this paper. The method is based on layer-by-layer spin-coating of both components, GNPs and crosslinker, and enables the deposition of films several tens of nanometers in thickness within a few minutes. X-ray diffraction and conductance measurements reveal the proper adjustment concentration of the crosslinker solution of the critical is in order to prevent the destabilization and coalescence of particles. UV/vis spectroscopy, atomic force microscopy, and conductivity measurements indicate that films prepared via layer-by-layer spin-coating are of comparable quality to coatings prepared via laborious layer-by-layer self-assembly using immersion baths. Because spin-coated films are not bound chemically to the substrate, they can be lifted-off by alkaline underetching and transferred onto 3d-electrodes to produce electrically addressable, freely suspended films. Comparative measurements of the sheet resistances indicate that the transfer process does not compromise the film quality.

  11. Freestanding films of crosslinked gold nanoparticles prepared via layer-by-layer spin-coating

    NASA Astrophysics Data System (ADS)

    Schlicke, Hendrik; Schröder, Jan H.; Trebbin, Martin; Petrov, Alexey; Ijeh, Michael; Weller, Horst; Vossmeyer, Tobias

    2011-07-01

    A new, extremely efficient method for the fabrication of films comprised of gold nanoparticles (GNPs) crosslinked by organic dithiols is presented in this paper. The method is based on layer-by-layer spin-coating of both components, GNPs and crosslinker, and enables the deposition of films several tens of nanometers in thickness within a few minutes. X-ray diffraction and conductance measurements reveal the proper adjustment concentration of the crosslinker solution of the critical is in order to prevent the destabilization and coalescence of particles. UV/vis spectroscopy, atomic force microscopy, and conductivity measurements indicate that films prepared via layer-by-layer spin-coating are of comparable quality to coatings prepared via laborious layer-by-layer self-assembly using immersion baths. Because spin-coated films are not bound chemically to the substrate, they can be lifted-off by alkaline underetching and transferred onto 3d-electrodes to produce electrically addressable, freely suspended films. Comparative measurements of the sheet resistances indicate that the transfer process does not compromise the film quality.

  12. Comparison of peroxidase-labeled DNA probes with radioactive RNA probes for detection of human papillomaviruses by in situ hybridization in paraffin sections.

    PubMed

    Park, J S; Kurman, R J; Kessis, T D; Shah, K V

    1991-01-01

    A study comparing in situ hybridization using nonradioactive DNA probes directly conjugated with horseradish peroxidase (HRP), and 35S-labeled antisense RNA probes for human papillomavirus (HPV) types 6/11, 16, and 18 was performed on formalin-fixed, paraffin-embedded tissue from 34 lesions of the cervix and vulva. These lesions included exophytic condylomas and intraepithelial and invasive neoplasms. HPV 6/11 was detected in two of four condylomata acuminata by both in situ techniques. HPV 16 was detected in 13 of 30 cases of intraepithelial and invasive neoplasms by both methods. Discordance between the two methods occurred in two instances. The radiolabeled probe but not the HRP probe detected HPV 16 in one case of cervical intraepithelial neoplasia (CIN 3), whereas the converse occurred in one case of vulvar intraepithelial neoplasia (VIN 3). HPV 18 was not detected in any of the specimens by either method. This study demonstrates that nonradioactive HRP-labeled probes for the detection of specific HPV types are as sensitive as the more laborious and potentially hazardous radioactive probes.

  13. An optimized chemical synthesis of human relaxin-2.

    PubMed

    Barlos, Kostas K; Gatos, Dimitrios; Vasileiou, Zoe; Barlos, Kleomenis

    2010-04-01

    Human gene 2 relaxin (RLX) is a member of the insulin superfamily and is a multi-functional factor playing a vital role in pregnancy, aging, fibrosis, cardioprotection, vasodilation, inflammation, and angiogenesis. RLX is currently applied in clinical trials to cure among others acute heart failure, fibrosis, and preeclampsia. The synthesis of RLX by chemical methods is difficult because of the insolubility of its B-chain and the required laborious and low yielding site-directed combination of its A (RLXA) and B (RLXB) chains. We report here that oxidation of the Met(25) residue of RLXB improves its solubility, allowing its effective solid-phase synthesis and application in random interchain combination reactions with RLXA. Linear Met(O)(25)-RLX B-chain (RLXBO) reacts with a mixture of isomers of bicyclic A-chain (bcRLXA) giving exclusively the native interchain combination. Applying this method Met(O)(25)-RLX (RLXO) was obtained in 62% yield and was easily converted to RLX in 78% yield, by reduction with ammonium iodide. Copyright (c) 2010 European Peptide Society and John Wiley & Sons, Ltd.

  14. CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API

    PubMed Central

    Ono, Keiichiro; Muetze, Tanja; Kolishovski, Georgi; Shannon, Paul; Demchak, Barry

    2015-01-01

    As bioinformatic workflows become increasingly complex and involve multiple specialized tools, so does the difficulty of reliably reproducing those workflows. Cytoscape is a critical workflow component for executing network visualization, analysis, and publishing tasks, but it can be operated only manually via a point-and-click user interface. Consequently, Cytoscape-oriented tasks are laborious and often error prone, especially with multistep protocols involving many networks. In this paper, we present the new cyREST Cytoscape app and accompanying harmonization libraries. Together, they improve workflow reproducibility and researcher productivity by enabling popular languages (e.g., Python and R, JavaScript, and C#) and tools (e.g., IPython/Jupyter Notebook and RStudio) to directly define and query networks, and perform network analysis, layouts and renderings. We describe cyREST’s API and overall construction, and present Python- and R-based examples that illustrate how Cytoscape can be integrated into large scale data analysis pipelines. cyREST is available in the Cytoscape app store (http://apps.cytoscape.org) where it has been downloaded over 1900 times since its release in late 2014. PMID:26672762

  15. DBS Programming: An Evolving Approach for Patients with Parkinson's Disease

    PubMed Central

    Zeilman, Pam; Fernandez, Hubert; Bajwa, Jawad A.

    2017-01-01

    Deep brain stimulation (DBS) surgery is a well-established therapy for control of motor symptoms in Parkinson's disease. Despite an appropriate targeting and an accurate placement of DBS lead, a thorough and efficient programming is critical for a successful clinical outcome. DBS programming is a time consuming and laborious manual process. The current approach involves use of general guidelines involving determination of the lead type, electrode configuration, impedance check, and battery check. However there are no validated and well-established programming protocols. In this review, we will discuss the current practice and the recent advances in DBS programming including the use of interleaving, fractionated current, directional steering of current, and the use of novel DBS pulses. These technological improvements are focused on achieving a more efficient control of clinical symptoms with the least possible side effects. Other promising advances include the introduction of computer guided programming which will likely impact the efficiency of programming for the clinicians and the possibility of remote Internet based programming which will improve access to DBS care for the patients. PMID:29147598

  16. PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts.

    PubMed

    Goetz, Thomas; von der Lieth, Claus-Wilhelm

    2005-07-01

    Since it is becoming increasingly laborious to manually extract useful information embedded in the ever-growing volumes of literature, automated intelligent text analysis tools are becoming more and more essential to assist in this task. PubFinder (www.glycosciences.de/tools/PubFinder) is a publicly available web tool designed to improve the retrieval rate of scientific abstracts relevant for a specific scientific topic. Only the selection of a representative set of abstracts is required, which are central for a scientific topic. No special knowledge concerning the query-syntax is necessary. Based on the selected abstracts, a list of discriminating words is automatically calculated, which is subsequently used for scoring all defined PubMed abstracts for their probability of belonging to the defined scientific topic. This results in a hit-list of references in the descending order of their likelihood score. The algorithms and procedures implemented in PubFinder facilitate the perpetual task for every scientist of staying up-to-date with current publications dealing with a specific subject in biomedicine.

