Activation of olefins via asymmetric Bronsted acid catalysis

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

Tsuji, Nobuya; Kennemur, Jennifer L.; Buyck, Thomas

The activation of olefins for asymmetric chemical synthesis traditionally relies on transition metal catalysts. In contrast, biological enzymes with Bronsted acidic sites of appropriate strength can protonate olefins and thereby generate carbocations that ultimately react to form natural products. Although chemists have recently designed chiral Bronsted acid catalysts to activate imines and carbonyl compounds, mimicking these enzymes to protonate simple olefins that then engage in asymmetric catalytic reactions has remained a substantial synthetic challenge. Here, we show that a class of confined and strong chiral Bronsted acids enables the catalytic asymmetric intramolecular hydroalkoxylation of unbiased olefins. In conclusion, the methodologymore » gives rapid access to biologically active 1,1-disubstituted tetrahydrofurans, including (–)-Boivinianin A.« less

Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes

PubMed Central

Mus, Florence; Crook, Matthew B.; Garcia, Kevin; Garcia Costas, Amaya; Geddes, Barney A.; Kouri, Evangelia D.; Paramasivan, Ponraj; Ryu, Min-Hyung; Oldroyd, Giles E. D.; Poole, Philip S.; Udvardi, Michael K.; Voigt, Christopher A.

2016-01-01

Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology. PMID:27084023

9-Fluorenylmethyl (Fm) Disulfides: Biomimetic Precursors for Persulfides

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

Park, Chung-Min; Johnson, Brett A.; Duan, Jicheng

Protein S-sulfhydration has been recognized as an important post-translational modification that regulates H2S signals. However, the reactivity and biological implications of the products of S-sulfhydration, i.e. persulfides, are still unclear. This is mainly due to the instability of persulfides and difficulty to access these molecules. Under physiological conditions persulfides mainly exist in anionic forms because of their low pKa values. However, current methods do not allow for the direct generation of persulfide anions under biomimetic and non-H2S conditions. Herein we report the development of a functional disulfide, FmSSPy-A (Fm =9-fluorenylmethyl; Py = pyridinyl). This reagent can effectively convert both smallmore » molecule and protein thiols (-SH) to form –S-SFm adducts under mild conditions. It allows for a H2S-free and biomimetic protocol to generate highly reactive persulfides (in their anionic forms). We also demonstrated the high nucleophilicity of persulfides toward a number of thiol-blocking reagents. This method holds promise for further understanding the chemical biology of persulfides and S-sulfhydration.« less

A system for success: BMC Systems Biology, a new open access journal.

PubMed

Hodgkinson, Matt J; Webb, Penelope A

2007-09-04

BMC Systems Biology is the first open access journal spanning the growing field of systems biology from molecules up to ecosystems. The journal has launched as more and more institutes are founded that are similarly dedicated to this new approach. BMC Systems Biology builds on the ongoing success of the BMC series, providing a venue for all sound research in the systems-level analysis of biology.

The EPA CompTox Chemistry Dashboard - an online resource ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Dashboard and its va

A hitchhiker's guide to the older literature of descriptive teratology.

PubMed

Beckwith, J Bruce

2007-12-15

Though relatively neglected in the age of molecular biology, the older literature of teratology includes superb illustrations and descriptions of malformations, and other information of permanent value to science and medicine. Accessing that literature can be challenging, as most is in works that are rare, published in languages other than English, and not available in digital form. This article describes some valuable sources of information concerning the antiquarian literature of descriptive teratology. (c) 2007 Wiley-Liss, Inc.

Self-formed cylindrical microcapillaries through surface migration of silicon and their application to single-cell analysis

NASA Astrophysics Data System (ADS)

Zeng, Fan; Luo, Yuan; Yobas, Levent; Wong, Man

2013-05-01

Surface migration of monocrystalline silicon has been applied to demonstrate self-formed cylindrical microcapillaries with diameters from 0.8 to 2.8 µm based on the microstructured substrate topography. The microcapillaries are entirely enclosed in silicon and can be conveniently etched to create fluidic access ports and microchannels for their subsequent integration into functional microfluidic devices. Moreover, the microcapillaries can be thermally oxidized through their access ports with silica walls remain intact upon release from surrounding silicon in an effort to enhance optical clarity. Straight microcapillaries and microcapillaries with perpendicular turns and crossings (junctions) have all been fabricated and validated for fluidic continuity with a fluorescein solution pumped through. The utility of the microcapillaries has been showcased on particle traps in which biological cells are probed for single-cell impedance spectroscopy. The approach disclosed, given its full compatibility with semiconductor device fabrication, offers great potential towards intelligent cell and molecule-based devices merging microelectronics and microfluidics.

