Improved molecular tools for sugar cane biotechnology.

Science.gov (United States)

Kinkema, Mark; Geijskes, Jason; Delucca, Paulo; Palupe, Anthony; Shand, Kylie; Coleman, Heather D; Brinin, Anthony; Williams, Brett; Sainz, Manuel; Dale, James L

2014-03-01

Sugar cane is a major source of food and fuel worldwide. Biotechnology has the potential to improve economically-important traits in sugar cane as well as diversify sugar cane beyond traditional applications such as sucrose production. High levels of transgene expression are key to the success of improving crops through biotechnology. Here we describe new molecular tools that both expand and improve gene expression capabilities in sugar cane. We have identified promoters that can be used to drive high levels of gene expression in the leaf and stem of transgenic sugar cane. One of these promoters, derived from the Cestrum yellow leaf curling virus, drives levels of constitutive transgene expression that are significantly higher than those achieved by the historical benchmark maize polyubiquitin-1 (Zm-Ubi1) promoter. A second promoter, the maize phosphonenolpyruvate carboxylate promoter, was found to be a strong, leaf-preferred promoter that enables levels of expression comparable to Zm-Ubi1 in this organ. Transgene expression was increased approximately 50-fold by gene modification, which included optimising the codon usage of the coding sequence to better suit sugar cane. We also describe a novel dual transcriptional enhancer that increased gene expression from different promoters, boosting expression from Zm-Ubi1 over eightfold. These molecular tools will be extremely valuable for the improvement of sugar cane through biotechnology.

eMovie: a storyboard-based tool for making molecular movies.

Science.gov (United States)

Hodis, Eran; Schreiber, Gideon; Rother, Kristian; Sussman, Joel L

2007-05-01

The 3D structures of macromolecules are difficult to grasp and also to communicate. By their nature, movies or animations are particularly useful for highlighting key features by offering a 'guided tour' of structures and conformation changes. However, high-quality movies are rarely seen because they are currently difficult and time consuming to make. By adopting the traditional movie 'storyboard' concept, which gives guidance and direction to filming, eMovie makes the creation of lengthy molecular animations much easier. This tool is a plug-in for the open-source molecular graphics program PyMOL, and enables experts and novices alike to produce informative and high-quality molecular animations.

Bio-AIMS Collection of Chemoinformatics Web Tools based on Molecular Graph Information and Artificial Intelligence Models.

Science.gov (United States)

Munteanu, Cristian R; Gonzalez-Diaz, Humberto; Garcia, Rafael; Loza, Mabel; Pazos, Alejandro

2015-01-01

The molecular information encoding into molecular descriptors is the first step into in silico Chemoinformatics methods in Drug Design. The Machine Learning methods are a complex solution to find prediction models for specific biological properties of molecules. These models connect the molecular structure information such as atom connectivity (molecular graphs) or physical-chemical properties of an atom/group of atoms to the molecular activity (Quantitative Structure - Activity Relationship, QSAR). Due to the complexity of the proteins, the prediction of their activity is a complicated task and the interpretation of the models is more difficult. The current review presents a series of 11 prediction models for proteins, implemented as free Web tools on an Artificial Intelligence Model Server in Biosciences, Bio-AIMS (http://bio-aims.udc.es/TargetPred.php). Six tools predict protein activity, two models evaluate drug - protein target interactions and the other three calculate protein - protein interactions. The input information is based on the protein 3D structure for nine models, 1D peptide amino acid sequence for three tools and drug SMILES formulas for two servers. The molecular graph descriptor-based Machine Learning models could be useful tools for in silico screening of new peptides/proteins as future drug targets for specific treatments.

Bring Your Own Device: Parental Guidance (PG) Suggested

Science.gov (United States)

Kiger, Derick; Herro, Dani

2015-01-01

Educators are incorporating students' mobile devices into the schooling experience via Bring Your Own Device (BYOD) initiatives. This is advantageous for many reasons, most notably, improving access to Internet resources and digital tools in support of teaching and learning. Obtaining parental support is key to BYOD success. Therefore, this study…

Bringing the Tools of Big Science to Bear on Local Environmental Challenges

Science.gov (United States)

Bronson, Scott; Jones, Keith W.; Brown, Maria

2013-01-01

We describe an interactive collaborative environmental education project that makes advanced laboratory facilities at Brookhaven National Laboratory accessible for one-year or multi-year science projects for the high school level. Cyber-enabled Environmental Science (CEES) utilizes web conferencing software to bring multi-disciplinary,…

Molecular tools for carotenogenesis analysis in the zygomycete Mucor circinelloides.

Science.gov (United States)

Torres-Martínez, Santiago; Ruiz-Vázquez, Rosa M; Garre, Victoriano; López-García, Sergio; Navarro, Eusebio; Vila, Ana

2012-01-01

The carotene producer fungus Mucor circinelloides is the zygomycete more amenable to genetic manipulations by using molecular tools. Since the initial development of an effective procedure of genetic transformation, more than two decades ago, the availability of new molecular approaches such as gene replacement techniques and gene expression inactivation by RNA silencing, in addition to the sequencing of its genome, has made Mucor a valuable organism for the study of a number of processes. Here we describe in detail the main techniques and methods currently used to manipulate M. circinelloides, including transformation, gene replacement, gene silencing, RNAi, and immunoprecipitation.

A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.

Science.gov (United States)

Purawat, Shweta; Ieong, Pek U; Malmstrom, Robert D; Chan, Garrett J; Yeung, Alan K; Walker, Ross C; Altintas, Ilkay; Amaro, Rommie E

2017-06-20

With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine. Additionally, the workflow tool reduces user input time by automating repetitive processes and facilitates access to GPU clusters, whose high-performance processing power makes simulations of large numerical scale possible. The presented workflow tool facilitates the management and deployment of large sets of MD simulations on heterogeneous computing resources. The workflow tool also performs systematic analysis on the simulation outputs and enhances simulation reproducibility, execution scalability, and MD method development including benchmarking and validation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Modeling, methodologies and tools for molecular and nano-scale communications modeling, methodologies and tools

CERN Document Server

Nakano, Tadashi; Moore, Michael

2017-01-01

(Preliminary) The book presents the state of art in the emerging field of molecular and nanoscale communication. It gives special attention to fundamental models, and advanced methodologies and tools used in the field. It covers a wide range of applications, e.g. nanomedicine, nanorobot communication, bioremediation and environmental managements. It addresses advanced graduate students, academics and professionals working at the forefront in their fields and at the interfaces between different areas of research, such as engineering, computer science, biology and nanotechnology.

Synthetic biology and molecular genetics in non-conventional yeasts: Current tools and future advances.

Science.gov (United States)

Wagner, James M; Alper, Hal S

2016-04-01

Coupling the tools of synthetic biology with traditional molecular genetic techniques can enable the rapid prototyping and optimization of yeast strains. While the era of yeast synthetic biology began in the well-characterized model organism Saccharomyces cerevisiae, it is swiftly expanding to include non-conventional yeast production systems such as Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. These yeasts already have roles in the manufacture of vaccines, therapeutic proteins, food additives, and biorenewable chemicals, but recent synthetic biology advances have the potential to greatly expand and diversify their impact on biotechnology. In this review, we summarize the development of synthetic biological tools (including promoters and terminators) and enabling molecular genetics approaches that have been applied in these four promising alternative biomanufacturing platforms. An emphasis is placed on synthetic parts and genome editing tools. Finally, we discuss examples of synthetic tools developed in other organisms that can be adapted or optimized for these hosts in the near future. Copyright © 2015 Elsevier Inc. All rights reserved.

Molecular beacon – tool for real time studying gene activity in stem cells

DEFF Research Database (Denmark)

Ilieva, Mirolyuba; Dufva, Martin

Cells respond to their internal genetic programs and external stimuli by modulating the synthesis of specific mRNAs. Direct observation of mRNA expression in living cells can provide valuable information with regards to understanding fundamental processes such cell differentiation, regeneration...... and cancerogenesis. Molecular beacon technology is based on fluorescence resonance energy transfer (FRET) and the complementary pairing principles. These fluorescent molecular probes are highly specific and sensitive and are one important tool in in vitro diagnostics. Here molecular beacons are used to follow...

Method for delivery of small molecules and proteins across the cell wall of algae using molecular transporters

Science.gov (United States)

Geihe, Erika; Trantow, Brian; Wender, Paul; Hyman, Joel M.; Parvin, Bahram

2017-11-14

The introduction of tools to study, control or expand the inner-workings of algae has been slow to develop. Provided are embodiments of a molecular method based on guanidinium-rich molecular transporters (GR-MoTrs) for bringing molecular cargos into algal cells. The methods of the disclosure have been shown to work in wild-type algae that have an intact cell wall. Developed using Chlamydomonas reinhardtii, this method is also successful with less studied algae, including Neochloris oleoabundans and Scenedesmus dimorphus, thus providing a new and versatile tool for algal research and modification. The method of delivering a cargo compound to an algal cell comprises contacting an algal cell with a guanidinium-rich delivery vehicle comprising a guanidinium-rich molecular transporter (GR-MoTr) linked to a cargo compound desired to be delivered to the algal cell, whereby the guanidinium-rich molecular transporter can traverse the algal cell wall, thereby delivering the cargo compound to the algal cell.

Bringing Foreign Language Learning into the 21st century | Thomas ...

African Journals Online (AJOL)

Bringing Foreign Language Learning into the 21st Century. The different challenges facing foreign language lecturers are considered as well as the different methods used to teach a foreign language. Technology and multimedia are proposed not only as tools and supports but also as a possible solution. With the change ...

Polymerase chain reaction: A molecular diagnostic tool in periodontology

Science.gov (United States)

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

2016-01-01

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

Ultrafast dissociation: An unexpected tool for probing molecular dynamics

International Nuclear Information System (INIS)

Morin, Paul; Miron, Catalin

2012-01-01

Highlights: ► Ultrafast dissociation has been investigated by means of XPS and mass spectrometry. ► The interplay between electron relaxation and molecular dynamics is evidenced. ► Extension toward polyatomics, clusters, adsorbed molecules is considered. ► Quantum effects (spectral hole, angular effects) evidence the molecular field anisotropy. -- Abstract: Ultrafast dissociation following core–shell excitation into an antibonding orbital led to the early observation in HBr of atomic Auger lines associated to the decay of dissociated excited atoms. The purpose of this article is to review the very large variety of systems where such a situation has been encountered, extending from simple diatomic molecules toward more complex systems like polyatomics, clusters, or adsorbed molecules. Interestingly, this phenomenon has revealed an extremely rich and powerful tool for probing nuclear dynamics and its subtle interplay with electron relaxation occurring on a comparable time scale. Consequently this review covers a surprisingly large period, starting in 1986 and still ongoing.

Molecular tools for bathing water assessment in Europe: Balancing social science research with a rapidly developing environmental science evidence-base.

Science.gov (United States)

Oliver, David M; Hanley, Nick D; van Niekerk, Melanie; Kay, David; Heathwaite, A Louise; Rabinovici, Sharyl J M; Kinzelman, Julie L; Fleming, Lora E; Porter, Jonathan; Shaikh, Sabina; Fish, Rob; Chilton, Sue; Hewitt, Julie; Connolly, Elaine; Cummins, Andy; Glenk, Klaus; McPhail, Calum; McRory, Eric; McVittie, Alistair; Giles, Amanna; Roberts, Suzanne; Simpson, Katherine; Tinch, Dugald; Thairs, Ted; Avery, Lisa M; Vinten, Andy J A; Watts, Bill D; Quilliam, Richard S

2016-02-01

The use of molecular tools, principally qPCR, versus traditional culture-based methods for quantifying microbial parameters (e.g., Fecal Indicator Organisms) in bathing waters generates considerable ongoing debate at the science-policy interface. Advances in science have allowed the development and application of molecular biological methods for rapid (~2 h) quantification of microbial pollution in bathing and recreational waters. In contrast, culture-based methods can take between 18 and 96 h for sample processing. Thus, molecular tools offer an opportunity to provide a more meaningful statement of microbial risk to water-users by providing near-real-time information enabling potentially more informed decision-making with regard to water-based activities. However, complementary studies concerning the potential costs and benefits of adopting rapid methods as a regulatory tool are in short supply. We report on findings from an international Working Group that examined the breadth of social impacts, challenges, and research opportunities associated with the application of molecular tools to bathing water regulations.

Molecular tools for diagnosis of visceral leishmaniasis: systematic review and meta-analysis of diagnostic test accuracy

NARCIS (Netherlands)

de Ruiter, C. M.; van der Veer, C.; Leeflang, M. M. G.; Deborggraeve, S.; Lucas, C.; Adams, E. R.

2014-01-01

Molecular methods have been proposed as highly sensitive tools for the detection of Leishmania parasites in visceral leishmaniasis (VL) patients. Here, we evaluate the diagnostic accuracy of these tools in a meta-analysis of the published literature. The selection criteria were original studies that

Molecular HIV screening.

Science.gov (United States)

Bourlet, Thomas; Memmi, Meriam; Saoudin, Henia; Pozzetto, Bruno

2013-09-01

Nuclear acid testing is more and more used for the diagnosis of infectious diseases. This paper focuses on the use of molecular tools for HIV screening. The term 'screening' will be used under the meaning of first-line HIV molecular techniques performed on a routine basis, which excludes HIV molecular tests designed to confirm or infirm a newly discovered HIV-seropositive patient or other molecular tests performed for the follow-up of HIV-infected patients. The following items are developed successively: i) presentation of the variety of molecular tools used for molecular HIV screening, ii) use of HIV molecular tools for the screening of blood products, iii) use of HIV molecular tools for the screening of organs and tissue from human origin, iv) use of HIV molecular tools in medically assisted procreation and v) use of HIV molecular tools in neonates from HIV-infected mothers.

Molecular epidemiology: new rules for new tools?

Science.gov (United States)

Merlo, Domenico Franco; Sormani, Maria Pia; Bruzzi, Paolo

2006-08-30

Molecular epidemiology combines biological markers and epidemiological observations in the study of the environmental and genetic determinants of cancer and other diseases. The potential advantages associated with biomarkers are manifold and include: (a) increased sensitivity and specificity to carcinogenic exposures; (b) more precise evaluation of the interplay between genetic and environmental determinants of cancer; (c) earlier detection of carcinogenic effects of exposure; (d) characterization of disease subtypes-etiologies patterns; (e) evaluation of primary prevention measures. These, in turn, may translate into better tools for etiologic research, individual risk assessment, and, ultimately, primary and secondary prevention. An area that has not received sufficient attention concerns the validation of these biomarkers as surrogate endpoints for cancer risk. Validation of a candidate biomarker's surrogacy is the demonstration that it possesses the properties required for its use as a substitute for a true endpoint. The principles underlying the validation process underwent remarkable developments and discussion in therapeutic research. However, the challenges posed by the application of these principles to epidemiological research, where the basic tool for this validation (i.e., the randomized study) is seldom possible, have not been thoroughly explored. The validation process of surrogacy must be applied rigorously to intermediate biomarkers of cancer risk before using them as risk predictors at the individual as well as at the population level.

Genetic, genomic, and molecular tools for studying the protoploid yeast, L. waltii.

Science.gov (United States)

Di Rienzi, Sara C; Lindstrom, Kimberly C; Lancaster, Ragina; Rolczynski, Lisa; Raghuraman, M K; Brewer, Bonita J

2011-02-01

Sequencing of the yeast Kluyveromyces waltii (recently renamed Lachancea waltii) provided evidence of a whole genome duplication event in the lineage leading to the well-studied Saccharomyces cerevisiae. While comparative genomic analyses of these yeasts have proven to be extremely instructive in modeling the loss or maintenance of gene duplicates, experimental tests of the ramifications following such genome alterations remain difficult. To transform L. waltii from an organism of the computational comparative genomic literature into an organism of the functional comparative genomic literature, we have developed genetic, molecular and genomic tools for working with L. waltii. In particular, we have characterized basic properties of L. waltii (growth, ploidy, molecular karyotype, mating type and the sexual cycle), developed transformation, cell cycle arrest and synchronization protocols, and have created centromeric and non-centromeric vectors as well as a genome browser for L. waltii. We hope that these tools will be used by the community to follow up on the ideas generated by sequence data and lead to a greater understanding of eukaryotic biology and genome evolution. 2010 John Wiley & Sons, Ltd.

ms 2: A molecular simulation tool for thermodynamic properties, release 3.0

Science.gov (United States)

Rutkai, Gábor; Köster, Andreas; Guevara-Carrion, Gabriela; Janzen, Tatjana; Schappals, Michael; Glass, Colin W.; Bernreuther, Martin; Wafai, Amer; Stephan, Simon; Kohns, Maximilian; Reiser, Steffen; Deublein, Stephan; Horsch, Martin; Hasse, Hans; Vrabec, Jadran

2017-12-01

A new version release (3.0) of the molecular simulation tool ms 2 (Deublein et al., 2011; Glass et al. 2014) is presented. Version 3.0 of ms 2 features two additional ensembles, i.e. microcanonical (NVE) and isobaric-isoenthalpic (NpH), various Helmholtz energy derivatives in the NVE ensemble, thermodynamic integration as a method for calculating the chemical potential, the osmotic pressure for calculating the activity of solvents, the six Maxwell-Stefan diffusion coefficients of quaternary mixtures, statistics for sampling hydrogen bonds, smooth-particle mesh Ewald summation as well as the ability to carry out molecular dynamics runs for an arbitrary number of state points in a single program execution.

Monitoring bioremediation of atrazine in soil microcosms using molecular tools

International Nuclear Information System (INIS)

Sagarkar, Sneha; Mukherjee, Shinjini; Nousiainen, Aura; Björklöf, Katarina; Purohit, Hemant J.; Jørgensen, Kirsten S.; Kapley, Atya

2013-01-01

Molecular tools in microbial community analysis give access to information on catabolic potential and diversity of microbes. Applied in bioremediation, they could provide a new dimension to improve pollution control. This concept has been demonstrated in the study using atrazine as model pollutant. Bioremediation of the herbicide, atrazine, was analyzed in microcosm studies by bioaugmentation, biostimulation and natural attenuation. Genes from the atrazine degrading pathway atzA/B/C/D/E/F, trzN, and trzD were monitored during the course of treatment and results demonstrated variation in atzC, trzD and trzN genes with time. Change in copy number of trzN gene under different treatment processes was demonstrated by real-time PCR. The amplified trzN gene was cloned and sequence data showed homology to genes reported in Arthrobacter and Nocardioides. Results demonstrate that specific target genes can be monitored, quantified and correlated to degradation analysis which would help in predicting the outcome of any bioremediation strategy. - Highlights: ► Degradation of herbicide, atrazine. ► Comparison of bioremediation via bioaugmentation, biostimulation and natural attenuation. ► Gene profile analysis in all treatments. ► Variation in trzN gene numbers correlated to degradation efficiency. ► Cloning and sequence analysis of trzN gene demonstrates very high homology to reported gene. - This study demonstrates the use of molecular tools in bioremediation to monitor and track target genes; correlates the results with degradation and thereby predicts the efficiency of treatment.

Intrageneric Primer Design: Bringing Bioinformatics Tools to the Class

Science.gov (United States)

Lima, Andre O. S.; Garces, Sergio P. S.

2006-01-01

Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private…

Molecular tools for the construction of peptide-based materials.

Science.gov (United States)

Ramakers, B E I; van Hest, J C M; Löwik, D W P M

2014-04-21

Proteins and peptides are fundamental components of living systems where they play crucial roles at both functional and structural level. The versatile biological properties of these molecules make them interesting building blocks for the construction of bio-active and biocompatible materials. A variety of molecular tools can be used to fashion the peptides necessary for the assembly of these materials. In this tutorial review we shall describe five of the main techniques, namely solid phase peptide synthesis, native chemical ligation, Staudinger ligation, NCA polymerisation, and genetic engineering, that have been used to great effect for the construction of a host of peptide-based materials.

TOXCAST, A TOOL FOR CATEGORIZATION AND ...

Science.gov (United States)

Across several EPA Program Offices (e.g., OPPTS, OW, OAR), there is a clear need to develop strategies and methods to screen large numbers of chemicals for potential toxicity, and to use the resulting information to prioritize the use of testing resources towards those entities and endpoints that present the greatest likelihood of risk to human health and the environment. This need could be addressed using the experience of the pharmaceutical industry in the use of advanced modern molecular biology and computational chemistry tools for the development of new drugs, with appropriate adjustment to the needs and desires of environmental toxicology. A conceptual approach named ToxCast has been developed to address the needs of EPA Program Offices in the area of prioritization and screening. Modern computational chemistry and molecular biology tools bring enabling technologies forward that can provide information about the physical and biological properties of large numbers of chemicals. The essence of the proposal is to conduct a demonstration project based upon a rich toxicological database (e.g., registered pesticides, or the chemicals tested in the NTP bioassay program), select a fairly large number (50-100 or more chemicals) representative of a number of differing structural classes and phenotypic outcomes (e.g., carcinogens, reproductive toxicants, neurotoxicants), and evaluate them across a broad spectrum of information domains that modern technology has pro

Bringing Your Baby Home

Science.gov (United States)

... for Educators Search English Español Bringing Your Baby Home KidsHealth / For Parents / Bringing Your Baby Home What's ... recall your baby's seemingly endless crying episodes. The Home Front Introducing your baby to others at home ...

Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

Science.gov (United States)

Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

2018-01-01

Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

Characteristics and evolution of the ecosystem of software tools supporting research in molecular biology.

Science.gov (United States)

Pazos, Florencio; Chagoyen, Monica

2018-01-16

Daily work in molecular biology presently depends on a large number of computational tools. An in-depth, large-scale study of that 'ecosystem' of Web tools, its characteristics, interconnectivity, patterns of usage/citation, temporal evolution and rate of decay is crucial for understanding the forces that shape it and for informing initiatives aimed at its funding, long-term maintenance and improvement. In particular, the long-term maintenance of these tools is compromised because of their specific development model. Hundreds of published studies become irreproducible de facto, as the software tools used to conduct them become unavailable. In this study, we present a large-scale survey of >5400 publications describing Web servers within the two main bibliographic resources for disseminating new software developments in molecular biology. For all these servers, we studied their citation patterns, the subjects they address, their citation networks and the temporal evolution of these factors. We also analysed how these factors affect the availability of these servers (whether they are alive). Our results show that this ecosystem of tools is highly interconnected and adapts to the 'trendy' subjects in every moment. The servers present characteristic temporal patterns of citation/usage, and there is a worrying rate of server 'death', which is influenced by factors such as the server popularity and the institutions that hosts it. These results can inform initiatives aimed at the long-term maintenance of these resources. © The Author(s) 2018. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Biopython: freely available Python tools for computational molecular biology and bioinformatics

DEFF Research Database (Denmark)

Cock, Peter J A; Antao, Tiago; Chang, Jeffrey T

2009-01-01

SUMMARY: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments......, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. AVAILABILITY: Biopython is freely available, with documentation and source code at (www...

Bringing up Gender: Academic Abjection?

Science.gov (United States)

Henderson, Emily F.

2014-01-01

The principal questions raised in this article are: what does it mean to bring up the topic of gender in a space where it is not known, and how can this moment of bringing up gender--or not bringing it up--be conceptualised? The article departs from the thoughts and questions that were provoked by an interview conducted with a Gender Studies…

DataGenno: building a new tool to bridge molecular and clinical genetics

Directory of Open Access Journals (Sweden)

Fabricio F Costa

2011-03-01

, DataGenno’s system and search engine will be able to provide tools that will facilitate the discovery and description of new genetic syndromes. In conclusion, we believe that DataGenno's portal will be a helpful and innovative tool for health care professionals, scientists, genetic counselors, and other professionals in the clinical genetics field.Keywords: genetic diseases, signs and symptoms, molecular genetics, genomics, search engine, database

Development and Application of Camelid Molecular Cytogenetic Tools

Science.gov (United States)

Avila, Felipe; Das, Pranab J.; Kutzler, Michelle; Owens, Elaine; Perelman, Polina; Rubes, Jiri; Hornak, Miroslav; Johnson, Warren E.

2014-01-01

Cytogenetic chromosome maps offer molecular tools for genome analysis and clinical cytogenetics and are of particular importance for species with difficult karyotypes, such as camelids (2n = 74). Building on the available human–camel zoo-fluorescence in situ hybridization (FISH) data, we developed the first cytogenetic map for the alpaca (Lama pacos, LPA) genome by isolating and identifying 151 alpaca bacterial artificial chromosome (BAC) clones corresponding to 44 specific genes. The genes were mapped by FISH to 31 alpaca autosomes and the sex chromosomes; 11 chromosomes had 2 markers, which were ordered by dual-color FISH. The STS gene mapped to Xpter/Ypter, demarcating the pseudoautosomal region, whereas no markers were assigned to chromosomes 14, 21, 22, 28, and 36. The chromosome-specific markers were applied in clinical cytogenetics to identify LPA20, the major histocompatibility complex (MHC)-carrying chromosome, as a part of an autosomal translocation in a sterile male llama (Lama glama, LGL; 2n = 73,XY). FISH with LPAX BACs and LPA36 paints, as well as comparative genomic hybridization, were also used to investigate the origin of the minute chromosome, an abnormally small LPA36 in infertile female alpacas. This collection of cytogenetically mapped markers represents a new tool for camelid clinical cytogenetics and has applications for the improvement of the alpaca genome map and sequence assembly. PMID:23109720

Molecular Imaging: A Useful Tool for the Development of Natural Killer Cell-Based Immunotherapies

Directory of Open Access Journals (Sweden)

Prakash Gangadaran

2017-09-01

Full Text Available Molecular imaging is a relatively new discipline that allows visualization, characterization, and measurement of the biological processes in living subjects, including humans, at a cellular and molecular level. The interaction between cancer cells and natural killer (NK cells is complex and incompletely understood. Despite our limited knowledge, progress in the search for immune cell therapies against cancer could be significantly improved by dynamic and non-invasive visualization and tracking of immune cells and by visualization of the response of cancer cells to therapies in preclinical and clinical studies. Molecular imaging is an essential tool for these studies, and a multimodal molecular imaging approach can be applied to monitor immune cells in vivo, for instance, to visualize therapeutic effects. In this review, we discuss the usefulness of NK cells in cancer therapies and the preclinical and clinical usefulness of molecular imaging in NK cell-based therapies. Furthermore, we discuss different molecular imaging modalities for use with NK cell-based therapies, and their preclinical and clinical applications in animal and human subjects. Molecular imaging has contributed to the development of NK cell-based therapies against cancers in animal models and to the refinement of current cell-based cancer immunotherapies. Developing sensitive and reproducible non-invasive molecular imaging technologies for in vivo NK cell monitoring and for real-time assessment of therapeutic effects will accelerate the development of NK cell therapies.

Synthesis of Novel Hydrocarbon Soluble Multifunctional Anionic Initiators: Tools for Synthesis of Novel Dendrimer and Molecular Brush Polymer Architectures

Science.gov (United States)

2015-02-09

Synthesis of Novel Dendrimer and Molecular Brush Polymer Architectures. Research Area:7.4 The views, opinions and/or findings contained in this report...journals: Final Report: Synthesis of Novel Hydrocarbon Soluble Multifunctional Anionic Initiators: Tools for Synthesis of Novel Dendrimer and Molecular

Model-based evaluation of the use of polycyclic aromatic hydrocarbons molecular diagnostic ratios as a source identification tool

International Nuclear Information System (INIS)

Katsoyiannis, Athanasios; Breivik, Knut

2014-01-01

Polycyclic Aromatic Hydrocarbons (PAHs) molecular diagnostic ratios (MDRs) are unitless concentration ratios of pair-PAHs with the same molecular weight (MW); MDRs have long been used as a tool for PAHs source identification purposes. In the present paper, the efficiency of the MDR methodology is evaluated through the use of a multimedia fate model, the calculation of characteristic travel distances (CTD) and the estimation of air concentrations for individual PAHs as a function of distance from an initial point source. The results show that PAHs with the same MW are sometimes characterized by substantially different CTDs and therefore their air concentrations and hence MDRs are predicted to change as the distance from the original source increases. From the assessed pair-PAHs, the biggest CTD difference is seen for Fluoranthene (107 km) vs. Pyrene (26 km). This study provides a strong indication that MDRs are of limited use as a source identification tool. -- Highlights: • Model-based evaluation of the PAHs molecular diagnostic ratios efficiency. • Individual PAHs are characterized by different characteristic travel distances. • MDRs are proven to be a limited tool for source identification. • Use of MDRs for other environmental media is likely unfeasible. -- PAHs molecular diagnostic ratios which change greatly as a function of distance from the emitting source are improper for source identification purposes

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.

Science.gov (United States)

Sánchez, Rubén; Serra, François; Tárraga, Joaquín; Medina, Ignacio; Carbonell, José; Pulido, Luis; de María, Alejandro; Capella-Gutíerrez, Salvador; Huerta-Cepas, Jaime; Gabaldón, Toni; Dopazo, Joaquín; Dopazo, Hernán

2011-07-01

Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing.

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

Science.gov (United States)

Sánchez, Rubén; Serra, François; Tárraga, Joaquín; Medina, Ignacio; Carbonell, José; Pulido, Luis; de María, Alejandro; Capella-Gutíerrez, Salvador; Huerta-Cepas, Jaime; Gabaldón, Toni; Dopazo, Joaquín; Dopazo, Hernán

2011-01-01

Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing. PMID:21646336

Can We Practically Bring Physics-based Modeling Into Operational Analytics Tools?

Energy Technology Data Exchange (ETDEWEB)

Granderson, Jessica [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Bonvini, Marco [Whisker Labs, Oakland, CA (United States); Piette, Mary Ann [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Page, Janie [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Lin, Guanjing [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Hu, R. Lilly [Univ. of California, Berkeley, CA (United States)

2017-08-11

We present that analytics software is increasingly used to improve and maintain operational efficiency in commercial buildings. Energy managers, owners, and operators are using a diversity of commercial offerings often referred to as Energy Information Systems, Fault Detection and Diagnostic (FDD) systems, or more broadly Energy Management and Information Systems, to cost-effectively enable savings on the order of ten to twenty percent. Most of these systems use data from meters and sensors, with rule-based and/or data-driven models to characterize system and building behavior. In contrast, physics-based modeling uses first-principles and engineering models (e.g., efficiency curves) to characterize system and building behavior. Historically, these physics-based approaches have been used in the design phase of the building life cycle or in retrofit analyses. Researchers have begun exploring the benefits of integrating physics-based models with operational data analytics tools, bridging the gap between design and operations. In this paper, we detail the development and operator use of a software tool that uses hybrid data-driven and physics-based approaches to cooling plant FDD and optimization. Specifically, we describe the system architecture, models, and FDD and optimization algorithms; advantages and disadvantages with respect to purely data-driven approaches; and practical implications for scaling and replicating these techniques. Finally, we conclude with an evaluation of the future potential for such tools and future research opportunities.

Molecular Tools for Diagnosis of Visceral Leishmaniasis: Systematic Review and Meta-Analysis of Diagnostic Test Accuracy

Science.gov (United States)

de Ruiter, C. M.; van der Veer, C.; Leeflang, M. M. G.; Deborggraeve, S.; Lucas, C.

2014-01-01

Molecular methods have been proposed as highly sensitive tools for the detection of Leishmania parasites in visceral leishmaniasis (VL) patients. Here, we evaluate the diagnostic accuracy of these tools in a meta-analysis of the published literature. The selection criteria were original studies that evaluate the sensitivities and specificities of molecular tests for diagnosis of VL, adequate classification of study participants, and the absolute numbers of true positives and negatives derivable from the data presented. Forty studies met the selection criteria, including PCR, real-time PCR, nucleic acid sequence-based amplification (NASBA), and loop-mediated isothermal amplification (LAMP). The sensitivities of the individual studies ranged from 29 to 100%, and the specificities ranged from 25 to 100%. The pooled sensitivity of PCR in whole blood was 93.1% (95% confidence interval [CI], 90.0 to 95.2), and the specificity was 95.6% (95% CI, 87.0 to 98.6). The specificity was significantly lower in consecutive studies, at 63.3% (95% CI, 53.9 to 71.8), due either to true-positive patients not being identified by parasitological methods or to the number of asymptomatic carriers in areas of endemicity. PCR for patients with HIV-VL coinfection showed high diagnostic accuracy in buffy coat and bone marrow, ranging from 93.1 to 96.9%. Molecular tools are highly sensitive assays for Leishmania detection and may contribute as an additional test in the algorithm, together with a clear clinical case definition. We observed wide variety in reference standards and study designs and now recommend consecutively designed studies. PMID:24829226

ANLIZE: a molecular mechanics force field visualization tool and its application to 18-crown-6.

Science.gov (United States)

Stolworthy, L D; Shirts, R B

1997-03-01

We describe a software tool that allows one to visualize and analyze the importance of each individual steric interaction in a molecular mechanics force field. ANLIZE is presently implemented for the Dreiding force field for use with the Cerius2 software package, but could be implemented in any molecular mechanics package with a graphical user interface. ANLIZE calculates individual interactions in the force field, sorts them by size, and displays them in several ways from a menu of choices. This allows the user to scan through selected interactions to visualize which interactions are the primary determinants of preferred conformations. The features of ANLIZE are illustrated using 18-crown-6 as an example, and the factors governing conformational preference in 18-crown-6 are demonstrated. Users of molecular mechanics packages are encouraged to demand this functionality from commercial software producers.

Cerebellum developmental challenges: From morphology to molecular issues

Directory of Open Access Journals (Sweden)

Andrei Cosma

2017-06-01

Full Text Available Introduction: It is known that, throughout the development of the nervous system, the cellular migratory routes are an important part of its expansion; therefore, the cerebellum is ‘sprinkled’ with cellular changes during its growth. The aim of this study was to analyse the morphological features of the cerebellum cells in all the layers, during its development. Material and methods: We examined 14 cases of human cerebellum, ranging between 1 to 12 months by histopathology and immunohistochemistry. Results: Haematoxylin and eosin staining method confirmed the age-linked migration of the cells from the external granular layer into the internal granular layer. Moreover, immunohistochemical evaluation using PROX1 and NFAP showed positivity for the Purkinje cells. However, these cells exposed negativity on NSE stained specimens. On the other hand, the transience of the EGL was analyzed using OCT3/4, which showed the migration of the EGL cells through the molecular layer to the IGL. Also, GFAP and NFAP proved to be a useful tool for the identification of the climbing fibres and the variation of their density connected the age of the patient. Conclusions: The human cerebellum undergoes different morphological and molecular changes throughout its evolution during embryogenesis. The markers used in our study have proved to present a differential, stage-dependant reactivity and appeared as useful tools for the identification of different cerebellar structures. Our study is a challenging attempt to understand the basics of cerebellar development at a morphological and molecular level and may bring new perspectives for a better approach of cerebellar associated pathologies.

CEREBELLUM DEVELOPMENTAL CHALLENGES: FROM MORPHOLOGY TO MOLECULAR ISSUES

Directory of Open Access Journals (Sweden)

Andrei Cosma ¹

2017-10-01

Full Text Available INTRODUCTION: It is known that, throughout the development of the nervous system, the cellular migratory routes are an important part of its expansion; therefore, the cerebellum is ‘sprinkled’ with cellular changes during its growth. The aim of this study was to analyse the morphological features of the cerebellum cells in all the layers, during its development. MATERIAL AND METHODS: We examined 14 cases of human cerebellum, ranging between 1 month to 12 years by histopathology and immunohistochemistry. RESULTS: Haematoxylin and eosin staining method confirmed the age-linked migration of the cells from the external granular layer into the internal granular layer. Moreover, immunohistochemical evaluation using PROX1 and NFAP showed positivity for the Purkinje cells. However, these cells exposed negativity on NSE stained specimens. On the other hand, the transience of the EGL was analysed using OCT3/4, which showed the migration of the EGL cells through the molecular layer to the IGL. Also, GFAP and NFAP proved to be a useful tool for the identification of the climbing fibres and the variation of their density connected the age of the patient. CONCLUSIONS: The human cerebellum undergoes different morphological and molecular changes throughout its evolution during embryogenesis. The markers used in our study have proved to present a differential, stage-dependant reactivity and appeared as useful tools for the identification of different cerebellar structures. Our study is a challenging attempt to understand the basics of cerebellar development at a morphological and molecular level and may bring new perspectives for a better approach of cerebellar associated pathologies.

Molecular tools for diagnosis of visceral leishmaniasis: systematic review and meta-analysis of diagnostic test accuracy.

Science.gov (United States)

de Ruiter, C M; van der Veer, C; Leeflang, M M G; Deborggraeve, S; Lucas, C; Adams, E R

2014-09-01

Molecular methods have been proposed as highly sensitive tools for the detection of Leishmania parasites in visceral leishmaniasis (VL) patients. Here, we evaluate the diagnostic accuracy of these tools in a meta-analysis of the published literature. The selection criteria were original studies that evaluate the sensitivities and specificities of molecular tests for diagnosis of VL, adequate classification of study participants, and the absolute numbers of true positives and negatives derivable from the data presented. Forty studies met the selection criteria, including PCR, real-time PCR, nucleic acid sequence-based amplification (NASBA), and loop-mediated isothermal amplification (LAMP). The sensitivities of the individual studies ranged from 29 to 100%, and the specificities ranged from 25 to 100%. The pooled sensitivity of PCR in whole blood was 93.1% (95% confidence interval [CI], 90.0 to 95.2), and the specificity was 95.6% (95% CI, 87.0 to 98.6). The specificity was significantly lower in consecutive studies, at 63.3% (95% CI, 53.9 to 71.8), due either to true-positive patients not being identified by parasitological methods or to the number of asymptomatic carriers in areas of endemicity. PCR for patients with HIV-VL coinfection showed high diagnostic accuracy in buffy coat and bone marrow, ranging from 93.1 to 96.9%. Molecular tools are highly sensitive assays for Leishmania detection and may contribute as an additional test in the algorithm, together with a clear clinical case definition. We observed wide variety in reference standards and study designs and now recommend consecutively designed studies. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Molecular profiling techniques as tools to detect potential unintended effects in genetically engineered maize

CSIR Research Space (South Africa)

Barros, E

2010-05-01

Full Text Available Molecular Profiling Techniques as Tools to Detect Potential Unintended Effects in Genetically Engineered Maize Eugenia Barros Introduction In the early stages of production and commercialization of foods derived from genetically engineered (GE) plants... systems. In a recent paper published in Plant Biotechnology Journal,4 we compared two transgenic white maize lines with the non-transgenic counterpart to investigate two possible sources of variation: genetic engineering and environmental variation...

Bring Your Own Device or Bring Your Own Distraction

Science.gov (United States)

Laxman, Kumar; Holt, Craig

2017-01-01

The purpose of this exploratory case study was to investigate the utilisation of Bring Your Own Device (BYOD) technologies in the classroom to determine if students and teachers perceive that the use of a digital device increased a learner's access to learning opportunities within the classroom, and, if the use of digital devices increased their…

[What do virtual reality tools bring to child and adolescent psychiatry?

Science.gov (United States)

Bioulac, S; de Sevin, E; Sagaspe, P; Claret, A; Philip, P; Micoulaud-Franchi, J A; Bouvard, M P

2018-06-01

Virtual reality is a relatively new technology that enables individuals to immerse themselves in a virtual world. It offers several advantages including a more realistic, lifelike environment that may allow subjects to "forget" they are being assessed, allow a better participation and an increased generalization of learning. Moreover, the virtual reality system can provide multimodal stimuli, such as visual and auditory stimuli, and can also be used to evaluate the patient's multimodal integration and to aid rehabilitation of cognitive abilities. The use of virtual reality to treat various psychiatric disorders in adults (phobic anxiety disorders, post-traumatic stress disorder, eating disorders, addictions…) and its efficacy is supported by numerous studies. Similar research for children and adolescents is lagging behind. This may be particularly beneficial to children who often show great interest and considerable success on computer, console or videogame tasks. This article will expose the main studies that have used virtual reality with children and adolescents suffering from psychiatric disorders. The use of virtual reality to treat anxiety disorders in adults is gaining popularity and its efficacy is supported by various studies. Most of the studies attest to the significant efficacy of the virtual reality exposure therapy (or in virtuo exposure). In children, studies have covered arachnophobia social anxiety and school refusal phobia. Despite the limited number of studies, results are very encouraging for treatment in anxiety disorders. Several studies have reported the clinical use of virtual reality technology for children and adolescents with autistic spectrum disorders (ASD). Extensive research has proven the efficiency of technologies as support tools for therapy. Researches are found to be focused on communication and on learning and social imitation skills. Virtual reality is also well accepted by subjects with ASD. The virtual environment offers

Improving molecular tools for global surveillance of measles virus⋆

Science.gov (United States)

Bankamp, Bettina; Byrd-Leotis, Lauren A.; Lopareva, Elena N.; Woo, Gibson K.S.; Liu, Chunyu; Jee, Youngmee; Ahmed, Hinda; Lim, Wilina W.; Ramamurty, Nalini; Mulders, Mick N.; Featherstone, David; Bellini, William J.; Rota, Paul A.

2017-01-01

Background The genetic characterization of wild-type measles viruses plays an important role in the description of viral transmission pathways and the verification of measles elimination. The 450 nucleotides that encode the carboxyl-terminus of the nucleoprotein (N-450) are routinely sequenced for genotype analysis. Objectives The objectives of this study were to develop improved primers and controls for RT-PCR reactions used for genotyping of measles samples and to develop a method to provide a convenient, safe, and inexpensive means to distribute measles RNA for RT-PCR assays and practice panels. Study design A newly designed, genetically defined synthetic RNA and RNA isolated from cells infected with currently circulating genotypes were used to compare the sensitivity of primer pairs in RT-PCR and nested PCR. FTA® cards loaded with lysates of measles infected cells were tested for their ability to preserve viral RNA and destroy virus infectivity. Results A new primer pair, MeV216/MeV214, was able to amplify N-450 from viruses representing 10 currently circulating genotypes and a genotype A vaccine strain and demonstrated 100-fold increased sensitivity compared to the previously used primer set. A nested PCR assay further increased the sensitivity of detection from patient samples. A synthetic positive control RNA was developed that produced PCR products that are distinguishable by size from PCR products amplified from clinical samples. FTA® cards completely inactivated measles virus and stabilized RNA for at least six months. Conclusions These improved molecular tools will advance molecular characterization of circulating measles viruses globally and provide enhanced quality control measures. PMID:23806666

Improving molecular tools for global surveillance of measles virus.

Science.gov (United States)

Bankamp, Bettina; Byrd-Leotis, Lauren A; Lopareva, Elena N; Woo, Gibson K S; Liu, Chunyu; Jee, Youngmee; Ahmed, Hinda; Lim, Wilina W; Ramamurty, Nalini; Mulders, Mick N; Featherstone, David; Bellini, William J; Rota, Paul A

2013-09-01

The genetic characterization of wild-type measles viruses plays an important role in the description of viral transmission pathways and the verification of measles elimination. The 450 nucleotides that encode the carboxyl-terminus of the nucleoprotein (N-450) are routinely sequenced for genotype analysis. The objectives of this study were to develop improved primers and controls for RT-PCR reactions used for genotyping of measles samples and to develop a method to provide a convenient, safe, and inexpensive means to distribute measles RNA for RT-PCR assays and practice panels. A newly designed, genetically defined synthetic RNA and RNA isolated from cells infected with currently circulating genotypes were used to compare the sensitivity of primer pairs in RT-PCR and nested PCR. FTA® cards loaded with lysates of measles infected cells were tested for their ability to preserve viral RNA and destroy virus infectivity. A new primer pair, MeV216/MeV214, was able to amplify N-450 from viruses representing 10 currently circulating genotypes and a genotype A vaccine strain and demonstrated 100-fold increased sensitivity compared to the previously used primer set. A nested PCR assay further increased the sensitivity of detection from patient samples. A synthetic positive control RNA was developed that produced PCR products that are distinguishable by size from PCR products amplified from clinical samples. FTA® cards completely inactivated measles virus and stabilized RNA for at least six months. These improved molecular tools will advance molecular characterization of circulating measles viruses globally and provide enhanced quality control measures. Published by Elsevier B.V.

Buried Volume Analysis for Propene Polymerization Catalysis Promoted by Group 4 Metals: a Tool for Molecular Mass Prediction

KAUST Repository

Falivene, Laura; Cavallo, Luigi; Talarico, Giovanni

2015-01-01

A comparison of the steric properties of homogeneous single site catalysts for propene polymerization using the percentage of buried volume (%VBur) as molecular descriptor is reported. The %VBur calculated on the neutral precursors of the active species seems to be a reliable tool to explain several experimental data related to the propene insertion and to the monomer chain transfer. Interestingly, a linear correlation between the buried volume calculated for a large set of neutral precursors and the energetic difference between propagation and termination steps calculated by DFT methods is found for Group 4 metal catalysts. The “master curves” derived for Ti, Zr and Hf confirm not only that the %VBur is an appropriate molecular descriptor for the systems considered but also that it could be used as tool for a large computational screening of new ligands.

Buried Volume Analysis for Propene Polymerization Catalysis Promoted by Group 4 Metals: a Tool for Molecular Mass Prediction

KAUST Repository

Falivene, Laura

2015-10-02

A comparison of the steric properties of homogeneous single site catalysts for propene polymerization using the percentage of buried volume (%VBur) as molecular descriptor is reported. The %VBur calculated on the neutral precursors of the active species seems to be a reliable tool to explain several experimental data related to the propene insertion and to the monomer chain transfer. Interestingly, a linear correlation between the buried volume calculated for a large set of neutral precursors and the energetic difference between propagation and termination steps calculated by DFT methods is found for Group 4 metal catalysts. The “master curves” derived for Ti, Zr and Hf confirm not only that the %VBur is an appropriate molecular descriptor for the systems considered but also that it could be used as tool for a large computational screening of new ligands.

Molecular dynamics simulation of subnanometric tool-workpiece contact on a force sensor-integrated fast tool servo for ultra-precision microcutting

International Nuclear Information System (INIS)

Cai, Yindi; Chen, Yuan-Liu; Shimizu, Yuki; Ito, So; Gao, Wei; Zhang, Liangchi

2016-01-01

Highlights: • Subnanometric contact between a diamond tool and a copper workpiece surface is investigated by MD simulation. • A multi-relaxation time technique is proposed to eliminate the influence of the atom vibrations. • The accuracy of the elastic-plastic transition contact depth estimation is improved by observing the residual defects. • The simulation results are beneficial for optimization of the next-generation microcutting instruments. - Abstract: This paper investigates the contact characteristics between a copper workpiece and a diamond tool in a force sensor-integrated fast tool servo (FS-FTS) for single point diamond microcutting and in-process measurement of ultra-precision surface forms of the workpiece. Molecular dynamics (MD) simulations are carried out to identify the subnanometric elastic-plastic transition contact depth, at which the plastic deformation in the workpiece is initiated. This critical depth can be used to optimize the FS-FTS as well as the cutting/measurement process. It is clarified that the vibrations of the copper atoms in the MD model have a great influence on the subnanometric MD simulation results. A multi-relaxation time method is then proposed to reduce the influence of the atom vibrations based on the fact that the dominant vibration component has a certain period determined by the size of the MD model. It is also identified that for a subnanometric contact depth, the position of the tool tip for the contact force to be zero during the retracting operation of the tool does not correspond to the final depth of the permanent contact impression on the workpiece surface. The accuracy for identification of the transition contact depth is then improved by observing the residual defects on the workpiece surface after the tool retracting.

FlaME: Flash Molecular Editor - a 2D structure input tool for the web

Directory of Open Access Journals (Sweden)

Dallakian Pavel

2011-02-01

Full Text Available Abstract Background So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME. In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. Implementation The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol( and setMol(. In addition, structures can be copied to the system clipboard. Conclusion A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application and the HTML elements on a web page, using JavaScript functions.

Molecular profiling--a tool for addressing emerging gaps in the comparative risk assessment of GMOs.

Science.gov (United States)

Heinemann, Jack A; Kurenbach, Brigitta; Quist, David

2011-10-01

Assessing the risks of genetically modified organisms (GMOs) is required by both international agreement and domestic legislation. Many view the use of the "omics" tools for profiling classes of molecules as useful in risk assessment, but no consensus has formed on the need or value of these techniques for assessing the risks of all GMOs. In this and many other cases, experts support case-by-case use of molecular profiling techniques for risk assessment. We review the latest research on the applicability and usefulness of molecular profiling techniques for GMO risk assessment. As more and more kinds of GMOs and traits are developed, broader use of molecular profiling in a risk assessment may be required to supplement the comparative approach to risk assessment. The literature-based discussions on the use of profiling appear to have settled on two findings: 1. profiling techniques are reliable and relevant, at least no less so than other techniques used in risk assessment; and 2. although not required routinely, regulators should be aware of when they are needed. The dismissal of routine molecular profiling may be confusing to regulators who then lack guidance on when molecular profiling might be worthwhile. Molecular profiling is an important way to increase confidence in risk assessments if the profiles are properly designed to address relevant risks and are applied at the correct stage of the assessment. Copyright © 2011 Elsevier Ltd. All rights reserved.

Can agile software tools bring the benefits of a task board to globally distributed teams?

NARCIS (Netherlands)

Katsma, Christiaan; Amrit, Chintan Amrit; van Hillegersberg, Jos; Sikkel, Nicolaas; Oshri, Ilan; Kotlarsky, Julia; Willcocks, Leslie P.

Software-based tooling has become an essential part of globally disitrbuted software development. In this study we focus on the usage of such tools and task boards in particular. We investigate the deployment of these tools through a field research in 4 different companies that feature agile and

Light and redox switchable molecular components for molecular electronics.

Science.gov (United States)

Browne, Wesley R; Feringa, Ben L

2010-01-01

The field of molecular and organic electronics has seen rapid progress in recent years, developing from concept and design to actual demonstration devices in which both single molecules and self-assembled monolayers are employed as light-responsive components. Research in this field has seen numerous unexpected challenges that have slowed progress and the initial promise of complex molecular-based computers has not yet been realised. Primarily this has been due to the realisation at an early stage that molecular-based nano-electronics brings with it the interface between the hard (semiconductor) and soft (molecular) worlds and the challenges which accompany working in such an environment. Issues such as addressability, cross-talk, molecular stability and perturbation of molecular properties (e.g., inhibition of photochemistry) have nevertheless driven development in molecular design and synthesis as well as our ability to interface molecular components with bulk metal contacts to a very high level of sophistication. Numerous groups have played key roles in progressing this field not least teams such as those led by Whitesides, Aviram, Ratner, Stoddart and Heath. In this short review we will however focus on the contributions from our own group and those of our collaborators, in employing diarylethene based molecular components.

Challenges for molecular and serological ZIKV infection confirmation.

Science.gov (United States)

de Vasconcelos, Zilton Farias Meira; Azevedo, Renata Campos; Thompson, Nathália; Gomes, Leonardo; Guida, Letícia; Moreira, Maria Elisabeth Lopes

2018-01-01

Zika Virus (ZIKV), member of Flaviviridae family and Flavivirus genus, has recently emerged as international public health emergency after its association with neonatal microcephaly cases. Clinical diagnosis hindrance involves symptom similarities produced by other arbovirus infections, therefore laboratory confirmation is of paramount importance. The most reliable test available is based on ZIKV RNA detection from body fluid samples. However, short viremia window periods and asymptomatic infections diminish the success rate for RT-PCR positivity. Beyond molecular detection, all serology tests in areas where other Flavivirus circulates proved to be a difficult task due to the broad range of cross-reactivity, especially with dengue pre-exposed individuals. Altogether, lack of serological diagnostic tools brings limitations to any retrospective evaluation. Those studies are central in the context of congenital infection that could occur asymptomatically and mask prevalence and risk rates.

Computational methods for molecular imaging

CERN Document Server

Shi, Kuangyu; Li, Shuo

2015-01-01

This volume contains original submissions on the development and application of molecular imaging computing. The editors invited authors to submit high-quality contributions on a wide range of topics including, but not limited to: • Image Synthesis & Reconstruction of Emission Tomography (PET, SPECT) and other Molecular Imaging Modalities • Molecular Imaging Enhancement • Data Analysis of Clinical & Pre-clinical Molecular Imaging • Multi-Modal Image Processing (PET/CT, PET/MR, SPECT/CT, etc.) • Machine Learning and Data Mining in Molecular Imaging. Molecular imaging is an evolving clinical and research discipline enabling the visualization, characterization and quantification of biological processes taking place at the cellular and subcellular levels within intact living subjects. Computational methods play an important role in the development of molecular imaging, from image synthesis to data analysis and from clinical diagnosis to therapy individualization. This work will bring readers fro...

Bringing Things Together

DEFF Research Database (Denmark)

Gundelach, Peter

2017-01-01

as facts, i.e. establish a scientific authoritative truth. In a case study from Denmark, the paper shows how the first survey - a study of seamstresses - was carried out by bringing several cognitive and organizational elements together: a network of researchers, a method for sampling, the construction...

Windows Developer Power Tools Turbocharge Windows development with more than 170 free and open source tools

CERN Document Server

Avery, James

2007-01-01

Software developers need to work harder and harder to bring value to their development process in order to build high quality applications and remain competitive. Developers can accomplish this by improving their productivity, quickly solving problems, and writing better code. A wealth of open source and free software tools are available for developers who want to improve the way they create, build, deploy, and use software. Tools, components, and frameworks exist to help developers at every point in the development process. Windows Developer Power Tools offers an encyclopedic guide to m

Bringing macromolecular machinery to life using 3D animation.