  17. Prick test: evolution towards automated reading.

    PubMed

    Justo, X; Díaz, I; Gil, J J; Gastaminza, G

    2016-08-01

    The prick test is one of the most common medical methods for diagnosing allergies, and it has been carried out in a similar and laborious manner over many decades. In an attempt to standardize the reading of the test, many researchers have tried to automate the process of measuring the allergic reactions found by developing systems and algorithms based on multiple technologies. This work reviews the techniques for automatic wheal measurement with the aim of pointing out their advantages and disadvantages and the progress in the field. Furthermore, it provides a classification scheme for the different technologies applied. The works discussed herein provide evidence that significant challenges still exist for the development of an automatic wheal measurement system that not only helps allergists in their medical practice but also allows for the standardization of the reading and data exchange. As such, the aim of the work was to serve as guideline for the development of a proper and feasible system. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  18. Comparison of peroxidase-labeled DNA probes with radioactive RNA probes for detection of human papillomaviruses by in situ hybridization in paraffin sections

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Park, J.S.; Kurman, R.J.; Kessis, T.D.

    1991-01-01

    A study comparing in situ hybridization using nonradioactive DNA probes directly conjugated with horseradish peroxidase (HRP), and {sup 35}S-labeled antisense RNA probes for human papillomavirus (HPV) types 6/11, 16, and 18 was performed on formalin-fixed, paraffin-embedded tissue from 34 lesions of the cervix and vulva. These lesions included exophytic condylomas and intraepithelial and invasive neoplasms. HPV 6/11 was detected in two of four condylomata acuminata by both in situ techniques. HPV 16 was detected in 13 of 30 cases of intraepithelial and invasive neoplasms by both methods. Discordance between the two methods occurred in two instances. The radiolabeled probe butmore » not the HRP probe detected HPV 16 in one case of cervical intraepithelial neoplasia (CIN 3), whereas the converse occurred in one case of vulvar intraepithelial neoplasia (VIN 3). HPV 18 was not detected in any of the specimens by either method. This study demonstrates that nonradioactive HRP-labeled probes for the detection of specific HPV types are as sensitive as the more laborious and potentially hazardous radioactive probes.« less

  19. Micro-beam Laue alignment of multi-reflection Bragg coherent diffraction imaging measurements.

    PubMed

    Hofmann, Felix; Phillips, Nicholas W; Harder, Ross J; Liu, Wenjun; Clark, Jesse N; Robinson, Ian K; Abbey, Brian

    2017-09-01

    Multi-reflection Bragg coherent diffraction imaging has the potential to allow three-dimensional (3D) resolved measurements of the full lattice strain tensor in specific micro-crystals. Until now such measurements were hampered by the need for laborious, time-intensive alignment procedures. Here a different approach is demonstrated, using micro-beam Laue X-ray diffraction to first determine the lattice orientation of the micro-crystal. This information is then used to rapidly align coherent diffraction measurements of three or more reflections from the crystal. Based on these, 3D strain and stress fields in the crystal are successfully determined. This approach is demonstrated on a focused ion beam milled micro-crystal from which six reflections could be measured. Since information from more than three independent reflections is available, the reliability of the phases retrieved from the coherent diffraction data can be assessed. Our results show that rapid, reliable 3D coherent diffraction measurements of the full lattice strain tensor in specific micro-crystals are now feasible and can be successfully carried out even in heavily distorted samples.

  20. From Organized High-Throughput Data to Phenomenological Theory using Machine Learning: The Example of Dielectric Breakdown

    DOE PAGES

    Kim, Chiho; Pilania, Ghanshyam; Ramprasad, Ramamurthy

    2016-02-02

    Understanding the behavior (and failure) of dielectric insulators experiencing extreme electric fields is critical to the operation of present and emerging electrical and electronic devices. Despite its importance, the development of a predictive theory of dielectric breakdown has remained a challenge, owing to the complex multiscale nature of this process. We focus on the intrinsic dielectric breakdown field of insulators—the theoretical limit of breakdown determined purely by the chemistry of the material, i.e., the elements the material is composed of, the atomic-level structure, and the bonding. Starting from a benchmark dataset (generated from laborious first principles computations) of the intrinsicmore » dielectric breakdown field of a variety of model insulators, simple predictive phenomenological models of dielectric breakdown are distilled using advanced statistical or machine learning schemes, revealing key correlations and analytical relationships between the breakdown field and easily accessible material properties. Lastly, the models are shown to be general, and can hence guide the screening and systematic identification of high electric field tolerant materials.« less

  1. A distributed cloud-based cyberinfrastructure framework for integrated bridge monitoring

    NASA Astrophysics Data System (ADS)

    Jeong, Seongwoon; Hou, Rui; Lynch, Jerome P.; Sohn, Hoon; Law, Kincho H.

    2017-04-01

    This paper describes a cloud-based cyberinfrastructure framework for the management of the diverse data involved in bridge monitoring. Bridge monitoring involves various hardware systems, software tools and laborious activities that include, for examples, a structural health monitoring (SHM), sensor network, engineering analysis programs and visual inspection. Very often, these monitoring systems, tools and activities are not coordinated, and the collected information are not shared. A well-designed integrated data management framework can support the effective use of the data and, thereby, enhance bridge management and maintenance operations. The cloud-based cyberinfrastructure framework presented herein is designed to manage not only sensor measurement data acquired from the SHM system, but also other relevant information, such as bridge engineering model and traffic videos, in an integrated manner. For the scalability and flexibility, cloud computing services and distributed database systems are employed. The information stored can be accessed through standard web interfaces. For demonstration, the cyberinfrastructure system is implemented for the monitoring of the bridges located along the I-275 Corridor in the state of Michigan.

  2. Rapid and non-destructive determination of rancidity levels in butter cookies by multi-spectral imaging.

    PubMed

    Xia, Qing; Liu, Changhong; Liu, Jinxia; Pan, Wenjuan; Lu, Xuzhong; Yang, Jianbo; Chen, Wei; Zheng, Lei

    2016-03-30

    Rancidity is an important attribute for quality assessment of butter cookies, while traditional methods for rancidity measurement are usually laborious, destructive and prone to operational error. In the present paper, the potential of applying multi-spectral imaging (MSI) technology with 19 wavelengths in the range of 405-970 nm to evaluate the rancidity in butter cookies was investigated. Moisture content, acid value and peroxide value were determined by traditional methods and then related with the spectral information by partial least squares regression (PLSR) and back-propagation artificial neural network (BP-ANN). The optimal models for predicting moisture content, acid value and peroxide value were obtained by PLSR. The correlation coefficient (r) obtained by PLSR models revealed that MSI had a perfect ability to predict moisture content (r = 0.909), acid value (r = 0.944) and peroxide value (r = 0.971). The study demonstrated that the rancidity level of butter cookies can be continuously monitored and evaluated in real-time by the multi-spectral imaging, which is of great significance for developing online food safety monitoring solutions. © 2015 Society of Chemical Industry.