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education

PubMed Central

Rose, Peter W.; Prlić, Andreas; Bi, Chunxiao; Bluhm, Wolfgang F.; Christie, Cole H.; Dutta, Shuchismita; Green, Rachel Kramer; Goodsell, David S.; Westbrook, John D.; Woo, Jesse; Young, Jasmine; Zardecki, Christine; Berman, Helen M.; Bourne, Philip E.; Burley, Stephen K.

2015-01-01

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine. PMID:25428375

Biological strategies for enhanced hydrolysis of lignocellulosic biomass during anaerobic digestion: Current status and future perspectives.

PubMed

Shrestha, Shilva; Fonoll, Xavier; Khanal, Samir Kumar; Raskin, Lutgarde

2017-12-01

Lignocellulosic biomass is the most abundant renewable bioresource on earth. In lignocellulosic biomass, the cellulose and hemicellulose are bound with lignin and other molecules to form a complex structure not easily accessible to microbial degradation. Anaerobic digestion (AD) of lignocellulosic biomass with a focus on improving hydrolysis, the rate limiting step in AD of lignocellulosic feedstocks, has received considerable attention. This review highlights challenges with AD of lignocellulosic biomass, factors contributing to its recalcitrance, and natural microbial ecosystems, such as the gastrointestinal tracts of herbivorous animals, capable of performing hydrolysis efficiently. Biological strategies that have been evaluated to enhance hydrolysis of lignocellulosic biomass include biological pretreatment, co-digestion, and inoculum selection. Strategies to further improve these approaches along with future research directions are outlined with a focus on linking studies of microbial communities involved in hydrolysis of lignocellulosics to process engineering. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural and molecular interrogation of intact biological systems

PubMed Central

Chung, Kwanghun; Wallace, Jenelle; Kim, Sung-Yon; Kalyanasundaram, Sandhiya; Andalman, Aaron S.; Davidson, Thomas J.; Mirzabekov, Julie J.; Zalocusky, Kelly A.; Mattis, Joanna; Denisin, Aleksandra K.; Pak, Sally; Bernstein, Hannah; Ramakrishnan, Charu; Grosenick, Logan; Gradinaru, Viviana; Deisseroth, Karl

2014-01-01

Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease. PMID:23575631

Total synthesis and biological activity of the proposed structure of phaeosphaeride A.

PubMed

Chatzimpaloglou, Anthoula; Yavropoulou, Maria P; Rooij, Karien E; Biedermann, Ralf; Mueller, Uwe; Kaskel, Stefan; Sarli, Vasiliki

2012-11-02

The total synthesis of the structure assigned to the natural product phaeosphaeride A 1a was accomplished. The key steps involve the addition of vinyllithium reagent 7 to the acetonide-protected aldehyde 8 to access the carbon backbone of 1a, the introduction of the methoxylamino group followed by intramolecular hetero-Michael cyclization, and methanol elimination to form the dihydropyran ring. In this study, both enantiomers of 1a were synthesized and tested for biological activity. Preliminary results showed that (6R,7R,8R)-1a and (6S,7S,8S)-1a inhibit STAT3-dependent transcriptional activity in a dose-dependent manner and exhibit antiproliferative properties in breast (MDA-MB-231) and pancreatic (PANC-1) cancer cells.

Environmental Impact Analysis Process. Environmental Assessment for Replacement Medical Clinic 61st Medical Squadron, Los Angeles Air Force Base

DTIC Science & Technology

1999-12-01

mass transit (buses, commuter trains and light rail ) serves Los Angeles County. Immediate public transit access to Los Angeles AFB is by bus only. 3.8...mostly paved. As a result, surface drainage enters the storm sewer system. Stormwater run-off from Area B of Los Angeles AFB, and specifically from...leaves the installation in the form of stormwater run-off. Little infiltration of rainfall is expected. 3.4 BIOLOGICAL RESOURCES As a result of the

Spiroacetal formation through telescoped cycloaddition and carbon-hydrogen bond functionalization: total synthesis of bistramide A.