Science.gov (United States)

Iwasa, Janet H

2015-04-01

Over the past decade, there has been a rapid rise in the use of three-dimensional (3D) animation to depict molecular and cellular processes. Much of the growth in molecular animation has been in the educational arena, but increasingly, 3D animation software is finding its way into research laboratories. In this review, I will discuss a number of ways in which 3d animation software can play a valuable role in visualizing and communicating macromolecular structures and dynamics. I will also consider the challenges of using animation tools within the research sphere. Copyright © 2015. Published by Elsevier Ltd.

Microfluidic technology for molecular diagnostics.

Science.gov (United States)

Robinson, Tom; Dittrich, Petra S

2013-01-01

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

Sharing tools and know-how

DEFF Research Database (Denmark)

Saad-Sulonen, Joanna

In this position paper I address the theme of designing for sharing in self-organized urban communities by bringing forward the aspect of sharing tools and know-how. I report the lessons learned from a case in Helsinki and open questions for discussion regarding some of the identified challenges...

Analysis about diamond tool wear in nano-metric cutting of single crystal silicon using molecular dynamics method

Science.gov (United States)

Wang, Zhiguo; Liang, Yingchun; Chen, Mingjun; Tong, Zhen; Chen, Jiaxuan

2010-10-01

Tool wear not only changes its geometry accuracy and integrity, but also decrease machining precision and surface integrity of workpiece that affect using performance and service life of workpiece in ultra-precision machining. Scholars made a lot of experimental researches and stimulant analyses, but there is a great difference on the wear mechanism, especially on the nano-scale wear mechanism. In this paper, the three-dimensional simulation model is built to simulate nano-metric cutting of a single crystal silicon with a non-rigid right-angle diamond tool with 0 rake angle and 0 clearance angle by the molecular dynamics (MD) simulation approach, which is used to investigate the diamond tool wear during the nano-metric cutting process. A Tersoff potential is employed for the interaction between carbon-carbon atoms, silicon-silicon atoms and carbon-silicon atoms. The tool gets the high alternating shear stress, the tool wear firstly presents at the cutting edge where intension is low. At the corner the tool is splitted along the {1 1 1} crystal plane, which forms the tipping. The wear at the flank face is the structure transformation of diamond that the diamond structure transforms into the sheet graphite structure. Owing to the tool wear the cutting force increases.

Implementation of exterior complex scaling in B-splines to solve atomic and molecular collision problems

International Nuclear Information System (INIS)

McCurdy, C William; MartIn, Fernando

2004-01-01

B-spline methods are now well established as widely applicable tools for the evaluation of atomic and molecular continuum states. The mathematical technique of exterior complex scaling has been shown, in a variety of other implementations, to be a powerful method with which to solve atomic and molecular scattering problems, because it allows the correct imposition of continuum boundary conditions without their explicit analytic application. In this paper, an implementation of exterior complex scaling in B-splines is described that can bring the well-developed technology of B-splines to bear on new problems, including multiple ionization and breakup problems, in a straightforward way. The approach is demonstrated for examples involving the continuum motion of nuclei in diatomic molecules as well as electronic continua. For problems involving electrons, a method based on Poisson's equation is presented for computing two-electron integrals over B-splines under exterior complex scaling

NASA Applications of Molecular Nanotechnology

Science.gov (United States)

Globus, Al; Bailey, David; Han, Jie; Jaffe, Richard; Levit, Creon; Merkle, Ralph; Srivastava, Deepak

1998-01-01

Laboratories throughout the world are rapidly gaining atomically precise control over matter. As this control extends to an ever wider variety of materials, processes and devices, opportunities for applications relevant to NASA's missions will be created. This document surveys a number of future molecular nanotechnology capabilities of aerospace interest. Computer applications, launch vehicle improvements, and active materials appear to be of particular interest. We also list a number of applications for each of NASA's enterprises. If advanced molecular nanotechnology can be developed, almost all of NASA's endeavors will be radically improved. In particular, a sufficiently advanced molecular nanotechnology can arguably bring large scale space colonization within our grasp.

Application of Molecular Tools for Gut Health of Pet Animals: A Review

Directory of Open Access Journals (Sweden)

Lipismita Samal

2011-04-01

Full Text Available Gut health is an important facet of well being of pet animals; it is in this context, various nutritional and biotechnological approaches have been proposed to manipulate the gut health by specifically targeting the colonic microbiota. Nutritional approaches include supplementation of antioxidants and phytochemicals like flavonoids, isoflavonoids and carotenoids. Biotechnological approaches include supplementation of probiotics, prebiotics, synbiotics in the diet and potential application of molecular tools like fluorescent in situ hybridization, denaturing gradient gel electrophoresis, quantitative dot blot hybridization, and restriction fragment length polymorphism etc. in studying the fecal microbiota composition. Post-genomic and related technologies, i.e. genomics, nutrigenomics, transcriptomics, proteomics, metabolomics and epigenomics in the study of gastrointestinal tract also put forward challenges for nutritionists and microbiologists to elucidate the complex interactions between gut microbiota and host.

Introduction to basic molecular biologic techniques for molecular imaging researches

International Nuclear Information System (INIS)

Kang, Joo Hyun

2004-01-01

Molecular imaging is a rapidly growing field due to the advances in molecular biology and imaging technologies. With the introduction of imaging reporter genes into the cell, diverse cellular processes can be monitored, quantified and imaged non-invasively in vivo. These processes include the gene expression, protein-protein interactions, signal transduction pathways, and monitoring of cells such as cancer cells, immune cells, and stem cells. In the near future, molecular imaging analysis will allow us to observe the incipience and progression of the disease. These will make us easier to give a diagnosis in the early stage of intractable diseases such as cancer, neuro-degenerative disease, and immunological disorders. Additionally, molecular imaging method will be a valuable tool for the real-time evaluation of cells in molecular biology and the basic biological studies. As newer and more powerful molecular imaging tools become available, it will be necessary to corporate clinicians, molecular biologists and biochemists for the planning, interpretation, and application of these techniques to their fullest potential. In order for such a multidisciplinary team to be effective, it is essential that a common understanding of basic biochemical and molecular biologic techniques is achieved. Basic molecular techniques for molecular imaging methods are presented in this paper

doit – Automation Tool

Directory of Open Access Journals (Sweden)

2010-09-01

Full Text Available

This article describes how traditional build-tools work, what are the shortcomings of this model for modern software development and finally how doit solve these problems. doit is written in python, it comes from the idea of bringing the power of build-tools to execute any kind of tasks.

BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine

Science.gov (United States)

Liu, Zhongyang; Guo, Feifei; Wang, Yong; Li, Chun; Zhang, Xinlei; Li, Honglei; Diao, Lihong; Gu, Jiangyong; Wang, Wei; Li, Dong; He, Fuchu

2016-02-01

Traditional Chinese Medicine (TCM), with a history of thousands of years of clinical practice, is gaining more and more attention and application worldwide. And TCM-based new drug development, especially for the treatment of complex diseases is promising. However, owing to the TCM’s diverse ingredients and their complex interaction with human body, it is still quite difficult to uncover its molecular mechanism, which greatly hinders the TCM modernization and internationalization. Here we developed the first online Bioinformatics Analysis Tool for Molecular mechANism of TCM (BATMAN-TCM). Its main functions include 1) TCM ingredients’ target prediction; 2) functional analyses of targets including biological pathway, Gene Ontology functional term and disease enrichment analyses; 3) the visualization of ingredient-target-pathway/disease association network and KEGG biological pathway with highlighted targets; 4) comparison analysis of multiple TCMs. Finally, we applied BATMAN-TCM to Qishen Yiqi dripping Pill (QSYQ) and combined with subsequent experimental validation to reveal the functions of renin-angiotensin system responsible for QSYQ’s cardioprotective effects for the first time. BATMAN-TCM will contribute to the understanding of the “multi-component, multi-target and multi-pathway” combinational therapeutic mechanism of TCM, and provide valuable clues for subsequent experimental validation, accelerating the elucidation of TCM’s molecular mechanism. BATMAN-TCM is available at http://bionet.ncpsb.org/batman-tcm.

Molecular Modeling: A Powerful Tool for Drug Design and Molecular ...

Indian Academy of Sciences (India)

eling studies is generally a two-dimensional drawing of a re- quired molecule. ... The most active area of theoretical research using molecular orbi tal theory has been in ... minimum energy structure for example, by using conjugated gradient algorithm .... QSARwas applied to understand how the structure might be modified ...

An empirical approach for evaluating the usability of model-driven tools

NARCIS (Netherlands)

Condori-Fernandez, Nelly; Panach, Jose Ignacio; Baars, Arthur Iwan; Vos, Tanja; Pastor, Oscar

2013-01-01

MDD tools are very useful to draw conceptual models and to automate code generation. Even though this would bring many benefits, wide adoption of MDD tools is not yet a reality. Various research activities are being undertaken to find why and to provide the required solutions. However, insufficient

Is high pressure liquid chromatography an effective screening tool for characterization of molecular defects in hemoglobinopathies?

Directory of Open Access Journals (Sweden)

Nikhil Moorchung

2013-01-01

Full Text Available Introduction: Hemoglobinopathies constitute entities that are generated by either abnormal hemoglobin or thalassemias. high pressure liquid chromatography (HPLC is one of the best methods for screening and detection of various hemoglobinopathies but it has intrinsic interpretive problems. The study was designed to evaluate the different mutations seen in cases of hemoglobinopathies and compare the same with screening tests. Materials and Methods: 68 patients of hemoglobinopathies were screened by HPLC. Mutation studies in the beta globin gene was performed using the polymerase chain reaction (PCR-based allele-specific Amplification Refractory Mutation System (ARMS. Molecular analysis for the sickle cell mutation was done by standard methods. Results: The IVS 1/5 mutation was the commonest mutation seen and it was seen in 26 (38.23% of the cases. This was followed by the IVS 1/1, codon 41/42, codon 8/9, del 22 mutation, codon 15 mutation and the -619 bp deletion. No mutation was seen in eight cases. There was a 100% concordance between the sickle cell trait as diagnosed by HPLC and genetic testing. Discussion and Conclusion: Our study underlies the importance of molecular testing in all cases of hemoglobinopathies. Although HPLC is a useful screening tool, molecular testing is very useful in accurately diagnosing the mutations. Molecular testing is especially applicable in cases with an abnormal hemoglobin (HbD, HbE and HbS because there may be a concomitant inheritance of a beta thalassemia mutation. Molecular testing is the gold standard when it comes to the diagnosis of hemoglobinopathies.

Molecular Modeling

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 5. Molecular Modeling: A Powerful Tool for Drug Design and Molecular Docking. Rama Rao Nadendla. General Article Volume 9 Issue 5 May 2004 pp 51-60. Fulltext. Click here to view fulltext PDF. Permanent link:

Exome sequencing is an efficient tool for variant late-infantile neuronal ceroid lipofuscinosis molecular diagnosis.

Directory of Open Access Journals (Sweden)

Liliana Catherine Patiño

Full Text Available The neuronal ceroid-lipofuscinoses (NCL is a group of neurodegenerative disorders characterized by epilepsy, visual failure, progressive mental and motor deterioration, myoclonus, dementia and reduced life expectancy. Classically, NCL-affected individuals have been classified into six categories, which have been mainly defined regarding the clinical onset of symptoms. However, some patients cannot be easily included in a specific group because of significant variation in the age of onset and disease progression. Molecular genetics has emerged in recent years as a useful tool for enhancing NCL subtype classification. Fourteen NCL genetic forms (CLN1 to CLN14 have been described to date. The variant late-infantile form of the disease has been linked to CLN5, CLN6, CLN7 (MFSD8 and CLN8 mutations. Despite advances in the diagnosis of neurodegenerative disorders mutations in these genes may cause similar phenotypes, which rends difficult accurate candidate gene selection for direct sequencing. Three siblings who were affected by variant late-infantile NCL are reported in the present study. We used whole-exome sequencing, direct sequencing and in silico approaches to identify the molecular basis of the disease. We identified the novel c.1219T>C (p.Trp407Arg and c.1361T>C (p.Met454Thr MFSD8 pathogenic mutations. Our results highlighted next generation sequencing as a novel and powerful methodological approach for the rapid determination of the molecular diagnosis of NCL. They also provide information regarding the phenotypic and molecular spectrum of CLN7 disease.

Plant molecular farming: Opportunities and challenges

Directory of Open Access Journals (Sweden)

Valkova Rumyana

2013-01-01

Full Text Available The modern human life is impossible without products derived from the classical, contemporary biotechnology. However, large scale production of biotechnology wares opens a discussion about the economic impact, waste management, biosafety, and bioethical issues. Plant molecular farming offers a relatively inexpensive option for yielding of many valuable products and demonstrates number of advantages over the classical technologies, but also brings the question of further development perspectives, hazard identification and risk assessment. This review is focused on those two questions: opportunities offered and challenges faced by modern plant molecular farming systems.

Exome sequencing of index patients with retinal dystrophies as a tool for molecular diagnosis.

Directory of Open Access Journals (Sweden)

Marta Corton

Full Text Available Retinal dystrophies (RD are a group of hereditary diseases that lead to debilitating visual impairment and are usually transmitted as a Mendelian trait. Pathogenic mutations can occur in any of the 100 or more disease genes identified so far, making molecular diagnosis a rather laborious process. In this work we explored the use of whole exome sequencing (WES as a tool for identification of RD mutations, with the aim of assessing its applicability in a diagnostic context.We ascertained 12 Spanish families with seemingly recessive RD. All of the index patients underwent mutational pre-screening by chip-based sequence hybridization and resulted to be negative for known RD mutations. With the exception of one pedigree, to simulate a standard diagnostic scenario we processed by WES only the DNA from the index patient of each family, followed by in silico data analysis. We successfully identified causative mutations in patients from 10 different families, which were later verified by Sanger sequencing and co-segregation analyses. Specifically, we detected pathogenic DNA variants (∼50% novel mutations in the genes RP1, USH2A, CNGB3, NMNAT1, CHM, and ABCA4, responsible for retinitis pigmentosa, Usher syndrome, achromatopsia, Leber congenital amaurosis, choroideremia, or recessive Stargardt/cone-rod dystrophy cases.Despite the absence of genetic information from other family members that could help excluding nonpathogenic DNA variants, we could detect causative mutations in a variety of genes known to represent a wide spectrum of clinical phenotypes in 83% of the patients analyzed. Considering the constant drop in costs for human exome sequencing and the relative simplicity of the analyses made, this technique could represent a valuable tool for molecular diagnostics or genetic research, even in cases for which no genotypes from family members are available.

Tool and its management for nuclear power plant

International Nuclear Information System (INIS)

Yan Rui

2000-01-01

The tool and its management are a necessary part for the operation and maintenance of NPP.And NPP tool management is,in fact.a process of study, allocation, development, procurement, utilization, decontamination and scrap of the tools needed in the operation and outage, and also includes the organization, coordination and control of the whole process. NPP shall strengthen the scientific management of the process from procurement to scrap. According to its scale and characteristics, NPP may, implement unified and centralized management policy, establish necessary tool management organization, define the responsibilities of the management departments, make relevant management regulations and perfect tool quality assurance system to bring the tools into full play.Furthermore, the development and application of special management software provides a quite efficient means for the realization of scientific management of tools in NPP

Molecular techniques as complementary tools in orchid mutagenesis

Energy Technology Data Exchange (ETDEWEB)

Mohd Nazir Basiran; Sakinah Ariffin [Malaysian Institute for Nuclear Technology Research (MINT), Bangi (Malaysia)

2002-02-01

Orchid breeders have always been dependent on hybridization technology to produce new orchid hybrids and varieties. The technology has proven very reliable and easy to use and has produced wide range of successful cultivars with attractive combinations of spray length, bud number, flower colour and form, vase life, fragrance, seasonality, and compactness. By introducing mutagenesis however, wide variations of flower colours, form and size can still be obtained in addition to overcoming the problem of sexual incompatibility and sterility. In addition, complementary use of molecular techniques will allow breeders to target more specific characteristic changes and cut short breeding time. PCR-based techniques used to analyse the DNA of mutagenic clones found polymorphic fragments that can be developed as molecular markers. This paper describes how mutagenesis and molecular techniques can be used to enhance orchid breeding efforts. (author)

Bring your own device (BYOD) to work trend report

CERN Document Server

Hayes, Bob

2013-01-01

Bring Your Own Device (BYOD) to Work examines the emerging BYOD (Bring Your Own Device to work) trend in corporate IT. BYOD is the practice of employees bringing personally-owned mobile devices (e.g., smartphones, tablets, laptops) to the workplace, and using those devices to access company resources such as email, file servers, and databases. BYOD presents unique challenges in data privacy, confidentiality, security, productivity, and acceptable use that must be met proactively by information security professionals. This report provides solid background on the practice, original res

Campaign effects and self-analysis Internet tool

Energy Technology Data Exchange (ETDEWEB)

Brange, Birgitte [Danish Electricity Saving Trust (Denmark); Fjordbak Larsen, Troels [IT Energy ApS (Denmark); Wilke, Goeran [Danish Electricity Saving Trust (Denmark)

2007-07-01

In October 2006, the Danish Electricity Saving Trust launched a large TV campaign targeting domestic electricity consumption. The campaign was based on the central message '1000 kWh/year per person is enough'. The campaign was accompanied by a new internet portal with updated information about numerous household appliances, and by analysis tools for bringing down electricity consumption to 1000 kWh/year per person. The effects of the campaign are monitored through repeated surveys and analysed in relation to usage of internet tools.

Value Innovation in Learner-Centered Design. How to Develop Valuable Learning Tools

Science.gov (United States)

Breuer, Henning; Schwarz, Heinrich; Feller, Kristina; Matsumoto, Mitsuji

2014-01-01

This paper shows how to address technological, cultural and social transformations with empirically grounded innovation. Areas in transition such as higher education and learning techniques today bring about new needs and opportunities for innovative tools and services. But how do we find these tools? The paper argues for using a strategy of…

Molecular identification of livestock breeds: a tool for modern conservation biology.

Science.gov (United States)

Yaro, Mohammed; Munyard, Kylie A; Stear, Michael J; Groth, David M

2017-05-01

Global livestock genetic diversity includes all of the species, breeds and strains of domestic animals, and their variations. Although a recent census indicated that there were 40 species and over 8000 breeds of domestic animals; for the purpose of conservation biology the diversity between and within breeds rather than species is regarded to be of crucial importance. This domestic animal genetic diversity has developed through three main evolutionary events, from speciation (about 3 million years ago) through domestication (about 12000 years ago) to specialised breeding (starting about 200 years ago). These events and their impacts on global animal genetic resources have been well documented in the literature. The key importance of global domestic animal resources in terms of economic, scientific and cultural heritage has also been addressed. In spite of their importance, there is a growing number of reports on the alarming erosion of domestic animal genetic resources. This erosion of is happening in spite of several global conservation initiatives designed to mitigate it. Herein we discuss these conservation interventions and highlight their strengths and weaknesses. However, pivotal to the success of these conservation initiatives is the reliability of the genetic assignment of individual members to a target breed. Finally, we discuss the prospect of using improved breed identification methodologies to develop a reliable breed-specific molecular identification tool that is easily applicable to populations of livestock breeds in various ecosystems. These identification tools, when developed, will not only facilitate the regular monitoring of threatened or endangered breed populations, but also enhance the development of more efficient and sustainable livestock production systems. © 2016 Cambridge Philosophical Society.

Molecular Modeling and Simulation Tools in the Development of Peptide-Based Biosensors for Mycotoxin Detection: Example of Ochratoxin

Directory of Open Access Journals (Sweden)

Aby A. Thyparambil

2017-12-01

Full Text Available Mycotoxin contamination of food and feed is now ubiquitous. Exposures to mycotoxin via contact or ingestion can potentially induce adverse health outcomes. Affordable mycotoxin-monitoring systems are highly desired but are limited by (a the reliance on technically challenging and costly molecular recognition by immuno-capture technologies; and (b the lack of predictive tools for directing the optimization of alternative molecular recognition modalities. Our group has been exploring the development of ochratoxin detection and monitoring systems using the peptide NFO4 as the molecular recognition receptor in fluorescence, electrochemical and multimodal biosensors. Using ochratoxin as the model mycotoxin, we share our perspective on addressing the technical challenges involved in biosensor fabrication, namely: (a peptide receptor design; and (b performance evaluation. Subsequently, the scope and utility of molecular modeling and simulation (MMS approaches to address the above challenges are described. Informed and enabled by phage display, the subsequent application of MMS approaches can rationally guide subsequent biomolecular engineering of peptide receptors, including bioconjugation and bioimmobilization approaches to be used in the fabrication of peptide biosensors. MMS approaches thus have the potential to reduce biosensor development cost, extend product life cycle, and facilitate multi-analyte detection of mycotoxins, each of which positively contributes to the overall affordability of mycotoxin biosensor monitoring systems.

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks.

Science.gov (United States)

Lepoivre, Cyrille; Bergon, Aurélie; Lopez, Fabrice; Perumal, Narayanan B; Nguyen, Catherine; Imbert, Jean; Puthier, Denis

2012-01-31

Deciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph. We extend the previously developed TranscriptomeBrowser database with a set of tables containing 1,594,978 human and mouse molecular interactions. The database includes: (i) predicted regulatory interactions (computed by scanning vertebrate alignments with a set of 1,213 position weight matrices), (ii) potential regulatory interactions inferred from systematic analysis of ChIP-seq experiments, (iii) regulatory interactions curated from the literature, (iv) predicted post-transcriptional regulation by micro-RNA, (v) protein kinase-substrate interactions and (vi) physical protein-protein interactions. In order to easily retrieve and efficiently analyze these interactions, we developed In-teractomeBrowser, a graph-based knowledge browser that comes as a plug-in for Transcriptome-Browser. The first objective of InteractomeBrowser is to provide a user-friendly tool to get new insight into any gene list by providing a context-specific display of putative regulatory and physical interactions. To achieve this, InteractomeBrowser relies on a "cell compartments-based layout" that makes use of a subset of the Gene Ontology to map gene products onto relevant cell compartments. This layout is particularly powerful for visual integration of heterogeneous biological information

Bring Your Own Technology (BYOT to Education

Directory of Open Access Journals (Sweden)

Joseph M. Woodside

2014-06-01

Full Text Available In an effort to reduce costs and increase worker satisfaction, many businesses have implemented a concept known as Bring Your Own Device (BYOD or Bring Your Own Technology (BYOT. Similarly, many school districts are beginning to implement BYOT policies and programs to improve educational learning opportunities for students who have a wide variety of technology devices. BYOT allow districts with limited budgets enable usage of technology while improving student engagement. This paper explores the technology devices, and educational implications of policies, device management, security and included components.

BYOD: Bring your own disaster

CERN Multimedia

Computer Security Team

2013-01-01

Have you ever heard of “BYOD”? No, it is not a pop band. Try again. It is short for “Bring Your Own Device” (the French use “AVEC” -  “Apporter Votre Equipement personnel de Communication”) and describes an option long since offered at CERN: the possibility to bring along your personal laptop, smartphone or PDA, use it on CERN premises and connect it to the CERN office network. But hold on. As practical as it is, there is also a dark side.   The primary advantage, of course, is having a digital work environment tuned to your needs and preferences. It allows you to continue working at home. Similarly, you always have your music, address books and bookmarks with you. However, as valuable as this is, it is also a responsibility. Laptop theft is happening - outside CERN but also on site. In France, 30% of stolen laptops were stolen out of cars or homes, and 10% during travel. At CERN, on average one ...

FORMED: Bringing Formal Methods to the Engineering Desktop

Science.gov (United States)

2016-02-01

FORMED: BRINGING FORMAL METHODS TO THE ENGINEERING DESKTOP BAE SYSTEMS FEBRUARY 2016 FINAL TECHNICAL REPORT APPROVED FOR PUBLIC RELEASE...This report is published in the interest of scientific and technical information exchange, and its publication does not constitute the Government’s...BRINGING FORMAL METHODS TO THE ENGINEERING DESKTOP 5a. CONTRACT NUMBER FA8750-14-C-0024 5b. GRANT NUMBER N/A 5c. PROGRAM ELEMENT NUMBER 63781D

Bringing it All Together: NODC's Geoportal Server as an Integration Tool for Interoperable Data Services

Science.gov (United States)

Casey, K. S.; Li, Y.

2011-12-01

The US National Oceanographic Data Center (NODC) has implemented numerous interoperable data technologies in recent years to enhance the discovery, understanding, and use of the vast quantities of data in the NODC archives. These services include OPeNDAP's Hyrax server, Unidata's THREDDS Data Server (TDS), NOAA's Live Access Server (LAS), and most recently the ESRI ArcGIS Server. Combined, these technologies enable NODC to provide access to its data holdings and products through most of the commonly-used standardized web services like the Data Access Protocol (DAP) and the Open Geospatial Consortium suite of services such as the Web Mapping Service (WMS) and Web Coverage Service (WCS). Despite the strong demand for and use of these services, the acronym-rich environment of services can also result in confusion for producers of data to the NODC archives, for consumers of data from the NODC archives, and for the data stewards at the archives as well. The situation is further complicated by the fact that NODC also maintains some ad hoc services like WODselect, and that not all services can be applied to all of the tens of thousands of collections in the NODC archive; where once every data set was available only through FTP and HTTP servers, now many are also available from the LAS, TDS, Hyrax, and ArcGIS Server. To bring order and clarity to this potentially confusing collection of services, NODC deployed the Geoportal Server into its Archive Management System as an integrating technology that brings together its various data access, visualization, and discovery services as well as its overall metadata management workflows. While providing an enhanced web-based interface for more integrated human-to-machine discovery and access, the deployment also enables NODC for the first time to support a robust set of machine-to-machine discovery services such as the Catalog Service for the Web (CS/W), OpenSearch, and Search and Retrieval via URL (SRU) . This approach allows NODC

Developing new chemical tools for solvent extraction

International Nuclear Information System (INIS)

Moyer, B.A.; Baes, C.F.; Burns, J.H.; Case, G.N.; Sachleben, R.A.; Bryan, S.A.; Lumetta, G.J.; McDowell, W.J.; Sachleben, R.A.

1993-01-01

Prospects for innovation and for greater technological impact in the field of solvent extraction (SX) seem as bright as ever, despite the maturation of SX as an economically significant separation method and as an important technique in the laboratory. New industrial, environmental, and analytical problems provide compelling motivation for diversifying the application of SX, developing new solvent systems, and seeking improved properties. Toward this end, basic research must be dedicated to enhancing the tools of SX: physical tools for probing the basis of extraction and molecular tools for developing new SX chemistries. In this paper, the authors describe their progress in developing and applying the general tools of equilibrium analysis and of ion recognition in SX. Nearly half a century after the field of SX began in earnest, coordination chemistry continues to provide the impetus for important advancements in understanding SX systems and in controlling SX chemistry. In particular, the physical tools of equilibrium analysis, X-ray crystallography, and spectroscopy are elucidating the molecular basis of SX in unprecedented detail. Moreover, the principles of ion recognition are providing the molecular tools with which to achieve new selectivities and new applications

Molecular imaging. Fundamentals and applications

International Nuclear Information System (INIS)

Tian, Jie

2013-01-01

Covers a wide range of new theory, new techniques and new applications. Contributed by many experts in China. The editor has obtained the National Science and Technology Progress Award twice. ''Molecular Imaging: Fundamentals and Applications'' is a comprehensive monograph which describes not only the theory of the underlying algorithms and key technologies but also introduces a prototype system and its applications, bringing together theory, technology and applications. By explaining the basic concepts and principles of molecular imaging, imaging techniques, as well as research and applications in detail, the book provides both detailed theoretical background information and technical methods for researchers working in medical imaging and the life sciences. Clinical doctors and graduate students will also benefit from this book.

Interactive exploratory data analysis tool in Alzheimer’s disease

Directory of Open Access Journals (Sweden)

Diana Furcila

2015-04-01

Thus, MorExAn provide us the possibility to relate histopathological data with neuropsychological and clinical variables. The aid of this interactive visualization tool brings us the possibility to find unexpected conclusions beyond the insight provided by simple statistics analysis, as well as to improve neuroscientists’ productivity.

wft4galaxy: a workflow testing tool for galaxy.

Science.gov (United States)

Piras, Marco Enrico; Pireddu, Luca; Zanetti, Gianluigi

2017-12-01

Workflow managers for scientific analysis provide a high-level programming platform facilitating standardization, automation, collaboration and access to sophisticated computing resources. The Galaxy workflow manager provides a prime example of this type of platform. As compositions of simpler tools, workflows effectively comprise specialized computer programs implementing often very complex analysis procedures. To date, no simple way to automatically test Galaxy workflows and ensure their correctness has appeared in the literature. With wft4galaxy we offer a tool to bring automated testing to Galaxy workflows, making it feasible to bring continuous integration to their development and ensuring that defects are detected promptly. wft4galaxy can be easily installed as a regular Python program or launched directly as a Docker container-the latter reducing installation effort to a minimum. Available at https://github.com/phnmnl/wft4galaxy under the Academic Free License v3.0. marcoenrico.piras@crs4.it. © The Author 2017. Published by Oxford University Press.

Logic circuits based on molecular spider systems.

Science.gov (United States)

Mo, Dandan; Lakin, Matthew R; Stefanovic, Darko

2016-08-01

Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized reactions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi-spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks

Directory of Open Access Journals (Sweden)

Lepoivre Cyrille

2012-01-01

Full Text Available Abstract Background Deciphering gene regulatory networks by in silico approaches is a crucial step in the study of the molecular perturbations that occur in diseases. The development of regulatory maps is a tedious process requiring the comprehensive integration of various evidences scattered over biological databases. Thus, the research community would greatly benefit from having a unified database storing known and predicted molecular interactions. Furthermore, given the intrinsic complexity of the data, the development of new tools offering integrated and meaningful visualizations of molecular interactions is necessary to help users drawing new hypotheses without being overwhelmed by the density of the subsequent graph. Results We extend the previously developed TranscriptomeBrowser database with a set of tables containing 1,594,978 human and mouse molecular interactions. The database includes: (i predicted regulatory interactions (computed by scanning vertebrate alignments with a set of 1,213 position weight matrices, (ii potential regulatory interactions inferred from systematic analysis of ChIP-seq experiments, (iii regulatory interactions curated from the literature, (iv predicted post-transcriptional regulation by micro-RNA, (v protein kinase-substrate interactions and (vi physical protein-protein interactions. In order to easily retrieve and efficiently analyze these interactions, we developed In-teractomeBrowser, a graph-based knowledge browser that comes as a plug-in for Transcriptome-Browser. The first objective of InteractomeBrowser is to provide a user-friendly tool to get new insight into any gene list by providing a context-specific display of putative regulatory and physical interactions. To achieve this, InteractomeBrowser relies on a "cell compartments-based layout" that makes use of a subset of the Gene Ontology to map gene products onto relevant cell compartments. This layout is particularly powerful for visual integration

Teaching molecular genetics: Chapter 1--Background principles and methods of molecular biology.

Science.gov (United States)

Knoers, Nine V A M; Monnens, Leo A H

2006-02-01

In this first chapter of the series "Teaching molecular genetics," an introduction to molecular genetics is presented. We describe the structure of DNA and genes and explain in detail the central dogma of molecular biology, that is, the flow of genetic information from DNA via RNA to polypeptide (protein). In addition, several basic and frequently used general molecular tools, such as restriction enzymes, Southern blotting, DNA amplification and sequencing are discussed, in order to lay the foundations for the forthcoming chapters.

The Quake-Catcher Network: Bringing Seismology to Homes and Schools

Science.gov (United States)

Lawrence, J. F.; Cochran, E. S.; Christensen, C. M.; Saltzman, J.; Taber, J.; Hubenthal, M.

2011-12-01

The Quake-Catcher Network (QCN) is a collaborative initiative for developing the world's largest, low-cost strong-motion seismic network by utilizing sensors in and attached to volunteer internet-connected computers. QCN is not only a research tool, but provides an educational tool for teaching earthquake science in formal and informal environments. A central mission of the Quake-Catcher Network is to provide scientific educational software and hardware so that K-12 teachers, students, and the general public can better understand and participate in the science of earthquakes and earthquake hazards. With greater understanding, teachers, students, and interested individuals can share their new knowledge, resulting in continued participation in the project, and better preparation for earthquakes in their homes, businesses, and communities. The primary educational outreach goals are 1) to present earthquake science and earthquake hazards in a modern and exciting way, and 2) to provide teachers and educators with seismic sensors, interactive software, and educational modules to assist in earthquake education. QCNLive (our interactive educational computer software) displays recent and historic earthquake locations and 3-axis real-time acceleration measurements. This tool is useful for demonstrations and active engagement for all ages, from K-college. QCN provides subsidized sensors at 49 for the general public and 5 for K-12 teachers. With your help, the Quake-Catcher Network can provide better understanding of earthquakes to a broader audience. Academics are taking QCN to classrooms across the United States and around the world. The next time you visit a K-12 classroom or teach a college class on interpreting seismograms, bring a QCN sensor and QCNLive software with you! To learn how, visit http://qcn.stanford.edu.

Exercise Brings Bone Benefits that Last

Science.gov (United States)

... Subscribe May 2014 Print this issue Health Capsule Exercise Brings Bone Benefits that Last En español Send ... lose bone. Studies of animals have shown that exercise during periods of rapid growth can lead to ...

Iterating between Tools to Create and Edit Visualizations.

Science.gov (United States)

Bigelow, Alex; Drucker, Steven; Fisher, Danyel; Meyer, Miriah

2017-01-01

A common workflow for visualization designers begins with a generative tool, like D3 or Processing, to create the initial visualization; and proceeds to a drawing tool, like Adobe Illustrator or Inkscape, for editing and cleaning. Unfortunately, this is typically a one-way process: once a visualization is exported from the generative tool into a drawing tool, it is difficult to make further, data-driven changes. In this paper, we propose a bridge model to allow designers to bring their work back from the drawing tool to re-edit in the generative tool. Our key insight is to recast this iteration challenge as a merge problem - similar to when two people are editing a document and changes between them need to reconciled. We also present a specific instantiation of this model, a tool called Hanpuku, which bridges between D3 scripts and Illustrator. We show several examples of visualizations that are iteratively created using Hanpuku in order to illustrate the flexibility of the approach. We further describe several hypothetical tools that bridge between other visualization tools to emphasize the generality of the model.

Practical tools to implement massive parallel pyrosequencing of PCR products in next generation molecular diagnostics.

Directory of Open Access Journals (Sweden)

Kim De Leeneer

Full Text Available Despite improvements in terms of sequence quality and price per basepair, Sanger sequencing remains restricted to screening of individual disease genes. The development of massively parallel sequencing (MPS technologies heralded an era in which molecular diagnostics for multigenic disorders becomes reality. Here, we outline different PCR amplification based strategies for the screening of a multitude of genes in a patient cohort. We performed a thorough evaluation in terms of set-up, coverage and sequencing variants on the data of 10 GS-FLX experiments (over 200 patients. Crucially, we determined the actual coverage that is required for reliable diagnostic results using MPS, and provide a tool to calculate the number of patients that can be screened in a single run. Finally, we provide an overview of factors contributing to false negative or false positive mutation calls and suggest ways to maximize sensitivity and specificity, both important in a routine setting. By describing practical strategies for screening of multigenic disorders in a multitude of samples and providing answers to questions about minimum required coverage, the number of patients that can be screened in a single run and the factors that may affect sensitivity and specificity we hope to facilitate the implementation of MPS technology in molecular diagnostics.

POLYANA-A tool for the calculation of molecular radial distribution functions based on Molecular Dynamics trajectories

Science.gov (United States)

Dimitroulis, Christos; Raptis, Theophanes; Raptis, Vasilios

2015-12-01

We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to 'hack' the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.

THE EVALUATION OF A TOOL FOR DISSEMINATION OF BIOTECHNOLOGY AND MOLECULAR BIOLOGY CONCEPTS IN FORMAL EDUCATION

Directory of Open Access Journals (Sweden)

F.M. Escanhoela

2007-05-01

Full Text Available Since 2003, the CBME Scientific Dissemination Coordination hasdeveloped a project related to the production and distribution of a scientificdissemination newspaper, called CBME InFORMAÇÃO, directed to high-schoolstudents and teachers. It is a quarterly publication and shows the concepts andadvances of studies in molecular biology and biotechnology. In order to evaluatethe newspaper, a research was accomplished in 2005. It involved 177 studentsfrom six high schools of São Carlos and region. In addition, opinions of fivescience teachers that worked with the newspaper in their classrooms, as well aseight Biology undergraduates were collected. The teachers received somequestionnaires that had to be answered by them and their students after a specifyactivity with the periodical – basically, the activities consisted of three stages:individual reading of the newspaper; formulation of questions by the teacher and,finally, group discussion on the chosen theme. The research confirmed theimportance of the use of the periodical as a tool in the formation of critical readersof facts related to the biotechnology and molecular biology, what should contributewith the citizenship development in the students. Moreover, it provided a possibilityto reorganize the periodical.

Assessment and applicability of evaluation tools: Current practice in a sample of European countries and steps towards a state-of-the-art approach. Road Infrastructure Safety Management Evaluation Tools (RISMET), Deliverables No. 4 and 5.

NARCIS (Netherlands)

Elvik, R.

2014-01-01

This report surveys current practice in a sample of European countries with respect to the use of ten different tools for safety management of road systems. The report also proposes steps that can be taken to bring the use of these management tools closer to their state-of-the-art versions. These

Combining self- and cross-docking as benchmark tools: the performance of DockBench in the D3R Grand Challenge 2

Science.gov (United States)

Salmaso, Veronica; Sturlese, Mattia; Cuzzolin, Alberto; Moro, Stefano

2018-01-01

Molecular docking is a powerful tool in the field of computer-aided molecular design. In particular, it is the technique of choice for the prediction of a ligand pose within its target binding site. A multitude of docking methods is available nowadays, whose performance may vary depending on the data set. Therefore, some non-trivial choices should be made before starting a docking simulation. In the same framework, the selection of the target structure to use could be challenging, since the number of available experimental structures is increasing. Both issues have been explored within this work. The pose prediction of a pool of 36 compounds provided by D3R Grand Challenge 2 organizers was preceded by a pipeline to choose the best protein/docking-method couple for each blind ligand. An integrated benchmark approach including ligand shape comparison and cross-docking evaluations was implemented inside our DockBench software. The results are encouraging and show that bringing attention to the choice of the docking simulation fundamental components improves the results of the binding mode predictions.

Bringing science to business

Science.gov (United States)

Lemetti, Paul

2005-06-01

Bringing science to business seems rather straight forward. Technology is constantly moving forward and new inventions are being brought into the market place. Science parks and technology parks have sprung out all around the globe competing against each other and trying to keep their own doors open by bringing in new business, thereby creating much needed income to keep their operations moving forward. However, only a small handful ofthese centers around the world can truly be considered successful. It is the relationship between the scientists, start-up business, local universities, local government, and invited bigger business that allows the parks to succeed. The individual scientist wishing to enter into business or just hoping to get his invention into the pool of potential ideas; which might end up in the hands of an entrepreneur or an established company, is not always that simple. Universal success principles must be embraced to ensure success. One must believe in oneself and to strive for excellence. One must be able to see the other persons viewpoint and adapt and change his behavior in order to succeed. One must learn to create trust as well as learn to trust. Furthermore, one must learn to focus on the why of the process and not on the how. A market must be identified and benefits of local area must be sold to potential investor or business partners. A local success has in part to do with local cooperation.

TdPIR minisatellite fingerprinting as a useful new tool for Torulaspora delbrueckii molecular typing.

Science.gov (United States)

Canonico, Laura; Comitini, Francesca; Ciani, Maurizio

2015-05-04

Torulaspora delbrueckii yeast strains are being increasingly applied at the industrial level, such as in the winemaking process, and so their identification and characterisation require effective, fast, accurate, reproducible and reliable approaches. Therefore, the development of typing techniques that allow discrimination at the strain level will provide an essential tool for those working with T. delbrueckii strains. Here, 28 T. delbrueckii strains from various substrates were characterised using different PCR-fingerprinting molecular methods: random amplified polymorphic DNA with polymerase chain reaction (RAPD-PCR), minisatellites SED1, AGA1, DAN4 and the newly designed T. delbrueckii (Td)PIR, and microsatellites (GAC)5 and (GTG)5. The aim was to determine and compare the efficacies, reproducibilities and discriminating powers of these molecular methods. RAPD-PCR using the M13 primers and the newly designed TdPIR3 minisatellite primer pair provided discrimination of the greatest number of T. delbrueckii strains. TdPIR3 clustered the 28 strains into 16 different groups with an efficiency of 100%, while M13 clustered the strains into 17 different groups, although with a lower efficiency of 89%. Moreover, the TdPIR3 primers showed reproducible profiles when the stringency of the PCR protocol was varied, which highlighted the great robustness of this technique. In contrast, variation of the stringency of the M13 PCR protocol resulted in modification of the amplified profiles, which suggested low reproducibility of this technique. Copyright © 2015 Elsevier B.V. All rights reserved.

Advanced Characterization of Molecular Interactions in TALSPEAK-like Separations Systems

Energy Technology Data Exchange (ETDEWEB)

Nash, Kenneth [Washington State Univ., Pullman, WA (United States); Guelis, Artem [Argonne National Lab. (ANL), Argonne, IL (United States); Lumetta, Gregg J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Sinkov, Sergey [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2015-10-21

Combining unit operations in advanced aqueous reprocessing schemes brings obvious process compactness advantages, but at the same time greater complexity in process design and operation. Unraveling these interactions requires increasingly sophisticated analytical tools and unique approaches for adequate analysis and characterization that probe molecular scale interactions. Conventional slope analysis methods of solvent extraction are too indirect to provide much insight into such interactions. This project proposed the development and verification of several analytical tools based on studies of TALSPEAK-like aqueous processes. As such, the chemistry of trivalent fission product lanthanides, americium, curium, plutonium, neptunium and uranium figure prominently in these studies. As the project was executed, the primary focus fell upon the chemistry or trivalent lanthanides and actinides. The intent of the investigation was to compare and contrast the results from these various complementary techniques/studies to provide a stronger basis for predicting the performance of extractant/diluent mixtures as media for metal ion separations. As many/most of these techniques require the presence of metal ions at elevated concentrations, it was expected that these studies would take this investigation into the realm of patterns of supramolecular organization of metal complexes and extractants in concentrated aqueous/organic media. We expected to advance knowledge of the processes that enable and limit solvent extraction reactions as a result of the application of fundamental chemical principles to explaining interactions in complex media.

Underworld - Bringing a Research Code to the Classroom

Science.gov (United States)

Moresi, L. N.; Mansour, J.; Giordani, J.; Farrington, R.; Kaluza, O.; Quenette, S.; Woodcock, R.; Squire, G.

2017-12-01

While there are many reasons to celebrate the passing of punch card programming and flickering green screens,the loss of the sense of wonder at the very existence of computers and the calculations they make possible shouldnot be numbered among them. Computers have become so familiar that students are often unaware that formal and careful design of algorithms andtheir implementations remains a valuable and important skill that has to be learned and practiced to achieveexpertise and genuine understanding. In teaching geodynamics and geophysics at undergraduate level, we aimed to be able to bring our researchtools into the classroom - even when those tools are advanced, parallel research codes that we typically deploy on hundredsor thousands of processors, and we wanted to teach not just the physical concepts that are modelled by these codes but asense of familiarity with computational modelling and the ability to discriminate a reliable model from a poor one. The underworld code (www.underworldcode.org) was developed for modelling plate-scale fluid mechanics and studyingproblems in lithosphere dynamics. Though specialised for this task, underworld has a straightforwardpython user interface that allows it to run within the environment of jupyter notebooks on a laptop (at modest resolution, of course).The python interface was developed for adaptability in addressing new research problems, but also lends itself to integration intoa python-driven learning environment. To manage the heavy demands of installing and running underworld in a teaching laboratory, we have developed a workflow in whichwe install docker containers in the cloud which support a number of students to run their own environment independently. We share ourexperience blending notebooks and static webpages into a single web environment, and we explain how we designed our graphics andanalysis tools to allow notebook "scripts" to be queued and run on a supercomputer.

Novel molecular diagnostic tools for malaria elimination: a review of options from the point of view of high-throughput and applicability in resource limited settings.

Science.gov (United States)

Britton, Sumudu; Cheng, Qin; McCarthy, James S

2016-02-16

As malaria transmission continues to decrease, an increasing number of countries will enter pre-elimination and elimination. To interrupt transmission, changes in control strategies are likely to require more accurate identification of all carriers of Plasmodium parasites, both symptomatic and asymptomatic, using diagnostic tools that are highly sensitive, high throughput and with fast turnaround times preferably performed in local health service settings. Currently available immunochromatographic lateral flow rapid diagnostic tests and field microscopy are unlikely to consistently detect infections at parasite densities less than 100 parasites/µL making them insufficiently sensitive for detecting all carriers. Molecular diagnostic platforms, such as PCR and LAMP, are currently available in reference laboratories, but at a cost both financially and in turnaround time. This review describes the recent progress in developing molecular diagnostic tools in terms of their capacity for high throughput and potential for performance in non-reference laboratories for malaria elimination.

Leveling the playing field: bringing development of biomarkers and molecular diagnostics up to the standards for drug development.

Science.gov (United States)

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

2012-03-15

Molecular diagnostics are becoming increasingly important in clinical research to stratify or identify molecularly profiled patient cohorts for targeted therapies, to modify the dose of a therapeutic, and to assess early response to therapy or monitor patients. Molecular diagnostics can also be used to identify the pharmacogenetic risk of adverse drug reactions. The articles in this CCR Focus section on molecular diagnosis describe the development and use of markers to guide medical decisions regarding cancer patients. They define sources of preanalytic variability that need to be minimized, as well as the regulatory and financial challenges involved in developing diagnostics and integrating them into clinical practice. They also outline a National Cancer Institute program to assist diagnostic development. Molecular diagnostic clinical tests require rigor in their development and clinical validation, with sensitivity, specificity, and validity comparable to those required for the development of therapeutics. These diagnostics must be offered at a realistic cost that reflects both their clinical value and the costs associated with their development. When genome-sequencing technologies move into the clinic, they must be integrated with and traceable to current technology because they may identify more efficient and accurate approaches to drug development. In addition, regulators may define progressive drug approval for companion diagnostics that requires further evidence regarding efficacy and safety before full approval can be achieved. One way to accomplish this is to emphasize phase IV postmarketing, hypothesis-driven clinical trials with biological characterization that would permit an accurate definition of the association of low-prevalence gene alterations with toxicity or response in large cohorts.

An educational tool for interactive parallel and distributed processing

DEFF Research Database (Denmark)

Pagliarini, Luigi; Lund, Henrik Hautop

2012-01-01

In this article we try to describe how the modular interactive tiles system (MITS) can be a valuable tool for introducing students to interactive parallel and distributed processing programming. This is done by providing a handson educational tool that allows a change in the representation...... of abstract problems related to designing interactive parallel and distributed systems. Indeed, the MITS seems to bring a series of goals into education, such as parallel programming, distributedness, communication protocols, master dependency, software behavioral models, adaptive interactivity, feedback......, connectivity, topology, island modeling, and user and multi-user interaction which can rarely be found in other tools. Finally, we introduce the system of modular interactive tiles as a tool for easy, fast, and flexible hands-on exploration of these issues, and through examples we show how to implement...

Heat Treatment of Cr- and Cr-V ledeburitic tool steels

Directory of Open Access Journals (Sweden)

Peter Jurči

2014-11-01

Full Text Available Cr- and Cr-V ledeburitic cold work tool steels belong to the most important tool materials for large series manufacturing. To enable high production stability, the tools must be heat treated before use. This overview paper brings a comprehensive study on the heat treatment of these materials, starting from the soft annealing and finishing with the tempering. Also, it describes the impact of any step of the heat treatment on the most important structural and mechanical characteristics, like the hardness, the toughness and the wear resistance. The widely used AIS D2- steel (conventionally manufactured and Vanadis 6 (PM are used as examples in most cases.

Bringing History Alive in the Classroom!

Science.gov (United States)

McRae, Lee, Ed.

1996-01-01

This document consists of the first four issues of a serial publication, "Bringing History Alive in the Classroom!" The volumes focus on: (1) "A Sampling of Renaissance Instruments," which includes: information on Christopher Columbus, Leondardo da Vinci, and William Shakespeare, a timeline from the middle ages through the renaissance, Queen…

Charge Transport Processes in Molecular Junctions

Science.gov (United States)

Smith, Christopher Eugene

Molecular electronics (ME) has evolved into a rich area of exploration that combines the fields of chemistry, materials, electronic engineering and computational modeling to explore the physics behind electronic conduction at the molecular level. Through studying charge transport properties of single molecules and nanoscale molecular materials the field has gained the potential to bring about new avenues for the miniaturization of electrical components where quantum phenomena are utilized to achieve solid state molecular device functionality. Molecular junctions are platforms that enable these studies and consist of a single molecule or a small group of molecules directly connected to electrodes. The work presented in this thesis has built upon the current understanding of the mechanisms of charge transport in ordered junctions using self-assembled monolayer (SAM) molecular thin films. Donor and acceptor compounds were synthesized and incorporated into SAMs grown on metal substrates then the transport properties were measured with conducting probe atomic force microscopy (CP-AFM). In addition to experimentally measured current-voltage (I-V) curves, the transport properties were addressed computationally and modeled theoretically. The key objectives of this project were to 1) investigate the impact of molecular structure on hole and electron charge transport, 2) understand the nature of the charge carriers and their structure-transport properties through long (chemically gated to modulate the transport. These results help advance our understanding of transport behavior in semiconducting molecular thin films, and open opportunities to engineer improved electronic functionality into molecular devices.

ASTROS: A multidisciplinary automated structural design tool

Science.gov (United States)

Neill, D. J.

1989-01-01

ASTROS (Automated Structural Optimization System) is a finite-element-based multidisciplinary structural optimization procedure developed under Air Force sponsorship to perform automated preliminary structural design. The design task is the determination of the structural sizes that provide an optimal structure while satisfying numerous constraints from many disciplines. In addition to its automated design features, ASTROS provides a general transient and frequency response capability, as well as a special feature to perform a transient analysis of a vehicle subjected to a nuclear blast. The motivation for the development of a single multidisciplinary design tool is that such a tool can provide improved structural designs in less time than is currently needed. The role of such a tool is even more apparent as modern materials come into widespread use. Balancing conflicting requirements for the structure's strength and stiffness while exploiting the benefits of material anisotropy is perhaps an impossible task without assistance from an automated design tool. Finally, the use of a single tool can bring the design task into better focus among design team members, thereby improving their insight into the overall task.

Nuclear imaging drug development tools

International Nuclear Information System (INIS)

Buchanan, L.; Jurek, P.; Redshaw, R.

2007-01-01

This article describes the development of nuclear imaging as an enabling technology in the pharmaceutical industry. Molecular imaging is maturing into an important tool with expanding applications from validating that a drug reaches the intended target through to market launch of a new drug. Molecular imaging includes anatomical imaging of organs or tissues, computerized tomography (CT), magnetic resonance imaging (MRI) and ultrasound.

Translating molecular medicine into clinical tools: doomed to fail by neglecting basic preanalytical principles

Directory of Open Access Journals (Sweden)

Mannello Ferdinando

2009-10-01

Full Text Available Abstract This commentary discusses a study on measurements of matrix metalloproteinase 9 (MMP-9 in serum of pseudoxanthoma elasticum patients recently published in Journal of Molecular Medicine. This study can be considered the typical "obstacle" to effective translational medicine as previously documented in JTM journal. Although serum has been frequently proven as inappropriate sample for determining numerous circulating MMPs, among them MMP-9, there are over and over again studies, as in this case, that measure MMP-9 in serum. Comparative measurements in serum and plasma samples demonstrated higher concentrations for MMP-9 in serum due to the additional release from leukocytes and platelets following the coagulation/fibrinolysis process. From this example it can be concluded that translating basic research discoveries into clinical tools needs a more intensive exchange between basic biomedical research and clinical scientists already in an early stage. Otherwise a lost of translation, as discussed in JTM journal, seems to be inevitable.

QR Code: An Interactive Mobile Advertising Tool

OpenAIRE

Ela Sibel Bayrak Meydanoglu

2013-01-01

Easy and rapid interaction between consumers and marketers enabled by mobile technology prompted  an increase in the usage of mobile media as an interactive marketing tool in recent years. One of the mobile technologies that can be used in interactive marketing for advertising is QR code (Quick Response Code). Interactive advertising brings back some advantages for the companies that apply it. For example, interaction with consumers provides significant information about consumers' preference...

Indigoid Photoswitches: Visible Light Responsive Molecular Tools.

Science.gov (United States)

Petermayer, Christian; Dube, Henry

2018-05-15

Indigoid photoswitches comprise a class of chromophores that are derived from the parent and well-known indigo dye. Different from most photoswitches their core structures absorb in the visible region of the spectrum in both isomeric states even without substitutions, which makes them especially interesting for applications not tolerant of high-energy UV light. Also different from most current photoswitching systems, they provide highly rigid structures that undergo large yet precisely controllable geometry changes upon photoisomerization. The favorable combination of pronounced photochromism, fast and efficient photoreactions, and high thermal bistability have led to a strongly increased interest in indigoid photoswitches over the last years. As a result, intriguing applications of these chromophores as reversible triggering units in supramolecular and biological chemistry, the field of molecular machines, or smart molecules have been put forward. In this Account current developments in the synthesis, mechanistic understanding of light responsiveness, advantageous properties as phototools, and new applications of indigoid photoswitches are summarized with the focus on hemithioindigo, hemiindigo, and indigo as key examples. Many methods for the synthesis of hemithioindigos are known, but derivatives with a fourth substituent at the double bond could not easily be prepared because of the resulting increased steric hindrance in the products. Recent efforts in our laboratory have provided two different methods to prepare these highly promising photoswitches in very efficient ways. One method is especially designed for the introduction of sterically hindered ketones while the second one allows rapid structural diversification in only three high-yielding synthetic steps. Given the lesser prominence of indigoid photoswitches, mechanistic understanding of their excited state behavior and therefore rational design opportunities for photophysical properties are also much

Rapid molecular diagnostics for multi-drug resistant tuberculosis in India.