  3. Data Recovery Effort of Nimbus Era Observations by the NASA GES DISC

    NASA Technical Reports Server (NTRS)

    Johnson, James; Esfandiari, Ed; Zamkoff, Emily; Gerasimov, Irina; Al-Jazrawi, Atheer; Alcott, Gary

    2017-01-01

    NASA launched seven Nimbus meteorological satellites in the 1960s and 70s. These satellites carried instruments for making observations of the Earth in the visible, infrared, ultraviolet, and microwave wavelengths. The original data archive consisted of a combination of magnetic tapes and various film media. As these media are well past their expected end of life, the valuable data they contain are now being migrated to the GES DISC modern online archive. The process involves recovering the digital data files from the tapes as well as scanning images of the data from film strips. This presentation will address the status and challenges of recovering the Nimbus data. The old data products were written on now obsolete hardware systems and outdated file formats. They lack any metadata standards and each product is often written in its own proprietary file structure. This requires creating metadata by reading the contents of the old data files. The job is tedious and laborious, as documentation may be incomplete, data files and tapes are sometimes corrupted, or were improperly copied at the time they were created.

  4. [Problems and ethical challenges in public health communication].

    PubMed

    Loss, J; Nagel, E

    2009-05-01

    Health communication, e.g., mass media campaigns, patient information leaflets or websites, plays an important role in public health. It contributes to citizen empowerment and helps them make informed decisions in health matters. However, public health communication can lead to adverse effects on both individual and societal level, e.g., by inaccurate or partial information, discriminatory messages, scandalizing coverage or inadequate tailoring to relevant target groups. It seems important to suggest ethical criteria for health information, e.g., (1) accuracy, completeness and balance, (2) transparency, (3) participation of the target group, (4) respect for human dignity, (5) social justice and equity, (6) appropriateness. Thoughtfulness is important in order not to stigmatize population subgroups. In addition, it is laborious to comprehensively and correctly present benefits and risks of a certain health behavior. Marketing principles guide how to 'sell' a certain health behavior, but health campaigns should not manipulate target persons for the sake of a population health aim. It remains unclear, however, how the different providers of health information can be held ethically responsible.

  5. Naming and Necessity: Sherborn’s Context in the 19th Century

    PubMed Central

    McOuat, Gordon

    2016-01-01

    Abstract By the late 19th Century, storms plaguing early Victorian systematics and nomenclature seemed to have abated. Vociferous disputes over radical renaming, the world-shaking clash of all-encompassing procrustean systems, struggles over centres of authority, and the issues of language and meaning had now been settled by the institution of a stable imperial museum and its catalogues, a set of rules for the naming of zoological objects, and a new professional class of zoologists. Yet, for all that tranquillity, the disputes simmered below the surface, re-emerging as bitter struggles over synonyms, trinomials, the subspecies category, the looming issues of the philosophy of scientific language, and the aggressive new American style of field biology – all pressed in upon the received practice of naming and classifying organisms and the threat of anarchy. In the midst rose an index. This paper will explore the context of CD Sherborn’s Index Animalium and those looming problems and issues which a laborious and comprehensive “index of nature” was meant to solve. PMID:26877652

  6. History of surface weather observations in the United States

    NASA Astrophysics Data System (ADS)

    Fiebrich, Christopher A.

    2009-04-01

    In this paper, the history of surface weather observations in the United States is reviewed. Local weather observations were first documented in the 17th Century along the East Coast. For many years, the progression of a weather observation from an initial reading to dissemination remained a slow and laborious process. The number of observers remained small and unorganized until agencies including the Surgeon General, Army, and General Land Office began to request regular observations at satellite locations in the 1800s. The Smithsonian was responsible for first organizing a large "network" of volunteer weather observers across the nation. These observers became the foundation for today's Cooperative Observer network. As applications of weather data continued to grow and users required the data with an ever-decreasing latency, automated weather networks saw rapid growth in the later part of the 20th century. Today, the number of weather observations across the U.S. totals in the tens of thousands due largely to privately-owned weather networks and amateur weather observers who submit observations over the internet.

  7. Efficient production of a folded and functional, highly disulfide-bonded beta-helix antifreeze protein in bacteria.

    PubMed

    Bar, Maya; Bar-Ziv, Roy; Scherf, Tali; Fass, Deborah

    2006-08-01

    The Tenebrio molitor thermal hysteresis protein has a cysteine content of 19%. This 84-residue protein folds as a compact beta-helix, with eight disulfide bonds buried in its core. Exposed on one face of the protein is an array of threonine residues, which constitutes the ice-binding face. Previous protocols for expression of this protein in recombinant expression systems resulted in inclusion bodies or soluble but largely inactive material. A long and laborious refolding procedure was performed to increase the fraction of active protein and isolate it from inactive fractions. We present a new protocol for production of fully folded and active T. molitor thermal hysteresis protein in bacteria, without the need for in vitro refolding. The protein coding sequence was fused to those of various carrier proteins and expressed at low temperature in a bacterial strain specially suited for production of disulfide-bonded proteins. The product, after a simple and robust purification procedure, was analyzed spectroscopically and functionally and was found to compare favorably to previously published data on refolded protein and protein obtained from its native source.

  8. [Techniques for rapid production of monoclonal antibodies for use with antibody technology].

    PubMed

    Kamada, Haruhiko

    2012-01-01

    A monoclonal antibody (Mab), due to its specific binding ability to a target protein, can potentially be one of the most useful tools for the functional analysis of proteins in recent proteomics-based research. However, the production of Mab is a very time-consuming and laborious process (i.e., preparation of recombinant antigens, immunization of animals, preparation of hybridomas), making it the rate-limiting step in using Mabs in high-throughput proteomics research, which heavily relies on comprehensive and rapid methods. Therefore, there is a great demand for new methods to efficiently generate Mabs against a group of proteins identified by proteome analysis. Here, we describe a useful method called "Antibody proteomic technique" for the rapid generations of Mabs to pharmaceutical target, which were identified by proteomic analyses of disease samples (ex. tumor tissue, etc.). We also introduce another method to find profitable targets on vasculature, which is called "Vascular proteomic technique". Our results suggest that this method for the rapid generation of Mabs to proteins may be very useful in proteomics-based research as well as in clinical applications.

  9. Non-contact assessment of COD and turbidity concentrations in water using diffuse reflectance UV-Vis spectroscopy.

    PubMed

    Agustsson, Jon; Akermann, Oliver; Barry, D Andrew; Rossi, Luca

    2014-08-01

    Water contamination is an important environmental concern underlining the need for reliable real-time information on contaminant concentrations in natural waters. Here, a new non-contact UV-Vis spectroscopic approach for monitoring contaminants in water, and especially wastewater, is proposed. Diffuse reflectance UV-Vis spectroscopy was applied to measure simultaneously the chemical oxygen demand (COD) and turbidity (TUR) concentrations in water. The measurements were carried out in the wavelength range from 200-1100 nm. The measured spectra were analysed using partial-least-squares (PLS) regression. The correlation coefficient between the measured and the reference concentrations of COD and TUR in the water samples were R(2) = 0.85 and 0.96, respectively. These results highlight the potential of non-contact UV-Vis spectroscopy for the assessment of water contamination. A system built on the concept would be able to monitor wastewater pollution continuously, without the need for laborious sample collection and subsequent laboratory analysis. Furthermore, since no parts of the system are in contact with the wastewater stream the need for maintenance is minimised.