PubMed

Han, Xun; Floreancig, Paul E

2014-10-06

Spiroacetals can be formed through a one-pot sequence of a hetero-Diels-Alder reaction, an oxidative carbon-hydrogen bond cleavage, and an acid treatment. This convergent approach expedites access to a complex molecular subunit which is present in numerous biologically active structures. The utility of the protocol is demonstrated through its application to a brief synthesis of the actin-binding cytotoxin bistramide A. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

ExplorEnz: the primary source of the IUBMB enzyme list

PubMed Central

McDonald, Andrew G.; Boyce, Sinéad; Tipton, Keith F.

2009-01-01

ExplorEnz is the MySQL database that is used for the curation and dissemination of the International Union of Biochemistry and Molecular Biology (IUBMB) Enzyme Nomenclature. A simple web-based query interface is provided, along with an advanced search engine for more complex Boolean queries. The WWW front-end is accessible at http://www.enzyme-database.org, from where downloads of the database as SQL and XML are also available. An associated form-based curatorial application has been developed to facilitate the curation of enzyme data as well as the internal and public review processes that occur before an enzyme entry is made official. Suggestions for new enzyme entries, or modifications to existing ones, can be made using the forms provided at http://www.enzyme-database.org/forms.php. PMID:18776214

Establishing a reliable framework for harnessing the creative power of the scientific crowd.

PubMed

Carter, Adrian J; Donner, Amy; Lee, Wen Hwa; Bountra, Chas

2017-02-01

Discovering new medicines is difficult and increasingly expensive. The pharmaceutical industry has responded to this challenge by embracing open innovation to access external ideas. Historically, partnerships were usually bilateral, and the drug discovery process was shrouded in secrecy. This model is rapidly changing. With the advent of the Internet, drug discovery has become more decentralised, bottom-up, and scalable than ever before. The term open innovation is now accepted as just one of many terms that capture different but overlapping levels of openness in the drug discovery process. Many pharmaceutical companies recognise the advantages of revealing some proprietary information in the form of results, chemical tools, or unsolved problems in return for valuable insights and ideas. For example, such selective revealing can take the form of openly shared chemical tools to explore new biological mechanisms or by publicly admitting what is not known in the form of an open call. The essential ingredient for addressing these problems is access to the wider scientific crowd. The business of crowdsourcing, a form of outsourcing in which individuals or organisations solicit contributions from Internet users to obtain ideas or desired services, has grown significantly to fill this need and takes many forms today. Here, we posit that open-innovation approaches are more successful when they establish a reliable framework for converting creative ideas of the scientific crowd into practice with actionable plans.

Establishing a reliable framework for harnessing the creative power of the scientific crowd

PubMed Central

Donner, Amy; Lee, Wen Hwa; Bountra, Chas

2017-01-01

Discovering new medicines is difficult and increasingly expensive. The pharmaceutical industry has responded to this challenge by embracing open innovation to access external ideas. Historically, partnerships were usually bilateral, and the drug discovery process was shrouded in secrecy. This model is rapidly changing. With the advent of the Internet, drug discovery has become more decentralised, bottom-up, and scalable than ever before. The term open innovation is now accepted as just one of many terms that capture different but overlapping levels of openness in the drug discovery process. Many pharmaceutical companies recognise the advantages of revealing some proprietary information in the form of results, chemical tools, or unsolved problems in return for valuable insights and ideas. For example, such selective revealing can take the form of openly shared chemical tools to explore new biological mechanisms or by publicly admitting what is not known in the form of an open call. The essential ingredient for addressing these problems is access to the wider scientific crowd. The business of crowdsourcing, a form of outsourcing in which individuals or organisations solicit contributions from Internet users to obtain ideas or desired services, has grown significantly to fill this need and takes many forms today. Here, we posit that open-innovation approaches are more successful when they establish a reliable framework for converting creative ideas of the scientific crowd into practice with actionable plans. PMID:28199324

Novel Paradigms for Dialysis Vascular Access: Downstream Vascular Biology–Is There a Final Common Pathway?