Science.gov (United States)

Ramachandran, Rajeswari; Muniyandi, M

2018-03-01

Rapid molecular diagnostic methods help in the detection of TB and Rifampicin resistance. These methods detect TB early, are accurate and play a crucial role in reducing the burden of drug resistant tuberculosis. Areas covered: This review analyses rapid molecular diagnostic tools used in the diagnosis of MDR-TB in India, such as the Line Probe Assay and GeneXpert. We have discussed the burden of MDR-TB and the impact of recent diagnostic tools on case detection and treatment outcomes. This review also discusses the costs involved in establishing these new techniques in India. Expert commentary: Molecular methods have considerable advantages for the programmatic management of drug resistant TB. These include speed, standardization of testing, potentially high throughput and reduced laboratory biosafety requirements. There is a desperate need for India to adopt modern, rapid, molecular tools with point-of-care tests being currently evaluated. New molecular diagnostic tests appear to be cost effective and also help in detecting missing cases. There is enough evidence to support the scaling up of these new tools in India.

Fleet DNA Brings Fleet Data to Life, Informs R&D | NREL

Science.gov (United States)

Fleet DNA Brings Fleet Data to Life, Informs R&D Science and Technology Highlights Highlights in Research & Development Fleet DNA Brings Fleet Data to Life, Informs R&D Key Research Results Achievement Built on over 11.5 million miles of vehicle operations data, Fleet DNA helps users

Implementation of new tools in molecular epidemiology studies of Echinococcus granulosus sensu lato in South America.

Science.gov (United States)

Avila, Héctor G; Santos, Guilherme B; Cucher, Marcela A; Macchiaroli, Natalia; Pérez, Matías G; Baldi, Germán; Jensen, Oscar; Pérez, Verónica; López, Raúl; Negro, Perla; Scialfa, Exequiel; Zaha, Arnaldo; Ferreira, Henrique B; Rosenzvit, Mara; Kamenetzky, Laura

2017-06-01

The aim of this work was to determine Echinococcus granulosus sensu lato species and genotypes in intermediate and definitive hosts and in human isolates from endemic regions of Argentina and Brazil including those where no molecular data is available by a combination of classical and alternative molecular tools. A total of 227 samples were isolated from humans, natural intermediate and definitive hosts. Amplification of cytochrome c oxidase subunit I gene fragment was performed and a combination of AluI digestion assay, High Resolution Melting analysis (HRM) assay and DNA sequencing was implemented for Echinococcus species/genotype determination. E. granulosus sensu stricto (G1) was found in sheep (n=35), cattle (n=67) and dogs (n=5); E. ortleppi (G5) in humans (n=3) and cattle (n=108); E. canadensis (G6) in humans (n=2) and E. canadensis (G7) in pigs (n=7). We reported for the first time the presence of E. ortleppi (G5) and E. canadensis (G6) in humans from San Juan and Catamarca Argentinean provinces and E. canadensis (G7) in pigs from Cordoba Argentinean province. In this work, we widened molecular epidemiology studies of E. granulosus s. l. in South America by analyzing several isolates from definitive and intermediate hosts, including humans from endemic regions were such information was scarce or unavailable. The presence of different species/genotypes in the same region and host species reinforce the need of rapid and specific techniques for accurate determination of Echinococcus species such as the ones proposed in this work. Copyright © 2017 Elsevier B.V. All rights reserved.

A Review of Bring Your Own Device on Security Issues

OpenAIRE

Morufu Olalere; Mohd Taufik Abdullah; Ramlan Mahmod; Azizol Abdullah

2015-01-01

Mobile computing has supplanted internet computing because of the proliferation of cloud-based applications and mobile devices (such as smartphones, palmtops, and tablets). As a result of this, workers bring their mobile devices to the workplace and use them for enterprise work. The policy of allowing the employees to work with their own personal mobile devices is called Bring Your Own Devices (BYOD). In this article, ...

Molecular images as a tool in research. From radiopharmacy to radiopharmacology

International Nuclear Information System (INIS)

Zubillaga, M.

2008-01-01

Full text: The rapidly emerging biomedical research discipline of Molecular Imaging (MI) enables the visualization, characterization and quantification of biologic process taking place at the cellular and sub-cellular levels within the intact living organism. The overall goal of MI is to interrogate biologic process in the cell of a living subject to report on and reveal their molecular abnormalities that form the basis of disease. This is in contrast to classical diagnostic imaging where documented findings are the result of the end effects of these molecular alterations, usually in the form of macroscopic and well-established gross pathology. MI includes the field of Nuclear Medicine (SPECT and PET) and other strategies that do not depend on radioactivity to produce imaging signals (optical, bioluminescence and Magnetic Resonance). The emergence of MI strategies has made possible the achievement of several important biomedical research goals that open the door to advancement of study in molecular medicine. These various accomplishments include: (1) development of non invasive 'in vivo' imaging methods to reflect gene expression and more complex events such as protein-protein interactions; (2) ability to monitor multiple molecular events near simultaneously; (3) capacity to follow cell trafficking and cell targeting; (4) optimization of drug and gene therapy; (5) capability of imaging drug effects at a molecular and cellular level; (6) assessment of disease progression at a molecular pathologic level; (7) advancement of the possibility of achieving all the above mentioned goals rapidly, reproducibly and quantitatively, in support of monitoring a time-dependent manner the experimental, developmental, environmental and therapeutic influences on gene products in a single living subject. Although many laboratory based proof-of-principle and validation studies have been conducted using MI approaches, a great deal more experimental research will be necessary to

Coupling scanning tunneling microscope and supersonic molecular beams: a unique tool for in situ investigation of the morphology of activated systems.

Science.gov (United States)

Smerieri, M; Reichelt, R; Savio, L; Vattuone, L; Rocca, M

2012-09-01

We report here on a new experimental apparatus combining a commercial low temperature scanning tunneling microscope with a supersonic molecular beam. This setup provides a unique tool for the in situ investigation of the topography of activated adsorption systems and opens thus new interesting perspectives. It has been tested towards the formation of the O/Ag(110) added rows reconstruction and of their hydroxylation, comparing data recorded upon O(2) exposure at thermal and hyperthermal energies.

Biomimetic molecular design tools that learn, evolve, and adapt

Science.gov (United States)

2017-01-01

A dominant hallmark of living systems is their ability to adapt to changes in the environment by learning and evolving. Nature does this so superbly that intensive research efforts are now attempting to mimic biological processes. Initially this biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science, medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known “S curve”, with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive, evolving, machine learning-based molecular design and optimization methods are approaching the period of very rapid growth and their impact is already being described as potentially disruptive. This paper describes new developments in biomimetic adaptive, evolving, learning computational molecular design methods and their potential impacts in chemistry, engineering, and medicine. PMID:28694872

Biomimetic molecular design tools that learn, evolve, and adapt

Directory of Open Access Journals (Sweden)

David A Winkler

2017-06-01

Full Text Available A dominant hallmark of living systems is their ability to adapt to changes in the environment by learning and evolving. Nature does this so superbly that intensive research efforts are now attempting to mimic biological processes. Initially this biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science, medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known “S curve”, with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive, evolving, machine learning-based molecular design and optimization methods are approaching the period of very rapid growth and their impact is already being described as potentially disruptive. This paper describes new developments in biomimetic adaptive, evolving, learning computational molecular design methods and their potential impacts in chemistry, engineering, and medicine.

Quantifying and Visualizing Uncertainties in Molecular Models

OpenAIRE

Rasheed, Muhibur; Clement, Nathan; Bhowmick, Abhishek; Bajaj, Chandrajit

2015-01-01

Computational molecular modeling and visualization has seen significant progress in recent years with sev- eral molecular modeling and visualization software systems in use today. Nevertheless the molecular biology community lacks techniques and tools for the rigorous analysis, quantification and visualization of the associated errors in molecular structure and its associated properties. This paper attempts at filling this vacuum with the introduction of a systematic statistical framework whe...

Making and Operating Molecular Machines: A Multidisciplinary Challenge.

Science.gov (United States)

Baroncini, Massimo; Casimiro, Lorenzo; de Vet, Christiaan; Groppi, Jessica; Silvi, Serena; Credi, Alberto

2018-02-01

Movement is one of the central attributes of life, and a key feature in many technological processes. While artificial motion is typically provided by macroscopic engines powered by internal combustion or electrical energy, movement in living organisms is produced by machines and motors of molecular size that typically exploit the energy of chemical fuels at ambient temperature to generate forces and ultimately execute functions. The progress in several areas of chemistry, together with an improved understanding of biomolecular machines, has led to the development of a large variety of wholly synthetic molecular machines. These systems have the potential to bring about radical innovations in several areas of technology and medicine. In this Minireview, we discuss, with the help of a few examples, the multidisciplinary aspects of research on artificial molecular machines and highlight its translational character.

The cognitive life of mechanical molecular models.

Science.gov (United States)

Charbonneau, Mathieu

2013-12-01

The use of physical models of molecular structures as research tools has been central to the development of biochemistry and molecular biology. Intriguingly, it has received little attention from scholars of science. In this paper, I argue that these physical models are not mere three-dimensional representations but that they are in fact very special research tools: they are cognitive augmentations. Despite the fact that they are external props, these models serve as cognitive tools that augment and extend the modeler's cognitive capacities and performance in molecular modeling tasks. This cognitive enhancement is obtained because of the way the modeler interacts with these models, the models' materiality contributing to the solving of the molecule's structure. Furthermore, I argue that these material models and their component parts were designed, built and used specifically to serve as cognitive facilitators and cognitive augmentations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bringing Internet-based education and intervention into mental health practice: afterdeployment.org

Directory of Open Access Journals (Sweden)

Josef I. Ruzek

2011-11-01

Full Text Available Internet-facilitated interventions may offer numerous advantages in reaching the large numbers of military service men and women exposed to traumatic events. The Internet is now a primary source of health-related information for consumers and research has shown the effectiveness of web-based interventions in addressing a range of mental health problems.Clinicians can learn how to bring Internet education and intervention into routine care, to help clients better understand mental health issues and learn skills for self-management of problems.The Afterdeployment.org (AD Internet site can be used by health care professionals serving U.S. military personnel returning from Iraq and Afghanistan, and their families. The site currently addresses 18 key domains of functioning, including post-traumatic stress, sleep, anger, alcohol and drugs, and military sexual trauma. It provides an extensive amount of client and family education that is suitable for immediate use by clients and providers, as well as the kinds of interactive workshop content and self-assessment tools that have been shown to be helpful in other treatment contexts. AD can be utilized in clinical practice in a variety of ways: as an adjunct to treatment for PTSD, to supplement existing treatments for a range of post-deployment problems, or as the primary focus of treatment for a client.AD represents a kind of service that is likely to become increasingly available in coming years and that is important for mental health providers to actively explore as a tool for extending their reach, improving their efficiency, and improving quality of care.For the abstract or full text in other languages, please see Supplementary files under Reading Tools online.

Modeling Complex Workflow in Molecular Diagnostics

Science.gov (United States)

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

2010-01-01

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

HIV-TRACE (Transmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens.

Science.gov (United States)

Kosakovsky Pond, Sergei L; Weaver, Steven; Leigh Brown, Andrew J; Wertheim, Joel O

2018-01-31

In modern applications of molecular epidemiology, genetic sequence data are routinely used to identify clusters of transmission in rapidly evolving pathogens, most notably HIV-1. Traditional 'shoeleather' epidemiology infers transmission clusters by tracing chains of partners sharing epidemiological connections (e.g., sexual contact). Here, we present a computational tool for identifying a molecular transmission analog of such clusters: HIV-TRACE (TRAnsmission Cluster Engine). HIV-TRACE implements an approach inspired by traditional epidemiology, by identifying chains of partners whose viral genetic relatedness imply direct or indirect epidemiological connections. Molecular transmission clusters are constructed using codon-aware pairwise alignment to a reference sequence followed by pairwise genetic distance estimation among all sequences. This approach is computationally tractable and is capable of identifying HIV-1 transmission clusters in large surveillance databases comprising tens or hundreds of thousands of sequences in near real time, i.e., on the order of minutes to hours. HIV-TRACE is available at www.hivtrace.org and from github.com/veg/hivtrace, along with the accompanying result visualization module from github.com/veg/hivtrace-viz. Importantly, the approach underlying HIV-TRACE is not limited to the study of HIV-1 and can be applied to study outbreaks and epidemics of other rapidly evolving pathogens. © The Author 2018. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Evolution of egg coats: linking molecular biology and ecology.

Science.gov (United States)

Shu, Longfei; Suter, Marc J-F; Räsänen, Katja

2015-08-01

One central goal of evolutionary biology is to explain how biological diversity emerges and is maintained in nature. Given the complexity of the phenotype and the multifaceted nature of inheritance, modern evolutionary ecological studies rely heavily on the use of molecular tools. Here, we show how molecular tools help to gain insight into the role of egg coats (i.e. the extracellular structures surrounding eggs and embryos) in evolutionary diversification. Egg coats are maternally derived structures that have many biological functions from mediating fertilization to protecting the embryo from environmental hazards. They show great molecular, structural and functional diversity across species, but intraspecific variability and the role of ecology in egg coat evolution have largely been overlooked. Given that much of the variation that influences egg coat function is ultimately determined by their molecular phenotype, cutting-edge molecular tools (e.g. proteomics, glycomics and transcriptomics), combined with functional assays, are needed for rigorous inferences on their evolutionary ecology. Here, we identify key research areas and highlight emerging molecular techniques that can increase our understanding of the role of egg coats in the evolution of biological diversity, from adaptation to speciation. © 2015 John Wiley & Sons Ltd.

Bringing New Families to the Museum One Baby at a Time

Science.gov (United States)

Herman, Alicia

2012-01-01

"Bring Your Baby to the Danforth Museum of Art" is a program for mothers. Unlike other museum programs that focus on the needs of children, Bring Your Baby caters to the intellectual interests of the adult parent. Parents learn about artworks, play with babies in a beautiful environment, and socialize with other families. The program is…

From electron microscopy to X-ray crystallography: molecular-replacement case studies

International Nuclear Information System (INIS)

Xiong, Yong

2008-01-01

Test studies have been conducted on five crystal structures of large molecular assemblies, in which EM maps are used as models for structure solution by molecular replacement using various standard MR packages such as AMoRe, MOLREP and Phaser. Multi-component molecular complexes are increasingly being tackled by structural biology, bringing X-ray crystallography into the purview of electron-microscopy (EM) studies. X-ray crystallography can utilize a low-resolution EM map for structure determination followed by phase extension to high resolution. Test studies have been conducted on five crystal structures of large molecular assemblies, in which EM maps are used as models for structure solution by molecular replacement (MR) using various standard MR packages such as AMoRe, MOLREP and Phaser. The results demonstrate that EM maps are viable models for molecular replacement. Possible difficulties in data analysis, such as the effects of the EM magnification error, and the effect of MR positional/rotational errors on phase extension are discussed

An Educational Tool for Interactive Parallel and Distributed Processing

DEFF Research Database (Denmark)

Pagliarini, Luigi; Lund, Henrik Hautop

2011-01-01

In this paper we try to describe how the Modular Interactive Tiles System (MITS) can be a valuable tool for introducing students to interactive parallel and distributed processing programming. This is done by providing an educational hands-on tool that allows a change of representation of the abs......In this paper we try to describe how the Modular Interactive Tiles System (MITS) can be a valuable tool for introducing students to interactive parallel and distributed processing programming. This is done by providing an educational hands-on tool that allows a change of representation...... of the abstract problems related to designing interactive parallel and distributed systems. Indeed, MITS seems to bring a series of goals into the education, such as parallel programming, distributedness, communication protocols, master dependency, software behavioral models, adaptive interactivity, feedback......, connectivity, topology, island modeling, user and multiuser interaction, which can hardly be found in other tools. Finally, we introduce the system of modular interactive tiles as a tool for easy, fast, and flexible hands-on exploration of these issues, and through examples show how to implement interactive...

High-throughput molecular binding analysis on open-microfluidic platform

OpenAIRE

Pan, Yuchen

2016-01-01

Biomolecular binding interactions underpin life sciences tools that are essential to fields as diverse as molecular biology and clinical chemistry. Merging needs in life science research entail fast, robust and quantitative binding reaction characterization, such as antibody selection, gene regulation screening and drug screening. Identification, characterization, and optimization of these diverse molecular binding reactions demands the availability of powerful, quantitative analytical tools....

Reflective Drawing as a Tool for Reflection in Design Research

Science.gov (United States)

Calvo, Mirian

2017-01-01

This article explores the role of drawing as a tool for reflection. It reports on a PhD research project that aims to identify and analyse the value that co-design processes can bring to participants and their communities. The research is associated with Leapfrog, a three-year project funded by the UK Arts and Humanities Research Council (AHRC).…

Molecular Imaging: A Promising Tool to Monitor Islet Transplantation

Directory of Open Access Journals (Sweden)

Ping Wang

2011-01-01

Full Text Available Replacement of insulin production by pancreatic islet transplantation has great potential as a therapy for type 1 diabetes mellitus. At present, the lack of an effective approach to islet grafts assessment limits the success of this treatment. The development of molecular imaging techniques has the potential to fulfill the goal of real-time noninvasive monitoring of the functional status and viability of the islet grafts. We review the application of a variety of imaging modalities for detecting endogenous and transplanted beta-cell mass. The review also explores the various molecular imaging strategies for assessing islet delivery, the metabolic effects on the islet grafts as well as detection of immunorejection. Here, we highlight the use of combined imaging and therapeutic interventions in islet transplantation and the in vivo monitoring of stem cells differentiation into insulin-producing cells.

Bringing "indigenous" ownership back

DEFF Research Database (Denmark)

Kragelund, Peter

2012-01-01

policies thrive again, this time disguised in terms such as ‘empowerment’, but just as politicised as in the 1970s. Zambia is at the heart of this development. In the light of liberalisation, booming commodity prices and the increasing importance of Chinese investors, this article seeks to further our...... understanding of how processes of exclusion interact with domestic politics in Zambia. It argues that the Citizens Economic Empowerment Commission, a new institution to bring ownership back to Zambians, builds on a long tradition of nationalist policies in Zambia, while its actual work is strictly related...... to the critique of the growing foreign dominance over the economy, and in particular of the upsurge in Chinese investments....

Molecular modeling

Directory of Open Access Journals (Sweden)

Aarti Sharma

2009-01-01

Full Text Available The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and the exponential growth of the knowledge of protein structures have made it possible for organic compounds to be tailored to decrease the harmful side effects and increase the potency. This article provides a detailed description of the techniques employed in molecular modeling. Molecular modeling is a rapidly developing discipline, and has been supported by the dramatic improvements in computer hardware and software in recent years.

The Annotation, Mapping, Expression and Network (AMEN suite of tools for molecular systems biology

Directory of Open Access Journals (Sweden)

Primig Michael

2008-02-01

Full Text Available Abstract Background High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpretation by life scientists. Many solutions currently exist, but they are often limited to specific steps in the complex process of data management and analysis and some require extensive informatics skills to be installed and run efficiently. Results We developed the Annotation, Mapping, Expression and Network (AMEN software as a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i uploading and pre-processing data from microarray expression profiling experiments, (ii detecting groups of significantly co-expressed genes, and (iii searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human. Conclusion AMEN is an innovative solution for molecular systems biological data analysis freely available under the GNU license. The program is available via a website at the Sourceforge portal which includes a user guide with concrete examples, links to external databases and helpful comments to implement additional functionalities. We emphasize that AMEN will continue to be developed and maintained by our laboratory because it has proven to be extremely useful for our genome biological research program.

Bringing Secrecy into the Open

DEFF Research Database (Denmark)

Costas, Jana; Grey, Christopher

2014-01-01

This paper brings into focus the concept of organizational secrecy, defined as the ongoing formal and informal social processes of intentional concealment of information from actors by actors in organizations. It is argued that existing literature on the topic is fragmented and predominantly...... focused on informational rather than social aspects of secrecy. The paper distinguishes between formal and informal secrecy and theorizes the social processes of these in terms of identity and control. It is proposed that organizational secrecy be added to the analytical repertoire of organization studies....

Fleet DNA Brings Fleet Data to Life, Informs R&D | News | NREL

Science.gov (United States)

Fleet DNA Brings Fleet Data to Life, Informs R&D Fleet DNA Brings Fleet Data to Life, Informs R De La Rosa, NREL 34672 The Fleet DNA clearinghouse of commercial vehicle operations data features Odyne-have tapped into Fleet DNA." The data-driven insight and decision-making capabilities

Skynet Junior Scholars: Bringing Astronomy to Deaf and Hard of Hearing Youth

Science.gov (United States)

Meredith, Kate; Williamson, Kathryn; Gartner, Constance; Hoette, Vivian L.; Heatherly, Sue Ann

2016-01-01

Skynet Junior Scholars (SJS), funded by the National Science Foundation, aims to engage middle school youth from diverse audiences in investigating the universe with research quality robotic telescopes. SJS project development goals include: 1) Online access to optical and radio telescopes, data analysis tools, and professional astronomers, 2) An age-appropriate web-based interface for controlling remote telescopes, 3) Inquiry-based standards-aligned instructional modules. From an accessibility perspective, the goal of the Skynet Junior Scholars project is to facilitate independent access to the project by all youth including those with blindness or low vision and those who are Deaf or Hard of Hearing.Deaf and Hard of Hearing (DHH) students have long been an underserved population within STEM fields, including astronomy. Two main barriers include: (1) insufficient corpus of American Sign Language (ASL) for astronomy terminology, and (2) DHH education professionals who lack astronomy background. A suite of vocabulary, accessible hands-on activities, and interaction with trained professionals, are critical for enhancing the background experiences of DHH youth, as they may come to an astronomy lesson lacking the basic "incidental learning" that is often taken for granted with hearing peers (for example, from astronomy in the media).A collaboration between the Skynet Junior Scholars (SJS) project and the Wisconsin School for the Deaf is bringing astronomy to the DHH community in an accessible way for the first time. We follow a group of seven DHH youth over one semester as they interact with the SJS tools and curriculum to understand how they assimilate astronomy experiences and benefit from access to telescopes both directly (on school campus and at Yerkes Observatory) and through Skynet's robotic telescope network (optical and radio telescopes, inquiry-based modules, data analysis tools, and professional astronomers). We report on our first findings of resources and

PET for molecular imaging of cancer: a tool for tailored therapy

International Nuclear Information System (INIS)

Kjaer, Andreas

2014-01-01

The concept of personalised medicine has led to a need for improved phenotyping as well as prediction of treatment response early after therapy initiation. Most of the molecular biology methods used today need tissue sampling for in vitro analysis. In contrast, molecular imaging allows for non-invasive studies at the molecular level in living, intact organisms. Accordingly, molecular imaging with PET has been one of the most successful techniques in such phenotyping and response prediction using FDG. In addition, recent development of new PET tracers has further improved the value of PET in tumor characterization. Such new PET tracers allow for visualization of tumor specific receptors and tissue characteristics such as ability to metastasize. Furthermore, PET has a high sensitivity and allows for quantification and is not prone to sampling error as seen with biopsies. We will present examples of development of probes targeting the somatostatin receptor type 2, over-expressed in neuroendocrine tumors, including our first-in-man studies of 64 Cu-DOTATATE. Also development in probes for visualization of the invasive phenotype will be presented. Finally, with the most recent development of true integrated PET/MRI scanners has now become possible to add information from MRI. The value of such hybrid imaging will also be briefly discussed. (author)

PET for molecular imaging of cancer: a tool for tailored therapy

International Nuclear Information System (INIS)

Kjaer, Andreas

2013-01-01

The concept of personalised medicine has led to a need for improved phenotyping as well as prediction of treatment response early after therapy initiation. Most of the molecular biology methods used today need tissue sampling for in vitro analysis. In contrast, molecular imaging allows for non-invasive studies at the molecular level in living, intact organisms. Accordingly, molecular imaging with PET has been one of the most successful techniques in such phenotyping and response prediction using FDG. In addition, recent development of new PET tracers has further improved the value of PET in tumor characterization. Such new PET tracers allow for visualization of tumor specific receptors and tissue characteristics such as ability to metastasize. Furthermore, PET has a high sensitivity and allows for quantification and is not prone to sampling error as seen with biopsies. We will present examples of development of probes targeting the somatostatin receptor type 2, over-expressed in neuroendocrine tumors, including our first-in-man studies of 64Cu-DOTATATE. Also development in probes for visualization of the invasive phenotype will be presented. Finally, with the most recent development of true integrated PET/MRI scanners it has now become possible to add information from MRI. The value of such hybrid imaging will also be briefly discussed. (author)

Dubna at Play Exhibition Science Bringing Nations Together

CERN Multimedia

1999-01-01

The small town of Dubna brings together the advantages of urban and country lifestyles. Dubna people spend a large part of their time outdoors taking part in all kind of sports or simply enjoying the beautiful surroundings.

Dubna at Play Exhibition Science Bringing Nations Together

CERN Multimedia

1997-01-01

The small town of Dubna brings together the advantages of urban and country lifestyles. Dubna people spend a large part of their time outdoors taking part in all kind of sports or simply enjoying the beautiful surroundings.

Microsoft Biology Initiative: .NET Bioinformatics Platform and Tools

Science.gov (United States)

Diaz Acosta, B.

2011-01-01

The Microsoft Biology Initiative (MBI) is an effort in Microsoft Research to bring new technology and tools to the area of bioinformatics and biology. This initiative is comprised of two primary components, the Microsoft Biology Foundation (MBF) and the Microsoft Biology Tools (MBT). MBF is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework—initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, documentation and training materials are freely downloadable from http://research.microsoft.com/bio. MBT is a collection of tools that enable biology and bioinformatics researchers to be more productive in making scientific discoveries.

Integrative pathway knowledge bases as a tool for systems molecular medicine.

Science.gov (United States)

Liang, Mingyu

2007-08-20

There exists a sense of urgency to begin to generate a cohesive assembly of biomedical knowledge as the pace of knowledge accumulation accelerates. The urgency is in part driven by the emergence of systems molecular medicine that emphasizes the combination of systems analysis and molecular dissection in the future of medical practice and research. A potentially powerful approach is to build integrative pathway knowledge bases that link organ systems function with molecules.

Physical tools for textile creativity and invention

DEFF Research Database (Denmark)

Heimdal, Elisabeth Jacobsen; Lenau, Torben Anker

2010-01-01

Two textile research projects (one completed and one ongoing) are described, where physical inspirational tools are developed and tested with the aim of stimulating textile creativity and invention, i.e. the use of textile materials in new kinds of products, thus bringing textiles into new contexts....... The first research project (completed) concerns how textile designers use new responsive materials and technologies, whereas the second (ongoing) concerns how architects and design engineers can use textile materials. In both projects, the developed inspirational tool is tested through workshops...... with the mentioned stakeholders. In these workshops, new ways of disseminating the results from research in textiles and textile design are experimented with. The submitted contribution therefore mainly addresses the role of interdisciplinarity in textile design research as well as the impact of new materials...

Design of extraction system in BRing at HIAF

Science.gov (United States)

Ruan, Shuang; Yang, Jiancheng; Zhang, Jinquan; Shen, Guodong; Ren, Hang; Liu, Jie; Shangguan, Jingbing; Zhang, Xiaoying; Zhang, Jingjing; Mao, Lijun; Sheng, Lina; Yin, Dayu; Wang, Geng; Wu, Bo; Yao, Liping; Tang, Meitang; Cai, Fucheng; Chen, Xiaoqiang

2018-06-01

The Booster Ring (BRing), which is the key part of HIAF (High Intensity heavy ion Accelerator Facility) complex at IMP (Institute of Modern Physics, Chinese Academy of Sciences), can provide uranium (A / q = 7) beam with a wide extraction energy range of 200-800 MeV/u. To fulfill a flexible beam extraction for multi-purpose experiments, both fast and slow extraction systems will be accommodated in the BRing. The fast extraction system is used for extracting short bunched beam horizontally in single-turn. The slow extraction system is used to provide quasi-continuous beam by the third order resonance and RF-knockout scheme. To achieve a compact structure, the two extraction systems are designed to share the same extraction channel. The general design of the fast and slow extraction systems and simulation results are discussed in this paper.

[Microdose clinical trial--impact of PET molecular imaging].

Science.gov (United States)

Yano, Tsuneo; Watanabe, Yasuyoshi

2010-10-01

Microdose (MD) clinical trial and exploratory IND study including sub-therapeutic dose and therapeutic dose which are higher than microdoses are expected to bring about innovations in drug development. The outlines of guidances for microdose clinical trial and ICH-M3 (R2) issued by the MHLW in June, 2008, and February, 2010, are first explained, respectively, and some examples of their application to clinical developments of therapeutic drugs in the infection and cancer fields are introduced. Especially, thanks to the progress of molecular imaging research, a new field of drug development is explored by using imaging biomarkers for efficacy or safety evaluation which visualize biomarkers by PET imaging agents. Finally, the roadmap for drug development in infection and cancer fields utilizing PET molecular imaging is discussed.

DNA Barcoding Investigations Bring Biology to Life

Science.gov (United States)

Musante, Susan

2010-01-01

This article describes how DNA barcoding investigations bring biology to life. Biologists recognize the power of DNA barcoding not just to teach biology through connections to the real world but also to immerse students in the exciting process of science. As an investigator in the Program for the Human Environment at Rockefeller University in New…

Pressure profiles of the BRing based on the simulation used in the CSRm

Science.gov (United States)

Wang, J. C.; Li, P.; Yang, J. C.; Yuan, Y. J.; Wu, B.; Chai, Z.; Luo, C.; Dong, Z. Q.; Zheng, W. H.; Zhao, H.; Ruan, S.; Wang, G.; Liu, J.; Chen, X.; Wang, K. D.; Qin, Z. M.; Yin, B.

2017-07-01

HIAF-BRing, a new multipurpose accelerator facility of the High Intensity heavy-ion Accelerator Facility project, requires an extremely high vacuum lower than 10-11 mbar to fulfill the requirements of radioactive beam physics and high energy density physics. To achieve the required process pressure, the bench-marked codes of VAKTRAK and Molflow+ are used to simulate the pressure profiles of the BRing system. In order to ensure the accuracy of the implementation of VAKTRAK, the computational results are verified by measured pressure data and compared with a new simulation code BOLIDE on the current synchrotron CSRm. Since the verification of VAKTRAK has been done, the pressure profiles of the BRing are calculated with different parameters such as conductance, out-gassing rates and pumping speeds. According to the computational results, the optimal parameters are selected to achieve the required pressure for the BRing.

MIPs as Tools in Environmental Biotechnology.

Science.gov (United States)

Mattiasson, Bo

2015-01-01

Molecular imprints are potentially fantastic constructions. They are selective, robust, and nonbiodegradable if produced from stable polymers. A range of different applications has been presented, everything from separation of enantiomers, via adsorbents for sample preparation before analysis to applications in wastewater treatment. This chapter deals with molecularly imprinted polymers (MIPs) as tools in environmental biotechnology, a field that has the potential to become very important in the future.

An Educational Tool for Creating Distributed Physical Games

DEFF Research Database (Denmark)

Lund, Henrik Hautop; Pagliarini, Luigi

2011-01-01

programming for physical games development. This is done by providing an educational tool that allows a change of representation of the problems related to game designing from a virtual to a physical representation. Indeed, MITS seems to be a valuable system for bringing into education a vast number of issues...... (such as parallel programming, distribution, communication protocols, master dependency, connectivity, topology, island modeling software behavioral models, adaptive interactivity, feedback, user and multi-user game interaction, etc.). This can both improve the education-related issues in computer......The development of physical interactive games demands extensive knowledge in engineering, computer science and gaming. In this paper we describe how the Modular Interactive Tiles System (MITS) can be a valuable tool for introducing students to interactive parallel and distributed processing...

Designing the molecular future

OpenAIRE

Schneider Gisbert

2011-01-01

Approximately 25 years ago the first computer applications were conceived for the purpose of automated 'de novo' drug design prominent pioneering tools being ALADDIN CAVEAT GENOA and DYLOMMS. Many of these early concepts were enabled by innovative techniques for ligand receptor interaction modeling like GRID MCSS DOCK and CoMFA which still provide the theoretical framework for several more recently developed molecular design algorithms. After a first wave of software tools and groundbreaking ...

Molecular Modelling

Directory of Open Access Journals (Sweden)

Aarti Sharma

2009-12-01

Full Text Available

Bringing the mountain to Mohammed

International Nuclear Information System (INIS)

Hibbs, S.M.; Bell, H.H.; Bowman, F.M.; Hitchin, C.; Jackson, M.

1987-01-01

New free electron laser (FEL) technology at Lawrence Livermore National Laboratory (LLNL) promises electron-cyclotron plasma heating at power levels, cost efficiency, and tunable frequency range far beyond the capabilities of existing technology. LLNL has the high-current induction linear accelerators needed to drive such an FEL. Thus, the first stage of the Microwave Tokamak Experiment (MTX), designed to test this new technology, was to bring the Alcator-C tokamak across the United States from the Massachusetts Institute of Technology (MIT) to LLNL in California. The authors discuss why the tokamak was moved across the country and described the move

Bringing nursing to the public.

Science.gov (United States)

Kazis, Cornelia; Schwendimann, René

2009-11-01

For the past 5 years, an unusual program has been evolving in the University of Basel's Institute of Nursing Science master's program in Basel, Switzerland. A special course designed to help nurses master public communication skills requires students to play the roles of journalist, exhibition curator, conference organizer, radio reporter, and news producer. Two faculty members, an experienced radio and newspaper journalist and a nurse scientist, teach and support the students. By developing their competence in media relations, participants prepare themselves to tackle the course's long-term goal of bringing the nursing profession into the public eye. Copyright 2009, SLACK Incorporated.

Molecular imaging in neurology and neuroscience

International Nuclear Information System (INIS)

Schreckenberger, M.

2007-01-01

Molecular imaging in neurology and neuroscience is a suspenseful and fast developing tool in order to quantitatively image genomics and proteomics by means of direct and indirect markers. Because of its high-sensitive tracer principle, nuclear medicine imaging has the pioneering task for the methodical progression of molecular imaging. The current development of molecular imaging in neurology changes from the use of indirect markers of gene and protein expression to the direct imaging of the molecular mechanisms. It is the aim of this article to give a short review on the status quo of molecular imaging in neurology with emphasis on clinically relevant aspects. (orig.)

Electronic Safety Resource Tools -- Supporting Hydrogen and Fuel Cell Commercialization

Energy Technology Data Exchange (ETDEWEB)

Barilo, Nick F.

2014-09-29

The Pacific Northwest National Laboratory (PNNL) Hydrogen Safety Program conducted a planning session in Los Angeles, CA on April 1, 2014 to consider what electronic safety tools would benefit the next phase of hydrogen and fuel cell commercialization. A diverse, 20-person team led by an experienced facilitator considered the question as it applied to the eight most relevant user groups. The results and subsequent evaluation activities revealed several possible resource tools that could greatly benefit users. The tool identified as having the greatest potential for impact is a hydrogen safety portal, which can be the central location for integrating and disseminating safety information (including most of the tools identified in this report). Such a tool can provide credible and reliable information from a trustworthy source. Other impactful tools identified include a codes and standards wizard to guide users through a series of questions relating to application and specific features of the requirements; a scenario-based virtual reality training for first responders; peer networking tools to bring users from focused groups together to discuss and collaborate on hydrogen safety issues; and a focused tool for training inspectors. Table ES.1 provides results of the planning session, including proposed new tools and changes to existing tools.

Molecular Tools for Facilitative Carbohydrate Transporters (Gluts).

Science.gov (United States)

Tanasova, Marina; Fedie, Joseph R

2017-09-19

Facilitative carbohydrate transporters-Gluts-have received wide attention over decades due to their essential role in nutrient uptake and links with various metabolic disorders, including diabetes, obesity, and cancer. Endeavors directed towards understanding the mechanisms of Glut-mediated nutrient uptake have resulted in a multidisciplinary research field spanning protein chemistry, chemical biology, organic synthesis, crystallography, and biomolecular modeling. Gluts became attractive targets for cancer research and medicinal chemistry, leading to the development of new approaches to cancer diagnostics and providing avenues for cancer-targeting therapeutics. In this review, the current state of knowledge of the molecular interactions behind Glut-mediated sugar uptake, Glut-targeting probes, therapeutics, and inhibitors are discussed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Theoretical Molecular Biophysics

CERN Document Server

Scherer, Philipp

2010-01-01

"Theoretical Molecular Biophysics" is an advanced study book for students, shortly before or after completing undergraduate studies, in physics, chemistry or biology. It provides the tools for an understanding of elementary processes in biology, such as photosynthesis on a molecular level. A basic knowledge in mechanics, electrostatics, quantum theory and statistical physics is desirable. The reader will be exposed to basic concepts in modern biophysics such as entropic forces, phase separation, potentials of mean force, proton and electron transfer, heterogeneous reactions coherent and incoherent energy transfer as well as molecular motors. Basic concepts such as phase transitions of biopolymers, electrostatics, protonation equilibria, ion transport, radiationless transitions as well as energy- and electron transfer are discussed within the frame of simple models.

Democratizing molecular diagnostics for the developing world.

Science.gov (United States)

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

2014-01-01

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

A molecular genetic toolbox for Yarrowia lipolytica

DEFF Research Database (Denmark)

Bredeweg, Erin L.; Pomraning, Kyle R.; Dai, Ziyu

2017-01-01

used these tools to build the "Yarrowia lipolytica Cell Atlas," a collection of strains with endogenous fluorescently tagged organelles in the same genetic background, in order to define organelle morphology in live cells. Conclusions: These molecular and isogenetic tools are useful for live assessment...

A survey of educational uses of molecular visualization freeware.

Science.gov (United States)

Craig, Paul A; Michel, Lea Vacca; Bateman, Robert C

2013-01-01

As biochemists, one of our most captivating teaching tools is the use of molecular visualization. It is a compelling medium that can be used to communicate structural information much more effectively with interactive animations than with static figures. We have conducted a survey to begin a systematic evaluation of the current classroom usage of molecular visualization. Participants (n = 116) were asked to complete 11 multiple choice and 3 open ended questions. To provide more depth to these results, interviews were conducted with 12 of the participants. Many common themes arose in the survey and the interviews: a shared passion for the use of molecular visualization in teaching, broad diversity in software preference, the lack of uniform standards for assessment, a desire for more quality resources, and the challenge of enabling students to incorporate visualization in their learning. The majority of respondents had used molecular visualization for more than 5 years and mentioned 32 different visualization tools used, with Jmol and PyMOL clearly standing out as the most frequently used programs at the present time. The most common uses of molecular visualization in teaching were lecture and lab illustrations, followed by exam questions, in-class or in-laboratory exercises, and student projects, which frequently included presentations. While a minority of instructors used a grading rubric/scoring matrix for assessment of student learning with molecular visualization, many expressed a desire for common use assessment tools. Copyright © 2013 International Union of Biochemistry and Molecular Biology, Inc.

MOLECULAR DIAGNOSTICS - ANOTHER PIECE IN THE ENVIRONMENTAL PUZZLE

Science.gov (United States)

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

Pressure profiles of the BRing based on the simulation used in the CSRm

Energy Technology Data Exchange (ETDEWEB)

Wang, J.C., E-mail: wangjiachen@impcas.ac.cn [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Li, P., E-mail: lipeng@impcas.ac.cn [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Yang, J.C.; Yuan, Y.J. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Wu, B. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Chai, Z.; Luo, C. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Dong, Z.Q. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zheng, W.H. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Zhao, H.; Ruan, S.; Wang, G.; Liu, J.; Chen, X.; Wang, K.D.; Qin, Z.M. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Yin, B. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)

2017-07-11

HIAF-BRing, a new multipurpose accelerator facility of the High Intensity heavy-ion Accelerator Facility project, requires an extremely high vacuum lower than 10{sup −11} mbar to fulfill the requirements of radioactive beam physics and high energy density physics. To achieve the required process pressure, the bench-marked codes of VAKTRAK and Molflow+ are used to simulate the pressure profiles of the BRing system. In order to ensure the accuracy of the implementation of VAKTRAK, the computational results are verified by measured pressure data and compared with a new simulation code BOLIDE on the current synchrotron CSRm. Since the verification of VAKTRAK has been done, the pressure profiles of the BRing are calculated with different parameters such as conductance, out-gassing rates and pumping speeds. According to the computational results, the optimal parameters are selected to achieve the required pressure for the BRing.

Molecular ions, Rydberg spectroscopy and dynamics

International Nuclear Information System (INIS)

Jungen, Ch.

2015-01-01

Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering

Molecular ions, Rydberg spectroscopy and dynamics

Energy Technology Data Exchange (ETDEWEB)

Jungen, Ch. [Laboratoire Aimé Cotton, Université de Paris-Sud, 91405 Orsay (France)

2015-01-22

Ion spectroscopy, Rydberg spectroscopy and molecular dynamics are closely related subjects. Multichannel quantum defect theory is a theoretical approach which draws on this close relationship and thereby becomes a powerful tool for the study of systems consisting of a positively charged molecular ion core interacting with an electron which may be loosely bound or freely scattering.

Insights into the HyPer biosensor as molecular tool for monitoring cellular antioxidant capacity

Directory of Open Access Journals (Sweden)

Helen Hernández

2018-06-01

Full Text Available Aerobic metabolism brings inexorably the production of reactive oxygen species (ROS, which are counterbalanced by intrinsic antioxidant defenses avoiding deleterious intracellular effects. Redox balance is the resultant of metabolic functioning under environmental inputs (i.e. diet, pollution and the activity of intrinsic antioxidant machinery. Monitoring of intracellular hydrogen peroxide has been successfully achieved by redox biosensor advent; however, to track the intrinsic disulfide bond reduction capacity represents a fundamental piece to understand better how redox homeostasis is maintained in living cells.In the present work, we compared the informative value of steady-state measurements and the kinetics of HyPer, a H2O2-sensitive fluorescent biosensor, targeted at the cytosol, mitochondrion and endoplasmic reticulum. From this set of data, biosensor signal recovery from an oxidized state raised as a suitable parameter to discriminate reducing capacity of a close environment. Biosensor recovery was pH-independent, condition demonstrated by experiments on pH-clamped cells, and sensitive to pharmacological perturbations of enzymatic disulfide reduction. Also, ten human cell lines were characterized according their H2O2-pulse responses, including their capacity to reduce disulfide bonds evaluated in terms of their migratory capacity.Finally, cellular migration experiments were conducted to study whether migratory efficiency was associated with the disulfide reduction activity. The migration efficiency of each cell type correlates with the rate of signal recovery measured from the oxidized biosensor. In addition, HyPer-expressing cells treated with N-acetyl-cysteine had accelerated recovery rates and major migratory capacities, both reversible effects upon treatment removal. Our data demonstrate that the HyPer signal recovery offers a novel methodological tool to track the cellular impact of redox active biomolecules. Keywords: Antioxidant

Insights into the HyPer biosensor as molecular tool for monitoring cellular antioxidant capacity.

Science.gov (United States)

Hernández, Helen; Parra, Alejandra; Tobar, Nicolas; Molina, Jessica; Kallens, Violeta; Hidalgo, Miltha; Varela, Diego; Martínez, Jorge; Porras, Omar

2018-06-01

Aerobic metabolism brings inexorably the production of reactive oxygen species (ROS), which are counterbalanced by intrinsic antioxidant defenses avoiding deleterious intracellular effects. Redox balance is the resultant of metabolic functioning under environmental inputs (i.e. diet, pollution) and the activity of intrinsic antioxidant machinery. Monitoring of intracellular hydrogen peroxide has been successfully achieved by redox biosensor advent; however, to track the intrinsic disulfide bond reduction capacity represents a fundamental piece to understand better how redox homeostasis is maintained in living cells. In the present work, we compared the informative value of steady-state measurements and the kinetics of HyPer, a H 2 O 2 -sensitive fluorescent biosensor, targeted at the cytosol, mitochondrion and endoplasmic reticulum. From this set of data, biosensor signal recovery from an oxidized state raised as a suitable parameter to discriminate reducing capacity of a close environment. Biosensor recovery was pH-independent, condition demonstrated by experiments on pH-clamped cells, and sensitive to pharmacological perturbations of enzymatic disulfide reduction. Also, ten human cell lines were characterized according their H 2 O 2 -pulse responses, including their capacity to reduce disulfide bonds evaluated in terms of their migratory capacity. Finally, cellular migration experiments were conducted to study whether migratory efficiency was associated with the disulfide reduction activity. The migration efficiency of each cell type correlates with the rate of signal recovery measured from the oxidized biosensor. In addition, HyPer-expressing cells treated with N-acetyl-cysteine had accelerated recovery rates and major migratory capacities, both reversible effects upon treatment removal. Our data demonstrate that the HyPer signal recovery offers a novel methodological tool to track the cellular impact of redox active biomolecules. Copyright © 2018 The Authors

A Comparative Study of Successful Central Nervous System Drugs Using Molecular Modeling

Science.gov (United States)

Kim, Hyosub; Sulaimon, Segun; Menezes, Sandra; Son, Anne; Menezes, Warren J. C.

2011-01-01

Molecular modeling is a powerful tool used for three-dimensional visualization and for exploring electrostatic forces involved in drug transport. This tool enhances student understanding of structure-property relationships, as well as actively engaging them in class. Molecular modeling of several central nervous system (CNS) drugs is used to…

CSR as a Marketing Tool : a Case Study of Fast Food Restaurant in Malaysia

OpenAIRE

Abdul Razak, Armiza

2014-01-01

The use of corporate social responsibility (CSR) as being an efficient marketing tool would be matter that is being researched, especially with the increasing awareness of consumers about the importance of commercial organizations doing business in ways that do not harm the consumers or the environment. The aim of the research will be to obtain data from qualitative data in order to determine whether using CSR as being a marketing tool would bring a higher level of efficiency in the marketing...

Molecular polymorphism as a tool for differentiating ground beetles (Carabus species): application of ubiquitin PCR/SSCP analysis.

Science.gov (United States)

Boge, A; Gerstmeier, R; Einspanier, R

1994-11-01

Differentiation between Carabus species (ground beetle) and subspecies is difficult, although there have been extensive studies. To address this problem we have applied PCR in combination with SSCP analysis focussing on the evolutionally conservative ubiquitin gene to elaborate a new approach to molecular differentiation between species. We report that Carabidae possess an ubiquitin gene and that its gene has a multimeric structure. Differential SSCP analysis was performed with the monomeric form of the gene to generate a clear SSCP pattern. Such PCR/SSCP resulted in reproducible patterns throughout our experiments. Comparing different Carabus species (Carabus granulatus, C. irregularis, C. violaceus and C. auronitens) we could observe clear interspecies differences but no differences between genders. Some species showed some remarkable differences between the individuals. We suggest that the ubiquitin PCR-SSCP technique might be an additional tool for the differentiation of ground beetles.

Molecular blood grouping of donors.

Science.gov (United States)

St-Louis, Maryse

2014-04-01

For many decades, hemagglutination has been the sole means to type blood donors. Since the first blood group gene cloning in the early 1990s, knowledge on the molecular basis of most red blood cell, platelet and neutrophil antigens brought the possibility of using nucleotide-based techniques to predict phenotype. This review will summarized methodologies available to genotype blood groups from laboratory developed assays to commercially available platforms, and how proficiency assays become more present. The author will also share her vision of the transfusion medicine future. The field is presently at the crossroads, bringing new perspectives to a century old practice. Copyright © 2014 Elsevier Ltd. All rights reserved.

Gene hunting: molecular analysis of the chicken genome

NARCIS (Netherlands)

Crooijmans, R.P.M.A.

2000-01-01

This dissertation describes the development of molecular tools to identify genes that are involved in production and health traits in poultry. To unravel the chicken genome, fluorescent molecular markers (microsatellite markers) were developed and optimized to perform high throughput

A fermionic molecular dynamics technique to model nuclear matter

International Nuclear Information System (INIS)

Vantournhout, K.; Jachowicz, N.; Ryckebusch, J.

2009-01-01

Full text: At sub-nuclear densities of about 10 14 g/cm 3 , nuclear matter arranges itself in a variety of complex shapes. This can be the case in the crust of neutron stars and in core-collapse supernovae. These slab like and rod like structures, designated as nuclear pasta, have been modelled with classical molecular dynamics techniques. We present a technique, based on fermionic molecular dynamics, to model nuclear matter at sub-nuclear densities in a semi classical framework. The dynamical evolution of an antisymmetric ground state is described making the assumption of periodic boundary conditions. Adding the concepts of antisymmetry, spin and probability distributions to classical molecular dynamics, brings the dynamical description of nuclear matter to a quantum mechanical level. Applications of this model vary from investigation of macroscopic observables and the equation of state to the study of fundamental interactions on the microscopic structure of the matter. (author)

Can wireless technology enable new diabetes management tools?

Science.gov (United States)

Hedtke, Paul A

2008-01-01

Mobile computing and communications technology embodied in the modern cell phone device can be employed to improve the lives of diabetes patients by giving them better tools for self-management. Several companies are working on the development of diabetes management tools that leverage the ubiquitous cell phone to bring self-management tools to the hand of the diabetes patient. Integration of blood glucose monitoring (BGM) technology with the cell phone platform adds a level of convenience for the person with diabetes, but, more importantly, allows BGM data to be automatically captured, logged, and processed in near real time in order to provide the diabetes patient with assistance in managing their blood glucose levels. Other automatic measurements can estimate physical activity, and information regarding medication events and food intake can be captured and analyzed in order to provide the diabetes patient with continual assistance in managing their therapy and behaviors in order to improve glycemic control. The path to realization of such solutions is not, however, without obstacles.

Cardiovascular Molecular Imaging

International Nuclear Information System (INIS)

Lee, Kyung Han

2009-01-01

Molecular imaging strives to visualize processes in living subjects at the molecular level. Monitoring biochemical processes at this level will allow us to directly track biological processes and signaling events that lead to pathophysiological abnormalities, and help make personalized medicine a reality by allowing evaluation of therapeutic efficacies on an individual basis. Although most molecular imaging techniques emerged from the field of oncology, they have now gradually gained acceptance by the cardiovascular community. Hence, the availability of dedicated high-resolution small animal imaging systems and specific targeting imaging probes is now enhancing our understanding of cardiovascular diseases and expediting the development of newer therapies. Examples include imaging approaches to evaluate and track the progress of recent genetic and cellular therapies for treatment of myocardial ischemia. Other areas include in vivo monitoring of such key molecular processes as angiogenesis and apoptosis. Cardiovascular molecular imaging is already an important research tool in preclinical experiments. The challenge that lies ahead is to implement these techniques into the clinics so that they may help fulfill the promise of molecular therapies and personalized medicine, as well as to resolve disappointments and controversies surrounding the field

Molecular epidemiology of foot and mouth disease, bluetongue and ...

African Journals Online (AJOL)

Molecular tools have become an increasingly important part of studying the epidemiology of infectious agents. These tools have allowed the aetiological agent within a population to be diagnosed rapidly with a greater degree of efficiency and accuracy than conventional diagnostic tools. They have enhanced understanding ...

Advances in algal-prokaryotic wastewater treatment: A review of nitrogen transformations, reactor configurations and molecular tools.

Science.gov (United States)

Wang, Meng; Keeley, Ryan; Zalivina, Nadezhda; Halfhide, Trina; Scott, Kathleen; Zhang, Qiong; van der Steen, Peter; Ergas, Sarina J

2018-07-01

The synergistic activity of algae and prokaryotic microorganisms can be used to improve the efficiency of biological wastewater treatment, particularly with regards to nitrogen removal. For example, algae can provide oxygen through photosynthesis needed for aerobic degradation of organic carbon and nitrification and harvested algal-prokaryotic biomass can be used to produce high value chemicals or biogas. Algal-prokaryotic consortia have been used to treat wastewater in different types of reactors, including waste stabilization ponds, high rate algal ponds and closed photobioreactors. This review addresses the current literature and identifies research gaps related to the following topics: 1) the complex interactions between algae and prokaryotes in wastewater treatment; 2) advances in bioreactor technologies that can achieve high nitrogen removal efficiencies in small reactor volumes, such as algal-prokaryotic biofilm reactors and enhanced algal-prokaryotic treatment systems (EAPS); 3) molecular tools that have expanded our understanding of the activities of algal and prokaryotic communities in wastewater treatment processes. Copyright © 2018 Elsevier Ltd. All rights reserved.

The PAANEEAC programme: bringing EIA professionals together

OpenAIRE

Nooteboom, Sibout; Boven, G.; Post, Reinoud

2015-01-01

markdownabstract__Abstract__ National EIA systems include many actors: EIA agencies, project proponents, sectoral authorities, environmental and social NGOs, consultants, academics, lawyers, politicians and even journalists. Their views and actions largely determine whether EIA systems are successfully strengthened. The PAANEEAC programme assisted national associations of EIA professionals in Central Africa to bring all these actors together, to become platforms for exchange, and to undertake...

Molecular docking.

Science.gov (United States)

Morris, Garrett M; Lim-Wilby, Marguerita

2008-01-01

Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand-protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the target, which is invaluable in lead optimization. The setting up of the input structures for the docking is just as important as the docking itself, and analyzing the results of stochastic search methods can sometimes be unclear. This chapter discusses the background and theory of molecular docking software, and covers the usage of some of the most-cited docking software.