  10. Semi-automatic recognition of marine debris on beaches

    NASA Astrophysics Data System (ADS)

    Ge, Zhenpeng; Shi, Huahong; Mei, Xuefei; Dai, Zhijun; Li, Daoji

    2016-05-01

    An increasing amount of anthropogenic marine debris is pervading the earth’s environmental systems, resulting in an enormous threat to living organisms. Additionally, the large amount of marine debris around the world has been investigated mostly through tedious manual methods. Therefore, we propose the use of a new technique, light detection and ranging (LIDAR), for the semi-automatic recognition of marine debris on a beach because of its substantially more efficient role in comparison with other more laborious methods. Our results revealed that LIDAR should be used for the classification of marine debris into plastic, paper, cloth and metal. Additionally, we reconstructed a 3-dimensional model of different types of debris on a beach with a high validity of debris revivification using LIDAR-based individual separation. These findings demonstrate that the availability of this new technique enables detailed observations to be made of debris on a large beach that was previously not possible. It is strongly suggested that LIDAR could be implemented as an appropriate monitoring tool for marine debris by global researchers and governments.

  11. Micro-beam Laue Alignment of Multi-Reflection Bragg Coherent Diffraction Imaging Measurements

    PubMed Central

    Hofmann, Felix; Phillips, Nicholas W.; Harder, Ross J.; Liu, Wenjun; Clark, Jesse N.; Robinson, Ian K.; Abbey, Brian

    2017-01-01

    Multi-reflection Bragg coherent diffraction imaging has the potential to allow 3D resolved measurements of the full lattice strain tensor in specific micro-crystals. Until now such measurements were hampered by the need for laborious, time-intensive alignment procedures. Here we demonstrate a different approach, using micro-beam Laue X-ray diffraction to first determine the lattice orientation of the micro-crystal. This information is then used to rapidly align coherent diffraction measurements of three or more reflections from the crystal. Based on these, 3D strain and stress fields in the crystal are successfully determined. This approach is demonstrated on a focussed ion beam milled micro-crystal from which six reflections could be measured. Since information from more than three independent reflections is available, the reliability of the phases retrieved from the coherent diffraction data can be assessed. Our results show that rapid, reliable 3D coherent diffraction measurements of the full lattice strain tensor in specific micro-crystals are now feasible and can be successfully carried out even in heavily distorted samples. PMID:28862628

  12. SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.

    PubMed

    Boniecki, Michal J; Lach, Grzegorz; Dawson, Wayne K; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M; Bujnicki, Janusz M

    2016-04-20

    RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Microfluidic size separation of cells and particles using a swinging bucket centrifuge.

    PubMed

    Yeo, Joo Chuan; Wang, Zhiping; Lim, Chwee Teck

    2015-09-01

    Biomolecular separation is crucial for downstream analysis. Separation technique mainly relies on centrifugal sedimentation. However, minuscule sample volume separation and extraction is difficult with conventional centrifuge. Furthermore, conventional centrifuge requires density gradient centrifugation which is laborious and time-consuming. To overcome this challenge, we present a novel size-selective bioparticles separation microfluidic chip on a swinging bucket minifuge. Size separation is achieved using passive pressure driven centrifugal fluid flows coupled with centrifugal force acting on the particles within the microfluidic chip. By adopting centrifugal microfluidics on a swinging bucket rotor, we achieved over 95% efficiency in separating mixed 20 μm and 2 μm colloidal dispersions from its liquid medium. Furthermore, by manipulating the hydrodynamic resistance, we performed size separation of mixed microbeads, achieving size efficiency of up to 90%. To further validate our device utility, we loaded spiked whole blood with MCF-7 cells into our microfluidic device and subjected it to centrifugal force for a mere duration of 10 s, thereby achieving a separation efficiency of over 75%. Overall, our centrifugal microfluidic device enables extremely rapid and label-free enrichment of different sized cells and particles with high efficiency.

  14. Inverse PCR-based method for isolating novel SINEs from genome.

    PubMed

    Han, Yawei; Chen, Liping; Guan, Lihong; He, Shunping

    2014-04-01

    Short interspersed elements (SINEs) are moderately repetitive DNA sequences in eukaryotic genomes. Although eukaryotic genomes contain numerous SINEs copy, it is very difficult and laborious to isolate and identify them by the reported methods. In this study, the inverse PCR was successfully applied to isolate SINEs from Opsariichthys bidens genome in Eastern Asian Cyprinid. A group of SINEs derived from tRNA(Ala) molecular had been identified, which were named Opsar according to Opsariichthys. SINEs characteristics were exhibited in Opsar, which contained a tRNA(Ala)-derived region at the 5' end, a tRNA-unrelated region, and AT-rich region at the 3' end. The tRNA-derived region of Opsar shared 76 % sequence similarity with tRNA(Ala) gene. This result indicated that Opsar could derive from the inactive or pseudogene of tRNA(Ala). The reliability of method was tested by obtaining C-SINE, Ct-SINE, and M-SINEs from Ctenopharyngodon idellus, Megalobrama amblycephala, and Cyprinus carpio genomes. This method is simpler than the previously reported, which successfully omitted many steps, such as preparation of probes, construction of genomic libraries, and hybridization.

  15. Comparison of surrogate indices for insulin sensitivity with parameters of the intravenous glucose tolerance test in early lactation dairy cattle.

    PubMed

    Alves-Nores, V; Castillo, C; Hernandez, J; Abuelo, A

    2017-10-01

    The aim of this study was to investigate the correlation between different surrogate indices and parameters of the intravenous glucose tolerance test (IVGTT) in dairy cows at the start of their lactation. Ten dairy cows underwent IVGTT on Days 3 to 7 after calving. Areas under the curve during the 90 min after infusion, peak and nadir concentrations, elimination rates, and times to reach half-maximal and basal concentrations for glucose, insulin, nonesterified fatty acids, and β-hydroxybutyrate were calculated. Surrogate indices were computed using the average of the IVGTT basal samples, and their correlation with the IVGTT parameters studied through the Spearman's rank test. No statistically significant or strong correlation coefficients (P > 0.05; |ρ| < 0.50) were observed between the insulin sensitivity measures derived from the IVGTT and any of the surrogate indices. Therefore, these results support that the assessment of insulin sensitivity in early lactation cattle cannot rely on the calculation of surrogate indices in just a blood sample, and the more laborious tests (ie, hyperinsulinemic euglycemic clamp test or IVGTT) should be employed to predict the sensitivity of the peripheral tissues to insulin accurately. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Long-term microfluidic glucose and lactate monitoring in hepatic cell culture