PubMed Central

2013-01-01

Summary Vascular access dysfunction is a major cause of morbidity and mortality in hemodialysis patients. The most common cause of vascular access dysfunction is venous stenosis from neointimal hyperplasia within the perianastomotic region of an arteriovenous fistula and at the graft-vein anastomosis of an arteriovenous graft. There have been few, if any, effective treatments for vascular access dysfunction because of the limited understanding of the pathophysiology of venous neointimal hyperplasia formation. This review will (1) describe the histopathologic features of hemodialysis access stenosis; (2) discuss novel concepts in the pathogenesis of neointimal hyperplasia development, focusing on downstream vascular biology; (3) highlight future novel therapies for treating downstream biology; and (4) discuss future research areas to improve our understanding of downstream biology and neointimal hyperplasia development. PMID:23990166

The antioxidant effect of derivatives pyroglutamic lactam

NASA Astrophysics Data System (ADS)

Rohadi, Atisya; Lazim, Azwani Mat; Hasbullah, Siti Aishah

2013-11-01

Diphenylpicrylhydrazyl (DPPH) is widely used for quickly accessing the ability of polyphenols to transfer labile H atoms to radicals. The antioxidant activity of all the synthesized compounds was screened by DPPH method. Compound (4) showed 54% antioxidant potential while all other compounds were found to have moderate to have moderate to mild antioxidant activity ranging from 47-52%. Pyroglutamic lactams have been synthesized stereoselectively in racemic form from levulinic acid as bifunctional adduct using convertible isocyanide in one-pot Ugi 4-center-3-component condensation reaction (U-4C-3CR). The product formed provides biologically interesting products in excellent yields in a short reaction time. The structures of the synthesized compounds were elucidated using spectroscopic data and elemental analysis.

The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

PubMed

Rose, Peter W; Prlić, Andreas; Bi, Chunxiao; Bluhm, Wolfgang F; Christie, Cole H; Dutta, Shuchismita; Green, Rachel Kramer; Goodsell, David S; Westbrook, John D; Woo, Jesse; Young, Jasmine; Zardecki, Christine; Berman, Helen M; Bourne, Philip E; Burley, Stephen K

2015-01-01

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Hypercrosslinked polymeric restricted access materials for analysis of biological fluids.

PubMed

Popov, Alekxander; Blinnikova, Zinaida K; Tsyurupa, Maria P; Davankov, Vadim A

2018-06-21

New restricted access materials based on microporous hypercrosslinked polystyrene have been developed. The materials are aimed at the use as packings for solid-phase extraction cartridges to isolate low-molecular-weight analytes from biological fluids (for instance, blood plasma or serum). Two features distinguish these polymers from all known restricted access materials. The first one consists in that the microporous hypercrosslinked polystyrene not only exclude proteins from the sorbent phase but also do not adsorb them on the bead outer surface and so they do not cause coagulation of blood protein components. Therefore, these materials do not require any chemical modification. The second distinguishing feature is the ability of hypercrosslinked sorbents to take up a wide variety of polar and non-polar organic compounds. The sorbents were obtained in the form of beads of 60-70 μm in diameter by crosslinking styrene copolymers with 1, 2 and 3% divinylbenzene with monochlorodimethyl ether to 100, 150 and 200%. The sorbents exhibit all typical properties of hypercrosslinked networks. They do not take up albumin, the major blood protein, and Cytochrome C, representative of smaller protein molecules, but are capable of adsorbing drugs, vitamins and phenyl carboxylic acids (markers of sepsis) from model aqueous solutions. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

76 FR 64379 - Agency Information Collection Activities: Proposed Collection; Comments Requested; eForm 6 Access...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-18

...] Agency Information Collection Activities: Proposed Collection; Comments Requested; eForm 6 Access Request... Form/Collection: eForm 6 Access Request. (3) Agency form number, if any, and the applicable component...: Respondents must complete the eForm 6 Access Request form in order to receive a user ID and password to obtain...

17 CFR 160.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2011 CFR

2011-04-01

... form of access number or access code, does not include a number or code in an encrypted form, as long... consumer reporting agency, an account number or similar form of access number or access code for a consumer... similar form of access number or access code: (1) To your agent or service provider solely in order to...

12 CFR 716.12 - Limits on sharing of account number information for marketing purposes.

Code of Federal Regulations, 2012 CFR

2012-01-01

... form of access number or access code, does not include a number or code in an encrypted form, as long... consumer reporting agency, an account number or similar form of access number or access code for a consumer... similar form of access number or access code: (1) To your agent or service provider solely in order to...

12 CFR 716.12 - Limits on sharing of account number information for marketing purposes.

Code of Federal Regulations, 2011 CFR

2011-01-01

... form of access number or access code, does not include a number or code in an encrypted form, as long... consumer reporting agency, an account number or similar form of access number or access code for a consumer... similar form of access number or access code: (1) To your agent or service provider solely in order to...