Molecular stratigraphy: a new tool for climatic assessment

Science.gov (United States)

Brassell, S. C.; Eglinton, G.; Marlowe, I. T.; Pflaumann, U.; Sarnthein, M.

1986-03-01

Variations in sea-surface temperatures over the past 500,000 years are inferred from the relative abundance behaviour of two organic compounds, C37 alkenones over the upper 8 metres of a sediment core from the eastern equatorial Atlantic. This molecular record, ascribed to contributions from prymnesiophyte algae, correlates well with the variations in the δ18 signal for the calcareous skeletons of certain planktonic foraminifera, thus providing the first demonstration of a new stratigraphical technique, which may be especially valuable where methods based on carbonate δ18 fail.

Molecular studies by electron spectroscopy

International Nuclear Information System (INIS)

Hansteen, J.M.

1977-01-01

Experience gained in experimental nuclear physics has played a large role in the development of electron spectroscopy as a powerful tool for studying chemical systems. The use of ESCA (Electron Spectroscopy for Chemical Analysis) for the mapping of molecular properties connected with inner as well as outer electron shells is reviewed, mainly from a phenomological point of view. Molecular Auger electron spectroscopy is described as a means of gaining information on details in molecular structure, simultaneously being extensively applied for surface studies. Future highly promising research areas for molecular electron spectroscopy are suggested to be (e,2e) processes as well as continued exploitation of synchrotron radiation from high energy nuclear devices. (Auth.)

Molecular Force Spectroscopy on Cells

Science.gov (United States)

Liu, Baoyu; Chen, Wei; Zhu, Cheng

2015-04-01

Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.

Improving transition voltage spectroscopy of molecular junctions

DEFF Research Database (Denmark)

Markussen, Troels; Chen, Jingzhe; Thygesen, Kristian Sommer

2011-01-01

Transition voltage spectroscopy (TVS) is a promising spectroscopic tool for molecular junctions. The principles in TVS is to find the minimum on a Fowler-Nordheim plot where ln(I/V2) is plotted against 1/V and relate the voltage at the minimum Vmin to the closest molecular level. Importantly, Vmin...

Bioresponsive probes for molecular imaging : Concepts and in vivo applications

NARCIS (Netherlands)

van Duijnhoven, S.M.J.; Robillard, M.S.; Langereis, S.; Grüll, H.

2015-01-01

Molecular imaging is a powerful tool to visualize and characterize biological processes at the cellular and molecular level in vivo. In most molecular imaging approaches, probes are used to bind to disease-specific biomarkers highlighting disease target sites. In recent years, a new subset of

Bioresponsive probes for molecular imaging: concepts and in vivo applications

NARCIS (Netherlands)

Duijnhoven, S.M. van; Robillard, M.S.; Langereis, S.; Grull, H.

2015-01-01

Molecular imaging is a powerful tool to visualize and characterize biological processes at the cellular and molecular level in vivo. In most molecular imaging approaches, probes are used to bind to disease-specific biomarkers highlighting disease target sites. In recent years, a new subset of

Earth Exploration Toolbook Workshops: Web-Conferencing and Teleconferencing Professional Development Bringing Earth Science Data Analysis and Visualization Tools to K-12 Teachers and Students

Science.gov (United States)

McAuliffe, C.; Ledley, T.

2008-12-01

our participants reported that they have not tried to locate a teaching resource in DLESE and forty-eight percent report that they have not to locate a teaching resource in NSDL. As part of an EET Data Analysis workshop, teachers actively visit both digital libraries. Virtual workshops using Web conferencing and teleconferencing are an effective and convenient way to deliver professional development that brings teachers from all over the nation together to learn new technology. Teachers report that the step-by-step facilitation along with the ability to ask questions and interact with their peers are some of the most useful aspects of the workshop. In this presentation, we will share successes and challenges of teachers as they implement these Earth science data analysis and visualization tools in their classrooms.

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

Science.gov (United States)

Canuto, V. M.; Battaglia, A.

1985-01-01

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

Molecular Responses to the Zika Virus in Mosquitoes

Directory of Open Access Journals (Sweden)

Catalina Alfonso-Parra

2018-05-01

Full Text Available The Zika virus (ZIKV, originally discovered in 1947, did not become a major concern until the virus swept across the Pacific and into the Americas in the last decade, bringing with it news of neurological complications and birth defects in ZIKV affected areas. This prompted researchers to dissect the molecular interactions between ZIKV and the mosquito vector in an attempt to better understand not only the changes that occur upon infection, but to also identify molecules that may potentially enhance or suppress a mosquito’s ability to become infected and/or transmit the virus. Here, we review what is currently known regarding ZIKV-mosquito molecular interactions, focusing on ZIKV infection of Aedes aegypti and Aedes albopictus, the primary species implicated in transmitting ZIKV during the recent outbreaks.

Bring Your Own Digital Device in Teacher Education

Science.gov (United States)

Newhouse, C. Paul; Cooper, Martin; Pagram, Jeremy

2015-01-01

This article reports on an investigation to advise a teacher education institution on the feasibility of having a "Bring Your Own Digital Device" policy for students. The investigation built on components of two research projects while adding the comprehensive testing of representative potential hardware and software platforms. The…

Bring Your Own Device and Nurse Managers' Decision Making.

Science.gov (United States)

Martinez, Karen; Borycki, Elizabeth; Courtney, Karen L

2017-02-01

The Bring Your Own Device phenomenon is important in the healthcare environment because this trend is changing the workplace in healthcare organizations, such as British Columbia. At present, there is little research that exists in Canada to provide a distinct understanding of the complexities and difficulties unique to this phenomenon within the nursing practice. This study focused on the experiences and perceptions of nurse managers regarding how they make decisions on the use of personal handheld devices in the workplace. Telephone interviews (N = 10) and qualitative descriptive analysis were used. Four major themes emerged: (1) management perspective, (2) opportunities, (3) disadvantages, and (4) solutions. Nurse managers and other executives in healthcare organizations and health information technology departments need to be aware of the practice and organizational implications of the Bring Your Own Device movement.

Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology.

Science.gov (United States)

Cock, Peter J A; Grüning, Björn A; Paszkiewicz, Konrad; Pritchard, Leighton

2013-01-01

The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of "effector" proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen's predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology. This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols. The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu).

Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology.

Science.gov (United States)

Li, Jinyang; Liu, Yi; Kim, Eunkyoung; March, John C; Bentley, William E; Payne, Gregory F

2017-04-01

The intestine is the site of digestion and forms a critical interface between the host and the outside world. This interface is composed of host epithelium and a complex microbiota which is "connected" through an extensive web of chemical and biological interactions that determine the balance between health and disease for the host. This biology and the associated chemical dialogues occur within a context of a steep oxygen gradient that provides the driving force for a variety of reduction and oxidation (redox) reactions. While some redox couples (e.g., catecholics) can spontaneously exchange electrons, many others are kinetically "insulated" (e.g., biothiols) allowing the biology to set and control their redox states far from equilibrium. It is well known that within cells, such non-equilibrated redox couples are poised to transfer electrons to perform reactions essential to immune defense (e.g., transfer from NADH to O 2 for reactive oxygen species, ROS, generation) and protection from such oxidative stresses (e.g., glutathione-based reduction of ROS). More recently, it has been recognized that some of these redox-active species (e.g., H 2 O 2 ) cross membranes and diffuse into the extracellular environment including lumen to transmit redox information that is received by atomically-specific receptors (e.g., cysteine-based sulfur switches) that regulate biological functions. Thus, redox has emerged as an important modality in the chemical signaling that occurs in the intestine and there have been emerging efforts to develop the experimental tools needed to probe this modality. We suggest that electrochemistry provides a unique tool to experimentally probe redox interactions at a systems level. Importantly, electrochemistry offers the potential to enlist the extensive theories established in signal processing in an effort to "reverse engineer" the molecular communication occurring in this complex biological system. Here, we review our efforts to develop this

Autonomous model protocell division driven by molecular replication.

Science.gov (United States)

Taylor, J W; Eghtesadi, S A; Points, L J; Liu, T; Cronin, L

2017-08-10

The coupling of compartmentalisation with molecular replication is thought to be crucial for the emergence of the first evolvable chemical systems. Minimal artificial replicators have been designed based on molecular recognition, inspired by the template copying of DNA, but none yet have been coupled to compartmentalisation. Here, we present an oil-in-water droplet system comprising an amphiphilic imine dissolved in chloroform that catalyses its own formation by bringing together a hydrophilic and a hydrophobic precursor, which leads to repeated droplet division. We demonstrate that the presence of the amphiphilic replicator, by lowering the interfacial tension between droplets of the reaction mixture and the aqueous phase, causes them to divide. Periodic sampling by a droplet-robot demonstrates that the extent of fission is increased as the reaction progresses, producing more compartments with increased self-replication. This bridges a divide, showing how replication at the molecular level can be used to drive macroscale droplet fission.Coupling compartmentalisation and molecular replication is essential for the development of evolving chemical systems. Here the authors show an oil-in-water droplet containing a self-replicating amphiphilic imine that can undergo repeated droplet division.

Dynamics and Thermodynamics of Molecular Machines

DEFF Research Database (Denmark)

Golubeva, Natalia

2014-01-01

to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical......Molecular machines, or molecular motors, are small biophysical devices that perform a variety of essential metabolic processes such as DNA replication, protein synthesis and intracellular transport. Typically, these machines operate by converting chemical energy into motion and mechanical work. Due...... mechanics. The first part focuses on noninteracting molecular machines described by a paradigmatic continuum model with the aim of comparing and contrasting such a description to the one offered by the widely used discrete models. Many molecular motors, for example, kinesin involved in cellular cargo...

Value Innovation in Learner-Centered Design. How to Develop Valuable Learning Tools.

Directory of Open Access Journals (Sweden)

Henning Breuer

2014-02-01

Full Text Available This paper shows how to address technological, cultural and social transformations with empirically grounded innovation. Areas in transition such as higher education and learning techniques today bring about new needs and opportunities for innovative tools and services. But how do we find these tools? The paper argues for using a strategy of (user value innovation that creatively combines ethnographic methods with strategic industry analysis. By focusing on unmet and emerging needs ethnographic research identifies learner values, needs and challenges but does not determine solutions. Blue-ocean strategy tools can identify new opportunities that alter existing offerings but give weak guidance on what will be most relevant to users. The triangulation of both is illustrated through an innovation project in higher education.

Understanding Managers Decision Making Process for Tools Selection in the Core Front End of Innovation

DEFF Research Database (Denmark)

Appio, Francesco P.; Achiche, Sofiane; McAloone, Tim C.

2011-01-01

New product development (NPD) describes the process of bringing a new product or service to the market. The Fuzzy Front End (FFE) of Innovation is the term describing the activities happening before the product development phase of NPD. In the FFE of innovation, several tools are used to facilita...... hypotheses are tested. A preliminary version of a theoretical model depicting the decision process of managers during tools selection in the FFE is proposed. The theoretical model is built from the constructed hypotheses....

Jane: a new tool for the cophylogeny reconstruction problem.

Science.gov (United States)

Conow, Chris; Fielder, Daniel; Ovadia, Yaniv; Libeskind-Hadas, Ran

2010-02-03

This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites), molecular systematics (associations of orderings and genes), and biogeography (associations of regions and orderings). The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools. The Jane software tool uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The tool allows the user to provide rich timing information on both the host and parasite trees. In addition the user can limit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costs for host switches between pairs of regions. Jane also provides a graphical user interface that allows the user to interactively experiment with modifications to the solutions found by the program. Jane is shown to be a useful tool for cophylogenetic reconstruction. Its functionality complements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology, molecular systematics, and biogeography.

Molecular modeling for the design of novel performance chemicals and materials

CERN Document Server

Rai, Beena

2012-01-01

Molecular modeling (MM) tools offer significant benefits in the design of industrial chemical plants and material processing operations. While the role of MM in biological fields is well established, in most cases MM works as an accessory in novel products/materials development rather than a tool for direct innovation. As a result, MM engineers and practitioners are often seized with the question: ""How do I leverage these tools to develop novel materials or chemicals in my industry?"" Molecular Modeling for the Design of Novel Performance Chemicals and Materials answers this important questio

IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels.

Directory of Open Access Journals (Sweden)

Kota Kasahara

Full Text Available Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering. This approach effectively revealed the ion conduction mechanisms and their dependence on the conditions, i.e., ion concentration and membrane voltage. Here, we present an easy-to-use computational toolkit for ion-binding state analysis, called IBiSA_tools. This toolkit consists of a C++ program and a series of Python and R scripts. From the trajectory file of MD simulations and a structure file, users can generate several images and statistics of ion conduction processes. A complex network named ion-binding state graph is generated in a standard graph format (graph modeling language; GML, which can be visualized by standard network analyzers such as Cytoscape. As a tutorial, a trajectory of a 50 ns MD simulation of the Kv1.2 channel is also distributed with the toolkit. Users can trace the entire process of ion-binding state analysis step by step. The novel method for analysis of ion conduction mechanisms of ion channels can be easily used by means of IBiSA_tools. This software is distributed under an open source license at the following URL: http://www.ritsumei.ac.jp/~ktkshr/ibisa_tools/.

Bringing the environment down to earth.

Science.gov (United States)

Reinhardt, F L

1999-01-01

The debate on business and the environment has typically been framed in simple yes-or-no terms: "Does it pay to be green?" But the environment, like other business issues, requires a more complex approach--one that demands more than such all-or-nothing thinking. Managers need to ask instead, "Under what circumstances do particular kinds of environmental investments deliver returns to shareholders?" This article presents five approaches that managers can take to identify those circumstances and integrate the environment into their business thinking. These approaches will enable companies with the right industry structure, competitive position, and managerial skills to reconcile their responsibility to shareholders with the pressure to be faithful stewards of the earth's resources. Some companies can distance themselves from competitors by differentiating their products and commanding higher prices for them. Others may be able to "manage" their competitors by imposing a set of private regulations or by helping to shape the rules written by government officials. Still others may be able to cut costs and help the environment simultaneously. Almost all can learn to improve their management of risk and thus reduce the outlays associated with accidents, lawsuits, and boycotts. And some companies may even be able to make systemic changes that will redefine competition in their markets. All five approaches can help managers bring the environment down to earth. And that means bringing the environment back into the fold of business problems and determining when it really pays to be green.

Analysis of Twisting of Cellulose Nanofibrils in Atomistic Molecular Dynamics Simulations

DEFF Research Database (Denmark)

Paavilainen, S.; Rog, T.; Vattulainen, I.

2011-01-01

We use atomistic molecular dynamics simulations to study the crystal structure of cellulose nanofibrils, whose sizes are comparable with the crystalline parts in commercial nanocellulose. The simulations show twisting, whose rate of relaxation is strongly temperature dependent. Meanwhile......, no significant bending or stretching of nanocellulose is discovered. Considerations of atomic-scale interaction patterns bring about that the twisting arises from hydrogen bonding within and between the chains in a fibril....

Neutron Scattering studies of magnetic molecular magnets

International Nuclear Information System (INIS)

Chaboussant, G.

2009-01-01

This work deals with inelastic neutron scattering studies of magnetic molecular magnets and focuses on their magnetic properties at low temperature and low energies. Several molecular magnets (Mn 12 , V 15 , Ni 12 , Mn 4 , etc.) are reviewed. Inelastic neutron scattering is shown to be a perfectly suited spectroscopy tool to -a) probe magnetic energy levels in such systems and -b) provide key information to understand the quantum tunnel effect of the magnetization in molecular spin clusters. (author)

Related Fact Checks: a tool for combating fake news

OpenAIRE

Guha, Sreya

2017-01-01

The emergence of "Fake News" and misinformation via online news and social media has spurred an interest in computational tools to combat this phenomenon. In this paper we present a new "Related Fact Checks" service, which can help a reader critically evaluate an article and make a judgment on its veracity by bringing up fact checks that are relevant to the article. We describe the core technical problems that need to be solved in building a "Related Fact Checks" service, and present results ...

Molecular Imaging in Nanotechnology and Theranostics.

Science.gov (United States)

Andreou, Chrysafis; Pal, Suchetan; Rotter, Lara; Yang, Jiang; Kircher, Moritz F

2017-06-01

The fields of biomedical nanotechnology and theranostics have enjoyed exponential growth in recent years. The "Molecular Imaging in Nanotechnology and Theranostics" (MINT) Interest Group of the World Molecular Imaging Society (WMIS) was created in order to provide a more organized and focused forum on these topics within the WMIS and at the World Molecular Imaging Conference (WMIC). The interest group was founded in 2015 and was officially inaugurated during the 2016 WMIC. The overarching goal of MINT is to bring together the many scientists who work on molecular imaging approaches using nanotechnology and those that work on theranostic agents. MINT therefore represents scientists, labs, and institutes that are very diverse in their scientific backgrounds and areas of expertise, reflecting the wide array of materials and approaches that drive these fields. In this short review, we attempt to provide a condensed overview over some of the key areas covered by MINT. Given the breadth of the fields and the given space constraints, we have limited the coverage to the realm of nanoconstructs, although theranostics is certainly not limited to this domain. We will also focus only on the most recent developments of the last 3-5 years, in order to provide the reader with an intuition of what is "in the pipeline" and has potential for clinical translation in the near future.

The role of binary and many-centre molecular interactions in spin crossover in the solid state. Part II. Non-ideality parameters defined via binary molecular potentials

International Nuclear Information System (INIS)

Koudriavtsev, A.B.; Linert, W.

2005-01-01

Parameters of the formalism [1-6] describing spin crossover in the solid state have been defined via molecular potentials in model systems of neutral and ionic complexes. In the first instance Lennard-Jones and electric dipole-dipole potentials have been used whereas in ionic systems Lennard-Jones and electric point-charge potentials have been used. Electric dipole-dipole interaction of neutral complexes brings about a positive excess energy controlled by the difference of electric dipole moments of HS and LS molecules. Differences of the order of Δμ = 1-2D cause an abrupt spin crossover in systems with T 1/2 = 100-150K. Magnetic coupling contributes both to the excess energy and excess entropy, however the overall effect is equivalent to a modest positive excess energy. Ionic systems in the absence of specific interactions are characterized by very small excess energies corresponding to practically linear van't Hoff plots. Detectable positive and negative excess energies in these systems may arise from interactions of ligands belonging to neighbouring complexes. The HOMO-LUMO overlap in HS-LS pairs can bring about a nontrivial variation of the shape of transition curves. Examples of regression analysis of experimental transition curves in terms of molecular potentials are given. (author)

The Engaged Microbiologist: Bringing the Microbiological Sciences to the K-12 Community.

Science.gov (United States)

Westenberg, David J

2016-03-01

Exposing K-12 students to cutting edge science that impacts their daily lives can bring classroom lessons to life. Citizen-science projects are an excellent way to bring high-level science to the classroom and help satisfy one of the cornerstone concepts of the Next Generation Science Standards (NGSS), "engaging in practices that scientists and engineers actually use." This can be a daunting task for teachers who may lack the background or resources to integrate these projects into the classroom. This is where scientific societies such as the American Society for Microbiology (ASM) can play a critical role. ASM encourages its members to engage with the K-12 community by providing networking opportunities and resources for ASM members and K-12 teachers to work together to bring microbiology into the classroom. Journal of Microbiology & Biology Education.

The Engaged Microbiologist: Bringing the Microbiological Sciences to the K–12 Community

Directory of Open Access Journals (Sweden)

David J. Westenberg

2015-12-01

Full Text Available Exposing K–12 students to cutting edge science that impacts their daily lives can bring classroom lessons to life. Citizen-science projects are an excellent way to bring high-level science to the classroom and help satisfy one of the cornerstone concepts of the Next Generation Science Standards (NGSS, “engaging in practices that scientists and engineers actually use.” This can be a daunting task for teachers who may lack the background or resources to integrate these projects into the classroom. This is where scientific societies such as the American Society for Microbiology (ASM can play a critical role. ASM encourages its members to engage with the K–12 community by providing networking opportunities and resources for ASM members and K–12 teachers to work together to bring microbiology into the classroom.

Bringing holistic treatments to the attention of medicine: acupuncture as an effective poststroke rehabilitation tool.

Science.gov (United States)

Farmer, Cecilia

2015-04-01

This article reviews 3 studies that explore the effects of acupuncture on poststroke patients suffering from chronic stroke symptoms. The 3 studies selected strive to show how acupuncture can be a safe, noninvasive, and cost-effect rehabilitation tool useful in adjunct with traditional rehabilitation. Chou et al (2009), Hopwood et al (2008), and Wayne et al (2005) all studied acupuncture's effects on quality of life. Additionally, both Hopwood et al and Wayne et al studied acupuncture's effects on mobility and activities of daily living. While the frequency, duration, and length of the entire treatment varied by study, overall, the results of all 3 studies suggest that acupuncture increases quality of life and improves mobility and activities of daily living. © The Author(s) 2014.

Improving Security in Bring Your Own Device (BYOD) Environment by Controlling Access

OpenAIRE

Muhammad, M.A.; Zadeh, P.B.; Ayesh, Aladdin, 1972-

2017-01-01

With the rapid increase in smartphones and tablets, Bring Your Own Devices (BYOD) has simplified computing by introducing the use of personally owned devices. These devices can be utilised in accessing business enterprise contents and networks. The effectiveness of BYOD offers several business benefits like employee job satisfaction, increased job efficiency and flexibility. However, allowing employees to bring their own devices could lead to a plethora of security issues; like data theft, un...

Math tools 500+ applications in science and arts

CERN Document Server

Glaeser, Georg

2017-01-01

In this book, topics such as algebra, trigonometry, calculus and statistics are brought to life through over 500 applications ranging from biology, physics and chemistry to astronomy, geography and music. With over 600 illustrations emphasizing the beauty of mathematics, Math Tools complements more theoretical textbooks on the market, bringing the subject closer to the reader and providing a useful reference to students. By highlighting the ubiquity of mathematics in practical fields, the book will appeal not only to students and teachers, but to anyone with a keen interest in mathematics and its applications.

Bringing climate change into natural resource management: proceedings.

Science.gov (United States)

L. Joyce; R. Haynes; R. White; R.J. Barbour

2007-01-01

These are the proceedings of the 2005 workshop titled implications of bringing climate into natural resource management in the Western United States. This workshop was an attempt to further the dialogue among scientists, land managers, landowners, interested stakeholders and the public about how individuals are addressing climate change in natural resource management....

Bringing Knowledge Back In: Perspectives from Liberal Education

Science.gov (United States)

Deng, Zongyi

2018-01-01

From the vantage point of liberal education, this article attempts to contribute to the conversation initiated by Michael Young and his colleagues on 'bringing knowledge back' into the current global discourse on curriculum policy and practice. The contribution is made through revisiting the knowledge-its-own-end thesis associated with Newman and…

Bioresponsive probes for molecular imaging:Concepts and in vivo applications

OpenAIRE

Duijnhoven, van, SMJ Sander; Robillard, MS Marc; Langereis, S Sander; Grüll, H Holger

2015-01-01

Molecular imaging is a powerful tool to visualize and characterize biological processes at the cellular and molecular level in vivo. In most molecular imaging approaches, probes are used to bind to disease-specific biomarkers highlighting disease target sites. In recent years, a new subset of molecular imaging probes, known as bioresponsive molecular probes, has been developed. These probes generally benefit from signal enhancement at the site of interaction with its target. There are mainly ...

From molecular design and materials construction to organic nanophotonic devices.

Science.gov (United States)

Zhang, Chuang; Yan, Yongli; Zhao, Yong Sheng; Yao, Jiannian

2014-12-16

CONSPECTUS: Nanophotonics has recently received broad research interest, since it may provide an alternative opportunity to overcome the fundamental limitations in electronic circuits. Diverse optical materials down to the wavelength scale are required to develop nanophotonic devices, including functional components for light emission, transmission, and detection. During the past decade, the chemists have made their own contributions to this interdisciplinary field, especially from the controlled fabrication of nanophotonic molecules and materials. In this context, organic micro- or nanocrystals have been developed as a very promising kind of building block in the construction of novel units for integrated nanophotonics, mainly due to the great versatility in organic molecular structures and their flexibility for the subsequent processing. Following the pioneering works on organic nanolasers and optical waveguides, the organic nanophotonic materials and devices have attracted increasing interest and developed rapidly during the past few years. In this Account, we review our research on the photonic performance of molecular micro- or nanostructures and the latest breakthroughs toward organic nanophotonic devices. Overall, the versatile features of organic materials are highlighted, because they brings tunable optical properties based on molecular design, size-dependent light confinement in low-dimensional structures, and various device geometries for nanophotonic integration. The molecular diversity enables abundant optical transitions in conjugated π-electron systems, and thus brings specific photonic functions into molecular aggregates. The morphology of these micro- or nanostructures can be further controlled based on the weak intermolecular interactions during molecular assembly process, making the aggregates show photon confinement or light guiding properties as nanophotonic materials. By adoption of some active processes in the composite of two or more

Tools and procedures for visualization of proteins and other biomolecules.

Science.gov (United States)

Pan, Lurong; Aller, Stephen G

2015-04-01

Protein, peptides, and nucleic acids are biomolecules that drive biological processes in living organisms. An enormous amount of structural data for a large number of these biomolecules has been described with atomic precision in the form of structural "snapshots" that are freely available in public repositories. These snapshots can help explain how the biomolecules function, the nature of interactions between multi-molecular complexes, and even how small-molecule drugs can modulate the biomolecules for clinical benefits. Furthermore, these structural snapshots serve as inputs for sophisticated computer simulations to turn the biomolecules into moving, "breathing" molecular machines for understanding their dynamic properties in real-time computer simulations. In order for the researcher to take advantage of such a wealth of structural data, it is necessary to gain competency in the use of computer molecular visualization tools for exploring the structures and visualizing three-dimensional spatial representations. Here, we present protocols for using two common visualization tools--the Web-based Jmol and the stand-alone PyMOL package--as well as a few examples of other popular tools. Copyright © 2015 John Wiley & Sons, Inc.

Laboratory Molecular Astrophysics as an Invaluable Tool in understanding Astronomical Observations.

Science.gov (United States)

Fraser, Helen Jane

2015-08-01

We are entering the decade of molecular astrochemistry: spectroscopic data pertaining to the interactions between baryonic matter and electromagnetic radiation are now at the forefront of astronomical observations. Elucidating such data is reliant on inputs from laboratory experiments, modeling, and theoretical chemistry / physics, a field that is intended to be a key focus for the proposed new commission in Laboratory Astrophysics.Here, we propose a “tour de force” review of some recent successes since the last GA in molecular astrophysics, particularly those that have been directly facilitated by laboratory data in Astrochemistry. It is vital to highlight to the astronomers that the absence of laboratory data from the literature would otherwise have precluded advances in our astronomical understanding, e.g:the detection of gas-phase water deep in pre-stellar cores,the detection of water and other molecular species in gravitationally lensed galaxies at z~6“Jumps” in the appearance or disappearance of molecules, including the very recent detection of the first branched organic molecule in the ISM, iso-propyl-cyanide,disentangling dense spectroscopic features in the sub-mm as measured by ALMA, Herschel and SOFIA, the so-called “weeds” and “flowers”,the first ''image'' of a CO snow-line in a protoplanetary disk.Looking forward, the advent of high spatial and spectral resolution telescopes, particularly ALMA, SKA E-ELT and JWST, will continue to drive forward the needs and interests of laboratory astrochemistry in the coming decade. We will look forward to five key areas where advances are expected, and both observational and laboratory techniques are evolving:-(a) understanding star forming regions at very high spatial and spectral senstivity and resolution(b) extragalactic astrochemistry(c) (exo-)planetary atmospheres, surfaces and Solar System sample return - linkinginterstellar and planetary chemistry(d) astrobiology - linking simple molecular

MEvoLib v1.0: the first molecular evolution library for Python.

Science.gov (United States)

Álvarez-Jarreta, Jorge; Ruiz-Pesini, Eduardo

2016-10-28

Molecular evolution studies involve many different hard computational problems solved, in most cases, with heuristic algorithms that provide a nearly optimal solution. Hence, diverse software tools exist for the different stages involved in a molecular evolution workflow. We present MEvoLib, the first molecular evolution library for Python, providing a framework to work with different tools and methods involved in the common tasks of molecular evolution workflows. In contrast with already existing bioinformatics libraries, MEvoLib is focused on the stages involved in molecular evolution studies, enclosing the set of tools with a common purpose in a single high-level interface with fast access to their frequent parameterizations. The gene clustering from partial or complete sequences has been improved with a new method that integrates accessible external information (e.g. GenBank's features data). Moreover, MEvoLib adjusts the fetching process from NCBI databases to optimize the download bandwidth usage. In addition, it has been implemented using parallelization techniques to cope with even large-case scenarios. MEvoLib is the first library for Python designed to facilitate molecular evolution researches both for expert and novel users. Its unique interface for each common task comprises several tools with their most used parameterizations. It has also included a method to take advantage of biological knowledge to improve the gene partition of sequence datasets. Additionally, its implementation incorporates parallelization techniques to enhance computational costs when handling very large input datasets.

Redox control of molecular motion in switchable artificial nanoscale devices.

Science.gov (United States)

Credi, Alberto; Semeraro, Monica; Silvi, Serena; Venturi, Margherita

2011-03-15

The design, synthesis, and operation of molecular-scale systems that exhibit controllable motions of their component parts is a topic of great interest in nanoscience and a fascinating challenge of nanotechnology. The development of this kind of species constitutes the premise to the construction of molecular machines and motors, which in a not-too-distant future could find applications in fields such as materials science, information technology, energy conversion, diagnostics, and medicine. In the past 25 years the development of supramolecular chemistry has enabled the construction of an interesting variety of artificial molecular machines. These devices operate via electronic and molecular rearrangements and, like the macroscopic counterparts, they need energy to work as well as signals to communicate with the operator. Here we outline the design principles at the basis of redox switching of molecular motion in artificial nanodevices. Redox processes, chemically, electrically, or photochemically induced, can indeed supply the energy to bring about molecular motions. Moreover, in the case of electrically and photochemically induced processes, electrochemical and photochemical techniques can be used to read the state of the system, and thus to control and monitor the operation of the device. Some selected examples are also reported to describe the most representative achievements in this research area.

New molecular probes of vascular inflammation

International Nuclear Information System (INIS)

Molecular Cardiovascular Imaging, Westfälische Wilhelms University Münster, Münster, (Germany))" data-affiliation=" (Department of Nuclear Medicine, University Hospital Münster, Münster, and DFG CRC 656 Molecular Cardiovascular Imaging, Westfälische Wilhelms University Münster, Münster, (Germany))" >VRACHIMIS, Alexis; HONOLD, Lisa; Cells in Motion Cluster of Excellence, Westfälische Wilhelms University Münster, Münster, (Germany))" data-affiliation=" (European Institute of Molecular Imaging, Westfälische Wilhelms University Münster, Münster, and DFG EXC 1003 Cells in Motion Cluster of Excellence, Westfälische Wilhelms University Münster, Münster, (Germany))" >FAUST, Andreas; Cells in Motion Cluster of Excellence, Westfälische Wilhelms University Münster, Münster, (Germany))" data-affiliation=" (European Institute of Molecular Imaging, Westfälische Wilhelms University Münster, Münster, and DFG EXC 1003 Cells in Motion Cluster of Excellence, Westfälische Wilhelms University Münster, Münster, (Germany))" >HERMANN, Sven; SCHÄFERS, Michael

2016-01-01

New molecular imaging approaches featuring the assessment of inflammatory processes in the vascular wall on top of existing anatomic and functional vessel imaging procedures could emerge as decisive tools for the understanding and prevention of cardiovascular events. In this respect imaging approaches addressing specific molecular and cellular targets in atherosclerosis are of high interest. This review summarizes the rationale and current status of nuclear imaging probes which possess high translational potential.

The CPEX Data Portal: Bringing Together Different Types of Data for Different Types of Users

Science.gov (United States)

Knosp, B.; Li, P.; Vu, Q. A.; Hristova-Veleva, S. M.; Turk, J.; Lambrigtsen, B.

2017-12-01

The NASA Convective Processes Experiment (CPEX) aircraft field campaign took place in the summer of 2017 in the North Atlantic / Caribbean Ocean region. During this campaign, the NASA DC-8 aircraft carried several instruments that took measurements with the goal of collecting data to help answer questions about convective storm initiation, organization, growth, and dissipation. To help researchers answer science questions about convective storms, the CPEX Data Portal (https://cpexportal.jpl.nasa.gov) was created to bring together relevant satellite and model data, along with aircraft data observed during the campaign. The CPEX Data Portal was designed for two major functions: 1) assist with mission planning by providing a near real-time snapshot of what was going on in the broader North Atlantic domain and 2) bring together different types of data after the aircraft flights had finished to allow researchers to dive deeper into the data. Both functions necessitated collecting a host of disparate data from different instrument types that inherently have differences in resolution, spatial and temporal domain, and quality. Additionally, users of this data portal had varying levels of experience with the different data types (e.g. some used aircraft data before, but not with satellite data). Users were also at different points in their careers - both students and seasoned researchers participated in the campaign and brought different understandings of the physical processes depicted in the portal's visualizations. The CPEX Data Portal team used the existing JPL Tropical Cyclone Information System's near real-time data portal software package to launch a campaign-specific portal to host data during and after the CPEX campaign. This web-based portal includes the ability to visualize pre-generated images of physical quantities from satellites, models, and aircraft instruments, and brings them together in a common virtual globe for given spatial and temporal criteria. Users

Molecular ecological network analyses.

Science.gov (United States)

Deng, Ye; Jiang, Yi-Huei; Yang, Yunfeng; He, Zhili; Luo, Feng; Zhou, Jizhong

2012-05-30

Understanding the interaction among different species within a community and their responses to environmental changes is a central goal in ecology. However, defining the network structure in a microbial community is very challenging due to their extremely high diversity and as-yet uncultivated status. Although recent advance of metagenomic technologies, such as high throughout sequencing and functional gene arrays, provide revolutionary tools for analyzing microbial community structure, it is still difficult to examine network interactions in a microbial community based on high-throughput metagenomics data. Here, we describe a novel mathematical and bioinformatics framework to construct ecological association networks named molecular ecological networks (MENs) through Random Matrix Theory (RMT)-based methods. Compared to other network construction methods, this approach is remarkable in that the network is automatically defined and robust to noise, thus providing excellent solutions to several common issues associated with high-throughput metagenomics data. We applied it to determine the network structure of microbial communities subjected to long-term experimental warming based on pyrosequencing data of 16 S rRNA genes. We showed that the constructed MENs under both warming and unwarming conditions exhibited topological features of scale free, small world and modularity, which were consistent with previously described molecular ecological networks. Eigengene analysis indicated that the eigengenes represented the module profiles relatively well. In consistency with many other studies, several major environmental traits including temperature and soil pH were found to be important in determining network interactions in the microbial communities examined. To facilitate its application by the scientific community, all these methods and statistical tools have been integrated into a comprehensive Molecular Ecological Network Analysis Pipeline (MENAP), which is open

Jane: a new tool for the cophylogeny reconstruction problem

Directory of Open Access Journals (Sweden)

Ovadia Yaniv

2010-02-01

Full Text Available Abstract Background This paper describes the theory and implementation of a new software tool, called Jane, for the study of historical associations. This problem arises in parasitology (associations of hosts and parasites, molecular systematics (associations of orderings and genes, and biogeography (associations of regions and orderings. The underlying problem is that of reconciling pairs of trees subject to biologically plausible events and costs associated with these events. Existing software tools for this problem have strengths and limitations, and the new Jane tool described here provides functionality that complements existing tools. Results The Jane software tool uses a polynomial time dynamic programming algorithm in conjunction with a genetic algorithm to find very good, and often optimal, solutions even for relatively large pairs of trees. The tool allows the user to provide rich timing information on both the host and parasite trees. In addition the user can limit host switch distance and specify multiple host switch costs by specifying regions in the host tree and costs for host switches between pairs of regions. Jane also provides a graphical user interface that allows the user to interactively experiment with modifications to the solutions found by the program. Conclusions Jane is shown to be a useful tool for cophylogenetic reconstruction. Its functionality complements existing tools and it is therefore likely to be of use to researchers in the areas of parasitology, molecular systematics, and biogeography.

Second-harmonic generation circular dichroism spectroscopy from tripod-like chiral molecular films

International Nuclear Information System (INIS)

Wang Xiao-Ou; Chen Li-An; Chen Li-Xue; Sun Xiu-Dong; Li Jun-Qing; Li Chun-Fei

2010-01-01

The second-harmonic generation (SHG) circular dichroism in the light of reflection from chiral films of tripod-like chiral molecules is investigated. The expressions of the second-harmonic generation circular dichroism are derived from our presented three-coupled-oscillator model for the tripod-like chiral molecules. Spectral dependence of the circular dichroism of SHG from film surface composed of tripod-like chiral molecules is simulated numerically and analysed. Influence of chiral parameters on the second-harmonic generation circular dichroism spectrum in chiral films is studied. The result shows that the second-harmonic generation circular dichroism is a sensitive method of detecting chirality compared with the ordinary circular dichroism in linear optics. All of our work indicates that the classical molecular models are very effective to explain the second-harmonic generation circular dichroism of chiral molecular system. The classical molecular model theory can give us a clear physical picture and brings us very instructive information about the link between the molecular configuration and the nonlinear processes

Molecular excitation dynamics and relaxation quantum theory and spectroscopy

CERN Document Server

Valkunas, Leonas; Mancal, Tomas

2013-01-01

Meeting the need for a work that brings together quantum theory and spectroscopy to convey excitation processes to advanced students and specialists wishing to conduct research and understand the entire field rather than just single aspects.Written by an experienced author and recognized authority in the field, this text covers numerous applications and offers examples taken from different disciplines. As a result, spectroscopists, molecular physicists, physical chemists, and biophysicists will all find this a must-have for their research. Also suitable as supplementary reading in graduate

Computer modeling of properties of complex molecular systems

Energy Technology Data Exchange (ETDEWEB)

Kulkova, E.Yu. [Moscow State University of Technology “STANKIN”, Vadkovsky per., 1, Moscow 101472 (Russian Federation); Khrenova, M.G.; Polyakov, I.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); Nemukhin, A.V. [Lomonosov Moscow State University, Chemistry Department, Leninskie Gory 1/3, Moscow 119991 (Russian Federation); N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow 119334 (Russian Federation)

2015-03-10

Large molecular aggregates present important examples of strongly nonhomogeneous systems. We apply combined quantum mechanics / molecular mechanics approaches that assume treatment of a part of the system by quantum-based methods and the rest of the system with conventional force fields. Herein we illustrate these computational approaches by two different examples: (1) large-scale molecular systems mimicking natural photosynthetic centers, and (2) components of prospective solar cells containing titan dioxide and organic dye molecules. We demonstrate that modern computational tools are capable to predict structures and spectra of such complex molecular aggregates.

Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging.

Science.gov (United States)

Gilad, Assaf A; Shapiro, Mikhail G

2017-06-01

Biomedical synthetic biology is an emerging field in which cells are engineered at the genetic level to carry out novel functions with relevance to biomedical and industrial applications. This approach promises new treatments, imaging tools, and diagnostics for diseases ranging from gastrointestinal inflammatory syndromes to cancer, diabetes, and neurodegeneration. As these cellular technologies undergo pre-clinical and clinical development, it is becoming essential to monitor their location and function in vivo, necessitating appropriate molecular imaging strategies, and therefore, we have created an interest group within the World Molecular Imaging Society focusing on synthetic biology and reporter gene technologies. Here, we highlight recent advances in biomedical synthetic biology, including bacterial therapy, immunotherapy, and regenerative medicine. We then discuss emerging molecular imaging approaches to facilitate in vivo applications, focusing on reporter genes for noninvasive modalities such as magnetic resonance, ultrasound, photoacoustic imaging, bioluminescence, and radionuclear imaging. Because reporter genes can be incorporated directly into engineered genetic circuits, they are particularly well suited to imaging synthetic biological constructs, and developing them provides opportunities for creative molecular and genetic engineering.

Bringing optics to Fab Labs in Europe

Science.gov (United States)

Adam, Aurèle; Zuidwijk, Thim; Urbach, Paul

2017-08-01

The Optics Group of Delft University of Technology plays a major role in teaching optics to bachelor and master students. In addition, the group has a long record of introducing, demonstrating and teaching optics to quite diverse groups of people from outside of the university. We will describe some of these activities and focus on a recently started project funded by the European Commission called Phablabs 4.0, which aims to bring photonics to European Fab labs.

Editorial: Biotechnology Journal brings more than biotechnology.

Science.gov (United States)

Jungbauer, Alois; Lee, Sang Yup

2015-09-01

Biotechnology Journal always brings the state-of-the-art biotechnologies to our readers. Different from other topical issues, this issue of Biotechnology Journal is complied with a series of exiting reviews and research articles from spontaneous submissions, again, addressing society's actual problems and needs. The progress is a real testimony how biotechnology contributes to achievements in healthcare, better utilization of resources, and a bio-based economy. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Proposal for Alzheimer’s diagnosis using molecular buffer and bus network

Directory of Open Access Journals (Sweden)

Mitatha S

2011-06-01

Full Text Available S Mitatha1, N Moongfangklang1, MA Jalil2, N Suwanpayak3, T Saktioto4, J Ali4, PP Yupapin31Hybrid Computing Research Laboratory, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, Thailand; 2Ibnu Sina Institute of Fundamental Science Studies, Nanotechnology Research Alliance, Universiti Teknologi Malaysia, Johor Bahru, Malaysia; 3Nanoscale Science and Engineering Research Alliance (N'SERA, Advanced Research Center for Photonics, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand; 4Institute of Advanced Photonics Science, Nanotechnology Research Alliance, Universiti Teknologi Malaysia, Johor Bahru, MalaysiaAbstract: A novel design of an optical trapping tool for tangle protein (tau tangles, ß-amyloid plaques and molecular motor storage and delivery using a PANDA ring resonator is proposed. The optical vortices can be generated and controlled to form the trapping tools in the same way as the optical tweezers. In theory, the trapping force is formed by the combination between the gradient field and scattering photons, and is reviewed. By using the intense optical vortices generated within the PANDA ring resonator, the required molecular volumes can be trapped and moved dynamically within the molecular buffer and bus network. The tangle protein and molecular motor can transport and connect to the required destinations, enabling availability for Alzheimer’s diagnosis.Keywords: Alzheimer’s disease, molecular diagnosis, optical trapping tool, molecular networks

SciServer Compute brings Analysis to Big Data in the Cloud

Science.gov (United States)

Raddick, Jordan; Medvedev, Dmitry; Lemson, Gerard; Souter, Barbara

2016-06-01

SciServer Compute uses Jupyter Notebooks running within server-side Docker containers attached to big data collections to bring advanced analysis to big data "in the cloud." SciServer Compute is a component in the SciServer Big-Data ecosystem under development at JHU, which will provide a stable, reproducible, sharable virtual research environment.SciServer builds on the popular CasJobs and SkyServer systems that made the Sloan Digital Sky Survey (SDSS) archive one of the most-used astronomical instruments. SciServer extends those systems with server-side computational capabilities and very large scratch storage space, and further extends their functions to a range of other scientific disciplines.Although big datasets like SDSS have revolutionized astronomy research, for further analysis, users are still restricted to downloading the selected data sets locally - but increasing data sizes make this local approach impractical. Instead, researchers need online tools that are co-located with data in a virtual research environment, enabling them to bring their analysis to the data.SciServer supports this using the popular Jupyter notebooks, which allow users to write their own Python and R scripts and execute them on the server with the data (extensions to Matlab and other languages are planned). We have written special-purpose libraries that enable querying the databases and other persistent datasets. Intermediate results can be stored in large scratch space (hundreds of TBs) and analyzed directly from within Python or R with state-of-the-art visualization and machine learning libraries. Users can store science-ready results in their permanent allocation on SciDrive, a Dropbox-like system for sharing and publishing files. Communication between the various components of the SciServer system is managed through SciServer‘s new Single Sign-on Portal.We have created a number of demos to illustrate the capabilities of SciServer Compute, including Python and R scripts

Driven: Bringing German Auto Concepts to the Classroom

Science.gov (United States)

Adney, Cara

2012-01-01

A world away from the red dirt of Oklahoma, David Shields and Shelly Smith felt right at home. A national grant took the Meridian Technology Center automotive teachers on a trip to Germany that car lovers only dream about. The tour to the major automakers last summer has them geared up and bringing fresh ideas to the classroom. They spent four…

Controlling charge current through a DNA based molecular transistor

Energy Technology Data Exchange (ETDEWEB)

Behnia, S., E-mail: s.behnia@sci.uut.ac.ir; Fathizadeh, S.; Ziaei, J.

2017-01-05

Molecular electronics is complementary to silicon-based electronics and may induce electronic functions which are difficult to obtain with conventional technology. We have considered a DNA based molecular transistor and study its transport properties. The appropriate DNA sequence as a central chain in molecular transistor and the functional interval for applied voltages is obtained. I–V characteristic diagram shows the rectifier behavior as well as the negative differential resistance phenomenon of DNA transistor. We have observed the nearly periodic behavior in the current flowing through DNA. It is reported that there is a critical gate voltage for each applied bias which above it, the electrical current is always positive. - Highlights: • Modeling a DNA based molecular transistor and studying its transport properties. • Choosing the appropriate DNA sequence using the quantum chaos tools. • Choosing the functional interval for voltages via the inverse participation ratio tool. • Detecting the rectifier and negative differential resistance behavior of DNA.

QR Code: An Interactive Mobile Advertising Tool

Directory of Open Access Journals (Sweden)

Ela Sibel Bayrak Meydanoglu

2013-10-01

Full Text Available Easy and rapid interaction between consumers and marketers enabled by mobile technology prompted  an increase in the usage of mobile media as an interactive marketing tool in recent years. One of the mobile technologies that can be used in interactive marketing for advertising is QR code (Quick Response Code. Interactive advertising brings back some advantages for the companies that apply it. For example, interaction with consumers provides significant information about consumers' preferences. Marketers can use information obtained from consumers for various marketing activities such as customizing advertisement messages, determining  target audience, improving future products and services. QR codes used in marketing campaigns can provide links to specific websites in which through various tools (e.g. questionnaires, voting information about the needs and wants of customers are collected. The aim of this basic research is to illustrate the contribution of  QR codes to the realization of the advantages gained by interactive advertising.

Three novel software tools for ASDEX Upgrade

International Nuclear Information System (INIS)

Martinov, S.; Löbhard, T.; Lunt, T.; Behler, K.; Drube, R.; Eixenberger, H.; Herrmann, A.; Lohs, A.; Lüddecke, K.; Merkel, R.; Neu, G.; ASDEX Upgrade Team; MPCDF Garching

2016-01-01

Highlights: • Key features of innovative software tools for data visualization and inspection are presented to the nuclear fusion research community. • 3D animation of experiment geometry together with diagnostic data and images allow better understanding of measurements and influence of machine construction details behind them. • Multi-video viewer with fusion relevant image manipulation abilities and event database features allows faster and better decision making from video streams coming from various plasma and machine diagnostics. • Platform independant Web technologies enable the inspection of diagnostic raw signals with virtually any kind of display device. - Abstract: Visualization of measurements together with experimental settings is a general subject in experiments analysis. The complex engineering design, 3D geometry, and manifold of diagnostics in larger fusion research experiments justify the development of special analysis and visualization programs. Novel ASDEX Upgrade (AUG) software tools bring together virtual navigation through 3D device models and advanced play-back and interpretation of video streams from plasma discharges. A third little tool allows the web-based platform independent observation of real-time diagnostic signals. While all three tools stem from spontaneous development ideas and are not considered mission critical for the operation of a fusion device, they with time and growing completeness shaped up as valuable helpers to visualize acquired data in fusion research. A short overview on the goals, the features, and the design as well as the operation of these tools is given in this paper.

Three novel software tools for ASDEX Upgrade

Energy Technology Data Exchange (ETDEWEB)

Martinov, S. [Max-Planck-Institut für Plasmaphysik, Boltzmannstr. 2, D-85748 Garching bei München (Germany); Löbhard, T. [Conovum GmbH & Co. KG, Nymphenburger Straße 13, D-80335 München (Germany); Lunt, T. [Max-Planck-Institut für Plasmaphysik, Boltzmannstr. 2, D-85748 Garching bei München (Germany); Behler, K., E-mail: karl.behler@ipp.mpg.de [Max-Planck-Institut für Plasmaphysik, Boltzmannstr. 2, D-85748 Garching bei München (Germany); Drube, R.; Eixenberger, H.; Herrmann, A.; Lohs, A. [Max-Planck-Institut für Plasmaphysik, Boltzmannstr. 2, D-85748 Garching bei München (Germany); Lüddecke, K. [Unlimited Computer Systems GmbH, Seeshaupterstr. 15, D-82393 Iffeldorf (Germany); Merkel, R.; Neu, G.; ASDEX Upgrade Team [Max-Planck-Institut für Plasmaphysik, Boltzmannstr. 2, D-85748 Garching bei München (Germany); MPCDF Garching [Max Planck Compu ting and Data Facility, Boltzmannstr. 2, D-85748 Garching (Germany)

2016-11-15

Highlights: • Key features of innovative software tools for data visualization and inspection are presented to the nuclear fusion research community. • 3D animation of experiment geometry together with diagnostic data and images allow better understanding of measurements and influence of machine construction details behind them. • Multi-video viewer with fusion relevant image manipulation abilities and event database features allows faster and better decision making from video streams coming from various plasma and machine diagnostics. • Platform independant Web technologies enable the inspection of diagnostic raw signals with virtually any kind of display device. - Abstract: Visualization of measurements together with experimental settings is a general subject in experiments analysis. The complex engineering design, 3D geometry, and manifold of diagnostics in larger fusion research experiments justify the development of special analysis and visualization programs. Novel ASDEX Upgrade (AUG) software tools bring together virtual navigation through 3D device models and advanced play-back and interpretation of video streams from plasma discharges. A third little tool allows the web-based platform independent observation of real-time diagnostic signals. While all three tools stem from spontaneous development ideas and are not considered mission critical for the operation of a fusion device, they with time and growing completeness shaped up as valuable helpers to visualize acquired data in fusion research. A short overview on the goals, the features, and the design as well as the operation of these tools is given in this paper.

Assessment of the Simulated Molecular Composition with the GECKO-A Modeling Tool Using Chamber Observations for α-Pinene.

Science.gov (United States)

Aumont, B.; Camredon, M.; Isaacman-VanWertz, G. A.; Karam, C.; Valorso, R.; Madronich, S.; Kroll, J. H.

2016-12-01

Gas phase oxidation of VOC is a gradual process leading to the formation of multifunctional organic compounds, i.e., typically species with higher oxidation state, high water solubility and low volatility. These species contribute to the formation of secondary organic aerosols (SOA) viamultiphase processes involving a myriad of organic species that evolve through thousands of reactions and gas/particle mass exchanges. Explicit chemical mechanisms reflect the understanding of these multigenerational oxidation steps. These mechanisms rely directly on elementary reactions to describe the chemical evolution and track the identity of organic carbon through various phases down to ultimate oxidation products. The development, assessment and improvement of such explicit schemes is a key issue, as major uncertainties remain on the chemical pathways involved during atmospheric oxidation of organic matter. An array of mass spectrometric techniques (CIMS, PTRMS, AMS) was recently used to track the composition of organic species during α-pinene oxidation in the MIT environmental chamber, providing an experimental database to evaluate and improve explicit mechanisms. In this study, the GECKO-A tool (Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere) is used to generate fully explicit oxidation schemes for α-pinene multiphase oxidation simulating the MIT experiment. The ability of the GECKO-A chemical scheme to explain the organic molecular composition in the gas and the condensed phases is explored. First results of this model/observation comparison at the molecular level will be presented.

MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures.

Directory of Open Access Journals (Sweden)

Fabiana A Caetano

2015-12-01

Full Text Available Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell.

Radiative transfer in molecular lines

Science.gov (United States)

Asensio Ramos, A.; Trujillo Bueno, J.; Cernicharo, J.

2001-07-01

The highly convergent iterative methods developed by Trujillo Bueno and Fabiani Bendicho (1995) for radiative transfer (RT) applications are generalized to spherical symmetry with velocity fields. These RT methods are based on Jacobi, Gauss-Seidel (GS), and SOR iteration and they form the basis of a new NLTE multilevel transfer code for atomic and molecular lines. The benchmark tests carried out so far are presented and discussed. The main aim is to develop a number of powerful RT tools for the theoretical interpretation of molecular spectra.