    PubMed Central

    Prill, Sebastian; Jaeger, Magnus S.; Duschl, Claus

    2014-01-01

    Monitoring cellular bioenergetic pathways provides the basis for a detailed understanding of the physiological state of a cell culture. Therefore, it is widely used as a tool amongst others in the field of in vitro toxicology. The resulting metabolic information allows for performing in vitro toxicology assays for assessing drug-induced toxicity. In this study, we demonstrate the value of a microsystem for the fully automated detection of drug-induced changes in cellular viability by continuous monitoring of the metabolic activity over several days. To this end, glucose consumption and lactate secretion of a hepatic tumor cell line were continuously measured using microfluidically addressed electrochemical sensors. Adapting enzyme-based electrochemical flat-plate sensors, originally designed for human whole-blood samples, to their use with cell culture medium supersedes the common manual and laborious colorimetric assays and off-line operated external measurement systems. The cells were exposed to different concentrations of the mitochondrial inhibitor rotenone and the cellular response was analyzed by detecting changes in the rates of the glucose and lactate metabolism. Thus, the system provides real-time information on drug-induced liver injury in vitro. PMID:24926387

  17. Exosome separation using microfluidic systems: size-based, immunoaffinity-based and dynamic methodologies.

    PubMed

    Yang, Fang; Liao, Xiangzhi; Tian, Yuan; Li, Guiying

    2017-04-01

    Exosomes, nanovesicles secreted by most types of cells, exist in virtually all bodily fluids. Their rich nucleic acid and protein content make them potentially valuable biomarkers for noninvasive molecular diagnostics. They also show promise, after further development, to serve as a drug delivery system. Unfortunately, existing exosome separation technologies, such as ultracentrifugation and methods incorporating magnetic beads, are time-consuming, laborious and separate only exosomes of low purity. Thus, a more effective separation method is highly desirable. Microfluidic platforms are ideal tools for exosome separation, since they enable fast, cost-efficient, portable and precise processing of nanoparticles and small volumes of liquid samples. Recently, several microfluidic-based exosome separation technologies have been studied. In this article, the advantages of the most recent technologies, as well as their limitations, challenges and potential uses in novel microfluidic exosome separation and collection applications is reviewed. This review outlines the uses of new powerful microfluidic exosome detection tools for biologists and clinicians, as well as exosome separation tools for microfluidic engineers. Current challenges of exosome separation methodologies are also described, in order to highlight areas for future research and development. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Protein and genome evolution in Mammalian cells for biotechnology applications.

    PubMed

    Majors, Brian S; Chiang, Gisela G; Betenbaugh, Michael J

    2009-06-01

    Mutation and selection are the essential steps of evolution. Researchers have long used in vitro mutagenesis, expression, and selection techniques in laboratory bacteria and yeast cultures to evolve proteins with new properties, termed directed evolution. Unfortunately, the nature of mammalian cells makes applying these mutagenesis and whole-organism evolution techniques to mammalian protein expression systems laborious and time consuming. Mammalian evolution systems would be useful to test unique mammalian cell proteins and protein characteristics, such as complex glycosylation. Protein evolution in mammalian cells would allow for generation of novel diagnostic tools and designer polypeptides that can only be tested in a mammalian expression system. Recent advances have shown that mammalian cells of the immune system can be utilized to evolve transgenes during their natural mutagenesis processes, thus creating proteins with unique properties, such as fluorescence. On a more global level, researchers have shown that mutation systems that affect the entire genome of a mammalian cell can give rise to cells with unique phenotypes suitable for commercial processes. This review examines the advances in mammalian cell and protein evolution and the application of this work toward advances in commercial mammalian cell biotechnology.

  19. miRToolsGallery: a tag-based and rankable microRNA bioinformatics resources database portal

    PubMed Central

    Chen, Liang; Heikkinen, Liisa; Wang, ChangLiang; Yang, Yang; Knott, K Emily

    2018-01-01

    Abstract Hundreds of bioinformatics tools have been developed for MicroRNA (miRNA) investigations including those used for identification, target prediction, structure and expression profile analysis. However, finding the correct tool for a specific application requires the tedious and laborious process of locating, downloading, testing and validating the appropriate tool from a group of nearly a thousand. In order to facilitate this process, we developed a novel database portal named miRToolsGallery. We constructed the portal by manually curating > 950 miRNA analysis tools and resources. In the portal, a query to locate the appropriate tool is expedited by being searchable, filterable and rankable. The ranking feature is vital to quickly identify and prioritize the more useful from the obscure tools. Tools are ranked via different criteria including the PageRank algorithm, date of publication, number of citations, average of votes and number of publications. miRToolsGallery provides links and data for the comprehensive collection of currently available miRNA tools with a ranking function which can be adjusted using different criteria according to specific requirements. Database URL: http://www.mirtoolsgallery.org PMID:29688355

  20. gyrB as a phylogenetic discriminator for members of the Bacillus anthracis-cereus-thuringiensis group

    NASA Technical Reports Server (NTRS)

    La Duc, Myron T.; Satomi, Masataka; Agata, Norio; Venkateswaran, Kasthuri

    2004-01-01

    Bacillus anthracis, the causative agent of the human disease anthrax, Bacillus cereus, a food-borne pathogen capable of causing human illness, and Bacillus thuringiensis, a well-characterized insecticidal toxin producer, all cluster together within a very tight clade (B. cereus group) phylogenetically and are indistinguishable from one another via 16S rDNA sequence analysis. As new pathogens are continually emerging, it is imperative to devise a system capable of rapidly and accurately differentiating closely related, yet phenotypically distinct species. Although the gyrB gene has proven useful in discriminating closely related species, its sequence analysis has not yet been validated by DNA:DNA hybridization, the taxonomically accepted "gold standard". We phylogenetically characterized the gyrB sequences of various species and serotypes encompassed in the "B. cereus group," including lab strains and environmental isolates. Results were compared to those obtained from analyses of phenotypic characteristics, 16S rDNA sequence, DNA:DNA hybridization, and virulence factors. The gyrB gene proved more highly differential than 16S, while, at the same time, as analytical as costly and laborious DNA:DNA hybridization techniques in differentiating species within the B. cereus group.

  1. Transglycosidase-like activity of Mucor hiemalis endoglycosidase mutants enabling the synthesis of glycoconjugates using a natural glycan donor.

    PubMed

    Sakaguchi, Kouta; Katoh, Toshihiko; Yamamoto, Kenji

    2016-11-01

    Glycan conversion of glycoprotein via the transglycosylation activity of endo-β-N-acetylglucosaminidase is a promising chemoenzymatic technology for the production of glycoproteins including bio-medicines with a homogeneous glycoform. Although Endo-M is a key enzyme in this process, its product undergoes rehydrolysis, which leads to a lower yield, and limits the practical application of this enzyme. We developed several Endo-M mutant enzymes including N175Q with glycosynthase-like activity and/or transglycosidase-like activity. We found that the Endo-M N175H mutant showed glycosynthase-like activity comparable to N175Q as well as transglycosidase-like activity superior to N175Q. Using a natural sialylglycopeptide as a donor substrate, N175H readily transferred the sialo-glycan onto an N-acetylglucosamine residue attached to bovine ribonuclease B (RNase B), yielding a nonnative sialoglycosylated RNase B. These results demonstrate that use of Endo-M N175H is an alternative glycoengineering technique, which provides a relatively high yield of transglycosylation product and avoids the laborious synthesis of a sugar oxazoline as a donor substrate. © 2015 International Union of Biochemistry and Molecular Biology, Inc.

  2. An algorithm for automated detection, localization and measurement of local calcium signals from camera-based imaging.