12 CFR 716.12 - Limits on sharing of account number information for marketing purposes.

Code of Federal Regulations, 2013 CFR

2013-01-01

... form of access number or access code, does not include a number or code in an encrypted form, as long... consumer reporting agency, an account number or similar form of access number or access code for a consumer... similar form of access number or access code: (1) To your agent or service provider solely in order to...

Cooperative Mission Concepts Using Biomorphic Explorers

NASA Technical Reports Server (NTRS)

Thakoor, S.; Miralles, C.; Martin, T.; Kahn, R.; Zurek, R.

2000-01-01

Inspired by the immense variety of naturally curious explorers (insects, animals, and birds), their wellintegrated biological sensor-processor suites, efficiently packaged in compact but highly dexterous forms, and their complex, intriguing, cooperative behavior, this paper focuses on "Biomorphic Explorers", their defination/classification, their designs, and presents planetary exploration scenarios based on the designs. Judicious blend of bio-inspired concepts and recent advances in micro-air vehicles, microsensors, microinstruments, MEMS, and microprocessors clearly suggests that the time of small, dedicated, low cost explorers that capture some of the key features of biological systems has arrived. Just as even small insects like ants, termites, honey bees etc working cooperatively in colonies can achieve big tasks, the biomorphic explorers hold the potential for obtaining science in-accessible by current large singular exploration platforms.

Automated assembly of oligosaccharides containing multiple cis-glycosidic linkages

NASA Astrophysics Data System (ADS)

Hahm, Heung Sik; Hurevich, Mattan; Seeberger, Peter H.

2016-09-01

Automated glycan assembly (AGA) has advanced from a concept to a commercial technology that rapidly provides access to diverse oligosaccharide chains as long as 30-mers. To date, AGA was mainly employed to incorporate trans-glycosidic linkages, where C2 participating protecting groups ensure stereoselective couplings. Stereocontrol during the installation of cis-glycosidic linkages cannot rely on C2-participation and anomeric mixtures are typically formed. Here, we demonstrate that oligosaccharides containing multiple cis-glycosidic linkages can be prepared efficiently by AGA using monosaccharide building blocks equipped with remote participating protecting groups. The concept is illustrated by the automated syntheses of biologically relevant oligosaccharides bearing various cis-galactosidic and cis-glucosidic linkages. This work provides further proof that AGA facilitates the synthesis of complex oligosaccharides with multiple cis-linkages and other biologically important oligosaccharides.

The Prescription Drug User Fee Act: Cause for Concern?

PubMed

Gabay, Michael

2018-04-01

The Prescription Drug User Fee Act (PDUFA) was originally enacted into law in 1992. PDUFA provides the Food and Drug Administration (FDA) with needed revenue in the form of various fees paid by drug and biologic manufacturers. The FDA utilizes this revenue to streamline the review and approval process for medications. Since the enactment of PDUFA, the median approval time for priority new drug applications and biologics license applications has reduced significantly. The FDA views PDUFA as a successful program that provides a consistent revenue stream to the agency, improves access to medications for patients, and allows industry to have a more predictable product review timeline. However, critics of PDUFA cite concerns including the potential for a lack of FDA independence and medication safety issues involving drugs approved after the existence of PDUFA.

Demonstration on Areca Catechu Tree Reuse with Supporting of Information Technology

NASA Astrophysics Data System (ADS)

Chao, F. L.; Wu, C. K.; Chao, A. K.

2018-04-01

Areca catechu can be commonly found in Taiwan and Asia. By the restriction of agriculture policy, often the tree is chopped down and left in the wild and became an extra burden on the local environment. In this study, reuse design cases and opportunities were collected as Blog, so that people can access more easily. To enhance the user’s awareness and information access it included the facets of its biology, culture history and reuse cases. Furthermore, we proposed demonstration supported with information technology. A blog can collect facts and examples with capabilities of multiple tags. This ability makes information search more accessible. The proposed approach combines both physical samples and visual elements in Blog which can be view by mobile phone. From the survey, Blog performs better than a regular internet search. Most people feel interesting, and some people were able to have own idea. Demonstration designs gather both elements will help to form a positive communication to the society with sustainable thinking.

Developing teachers' understanding of molecular biology: Building a foundation for students.