International Conference on Intelligent Systems for Molecular Biology (ISMB)

Energy Technology Data Exchange (ETDEWEB)

Goldberg, Debra; Hibbs, Matthew; Kall, Lukas; Komandurglayavilli, Ravikumar; Mahony, Shaun; Marinescu, Voichita; Mayrose, Itay; Minin, Vladimir; Neeman, Yossef; Nimrod, Guy; Novotny, Marian; Opiyo, Stephen; Portugaly, Elon; Sadka, Tali; Sakabe, Noboru; Sarkar, Indra; Schaub, Marc; Shafer, Paul; Shmygelska, Olena; Singer, Gregory; Song, Yun; Soumyaroop, Bhattacharya; Stadler, Michael; Strope, Pooja; Su, Rong; Tabach, Yuval; Tae, Hongseok; Taylor, Todd; Terribilini, Michael; Thomas, Asha; Tran, Nam; Tseng, Tsai-Tien; Vashist, Akshay; Vijaya, Parthiban; Wang, Kai; Wang, Ting; Wei, Lai; Woo, Yong; Wu, Chunlei; Yamanishi, Yoshihiro; Yan, Changhui; Yang, Jack; Yang, Mary; Ye, Ping; Zhang, Miao

2009-12-29

The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 13 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on "intelligent systems" and actual biological data makes ISMB a unique and highly important meeting, and 13 years of experience in holding the conference has resulted in a consistently well organized, well attended, and highly respected annual conference. The ISMB 2005 meeting was held June 25-29, 2005 at the Renaissance Center in Detroit, Michigan. The meeting attracted over 1,730 attendees. The science presented was exceptional, and in the course of the five-day meeting, 56 scientific papers, 710 posters, 47 Oral Abstracts, 76 Software demonstrations, and 14 tutorials were presented. The attendees represented a broad spectrum of backgrounds with 7% from commercial companies, over 28% qualifying for student registration, and 41 countries were represented at the conference, emphasizing its important international aspect. The ISMB conference is especially important because the cultures of computer science and biology are so disparate. ISMB, as a full-scale technical conference with refereed proceedings that have been indexed by both MEDLINE and Current Contents since 1996, bridges this cultural gap.

Illuminating odors: when optogenetics brings to light unexpected olfactory abilities

Science.gov (United States)

Grimaud, Julien

2016-01-01

For hundreds of years, the sense of smell has generated great interest in the world literature, oenologists, and perfume makers but less of scientists. Only recently this sensory modality has gained new attraction in neuroscience when original tools issued from physiology, anatomy, or molecular biology were available to decipher how the brain makes sense of olfactory cues. However, this move was promptly dampened by the difficulties of developing quantitative approaches to study the relationship between the physical characteristics of stimuli and the sensations they create. An upswing of olfactory investigations occurred when genetic tools could be used in combination with devices borrowed from the physics of light (a hybrid technique called optogenetics) to scrutinize the olfactory system and to provide greater physiological precision for studying olfactory-driven behaviors. This review aims to present the most recent studies that have used light to activate components of the olfactory pathway, such as olfactory receptor neurons, or neurons located further downstream, while leaving intact others brain circuits. With the use of optogenetics to unravel the mystery of olfaction, scientists have begun to disentangle how the brain makes sense of smells. In this review, we shall discuss how the brain recognizes odors, how it memorizes them, and how animals make decisions based on odorants they are capable of sensing. Although this review deals with olfaction, the role of light will be central throughout. PMID:27194792

Features of course definition system control for a mode of preliminary bringing to horizon

Directory of Open Access Journals (Sweden)

О.А. Сущенко

2004-03-01

Full Text Available  The features of course definition system consisting of   platform in gimbal suspension, tuned rotor gyroscopes and pendulous accelerometers for a mode of preliminary bringing to horizon are reviewed. The mathematical description of the mode of preliminary bringing to horizon is derived and the appropriate control moments are determined.

Tools and solutions for environmental reporting and energy management

International Nuclear Information System (INIS)

Suhonen, T.

2004-01-01

Especially two areas of energy applications - environmental reporting and energy management - are emphasized due to the current EU legislation and opening energy markets. Emissions reporting is driven by several EU directives and international agreements, like Emissions Trading Scheme. The directives guide implementation of the emission information management and reporting procedures, but requirements and differences defined by the local authorities are challenging both for the system supplier and for the energy producer. Energy management of industrial energy production (CHP) is an application, which offers real-time tools for forecasting mill's energy need and optimizing the energy balance between a mill's own production, purchases and consumption. This can bring significant reductions in mill energy costs and consumption. For these applications, the exact and well-managed information is needed. Data is retrieved from plant historians and event databases, ERP's and external sources. Calculation applications generate characteristic values (KPI's), which are used for monitoring operation, improving plant availability and boosting performance. Common office tools, like MS Excel, are the most convenient tools for reporting and processing information. Integration tools are needed to combine data from several sources to a single channel, handling messaging between applications and distributing information. (author)

A Diagnostic Assessment for Introductory Molecular and Cell Biology

Science.gov (United States)

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

2010-01-01

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

Final Report "CoDeveloper: A Secure Web-Invocable Collaborative Software Development Tool"

Energy Technology Data Exchange (ETDEWEB)

Svetlana Shasharina

2005-11-27

Modern scientific simulations generate large datasets at remote sites with appropriate resources (supercomputers and clusters). Bringing these large datasets to the computers of all members of a distributed team of collaborators is often impractical or even impossible: there might not be enough bandwidth, storage capacity or appropriate data analysis and visualization tools locally available. To address the need to access remote data, avoid heavy Internet traffic and unnecessary data replication, Tech-X Corporation developed a tool, which allows running remote data visualization collaboratively and sharing the visualization objects as they get generated. The size of these objects is typically much smaller than the size of the original data. For marketing reasons, we renamed the product CoReViz. The detailed information on this product can be found at http://www.txcorp.com/products/CoReViz/. We installed and tested this tool at multiple machines at Tech-X and on seaborg at NERSC. In what follows, we give a detailed description of this tool.

Control of molecular rotation with an optical centrifuge

Science.gov (United States)

Korobenko, Aleksey

2017-04-01

The main purpose of this work is the experimental study of the applicability of an optical centrifuge - a novel tool, utilizing non-resonant broadband laser radiation to excite molecular rotation - to produce and control molecules in extremely high rotational states, so called molecular ``super rotors'', and to study their optical, magnetic, acoustic, hydrodynamic and quantum mechanical properties.

SOYBEAN - MOLECULAR ASPECTS OF BREEDING

Directory of Open Access Journals (Sweden)

Aleksandra Sudarić

2012-12-01

Full Text Available The book Soybean: Molecular Aspects of Breeding focuses recent progress in our understanding of the genetics and molecular biology of soybean. This book is divided into four parts and contains 22 chapters. Part I, Molecular Biology and Biotechnology focuses advances in molecular biology and laboratory procedures that have been developed recently to manipulate DNA. Part II, Breeding for abiotic stress covers proteomics approaches form as a powerful tool for investigating the molecular mechanisms of the plant responses to various types of abiotic stresses. Part III, Breeding for biotic stress addresses issues related to application of molecular based strategies in order to increase soybean resistance to various biotic factors. Part IV, Recent Technology reviews recent technologies into the realm of soybean monitoring, processing and product use. While the information accumulated in this book is of primary interest for plant breeders, valuable insights are also offered to agronomists, molecular biologists, physiologists, plant pathologists, food scientists and students. The book is a result of efforts made by many experts from different countries (USA, Japan, Croatia, Serbia, China, Canada, Malawi, Iran, Hong Kong, Brasil, Mexico.

OralCard: a bioinformatic tool for the study of oral proteome.

Science.gov (United States)

Arrais, Joel P; Rosa, Nuno; Melo, José; Coelho, Edgar D; Amaral, Diana; Correia, Maria José; Barros, Marlene; Oliveira, José Luís

2013-07-01

The molecular complexity of the human oral cavity can only be clarified through identification of components that participate within it. However current proteomic techniques produce high volumes of information that are dispersed over several online databases. Collecting all of this data and using an integrative approach capable of identifying unknown associations is still an unsolved problem. This is the main motivation for this work. We present the online bioinformatic tool OralCard, which comprises results from 55 manually curated articles reflecting the oral molecular ecosystem (OralPhysiOme). It comprises experimental information available from the oral proteome both of human (OralOme) and microbial origin (MicroOralOme) structured in protein, disease and organism. This tool is a key resource for researchers to understand the molecular foundations implicated in biology and disease mechanisms of the oral cavity. The usefulness of this tool is illustrated with the analysis of the oral proteome associated with diabetes melitus type 2. OralCard is available at http://bioinformatics.ua.pt/oralcard. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bringing Curriculum Theory and Didactics Together: A Deweyan Perspective

Science.gov (United States)

Deng, Zongyi

2016-01-01

Using Dewey's method of resolution for resolving a dualism exemplified in "The Child and the Curriculum," this article reconciles and brings together two rival schools of thought--curriculum theory and didactics--in China. The central thesis is that the rapprochement requires a reconceptualisation of curriculum theory and didactics in…

Quantifying transition voltage spectroscopy of molecular junctions: Ab initio calculations

DEFF Research Database (Denmark)

Chen, Jingzhe; Markussen, Troels; Thygesen, Kristian Sommer

2010-01-01

Transition voltage spectroscopy (TVS) has recently been introduced as a spectroscopic tool for molecular junctions where it offers the possibility to probe molecular level energies at relatively low bias voltages. In this work we perform extensive ab initio calculations of the nonlinear current...

Leishmania OligoC-TesT as a simple, rapid, and standardized tool for molecular diagnosis of cutaneous leishmaniasis in Peru.

Science.gov (United States)

Espinosa, Diego; Boggild, Andrea K; Deborggraeve, Stijn; Laurent, Thierry; Valencia, Cristian; Pacheco, Rosa; Miranda-Verástegui, César; Llanos-Cuentas, Alejandro; Leclipteux, Thierry; Dujardin, Jean-Claude; Büscher, Philippe; Arévalo, Jorge

2009-08-01

Molecular methods such as PCR have become attractive tools for diagnosis of cutaneous leishmaniasis (CL), both for their high sensitivity and for their specificity. However, their practical use in routine diagnosis is limited due to the infrastructural requirements and the lack of any standardization. Recently, a simplified and standardized PCR format for molecular detection of Leishmania was developed. The Leishmania OligoC-TesT is based on simple and rapid detection using a dipstick with PCR-amplified Leishmania DNA. In this study, we estimated the diagnostic accuracy of the Leishmania OligoC-TesT for 61 specimens from 44 CL-suspected patients presenting at the leishmaniasis clinic of the Instituto de Medicina Tropical Alexander von Humboldt, Peru. On the basis of parasitological detection and the leishmanin skin test (LST), patients were classified as (i) confirmed CL cases, (ii) LST-positive cases, and (iii) LST-negative cases. The sensitivities of the Leishmania OligoC-TesT was 74% (95% confidence interval (CI), 60.5% to 84.1%) for lesion aspirates and 92% (95% CI, 81.2% to 96.9%) for scrapings. A significantly higher sensitivity was observed with a conventional PCR targeting the kinetoplast DNA on the aspirates (94%) (P = 0.001), while there was no significant difference in sensitivity for the lesion scrapings (88%) (P = 0.317). In addition, the Leishmania OligoC-TesT was evaluated for 13 CL-suspected patients in two different peripheral health centers in the central jungle of Peru. Our findings clearly indicate the high accuracy of the Leishmania OligoC-TesT for lesion scrapings for simple and rapid molecular diagnosis of CL in Peru.

Leishmania OligoC-TesT as a Simple, Rapid, and Standardized Tool for Molecular Diagnosis of Cutaneous Leishmaniasis in Peru▿

Science.gov (United States)

Espinosa, Diego; Boggild, Andrea K.; Deborggraeve, Stijn; Laurent, Thierry; Valencia, Cristian; Pacheco, Rosa; Miranda-Verástegui, César; Llanos-Cuentas, Alejandro; Leclipteux, Thierry; Dujardin, Jean-Claude; Büscher, Philippe; Arévalo, Jorge

2009-01-01

Molecular methods such as PCR have become attractive tools for diagnosis of cutaneous leishmaniasis (CL), both for their high sensitivity and for their specificity. However, their practical use in routine diagnosis is limited due to the infrastructural requirements and the lack of any standardization. Recently, a simplified and standardized PCR format for molecular detection of Leishmania was developed. The Leishmania OligoC-TesT is based on simple and rapid detection using a dipstick with PCR-amplified Leishmania DNA. In this study, we estimated the diagnostic accuracy of the Leishmania OligoC-TesT for 61 specimens from 44 CL-suspected patients presenting at the leishmaniasis clinic of the Instituto de Medicina Tropical Alexander von Humboldt, Peru. On the basis of parasitological detection and the leishmanin skin test (LST), patients were classified as (i) confirmed CL cases, (ii) LST-positive cases, and (iii) LST-negative cases. The sensitivities of the Leishmania OligoC-TesT was 74% (95% confidence interval (CI), 60.5% to 84.1%) for lesion aspirates and 92% (95% CI, 81.2% to 96.9%) for scrapings. A significantly higher sensitivity was observed with a conventional PCR targeting the kinetoplast DNA on the aspirates (94%) (P = 0.001), while there was no significant difference in sensitivity for the lesion scrapings (88%) (P = 0.317). In addition, the Leishmania OligoC-TesT was evaluated for 13 CL-suspected patients in two different peripheral health centers in the central jungle of Peru. Our findings clearly indicate the high accuracy of the Leishmania OligoC-TesT for lesion scrapings for simple and rapid molecular diagnosis of CL in Peru. PMID:19553579

Computational Immunology Meets Bioinformatics: The Use of Prediction Tools for Molecular Binding in the Simulation of the Immune System

DEFF Research Database (Denmark)

Rapin, N.; Lund, Ole; Bernaschi, M.

2010-01-01

potential measurements, for assessing molecular binding in the context of immune complexes. We benchmark the resulting model by simulating a classical immunization experiment that reproduces the development of immune memory. We also investigate the role of major histocompatibility complex (MHC) haplotype...... proliferate more than any other. These results show that the simulator produces dynamics that are stable and consistent with basic immunological knowledge. We believe that the combination of genomic information and simulation of the dynamics of the immune system, in one single tool, can offer new perspectives......We present a new approach to the study of the immune system that combines techniques of systems biology with information provided by data-driven prediction methods. To this end, we have extended an agent-based simulator of the immune response, C-IMMSIM, such that it represents pathogens, as well...

Fads and Fancies: The Use of New Management Tools in UK Universities

Directory of Open Access Journals (Sweden)

John Taylor

2012-08-01

Full Text Available Over the last 20 years, British universities have often looked to business for ideas that might help them cope with growing financial and competitive pressures, increasing expectations of quality and new forms of accountability. The impact of this “new managerialism” has been researched in broad terms, especially looking at the inter-relationship between academic staff and university managers. By contrast, very little has been written about one, highly practical expression of the new managerialism, namely the use of new management tools. This paper brings together separate studies of three such tools: the balanced scorecard, knowledge management and lean thinking. In each case, issues of motivation, leadership and implementation are considered, leading to an overall set of factors that influence the use of such tools in higher education and a model for wider consideration.

Biblionef SA: Bringing books to the bookless | Williams | Innovation

African Journals Online (AJOL)

Biblionef SA: Bringing books to the bookless. Jean Williams. Abstract. No abstract available. Innovation (2003) No. 26, pp 43-47. Full Text: EMAIL FULL TEXT EMAIL FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT · AJOL African Journals Online. HOW TO USE AJOL... for Researchers · for Librarians ...

Molecular Tools for Monitoring the Ecological Sustainability of a Stone Bio-Consolidation Treatment at the Royal Chapel, Granada.

Directory of Open Access Journals (Sweden)

Fadwa Jroundi

Full Text Available Biomineralization processes have recently been applied in situ to protect and consolidate decayed ornamental stone of the Royal Chapel in Granada (Spain. While this promising method has demonstrated its efficacy regarding strengthening of the stone, little is known about its ecological sustainability.Here, we report molecular monitoring of the stone-autochthonous microbiota before and at 5, 12 and 30 months after the bio-consolidation treatment (medium/long-term monitoring, employing the well-known molecular strategy of DGGE analyses. Before the bio-consolidation treatment, the bacterial diversity showed the exclusive dominance of Actinobacteria (100%, which decreased in the community (44.2% after 5 months, and Gamma-proteobacteria (30.24% and Chloroflexi (25.56% appeared. After 12 months, Gamma-proteobacteria vanished from the community and Cyanobacteria (22.1% appeared and remained dominant after thirty months, when the microbiota consisted of Actinobacteria (42.2% and Cyanobacteria (57.8% only. Fungal diversity showed that the Ascomycota phylum was dominant before treatment (100%, while, after five months, Basidiomycota (6.38% appeared on the stone, and vanished again after twelve months. Thirty months after the treatment, the fungal population started to stabilize and Ascomycota dominated on the stone (83.33% once again. Members of green algae (Chlorophyta, Viridiplantae appeared on the stone at 5, 12 and 30 months after the treatment and accounted for 4.25%, 84.77% and 16.77%, respectively.The results clearly show that, although a temporary shift in the bacterial and fungal diversity was observed during the first five months, most probably promoted by the application of the bio-consolidation treatment, the microbiota tends to regain its initial stability in a few months. Thus, the treatment does not seem to have any negative side effects on the stone-autochthonous microbiota over that time. The molecular strategy employed here is suggested

Modelling human behaviour in a bumper car ride using molecular dynamics tools: a student project

Science.gov (United States)

Buendía, Jorge J.; Lopez, Hector; Sanchis, Guillem; Pardo, Luis Carlos

2017-05-01

Amusement parks are excellent laboratories of physics, not only to check physical laws, but also to investigate if those physical laws might also be applied to human behaviour. A group of Physics Engineering students from Universitat Politècnica de Catalunya has investigated if human behaviour, when driving bumper cars, can be modelled using tools borrowed from the analysis of molecular dynamics simulations, such as the radial and angular distribution functions. After acquiring several clips and obtaining the coordinates of the cars, those magnitudes are computed and analysed. Additionally, an analogous hard disks system is simulated to compare its distribution functions to those obtained from the cars’ coordinates. Despite the clear difference between bumper cars and a hard disk-like particle system, the obtained distribution functions are very similar. This suggests that there is no important effect of the individuals in the collective behaviour of the system in terms of structure. The research, performed by the students, has been undertaken in the frame of a motivational project designed to approach the scientific method for university students named FISIDABO. This project offers both the logistical and technical support to undertake the experiments designed by students at the amusement park of Barcelona TIBIDABO and accompanies them all along the scientific process.

Optimization of preservation and processing of sea anemones for microbial community analysis using molecular tools.

Science.gov (United States)

Rocha, Joana; Coelho, Francisco J R C; Peixe, Luísa; Gomes, Newton C M; Calado, Ricardo

2014-11-11

For several years, knowledge on the microbiome associated with marine invertebrates was impaired by the challenges associated with the characterization of bacterial communities. With the advent of culture independent molecular tools it is possible to gain new insights on the diversity and richness of microorganisms associated with marine invertebrates. In the present study, we evaluated if different preservation and processing methodologies (prior to DNA extraction) can affect the bacterial diversity retrieved from snakelocks anemone Anemonia viridis. Denaturing gradient gel electrophoresis (DGGE) community fingerprints were used as proxy to determine the bacterial diversity retrieved (H'). Statistical analyses indicated that preservation significantly affects H'. The best approach to preserve and process A. viridis biomass for bacterial community fingerprint analysis was flash freezing in liquid nitrogen (preservation) followed by the use of a mechanical homogenizer (process), as it consistently yielded higher H'. Alternatively, biomass samples can be processed fresh followed by cell lyses using a mechanical homogenizer or mortar &pestle. The suitability of employing these two alternative procedures was further reinforced by the quantification of the 16S rRNA gene; no significant differences were recorded when comparing these two approaches and the use of liquid nitrogen followed by processing with a mechanical homogenizer.

Amino Acid Molecular Units: Building Primary and Secondary Protein Structures

Directory of Open Access Journals (Sweden)

Aparecido R. Silva

2008-05-01

Full Text Available In order to guarantee the learning quality and suitable knowledge  use  about structural biology, it is fundamental to  exist, since the beginning of  students’ formation, the possibility of clear visualization of biomolecule structures. Nevertheless, the didactic books can only bring  schematic  drawings; even more elaborated figures and graphic computation  do not permit the necessary interaction.  The representation of three-dimensional molecular structures with ludic models, built with representative units, have supplied to the students and teachers a successfully experience to  visualize such structures and correlate them to the real molecules.  The design and applicability of the representative units were discussed with researchers and teachers before mould implementation.  In this stage  it  will be presented the  developed  kit  containing the  representative  plastic parts of the main amino acids.  The kit can demonstrate the interaction among the amino acids  functional groups  (represented by colors, shapes,  sizes and  the peptidic bonds between them  facilitating the assembly and visuali zation of the primary and secondary protein structure.  The models were designed for  Ca,  amino,  carboxyl groups  and  hydrogen. The  lateral chains have  well defined models that represent their geometrical shape.  The completed kit set  will be presented in this meeting (patent requested.  In the last phase of the project will be realized  an effective evaluation  of the kit  as a facilitative didactic tool of the teaching/learning process in the Structural Molecular Biology area.

IVSPlat 1.0: an integrated virtual screening platform with a molecular graphical interface.

Science.gov (United States)

Sun, Yin Xue; Huang, Yan Xin; Li, Feng Li; Wang, Hong Yan; Fan, Cong; Bao, Yong Li; Sun, Lu Guo; Ma, Zhi Qiang; Kong, Jun; Li, Yu Xin

2012-01-05

The virtual screening (VS) of lead compounds using molecular docking and pharmacophore detection is now an important tool in drug discovery. VS tasks typically require a combination of several software tools and a molecular graphics system. Thus, the integration of all the requisite tools in a single operating environment could reduce the complexity of running VS experiments. However, only a few freely available integrated software platforms have been developed. A free open-source platform, IVSPlat 1.0, was developed in this study for the management and automation of VS tasks. We integrated several VS-related programs into a molecular graphics system to provide a comprehensive platform for the solution of VS tasks based on molecular docking, pharmacophore detection, and a combination of both methods. This tool can be used to visualize intermediate and final results of the VS execution, while also providing a clustering tool for the analysis of VS results. A case study was conducted to demonstrate the applicability of this platform. IVSPlat 1.0 provides a plug-in-based solution for the management, automation, and visualization of VS tasks. IVSPlat 1.0 is an open framework that allows the integration of extra software to extend its functionality and modified versions can be freely distributed. The open source code and documentation are available at http://kyc.nenu.edu.cn/IVSPlat/.

Application of Machine Learning tools to recognition of molecular patterns in STM images

Science.gov (United States)

Maksov, Artem; Ziatdinov, Maxim; Fujii, Shintaro; Kiguchi, Manabu; Higashibayashi, Shuhei; Sakurai, Hidehiro; Kalinin, Sergei; Sumpter, Bobby

The ability to utilize individual molecules and molecular assemblies as data storage elements has motivated scientist for years, concurrent with the continuous effort to shrink a size of data storage devices in microelectronics industry. One of the critical issues in this effort lies in being able to identify individual molecular assembly units (patterns), on a large scale in an automated fashion of complete information extraction. Here we present a novel method of applying machine learning techniques for extraction of positional and rotational information from scanning tunneling microscopy (STM) images of π-bowl sumanene molecules on gold. We use Markov Random Field (MRF) model to decode the polar rotational states for each molecule in a large scale STM image of molecular film. We further develop an algorithm that uses a convolutional Neural Network combined with MRF and input from density functional theory to classify molecules into different azimuthal rotational classes. Our results demonstrate that a molecular film is partitioned into distinctive azimuthal rotational domains consisting typically of 20-30 molecules. In each domain, the ``bowl-down'' molecules are generally surrounded by six nearest neighbor molecules in ``bowl-up'' configuration, and the resultant overall structure form a periodic lattice of rotational and polar states within each domain. Research was supported by the US Department of Energy.

Nuclear molecular halo: the ubiquitous occurrence of van der Waals molecular states near threshold in molecular, nuclear and particle physics

International Nuclear Information System (INIS)

Gai, Moshe

1999-01-01

The observation of large E1 strength near threshold in the electromagnetic dissociation of 11 Li poses a fundamental question: Is the large E1 strength due to the threshold or is it due to a low lying E1 state? Such molecular cluster states were observed in 18 O and in several nuclei near the drip line. We discuss the nature of the threshold effect as well as review the situation in Molecular (and Particle Physics) where such Molecular States are observed near the dissociation limit. We suggest that the situation in 11 Li is reminiscent of the argon-benzene molecule where the argon atom is loosely bound by a polarization (van der Waals) mechanism and thus leads to a very extended object lying near the dissociation limit. Such states are also suggested to dominate the structure of mesons [α 0 (980), f 0 (975)] and baryons [λ(1405)] with proposed Kaon molecular structure (Dalitz) near threshold. The inspection of such states throughout Physics allows us to gain insight into this phenomenon and suggest that a new collective Molecular Dipole Degree of Freedom plays a major role in the structure of hadrons (halo nuclei, mesons and baryons), and that quantitative tools such as the E1 Molecular Sum Rule are useful for elucidating the nature of the observed low lying E1 strength in halo nuclei. (author)

Alterações moleculares no Mieloma Múltiplo Molecular abnormalities in Multiple Myeloma

Directory of Open Access Journals (Sweden)

Esteban Braggio

2007-03-01

Full Text Available Nos últimos anos tem acontecido uma revolução no conhecimento dos mecanismos moleculares envolvidos na patogênese do mieloma múltiplo, principalmente devido à incorporação de técnicas de citogenética molecular (hibridização in situ fluorescente - FISH e biologia molecular (Reação em cadeia da polimerase - PCR, hibridização genômica comparativa baseada em microarranjos - aCGH e microarranjos de RNA. Estas técnicas permitem estudar as células em interfase e detectar alterações cromossômicas crípticas, superando assim problemas metodológicos relacionados à análise por citogenética convencional. Por outro lado, a complexidade metodológica relacionada com a realização das técnicas de FISH e biologia molecular tem impossibilitado que sejam amplamente utilizadas na rotina laboratorial. Este trabalho tem como objetivo fazer uma revisão das principais vias moleculares alteradas no mieloma múltiplo, o seu valor prognóstico e a sua utilização na estratificação dos pacientes em diferentes grupos de risco. São detalhadas diferentes abordagens metodológicas e uma ênfase especial é dada em relação à importância da análise se restringir exclusivamente às células plasmocitárias. Por último, discutimos uma série de prioridades e estratégias de estudo na rotina laboratorial.In recent years, we have seen an explosion in knowledge on genetic and cytogenetic mechanisms involved in the pathogenesis of multiple myeloma, mainly due to the incorporation of molecular tools in its study (fluorescence in situ hybridization - FISH, Real time PCR and RNA microarrays. These tools have enabled the study of cells in interphase and to detect cryptic chromosomal abnormalities, replacing cytogenetic techniques. The technical complexities associated with the performance of these tests, however, have limited their widespread applicability in routine clinical practice. The aim of this work is to review the present status of our

[Relevance of big data for molecular diagnostics].

Science.gov (United States)

Bonin-Andresen, M; Smiljanovic, B; Stuhlmüller, B; Sörensen, T; Grützkau, A; Häupl, T

2018-04-01

Big data analysis raises the expectation that computerized algorithms may extract new knowledge from otherwise unmanageable vast data sets. What are the algorithms behind the big data discussion? In principle, high throughput technologies in molecular research already introduced big data and the development and application of analysis tools into the field of rheumatology some 15 years ago. This includes especially omics technologies, such as genomics, transcriptomics and cytomics. Some basic methods of data analysis are provided along with the technology, however, functional analysis and interpretation requires adaptation of existing or development of new software tools. For these steps, structuring and evaluating according to the biological context is extremely important and not only a mathematical problem. This aspect has to be considered much more for molecular big data than for those analyzed in health economy or epidemiology. Molecular data are structured in a first order determined by the applied technology and present quantitative characteristics that follow the principles of their biological nature. These biological dependencies have to be integrated into software solutions, which may require networks of molecular big data of the same or even different technologies in order to achieve cross-technology confirmation. More and more extensive recording of molecular processes also in individual patients are generating personal big data and require new strategies for management in order to develop data-driven individualized interpretation concepts. With this perspective in mind, translation of information derived from molecular big data will also require new specifications for education and professional competence.

Disulfide Bridges: Bringing Together Frustrated Structure in a Bioactive Peptide.

Science.gov (United States)

Zhang, Yi; Schulten, Klaus; Gruebele, Martin; Bansal, Paramjit S; Wilson, David; Daly, Norelle L

2016-04-26

Disulfide bridges are commonly found covalent bonds that are usually believed to maintain structural stability of proteins. Here, we investigate the influence of disulfide bridges on protein dynamics through molecular dynamics simulations on the cysteine-rich trypsin inhibitor MCoTI-II with three disulfide bridges. Correlation analysis of the reduced cyclic peptide shows that two of the three disulfide distances (Cys(11)-Cys(23) and Cys(17)-Cys(29)) are anticorrelated within ∼1 μs of bridge formation or dissolution: when the peptide is in nativelike structures and one of the distances shortens to allow bond formation, the other tends to lengthen. Simulations over longer timescales, when the denatured state is less structured, do not show the anticorrelation. We propose that the native state contains structural elements that frustrate one another's folding, and that the two bridges are critical for snapping the frustrated native structure into place. In contrast, the Cys(4)-Cys(21) bridge is predicted to form together with either of the other two bridges. Indeed, experimental chromatography and nuclear magnetic resonance data show that an engineered peptide with the Cys(4)-Cys(21) bridge deleted can still fold into its near-native structure even in its noncyclic form, confirming the lesser role of the Cys(4)-Cys(21) bridge. The results highlight the importance of disulfide bridges in a small bioactive peptide to bring together frustrated structure in addition to maintaining protein structural stability. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Molecular methods in nuclear medicine therapy

International Nuclear Information System (INIS)

Lee, Kyung Han

2001-01-01

Nuclear medicine has traditionally contributed to molecular oncology by allowing noninvasive monitoring of tumor metabolism, growth and genetic changes, thereby providing a basis for appropriate biology-based treatment planning. However, NM techniques are now being applied as an active therapeutic tool in novel molecular approaches for cancer treatment. Such areas include research on cancer therapy with radiolabeled ligands or oligonucleotides, and utilization of synergism between NM radiotherapy and gene transfer techniques. Here we will focus on novel aspects of nuclear medicine therapy

Early wound infection identification using the WIRE tool in community health care settings: An audit report.

Science.gov (United States)

Siaw-Sakyi, Vincent

2017-12-01

Wound infection is proving to be a challenge for health care professionals. The associated complications and cost of wound infection is immense and can lead to death in extreme cases. Current management of wound infection is largely subjective and relies on the knowledge of the health care professional to identify and initiate treatment. In response, we have developed an infection prediction and assessment tool. The Wound Infection Risk-Assessment and Evaluation tool (WIRE) and its management strategy is a tool with the aim to bring objectivity to infection prediction, assessment and management. A local audit carried out indicated a high infection prediction rate. More work is being done to improve its effectiveness.

Issues and Solutions for Bringing Heterogeneous Water Cycle Data Sets Together

Science.gov (United States)

Acker, James; Kempler, Steven; Teng, William; Belvedere, Deborah; Liu, Zhong; Leptoukh, Gregory

2010-01-01

The water cycle research community has generated many regional to global scale products using data from individual NASA missions or sensors (e.g., TRMM, AMSR-E); multiple ground- and space-based data sources (e.g., Global Precipitation Climatology Project [GPCP] products); and sophisticated data assimilation systems (e.g., Land Data Assimilation Systems [LDAS]). However, it is often difficult to access, explore, merge, analyze, and inter-compare these data in a coherent manner due to issues of data resolution, format, and structure. These difficulties were substantiated at the recent Collaborative Energy and Water Cycle Information Services (CEWIS) Workshop, where members of the NASA Energy and Water cycle Study (NEWS) community gave presentations, provided feedback, and developed scenarios which illustrated the difficulties and techniques for bringing together heterogeneous datasets. This presentation reports on the findings of the workshop, thus defining the problems and challenges of multi-dataset research. In addition, the CEWIS prototype shown at the workshop will be presented to illustrate new technologies that can mitigate data access roadblocks encountered in multi-dataset research, including: (1) Quick and easy search and access of selected NEWS data sets. (2) Multi-parameter data subsetting, manipulation, analysis, and display tools. (3) Access to input and derived water cycle data (data lineage). It is hoped that this presentation will encourage community discussion and feedback on heterogeneous data analysis scenarios, issues, and remedies.

Molecular markers in breast cancer: new tools in imaging and prognosis

NARCIS (Netherlands)

Vermeulen, J.F.

2012-01-01

Breast cancer is the most frequently diagnosed cancer in women. Although breast cancer is mainly diagnosed by mammography, other imaging modalities (e.g. MRI, PET) are increasingly used. The most recent developments in the field of molecular imaging comprise the application of near-infrared

Software engineering methodologies and tools

Science.gov (United States)

Wilcox, Lawrence M.

1993-01-01

Over the years many engineering disciplines have developed, including chemical, electronic, etc. Common to all engineering disciplines is the use of rigor, models, metrics, and predefined methodologies. Recently, a new engineering discipline has appeared on the scene, called software engineering. For over thirty years computer software has been developed and the track record has not been good. Software development projects often miss schedules, are over budget, do not give the user what is wanted, and produce defects. One estimate is there are one to three defects per 1000 lines of deployed code. More and more systems are requiring larger and more complex software for support. As this requirement grows, the software development problems grow exponentially. It is believed that software quality can be improved by applying engineering principles. Another compelling reason to bring the engineering disciplines to software development is productivity. It has been estimated that productivity of producing software has only increased one to two percent a year in the last thirty years. Ironically, the computer and its software have contributed significantly to the industry-wide productivity, but computer professionals have done a poor job of using the computer to do their job. Engineering disciplines and methodologies are now emerging supported by software tools that address the problems of software development. This paper addresses some of the current software engineering methodologies as a backdrop for the general evaluation of computer assisted software engineering (CASE) tools from actual installation of and experimentation with some specific tools.

A combined reaction class approach with integrated molecular orbital+molecular orbital (IMOMO) methodology: A practical tool for kinetic modeling

International Nuclear Information System (INIS)

Truong, Thanh N.; Maity, Dilip K.; Truong, Thanh-Thai T.

2000-01-01

We present a new practical computational methodology for predicting thermal rate constants of reactions involving large molecules or a large number of elementary reactions in the same class. This methodology combines the integrated molecular orbital+molecular orbital (IMOMO) approach with our recently proposed reaction class models for tunneling. With the new methodology, we show that it is possible to significantly reduce the computational cost by several orders of magnitude while compromising the accuracy in the predicted rate constants by less than 40% over a wide range of temperatures. Another important result is that the computational cost increases only slightly as the system size increases. (c) 2000 American Institute of Physics

36 CFR 1280.8 - May I bring a seeing-eye dog or other assistance animal?

Science.gov (United States)

2010-07-01

... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false May I bring a seeing-eye dog or other assistance animal? 1280.8 Section 1280.8 Parks, Forests, and Public Property NATIONAL... dog or other assistance animal? Yes, persons with disabilities may bring guide dogs or other animals...

29 CFR 779.110 - Employees in retailing whose activities may bring them under the Act.

Science.gov (United States)

2010-07-01

... 29 Labor 3 2010-07-01 2010-07-01 false Employees in retailing whose activities may bring them under the Act. 779.110 Section 779.110 Labor Regulations Relating to Labor (Continued) WAGE AND HOUR... Production of Goods for Commerce § 779.110 Employees in retailing whose activities may bring them under the...

Illuminating odors: when optogenetics brings to light unexpected olfactory abilities.

Science.gov (United States)

Grimaud, Julien; Lledo, Pierre-Marie

2016-06-01

For hundreds of years, the sense of smell has generated great interest in the world literature, oenologists, and perfume makers but less of scientists. Only recently this sensory modality has gained new attraction in neuroscience when original tools issued from physiology, anatomy, or molecular biology were available to decipher how the brain makes sense of olfactory cues. However, this move was promptly dampened by the difficulties of developing quantitative approaches to study the relationship between the physical characteristics of stimuli and the sensations they create. An upswing of olfactory investigations occurred when genetic tools could be used in combination with devices borrowed from the physics of light (a hybrid technique called optogenetics) to scrutinize the olfactory system and to provide greater physiological precision for studying olfactory-driven behaviors. This review aims to present the most recent studies that have used light to activate components of the olfactory pathway, such as olfactory receptor neurons, or neurons located further downstream, while leaving intact others brain circuits. With the use of optogenetics to unravel the mystery of olfaction, scientists have begun to disentangle how the brain makes sense of smells. In this review, we shall discuss how the brain recognizes odors, how it memorizes them, and how animals make decisions based on odorants they are capable of sensing. Although this review deals with olfaction, the role of light will be central throughout. © 2016 Grimaud and Lledo; Published by Cold Spring Harbor Laboratory Press.

Molecular biology approaches in bioadhesion research

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Marcelo Rodrigues

2014-07-01

Full Text Available The use of molecular biology tools in the field of bioadhesion is still in its infancy. For new research groups who are considering taking a molecular approach, the techniques presented here are essential to unravelling the sequence of a gene, its expression and its biological function. Here we provide an outline for addressing adhesion-related genes in diverse organisms. We show how to gradually narrow down the number of candidate transcripts that are involved in adhesion by (1 generating a transcriptome and a differentially expressed cDNA list enriched for adhesion-related transcripts, (2 setting up a BLAST search facility, (3 perform an in situ hybridization screen, and (4 functional analyses of selected genes by using RNA interference knock-down. Furthermore, latest developments in genome-editing are presented as new tools to study gene function. By using this iterative multi-technologies approach, the identification, isolation, expression and function of adhesion-related genes can be studied in most organisms. These tools will improve our understanding of the diversity of molecules used for adhesion in different organisms and these findings will help to develop innovative bio-inspired adhesives.

"On-off" switchable tool for food sample preparation: merging molecularly imprinting technology with stimuli-responsive blocks. Current status, challenges and highlighted applications.

Science.gov (United States)

Garcia, Raquel; Gomes da Silva, Marco D R; Cabrita, Maria João

2018-01-01

Sample preparation still remains a great challenge in the analytical workflow representing the most time-consuming and laborious step in analytical procedures. Ideally, sample pre-treatment procedures must be more selective, cheap, quick and environmental friendly. Molecular imprinting technology is a powerful tool in the development of highly selective sample preparation methodologies enabling to preconcentrate the analytes from a complex food matrix. Actually, the design and development of molecularly imprinted polymers-based functional materials that merge an enhancement of selectivity with a controllable and switchable mode of action by means of specific stimulus constitutes a hot research topic in the field of food analysis. Thus, combining the stimuli responsive mechanism and imprinting technology a new generation of materials are emerging. The application of these smart materials in sample preparation is in early stage of development, nevertheless new improvements will promote a new driven in the demanding field of food sample preparation. The new trends in the advancement of food sample preparation using these smart materials will be presented in this review and highlighted the most relevant applications in this particular area of knowledge. Copyright © 2017 Elsevier B.V. All rights reserved.

CSS Preprocessing: Tools and Automation Techniques

Directory of Open Access Journals (Sweden)

Ricardo Queirós

2018-01-01

Full Text Available Cascading Style Sheets (CSS is a W3C specification for a style sheet language used for describing the presentation of a document written in a markup language, more precisely, for styling Web documents. However, in the last few years, the landscape for CSS development has changed dramatically with the appearance of several languages and tools aiming to help developers build clean, modular and performance-aware CSS. These new approaches give developers mechanisms to preprocess CSS rules through the use of programming constructs, defined as CSS preprocessors, with the ultimate goal to bring those missing constructs to the CSS realm and to foster stylesheets structured programming. At the same time, a new set of tools appeared, defined as postprocessors, for extension and automation purposes covering a broad set of features ranging from identifying unused and duplicate code to applying vendor prefixes. With all these tools and techniques in hands, developers need to provide a consistent workflow to foster CSS modular coding. This paper aims to present an introductory survey on the CSS processors. The survey gathers information on a specific set of processors, categorizes them and compares their features regarding a set of predefined criteria such as: maturity, coverage and performance. Finally, we propose a basic set of best practices in order to setup a simple and pragmatic styling code workflow.

Molecular markers in bladder cancer: Novel research frontiers.

Science.gov (United States)

Sanguedolce, Francesca; Cormio, Antonella; Bufo, Pantaleo; Carrieri, Giuseppe; Cormio, Luigi

2015-01-01

Bladder cancer (BC) is a heterogeneous disease encompassing distinct biologic features that lead to extremely different clinical behaviors. In the last 20 years, great efforts have been made to predict disease outcome and response to treatment by developing risk assessment calculators based on multiple standard clinical-pathological factors, as well as by testing several molecular markers. Unfortunately, risk assessment calculators alone fail to accurately assess a single patient's prognosis and response to different treatment options. Several molecular markers easily assessable by routine immunohistochemical techniques hold promise for becoming widely available and cost-effective tools for a more reliable risk assessment, but none have yet entered routine clinical practice. Current research is therefore moving towards (i) identifying novel molecular markers; (ii) testing old and new markers in homogeneous patients' populations receiving homogeneous treatments; (iii) generating a multimarker panel that could be easily, and thus routinely, used in clinical practice; (iv) developing novel risk assessment tools, possibly combining standard clinical-pathological factors with molecular markers. This review analyses the emerging body of literature concerning novel biomarkers, ranging from genetic changes to altered expression of a huge variety of molecules, potentially involved in BC outcome and response to treatment. Findings suggest that some of these indicators, such as serum circulating tumor cells and tissue mitochondrial DNA, seem to be easily assessable and provide reliable information. Other markers, such as the phosphoinositide-3-kinase (PI3K)/AKT (serine-threonine kinase)/mTOR (mammalian target of rapamycin) pathway and epigenetic changes in DNA methylation seem to not only have prognostic/predictive value but also, most importantly, represent valuable therapeutic targets. Finally, there is increasing evidence that the development of novel risk assessment tools

Novel gene expression tools for rice biotechnology

Science.gov (United States)

Biotechnology is an effective and important method of improving both quality and agronomic traits in rice. We are developing novel molecular tools for genetic engineering, with a focus on developing novel transgene expression control elements (i.e. promoters) for rice. A suite of monocot grass promo...

The Chemistry and Flow Dynamics of Molecular Biological Tools Used to Confirm In Situ Bioremediation of Benzene, TBA, and MTBE

Science.gov (United States)

North, K. P.; Mackay, D. M.; Scow, K. M.

2010-12-01

In situ bioremediation has typically been confirmed by collecting sediment and groundwater samples to directly demonstrate a degradation process in a laboratory microcosm. However, recent advances in molecular biological tools present options for demonstrating degradation processes with field-based tools that are less time-consuming. We have been investigating the capability of some of these molecular biological tools to evaluate in situ biodegradation of tert-butyl alcohol (TBA), methyl tert-butyl ether (MTBE), and benzene at two field sites in California. At both sites, we have deployed Bio-Traps® (“traps”), made of Bio-Sep® beads in slotted PVC pipe, which provide ideal environments for microbial colonization. Stable Isotope Probing can be accomplished by sorbing the13C-labeled organic contaminant of concern onto Bio-Sep® beads (“baiting”); incorporation of 13C into the biomass collected by the trap would indicate that the microbial community was capable of degrading the labeled compound. In addition, we examined the chemistry and flow dynamics of these traps and present those results here. We performed a field experiment and a lab experiment to, in part, define the rate that different baits leached off various traps. At a TBA- and MTBE-contaminated site at Vandenberg AFB, Lompoc, CA, the TBA-dominant plume was effectively treated by recirculation/oxygenation of groundwater, decreasing TBA and MTBE concentrations to detection limits along predicted flowpaths created by two pairs of recirculation wells. We used the generated aerobic treatment zone to deploy traps baited with 13C-labeled MTBE or TBA in a novel, ex situ experimental setup. The groundwater flow extracted from the aerobic treatment zone was split through several chambers, each containing a trap and monitoring of influent and effluent. The chamber effluent was measured throughout a six-week deployment and analyzed for both TBA and MTBE; the majority of mass leached from the baited traps did

Molecular docking as a popular tool in drug design, an in silico travel

Directory of Open Access Journals (Sweden)

de Ruyck J

2016-06-01

Full Text Available Jerome de Ruyck, Guillaume Brysbaert, Ralf Blossey, Marc F Lensink University Lille, CNRS UMR8576 UGSF, Lille, FranceAbstract: New molecular modeling approaches, driven by rapidly improving computational platforms, have allowed many success stories for the use of computer-assisted drug design in the discovery of new mechanism- or structure-based drugs. In this overview, we highlight three aspects of the use of molecular docking. First, we discuss the combination of molecular and quantum mechanics to investigate an unusual enzymatic mechanism of a flavoprotein. Second, we present recent advances in anti-infectious agents' synthesis driven by structural insights. At the end, we focus on larger biological complexes made by protein–protein interactions and discuss their relevance in drug design. This review provides information on how these large systems, even in the presence of the solvent, can be investigated with the outlook of drug discovery.Keywords: structure-based drug design, protein–protein docking, quaternary structure prediction, residue interaction networks, RINs, water position

Recent Advances in Cardiac Computed Tomography: Dual Energy, Spectral and Molecular CT Imaging

Science.gov (United States)

Danad, Ibrahim; Fayad, Zahi A.; Willemink, Martin J.; Min, James K.

2015-01-01

Computed tomography (CT) evolved into a powerful diagnostic tool and it is impossible to imagine current clinical practice without CT imaging. Due to its widespread availability, ease of clinical application, superb sensitivity for detection of CAD, and non-invasive nature, CT has become a valuable tool within the armamentarium of the cardiologist. In the last few years, numerous technological advances in CT have occurred—including dual energy CT (DECT), spectral CT and CT-based molecular imaging. By harnessing the advances in technology, cardiac CT has advanced beyond the mere evaluation of coronary stenosis to an imaging modality tool that permits accurate plaque characterization, assessment of myocardial perfusion and even probing of molecular processes that are involved in coronary atherosclerosis. Novel innovations in CT contrast agents and pre-clinical spectral CT devices have paved the way for CT-based molecular imaging. PMID:26068288

Effect of B-ring substitution pattern on binding mode of propionamide selective androgen receptor modulators.

Science.gov (United States)

Bohl, Casey E; Wu, Zengru; Chen, Jiyun; Mohler, Michael L; Yang, Jun; Hwang, Dong Jin; Mustafa, Suni; Miller, Duane D; Bell, Charles E; Dalton, James T

2008-10-15

Selective androgen receptor modulators (SARMs) are essentially prostate sparing androgens, which provide therapeutic potential in osteoporosis, male hormone replacement, and muscle wasting. Herein we report crystal structures of the androgen receptor (AR) ligand-binding domain (LBD) complexed to a series of potent synthetic nonsteroidal SARMs with a substituted pendant arene referred to as the B-ring. We found that hydrophilic B-ring para-substituted analogs exhibit an additional region of hydrogen bonding not seen with steroidal compounds and that multiple halogen substitutions affect the B-ring conformation and aromatic interactions with Trp741. This information elucidates interactions important for high AR binding affinity and provides new insight for structure-based drug design.

Field-programmable custom computing technology architectures, tools, and applications

CERN Document Server

Luk, Wayne; Pocek, Ken

2000-01-01

Field-Programmable Custom Computing Technology: Architectures, Tools, and Applications brings together in one place important contributions and up-to-date research results in this fast-moving area. In seven selected chapters, the book describes the latest advances in architectures, design methods, and applications of field-programmable devices for high-performance reconfigurable systems. The contributors to this work were selected from the leading researchers and practitioners in the field. It will be valuable to anyone working or researching in the field of custom computing technology. It serves as an excellent reference, providing insight into some of the most challenging issues being examined today.

Practical ways of bringing innovations and creativity into the school ...

African Journals Online (AJOL)

This article describes the practical ways of bringing innovations and creativity into the school library media programme in Nigeria. Discussion focused on areas on creativity and innovations such as environmental design, staffing, outreach activities, library cooperation, and introduction of ICT system. Keywords: Innovations ...

The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

Science.gov (United States)

Chen, Jundong

2018-03-01

Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

Agent-Based Modeling in Molecular Systems Biology.

Science.gov (United States)

Soheilypour, Mohammad; Mofrad, Mohammad R K

2018-06-08

Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

Computational tool for simulation of power and refrigeration cycles

Science.gov (United States)

Córdoba Tuta, E.; Reyes Orozco, M.

2016-07-01

Small improvement in thermal efficiency of power cycles brings huge cost savings in the production of electricity, for that reason have a tool for simulation of power cycles allows modeling the optimal changes for a best performance. There is also a big boom in research Organic Rankine Cycle (ORC), which aims to get electricity at low power through cogeneration, in which the working fluid is usually a refrigerant. A tool to design the elements of an ORC cycle and the selection of the working fluid would be helpful, because sources of heat from cogeneration are very different and in each case would be a custom design. In this work the development of a multiplatform software for the simulation of power cycles and refrigeration, which was implemented in the C ++ language and includes a graphical interface which was developed using multiplatform environment Qt and runs on operating systems Windows and Linux. The tool allows the design of custom power cycles, selection the type of fluid (thermodynamic properties are calculated through CoolProp library), calculate the plant efficiency, identify the fractions of flow in each branch and finally generates a report very educational in pdf format via the LaTeX tool.

MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories

KAUST Repository

Abdel-Azeim, Safwat

2014-05-06

Background: Molecular Dynamics ( MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. Results: On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. Conclusions: MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.

Amphibian molecular ecology and how it has informed conservation.

Science.gov (United States)

McCartney-Melstad, Evan; Shaffer, H Bradley

2015-10-01

Molecular ecology has become one of the key tools in the modern conservationist's kit. Here we review three areas where molecular ecology has been applied to amphibian conservation: genes on landscapes, within-population processes, and genes that matter. We summarize relevant analytical methods, recent important studies from the amphibian literature, and conservation implications for each section. Finally, we include five in-depth examples of how molecular ecology has been successfully applied to specific amphibian systems. © 2015 John Wiley & Sons Ltd.

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

Science.gov (United States)

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

2017-07-01

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

Systems biology for molecular life sciences and its impact in biomedicine.

Science.gov (United States)

Medina, Miguel Ángel

2013-03-01

Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

Model Testing - Bringing the Ocean into the Laboratory

DEFF Research Database (Denmark)

Aage, Christian

2000-01-01

Hydrodynamic model testing, the principle of bringing the ocean into the laboratory to study the behaviour of the ocean itself and the response of man-made structures in the ocean in reduced scale, has been known for centuries. Due to an insufficient understanding of the physics involved, however......, the early model tests often gave incomplete or directly misleading results.This keynote lecture deals with some of the possibilities and problems within the field of hydrodynamic and hydraulic model testing....

Silane and Germane Molecular Electronics.

Science.gov (United States)

Su, Timothy A; Li, Haixing; Klausen, Rebekka S; Kim, Nathaniel T; Neupane, Madhav; Leighton, James L; Steigerwald, Michael L; Venkataraman, Latha; Nuckolls, Colin

2017-04-18

This Account provides an overview of our recent efforts to uncover the fundamental charge transport properties of Si-Si and Ge-Ge single bonds and introduce useful functions into group 14 molecular wires. We utilize the tools of chemical synthesis and a scanning tunneling microscopy-based break-junction technique to study the mechanism of charge transport in these molecular systems. We evaluated the fundamental ability of silicon, germanium, and carbon molecular wires to transport charge by comparing conductances within families of well-defined structures, the members of which differ only in the number of Si (or Ge or C) atoms in the wire. For each family, this procedure yielded a length-dependent conductance decay parameter, β. Comparison of the different β values demonstrates that Si-Si and Ge-Ge σ bonds are more conductive than the analogous C-C σ bonds. These molecular trends mirror what is seen in the bulk. The conductance decay of Si and Ge-based wires is similar in magnitude to those from π-based molecular wires such as paraphenylenes However, the chemistry of the linkers that attach the molecular wires to the electrodes has a large influence on the resulting β value. For example, Si- and Ge-based wires of many different lengths connected with a methyl-thiomethyl linker give β values of 0.36-0.39 Å -1 , whereas Si- and Ge-based wires connected with aryl-thiomethyl groups give drastically different β values for short and long wires. This observation inspired us to study molecular wires that are composed of both π- and σ-orbitals. The sequence and composition of group 14 atoms in the σ chain modulates the electronic coupling between the π end-groups and dictates the molecular conductance. The conductance behavior originates from the coupling between the subunits, which can be understood by considering periodic trends such as bond length, polarizability, and bond polarity. We found that the same periodic trends determine the electric field

Bringing Work Home: Take-Home Pesticide Exposure Among Farm Families

NARCIS (Netherlands)

Curwin, B.D.

2006-01-01

In this thesis take-home pesticide exposure among farm families, with an emphasis on herbicides, was investigated. Take-home exposure occurs when a worker unwittingly brings home a substance on his or her clothing or shoes, thereby potentially exposing his or her family. The pesticides investigated

Bringing the LHC and ATLAS to a regional planetarium

CERN Document Server

Schwienhorst, Reinhard

2011-01-01

An outreach effort has started at Michigan State University to bring particle physics, the Large Hadron Collider, and the ATLAS experiment to a general audience at the Abrams planetarium on the MSU campus. A team of undergraduate students majoring in physics, communications arts & sciences, and journalism are putting together short clips about ATLAS and the LHC to be shown at the planetarium.

Molecular Dynamics of Flexible Polar Cations in a Variable Confined Space: Toward Exceptional Two-Step Nonlinear Optical Switches.

Science.gov (United States)

Xu, Wei-Jian; He, Chun-Ting; Ji, Cheng-Min; Chen, Shao-Li; Huang, Rui-Kang; Lin, Rui-Biao; Xue, Wei; Luo, Jun-Hua; Zhang, Wei-Xiong; Chen, Xiao-Ming

2016-07-01

The changeable molecular dynamics of flexible polar cations in the variable confined space between inorganic chains brings about a new type of two-step nonlinear optical (NLO) switch with genuine "off-on-off" second harmonic generation (SHG) conversion between one NLO-active state and two NLO-inactive states. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Culture-Independent Molecular Tools for Soil and Rhizosphere Microbiology

Directory of Open Access Journals (Sweden)

Peer M. Schenk

2013-08-01

Full Text Available Soil microbial communities play an important role in plant health and soil quality. Researchers have developed a wide range of methods for studying the structure, diversity, and activity of microbes to better understand soil biology and plant-microbe interactions. Functional microbiological analyses of the rhizosphere have given new insights into the role of microbial communities in plant nutrition and plant protection against diseases. In this review, we present the most commonly used traditional as well as new culture-independent molecular methods to assess the diversity and function of soil microbial communities. Furthermore, we discuss advantages and disadvantages of these techniques and provide a perspective on emerging technologies for soil microbial community profiling.