    PubMed

    Ellefsen, Kyle L; Settle, Brett; Parker, Ian; Smith, Ian F

    2014-09-01

    Local Ca(2+) transients such as puffs and sparks form the building blocks of cellular Ca(2+) signaling in numerous cell types. They have traditionally been studied by linescan confocal microscopy, but advances in TIRF microscopy together with improved electron-multiplied CCD (EMCCD) cameras now enable rapid (>500 frames s(-1)) imaging of subcellular Ca(2+) signals with high spatial resolution in two dimensions. This approach yields vastly more information (ca. 1 Gb min(-1)) than linescan imaging, rendering visual identification and analysis of local events imaged both laborious and subject to user bias. Here we describe a routine to rapidly automate identification and analysis of local Ca(2+) events. This features an intuitive graphical user-interfaces and runs under Matlab and the open-source Python software. The underlying algorithm features spatial and temporal noise filtering to reliably detect even small events in the presence of noisy and fluctuating baselines; localizes sites of Ca(2+) release with sub-pixel resolution; facilitates user review and editing of data; and outputs time-sequences of fluorescence ratio signals for identified event sites along with Excel-compatible tables listing amplitudes and kinetics of events. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. ovoD Co-selection: A Method for Enriching CRISPR/Cas9-Edited Alleles in Drosophila.

    PubMed

    Ewen-Campen, Ben; Perrimon, Norbert

    2018-06-22

    Screening for successful CRISPR/Cas9 editing events remains a time consuming technical bottleneck in the field of Drosophila genome editing. This step can be particularly laborious for events that do not cause a visible phenotype, or those which occur at relatively low frequency. A promising strategy to enrich for desired CRISPR events is to co-select for an independent CRISPR event that produces an easily detectable phenotype. Here, we describe a simple negative co-selection strategy involving CRISPR-editing of a dominant female sterile allele, ovo D1 In this system (" ovo D co-selection"), the only functional germ cells in injected females are those that have been edited at the ovo D1 locus, and thus all offspring of these flies have undergone editing of at least one locus. We demonstrate that ovo D co-selection can be used to enrich for knock-out mutagenesis via nonhomologous end-joining (NHEJ), and for knock-in alleles via homology-directed repair (HDR). Altogether, our results demonstrate that ovoD co-selection reduces the amount of screening necessary to isolate desired CRISPR events in Drosophila. Copyright © 2018, G3: Genes, Genomes, Genetics.

  4. Boundary condition determined wave functions for the ground states of one- and two-electron homonuclear molecules

    NASA Astrophysics Data System (ADS)

    Patil, S. H.; Tang, K. T.; Toennies, J. P.

    1999-10-01

    Simple analytical wave functions satisfying appropriate boundary conditions are constructed for the ground states of one-and two-electron homonuclear molecules. Both the asymptotic condition when one electron is far away and the cusp condition when the electron coalesces with a nucleus are satisfied by the proposed wave function. For H2+, the resulting wave function is almost identical to the Guillemin-Zener wave function which is known to give very good energies. For the two electron systems H2 and He2++, the additional electron-electron cusp condition is rigorously accounted for by a simple analytic correlation function which has the correct behavior not only for r12→0 and r12→∞ but also for R→0 and R→∞, where r12 is the interelectronic distance and R, the internuclear distance. Energies obtained from these simple wave functions agree within 2×10-3 a.u. with the results of the most sophisticated variational calculations for all R and for all systems studied. This demonstrates that rather simple physical considerations can be used to derive very accurate wave functions for simple molecules thereby avoiding laborious numerical variational calculations.

  5. Can enzyme engineering benefit from the modulation of protein motions? Lessons learned from NMR relaxation dispersion experiments.

    PubMed

    Doucet, Nicolas

    2011-04-01

    Despite impressive progress in protein engineering and design, our ability to create new and efficient enzyme activities remains a laborious and time-consuming endeavor. In the past few years, intricate combinations of rational mutagenesis, directed evolution and computational methods have paved the way to exciting engineering examples and are now offering a new perspective on the structural requirements of enzyme activity. However, these structure-function analyses are usually guided by the time-averaged static models offered by enzyme crystal structures, which often fail to describe the functionally relevant 'invisible states' adopted by proteins in space and time. To alleviate such limitations, NMR relaxation dispersion experiments coupled to mutagenesis studies have recently been applied to the study of enzyme catalysis, effectively complementing 'structure-function' analyses with 'flexibility-function' investigations. In addition to offering quantitative, site-specific information to help characterize residue motion, these NMR methods are now being applied to enzyme engineering purposes, providing a powerful tool to help characterize the effects of controlling long-range networks of flexible residues affecting enzyme function. Recent advancements in this emerging field are presented here, with particular attention to mutagenesis reports highlighting the relevance of NMR relaxation dispersion tools in enzyme engineering.

  6. High clearance phenotyping systems for season-long measurement of corn, sorghum and other row crops to complement unmanned aerial vehicle systems

    NASA Astrophysics Data System (ADS)

    Murray, Seth C.; Knox, Leighton; Hartley, Brandon; Méndez-Dorado, Mario A.; Richardson, Grant; Thomasson, J. Alex; Shi, Yeyin; Rajan, Nithya; Neely, Haly; Bagavathiannan, Muthukumar; Dong, Xuejun; Rooney, William L.

    2016-05-01

    The next generation of plant breeding progress requires accurately estimating plant growth and development parameters to be made over routine intervals within large field experiments. Hand measurements are laborious and time consuming and the most promising tools under development are sensors carried by ground vehicles or unmanned aerial vehicles, with each specific vehicle having unique limitations. Previously available ground vehicles have primarily been restricted to monitoring shorter crops or early growth in corn and sorghum, since plants taller than a meter could be damaged by a tractor or spray rig passing over them. Here we have designed two and already constructed one of these self-propelled ground vehicles with adjustable heights that can clear mature corn and sorghum without damage (over three meters of clearance), which will work for shorter row crops as well. In addition to regular RGB image capture, sensor suites are incorporated to estimate plant height, vegetation indices, canopy temperature and photosynthetically active solar radiation, all referenced using RTK GPS to individual plots. These ground vehicles will be useful to validate data collected from unmanned aerial vehicles and support hand measurements taken on plots.

  7. Next-generation sequencing library construction on a surface.

    PubMed

    Feng, Kuan; Costa, Justin; Edwards, Jeremy S

    2018-05-30

    Next-generation sequencing (NGS) has revolutionized almost all fields of biology, agriculture and medicine, and is widely utilized to analyse genetic variation. Over the past decade, the NGS pipeline has been steadily improved, and the entire process is currently relatively straightforward. However, NGS instrumentation still requires upfront library preparation, which can be a laborious process, requiring significant hands-on time. Herein, we present a simple but robust approach to streamline library preparation by utilizing surface bound transposases to construct DNA libraries directly on a flowcell surface. The surface bound transposases directly fragment genomic DNA while simultaneously attaching the library molecules to the flowcell. We sequenced and analysed a Drosophila genome library generated by this surface tagmentation approach, and we showed that our surface bound library quality was comparable to the quality of the library from a commercial kit. In addition to the time and cost savings, our approach does not require PCR amplification of the library, which eliminates potential problems associated with PCR duplicates. We described the first study to construct libraries directly on a flowcell. We believe our technique could be incorporated into the existing Illumina sequencing pipeline to simplify the workflow, reduce costs, and improve data quality.