PubMed

Boulay, Rachel; Parisky, Alex; Campbell, Chris

2010-01-01

Molecular biology often uses participation in active research laboratories as a form of educational training. However, this approach to learning severely restricts access. As a way of addressing this need, the University of Hawaii launched a project to expand this model to include newly developed online training materials in addition to a hands-on laboratory experience. This paper further explores the process of material development and assessment plans. A pilot case study of a group of advanced biology teachers who embark on learning molecular biology over a four-month period through online training materials and working side-by-side with medical researchers in a laboratory is described. Teachers were positive in reporting about the many areas they gained instruction in although some feedback suggested that the initial online materials over-emphasised abstract concepts and laboratory techniques and did not adequately connect to the active research problems or local context of most interest to teachers and students. The experiences of the teachers are shared in an effort to gain insight on how teachers perceive their participation in the study.

Synthetic Biology and Biosecurity: Challenging the “Myths”

PubMed Central

Jefferson, Catherine; Lentzos, Filippa; Marris, Claire

2014-01-01

Synthetic biology, a field that aims to “make biology easier to engineer,” is routinely described as leading to an increase in the “dual-use” threat, i.e., the potential for the same scientific research to be “used” for peaceful purposes or “misused” for warfare or terrorism. Fears have been expressed that the “de-skilling” of biology, combined with online access to the genomic DNA sequences of pathogenic organisms and the reduction in price for DNA synthesis, will make biology increasingly accessible to people operating outside well-equipped professional research laboratories, including people with malevolent intentions. The emergence of do-it-yourself (DIY) biology communities and of the student iGEM competition has come to epitomize this supposed trend toward greater ease of access and the associated potential threat from rogue actors. In this article, we identify five “myths” that permeate discussions about synthetic biology and biosecurity, and argue that they embody misleading assumptions about both synthetic biology and bioterrorism. We demonstrate how these myths are challenged by more realistic understandings of the scientific research currently being conducted in both professional and DIY laboratories, and by an analysis of historical cases of bioterrorism. We show that the importance of tacit knowledge is commonly overlooked in the dominant narrative: the focus is on access to biological materials and digital information, rather than on human practices and institutional dimensions. As a result, public discourse on synthetic biology and biosecurity tends to portray speculative scenarios about the future as realities in the present or the near future, when this is not warranted. We suggest that these “myths” play an important role in defining synthetic biology as a “promissory” field of research and as an “emerging technology” in need of governance. PMID:25191649

Synthetic biology and biosecurity: challenging the "myths".

PubMed

Jefferson, Catherine; Lentzos, Filippa; Marris, Claire

2014-01-01

Synthetic biology, a field that aims to "make biology easier to engineer," is routinely described as leading to an increase in the "dual-use" threat, i.e., the potential for the same scientific research to be "used" for peaceful purposes or "misused" for warfare or terrorism. Fears have been expressed that the "de-skilling" of biology, combined with online access to the genomic DNA sequences of pathogenic organisms and the reduction in price for DNA synthesis, will make biology increasingly accessible to people operating outside well-equipped professional research laboratories, including people with malevolent intentions. The emergence of do-it-yourself (DIY) biology communities and of the student iGEM competition has come to epitomize this supposed trend toward greater ease of access and the associated potential threat from rogue actors. In this article, we identify five "myths" that permeate discussions about synthetic biology and biosecurity, and argue that they embody misleading assumptions about both synthetic biology and bioterrorism. We demonstrate how these myths are challenged by more realistic understandings of the scientific research currently being conducted in both professional and DIY laboratories, and by an analysis of historical cases of bioterrorism. We show that the importance of tacit knowledge is commonly overlooked in the dominant narrative: the focus is on access to biological materials and digital information, rather than on human practices and institutional dimensions. As a result, public discourse on synthetic biology and biosecurity tends to portray speculative scenarios about the future as realities in the present or the near future, when this is not warranted. We suggest that these "myths" play an important role in defining synthetic biology as a "promissory" field of research and as an "emerging technology" in need of governance.

Studies on Monitoring and Tracking Genetic Resources: An Executive Summary

PubMed Central

Garrity, George M.; Thompson, Lorraine M.; Ussery, David W.; Paskin, Norman; Baker, Dwight; Desmeth, Philippe; Schindel, D.E.; Ong, P.S.