The emergence of use of a rake-like tool: a longitudinal study in human infants

Directory of Open Access Journals (Sweden)

Jacqueline eFagard

2014-05-01

Full Text Available We describe the results of a longitudinal study on five infants from age 12 to 20 months, presented with an out of reach toy and a rake-like tool within reach. Five conditions of spatial relationship between toy and rake were tested. Outcomes and types of behavior were analyzed. There were successes observed around 12 months in the condition of spatial contiguity between rake and toy, but these could not be interpreted as corresponding to full understanding of the use of the rake. At this age and for the following months, in the conditions involving spatial separation between rake and toy, infants’ strategies fluctuated between paying attention to the toy only, exploring the rake for its own sake, and connecting rake and toy but with no apparent attempt to bring the toy closer. Only between 16 and 20 months did infants fairly suddenly start to intentionally try to bring the toy closer with the tool: at this stage the infants also became able to learn from their failures and to correct their actions, as well as to benefit from demonstration from an adult. We examine the individual differences in the pattern of change in behaviors leading to tool use in the five infants, and find no increase in any one type of behaviour that systematically precedes success. We conclude that sudden success at 18 months probably corresponds to the coming together of a variety of capacities.

Bring Your Own Device Technology: Preliminary Results from a Mixed Methods Study to Explore Student Experience of In-Class Response Systems in Post-Secondary Education

Directory of Open Access Journals (Sweden)

Matthew Numer

2015-02-01

Full Text Available This research examines the effectiveness of Bring Your Own Device (BYOD technology in a postsecondary classroom. Despite recent advances in the technological tools available to educators, there is a significant gap in the literature regarding student efficacy, engagement and contribution to learning. This paper will present the preliminary findings of the first phases of an evaluation project measuring student interaction with BYOD technology in a large group setting. Employing a mixed methods design, the findings from two focus groups and two online surveys will be discussed. This project involved students in the Winter and Fall 2014 semesters of a fourth year Human Sexuality course which has enrolment of approximately 400 per semester. The findings suggest that BYOD technology contributes to student engagement and participation in the classroom setting. Further, the findings suggest that students are comfortable in using this tool, and perceived the experience as enjoyable.

[The new tools of microbiological diagnosis of tuberculosis].

Science.gov (United States)

Guillet-Caruba, C; Martinez, V; Doucet-Populaire, F

2014-12-01

This review focuses on the role of new tools in the "modern" microbiological diagnosis of tuberculosis. Traditional techniques of microscopy and culture remain essential to diagnostic certainty, but some innovations replace daily the older techniques such as the identification of Mycobacterium tuberculosis complex by immunochromatography or mass spectrometry MALDI-TOF type from positive cultures, or susceptibility testing in liquid medium. New tools that use molecular techniques have become important. They all have in common to optimize the fight against tuberculosis by reducing diagnostic delay. They also allow rapid detection of drug resistance. However, the techniques of gene amplification directly from clinical samples are still less sensitive than culture. Bacteriological diagnosis of tuberculosis disease therefore still relies on the complementarities of different phenotypic and molecular techniques. Copyright © 2014 Société nationale française de médecine interne (SNFMI). Published by Elsevier SAS. All rights reserved.

Ninth Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools

DEFF Research Database (Denmark)

Daniel Moldt, Gremany Laure Petrucci, France Rüdiger Vlak, Germany Lee Wagenhals, USA Karsten Wolf, Germany Jianli Xu, Finland The programme committee has accepted 10 papers for presentation. Most of these deal with different projects in which Coloured Petri Nets and their tools have been put......This booklet contains the proceedings of the Ninth Workshop on Pratical Use of Coloured Petri Nets and CPN Tools, October 20-22, 2008. The workshop is organised by the CPN group at the Department of Computer Science, Aarhus University, Denmark. Coloured Petri Nets and the CPN Tools are now licensed...... to more than 7,200 users in 138 countries. The aim of the workshop is to bring together some of the users and in this way provide a forum for those who are interested in the practical use of Coloured Petri nets and their tools. The submitted papers were evaluated by a programme committee...

GTZ: a fast compression and cloud transmission tool optimized for FASTQ files.

Science.gov (United States)

Xing, Yuting; Li, Gen; Wang, Zhenguo; Feng, Bolun; Song, Zhuo; Wu, Chengkun

2017-12-28

The dramatic development of DNA sequencing technology is generating real big data, craving for more storage and bandwidth. To speed up data sharing and bring data to computing resource faster and cheaper, it is necessary to develop a compression tool than can support efficient compression and transmission of sequencing data onto the cloud storage. This paper presents GTZ, a compression and transmission tool, optimized for FASTQ files. As a reference-free lossless FASTQ compressor, GTZ treats different lines of FASTQ separately, utilizes adaptive context modelling to estimate their characteristic probabilities, and compresses data blocks with arithmetic coding. GTZ can also be used to compress multiple files or directories at once. Furthermore, as a tool to be used in the cloud computing era, it is capable of saving compressed data locally or transmitting data directly into cloud by choice. We evaluated the performance of GTZ on some diverse FASTQ benchmarks. Results show that in most cases, it outperforms many other tools in terms of the compression ratio, speed and stability. GTZ is a tool that enables efficient lossless FASTQ data compression and simultaneous data transmission onto to cloud. It emerges as a useful tool for NGS data storage and transmission in the cloud environment. GTZ is freely available online at: https://github.com/Genetalks/gtz .

Bring-Your-Own-Device (BYOD): An Evaluation of Associated Risks to Corporate Information Security

OpenAIRE

Yeboah-Boateng, Ezer Osei; Boaten, Francis Edmund

2016-01-01

This study evaluates the cyber-risks to Business Information Assets posed by the adoption of Bring-Your-Own-Device (BYOD) to the workplace. BYOD is an emerging trend where employees bring and use personal computing devices on the companys network to access applications and sensitive data like emails, calendar and scheduling applications, documents, etc. Employees are captivated by BYOD because they can have access to private items as well as perform certain job functions while being unrestric...

Educational challenges of molecular life science: Characteristics and implications for education and research.

Science.gov (United States)

Tibell, Lena A E; Rundgren, Carl-Johan

2010-01-01

Molecular life science is one of the fastest-growing fields of scientific and technical innovation, and biotechnology has profound effects on many aspects of daily life-often with deep, ethical dimensions. At the same time, the content is inherently complex, highly abstract, and deeply rooted in diverse disciplines ranging from "pure sciences," such as math, chemistry, and physics, through "applied sciences," such as medicine and agriculture, to subjects that are traditionally within the remit of humanities, notably philosophy and ethics. Together, these features pose diverse, important, and exciting challenges for tomorrow's teachers and educational establishments. With backgrounds in molecular life science research and secondary life science teaching, we (Tibell and Rundgren, respectively) bring different experiences, perspectives, concerns, and awareness of these issues. Taking the nature of the discipline as a starting point, we highlight important facets of molecular life science that are both characteristic of the domain and challenging for learning and education. Of these challenges, we focus most detail on content, reasoning difficulties, and communication issues. We also discuss implications for education research and teaching in the molecular life sciences.

Frontier Fields: A Cost-Effective Approach to Bringing Authentic Science to the Education Community

Science.gov (United States)

Eisenhamer, B.; Lawton, B.; Summers, F.; Ryer, H.

2015-11-01

For more than two decades, the Hubble EPO program has sought to bring the wonders of the universe to the education community and the public, and to engage audiences in the adventure of scientific discovery. Program components include standards-based, curriculum-support materials, exhibits and exhibit components, and professional development workshops. The main underpinnings of the program's infrastructure are scientist-educator development teams, partnerships, and an embedded program evaluation component. The Space Telescope Science Institute's Office of Public Outreach is leveraging this existing infrastructure to bring the Frontier Fields science program to the education community in a cost-effective way. Frontier Fields observations and results have been, and will continue to be, embedded into existing product lines and professional development offerings. We also are leveraging our new social media strategy to bring the science program to the public in the form of an ongoing blog.

Characterization of microbial communities in pest colonized books by molecular biology tools

Directory of Open Access Journals (Sweden)

Franco Palla

2011-08-01

Full Text Available This work presents the identification of bacteria and fungi colonies in insect infesting books, by cultural-independent methodologies based on molecular biology techniques. Microbial genomic DNA extraction, in vitro amplification of specific target sequences by polymerase chain reactions (PCR, sequencing and sequence analysis were performed. These procedures minimized the samples amount, optimized the diagnostic studies on bacteria and fungi colonization and allowed the identification of many species also in complex microbial consortia. The molecular techniques for sure accomplish and integrate the microbiological standard methods (in vitro culture and morphological analyses (OM, SEM, CLSM, in order to understand the role of microorganisms in bio-deterioration of cultural assets. This monitoring is also indispensable to shed light on the risk for visitors and/or professionals to contract potential illnesses within indoor environments.

Prospects of molecular markers in Fusarium species diversity

DEFF Research Database (Denmark)

Nayaka, S. Chandra; Wulff, Ednar Gadelha; Udayashankar, A.C.

2011-01-01

focuses of various molecular-based techniques employed to study the diversity of Fusarium species causing diseases in major food crops. An introduction of fusarial diseases and their mycotoxins and molecular-marker-based methods for detection introduce the concept of marker application. Various well...... for generation of probes and their use in phylogeny of Fusarium spp. are also presented. The concluding part emphasizes the value of molecular markers for assessing genetic variability and reveals that molecular tools are indispensable for providing information not only of one Fusarium species but on whole......-known molecular techniques such as random amplified polymorphic DNA, amplification fragment length polymorphism, etc. to more modern ones such as DNA microarrays, DNA barcoding, and pyrosequencing and their application form the core of the review. Target regions in the genome which can be potential candidates...

Molecular galactose-galectin association in neuroblastoma cells: An unconventional tool for qualitative/quantitative screening.

Science.gov (United States)

Pastorino, Fabio; Ponzoni, Mirco; Simone, Giuseppina

2017-05-01

Galectin decorates the cell membrane and forms an extracellular molecular association with galactoside units. Here, galactoside probes have been used to study galectin expression in neuroblastoma cells. The hypothesis behind this investigation has been that the molecular mechanisms by which glycans modulate neural metastatic cells involve a protein-carbohydrate association, galectin-galactose. Preliminary screening to validate the hypothesis has been performed with galactose moieties anchored to beads. The molecular association has been studied by FACS. In vitro experiments reveal the molecular binding preferences of the metastatic neuroblastoma cells. Ex vivo, the galactose probes discriminate healthy tissues. The unconventional assay in microfluidics used in this study displayed results analogous to the above (GI-LI-N cell capture efficiency overcomes IMR-32). At the point of equilibrium of shear and binding forces, the capture yield inside the chamber was measured to 60 ± 4.4% in GI-LI-N versus 40 ± 2.1% in IMR-32. Staining of the fished cells and subsequent conjugation with red beads bearing the galactose also have evidenced that microfluidics can be used to study and quantify the molecular association of galectin-galactose. Most importantly, a crucial insight for obtaining single-cell qualitative/quantitative glycome analysis has been achieved. Finally, the specificity of the assay performed in microfluidics is demonstrated by comparing GI-LI-N fishing efficiency in galactose and fucose environments. The residual adhesion to fucose confirmed the existence of receptors for this glycan and that its eventual unspecific binding (i.e. due to electrostatic interactions) is insignificant compared with the molecular binding. Identification and understanding of this mechanism of discrimination can be relevant for diagnostic monitoring and for producing probes tailored to interfere with galectin activities associated with the malignant phenotype. Besides, the given

Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis.

Directory of Open Access Journals (Sweden)

Emmanuel Dias-Neto

2009-12-01

Full Text Available Combinatorial phage display has been used in the last 20 years in the identification of protein-ligands and protein-protein interactions, uncovering relevant molecular recognition events. Rate-limiting steps of combinatorial phage display library selection are (i the counting of transducing units and (ii the sequencing of the encoded displayed ligands. Here, we adapted emerging genomic technologies to minimize such challenges.We gained efficiency by applying in tandem real-time PCR for rapid quantification to enable bacteria-free phage display library screening, and added phage DNA next-generation sequencing for large-scale ligand analysis, reporting a fully integrated set of high-throughput quantitative and analytical tools. The approach is far less labor-intensive and allows rigorous quantification; for medical applications, including selections in patients, it also represents an advance for quantitative distribution analysis and ligand identification of hundreds of thousands of targeted particles from patient-derived biopsy or autopsy in a longer timeframe post library administration. Additional advantages over current methods include increased sensitivity, less variability, enhanced linearity, scalability, and accuracy at much lower cost. Sequences obtained by qPhage plus pyrosequencing were similar to a dataset produced from conventional Sanger-sequenced transducing-units (TU, with no biases due to GC content, codon usage, and amino acid or peptide frequency. These tools allow phage display selection and ligand analysis at >1,000-fold faster rate, and reduce costs approximately 250-fold for generating 10(6 ligand sequences.Our analyses demonstrates that whereas this approach correlates with the traditional colony-counting, it is also capable of a much larger sampling, allowing a faster, less expensive, more accurate and consistent analysis of phage enrichment. Overall, qPhage plus pyrosequencing is superior to TU-counting plus Sanger

Role of Open Source Tools and Resources in Virtual Screening for Drug Discovery.

Science.gov (United States)

Karthikeyan, Muthukumarasamy; Vyas, Renu

2015-01-01

Advancement in chemoinformatics research in parallel with availability of high performance computing platform has made handling of large scale multi-dimensional scientific data for high throughput drug discovery easier. In this study we have explored publicly available molecular databases with the help of open-source based integrated in-house molecular informatics tools for virtual screening. The virtual screening literature for past decade has been extensively investigated and thoroughly analyzed to reveal interesting patterns with respect to the drug, target, scaffold and disease space. The review also focuses on the integrated chemoinformatics tools that are capable of harvesting chemical data from textual literature information and transform them into truly computable chemical structures, identification of unique fragments and scaffolds from a class of compounds, automatic generation of focused virtual libraries, computation of molecular descriptors for structure-activity relationship studies, application of conventional filters used in lead discovery along with in-house developed exhaustive PTC (Pharmacophore, Toxicophores and Chemophores) filters and machine learning tools for the design of potential disease specific inhibitors. A case study on kinase inhibitors is provided as an example.

Understanding molecular simulation from algorithms to applications

CERN Document Server

Frenkel, Daan

2001-01-01

Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the ""recipes"" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practic

Contingent Commitments: Bringing Part-Time Faculty into Focus. Methodology Supplement

Science.gov (United States)

Center for Community College Student Engagement, 2014

2014-01-01

Center reporting prior to 2013 focused primarily on descriptive statistics (frequencies and means) of student and faculty behaviors. The goal of the analyses reported here and in "Contingent Commitments: Bringing Part-Time Faculty into Focus" is to understand the engagement of part-time or contingent faculty in various activities that…

CADRE-SS, an in Silico Tool for Predicting Skin Sensitization Potential Based on Modeling of Molecular Interactions.

Science.gov (United States)

Kostal, Jakub; Voutchkova-Kostal, Adelina

2016-01-19

Using computer models to accurately predict toxicity outcomes is considered to be a major challenge. However, state-of-the-art computational chemistry techniques can now be incorporated in predictive models, supported by advances in mechanistic toxicology and the exponential growth of computing resources witnessed over the past decade. The CADRE (Computer-Aided Discovery and REdesign) platform relies on quantum-mechanical modeling of molecular interactions that represent key biochemical triggers in toxicity pathways. Here, we present an external validation exercise for CADRE-SS, a variant developed to predict the skin sensitization potential of commercial chemicals. CADRE-SS is a hybrid model that evaluates skin permeability using Monte Carlo simulations, assigns reactive centers in a molecule and possible biotransformations via expert rules, and determines reactivity with skin proteins via quantum-mechanical modeling. The results were promising with an overall very good concordance of 93% between experimental and predicted values. Comparison to performance metrics yielded by other tools available for this endpoint suggests that CADRE-SS offers distinct advantages for first-round screenings of chemicals and could be used as an in silico alternative to animal tests where permissible by legislative programs.

Alkynes as a versatile platform for construction of chemical molecular complexity and realization of molecular 3D printing

International Nuclear Information System (INIS)

Galkin, K I; Ananikov, V P

2016-01-01

The current level of scientific and technological development requires the formation of general tools and techniques. One of the most versatile technologies is 3D printing, which allows fast and efficient creation of materials and biological objects of desired shape and composition. Today, methods have been developed for 3D printing of macro- and nano-sized objects and for production of films and deposited materials with molecular precision but the most promising technology is printing at the molecular level (molecular 3D printing) for the purpose of direct construction of molecular complexity. This process is currently at the initial stage concerning selection of simple molecules to be used as building blocks possessing flexibility, availability and ease of modification. In this review, we examine the possible versatile synthons suitable for preparation of the main types of organic compounds using molecular 3D printing. The surveyed data strongly indicate that alkyne molecules may be used as a building material in a molecular 3D printer working on hydrocarbons. The bibliography includes 428 references

[Molecular markers: an important tool in the diagnosis, treatment and epidemiology of invasive aspergillosis].

Science.gov (United States)

Frías-de León, María Guadalupe; Acosta-Altamirano, Gustavo; Duarte-Escalante, Esperanza; Martínez-Hernández, José Enrique; Martínez-Rivera, María de Los Ángeles; Reyes-Montes, María Del Rocío

2014-01-01

Increase in the incidence of invasive aspergillosis has represented a difficult problem for management of patients with this infection due to its high rate of mortality, limited knowledge concerning its diagnosis, and therapeutic practice. The difficulty in management of patients with aspergillosis initiates with detection of the fungus in the specimens of immunosuppressed patients infected with Aspergillus fumigatus; in addition, difficulty exists in terms of the development of resistance to antifungals as a consequence of their indiscriminate use in prophylactic and therapeutic practice and to ignorance concerning the epidemiological data of aspergillosis. With the aim of resolving these problems, molecular markers is employed at present with specific and accurate results. However, in Mexico, the use of molecular markers has not yet been implemented in the routine of intrahospital laboratories; despite the fact that these molecular markers has been widely referred in the literature, it is necessary for it to validated and standardized to ensure that the results obtained in any laboratory would be reliable and comparable. In the present review, we present an update on the usefulness of molecular markers in accurate identification of A. fumigatus, detection of resistance to antifugal triazoles, and epidemiological studies for establishing the necessary measures for prevention and control of aspergillosis.

ADM3, TFF3 and LGALS3 are discriminative molecular markers in fine-needle aspiration biopsies of benign and malignant thyroid tumours

Science.gov (United States)

Karger, S; Krause, K; Gutknecht, M; Schierle, K; Graf, D; Steinert, F; Dralle, H; Führer, D

2012-01-01

Background: Previously, we reported a six-marker gene set, which allowed a molecular discrimination of benign and malignant thyroid tumours. Now, we evaluated these markers in fine-needle aspiration biopsies (FNAB) in a prospective, independent series of thyroid tumours with proven histological outcome. Methods: Quantitative RT–PCR was performed (ADM3, HGD1, LGALS3, PLAB, TFF3, TG) in the needle wash-out of 156 FNAB of follicular adenoma (FA), adenomatous nodules, follicular and papillary thyroid cancers (TC) and normal thyroid tissues (NT). Results: Significant expression differences were found for TFF3, HGD1, ADM3 and LGALS3 in FNAB of TC compared with benign thyroid nodules and NT. Using two-marker gene sets, a specific FNAB distinction of benign and malignant tumours was achieved with negative predictive values (NPV) up to 0.78 and positive predictive values (PPV) up to 0.84. Two FNAB marker gene combinations (ADM3/TFF3; ADM3/ACTB) allowed the distinction of FA and malignant follicular neoplasia with NPV up to 0.94 and PPV up to 0.86. Conclusion: We demonstrate that molecular FNAB diagnosis of benign and malignant thyroid tumours including follicular neoplasia is possible with recently identified marker gene combinations. We propose multi-centre FNAB studies on these markers to bring this promising diagnostic tool closer to clinical practice. PMID:22223087

Bringing the light to high throughput screening: use of optogenetic tools for the development of recombinant cellular assays

Science.gov (United States)

Agus, Viviana; Di Silvio, Alberto; Rolland, Jean Francois; Mondini, Anna; Tremolada, Sara; Montag, Katharina; Scarabottolo, Lia; Redaelli, Loredana; Lohmer, Stefan

2015-03-01

The use of light-activated proteins represents a powerful tool to control biological processes with high spatial and temporal precision. These so called "optogenetic" technologies have been successfully validated in many recombinant systems, and have been widely applied to the study of cellular mechanisms in intact tissues or behaving animals; to do that, complex, high-intensity, often home-made instrumentations were developed to achieve the optimal power and precision of light stimulation. In our study we sought to determine if this optical modulation can be obtained also in a miniaturized format, such as a 384-well plate, using the instrumentations normally dedicated to fluorescence analysis in High Throughput Screening (HTS) activities, such as for example the FLIPR (Fluorometric Imaging Plate Reader) instrument. We successfully generated optogenetic assays for the study of different ion channel targets: the CaV1.3 calcium channel was modulated by the light-activated Channelrhodopsin-2, the HCN2 cyclic nucleotide gated (CNG) channel was modulated by the light activated bPAC adenylyl cyclase, and finally the genetically encoded voltage indicator ArcLight was efficiently used to measure potassium, sodium or chloride channel activity. Our results showed that stable, robust and miniaturized cellular assays can be developed using different optogenetic tools, and efficiently modulated by the FLIPR instrument LEDs in a 384-well format. The spatial and temporal resolution delivered by this technology might enormously advantage the early stages of drug discovery, leading to the identification of more physiological and effective drug molecules.

How can we bring public health in all policies? Strategies for healthy societies

Directory of Open Access Journals (Sweden)

Fabrizio Bert

2015-04-01

Full Text Available New scenarios are emerging in the European and worldwide context: the ageing of society, the climate changes, the increasing of health inequalities and the financial crisis. In this context, the scientific community and the decision-makers agree on the role of health in all policies (HiAP strategy in improving the population’s health. The HiAP takes into account factors not strictly related to health but with important health consequences. To bring public health in all policies a change is needed, but there are some obstacles to overcome: for instance, the lack of evidence regarding the governance tools and frameworks for HiAP, the difficulty of convincing stakeholders and producing a cultural change in the political positioning of decision-makers. Consequently, it is necessary: i to implement stronger and responsible decision-support approaches, such as health impact assessment and health technology assessment; ii to encourage and coordinate all relevant sectors in playing their part in reducing health gaps within the European Union; iii to strengthen cooperation and make better use of existing networks and existing public health and related institutions. The final aim will be to monitor the impact of the health determinants in order to promote the effective implementation of HiAP approach.

The GEDI Performance Tool

Science.gov (United States)

Hancock, S.; Armston, J.; Tang, H.; Patterson, P. L.; Healey, S. P.; Marselis, S.; Duncanson, L.; Hofton, M. A.; Kellner, J. R.; Luthcke, S. B.; Sun, X.; Blair, J. B.; Dubayah, R.

2017-12-01

NASA's Global Ecosystem Dynamics Investigation will mount a multi-track, full-waveform lidar on the International Space Station (ISS) that is optimised for the measurement of forest canopy height and structure. GEDI will use ten laser tracks, two 10 mJ "power beams" and eight 5 mJ "coverage beams" to produce global (51.5oS to 51.5oN) maps of above ground biomass (AGB), canopy height, vegetation structure and other biophysical parameters. The mission has a requirement to generate a 1 km AGB map with 80% of pixels with ≤ 20% standard error or 20 Mg·ha-1, whichever is greater. To assess performance and compare to mission requirements, an end-to-end simulator has been developed. The simulator brings together tools to propagate the effects of measurement and sampling error on GEDI data products. The simulator allows us to evaluate the impact of instrument performance, ISS orbits, processing algorithms and losses of data that may occur due to clouds, snow, leaf-off conditions, and areas with an insufficient signal-to-noise ratio (SNR). By evaluating the consequences of operational decisions on GEDI data products, this tool provides a quantitative framework for decision-making and mission planning. Here we demonstrate the performance tool by using it to evaluate the trade-off between measurement and sampling error on the 1 km AGB data product. Results demonstrate that the use of coverage beams during the day (lowest GEDI SNR case) over very dense forests (>95% canopy cover) will result in some measurement bias. Omitting these low SNR cases increased the sampling error. Through this an SNR threshold for a given expected canopy cover can be set. The other applications of the performance tool are also discussed, such as assessing the impact of decisions made in the AGB modelling and signal processing stages on the accuracy of final data products.

Bringing back the book through digital experiences: e-Books and ...

African Journals Online (AJOL)

Bringing back the book through digital experiences: e-Books and digital media as platforms for reading among school children. ... for technology has changed the format of books and reading platforms from print to ereaders. ... print. Findings further showed that there is no significant difference in the attitude of boys and girls ...

21 CFR 1005.24 - Costs of bringing product into compliance.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Costs of bringing product into compliance. 1005.24 Section 1005.24 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... include: (a) Travel expenses of the supervising officer; (b) Per diem in lieu of subsistence of the...

Advances in e-health and telemedicine: strategy to bring health service users

Directory of Open Access Journals (Sweden)

Wilson Giovanni Jiménez Barbosa

2015-08-01

Full Text Available Background: The e-health and telemedicine have emerged as tools to facilitate access to health services, both populations far from the centres, and those who reside near them is not easily accessible or require constant controls by their professionals health traffickers. Objective: To reflect on the uses, progress and difficulties faced by Information and Communication Technologies (ICT as a strategy to bring health services to users. Methodology: qualitative hermeneutic research; advanced in two phases. The first, theoretical review by finding relevant articles in scientific databases. The second phase, critical analysis of literature found, in order to understand the dynamics generated from the use of ICT in the health sector, its current uses and prospected, and the risk that can generate its implementation for providers and patients. Results: The e-health and telemedicine have advanced in their development process andColombiahas not been outside, but there are still drawbacks of ethical, legal and operational order, which are not static and show great variation over time, becoming challenges are not independent but are associated with the dynamic progress of ICT. Conclusion: e-health and telemedicine are valid strategies to improve access to health services to communities. But require the development of processes to prevent, mitigate and / or exceed the inconveniences that may arise from its use. 

MySQL High Availability Tools for Building Robust Data Centers

CERN Document Server

Bell, Charles; Thalmann, Lars

2010-01-01

Server bottlenecks and failures are a fact of life in any database deployment, but they don't have to bring everything to a halt. MySQL has several features that can help you protect your system from outages, whether it's running on hardware, virtual machines, or in the cloud. MySQL High Availability explains how to use these replication, cluster, and monitoring features in a wide range of real-life situations. Written by engineers who designed many of the tools covered inside, this book reveals undocumented or hard-to-find aspects of MySQL reliability and high availability -- knowledge that

Inorganic-Organic Coating via Molecular Layer Deposition Enables Long Life Sodium Metal Anode.

Science.gov (United States)

Zhao, Yang; Goncharova, Lyudmila V; Zhang, Qian; Kaghazchi, Payam; Sun, Qian; Lushington, Andrew; Wang, Biqiong; Li, Ruying; Sun, Xueliang

2017-09-13

Metallic Na anode is considered as a promising alternative candidate for Na ion batteries (NIBs) and Na metal batteries (NMBs) due to its high specific capacity, and low potential. However, the unstable solid electrolyte interphase layer caused by serious corrosion and reaction in electrolyte will lead to big challenges, including dendrite growth, low Coulombic efficiency and even safety issues. In this paper, we first demonstrate the inorganic-organic coating via advanced molecular layer deposition (alucone) as a protective layer for metallic Na anode. By protecting Na anode with controllable alucone layer, the dendrites and mossy Na formation have been effectively suppressed and the lifetime has been significantly improved. Moreover, the molecular layer deposition alucone coating shows better performances than the atomic layer deposition Al 2 O 3 coating. The novel design of molecular layer deposition protected Na metal anode may bring in new opportunities to the realization of the next-generation high energy-density NIBs and NMBs.

Applying knowledge engineering tools for the personal computer to the operation and maintenance of radiopharmaceutical production systems

International Nuclear Information System (INIS)

Alexoff, D.L.

1990-01-01

A practical consequence of over three decades of Artificial Intelligence (AI) research has been the emergence of Personal Computer-based AI programming tools. A special class of this microcomputer-based software, called expert systems shells, is now applied routinely outside the realm of classical AI to solve many types of problems, particularly in analytical chemistry. These AI tools offer not only some of the advantages inherent to symbolic programming languages, but, as significant, they bring with them advanced program development environments which can facilitate software development and maintenance. Exploitation of this enhanced programming environment was a major motivation for using an AI tool. The goal of this work is to evaluate the use of an example-based expert system shell (1st Class FUSION, 1st Class Expert Systems, Inc.) as a programming tool for developing software useful for automated radiopharmaceutical production

A New Molecular Surveillance System for Leishmaniasis

Science.gov (United States)

Pandey, Kishor; Pandey, Basu Dev; Mallik, Arun Kumar; Acharya, Jyoti; Kato, Kentaro; Kaneko, Osamu; Ferreira, Pedro Eduardo

2014-01-01

Abstract. Presently, global efforts are being made to control and eradicate the deadliest tropical diseases through the improvement of adequate interventions. A critical point for programs to succeed is the prompt and accurate diagnosis in endemic regions. Rapid diagnostic tests (RDTs) are being massively deployed and used to improve diagnosis in tropical countries. In the present report, we evaluated the hypothesis of, after use for diagnosis, the reuse of the Leishmania RDT kit as a DNA source, which can be used downstream as a molecular surveillance and/or quality control tool. As a proof of principle, a polymerase chain reaction-based method was used to detect Leishmania spp. minicircle kinetoplast DNA from leishmaniasis RDT kits. Our results show that Leishmania spp. DNA can be extracted from used RDTs and may constitute an important, reliable, and affordable tool to assist in future leishmaniasis molecular surveillance methods. PMID:24752687

Greenhouse gas emission trading schemes: a new tool for the environmental regulator's kit

International Nuclear Information System (INIS)

Soleille, Sebastien

2006-01-01

As the European Union greenhouse gas emission trading scheme (ETS) is emerging, it seems interesting to look back on previous experiments and to bring together a few elements of reflection about the pertinence of ETS as a new policy tool to regulate industrial pollution. So far, several regulatory tools have been used to decrease pollution. This article focuses on two of them, command-and-control (CAC) and ETS. There is no simple answer to which one is more efficient. It depends strongly on the context. Given a few elements outlined in this paper, the choice of an ETS to abate industrial emissions of greenhouse gases in the European Union (EU) can be considered pertinent. But, ultimately, what makes a scheme environmentally efficient is not the tool in itself (ETS or CAC) but the ambition of the target. Hence the design of the National Allocation Plans setting the emission caps are of paramount importance. They will make the EU ETS either a useless mess or an effective climate change mitigation policy tool

AAVSO Target Tool: A Web-Based Service for Tracking Variable Star Observations (Abstract)

Science.gov (United States)

Burger, D.; Stassun, K. G.; Barnes, C.; Kafka, S.; Beck, S.; Li, K.

2018-06-01

(Abstract only) The AAVSO Target Tool is a web-based interface for bringing stars in need of observation to the attention of AAVSOís network of amateur and professional astronomers. The site currently tracks over 700 targets of interest, collecting data from them on a regular basis from AAVSOís servers and sorting them based on priority. While the target tool does not require a login, users can obtain visibility times for each target by signing up and entering a telescope location. Other key features of the site include filtering by AAVSO observing section, sorting by different variable types, formatting the data for printing, and exporting the data to a CSV file. The AAVSO Target Tool builds upon seven years of experience developing web applications for astronomical data analysis, most notably on Filtergraph (Burger, D., et al. 2013, Astronomical Data Analysis Software and Systems XXII, Astronomical Society of the Pacific, San Francisco, 399), and is built using the web2py web framework based on the python programming language. The target tool is available at http://filtergraph.com/aavso.

Application of atomic force microscopy as a nanotechnology tool in food science.

Science.gov (United States)

Yang, Hongshun; Wang, Yifen; Lai, Shaojuan; An, Hongjie; Li, Yunfei; Chen, Fusheng

2007-05-01

Atomic force microscopy (AFM) provides a method for detecting nanoscale structural information. First, this review explains the fundamentals of AFM, including principle, manipulation, and analysis. Applications of AFM are then reported in food science and technology research, including qualitative macromolecule and polymer imaging, complicated or quantitative structure analysis, molecular interaction, molecular manipulation, surface topography, and nanofood characterization. The results suggested that AFM could bring insightful knowledge on food properties, and the AFM analysis could be used to illustrate some mechanisms of property changes during processing and storage. However, the current difficulty in applying AFM to food research is lacking appropriate methodology for different food systems. Better understanding of AFM technology and developing corresponding methodology for complicated food systems would lead to a more in-depth understanding of food properties at macromolecular levels and enlarge their applications. The AFM results could greatly improve the food processing and storage technologies.

"Bring Your Own Device": Considering Potential Risks to Student Health

Science.gov (United States)

Merga, Margaret K.

2016-01-01

Background and context: Schools in Australia and internationally are increasingly adopting a Bring Your Own Device (BYOD) approach to teaching and learning. The review: While discussion of a BYOD approach has taken place, there is a dearth of consideration of the potential impact of BYOD policy on student health. Implementation of a BYOD policy…

A Review of Bring Your Own Device on Security Issues

Directory of Open Access Journals (Sweden)

Morufu Olalere

2015-04-01

Full Text Available Mobile computing has supplanted internet computing because of the proliferation of cloud-based applications and mobile devices (such as smartphones, palmtops, and tablets. As a result of this, workers bring their mobile devices to the workplace and use them for enterprise work. The policy of allowing the employees to work with their own personal mobile devices is called Bring Your Own Devices (BYOD. In this article, we discuss BYOD’s background, prevalence, benefits, challenges, and possible security attacks. We then review contributions of academic researchers on BYOD. The Universiti Putra Malaysia online databases (such as IEEE Xplore digital library, Elsevier, Springer, ACM digital library were used to search for peer-reviewed academic publications and other relevant publications on BYOD. The Google Scholar search engine was also used. Our thorough review shows that security issues comprise the most significant challenge confronting BYOD policy and that very little has been done to tackle this security challenge. It is our hope that this review will provide a theoretical background for future research and enable researchers to identify researchable areas of BYOD.

Bringing Together Interactive Digital Storytelling with Tangible Interaction : Challenges and Opportunities

NARCIS (Netherlands)

Catala, Alejandro; Theune, Mariët; Sylla, Cristina; Ribeiro, Pedro; Nunes, Nuno; Oakley, Ian; Nisi, Valentina

2017-01-01

This workshop aims to explore challenges and potential opportunities in bringing interactive digital storytelling into the realm of tangible and embodied interaction. To this end, experts from both fields are invited to present and discuss their ideas. Besides fostering discussion and potential

Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

KAUST Repository

Rashid, Mamoon; Stingl, Ulrich

2015-01-01

Novel methods in microbial ecology are revolutionizing our understanding of the structure and function of microbes in the environment, but concomitant advances in applications of these tools to biotechnology are mostly lagging behind. After more than a century of efforts to improve microbial culturing techniques, about 70–80% of microbial diversity – recently called the “microbial dark matter” – remains uncultured. In early attempts to identify and sample these so far uncultured taxonomic lineages, methods that amplify and sequence ribosomal RNA genes were extensively used. Recent developments in cell separation techniques, DNA amplification, and high-throughput DNA sequencing platforms have now made the discovery of genes/genomes of uncultured microorganisms from different environments possible through the use of metagenomic techniques and single-cell genomics. When used synergistically, these metagenomic and single-cell techniques create a powerful tool to study microbial diversity. These genomics techniques have already been successfully exploited to identify sources for i) novel enzymes or natural products for biotechnology applications, ii) novel genes from extremophiles, and iii) whole genomes or operons from uncultured microbes. More can be done to utilize these tools more efficiently in biotechnology.

Contemporary molecular tools in microbial ecology and their application to advancing biotechnology.

Science.gov (United States)

Rashid, Mamoon; Stingl, Ulrich

2015-12-01

Novel methods in microbial ecology are revolutionizing our understanding of the structure and function of microbes in the environment, but concomitant advances in applications of these tools to biotechnology are mostly lagging behind. After more than a century of efforts to improve microbial culturing techniques, about 70-80% of microbial diversity - recently called the "microbial dark matter" - remains uncultured. In early attempts to identify and sample these so far uncultured taxonomic lineages, methods that amplify and sequence ribosomal RNA genes were extensively used. Recent developments in cell separation techniques, DNA amplification, and high-throughput DNA sequencing platforms have now made the discovery of genes/genomes of uncultured microorganisms from different environments possible through the use of metagenomic techniques and single-cell genomics. When used synergistically, these metagenomic and single-cell techniques create a powerful tool to study microbial diversity. These genomics techniques have already been successfully exploited to identify sources for i) novel enzymes or natural products for biotechnology applications, ii) novel genes from extremophiles, and iii) whole genomes or operons from uncultured microbes. More can be done to utilize these tools more efficiently in biotechnology. Copyright © 2015 Elsevier Inc. All rights reserved.

Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

KAUST Repository

Rashid, Mamoon

2015-09-25

Novel methods in microbial ecology are revolutionizing our understanding of the structure and function of microbes in the environment, but concomitant advances in applications of these tools to biotechnology are mostly lagging behind. After more than a century of efforts to improve microbial culturing techniques, about 70–80% of microbial diversity – recently called the “microbial dark matter” – remains uncultured. In early attempts to identify and sample these so far uncultured taxonomic lineages, methods that amplify and sequence ribosomal RNA genes were extensively used. Recent developments in cell separation techniques, DNA amplification, and high-throughput DNA sequencing platforms have now made the discovery of genes/genomes of uncultured microorganisms from different environments possible through the use of metagenomic techniques and single-cell genomics. When used synergistically, these metagenomic and single-cell techniques create a powerful tool to study microbial diversity. These genomics techniques have already been successfully exploited to identify sources for i) novel enzymes or natural products for biotechnology applications, ii) novel genes from extremophiles, and iii) whole genomes or operons from uncultured microbes. More can be done to utilize these tools more efficiently in biotechnology.

Decision support tools in conservation: a workshop to improve user-centred design

Directory of Open Access Journals (Sweden)

David Rose

2017-09-01

Full Text Available A workshop held at the University of Cambridge in May 2017 brought developers, researchers, knowledge brokers, and users together to discuss user-centred design of decision support tools. Decision support tools are designed to take users through logical decision steps towards an evidence-informed final decision. Although they may exist in different forms, including on paper, decision support tools are generally considered to be computer- (online, software or app-based. Studies have illustrated the potential value of decision support tools for conservation, and there are several papers describing the design of individual tools. Rather less attention, however, has been placed on the desirable characteristics for use, and even less on whether tools are actually being used in practice. This is concerning because if tools are not used by their intended end user, for example a policy-maker or practitioner, then its design will have wasted resources. Based on an analysis of papers on tool use in conservation, there is a lack of social science research on improving design, and relatively few examples where users have been incorporated into the design process. Evidence from other disciplines, particularly human-computer interaction research, illustrates that involving users throughout the design of decision support tools increases the relevance, usability, and impact of systems. User-centred design of tools is, however, seldom mentioned in the conservation literature. The workshop started the necessary process of bringing together developers and users to share knowledge about how to conduct good user-centred design of decision support tools. This will help to ensure that tools are usable and make an impact in conservation policy and practice.

Molecular Biology for the Environment: an EC-US hands-on Course in Environmental Biotechnology

Energy Technology Data Exchange (ETDEWEB)

Victor de Lorenzo; Juan Luis Ramos; Jerome Kukor; Gerben J. Zylstra

2004-02-15

One of the central goals of this activity is to bring together young scientists (at the late Ph.D. or early postdoctoral stages of their careers) in a forum that should result in future collaborations. The course is designed to give scientists hands-on experience in modern, up-to-date biotechnological methods at the interface between molecular biology and environmental biotechnology for the analysis of microorganisms and their activities with regard to the remediation of pollutants in the environment.

Importance and pitfalls of molecular analysis to parasite epidemiology.

Science.gov (United States)

Constantine, Clare C

2003-08-01

Molecular tools are increasingly being used to address questions about parasite epidemiology. Parasites represent a diverse group and they might not fit traditional population genetic models. Testing hypotheses depends equally on correct sampling, appropriate tool and/or marker choice, appropriate analysis and careful interpretation. All methods of analysis make assumptions which, if violated, make the results invalid. Some guidelines to avoid common pitfalls are offered here.

Nuances of Morphology in Myelodysplastic Diseases in the Age of Molecular Diagnostics.

Science.gov (United States)

Shaver, Aaron C; Seegmiller, Adam C

2017-10-01

Morphologic dysplasia is an important factor in diagnosis of myelodysplastic syndrome (MDS). However, the role of dysplasia is changing as new molecular genetic and genomic technologies take a more prominent place in diagnosis. This review discusses the role of morphology in the diagnosis of MDS and its interactions with cytogenetic and molecular testing. Recent changes in diagnostic criteria have attempted to standardize approaches to morphologic diagnosis of MDS, recognizing significant inter-observer variability in assessment of dysplasia. Definitive correlates between cytogenetic/molecular and morphologic findings have been described in only a small set of cases. However, these genetic and morphologic tools do play a complementary role in the diagnosis of both MDS and other myeloid neoplasms. Diagnosis of MDS requires a multi-factorial approach, utilizing both traditional morphologic as well as newer molecular genetic techniques. Understanding these tools, and the interplay between them, is crucial in the modern diagnosis of myeloid neoplasms.

Radiation damage at the molecular level: Nanodosimetry

International Nuclear Information System (INIS)

Blanco, F.; Munoz, A.; Lagares, J. I.; Nunez, L.; Garcia, G.

2013-01-01

One of the main practical use of the model is its use as a tool of nanodosimetry which basically consists in characterizing the effect of radiation on nano volumes (comparable to the DNA of volumes) in terms of link breaks and molecular dissociations. (Author)

Bringing indigenous ownership back to the private sector

DEFF Research Database (Denmark)

Kragelund, Peter

. This time disguised in terms like empowerment and unequal opportunities but just as politicised as in the 1970s. In light of the current anti-Chinese sentiments in Zambia, this paper seeks to further our understanding of private sector policy making in Zambia. It argues that populist politics, referring...... been particularly present in all sectors of the Zambian economy. Foreign ownership, however, is not new to African societies and several African countries pursued indigenisation policies in the wake of independence to bring ownership back to their own citizens. Now indigenisation policies thrive again...

The rebirth of the morphogenetic field as an explanatory tool in biology

Directory of Open Access Journals (Sweden)

Perović Slobodan

2013-01-01

Full Text Available I discuss two uses of the concept of the morphogenetic field, a tool of the 19th century biology motivated by particular ontological views of the time, which has been re-emerging and increasingly relevant in explaining microbiological phenomena. I also consider the relation of these uses to the Central Dogma of modern biology as well as Modern Synthesis of Darwinism and genetics. An induced morphogenetic field is determined by a physical (e.g., gravitational field, or it acquires a physical (e.g., visco-elastic field’s characteristics. Such a morphogenetic field presents only a weak challenge to the Central Dogma of Modern Synthesis by indirectly, albeit severely, constraining variability at the molecular level. I discuss explanations that introduce structural inheritance in ciliate protozoa, as well as the experimental evidence on which these arguments are based. The global cellular morphogenetic field is a unit of such inheritance. I discuss relevant cases of structural inheritance in ciliates that bring about internal cellular as well as functional changes and point out that DNA is absent in the cortex and that RNA controls neither intermediary nor the global level of the field. I go on to argue that utilizing knowledge of known physical fields may advance explanations and understanding of the morphogenetic field in ciliates as the unit of both development and inheritance. [Projekat Ministarstva nauke Republike Srbije, br. 179041: Dynamic Systems in nature and society: Philosophical and empirical aspects

Molecular Twister: A Game for Exploring Solution Chemistry

Directory of Open Access Journals (Sweden)

Sawyer R. Masonjones

2014-02-01

Full Text Available pH is an essential biological concept with critical importance at various scales, from the molecular level, dealing with blood buffers, homeostasis, and proton gradients, all the way up to the ecosystem level, with soil chemistry and acid rain. However, pH is also a concept that spawns student misconceptions and misunderstanding in terms of what is happening in a solution on the atomic level. The Molecular Twister game, created for a Florida Department of Education funded professional development workshop for Florida high school teachers hosted at the University of Tampa  (Science Math Masters, seeks to model pH in such a way that students can visually and kinesthetically learn the concept in a few minutes. In addition, the basic design of the game pieces allow for teaching extensions to include more complex acid-base reactions. Challenge questions are provided to allow teachers to bring relevancy to the game, using examples of acid-base chemistry pulled from cases in human health and the environment.

Horror Autoinflammaticus: The Molecular Pathophysiology of Autoinflammatory Disease*

Science.gov (United States)

Masters, Seth L.; Simon, Anna; Aksentijevich, Ivona; Kastner, Daniel L.

2010-01-01

The autoinflammatory diseases are characterized by seemingly unprovoked episodes of inflammation, without high-titer autoantibodies or antigen-specific T cells. The concept was proposed ten years ago with the identification of the genes underlying hereditary periodic fever syndromes. This nosology has taken root because of the dramatic advances in our knowledge of the genetic basis of both mendelian and complex autoinflammatory diseases, and with the recognition that these illnesses derive from genetic variants of the innate immune system. Herein we propose an updated classification scheme based on the molecular insights garnered over the past decade, supplanting a clinical classification that has served well but is opaque to the genetic, immunologic, and therapeutic interrelationships now before us. We define six categories of autoinflammatory disease: IL-1β activation disorders (inflammasomopathies), NF-κB activation syndromes, protein misfolding disorders, complement regulatory diseases, disturbances in cytokine signaling, and macrophage activation syndromes. A system based on molecular pathophysiology will bring greater clarity to our discourse while catalyzing new hypotheses both at the bench and at the bedside. PMID:19302049

Molecular electrostatics for probing lone pair-π interactions.

Science.gov (United States)

Mohan, Neetha; Suresh, Cherumuttathu H; Kumar, Anmol; Gadre, Shridhar R

2013-11-14

An electrostatics-based approach has been proposed for probing the weak interactions between lone pair containing molecules and π deficient molecular systems. For electron-rich molecules, the negative minima in molecular electrostatic potential (MESP) topography give the location of electron localization and the MESP value at the minimum (Vmin) quantifies the electron-rich character of that region. Interactive behavior of a lone pair bearing molecule with electron deficient π-systems, such as hexafluorobenzene, 1,3,5-trinitrobenzene, 2,4,6-trifluoro-1,3,5-triazine and 1,2,4,5-tetracyanobenzene explored within DFT brings out good correlation of the lone pair-π interaction energy (E(int)) with the Vmin value of the electron-rich system. Such interaction is found to be portrayed well with the Electrostatic Potential for Intermolecular Complexation (EPIC) model. On the basis of the precise location of MESP minimum, a prediction for the orientation of a lone pair bearing molecule with an electron deficient π-system is possible in the majority of the cases studied.

Molecular markers in the epidemiology and diagnosis of coccidioidomycosis.

Science.gov (United States)

Duarte-Escalante, Esperanza; Frías-De-León, María Guadalupe; Zúñiga, Gerardo; Martínez-Herrera, Erick; Acosta-Altamirano, Gustavo; Reyes-Montes, María Del Rocío

2014-01-01

The prevalence of coccidioidomycosis in endemic areas has been observed to increase daily. To understand the causes of the spread of the disease and design strategies for fungal detection in clinical and environmental samples, scientists have resorted to molecular tools that allow fungal detection in a natural environment, reliable identification in clinical cases and the study of biological characteristics, such as reproductive and genetic structure, demographic history and diversification. We conducted a review of the most important molecular markers in the epidemiology of Coccidioides spp. and the diagnosis of coccidioidomycosis. A literature search was performed for scientific publications concerning the application of molecular tools for the epidemiology and diagnosis of coccidioidomycosis. The use of molecular markers in the epidemiological study and diagnosis of coccidioidomycosis has allowed for the typing of Coccidioides spp. isolates, improved understanding of their mode of reproduction, genetic variation and speciation and resulted in the development specific, rapid and sensitive strategies for detecting the fungus in environmental and clinical samples. Molecular markers have revealed genetic variability in Coccidioides spp. This finding influences changes in the epidemiology of coccidioidomycosis, such as the emergence of more virulent or antifungal resistant genotypes. Furthermore, the molecular markers currently used to identify Coccidioides immitis and Coccidioides posadasii are specific and sensitive. However, they must be validated to determine their application in diagnosis. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Molecular Laser Spectroscopy as a Tool for Gas Analysis Applications

Directory of Open Access Journals (Sweden)

Javis Anyangwe Nwaboh

2011-01-01

Full Text Available We have used the traceable infrared laser spectrometric amount fraction measurement (TILSAM method to perform absolute concentration measurements of molecular species using three laser spectroscopic techniques. We report results performed by tunable diode laser absorption spectroscopy (TDLAS, quantum cascade laser absorption spectroscopy (QCLAS, and cavity ring down spectroscopy (CRDS, all based on the TILSAM methodology. The measured results of the different spectroscopic techniques are in agreement with respective gravimetric values, showing that the TILSAM method is feasible with all different techniques. We emphasize the data quality objectives given by traceability issues and uncertainty analyses.

Bringing Pulsed Laser Welding into Production

DEFF Research Database (Denmark)

Olsen, Flemmming Ove

1996-01-01

In this paper, some research and develop-ment activities within pulsed laser welding technology at the Tech-nical University of Denmark will be described. The laser group at the Insti-tute for Manufacturing Technology has nearly 20 years of experience in laser materials process-ing. Inter......-nationally the group is mostly known for its contri-butions to the development of the laser cutting process, but further it has been active within laser welding, both in assisting industry in bringing laser welding into production in several cases and in performing fundamental R & D. In this paper some research...... activities concerning the weldability of high alloyed austenitic stainless steels for mass production industry applying industrial lasers for fine welding will be described. Studies on hot cracking sensitivity of high alloyed austenitic stainless steel applying both ND-YAG-lasers and CO2-lasers has been...

Bringing Space Weather Down to Earth

Science.gov (United States)

Reiff, P. H.; Sumners, C.

2005-05-01

Most of the public has no idea what Space Weather is, but a number of innovative programs, web sites, magazine articles, TV shows and planetarium shows have taken space weather from an unknown quantity to a much more visible field. This paper reviews new developments, including the new Space Weather journal, the very popular spaceweather.com website, new immersive planetarium shows that can go "on the road", and well-publicized Sun-Earth Day activities. Real-time data and reasonably accurate spaceweather forecasts are available from several websites, with many subscribers. Even the renaissance of amateur radio because of Homeland Security brings a new generation of learners to wonder what is going on in the Sun today. The NSF Center for Integrated Space Weather Modeling has a dedicated team to reach both the public and a greater diversity of new scientists.

On simulation of local fluxes in molecular junctions

Science.gov (United States)

Cabra, Gabriel; Jensen, Anders; Galperin, Michael

2018-05-01

We present a pedagogical review of the current density simulation in molecular junction models indicating its advantages and deficiencies in analysis of local junction transport characteristics. In particular, we argue that current density is a universal tool which provides more information than traditionally simulated bond currents, especially when discussing inelastic processes. However, current density simulations are sensitive to the choice of basis and electronic structure method. We note that while discussing the local current conservation in junctions, one has to account for the source term caused by the open character of the system and intra-molecular interactions. Our considerations are illustrated with numerical simulations of a benzenedithiol molecular junction.

Molecular biology applications to infectious diseases diagnostic; Aplicaciones de la Biologica Molecular al diagnostico de enfermedades infecciosas

Energy Technology Data Exchange (ETDEWEB)

NONE

2001-07-01

This project goes directed to the applications of the techniques of molecular biology in hepatitis virus.A great advance of these techniques it allows its application to the diagnose molecular and it becomes indispensable to have these fundamental tools in the field of the Health Public for the detection precocious, pursuit of the treatment, the one predicts and the evolution of the patient hepatitis bearing virus technical.Use of molecular biology to increase the handling and the control of the patients with hepatitis B and C and to detect an adult numbers of positive cases by means of the training and integration of all the countries participating.Implement the technique of PCR to identify the virus of the hepatitis B and C,implement quantification methods and genotipification for these virus.

BRINGING STRATEGIC THINKING TO A CHINESE TOBACCO LOGISTICS CENTER

OpenAIRE

Zhao, Liubaihe

2012-01-01

Recently operation and logistics activities have played a more strategic role as tobacco business enterprises’ main functions. Because of the increasing costs of e.g. warehousing and inventory, transportation, personnel and other relevant materials, the different parties in the supply chain are facing more challenges and opportunities. On the one hand, this brings about improvements to the process flow and communications within the logistics activities for the sake of saving materials and ...

Moving Genetic Biomonitoring from a Concept to a Tool

Science.gov (United States)

Molecular genetic techniques like DNA barcoding and environmental DNA have been proposed as tools for aquatic biomonitoring for nearly a decade, but have yet to break through into widespread acceptance. The potential benefits of these methods, such as quicker, cheaper, more detai...