  8. Optical Method For Monitoring Tool Control For Green Burnishing With Using Of Algorithms With Adaptive Settings

    NASA Astrophysics Data System (ADS)

    Lukyanov, A. A.; Grigoriev, S. N.; Bobrovskij, I. N.; Melnikov, P. A.; Bobrovskij, N. M.

    2017-05-01

    With regard to the complexity of the new technology and increase its reliability requirements laboriousness of control operations in industrial quality control systems increases significantly. The importance of quality management control due to the fact that its promotes the correct use of production conditions, the relevant requirements are required. Digital image processing allows to reach a new technological level of production (new technological way). The most complicated automated interpretation of information is the basis for decision-making in the management of production processes. In the case of surface analysis of tools used for processing with the using of metalworking fluids (MWF) it is more complicated. The authors suggest new algorithm for optical inspection of the wear of the cylinder tool for burnishing, which used in surface plastic deformation without using of MWF. The main advantage of proposed algorithm is the possibility of automatic recognition of images of burnisher tool with the subsequent allocation of its boundaries, finding a working surface and automatically allocating the defects and wear area. Software that implements the algorithm was developed by the authors in Matlab programming environment, but can be implemented using other programming languages.

  9. Physics-Based Image Segmentation Using First Order Statistical Properties and Genetic Algorithm for Inductive Thermography Imaging.

    PubMed

    Gao, Bin; Li, Xiaoqing; Woo, Wai Lok; Tian, Gui Yun

    2018-05-01

    Thermographic inspection has been widely applied to non-destructive testing and evaluation with the capabilities of rapid, contactless, and large surface area detection. Image segmentation is considered essential for identifying and sizing defects. To attain a high-level performance, specific physics-based models that describe defects generation and enable the precise extraction of target region are of crucial importance. In this paper, an effective genetic first-order statistical image segmentation algorithm is proposed for quantitative crack detection. The proposed method automatically extracts valuable spatial-temporal patterns from unsupervised feature extraction algorithm and avoids a range of issues associated with human intervention in laborious manual selection of specific thermal video frames for processing. An internal genetic functionality is built into the proposed algorithm to automatically control the segmentation threshold to render enhanced accuracy in sizing the cracks. Eddy current pulsed thermography will be implemented as a platform to demonstrate surface crack detection. Experimental tests and comparisons have been conducted to verify the efficacy of the proposed method. In addition, a global quantitative assessment index F-score has been adopted to objectively evaluate the performance of different segmentation algorithms.

  10. A simplified approach to construct infectious cDNA clones of a tobamovirus in a binary vector.

    PubMed

    Junqueira, Bruna Rayane Teodoro; Nicolini, Cícero; Lucinda, Natalia; Orílio, Anelise Franco; Nagata, Tatsuya

    2014-03-01

    Infectious cDNA clones of RNA viruses are important tools to study molecular processes such as replication and host-virus interactions. However, the cloning steps necessary for construction of cDNAs of viral RNA genomes in binary vectors are generally laborious. In this study, a simplified method of producing an agro-infectious Pepper mild mottle virus (PMMoV) clone is described in detail. Initially, the complete genome of PMMoV was amplified by a single-step RT-PCR, cloned, and subcloned into a small plasmid vector under the T7 RNA polymerase promoter to confirm the infectivity of the cDNA clone through transcript inoculation. The complete genome was then transferred to a binary vector using a single-step, overlap-extension PCR. The selected clones were agro-infiltrated to Nicotiana benthamiana plants and showed to be infectious, causing typical PMMoV symptoms. No differences in host responses were observed when the wild-type PMMoV isolate, the T7 RNA polymerase-derived transcripts and the agroinfiltration-derived viruses were inoculated to N. benthamiana, Capsicum chinense PI 159236 and Capsicum annuum plants. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. Bi-PROF

    PubMed Central

    Gries, Jasmin; Schumacher, Dirk; Arand, Julia; Lutsik, Pavlo; Markelova, Maria Rivera; Fichtner, Iduna; Walter, Jörn; Sers, Christine; Tierling, Sascha

    2013-01-01

    The use of next generation sequencing has expanded our view on whole mammalian methylome patterns. In particular, it provides a genome-wide insight of local DNA methylation diversity at single nucleotide level and enables the examination of single chromosome sequence sections at a sufficient statistical power. We describe a bisulfite-based sequence profiling pipeline, Bi-PROF, which is based on the 454 GS-FLX Titanium technology that allows to obtain up to one million sequence stretches at single base pair resolution without laborious subcloning. To illustrate the performance of the experimental workflow connected to a bioinformatics program pipeline (BiQ Analyzer HT) we present a test analysis set of 68 different epigenetic marker regions (amplicons) in five individual patient-derived xenograft tissue samples of colorectal cancer and one healthy colon epithelium sample as a control. After the 454 GS-FLX Titanium run, sequence read processing and sample decoding, the obtained alignments are quality controlled and statistically evaluated. Comprehensive methylation pattern interpretation (profiling) assessed by analyzing 102-104 sequence reads per amplicon allows an unprecedented deep view on pattern formation and methylation marker heterogeneity in tissues concerned by complex diseases like cancer. PMID:23803588

  12. Topological leakage detection and freeze-and-grow propagation for improved CT-based airway segmentation

    NASA Astrophysics Data System (ADS)

    Nadeem, Syed Ahmed; Hoffman, Eric A.; Sieren, Jered P.; Saha, Punam K.

    2018-03-01

    Numerous large multi-center studies are incorporating the use of computed tomography (CT)-based characterization of the lung parenchyma and bronchial tree to understand chronic obstructive pulmonary disease status and progression. To the best of our knowledge, there are no fully automated airway tree segmentation methods, free of the need for user review. A failure in even a fraction of segmentation results necessitates manual revision of all segmentation masks which is laborious considering the thousands of image data sets evaluated in large studies. In this paper, we present a novel CT-based airway tree segmentation algorithm using topological leakage detection and freeze-and-grow propagation. The method is fully automated requiring no manual inputs or post-segmentation editing. It uses simple intensity-based connectivity and a freeze-and-grow propagation algorithm to iteratively grow the airway tree starting from an initial seed inside the trachea. It begins with a conservative parameter and then, gradually shifts toward more generous parameter values. The method was applied on chest CT scans of fifteen subjects at total lung capacity. Airway segmentation results were qualitatively assessed and performed comparably to established airway segmentation method with no major visual leakages.

  13. Phenotype detection in morphological mutant mice using deformation features.

    PubMed

    Roy, Sharmili; Liang, Xi; Kitamoto, Asanobu; Tamura, Masaru; Shiroishi, Toshihiko; Brown, Michael S

    2013-01-01

    Large-scale global efforts are underway to knockout each of the approximately 25,000 mouse genes and interpret their roles in shaping the mammalian embryo. Given the tremendous amount of data generated by imaging mutated prenatal mice, high-throughput image analysis systems are inevitable to characterize mammalian development and diseases. Current state-of-the-art computational systems offer only differential volumetric analysis of pre-defined anatomical structures between various gene-knockout mice strains. For subtle anatomical phenotypes, embryo phenotyping still relies on the laborious histological techniques that are clearly unsuitable in such big data environment. This paper presents a system that automatically detects known phenotypes and assists in discovering novel phenotypes in muCT images of mutant mice. Deformation features obtained from non-linear registration of mutant embryo to a normal consensus average image are extracted and analyzed to compute phenotypic and candidate phenotypic areas. The presented system is evaluated using C57BL/10 embryo images. All cases of ventricular septum defect and polydactyly, well-known to be present in this strain, are successfully detected. The system predicts potential phenotypic areas in the liver that are under active histological evaluation for possible phenotype of this mouse line.