2009-01-01

The principles underlying fair and equitable sharing of benefits derived from the utilization of genetic resources are set out in Article 15 of the UN Convention on Biological Diversity, which stipulate that access to genetic resources is subject to the prior informed consent of the country where such resources are located and to mutually agreed terms regarding the sharing of benefits that could be derived from such access. One issue of particular concern for provider countries is how to monitor and track genetic resources once they have left the provider country and enter into use in a variety of forms. This report was commissioned to provide a detailed review of advances in DNA sequencing technologies, as those methods apply to identification of genetic resources, and the use of globally unique persistent identifiers for persistently linking to data and other forms of digital documentation that is linked to individual genetic resources. While the report was written for an audience with a mixture of technical, legal, and policy backgrounds it is relevant to the genomics community as it is an example of downstream application of genomics information. PMID:21304641

Random walks with random velocities.

PubMed

Zaburdaev, Vasily; Schmiedeberg, Michael; Stark, Holger

2008-07-01

We consider a random walk model that takes into account the velocity distribution of random walkers. Random motion with alternating velocities is inherent to various physical and biological systems. Moreover, the velocity distribution is often the first characteristic that is experimentally accessible. Here, we derive transport equations describing the dispersal process in the model and solve them analytically. The asymptotic properties of solutions are presented in the form of a phase diagram that shows all possible scaling regimes, including superdiffusive, ballistic, and superballistic motion. The theoretical results of this work are in excellent agreement with accompanying numerical simulations.

Institutions, incentives and the future of fisheries

PubMed Central

Hilborn, Ray; Orensanz, J. M. (Lobo); Parma, Ana M.

2005-01-01

Fisheries around the world are managed with a broad range of institutional structures. Some of these have been quite disastrous, whereas others have proven both biologically and economically successful. Unsuccessful systems have generally involved either open access, attempts at top-down control with poor ability to monitor and implement regulations, or reliance on consensus. Successful systems range from local cooperatives to strong governmental control, to various forms of property rights, but usually involve institutional systems that provide incentives to individual operators that lead to behaviour consistent with conservation. PMID:15744918

The antioxidant effect of derivatives pyroglutamic lactam

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

Rohadi, Atisya; Lazim, Azwani Mat; Hasbullah, Siti Aishah

Diphenylpicrylhydrazyl (DPPH) is widely used for quickly accessing the ability of polyphenols to transfer labile H atoms to radicals. The antioxidant activity of all the synthesized compounds was screened by DPPH method. Compound (4) showed 54% antioxidant potential while all other compounds were found to have moderate to have moderate to mild antioxidant activity ranging from 47–52%. Pyroglutamic lactams have been synthesized stereoselectively in racemic form from levulinic acid as bifunctional adduct using convertible isocyanide in one-pot Ugi 4-center-3-component condensation reaction (U-4C-3CR). The product formed provides biologically interesting products in excellent yields in a short reaction time. The structures ofmore » the synthesized compounds were elucidated using spectroscopic data and elemental analysis.« less

40. Perimeter acquisition radar building room #510B, chemical, biological, and ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

40. Perimeter acquisition radar building room #510B, chemical, biological, and radiological (CBR) air filter room no. 1 - Stanley R. Mickelsen Safeguard Complex, Perimeter Acquisition Radar Building, Limited Access Area, between Limited Access Patrol Road & Service Road A, Nekoma, Cavalier County, ND

S-Layer Nanosheet Binding of Zn and Gd

DOE Data Explorer

Ajo-Franklin, Caroline (ORCID:0000000189096712); Charrier, Marimikel; Yang, Li

2016-04-15

This data characterizes binding of Zn2+ and Gd3+ to engineered nanosheets at 40C and in a brine solution. The engineered nanosheets are composed of surface-layer (S-layer) proteins which form 2 D crystalline sheets and display Zn2+- or Gd3+-binding domains on these sheets. Their ability to bind Zn2+ is compared to S-layer nanosheets that do not contain Zn2+-binding domains. We found that the purification method of these nanosheets was a critical determinant of their function and thus have provided data on the binding from two different purification methods. A key distinction of this dataset from other datasets is that the engineered nanosheets were expressed and purified from E. coli grown at 37C as described in (Kinns, 2010; Howorka, 2000), Kinns, H., et al. Identifying assembly-inhibiting and assembly-tolerant sites in the SbsB S-layer protein from Geobacillus stearothermophilus. Journal of Molecular Biology, 2010. 395(4): p. 742-753. Howorka, S., et al. Surface-accessible residues in the monomeric and assembled forms of a bacterial surface layer protein. Journal of Biological Chemistry, 2000. 275(48): p. 37876-37886.