Tools for characterizing biomembranes : final LDRD report.

Energy Technology Data Exchange (ETDEWEB)

Alam, Todd Michael; Stevens, Mark; Holland, Gregory P.; McIntyre, Sarah K.

2007-10-01

A suite of experimental nuclear magnetic resonance (NMR) spectroscopy tools were developed to investigate lipid structure and dynamics in model membrane systems. By utilizing both multinuclear and multidimensional NMR experiments a range of different intra- and inter-molecular contacts were probed within the membranes. Examples on pure single component lipid membranes and on the canonical raft forming mixture of DOPC/SM/Chol are presented. A unique gel phase pretransition in SM was also identified and characterized using these NMR techniques. In addition molecular dynamics into the hydrogen bonding network unique to sphingomyelin containing membranes were evaluated as a function of temperature, and are discussed.

In Silico PCR Tools for a Fast Primer, Probe, and Advanced Searching.

Science.gov (United States)

Kalendar, Ruslan; Muterko, Alexandr; Shamekova, Malika; Zhambakin, Kabyl

2017-01-01

The polymerase chain reaction (PCR) is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. The principle of this technique has been further used and applied in plenty of other simple or complex nucleic acid amplification technologies (NAAT). In parallel to laboratory "wet bench" experiments for nucleic acid amplification technologies, in silico or virtual (bioinformatics) approaches have been developed, among which in silico PCR analysis. In silico NAAT analysis is a useful and efficient complementary method to ensure the specificity of primers or probes for an extensive range of PCR applications from homology gene discovery, molecular diagnosis, DNA fingerprinting, and repeat searching. Predicting sensitivity and specificity of primers and probes requires a search to determine whether they match a database with an optimal number of mismatches, similarity, and stability. In the development of in silico bioinformatics tools for nucleic acid amplification technologies, the prospects for the development of new NAAT or similar approaches should be taken into account, including forward-looking and comprehensive analysis that is not limited to only one PCR technique variant. The software FastPCR and the online Java web tool are integrated tools for in silico PCR of linear and circular DNA, multiple primer or probe searches in large or small databases and for advanced search. These tools are suitable for processing of batch files that are essential for automation when working with large amounts of data. The FastPCR software is available for download at http://primerdigital.com/fastpcr.html and the online Java version at http://primerdigital.com/tools/pcr.html .

Molecular gastronomy, a scientific look at cooking.

Science.gov (United States)

This, Hervé

2009-05-19

Food preparation is such a routine activity that we often do not question the process. For example, why do we cook as we do? Why do we eat certain foods and avoid other perfectly edible ingredients? To help answer these questions, it is extremely important to study the chemical changes that food undergoes during preparation; even simply cutting a vegetable can lead to enzymatic reactions. For many years, these molecular transformations were neglected by the food science field. In 1988, the scientific discipline called "molecular gastronomy" was created, and the field is now developing in many countries. Its many applications fall into two categories. First, there are technology applications for restaurants, for homes, or even for the food industry. In particular, molecular gastronomy has led to "molecular cooking", a way of food preparation that uses "new" tools, ingredients, and methods. According to a British culinary magazine, the three "top chefs" of the world employ elements of molecular cooking. Second, there are educational applications of molecular gastronomy: new insights into the culinary processes have led to new culinary curricula for chefs in many countries such as France, Canada, Italy, and Finland, as well as educational programs in schools. In this Account, we focus on science, explain why molecular gastronomy had to be created, and consider its tools, concepts, and results. Within the field, conceptual tools have been developed in order to make the necessary studies. The emphasis is on two important parts of recipes: culinary definitions (describing the objective of recipes) and culinary "precisions" (information that includes old wives' tales, methods, tips, and proverbs, for example). As for any science, the main objective of molecular gastronomy is, of course, the discovery of new phenomena and new mechanisms. This explains why culinary precisions are so important: cooks of the past could see, but not interpret, phenomena that awaited scientific

New concepts for molecular magnets

Science.gov (United States)

Pilawa, Bernd

1999-03-01

Miller and Epstein (1994) define molecular magnets as magnetic materials which are prepared by the low-temperature methods of the preparative chemistry. This definition includes molecular crystals of neutral radicals, radical salts and charge transfer complexes as well as metal complexes and polymers with unpaired spins (Dormann 1995). The challenge of molecular magnets consists in tailoring magnetic properties by specific modifications of the molecular units. The combination of magnetism with mechanical or electrical properties of molecular compounds promise materials of high technical interest (Gatteschi 1994a and 1994b, Möhwald 1996) and both the chemical synthesis of new molecular materials with magnetic properties as well as the physical investigation and explanation of these properties is important, in order to achieve any progress. This work deals with the physical characterization of the magnetic properties of molecular materials. It is organized as follows. In the first part molecular crystals of neutral radicals are studied. After briefly discussing the general magnetic properties of these materials and after an overview over the physical principles of exchange interaction between organic radicals I focus on the interplay between the crystallographic structure and the magnetic properties of various derivatives of the verdazyl and nitronyl nitroxide radicals. The magnetic properties of metal complexes are the subject of the second part. After an overview over the experimental and theoretical tools which are used for the investigation of the magnetic properties I shortly discuss the exchange coupling of transition metal ions and the magnetic properties of complexes of two and three metal ions. Special emphasis is given to spin cluster compounds. Spin cluster denote complexes of many magnetic ions. They are attractive as building blocks of molecular magnets as well as magnetic model compounds for the study of spin frustration, molecular super

The fundamentals of atomic and molecular physics

CERN Document Server

Brooks, Robert L

2013-01-01

The Fundamentals of Atomic and Molecular Physics is intended as an introduction to the field for advanced undergraduates who have taken quantum mechanics. Each chapter builds upon the previous, using the same tools and methods throughout. As the students progress through the book, their ability to use these tools will steadily increase, along with their confidence in their efficacy. The book treats the two-electron atom as the simplest example of the many-electron atom—as opposed to using techniques that are not applicable to many-electron atoms—so that it is unnecessary to develop additional equations when turning to multielectron atoms, such as carbon. External fields are treated using both perturbation theory and direct diagonalization and spontaneous emission is developed from first principles. Only diatomic molecules are considered with the hydrogen molecular ion and neutral molecule treated in some detail. This comprehensive coverage of the quantum mechanics of complex atoms and simple diatomic mole...

Molecular Imaging Challenges With PET

CERN Document Server

Lecoq, P

2010-01-01

The future trends in molecular imaging and associated challenges for in-vivo functional imaging are illustrated on the basis of a few examples, such as atherosclerosis vulnerable plaques imaging or stem cells tracking. A set of parameters are derived to define the specifications of a new generation of in-vivo imaging devices in terms of sensitivity, spatial resolution and signal-to-noise ratio. The limitations of strategies used in present PET scanners are discussed and new approaches are proposed taking advantage of recent progress on materials, photodetectors and readout electronics. A special focus is put on metamaterials, as a new approach to bring more functionality to detection devices. It is shown that the route is now open towards a fully digital detector head with very high photon counting capability over a large energy range, excellent timing precision and possibility of imaging the energy deposition process.

A room-temperature non-volatile CNT-based molecular memory cell

Science.gov (United States)

Ye, Senbin; Jing, Qingshen; Han, Ray P. S.

2013-04-01

Recent experiments with a carbon nanotube (CNT) system confirmed that the innertube can oscillate back-and-forth even under a room-temperature excitation. This demonstration of relative motion suggests that it is now feasible to build a CNT-based molecular memory cell (MC), and the key to bring the concept to reality is the precision control of the moving tube for sustained and reliable read/write (RW) operations. Here, we show that by using a 2-section outertube design, we are able to suitably recalibrate the system energetics and obtain the designed performance characteristics of a MC. Further, the resulting energy modification enables the MC to operate as a non-volatile memory element at room temperatures. Our paper explores a fundamental understanding of a MC and its response at the molecular level to roadmap a novel approach in memory technologies that can be harnessed to overcome the miniaturization limit and memory volatility in memory technologies.

Application of genomic tools in plant breeding.

Science.gov (United States)

Pérez-de-Castro, A M; Vilanova, S; Cañizares, J; Pascual, L; Blanca, J M; Díez, M J; Prohens, J; Picó, B

2012-05-01

Plant breeding has been very successful in developing improved varieties using conventional tools and methodologies. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information. The analysis of NGS data by means of bioinformatics developments allows discovering new genes and regulatory sequences and their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Genomic approaches include TILLING and EcoTILLING, which make possible to screen mutant and germplasm collections for allelic variants in target genes. Re-sequencing of genomes is very useful for the genome-wide discovery of markers amenable for high-throughput genotyping platforms, like SSRs and SNPs, or the construction of high density genetic maps. All these tools and resources facilitate studying the genetic diversity, which is important for germplasm management, enhancement and use. Also, they allow the identification of markers linked to genes and QTLs, using a diversity of techniques like bulked segregant analysis (BSA), fine genetic mapping, or association mapping. These new markers are used for marker assisted selection, including marker assisted backcross selection, 'breeding by design', or new strategies, like genomic selection. In conclusion, advances in genomics are providing breeders with new tools and methodologies that allow a great leap forward in plant breeding, including the 'superdomestication' of crops and the genetic dissection and breeding for complex traits.

Laser-cooled atomic ions as probes of molecular ions

Energy Technology Data Exchange (ETDEWEB)

Brown, Kenneth R.; Viteri, C. Ricardo; Clark, Craig R.; Goeders, James E.; Khanyile, Ncamiso B.; Vittorini, Grahame D. [Schools of Chemistry and Biochemistry, Computational Science and Engineering and Physics, Georgia Institute of Technology, Atlanta, GA 30332 (United States)

2015-01-22

Trapped laser-cooled atomic ions are a new tool for understanding cold molecular ions. The atomic ions not only sympathetically cool the molecular ions to millikelvin temperatures, but the bright atomic ion fluorescence can also serve as a detector of both molecular reactions and molecular spectra. We are working towards the detection of single molecular ion spectra by sympathetic heating spectroscopy. Sympathetic heating spectroscopy uses the coupled motion of two trapped ions to measure the spectra of one ion by observing changes in the fluorescence of the other ion. Sympathetic heating spectroscopy is a generalization of quantum logic spectroscopy, but does not require ions in the motional ground state or coherent control of the ion internal states. We have recently demonstrated this technique using two isotopes of Ca{sup +} [Phys. Rev. A, 81, 043428 (2010)]. Limits of the method and potential applications for molecular spectroscopy are discussed.

Molecular medicine: a path towards a personalized medicine.

Science.gov (United States)

Miranda, Debora Marques de; Mamede, Marcelo; Souza, Bruno Rezende de; Almeida Barros, Alexandre Guimarães de; Magno, Luiz Alexandre; Alvim-Soares, Antônio; Rosa, Daniela Valadão; Castro, Célio José de; Malloy-Diniz, Leandro; Gomez, Marcus Vinícius; Marco, Luiz Armando De; Correa, Humberto; Romano-Silva, Marco Aurélio

2012-03-01

Psychiatric disorders are among the most common human illnesses; still, the molecular and cellular mechanisms underlying their complex pathophysiology remain to be fully elucidated. Over the past 10 years, our group has been investigating the molecular abnormalities in major signaling pathways involved in psychiatric disorders. Recent evidences obtained by the Instituto Nacional de Ciência e Tecnologia de Medicina Molecular (National Institute of Science and Technology - Molecular Medicine, INCT-MM) and others using behavioral analysis of animal models provided valuable insights into the underlying molecular alterations responsible for many complex neuropsychiatric disorders, suggesting that "defects" in critical intracellular signaling pathways have an important role in regulating neurodevelopment, as well as in pathophysiology and treatment efficacy. Resources from the INCT have allowed us to start doing research in the field of molecular imaging. Molecular imaging is a research discipline that visualizes, characterizes, and quantifies the biologic processes taking place at cellular and molecular levels in humans and other living systems through the results of image within the reality of the physiological environment. In order to recognize targets, molecular imaging applies specific instruments (e.g., PET) that enable visualization and quantification in space and in real-time of signals from molecular imaging agents. The objective of molecular medicine is to individualize treatment and improve patient care. Thus, molecular imaging is an additional tool to achieve our ultimate goal.

Molecular Classification of Lobular Carcinoma of the Breast

Science.gov (United States)

Fu, Denggang; Zuo, Qi; Huang, Qi; Su, Li; Ring, Huijun Z.; Ring, Brian Z.

2017-01-01

The morphology of breast tumors is complicated and diagnosis can be difficult. We present here a novel diagnostic model which we validate on both array-based and RNA sequencing platforms which reliably distinguishes this tumor type across multiple cohorts. We also examine how this molecular classification predicts sensitivity to common chemotherapeutics in cell-line based assays. A total of 1845 invasive breast cancer cases in six cohorts were collected, split into discovery and validation cohorts, and a classifier was created and compared to pathological diagnosis, grade and survival. In the validation cohorts the concordance of predicted diagnosis with a pathological diagnosis was 92%, and 97% when inconclusively classified cases were excluded. Tumor-derived cell lines were classified with the model as having predominantly ductal or lobular-like molecular physiologies, and sensitivity of these lines to relevant compounds was analyzed. A diagnostic tool can be created that reliably distinguishes lobular from ductal carcinoma and allows the classification of cell lines on the basis of molecular profiles associated with these tumor types. This tool may assist in improved diagnosis and aid in explorations of the response of lobular type breast tumor models to different compounds. PMID:28303886

Communication tools between Grid virtual organisations, middleware deployers and sites

CERN Document Server

Dimou, Maria

2008-01-01

Grid Deployment suffers today from the difficulty to reach users and site administrators when a package or a configuration parameter changes. Release notes, twiki pages and news’ broadcasts are not efficient enough. The interest of using GGUS as an efficient and effective intra-project communication tool is the message to the user community presented here. The purpose of GGUS is to bring together End Users and Supporters in the Regions where the Grid is deployed and in operation. Today’s Grid usage is still very far from the simplicity and functionality of the web. While pressing for middleware usability, we try to turn the Global Grid User Support (GGUS) into the central tool for identifying areas in the support environment that need attention. To do this, we exploit GGUS' capacity to expand, by including new Support Units that follow the project's operational structure. Using tailored GGUS database searches we obtain concrete results that prove where we need to improve procedures, Service Level Agreemen...

Laurentide: The Crime Fighting Geologist, A Comic-Book Curriculum Tool

Science.gov (United States)

McGillis, A.; Gilbert, L. A.; Enright, K. P.

2014-12-01

When the police are just too ill informed on matters of earth science to solve the case it is up to Laurentide and her crew of geologists to bring justice to evildoers. Using every tool available, from a rock hammer to LiDAR, Laurentide fights crime while teaching her apprentice Esker about how geologists uncover mysteries everyday. This is the first of what will be a series of free teaching materials targeted at grades 5-8 based around the National Science Education Standards. Students will get the chance to practice problem solving and data analysis in order to solve mysteries with a combination of comic book style story telling and hands-on worksheets. The pilot story, "The Caper of the Ridiculously Cheap Condominiums" will cover 4 of the 9 Earth Science Literacy Principles 'Big Ideas'. Material will explore earthquakes, the hazards and risks they present, and the tools geologists use to map faults and estimate reoccurrence intervals.

Bring Back Our Girls, Social Mobilization: Implications for Cross-Cultural Research

Science.gov (United States)

Olutokunbo, Adekalu Samuel; Suandi, Turiman; Cephas, Oluwaseyitan Rotimi; Abu-Samah, Irza Hanie

2015-01-01

Social mobilization is a proactive measure for community development that salvages the society from destruction and disaster. From sociological perspective, this paper discusses the concept of social mobilization and its implications for cross-cultural research. To do this, the study uses the "Bring Back Our Girls" Global Campaign, as…

Crawl and crowd to bring machine translation to under-resourced languages

NARCIS (Netherlands)

Toral Ruiz, Antonio

2017-01-01

We present a widely applicable methodology to bring machine translation (MT) to under-resourced languages in a cost-effective and rapid manner. Our proposal relies on web crawling to automatically acquire parallel data to train statistical MT systems if any such data can be found for the language

Towards high-throughput molecular detection of Plasmodium: new approaches and molecular markers

Directory of Open Access Journals (Sweden)

Rogier Christophe

2009-04-01

Full Text Available Abstract Background Several strategies are currently deployed in many countries in the tropics to strengthen malaria control toward malaria elimination. To measure the impact of any intervention, there is a need to detect malaria properly. Mostly, decisions still rely on microscopy diagnosis. But sensitive diagnosis tools enabling to deal with a large number of samples are needed. The molecular detection approach offers a much higher sensitivity, and the flexibility to be automated and upgraded. Methods Two new molecular methods were developed: dot18S, a Plasmodium-specific nested PCR based on the 18S rRNA gene followed by dot-blot detection of species by using species-specific probes and CYTB, a Plasmodium-specific nested PCR based on cytochrome b gene followed by species detection using SNP analysis. The results were compared to those obtained with microscopic examination and the "standard" 18S rRNA gene based nested PCR using species specific primers. 337 samples were diagnosed. Results Compared to the microscopy the three molecular methods were more sensitive, greatly increasing the estimated prevalence of Plasmodium infection, including P. malariae and P. ovale. A high rate of mixed infections was uncovered with about one third of the villagers infected with more than one malaria parasite species. Dot18S and CYTB sensitivity outranged the "standard" nested PCR method, CYTB being the most sensitive. As a consequence, compared to the "standard" nested PCR method for the detection of Plasmodium spp., the sensitivity of dot18S and CYTB was respectively 95.3% and 97.3%. Consistent detection of Plasmodium spp. by the three molecular methods was obtained for 83% of tested isolates. Contradictory results were mostly related to detection of Plasmodium malariae and Plasmodium ovale in mixed infections, due to an "all-or-none" detection effect at low-level parasitaemia. Conclusion A large reservoir of asymptomatic infections was uncovered using the

Software Tools | Office of Cancer Clinical Proteomics Research

Science.gov (United States)

The CPTAC program develops new approaches to elucidate aspects of the molecular complexity of cancer made from large-scale proteogenomic datasets, and advance them toward precision medicine.  Part of the CPTAC mission is to make data and tools available and accessible to the greater research community to accelerate the discovery process.

Beyond a pedagogical tool: 30 years of Molecular biology of the cell.

Science.gov (United States)

Serpente, Norberto

2013-02-01

In 1983, a bulky and profusely illustrated textbook on molecular and cell biology began to inhabit the shelves of university libraries worldwide. The effect of capturing the eyes and souls of biologists was immediate as the book provided them with a new and invigorating outlook on what cells are and what they do.

Using molecular tools to identify the geographical origin of a case of human brucellosis.

Science.gov (United States)

Muchowski, J K; Koylass, M S; Dainty, A C; Stack, J A; Perrett, L; Whatmore, A M; Perrier, C; Chircop, S; Demicoli, N; Gatt, A B; Caruana, P A; Gopaul, K K

2015-10-01

Although Malta is historically linked with the zoonosis brucellosis, there had not been a case of the disease in either the human or livestock population for several years. However, in July 2013 a case of human brucellosis was identified on the island. To determine whether this recent case originated in Malta, four isolates from this case were subjected to molecular analysis. Molecular profiles generated using multilocus sequence analysis and multilocus variable number tandem repeat for the recent human case isolates and 11 Brucella melitensis strains of known Maltese origin were compared with others held on in-house and global databases. While the 11 isolates of Maltese origin formed a distinct cluster, the recent human isolation was not associated with these strains but instead clustered with isolates originating from the Horn of Africa. These data was congruent with epidemiological trace-back showed that the individual had travelled to Malta from Eritrea. This work highlights the potential of using molecular typing data to aid in epidemiological trace-back of Brucella isolations and assist in monitoring of the effectiveness of brucellosis control schemes.

Science and Sport bringing people together

CERN Multimedia

Staff Association

2018-01-01

ASCERI is the Association of the Sports Communities of the European Research Institutes and aims to contribute to a united Europe through regular sports meetings, bringing together members of public Research Institutes at European level. The Association's members come from over 42 Research Institutes spanning 15 countries. The association was born from the German "Kernforschungszentrum Karlsruhe" (KfK) football team who had the idea to play against other teams from institutes also involved in nuclear research. Therefore, six teams from different German centres were invited to take part in a "Reaktoren Fußballturnier" in Karlsruhe on 2 July 1966. Ever since, The Winter-ATOMIADE has taken place every three years and alternating with the Summer-ATOMIADE and a Mini Atomiade in between with numerous sports and leisure activities including football, skiing, golf, athletics, tennis, volleyball to name a few. CERN has been a regular participant ...

Candidate gene molecular markers as tools for analyzing genetic susceptibility to morbillivirus infection in stranded Cetaceans

Czech Academy of Sciences Publication Activity Database

Stejskalová, K.; Bayerova, Z.; Futas, J.; Hrazdilová, K.; Klumplerova, M.; Oppelt, J.; Šplíchalová, P.; Di Guardo, G.; Mazzariol, S.; Di Francesco, C. E.; Di Francesco, G.; Terracciano, G.; Paiu, R.M.; Ursache, T. D.; Modrý, David; Horin, P.

2017-01-01

Roč. 90, č. 6 (2017), s. 343-353 ISSN 2059-2302 Institutional support: RVO:60077344 Keywords : Cetacea * haplotype * immunity * innate * mhc-dqb * Phocoena phocoena * polymorphism * single nucleotide * Stenella coeruleoalba Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology

Bring Me Men: Intertextual Identity Formation at the US Air Force Academy

National Research Council Canada - National Science Library

Schifani, Katherine L

2008-01-01

.... It took twenty-one years from when the first class entered in 1955 before the Air Force Academy saw its first women, one walking famously on her first day in front of the "Bring Me Men..." ramp (BMMR...

Building ProteomeTools based on a complete synthetic human proteome

Science.gov (United States)

Zolg, Daniel P.; Wilhelm, Mathias; Schnatbaum, Karsten; Zerweck, Johannes; Knaute, Tobias; Delanghe, Bernard; Bailey, Derek J.; Gessulat, Siegfried; Ehrlich, Hans-Christian; Weininger, Maximilian; Yu, Peng; Schlegl, Judith; Kramer, Karl; Schmidt, Tobias; Kusebauch, Ulrike; Deutsch, Eric W.; Aebersold, Ruedi; Moritz, Robert L.; Wenschuh, Holger; Moehring, Thomas; Aiche, Stephan; Huhmer, Andreas; Reimer, Ulf; Kuster, Bernhard

2018-01-01

The ProteomeTools project builds molecular and digital tools from the human proteome to facilitate biomedical and life science research. Here, we report the generation and multimodal LC-MS/MS analysis of >330,000 synthetic tryptic peptides representing essentially all canonical human gene products and exemplify the utility of this data. The resource will be extended to >1 million peptides and all data will be shared with the community via ProteomicsDB and proteomeXchange. PMID:28135259

Current state of molecular imaging research

International Nuclear Information System (INIS)

Grimm, J.; Wunder, A.

2005-01-01

The recent years have seen significant advances in both molecular biology, allowing the identification of genes and pathways related to disease, and imaging technologies that allow for improved spatial and temporal resolution, enhanced sensitivity, better depth penetration, improved image processing, and beneficial combinations of different imaging modalities. These advances have led to a paradigm shift in the scope of diagnostic imaging. The traditional role of radiological diagnostic imaging is to define gross anatomy and structure in order to detect pathological abnormalities. Available contrast agents are mostly non-specific and can be used to image physiological processes such as changes in blood volume, flow, and perfusion but not to demonstrate pathological alterations at molecular levels. However, alterations at the anatomical-morphological level are relatively late manifestations of underlying molecular changes. Using molecular probes or markers that bind specifically to molecular targets allows for the non-invasive visualization and quantitation of biological processes such as gene expression, apoptosis, or angiogenesis at the molecular level within intact living organisms. This rapidly evolving, multidisciplinary approach, referred to as molecular imaging, promises to enable early diagnosis, can provide improved classification of stage and severity of disease, an objective assessment of treatment efficacy, and a reliable prognosis. Furthermore, molecular imaging is an important tool for the evaluation of physiological and pathophysiological processes, and for the development of new therapies. This article comprises a review of current technologies of molecular imaging, describes the development of contrast agents and various imaging modalities, new applications in specific disease models, and potential future developments. (orig.)

Peroxisome Proliferator-Activated Receptor (PPAR) in Regenerative Medicine: Molecular Mechanism for PPAR in Stem Cells' Adipocyte Differentiation.

Science.gov (United States)

Xie, Qiang; Tian, Taoran; Chen, Zhaozhao; Deng, Shuwen; Sun, Ke; Xie, Jing; Cai, Xiaoxiao

2016-01-01

Regenerative medicine plays an indispensable role in modern medicine and many trials and researches have therefore been developed to fit our medical needs. Tissue engineering has proven that adipose tissue can widely be used and brings advantages to regenerative medicine. Moreover, a trait of adipose stem cells being isolated and grown in vitro is a cornerstone to various applications. Since the adipose tissue has been widely used in regenerative medicine, numerous studies have been conducted to seek methods for gaining more adipocytes. To investigate molecular mechanism for adipocyte differentiation, peroxisome proliferator-activated receptor (PPAR) has been widely studied to find out its functional mechanism, as a key factor for adipocyte differentiation. However, the precise molecular mechanism is still unknown. This review thus summarizes recent progress on the study of molecular mechanism and role of PPAR in adipocyte differentiation.

Automated processing of data generated by molecular dynamics

International Nuclear Information System (INIS)

Lobato Hoyos, Ivan; Rojas Tapia, Justo; Instituto Peruano de Energia Nuclear, Lima

2008-01-01

A new integrated tool for automated processing of data generated by molecular dynamics packages and programs have been developed. The program allows to calculate important quantities such as pair correlation function, the analysis of common neighbors, counting nanoparticles and their size distribution, conversion of output files between different formats. The work explains in detail the modules of the tool, the interface between them. The uses of program are illustrated in application examples in the calculation of various properties of silver nanoparticles. (author)

Subtle Monte Carlo Updates in Dense Molecular Systems

DEFF Research Database (Denmark)

Bottaro, Sandro; Boomsma, Wouter; Johansson, Kristoffer E.

2012-01-01

Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as the native state of globular proteins. Here, we introduce...... as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater efficiency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results...... suggest our method as a valuable tool in the study of molecules in atomic detail, offering a potential alternative to molecular dynamics for probing long time-scale conformational transitions....

Archaeopteryx: Bringing the Dino-Bird to Life

International Nuclear Information System (INIS)

Bergmann, Uwe

2011-01-01

Some 150 million years ago, a strange creature died in a tropical lagoon that today is located in Bavaria, Germany. In 1861, a single feather of this creature was discovered. Not long afterward, a complete fossil was found with the same bird-like feathers but dinosaur-like anatomical features. Darwin had just published 'On the Origin of Species'; could this be the missing link that Darwin's supporters hoped to find? Recently, two of the now eleven discovered Archaeopteryx fossils, and that first feather, were brought to SLAC, where, using the intense X-ray beam, researchers searched for the chemical remains of the original living creatures. Please join us for this lecture, which will explain how the studies attempt to bring the original dino-bird back to life.

An Engineering Tool for the Prediction of Internal Dielectric Charging

Science.gov (United States)

Rodgers, D. J.; Ryden, K. A.; Wrenn, G. L.; Latham, P. M.; Sorensen, J.; Levy, L.

1998-11-01

A practical internal charging tool has been developed. It provides an easy-to-use means for satellite engineers to predict whether on-board dielectrics are vulnerable to electrostatic discharge in the outer radiation belt. The tool is designed to simulate irradiation of single-dielectric planar or cylindrical structures with or without shielding. Analytical equations are used to describe current deposition in the dielectric. This is fast and gives charging currents to sufficient accuracy given the uncertainties in other aspects of the problem - particularly material characteristics. Time-dependent internal electric fields are calculated, taking into account the effect on conductivity of electric field, dose rate and temperature. A worst-case model of electron fluxes in the outer belt has been created specifically for the internal charging problem and is built into the code. For output, the tool gives a YES or NO decision on the susceptibility of the structure to internal electrostatic breakdown and if necessary, calculates the required changes to bring the system below the breakdown threshold. A complementary programme of laboratory irradiations has been carried out to validate the tool. The results for Epoxy-fibreglass samples show that the code models electric field realistically for a wide variety of shields, dielectric thicknesses and electron spectra. Results for Teflon samples indicate that some further experimentation is required and the radiation-induced conductivity aspects of the code have not been validated.

Using vibrational molecular spectroscopy to reveal association of steam-flaking induced carbohydrates molecular structural changes with grain fractionation, biodigestion and biodegradation

Science.gov (United States)

Xu, Ningning; Liu, Jianxin; Yu, Peiqiang

2018-04-01

Advanced vibrational molecular spectroscopy has been developed as a rapid and non-destructive tool to reveal intrinsic molecular structure conformation of biological tissues. However, this technique has not been used to systematically study flaking induced structure changes at a molecular level. The objective of this study was to use vibrational molecular spectroscopy to reveal association between steam flaking induced CHO molecular structural changes in relation to grain CHO fractionation, predicted CHO biodegradation and biodigestion in ruminant system. The Attenuate Total Reflectance Fourier-transform Vibrational Molecular Spectroscopy (ATR-Ft/VMS) at SRP Key Lab of Molecular Structure and Molecular Nutrition, Ministry of Agriculture Strategic Research Chair Program (SRP, University of Saskatchewan) was applied in this study. The fractionation, predicted biodegradation and biodigestion were evaluated using the Cornell Net Carbohydrate Protein System. The results show that: (1) The steam flaking induced significant changes in CHO subfractions, CHO biodegradation and biodigestion in ruminant system. There were significant differences between non-processed (raw) and steam flaked grain corn (P R2 = 0.87, RSD = 0.74, P R2 = 0.87, RSD = 0.24, P < .01). In summary, the processing induced molecular CHO structure changes in grain corn could be revealed by the ATR-Ft/VMS vibrational molecular spectroscopy. These molecular structure changes in grain were potentially associated with CHO biodegradation and biodigestion.

The Jukes-Cantor Model of Molecular Evolution

Science.gov (United States)

Erickson, Keith

2010-01-01

The material in this module introduces students to some of the mathematical tools used to examine molecular evolution. This topic is standard fare in many mathematical biology or bioinformatics classes, but could also be suitable for classes in linear algebra or probability. While coursework in matrix algebra, Markov processes, Monte Carlo…

Molecular environmental geochemistry

Science.gov (United States)

O'Day, Peggy A.

1999-05-01

The chemistry, mobility, and bioavailability of contaminant species in the natural environment are controlled by reactions that occur in and among solid, aqueous, and gas phases. These reactions are varied and complex, involving changes in chemical form and mass transfer among inorganic, organic, and biochemical species. The field of molecular environmental geochemistry seeks to apply spectroscopic and microscopic probes to the mechanistic understanding of environmentally relevant chemical processes, particularly those involving contaminants and Earth materials. In general, empirical geochemical models have been shown to lack uniqueness and adequate predictive capability, even in relatively simple systems. Molecular geochemical tools, when coupled with macroscopic measurements, can provide the level of chemical detail required for the credible extrapolation of contaminant reactivity and bioavailability over ranges of temperature, pressure, and composition. This review focuses on recent advances in the understanding of molecular chemistry and reaction mechanisms at mineral surfaces and mineral-fluid interfaces spurred by the application of new spectroscopies and microscopies. These methods, such as synchrotron X-ray absorption and scattering techniques, vibrational and resonance spectroscopies, and scanning probe microscopies, provide direct chemical information that can elucidate molecular mechanisms, including element speciation, ligand coordination and oxidation state, structural arrangement and crystallinity on different scales, and physical morphology and topography of surfaces. Nonvacuum techniques that allow examination of reactions in situ (i.e., with water or fluids present) and in real time provide direct links between molecular structure and reactivity and measurements of kinetic rates or thermodynamic properties. Applications of these diverse probes to laboratory model systems have provided fundamental insight into inorganic and organic reactions at

Diversity in parasitic helminths of Australasian marsupials and monotremes: a molecular perspective.

Science.gov (United States)

Beveridge, Ian; Gasser, Robin B

2014-10-15

Marsupials and monotremes are a prominent part of the mammalian fauna in Australia, and harbour an extremely diverse and highly distinctive array of helminth parasites. Their study has been relatively neglected, likely because they have no direct, adverse socioeconomic impact. As the body plans of helminths generally are very simple and morphological characterisation likely underestimates true diversity, molecular tools have been employed to assess genetic diversity. Using biochemical and/or molecular methods, recent studies show extensive diversity in helminths of marsupials, with cryptic species being commonly encountered. The purpose of this article is to review current knowledge about the diversity of parasitic helminths of marsupials and monotremes, to raise questions as to whether current molecular data can be used to estimate diversity, what mechanisms lead to such diversity, to critically appraise the molecular tools that have been employed thus far to explore diversity and to discuss the directions which might be taken in the future employing improved techniques. Copyright © 2014 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Molecular Rift: Virtual Reality for Drug Designers.

Science.gov (United States)

Norrby, Magnus; Grebner, Christoph; Eriksson, Joakim; Boström, Jonas

2015-11-23

Recent advances in interaction design have created new ways to use computers. One example is the ability to create enhanced 3D environments that simulate physical presence in the real world--a virtual reality. This is relevant to drug discovery since molecular models are frequently used to obtain deeper understandings of, say, ligand-protein complexes. We have developed a tool (Molecular Rift), which creates a virtual reality environment steered with hand movements. Oculus Rift, a head-mounted display, is used to create the virtual settings. The program is controlled by gesture-recognition, using the gaming sensor MS Kinect v2, eliminating the need for standard input devices. The Open Babel toolkit was integrated to provide access to powerful cheminformatics functions. Molecular Rift was developed with a focus on usability, including iterative test-group evaluations. We conclude with reflections on virtual reality's future capabilities in chemistry and education. Molecular Rift is open source and can be downloaded from GitHub.

Gastronomic botany and molecular gastronomy

OpenAIRE

Pérez-Urria Carril, Elena; Gómez Garay, Aranzazu; Ávalos García, Adolfo; Martín Calvarro, Luisa; Pintos López, Beatriz; Saco Sierra, M. Dolores; Martín Gómez, M. Soledad; Pérez Alonso, M. José; Puelles Gallo, María; Palá Paúl, Jesús; Cifuentes Cuencas, Blanca; Llamas Ramos, José Eugenio

2011-01-01

Complutense University of Madrid through the "Vicerrectorado de Calidad" develops projects to innovate and improve teaching quality. Among these projects is "Gastronomic Botany and Molecular Gastronomy" which aims to develop new materials and tools for the Virtual Campus and consequently offer new possibilities for teaching and training. Also this project organize and structure a new teaching matter for post-graduate education that will be an example of approach, relationship and cooper...

Biology Needs Evolutionary Software Tools: Let’s Build Them Right

Science.gov (United States)

Team, Galaxy; Goecks, Jeremy; Taylor, James

2018-01-01

Abstract Research in population genetics and evolutionary biology has always provided a computational backbone for life sciences as a whole. Today evolutionary and population biology reasoning are essential for interpretation of large complex datasets that are characteristic of all domains of today’s life sciences ranging from cancer biology to microbial ecology. This situation makes algorithms and software tools developed by our community more important than ever before. This means that we, developers of software tool for molecular evolutionary analyses, now have a shared responsibility to make these tools accessible using modern technological developments as well as provide adequate documentation and training. PMID:29688462

Molecular biology applications to infectious diseases diagnostic

International Nuclear Information System (INIS)

2001-01-01

This project goes directed to the applications of the techniques of molecular biology in hepatitis virus.A great advance of these techniques it allows its application to the diagnose molecular and it becomes indispensable to have these fundamental tools in the field of the Health Public for the detection precocious, pursuit of the treatment, the one predicts and the evolution of the patient hepatitis bearing virus technical.Use of molecular biology to increase the handling and the control of the patients with hepatitis B and C and to detect an adult numbers of positive cases by means of the training and integration of all the countries participating.Implement the technique of PCR to identify the virus of the hepatitis B and C,implement quantification methods and genotipification for these virus

Modified T-cells (using TCR and CTAs, chimeric antigen receptor (CAR and other molecular tools in recent gene therapy

Directory of Open Access Journals (Sweden)

A.S. Odiba

2018-07-01

Full Text Available T-cell-based cancer immunotherapy by the transfer of cloned TCRs that are isolated from tumor penetrating T-cells becomes a possibility through NY-ESOc259; a human-derived affinity-enhanced TCR that provides a level of sufficiency in long-term safety and efficacy. NY-ESOc259 recognizes a peptide common to CTAs (LAGE-1 and NY-ESO-1 in melanoma. Risks associated with insertion related transformation in gene therapy have been alleviated through strategies that include the engineering of transcription activator like effector nucleases (TALEN, RNA-guided nucleases (CRISPR/Cas9, Zinc-finger nucleases (ZFN. Cancer immunotherapy based on the genetic modification of autologous T-cells (dependent on the engineered autologous CD8+ T-cells, designed to distinguish and destroy cells bearing tumor-specific antigens via a CAR is able to exterminate B-cell leukemias and lymphomas that are resilient to conventional therapies. A tool with a very large reservoir of potentials in molecular therapy strategy is the Pluripotent Stem Cells (PSC, with pluripotency factors that include Klf4, Sox2, c-Myc, Oct4, differentiating into disease-associated cell phenotypes of three germ layers, comprising of mesoderm (e.g. cardiac cells, blood and muscle, endoderm (liver, pancreas and ectoderm (epidermis, neurons. It finds good application in disease modelling as well as therapeutic options in the restoration of CGD by using AAVS1 as the vector where the therapeutic cassette is integrated into the locus to restore superoxide production in the granulocytes. Fascinatingly, Clinical trial involving iPSC are already underway where scientists have plans to use iPSC-derived cells to treat macular degeneration (a devastating age-related eye disease. Application of these findings has redefined incurable diseases disorders as curable. Keywords: Clinical trials, Disorders, Gene therapy, Molecular biology, Pharmacotherapy, Vector

Bring learning into action

Directory of Open Access Journals (Sweden)

Annemieke van den Berg

2018-05-01

Full Text Available Context: This critical reflection is about the positive effects for educational and research settings of participation in a two-day programme entitled ‘Using participatory action research and appreciative inquiry to research healthcare practice’. Aims: To reflect on the journey of positive developments in research and education that started with participation in this programme. Using Caring Conversations (Dewar, 2011 as a reflective framework of questions, this article discusses the journey in order to encourage others to consider the approach of appreciative inquiry to bring to life the concept of co-creation in research and education. Conclusions and implications for practice: Participation in this programme has led to the implementation of a variety of actions in educational and research settings. Central to all these actions is an appreciative approach to co-creation as a counterpart to today’s prevailing problem-based viewpoint. A possible factor behind these developments was the power of vulnerability experienced during the programme, a shared process of transformational learning. Implications for practice: This critical reflection: Provides an invitation to shift from a problem-based focus to a positive revolution Provides an appreciative reflective story about the power of vulnerability as an inspiration for others to move out of their comfort zone and seek to discover their own exceptionality Supports a shift from a facilitator-led to a co-creation approach in doing research and teaching with older adults

Stereochemical errors and their implications for molecular dynamics simulations

Directory of Open Access Journals (Sweden)

Freddolino Peter L

2011-05-01

Full Text Available Abstract Background Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations. Results Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules. Conclusions Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.

Simrank: Rapid and sensitive general-purpose k-mer search tool

Energy Technology Data Exchange (ETDEWEB)

DeSantis, T.Z.; Keller, K.; Karaoz, U.; Alekseyenko, A.V; Singh, N.N.S.; Brodie, E.L; Pei, Z.; Andersen, G.L; Larsen, N.

2011-04-01

Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project (http://nihroadmap.nih.gov/hmp). Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available. Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset. Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity.

Bring-Your-Own-Device: Turning Cell Phones into Forces for Good

Science.gov (United States)

Imazeki, Jennifer

2014-01-01

Over the last few years, classroom response systems (or "clickers") have become increasingly common. Although most systems require students to use a standalone handheld device, bring-your-own-device (BYOD) systems allow students to use devices they already own (e.g., a cell phone, tablet or laptop) to submit responses via text message or…

Methods and Tools to allow molecular flow simulations to be coupled to higher level continuum descriptions of flows in porous/fractured media and aerosol/dust dynamics

Energy Technology Data Exchange (ETDEWEB)

Loyalka, Sudarshan [Univ. of Missouri, Columbia, MO (United States)

2015-04-09

The purpose of this project was to develop methods and tools that will aid in safety evaluation of nuclear fuels and licensing of nuclear reactors relating to accidents.The objectives were to develop more detailed and faster computations of fission product transport and aerosol evolution as they generally relate to nuclear fuel and/or nuclear reactor accidents. The two tasks in the project related to molecular transport in nuclear fuel and aerosol transport in reactor vessel and containment. For both the tasks, explorations of coupling of Direct Simulation Monte Carlo with Navier-Stokes solvers or the Sectional method were not successful. However, Mesh free methods for the Direct Simulation Monte Carlo method were successfully explored.These explorations permit applications to porous and fractured media, and arbitrary geometries.The computations were carried out in Mathematica and are fully parallelized. The project has resulted in new computational tools (algorithms and programs) that will improve the fidelity of computations to actual physics, chemistry and transport of fission products in the nuclear fuel and aerosol in reactor primary and secondary containments.

Molecular detection of pathogens in water--the pros and cons of molecular techniques.

Science.gov (United States)

Girones, Rosina; Ferrús, Maria Antonia; Alonso, José Luis; Rodriguez-Manzano, Jesus; Calgua, Byron; Corrêa, Adriana de Abreu; Hundesa, Ayalkibet; Carratala, Anna; Bofill-Mas, Sílvia

2010-08-01

Pollution of water by sewage and run-off from farms produces a serious public health problem in many countries. Viruses, along with bacteria and protozoa in the intestine or in urine are shed and transported through the sewer system. Even in highly industrialized countries, pathogens, including viruses, are prevalent throughout the environment. Molecular methods are used to monitor viral, bacterial, and protozoan pathogens, and to track pathogen- and source-specific markers in the environment. Molecular techniques, specifically polymerase chain reaction-based methods, provide sensitive, rapid, and quantitative analytical tools with which to study such pathogens, including new or emerging strains. These techniques are used to evaluate the microbiological quality of food and water, and to assess the efficiency of virus removal in drinking and wastewater treatment plants. The range of methods available for the application of molecular techniques has increased, and the costs involved have fallen. These developments have allowed the potential standardization and automation of certain techniques. In some cases they facilitate the identification, genotyping, enumeration, viability assessment, and source-tracking of human and animal contamination. Additionally, recent improvements in detection technologies have allowed the simultaneous detection of multiple targets in a single assay. However, the molecular techniques available today and those under development require further refinement in order to be standardized and applicable to a diversity of matrices. Water disinfection treatments may have an effect on the viability of pathogens and the numbers obtained by molecular techniques may overestimate the quantification of infectious microorganisms. The pros and cons of molecular techniques for the detection and quantification of pathogens in water are discussed. (c) 2010 Elsevier Ltd. All rights reserved.

Integration of ROOT notebook as an ATLAS analysis web-based tool in outreach and public data release projects

CERN Document Server

AUTHOR|(INSPIRE)INSPIRE-00237353; The ATLAS collaboration

2017-01-01

Integration of the ROOT data analysis framework with the Jupyter Notebook technology presents the potential of enhancement and expansion of educational and training programs. It can be beneficial for university students in their early years, new PhD students and post-doctoral researchers, as well as for senior researchers and teachers who want to refresh their data analysis skills or to introduce a more friendly and yet very powerful open source tool in the classroom. Such tools have been already tested in several environments. A fully web-based integration of the tools and the Open Access Data repositories brings the possibility to go a step forward in the ATLAS quest of making use of several CERN projects in the field of the education and training, developing new computing solutions on the way.

Bringing a Finnish Company to the Russian E-Market

OpenAIRE

Veselova, Victoria

2012-01-01

The main objective of the project was to enable a small business case company that is operating in the town of Lappeenranta, Finland, to reach successfully its target segment (Russian consumers) with the help of digital technology in order to increase sales both in its physical shop and in online store. In order to reach the aim of the project and bring Russian consumers and the case company together by the means of electronic marketing, a marketing plan for the promotional campaigns of th...

Bring Your Own Device in the Information Literacy Classroom

OpenAIRE

Stonebraker, Ilana; Robertshaw, M Brooke; Kirkwood, Hal; Dugan, Mary

2014-01-01

In the 2013 school year, a team of librarians in the Parrish Library of Management and Economics at Purdue University taught a business information literacy course to approximately 500 management students in eight 70-person sessions. Due to limitations on a set of iPads borrowed from another department, one of two concurrent classes was taught with a set of iPads, while another had a Bring Your Own Device (BYOD) policy, where students brought their own laptops or iPads. Focus groups, observat...

[Manipulation of the human genome: ethics and law].

Science.gov (United States)

Goulart, Maria Carolina Vaz; Iano, Flávia Godoy; Silva, Paulo Maurício; Sales-Peres, Silvia Helena de Carvalho; Sales-Peres, Arsênio

2010-06-01

The molecular biology has provided the basic tool for geneticists deepening in the molecular mechanisms that influence different diseases. It should be noted the scientific and moral responsibility of the researchers, because the scientists should imagine the moral consequences of the commercial application of genetic tests, since this fact involves not only the individual and their families, but the entire population. Besides being also necessary to make a reflection on how this information from the human genome will be used, for good or bad. The objective of this review was to bring the light of knowledge, data on characteristics of the ethical application of molecular biology, linking it with the rights of human beings. After studying literature, it might be observed that the Human Genome Project has generated several possibilities, such as the identification of genes associated with diseases with synergistic properties, but sometimes modifying behavior to genetically intervene in humans, bringing benefits or social harm. The big challenge is to decide what humanity wants on this giant leap.

Molecular Imaging and Precision Medicine in Dementia and Movement Disorders.

Science.gov (United States)

Mallik, Atul K; Drzezga, Alexander; Minoshima, Satoshi

2017-01-01

Precision medicine (PM) has been defined as "prevention and treatment strategies that take individual variability into account." Molecular imaging (MI) is an ideally suited tool for PM approaches to neurodegenerative dementia and movement disorders (MD). Here we review PM approaches and discuss how they may be applied to other associated neurodegenerative dementia and MD. With ongoing major therapeutic research initiatives that include the use of molecular imaging, we look forward to established interventions targeted to specific molecular pathophysiology and expect the potential benefit of MI PM approaches in neurodegenerative dementia and MD will only increase. Copyright © 2016 Elsevier Inc. All rights reserved.

Design strategies for organic semiconductors beyond the molecular formula.

Science.gov (United States)

Henson, Zachary B; Müllen, Klaus; Bazan, Guillermo C

2012-09-01

Organic semiconducting materials based on polymers and molecular systems containing an electronically delocalized structure are the basis of emerging optoelectronic technologies such as plastic solar cells and flexible transistors. For isolated molecules, guidelines exist that rely on the molecular formula to tailor the frontier (highest occupied or lowest unoccupied) molecular orbital energy levels and optical absorption profiles. Much less control can be achieved over relevant properties, however, as one makes the transition to the ensemble behaviour characteristic of the solid state. Polymeric materials are also challenging owing to the statistical description of the average number of repeat units. Here we draw attention to the limitations of molecular formulae as predictive tools for achieving properties relevant to device performances. Illustrative examples highlight the relevance of organization across multiple length scales, and how device performances--although relevant for practical applications--poorly reflect the success of molecular design.

Design tools for complex dynamic security systems.

Energy Technology Data Exchange (ETDEWEB)

Byrne, Raymond Harry; Rigdon, James Brian; Rohrer, Brandon Robinson; Laguna, Glenn A.; Robinett, Rush D. III (.; ); Groom, Kenneth Neal; Wilson, David Gerald; Bickerstaff, Robert J.; Harrington, John J.

2007-01-01

The development of tools for complex dynamic security systems is not a straight forward engineering task but, rather, a scientific task where discovery of new scientific principles and math is necessary. For years, scientists have observed complex behavior but have had difficulty understanding it. Prominent examples include: insect colony organization, the stock market, molecular interactions, fractals, and emergent behavior. Engineering such systems will be an even greater challenge. This report explores four tools for engineered complex dynamic security systems: Partially Observable Markov Decision Process, Percolation Theory, Graph Theory, and Exergy/Entropy Theory. Additionally, enabling hardware technology for next generation security systems are described: a 100 node wireless sensor network, unmanned ground vehicle and unmanned aerial vehicle.

Molecular diagnosis and immunotherapy.

Science.gov (United States)

Sastre, Joaquín; Sastre-Ibañez, Marina

2016-12-01

To describe recent insights into how molecular diagnosis can improve indication and selection of suitable allergens for specific immunotherapy and increase the safety of this therapy. As specific allergen immunotherapy targets specific allergens, identification of the disease-eliciting allergen is a prerequisite for accurate prescription of treatment. In areas of complex sensitization to aeroallergens or in cases of hymenoptera venom allergy, the use of molecular diagnosis has demonstrated that it may lead to a change in indication and selection of allergens for immunotherapy in a large proportion of patients when compared with diagnosis based on skin prick testing and/or specific IgE determination with commercial extracts. These changes in immunotherapy prescription aided by molecular diagnosis have been demonstrated to be cost-effective in some scenarios. Certain patterns of sensitization to grass or olive pollen and bee allergens may identify patients with higher risk of adverse reaction during immunotherapy. Molecular diagnosis, when used with other tools and patients' clinical records, can help clinicians better to select the most appropriate patients and allergens for specific immunotherapy and, in some cases, predict the risk of adverse reactions. The pattern of sensitization to allergens could potentially predict the efficacy of allergen immunotherapy provided that these immunotherapy products contain a sufficient amount of these allergens. Nevertheless, multiplex assay remains a third-level approach, not to be used as screening method in current practice.

Archaeopteryx: Bringing the Dino-Bird to Life

Energy Technology Data Exchange (ETDEWEB)

Bergmann, Uwe

2011-01-25

Some 150 million years ago, a strange creature died in a tropical lagoon that today is located in Bavaria, Germany. In 1861, a single feather of this creature was discovered. Not long afterward, a complete fossil was found with the same bird-like feathers but dinosaur-like anatomical features. Darwin had just published 'On the Origin of Species'; could this be the missing link that Darwin's supporters hoped to find? Recently, two of the now eleven discovered Archaeopteryx fossils, and that first feather, were brought to SLAC, where, using the intense X-ray beam, researchers searched for the chemical remains of the original living creatures. Please join us for this lecture, which will explain how the studies attempt to bring the original dino-bird back to life.

The Wild-Card Character of "Bring Your Own:" A Panel Discussion

Science.gov (United States)

Campbell, W. Gardner; Fitch, Megan; German, Robert F., Jr.; Hulvey, Dale; McIntosh, Keith; McPherson, Michael R.; O'Keefe, John

2013-01-01

Panelists on the front lines of higher education information technology share their thoughts on Bring Your Own Device (BYOD) and what it could mean for colleges and universities. Five questions were asked of each panelist. These were: (1) How strategically important to higher education is the BYOD phenomenon? Is it simply a passing fad? (2) Should…

Bring Your Own Device--A Snapshot of Two Australian Primary Schools

Science.gov (United States)

Maher, Damian; Twining, Peter

2017-01-01

Background: The use of 1:1 and Bring Your Own Device strategies in schools is in its infancy and little is known about how mobile devices such as tablets are being used to support educational practice. Purpose: In this article, two suburban primary schools in Sydney, Australia were focused on with an aim to understand how mobile device strategies…

Molecular Imprinting Technology in Quartz Crystal Microbalance (QCM) Sensors

Science.gov (United States)

Emir Diltemiz, Sibel; Keçili, Rüstem; Ersöz, Arzu; Say, Rıdvan

2017-01-01

Molecularly imprinted polymers (MIPs) as artificial antibodies have received considerable scientific attention in the past years in the field of (bio)sensors since they have unique features that distinguish them from natural antibodies such as robustness, multiple binding sites, low cost, facile preparation and high stability under extreme operation conditions (higher pH and temperature values, etc.). On the other hand, the Quartz Crystal Microbalance (QCM) is an analytical tool based on the measurement of small mass changes on the sensor surface. QCM sensors are practical and convenient monitoring tools because of their specificity, sensitivity, high accuracy, stability and reproducibility. QCM devices are highly suitable for converting the recognition process achieved using MIP-based memories into a sensor signal. Therefore, the combination of a QCM and MIPs as synthetic receptors enhances the sensitivity through MIP process-based multiplexed binding sites using size, 3D-shape and chemical function having molecular memories of the prepared sensor system toward the target compound to be detected. This review aims to highlight and summarize the recent progress and studies in the field of (bio)sensor systems based on QCMs combined with molecular imprinting technology. PMID:28245588

Molecular Imprinting Technology in Quartz Crystal Microbalance (QCM Sensors

Directory of Open Access Journals (Sweden)

Sibel Emir Diltemiz

2017-02-01

Full Text Available Molecularly imprinted polymers (MIPs as artificial antibodies have received considerable scientific attention in the past years in the field of (biosensors since they have unique features that distinguish them from natural antibodies such as robustness, multiple binding sites, low cost, facile preparation and high stability under extreme operation conditions (higher pH and temperature values, etc.. On the other hand, the Quartz Crystal Microbalance (QCM is an analytical tool based on the measurement of small mass changes on the sensor surface. QCM sensors are practical and convenient monitoring tools because of their specificity, sensitivity, high accuracy, stability and reproducibility. QCM devices are highly suitable for converting the recognition process achieved using MIP-based memories into a sensor signal. Therefore, the combination of a QCM and MIPs as synthetic receptors enhances the sensitivity through MIP process-based multiplexed binding sites using size, 3D-shape and chemical function having molecular memories of the prepared sensor system toward the target compound to be detected. This review aims to highlight and summarize the recent progress and studies in the field of (biosensor systems based on QCMs combined with molecular imprinting technology.