  14. Assaying Wnt5A-mediated Invasion in Melanoma Cells

    PubMed Central

    O'Connell, Michael P.; French, Amanda D.; Leotlela, Poloko D.; Weeraratna, Ashani T.

    2009-01-01

    Wnt5A has been implicated in melanoma metastasis, and the progression of other cancers including pancreatic, gastric, prostate and lung cancers. Assays to test motility and invasion include both in vivo assays, and in vitro assays. The former assays include the use of tail vein or footpad injections of metastatic cells, and are often laborious and expensive. In vitro invasion assays provide quick readouts that can help to establish conditions that either activate or inhibit melanoma cell motility, and to assess whether the conditions in question are worth translating into an in vivo model. Here we describe two standard methods for assaying motility and invasion in vitro including wound healing assays and Matrigel invasion assays (Boyden chamber assays). In addition, we and several other laboratories have previously shown that melanoma cells require MMP-2 for their invasion, and have recently shown that Wnt5A treatment can increase the levels of this enzyme in melanoma cells, as demonstrated by gelatin zymography. The use of these techniques can help to assess the migratory capacity of melanoma cells in response to Wnt treatment. PMID:19099260

  15. MEPSA: minimum energy pathway analysis for energy landscapes.

    PubMed

    Marcos-Alcalde, Iñigo; Setoain, Javier; Mendieta-Moreno, Jesús I; Mendieta, Jesús; Gómez-Puertas, Paulino

    2015-12-01

    From conformational studies to atomistic descriptions of enzymatic reactions, potential and free energy landscapes can be used to describe biomolecular systems in detail. However, extracting the relevant data of complex 3D energy surfaces can sometimes be laborious. In this article, we present MEPSA (Minimum Energy Path Surface Analysis), a cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective. Some of its most relevant features are: identification of all the barriers and minima of the landscape at once, description of maxima edge profiles, detection of the lowest energy path connecting two minima and generation of transition state theory diagrams along these paths. In addition to a built-in plotting system, MEPSA can save most of the generated data into easily parseable text files, allowing more versatile uses of MEPSA's output such as the generation of molecular dynamics restraints from a calculated path. MEPSA is freely available (under GPLv3 license) at: http://bioweb.cbm.uam.es/software/MEPSA/ CONTACT: pagomez@cbm.csic.es. Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  16. Comparison of sample preparation methods combined with fast gas chromatography-mass spectrometry for ultratrace analysis of pesticide residues in baby food.

    PubMed

    Hercegová, Andrea; Dömötörová, Milena; Kruzlicová, Dása; Matisová, Eva

    2006-05-01

    Four sample preparation techniques were compared for the ultratrace analysis of pesticide residues in baby food: (a) modified Schenck's method based on ACN extraction with SPE cleaning; (b) quick, easy, cheap, effective, rugged, and safe (QuEChERS) method based on ACN extraction and dispersive SPE; (c) modified QuEChERS method which utilizes column-based SPE instead of dispersive SPE; and (d) matrix solid phase dispersion (MSPD). The methods were combined with fast gas chromatographic-mass spectrometric analysis. The effectiveness of clean-up of the final extract was determined by comparison of the chromatograms obtained. Time consumption, laboriousness, demands on glassware and working place, and consumption of chemicals, especially solvents, increase in the following order QuEChERS < modified QuEChERS < MSPD < modified Schenck's method. All methods offer satisfactory analytical characteristics at the concentration levels of 5, 10, and 100 microg/kg in terms of recoveries and repeatability. Recoveries obtained for the modified QuEChERS method were lower than for the original QuEChERS. In general the best LOQs were obtained for the modified Schenck's method. Modified QuEChERS method provides 21-72% better LOQs than the original method.

  17. OpenComet: An automated tool for comet assay image analysis

    PubMed Central

    Gyori, Benjamin M.; Venkatachalam, Gireedhar; Thiagarajan, P.S.; Hsu, David; Clement, Marie-Veronique

    2014-01-01

    Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time. PMID:24624335

  18. OpenComet: an automated tool for comet assay image analysis.

    PubMed

    Gyori, Benjamin M; Venkatachalam, Gireedhar; Thiagarajan, P S; Hsu, David; Clement, Marie-Veronique

    2014-01-01

    Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time.

  19. Novel method for the high-throughput processing of slides for the comet assay.

    PubMed

    Karbaschi, Mahsa; Cooke, Marcus S

    2014-11-26

    Single cell gel electrophoresis (the comet assay), continues to gain popularity as a means of assessing DNA damage. However, the assay's low sample throughput and laborious sample workup procedure are limiting factors to its application. "Scoring", or individually determining DNA damage levels in 50 cells per treatment, is time-consuming, but with the advent of high-throughput scoring, the limitation is now the ability to process significant numbers of comet slides. We have developed a novel method by which multiple slides may be manipulated, and undergo electrophoresis, in batches of 25 rather than individually and, importantly, retains the use of standard microscope comet slides, which are the assay convention. This decreases assay time by 60%, and benefits from an electrophoresis tank with a substantially smaller footprint, and more uniform orientation of gels during electrophoresis. Our high-throughput variant of the comet assay greatly increases the number of samples analysed, decreases assay time, number of individual slide manipulations, reagent requirements and risk of damage to slides. The compact nature of the electrophoresis tank is of particular benefit to laboratories where bench space is at a premium. This novel approach is a significant advance on the current comet assay procedure.

  20. A Simple and Efficient Method of Slow Freezing for Human Embryonic Stem Cells and Induced Pluripotent Stem Cells.

    PubMed

    Imaizumi, Keitaro; Iha, Momoe; Nishishita, Naoki; Kawamata, Shin; Nishikawa, Shinichi; Akuta, Teruo

    2016-01-01

    Protocols available for the cryopreservation of human embryonic stem (ES) and induced pluripotent stem (iPS) cells are very inefficient and laborious compared to those for the cryopreservation of murine ES/iPS cells or other general cell lines. While the vitrification method may be adequate when working with small numbers of human ES/iPS cells, it requires special skills and is unsuitable when working with large cell numbers. Here, we describe a simple and efficient method for the cryopreservation of hES/hiPS cells that is based on a conventional slow freezing method that uses a combination of Pronase/EDTA for Stem™ and CP-5E™ [final concentrations: 6 % hydroxyethyl starch, 5 % DMSO, and 5 % ethylene glycol in saline]. CP-5E™ is highly effective for the cryopreservation of small cell clumps produced by hES/hiPS colony detachment in the presence of Pronase and EDTA (Pronase/EDTA for Stem™, a formulation containing multiple digestive enzymes from Streptomyces griseus). This novel method would be quite useful for large-scale hES/iPS cell banking for use in clinical applications.