Characterization of microbial communities in pest colonized books by molecular biology tools

OpenAIRE

Franco Palla

2011-01-01

This work presents the identification of bacteria and fungi colonies in insect infesting books, by cultural-independent methodologies based on molecular biology techniques. Microbial genomic DNA extraction, in vitro amplification of specific target sequences by polymerase chain reactions (PCR), sequencing and sequence analysis were performed. These procedures minimized the samples amount, optimized the diagnostic studies on bacteria and fungi colonization and allowed the identification of man...

Scoria: a Python module for manipulating 3D molecular data.

Science.gov (United States)

Ropp, Patrick; Friedman, Aaron; Durrant, Jacob D

2017-09-18

Third-party packages have transformed the Python programming language into a powerful computational-biology tool. Package installation is easy for experienced users, but novices sometimes struggle with dependencies and compilers. This presents a barrier that can hinder the otherwise broad adoption of new tools. We present Scoria, a Python package for manipulating three-dimensional molecular data. Unlike similar packages, Scoria requires no dependencies, compilation, or system-wide installation. One can incorporate the Scoria source code directly into their own programs. But Scoria is not designed to compete with other similar packages. Rather, it complements them. Our package leverages others (e.g. NumPy, SciPy), if present, to speed and extend its own functionality. To show its utility, we use Scoria to analyze a molecular dynamics trajectory. Our FootPrint script colors the atoms of one chain by the frequency of their contacts with a second chain. We are hopeful that Scoria will be a useful tool for the computational-biology community. A copy is available for download free of charge (Apache License 2.0) at http://durrantlab.com/scoria/ . Graphical abstract .

Rational Design of Molecular Gelator - Solvent Systems Guided by Solubility Parameters

Science.gov (United States)

Lan, Yaqi

Self-assembled architectures, such as molecular gels, have attracted wide interest among chemists, physicists and engineers during the past decade. However, the mechanism behind self-assembly remains largely unknown and no capability exists to predict a priori whether a small molecule will gelate a specific solvent or not. The process of self-assembly, in molecular gels, is intricate and must balance parameters influencing solubility and those contrasting forces that govern epitaxial growth into axially symmetric elongated aggregates. Although the gelator-gelator interactions are of paramount importance in understanding gelation, the solvent-gelator specific (i.e., H-bonding) and nonspecific (dipole-dipole, dipole-induced and instantaneous dipole induced forces) intermolecular interactions are equally important. Solvent properties mediate the self-assembly of molecular gelators into their self-assembled fibrillar networks. Herein, solubility parameters of solvents, ranging from partition coefficients (logP), to Henry's law constants (HLC), to solvatochromic ET(30) parameters, to Kamlet-Taft parameters (beta, alpha and pi), to Hansen solubility parameters (deltap, deltad, deltah), etc., are correlated with the gelation ability of numerous classes of molecular gelators. Advanced solvent clustering techniques have led to the development of a priori tools that can identify the solvents that will be gelled and not gelled by molecular gelators. These tools will greatly aid in the development of novel gelators without solely relying on serendipitous discoveries.

Use of molecular markers in plant breeding = [Het gebruik van moleculaire merkers in de plantenveredeling

NARCIS (Netherlands)

Berloo, van R.

2000-01-01

Molecular markers provide plant breeding with an important and valuable new source of information. Linkage between molecular markers can be translated to genetic linkage maps, which have become an important tool in plant and animal genetics. Linkage between (quantitative) trait-data and

Molecular Imprinting of Macromolecules for Sensor Applications.

Science.gov (United States)

Saylan, Yeşeren; Yilmaz, Fatma; Özgür, Erdoğan; Derazshamshir, Ali; Yavuz, Handan; Denizli, Adil

2017-04-19

Molecular recognition has an important role in numerous living systems. One of the most important molecular recognition methods is molecular imprinting, which allows host compounds to recognize and detect several molecules rapidly, sensitively and selectively. Compared to natural systems, molecular imprinting methods have some important features such as low cost, robustness, high recognition ability and long term durability which allows molecularly imprinted polymers to be used in various biotechnological applications, such as chromatography, drug delivery, nanotechnology, and sensor technology. Sensors are important tools because of their ability to figure out a potentially large number of analytical difficulties in various areas with different macromolecular targets. Proteins, enzymes, nucleic acids, antibodies, viruses and cells are defined as macromolecules that have wide range of functions are very important. Thus, macromolecules detection has gained great attention in concerning the improvement in most of the studies. The applications of macromolecule imprinted sensors will have a spacious exploration according to the low cost, high specificity and stability. In this review, macromolecules for molecularly imprinted sensor applications are structured according to the definition of molecular imprinting methods, developments in macromolecular imprinting methods, macromolecular imprinted sensors, and conclusions and future perspectives. This chapter follows the latter strategies and focuses on the applications of macromolecular imprinted sensors. This allows discussion on how sensor strategy is brought to solve the macromolecules imprinting.

Collaborative Inquiry Learning: Models, tools, and challenges

Science.gov (United States)

Bell, Thorsten; Urhahne, Detlef; Schanze, Sascha; Ploetzner, Rolf

2010-02-01

Collaborative inquiry learning is one of the most challenging and exciting ventures for today's schools. It aims at bringing a new and promising culture of teaching and learning into the classroom where students in groups engage in self-regulated learning activities supported by the teacher. It is expected that this way of learning fosters students' motivation and interest in science, that they learn to perform steps of inquiry similar to scientists and that they gain knowledge on scientific processes. Starting from general pedagogical reflections and science standards, the article reviews some prominent models of inquiry learning. This comparison results in a set of inquiry processes being the basis for cooperation in the scientific network NetCoIL. Inquiry learning is conceived in several ways with emphasis on different processes. For an illustration of the spectrum, some main conceptions of inquiry and their focuses are described. In the next step, the article describes exemplary computer tools and environments from within and outside the NetCoIL network that were designed to support processes of collaborative inquiry learning. These tools are analysed by describing their functionalities as well as effects on student learning known from the literature. The article closes with challenges for further developments elaborated by the NetCoIL network.

CISP: Simulation Platform for Collective Instabilities in the BRing of HIAF project

Science.gov (United States)

Liu, J.; Yang, J. C.; Xia, J. W.; Yin, D. Y.; Shen, G. D.; Li, P.; Zhao, H.; Ruan, S.; Wu, B.

2018-02-01

To simulate collective instabilities during the complicated beam manipulation in the BRing (Booster Ring) of HIAF (High Intensity heavy-ion Accelerator Facility) or other high intensity accelerators, a code, named CISP (Simulation Platform for Collective Instabilities), is designed and constructed in China's IMP (Institute of Modern Physics). The CISP is a scalable multi-macroparticle simulation platform that can perform longitudinal and transverse tracking when chromaticity, space charge effect, nonlinear magnets and wakes are included. And due to its well object-oriented design, the CISP is also a basic platform used to develop many other applications (like feedback). Several simulations, completed by the CISP in this paper, agree with analytical results very well, which shows that the CISP is fully functional now and it is a powerful platform for the further collective instability research in the BRing or other accelerators. In the future, the CISP can also be extended easily into a physics control system for HIAF or other facilities.

Molecular Dynamics: New Frontier in Personalized Medicine.

Science.gov (United States)

Sneha, P; Doss, C George Priya

2016-01-01

The field of drug discovery has witnessed infinite development over the last decade with the demand for discovery of novel efficient lead compounds. Although the development of novel compounds in this field has seen large failure, a breakthrough in this area might be the establishment of personalized medicine. The trend of personalized medicine has shown stupendous growth being a hot topic after the successful completion of Human Genome Project and 1000 genomes pilot project. Genomic variant such as SNPs play a vital role with respect to inter individual's disease susceptibility and drug response. Hence, identification of such genetic variants has to be performed before administration of a drug. This process requires high-end techniques to understand the complexity of the molecules which might bring an insight to understand the compounds at their molecular level. To sustenance this, field of bioinformatics plays a crucial role in revealing the molecular mechanism of the mutation and thereby designing a drug for an individual in fast and affordable manner. High-end computational methods, such as molecular dynamics (MD) simulation has proved to be a constitutive approach to detecting the minor changes associated with an SNP for better understanding of the structural and functional relationship. The parameters used in molecular dynamic simulation elucidate different properties of a macromolecule, such as protein stability and flexibility. MD along with docking analysis can reveal the synergetic effect of an SNP in protein-ligand interaction and provides a foundation for designing a particular drug molecule for an individual. This compelling application of computational power and the advent of other technologies have paved a promising way toward personalized medicine. In this in-depth review, we tried to highlight the different wings of MD toward personalized medicine. © 2016 Elsevier Inc. All rights reserved.

Rose George: Deep Sea and Foreign Going: Inside Shipping, the Invisible Industry that Brings you 90% of Everything

DEFF Research Database (Denmark)

Taudal Poulsen, René

2014-01-01

Book review of: Rose George: Deep Sea and Foreign Going: Inside Shipping, the Invisible Industry that Brings you 90% of Everything. London :Portobello Books, 2013. 320 pp. ISBN 9781846272639......Book review of: Rose George: Deep Sea and Foreign Going: Inside Shipping, the Invisible Industry that Brings you 90% of Everything. London :Portobello Books, 2013. 320 pp. ISBN 9781846272639...

Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of Oncidium Gower Ramsey

Directory of Open Access Journals (Sweden)

Tung Shu-Yun

2011-04-01

Full Text Available Abstract Background Orchids comprise one of the largest families of flowering plants and generate commercially important flowers. However, model plants, such as Arabidopsis thaliana do not contain all plant genes, and agronomic and horticulturally important genera and species must be individually studied. Results Several molecular biology tools were used to isolate flower-specific gene promoters from Oncidium 'Gower Ramsey' (Onc. GR. A cDNA library of reproductive tissues was used to construct a microarray in order to compare gene expression in flowers and leaves. Five genes were highly expressed in flower tissues, and the subcellular locations of the corresponding proteins were identified using lip transient transformation with fluorescent protein-fusion constructs. BAC clones of the 5 genes, together with 7 previously published flower- and reproductive growth-specific genes in Onc. GR, were identified for cloning of their promoter regions. Interestingly, 3 of the 5 novel flower-abundant genes were putative trypsin inhibitor (TI genes (OnTI1, OnTI2 and OnTI3, which were tandemly duplicated in the same BAC clone. Their promoters were identified using transient GUS reporter gene transformation and stable A. thaliana transformation analyses. Conclusions By combining cDNA microarray, BAC library, and bombardment assay techniques, we successfully identified flower-directed orchid genes and promoters.

Building bridges between cellular and molecular structural biology.

Science.gov (United States)

Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J

2017-07-06

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

Public - private interdependence: An effective tool in water supply services

Directory of Open Access Journals (Sweden)

Ana Elena Iosif

2014-11-01

Full Text Available The paper aims to study the impact of certain determinants on the choice of local authorities to use public - private interdependence for the provision of water supply services, based on the Spanish and Romanian local experiences. Being aware of their impact, the authorities could place a particular focus on the determinants that lead to local development. Several studies reveal that public – private interdependence is a powerful tool for building local development (Melo & do Carmo, 2008; Dessi & Floris, 2009 and states are interested in finding out ways to obtain it. The complex methodology of the paper was designed in accordance with the particularities of each country studied. Gathering the data for Romania implied conducting several interviews, and for Spain survey, exploratory analysis and semi-structured interviews were applied. The determinants’ influence was tested through logit or linear probability model. The analysis validates that population, density of population, indirect taxes, affiliation of the city representative to a certain political party is influencing the option of local public authorities. The paper brings recommendations on promoting public - private interdependence in water supply services. The paper is mainly valuable for the parallel that is made between Spain and Romania in water supply services and it brings progress in comparative country cases.

DNA-based molecular markers as tools for the discovery of γ-induced mutants in cereals and soybean

International Nuclear Information System (INIS)

Bondarenco, E.; Bondarenco, V.; Barbacar, N.; Coretchi, L.

2009-01-01

γ-induced mutagenesis is one of the present techniques effective in producing crops with enhanced quality and novel properties. The fast detection of mutants can be nowadays assured by the employment of DNA-based molecular markers. Different kinds of molecular markers are being widely used all over the world to monitor DNA sequence variation and identification of desired traits. In the given paper we present a short overview of the types of molecular markers and the first steps of the attempt of their use for mutants' characterization in the Republic of Moldova (authors)

Multi-tissue RNA-seq and transcriptome characterisation of the spiny dogfish shark (Squalus acanthias) provides a molecular tool for biological research and reveals new genes involved in osmoregulation

DEFF Research Database (Denmark)

Chana Munoz, Andres; Jendroszek, Agnieszka; Sønnichsen, Malene

2017-01-01

The spiny dogfish shark (Squalus acanthias) is one of the most commonly used cartilaginous fishes in biological research, especially in the fields of nitrogen metabolism, ion transporters and osmoregulation. Nonetheless, transcriptomic data for this organism is scarce. In the present study, a multi......-tissue RNA-seq experiment and de novo transcriptome assembly was performed in four different spiny dogfish tissues (brain, liver, kidney and ovary), providing an annotated sequence resource. The characterization of the transcriptome greatly increases the scarce sequence information for shark species. Reads...... and provides a new molecular tool to assist biological research in cartilaginous fishes....

Bring back the Glory!

Directory of Open Access Journals (Sweden)

James Q. Whitman

2004-01-01

Full Text Available This paper, drafted in response to Dr. Kiesow’s question, »Wozu Rechtsgeschichte?«, begins with a backward glance at the nineteenth century, when legal history played a leading role in the intellectual life of the western world. Since those great days, when legal history attracted figures like Karl Marx and Max Weber, the field has fallen on hard times. This is in large part the inevitable consequence of the declining prestige of law itself, which no longer seems to matter in the way that it did in the nineteenth century. Nevertheless, the paper pleads for something of a Return of Grand Theory in legal history. It is true that we can never bring back the glory years. But we can be figures of importance in the public debates of our time if we remain mindful of what it is that gives law itself its enduring social importance. Law reflects, in an unsystematic but telling way, some of the basic value commitments of society-commitments such as the contemporary American commitment to the free market, or the contemporary European commitment to »human dignity«. Law also reflects stylized histories of a given society’s past-histories like that of the American triumph over race slavery, or the European triumph over Nazism. These value commitments and stylized histories are the natural territory of legal historians, who can best claim a role for themselves in public debate if they think of themselves as historians of values, rather than as historians of social realities.

Observational Constraints for Modeling Diffuse Molecular Clouds

Science.gov (United States)

Federman, S. R.

2014-02-01

Ground-based and space-borne observations of diffuse molecular clouds suggest a number of areas where further improvements to modeling efforts is warranted. I will highlight those that have the widest applicability. The range in CO fractionation caused by selective isotope photodissociation, in particular the large 12C16O/13C16O ratios observed toward stars in Ophiuchus, is not reproduced well by current models. Our ongoing laboratory measurements of oscillator strengths and predissociation rates for Rydberg transitions in CO isotopologues may help clarify the situtation. The CH+ abundance continues to draw attention. Small scale structure seen toward ζ Per may provide additional constraints on the possible synthesis routes. The connection between results from optical transitions and those from radio and sub-millimeter wave transitions requires further effort. A study of OH+ and OH toward background stars reveals that these species favor different environments. This brings to focus the need to model each cloud along the line of sight separately, and to allow the physical conditions to vary within an individual cloud, in order to gain further insight into the chemistry. Now that an extensive set of data on molecular excitation is available, the models should seek to reproduce these data to place further constraints on the modeling results.

Assessing Date Palm Genetic Diversity Using Different Molecular Markers.

Science.gov (United States)

Atia, Mohamed A M; Sakr, Mahmoud M; Adawy, Sami S

2017-01-01

Molecular marker technologies which rely on DNA analysis provide powerful tools to assess biodiversity at different levels, i.e., among and within species. A range of different molecular marker techniques have been developed and extensively applied for detecting variability in date palm at the DNA level. Recently, the employment of gene-targeting molecular marker approaches to study biodiversity and genetic variations in many plant species has increased the attention of researchers interested in date palm to carry out phylogenetic studies using these novel marker systems. Molecular markers are good indicators of genetic distances among accessions, because DNA-based markers are neutral in the face of selection. Here we describe the employment of multidisciplinary molecular marker approaches: amplified fragment length polymorphism (AFLP), start codon targeted (SCoT) polymorphism, conserved DNA-derived polymorphism (CDDP), intron-targeted amplified polymorphism (ITAP), simple sequence repeats (SSR), and random amplified polymorphic DNA (RAPD) to assess genetic diversity in date palm.

Descendit ad [in] inferna:'A matter of no small moment in bringing ...

African Journals Online (AJOL)

Descendit ad [in] inferna:'A matter of no small moment in bringing about redemption' ... and make one suspicious about certain ecclesiastical biases. Spatial terms in the Creed should therefore not be demythologised, but rather be transformed in accordance with the insights of the contemporary physics of time and space.

Explore: An Action to Bring Science and Technology Closer to Secondary School

Science.gov (United States)

Torras-Melenchon, Nuria; Grau, M. Dolors; Font-Soldevila, Josep; Freixas, Josep

2015-01-01

This paper presents the experience of an initiative, the EXPLORE courses, designed to bring science and technology closer to secondary school. The EXPLORE courses, organised by "EXPLORATORI: Natural Resources" project, are particularly addressed to secondary school teachers and are conducted at Catalonia (North East of Spain). The main…

Developing a web page: bringing clinics online.

Science.gov (United States)

Peterson, Ronnie; Berns, Susan

2004-01-01

Introducing clinical staff education, along with new policies and procedures, to over 50 different clinical sites can be a challenge. As any staff educator will confess, getting people to attend an educational inservice session can be difficult. Clinical staff request training, but no one has time to attend training sessions. Putting the training along with the policies and other information into "neat" concise packages via the computer and over the company's intranet was the way to go. However, how do you bring the clinics online when some of the clinical staff may still be reluctant to turn on their computers for anything other than to gather laboratory results? Developing an easy, fun, and accessible Web page was the answer. This article outlines the development of the first training Web page at the University of Wisconsin Medical Foundation, Madison, WI.

APT, The Phase I tool for HST Cycle 12

Science.gov (United States)

Blacker, Brett S.; Bertch, Maria; Curtis, Gary; Douglas, Robert E., Jr.; Krueger, Anthony P.

2002-12-01

In the continuing effort to streamline our systems and improve service to the science community, the Space Telescope Science Institute (STScI) is developing and releasing, APT The Astronomer’s Proposal Tool as the new interface for Hubble Space Telescope (HST) Phase I and Phase II proposal submissions for HST Cycle 12. APT, was formerly called the Scientist’s Expert Assistant (SEA), which started as a prototype effort to try and bring state of the art technology, more visual tools and power into the hands of proposers so that they can optimize the scientific return of their programs as well as HST. Proposing for HST and other missions, consists of requesting observing time and/or archival research funding. This step is called Phase I, where the scientific merit of a proposal is considered by a community based peer-review process. Accepted proposals then proceed thru Phase II, where the observations are specified in sufficient detail to enable scheduling on the telescope. In this paper, we will present our concept and implementation plans for our Phase I development and submission tool, APT. More importantly, we will go behind the scenes and discuss why it’s important for the Science Policies Division (SPD) and other groups at the STScI to have a new submission tool and submission output products. This paper is an update of the status of the HST Phase I Proposal Processing System that was described in the published paper “A New Era for HST Phase I Development and Submission.”

Interdisciplinary research center devoted to molecular environmental science opens

Science.gov (United States)

Vaughan, David J.

In October, a new research center opened at the University of Manchester in the United Kingdom. The center is the product of over a decade of ground-breaking interdisciplinary research in the Earth and related biological and chemical sciences at the university The center also responds to the British governments policy of investing in research infrastructure at key universities.The Williamson Research Centre, the first of its kind in Britain and among the first worldwide, is devoted to the emerging field of molecular environmental science. This field also aims to bring about a revolution in understanding of our environment. Though it may be a less violent revolution than some, perhaps, its potential is high for developments that could affect us all.

Atomdroid: a computational chemistry tool for mobile platforms.

Science.gov (United States)

Feldt, Jonas; Mata, Ricardo A; Dieterich, Johannes M

2012-04-23

We present the implementation of a new molecular mechanics program designed for use in mobile platforms, the first specifically built for these devices. The software is designed to run on Android operating systems and is compatible with several modern tablet-PCs and smartphones available in the market. It includes molecular viewer/builder capabilities with integrated routines for geometry optimizations and Monte Carlo simulations. These functionalities allow it to work as a stand-alone tool. We discuss some particular development aspects, as well as the overall feasibility of using computational chemistry software packages in mobile platforms. Benchmark calculations show that through efficient implementation techniques even hand-held devices can be used to simulate midsized systems using force fields.

Molecular diversity of avian schistosomes in Danish freshwater snails

DEFF Research Database (Denmark)

Christiansen, Anne Ø.; Olsen, Annette; Buchmann, Kurt

2016-01-01

Avian schistosomes are widespread parasites of snails and waterfowl and may cause cercarial dermatitis (swimmer's itch) in humans, a disease that is frequently reported in European countries. These parasites are known to occur in Denmark, but here, we applied a new approach using molecular tools ...

Consumer Advertising: Its Role in Bringing a Product to Market. Revised Edition.

Science.gov (United States)

Procter and Gamble Educational Services, Cincinnati, OH.

This kit, designed for high school classes, considers advertising from both consumers' and manufacturers' perspectives. The role of advertising in relation to free enterprise principles is discussed in chapter 1, while chapter 2 provides a history of U.S. advertising processes and development. Chapter 3 describes advertising's role in bringing a…

Nested-PCR real time as alternative molecular tool for detection of Borrelia burgdorferi compared to the classical serological diagnosis of the blood.

Science.gov (United States)

Sroka-Oleksiak, Agnieszka; Ufir, Krzysztof; Salamon, Dominika; Bulanda, Malgorzata; Gosiewski, Tomasz

Lyme disease, caused by Borrelia burgdorferi, is a multisystem disease that often makes difficulties to recognize caused by their genetic heterogenity. Currently, the gold standard for the detection of Lyme disease (LD) is serologic diagnostics based mainly on tests: ELISA and Western blot (WB). These methods, however, are subject to consider- able defect, especially in the initial phase of infection due to the occurrence of so-called serological window period and low specificity. For this reason, they might be replaced by molecular methods, for example polymerase chain reaction (PCR), which should be more sensitivity and specificity. In the present study we attempt to optimize the PCR reaction conditions and enhance existing test sensitivity by applying the equivalent of real time PCR - nested PCR for detection B. burgdorferi DNA in the patient's blood. The study involved 94 blood samples of patients with suspected LD. From each sample, 1.5 ml of blood was used for the isolation of bacterial DNA and PCR real time am- plification and its equivalent, in nested version. The remaining part earmarked for serologi- cal testing. Optimization of the reaction conditions made experimentally, using gradient of the temperature and gradient of the magnesium ions concentration for reaction real time in nested-PCR and PCR version. The results show that the nested-PCR real time, has a much higher sensitivity 45 (47.8%) of positive results for the detection of B. burgdorferi compared to the single- variety, without a preceding pre-amplification 2 (2.1%). Serological methods allowed the detection of infection in 41 (43.6%) samples. These results support of the nested PCR method as a better molecular tool for the detection of B. burgdorferi infection than classical PCR real time reaction. The nested-PCR real time method may be considered as a complement to ELISA and WB mainly in the early stages of infection, when in the blood circulating B. burgdorferi cells. By contrast, the

Bringing science to the policy table

CERN Multimedia

2014-01-01

“They shall beat their swords into plowshares, and their spears into pruning hooks. Nation shall not lift up sword against nation. Neither shall they learn war anymore." So says Isaiah 2:4, as transcribed on the famous wall in Ralph Bunche park, just the other side of 1st Avenue from the UN’s New York headquarters, where we held a celebration of our 60th anniversary year on Monday 20 October. I used the quotation in my opening address, since it is such a perfect fit to the theme of 60 years of science for peace and development.   The event was organised with the United Nations Economic and Social Council, ECOSOC, in the framework of CERN’s observer status at the UN, and although focused on CERN, its aim was broader. Presentations used CERN as an example to bring out the vital importance of science in general to the themes of peace and development. The event was presided over by Martin Sajdik, President of ECOSOC, and we were privileged to have presentat...

Poster power brings together electronics community

CERN Multimedia

2006-01-01

An 'Electronics at CERN' poster session was displayed on the mezzanine in building 500 for two days from 30 November. The display consisted of 20 posters and brought together a wide range of electronic projects designed and assembled by CERN teams and other collaborators involved in the building of the LHC. This was the first time this event had been held. As its organiser John Evans (IT/DES) explained, 'the idea came from the experience of attending conferences outside CERN, where you may find projects from CERN you didn't know about. It's nice to bring them together so we can all benefit from the efforts made.' The work on show spanned different departments and experiments, ranging from microelectronics to equipment designed for giant magnets. The invited audience was equally broad and included engineers, physicists as well as the electronics community at CERN. An informal gathering of all the exhibitors also offered an opportunity to view and discuss the work over a cup of coffee. 'The poster session acts...

Advances in Molecular Rotational Spectroscopy for Applied Science

Science.gov (United States)

Harris, Brent; Fields, Shelby S.; Pulliam, Robin; Muckle, Matt; Neill, Justin L.

2017-06-01

Advances in chemical sensitivity and robust, solid-state designs for microwave/millimeter-wave instrumentation compel the expansion of molecular rotational spectroscopy as research tool into applied science. It is familiar to consider molecular rotational spectroscopy for air analysis. Those techniques for molecular rotational spectroscopy are included in our presentation of a more broad application space for materials analysis using Fourier Transform Molecular Rotational Resonance (FT-MRR) spectrometers. There are potentially transformative advantages for direct gas analysis of complex mixtures, determination of unknown evolved gases with parts per trillion detection limits in solid materials, and unambiguous chiral determination. The introduction of FT-MRR as an alternative detection principle for analytical chemistry has created a ripe research space for the development of new analytical methods and sampling equipment to fully enable FT-MRR. We present the current state of purpose-built FT-MRR instrumentation and the latest application measurements that make use of new sampling methods.

Molecular and radiological diagnosis of sclerosing bone dysplasias

International Nuclear Information System (INIS)

Hul, Wim van; Vanhoenacker, Filip; Balemans, Wendy; Janssens, Katrien; Schepper, A.M. de

2001-01-01

Bone mineral density (BMD) is a quantitative trait for which the heritability of the variance is estimated to be up to 80%, based on epidemiological and twin studies. Further illustration of the involvement of genetic factors in bone homeostasis, is the existence of an extended group of genetic conditions associated with an abnormal bone density. The group of conditions with increased bone density has long been poorly studied and understood at the molecular genetic level but recently, thanks to recent developments in molecular genetics and genomics, for some of them major breakthroughs have been made. These findings will make the molecular analysis of such patients an additional tool in diagnostics and in genetic counseling. However, the initial identification of affected patients is still largely dependent upon recognition of clinical and radiological stigmata of the disease. Therefore, in this overview of sclerosing bone dysplasias, the classical clinical and radiological signs of this group of disorders will be discussed along with the new molecular insights

Molecular and radiological diagnosis of sclerosing bone dysplasias

Energy Technology Data Exchange (ETDEWEB)

Hul, Wim van E-mail: vhul@uia.ac.be; Vanhoenacker, Filip; Balemans, Wendy; Janssens, Katrien; Schepper, A.M. de

2001-12-01

Bone mineral density (BMD) is a quantitative trait for which the heritability of the variance is estimated to be up to 80%, based on epidemiological and twin studies. Further illustration of the involvement of genetic factors in bone homeostasis, is the existence of an extended group of genetic conditions associated with an abnormal bone density. The group of conditions with increased bone density has long been poorly studied and understood at the molecular genetic level but recently, thanks to recent developments in molecular genetics and genomics, for some of them major breakthroughs have been made. These findings will make the molecular analysis of such patients an additional tool in diagnostics and in genetic counseling. However, the initial identification of affected patients is still largely dependent upon recognition of clinical and radiological stigmata of the disease. Therefore, in this overview of sclerosing bone dysplasias, the classical clinical and radiological signs of this group of disorders will be discussed along with the new molecular insights.

Individual Biomarkers Using Molecular Personalized Medicine Approaches.

Science.gov (United States)

Zenner, Hans P

2017-01-01

Molecular personalized medicine tries to generate individual predictive biomarkers to assist doctors in their decision making. These are thought to improve the efficacy and lower the toxicity of a treatment. The molecular basis of the desired high-precision prediction is modern "omex" technologies providing high-throughput bioanalytical methods. These include genomics and epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, imaging, and functional analyses. In most cases, producing big data also requires a complex biomathematical analysis. Using molecular personalized medicine, the conventional physician's check of biomarker results may no longer be sufficient. By contrast, the physician may need to cooperate with the biomathematician to achieve the desired prediction on the basis of the analysis of individual big data typically produced by omex technologies. Identification of individual biomarkers using molecular personalized medicine approaches is thought to allow a decision-making for the precise use of a targeted therapy, selecting the successful therapeutic tool from a panel of preexisting drugs or medical products. This should avoid the treatment of nonresponders and responders that produces intolerable unwanted effects. © 2017 S. Karger AG, Basel.

New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0.

Science.gov (United States)

Clark, Alex M; Sarker, Malabika; Ekins, Sean

2014-01-01

We recently developed a freely available mobile app (TB Mobile) for both iOS and Android platforms that displays Mycobacterium tuberculosis (Mtb) active molecule structures and their targets with links to associated data. The app was developed to make target information available to as large an audience as possible. We now report a major update of the iOS version of the app. This includes enhancements that use an implementation of ECFP_6 fingerprints that we have made open source. Using these fingerprints, the user can propose compounds with possible anti-TB activity, and view the compounds within a cluster landscape. Proposed compounds can also be compared to existing target data, using a näive Bayesian scoring system to rank probable targets. We have curated an additional 60 new compounds and their targets for Mtb and added these to the original set of 745 compounds. We have also curated 20 further compounds (many without targets in TB Mobile) to evaluate this version of the app with 805 compounds and associated targets. TB Mobile can now manage a small collection of compounds that can be imported from external sources, or exported by various means such as email or app-to-app inter-process communication. This means that TB Mobile can be used as a node within a growing ecosystem of mobile apps for cheminformatics. It can also cluster compounds and use internal algorithms to help identify potential targets based on molecular similarity. TB Mobile represents a valuable dataset, data-visualization aid and target prediction tool.

High-throughput SNP genotyping: combining tag SNPs and molecular beacons

CSIR Research Space (South Africa)

Barreiro, LB

2009-10-01

Full Text Available In the last decade, molecular beacons have emerged to become a widely used tool in the multiplex typing of single nucleotide polymorphisms (SNPs). Improvements in detection technologies in instrumentation and chemistries to label these probes have...

White piedra: molecular identification of Trichosporon inkin in members of the same family.

Science.gov (United States)

Richini-Pereira, Virgínia Bodelão; Camargo, Rosângela Maria Pires de; Bagagli, Eduardo; Marques, Silvio Alencar

2012-06-01

White piedra is a superficial mycosis caused by the genus Trichosporon and characterized by nodules on hair shaft. The authors report a family referred to as pediculosis. Mycological culture on Mycosel® plus molecular identification was performed to precisely identify the etiology. A Trichosporon spp. infection was revealed. The molecular procedure identified the agent as Trichosporon inkin. White piedra and infection caused by T. inkin are rarely reported in Southern Brazil. The molecular tools are essentials on identifying the Trichosporon species.

Lanthanides in molecular magnetism: old tools in a new field.

Science.gov (United States)

Sorace, Lorenzo; Benelli, Cristiano; Gatteschi, Dante

2011-06-01

In this tutorial review we discuss some basic aspects concerning the magnetic properties of rare-earth ions, which are currently the subject of a renovated interest in the field of molecular magnetism, after the discovery that slow relaxation of the magnetization at liquid nitrogen temperature can occur in mononuclear complexes of these ions. Focusing on Dy(III) derivatives a tutorial discussion is given of the relation of the crystal field parameters, which determine the anisotropy of these systems and consequently their interesting magnetic properties, with the geometry of the coordination sphere around the lanthanide centre and with the pattern of f orbitals. The problem of systems of low point symmetry is also addressed by showing how detailed single crystal investigation, coupled to more sophisticated calculation procedures, is an absolute necessity to obtain meaningful structure-property relationships in these systems.

Development of remote pipe cutting tool for divertor cassettes in JT-60SA

International Nuclear Information System (INIS)

Hayashi, Takao; Sakurai, Shinji; Shibanuma, Kiyoshi; Sakasai, Akira

2014-01-01

Remote pipe cutting tool accessing from inside pipe has been newly developed for JT-60SA. The tool head equips a disk-shaped cutter blade and four rollers which are subjected to the reaction force. The tool pushes out the cutter blade by decreasing the distance between two cams. The tool cuts a cooling pipe by both pushing out the cutter blade and rotating the tool head itself. The roller holder is not pushed out anymore after touching the inner wall of the pipe. In other words, only cutter blade is pushed out after bringing the tool axis into the pipe axis. Outer diameter of the cutting tool head is 44 mm. The cutting tool is able to push out the cutter blade up to 32.5 mm in radius, i.e. 65 mm in diameter, which is enough to cut the pipe having an outer diameter of 59.8 mm. The thickness and material of the cooling pipe are 2.8 mm and SUS316L, respectively. The length of the cutting tool head is about 1 m. The tool is able to cut a pipe locates about 480 mm in depth from the mounting surface on the divertor cassette. The pipe cutting system equips two cutting heads and they are able to cut two pipes at the same time in order to remove the inner target plate. Reproducibility of the cross-sectional shape of the cut pipe is required for re-welding. The degree of reproducibility is inside 0.1 mm except for burr at outside of the pipe, which is enough to re-weld the cut pipe. Some swarf is generated during cutting the double-layered pipe assuming a plug located on the top of the pipe. The swarf is deposited on the bottom of the plug and collected by pulling out the plug in the actual equipment

Bringing Science to Life for Students, Teachers and the Community

Science.gov (United States)

Pratt, K.

2012-04-01

Bringing Science to Life for Students, Teachers and the Community Prior to 2008, 5th grade students at two schools of the New Haven Unified School District consistently scored in the bottom 20% of the California State Standards Test for science. Teachers in the upper grades reported not spending enough time teaching science, which is attributed to lack of time, resources or knowledge of science. A proposal was written to the National Oceanic and Atmospheric Administration's Bay Watershed Education Grant program and funding was received for Bringing Science to Life for Students, Teachers and the Community to address these concerns and instill a sense of stewardship in our students. This program engages and energizes students in learning science and the protection of the SF Bay Watershed, provides staff development for teachers, and educates the community about conservation of our local watershed. The project includes a preparation phase, outdoor phase, an analysis and reporting phase, and teacher training and consists of two complete units: 1) The San Francisco Bay Watershed Unit and 2) the Marine Environment Unit. At the end of year 5, our teachers were teaching more science, the community was engaged in conservation of the San Francisco Bay Watershed and most importantly, student scores increased on the California Science Test at one site by over 121% and another site by 152%.

Pydna: a simulation and documentation tool for DNA assembly strategies using python.

Science.gov (United States)

Pereira, Filipa; Azevedo, Flávio; Carvalho, Ângela; Ribeiro, Gabriela F; Budde, Mark W; Johansson, Björn

2015-05-02

Recent advances in synthetic biology have provided tools to efficiently construct complex DNA molecules which are an important part of many molecular biology and biotechnology projects. The planning of such constructs has traditionally been done manually using a DNA sequence editor which becomes error-prone as scale and complexity of the construction increase. A human-readable formal description of cloning and assembly strategies, which also allows for automatic computer simulation and verification, would therefore be a valuable tool. We have developed pydna, an extensible, free and open source Python library for simulating basic molecular biology DNA unit operations such as restriction digestion, ligation, PCR, primer design, Gibson assembly and homologous recombination. A cloning strategy expressed as a pydna script provides a description that is complete, unambiguous and stable. Execution of the script automatically yields the sequence of the final molecule(s) and that of any intermediate constructs. Pydna has been designed to be understandable for biologists with limited programming skills by providing interfaces that are semantically similar to the description of molecular biology unit operations found in literature. Pydna simplifies both the planning and sharing of cloning strategies and is especially useful for complex or combinatorial DNA molecule construction. An important difference compared to existing tools with similar goals is the use of Python instead of a specifically constructed language, providing a simulation environment that is more flexible and extensible by the user.

Managing and monitoring tuberculosis using web-based tools in combination with traditional approaches.

Science.gov (United States)

Chapman, Ann Ln; Darton, Thomas C; Foster, Rachel A

2013-01-01

Tuberculosis (TB) remains a global health emergency. Ongoing challenges include the coordination of national and international control programs, high levels of drug resistance in many parts of the world, and availability of accurate and rapid diagnostic tests. The increasing availability and reliability of Internet access throughout both affluent and resource-limited countries brings new opportunities to improve TB management and control through the integration of web-based technologies with traditional approaches. In this review, we explore current and potential future use of web-based tools in the areas of TB diagnosis, treatment, epidemiology, service monitoring, and teaching and training.

Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection

Science.gov (United States)

Cox, Courtney E.; Phifer, Jeremy R.; Ferreira da Silva, Larissa; Gonçalves Nogueira, Gabriel; Ley, Ryan T.; O'Loughlin, Elizabeth J.; Pereira Barbosa, Ana Karolyne; Rygelski, Brett T.; Paluch, Andrew S.

2017-02-01

Solubility parameter based methods have long been a valuable tool for solvent formulation and selection. Of these methods, the MOdified Separation of Cohesive Energy Density (MOSCED) has recently been shown to correlate well the equilibrium solubility of multifunctional non-electrolyte solids. However, before it can be applied to a novel solute, a limited amount of reference solubility data is required to regress the necessary MOSCED parameters. Here we demonstrate for the solutes methylparaben, ethylparaben, propylparaben, butylparaben, lidocaine and ephedrine how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here the SMD or SM8 solvation model, can instead be used to generate the necessary reference data, resulting in a predictive flavor of MOSCED. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. We find the method is able to well correlate the (mole fraction) equilibrium solubility in non-aqueous solvents over four orders of magnitude with good quantitative agreement.

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.

Science.gov (United States)

Kumar, Sudhir; Stecher, Glen; Li, Michael; Knyaz, Christina; Tamura, Koichiro

2018-06-01

The Molecular Evolutionary Genetics Analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.

Bringing Vision to Practice: Planning and Provisioning the New Library Resource Center

Science.gov (United States)

Wilson, Lisa

2004-01-01

The most critical factor in creating a successful school library is the development of a clear vision of the mission and functionality of this integral learning space. However, the process of bringing a vision to realization involves harsh realities and sensible planning. The budget will determine many purchasing decisions and therefore it is…

Brown Spider (Loxosceles genus Venom Toxins: Tools for Biological Purposes

Directory of Open Access Journals (Sweden)

Andrea Senff-Ribeiro

2011-03-01

Full Text Available Venomous animals use their venoms as tools for defense or predation. These venoms are complex mixtures, mainly enriched of proteic toxins or peptides with several, and different, biological activities. In general, spider venom is rich in biologically active molecules that are useful in experimental protocols for pharmacology, biochemistry, cell biology and immunology, as well as putative tools for biotechnology and industries. Spider venoms have recently garnered much attention from several research groups worldwide. Brown spider (Loxosceles genus venom is enriched in low molecular mass proteins (5–40 kDa. Although their venom is produced in minute volumes (a few microliters, and contain only tens of micrograms of protein, the use of techniques based on molecular biology and proteomic analysis has afforded rational projects in the area and permitted the discovery and identification of a great number of novel toxins. The brown spider phospholipase-D family is undoubtedly the most investigated and characterized, although other important toxins, such as low molecular mass insecticidal peptides, metalloproteases and hyaluronidases have also been identified and featured in literature. The molecular pathways of the action of these toxins have been reported and brought new insights in the field of biotechnology. Herein, we shall see how recent reports describing discoveries in the area of brown spider venom have expanded biotechnological uses of molecules identified in these venoms, with special emphasis on the construction of a cDNA library for venom glands, transcriptome analysis, proteomic projects, recombinant expression of different proteic toxins, and finally structural descriptions based on crystallography of toxins.

Atomic Force Microscopy - A Tool to Unveil the Mystery of Biological ...

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 7. Atomic Force Microscopy - A Tool to Unveil the Mystery of Biological Systems ... Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560 ...

Cloning Yeast Actin cDNA Leads to an Investigative Approach for the Molecular Biology Laboratory

Science.gov (United States)

Black, Michael W.; Tuan, Alice; Jonasson, Erin

2008-01-01

The emergence of molecular tools in multiple disciplines has elevated the importance of undergraduate laboratory courses that train students in molecular biology techniques. Although it would also be desirable to provide students with opportunities to apply these techniques in an investigative manner, this is generally not possible in the…

Molecular characterization of olive cultivars grown in Iraq using ...

African Journals Online (AJOL)

The results of this research confirmed AFLP and SSR to be useful tools in genetic relationships among olive cultivars, in creating a molecular database for Iraqi olive cultivars, in breeding strategies and in correct cultivar identification. Keywords: Olea europaea, genetic diversity, amplified fragment length polymorphism ...

BioVersys Works to Bring Antibiotic Resistance to an End.

Science.gov (United States)

Tigges, Marcel; Gitzinger, Marc

2014-12-01

BioVersys, founded in 2008, is working on bringing a technology for screening and for the development of 'transcriptional regulator inhibiting compounds' (TRICs) to patients in order to overcome antibiotic resistance. The co-founders share their view on what makes successful scientists pursue a career as start-up entrepreneurs rather than a classic academic career. They describe the history and milestones of their company, and how their everyday work differs from that of peers in an academic or industrial research setting.

Bringing the physical sciences into your cell biology research.

Science.gov (United States)

Robinson, Douglas N; Iglesias, Pablo A

2012-11-01

Historically, much of biology was studied by physicists and mathematicians. With the advent of modern molecular biology, a wave of researchers became trained in a new scientific discipline filled with the language of genes, mutants, and the central dogma. These new molecular approaches have provided volumes of information on biomolecules and molecular pathways from the cellular to the organismal level. The challenge now is to determine how this seemingly endless list of components works together to promote the healthy function of complex living systems. This effort requires an interdisciplinary approach by investigators from both the biological and the physical sciences.

Molecular simulations of hydrocarbon lubricants: Impact of molecular architecture on performance properties

Science.gov (United States)

Kioupis, Loukas I.

2000-07-01

With the increased power of modern computers, molecular modeling has been used widely and proven to be a valuable tool for elucidating the physical processes important in many industrial and engineering problems. Of particular interest to us is the rheology and physical chemistry of complex fluids, such as hydrocarbon lubricants and polymers. The goal is to provide qualitative and quantitative molecular-level explanations for the behavior of such fluids, and provide guidance in the development of new improved materials. For example, during the production of poly-α-olefin (PAO) synthetic lubricants, the number of the isomer skeletal structures that can be obtained is staggering. Which of the countless PAO isomers produce a lubricant with superior performance properties? How does it behave under different operational conditions of temperature, pressure, and shear rate? A fundamental understanding of the effect that molecular structure has on the oil's rheological and lubricant performance is first needed, in order to answer these questions. To serve this purpose, we have developed efficient molecular dynamics (MD) simulation programs, which utilize multiple time step algorithms and parallel computational techniques. This enables us to conduct simulations of typical PAO isomers and compute the viscosity, as well as several other dynamic and static properties, as a function of temperature, pressure, and shear rate. The key molecular mechanisms that determine important macroscopic properties, such as viscosity index, viscosity-pressure coefficient, traction coefficient, and shear thinning behavior are discussed. Based on this analysis, lubricant and traction fluid structures that have a high likelihood of having desirable properties are proposed. In addition, studies on simple alkane mixtures are presented, in an attempt to understand the more complex polydisperse lubricant fluids, their blends, and their interaction with additives.

Laser Controlled Molecular Orientation Dynamics

International Nuclear Information System (INIS)

Atabek, O.

2004-01-01

Molecular orientation is a challenging control issue covering a wide range of applications from reactive collisions, high order harmonic generation, surface processing and catalysis, to nanotechnologies. The laser control scenario rests on the following three steps: (i) depict some basic mechanisms producing dynamical orientation; (ii) use them both as computational and interpretative tools in optimal control schemes involving genetic algorithms; (iii) apply what is learnt from optimal control to improve the basic mechanisms. The existence of a target molecular rotational state combining the advantages of efficient and post-pulse long duration orientation is shown. A strategy is developed for reaching such a target in terms of a train of successive short laser pulses applied at predicted time intervals. Each individual pulse imparts a kick to the molecule which orients. Transposition of such strategies to generic systems is now under investigation

Bringing Gravity to Space

Science.gov (United States)

Norsk, P.; Shelhamer, M.

2016-01-01

This panel will present NASA's plans for ongoing and future research to define the requirements for Artificial Gravity (AG) as a countermeasure against the negative health effects of long-duration weightlessness. AG could mitigate the gravity-sensitive effects of spaceflight across a host of physiological systems. Bringing gravity to space could mitigate the sensorimotor and neuro-vestibular disturbances induced by G-transitions upon reaching a planetary body, and the cardiovascular deconditioning and musculoskeletal weakness induced by weightlessness. Of particular interest for AG during deep-space missions is mitigation of the Visual Impairment Intracranial Pressure (VIIP) syndrome that the majority of astronauts exhibit in space to varying degrees, and which presumably is associated with weightlessness-induced fluid shift from lower to upper body segments. AG could be very effective for reversing the fluid shift and thus help prevent VIIP. The first presentation by Dr. Charles will summarize some of the ground-based and (very little) space-based research that has been conducted on AG by the various space programs. Dr. Paloski will address the use of AG during deep-space exploration-class missions and describe the different AG scenarios such as intra-vehicular, part-of-vehicle, or whole-vehicle centrifugations. Dr. Clement will discuss currently planned NASA research as well as how to coordinate future activities among NASA's international partners. Dr. Barr will describe some possible future plans for using space- and ground-based partial-G analogs to define the relationship between physiological responses and G levels between 0 and 1. Finally, Dr. Stenger will summarize how the human cardiovascular system could benefit from intermittent short-radius centrifugations during long-duration missions.

Development of molecular tools based on the dopamine D3 receptor ligand FAUC 329 showing inhibiting effects on drug and food maintained behavior.

Science.gov (United States)

Stößel, Anne; Brox, Regine; Purkayastha, Nirupam; Hübner, Harald; Hocke, Carsten; Prante, Olaf; Gmeiner, Peter

2017-07-01

Dopamine D 3 receptor-mediated networks have been associated with a wide range of neuropsychiatric diseases, drug addiction and food maintained behavior, which makes D 3 a highly promising biological target. The previously described dopamine D 3 receptor ligand FAUC 329 (1) showed protective effects against dopamine depletion in a MPTP mouse model of Parkinson's disease. We used the radioligand [ 18 F]2, a [ 18 F]fluoroethoxy substituted analog of the lead compound 1 as a molecular tool for visualization of D 3 -rich brain regions including the islands of Calleja. Furthermore, structural modifications are reported leading to the pyrimidylpiperazine derivatives 3 and 9 displaying superior subtype selectivity and preference over serotonergic receptors. Evaluation of the lead compound 1 on cocaine-seeking behavior in non-human primates showed a substantial reduction in cocaine self-administration behavior and food intake. Copyright © 2017 Elsevier Ltd. All rights reserved.

MoCha: Molecular Characterization of Unknown Pathways.

Science.gov (United States)

Lobo, Daniel; Hammelman, Jennifer; Levin, Michael

2016-04-01

Automated methods for the reverse-engineering of complex regulatory networks are paving the way for the inference of mechanistic comprehensive models directly from experimental data. These novel methods can infer not only the relations and parameters of the known molecules defined in their input datasets, but also unknown components and pathways identified as necessary by the automated algorithms. Identifying the molecular nature of these unknown components is a crucial step for making testable predictions and experimentally validating the models, yet no specific and efficient tools exist to aid in this process. To this end, we present here MoCha (Molecular Characterization), a tool optimized for the search of unknown proteins and their pathways from a given set of known interacting proteins. MoCha uses the comprehensive dataset of protein-protein interactions provided by the STRING database, which currently includes more than a billion interactions from over 2,000 organisms. MoCha is highly optimized, performing typical searches within seconds. We demonstrate the use of MoCha with the characterization of unknown components from reverse-engineered models from the literature. MoCha is useful for working on network models by hand or as a downstream step of a model inference engine workflow and represents a valuable and efficient tool for the characterization of unknown pathways using known data from thousands of organisms. MoCha and its source code are freely available online under the GPLv3 license.

Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments.

Science.gov (United States)

Chaudhary, Prem Prashant; Brablcová, Lenka; Buriánková, Iva; Rulík, Martin

2013-09-01

Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.

pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

Directory of Open Access Journals (Sweden)

Ardita Shkurti

2016-01-01

Full Text Available The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse and process, in reasonable timescales, the large generated amounts of molecular simulation data. In light of this, we have developed and present here pyPcazip: a suite of software tools for compression and analysis of molecular dynamics (MD simulation data. The software is compatible with trajectory file formats generated by most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelised to permit the efficient processing of very large datasets. pyPcazip is a Unix based open-source software (BSD licenced written in Python.

The 'added value' GPs bring to commissioning: a qualitative study in primary care.

Science.gov (United States)

Perkins, Neil; Coleman, Anna; Wright, Michael; Gadsby, Erica; McDermott, Imelda; Petsoulas, Christina; Checkland, Kath

2014-11-01

The 2012 Health and Social Care Act in England replaced primary care trusts with clinical commissioning groups (CCGs) as the main purchasing organisations. These new organisations are GP-led, and it was claimed that this increased clinical input would significantly improve commissioning practice. To explore some of the key assumptions underpinning CCGs, and to examine the claim that GPs bring 'added value' to commissioning. In-depth interviews with clinicians and managers across seven CCGs in England between April and September 2013. A total of 40 clinicians and managers were interviewed. Interviews focused on the perceived 'added value' that GPs bring to commissioning. Claims to GP 'added value' centred on their intimate knowledge of their patients. It was argued that this detailed and concrete knowledge improves service design and that a close working relationship between GPs and managers strengthens the ability of managers to negotiate. However, responders also expressed concerns about the large workload that they face and about the difficulty in engaging with the wider body of GPs. GPs have been involved in commissioning in many ways since fundholding in the 1990s, and claims such as these are not new. The key question is whether these new organisations better support and enable the effective use of this knowledge. Furthermore, emphasis on experiential knowledge brings with it concerns about representativeness and the extent to which other voices are heard. Finally, the implicit privileging of GPs' personal knowledge ahead of systematic public health intelligence also requires exploration. © British Journal of General Practice 2014.

Smart Technology Brings Power to the People

Energy Technology Data Exchange (ETDEWEB)

Hammerstrom, Donald J.; Gephart, Julie M.

2006-12-01

Imagine you’re at home one Saturday morning on the computer, as your son takes a shower, your daughter is watching TV, and a load of laundry is in your washer and dryer. Meanwhile, the fragrance of fresh-brewed coffee fills the house. You hear a momentary beep from the dryer that tells you that if you were to look, a high-energy price indicator would be displayed on the front panels of some of your favorite appliances. This tells you that you could save money right now by using less energy. (You’ve agreed to this arrangement to help your utility avoid a substation upgrade. In return, you get a lower rate most of the time.) So you turn off some of the unneeded lights in your home and opt to wait until evening to run the dishwasher. Meanwhile, some of your largest appliances have automatically responded to this signal and have already reduced your home’s energy consumption, saving you money. On January 11, 2006, demonstration projects were launched in 200 homes in the Pacific Northwest region of the United States to test and speed adoption of new smart grid technologies that can make the power grid more resilient and efficient. Pacific Northwest National Laboratory, a U.S. Department of Energy national laboratory in Richland, Washington, is managing the yearlong study called the Pacific Northwest GridWise™ Testbed Demonstration, a project funded primarily by DOE. Through the GridWise™ Demonstration projects, researchers are gaining insight into energy consumers’ behavior while testing new technologies designed to bring the electric transmission system into the information age. Northwest utilities, appliance manufacturers and technology companies are also supporting this effort to demonstrate the devices and assess the resulting consumer response. A combination of devices, software and advanced analytical tools will give homeowners more information about their energy use and cost, and we want to know if this will modify their behavior. Approximately 100

Where has the public gone and will communications technology bring them back?

International Nuclear Information System (INIS)

Hutterman, L.; Smith, R.

1997-01-01

This paper addresses the decreasing number of persons interested and participating in the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) or open-quotes Superfundclose quotes process. It also looks at communications technology to bring people back into participation in the Superfund process. The material studied and the technologies evaluated involve the Environmental Restoration Program at the Idaho National Engineering and Environmental Laboratory. The conclusions are probably valid for most DOE Superfund activities. Where has the public gone? The public has taken an interest in issues that they perceive have greater impact on their quality of life and that have an adverse impact on the environment, such as the shipment and storage of spent nuclear fuel. Will communications technology bring them back? Technology can do many things: it can reduce cost; it can allow quicker access to and from the public; it can offer more information; and it can increase interest because of its novelty for short periods of time, but it will not, in and of its own, create public involvement

Nanopore wall-liquid interaction under scope of molecular dynamics study: Review