Adapting federated cyberinfrastructure for shared data collection facilities in structural biology

PubMed Central

Stokes-Rees, Ian; Levesque, Ian; Murphy, Frank V.; Yang, Wei; Deacon, Ashley; Sliz, Piotr

2012-01-01

Early stage experimental data in structural biology is generally unmaintained and inaccessible to the public. It is increasingly believed that this data, which forms the basis for each macromolecular structure discovered by this field, must be archived and, in due course, published. Furthermore, the widespread use of shared scientific facilities such as synchrotron beamlines complicates the issue of data storage, access and movement, as does the increase of remote users. This work describes a prototype system that adapts existing federated cyberinfra­structure technology and techniques to significantly improve the operational environment for users and administrators of synchrotron data collection facilities used in structural biology. This is achieved through software from the Virtual Data Toolkit and Globus, bringing together federated users and facilities from the Stanford Synchrotron Radiation Lightsource, the Advanced Photon Source, the Open Science Grid, the SBGrid Consortium and Harvard Medical School. The performance and experience with the prototype provide a model for data management at shared scientific facilities. PMID:22514186

Adapting federated cyberinfrastructure for shared data collection facilities in structural biology.

PubMed

Stokes-Rees, Ian; Levesque, Ian; Murphy, Frank V; Yang, Wei; Deacon, Ashley; Sliz, Piotr

2012-05-01

Early stage experimental data in structural biology is generally unmaintained and inaccessible to the public. It is increasingly believed that this data, which forms the basis for each macromolecular structure discovered by this field, must be archived and, in due course, published. Furthermore, the widespread use of shared scientific facilities such as synchrotron beamlines complicates the issue of data storage, access and movement, as does the increase of remote users. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to significantly improve the operational environment for users and administrators of synchrotron data collection facilities used in structural biology. This is achieved through software from the Virtual Data Toolkit and Globus, bringing together federated users and facilities from the Stanford Synchrotron Radiation Lightsource, the Advanced Photon Source, the Open Science Grid, the SBGrid Consortium and Harvard Medical School. The performance and experience with the prototype provide a model for data management at shared scientific facilities.

Breeding biology and the evolution of dynamic sexual dichromatism in frogs.

PubMed

Bell, R C; Webster, G N; Whiting, M J

2017-12-01

Dynamic sexual dichromatism is a temporary colour change between the sexes and has evolved independently in a wide range of anurans, many of which are explosive breeders wherein males physically compete for access to females. Behavioural studies in a few species indicate that dynamic dichromatism functions as a visual signal in large breeding aggregations; however, the prevalence of this trait and the social and environmental factors underlying its expression are poorly understood. We compiled a database of 178 anurans with dynamic dichromatism that include representatives from 15 families and subfamilies. Dynamic dichromatism is common in two of the three subfamilies of hylid treefrogs. Phylogenetic comparative analyses of 355 hylid species (of which 95 display dynamic dichromatism) reveal high transition rates between dynamic dichromatism, ontogenetic (permanent) dichromatism and monochromatism reflecting the high evolutionary lability of this trait. Correlated evolution in hylids between dynamic dichromatism and forming large breeding aggregations indicates that the evolution of large breeding aggregations precedes the evolution of dynamic dichromatism. Multivariate phylogenetic logistic regression recovers the interaction between biogeographic distribution and forming breeding aggregations as a significant predictor of dynamic dichromatism in hylids. Accounting for macroecological differences between temperate and tropical regions, such as seasonality and the availability of breeding sites, may improve our understanding of ecological contexts in which dynamic dichromatism is likely to arise in tropical lineages and why it is retained in some temperate species and lost in others. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Organization of marine phenology data in support of planning and conservation in ocean and coastal ecosystems

USGS Publications Warehouse

Thomas, Kathryn A.; Fornwall, Mark D.; Weltzin, Jake F.; Griffis, R.B.

2014-01-01

Among the many effects of climate change is its influence on the phenology of biota. In marine and coastal ecosystems, phenological shifts have been documented for multiple life forms; however, biological data related to marine species' phenology remain difficult to access and is under-used. We conducted an assessment of potential sources of biological data for marine species and their availability for use in phenological analyses and assessments. Our evaluations showed that data potentially related to understanding marine species' phenology are available through online resources of governmental, academic, and non-governmental organizations, but appropriate datasets are often difficult to discover and access, presenting opportunities for scientific infrastructure improvement. The developing Federal Marine Data Architecture when fully implemented will improve data flow and standardization for marine data within major federal repositories and provide an archival repository for collaborating academic and public data contributors. Another opportunity, largely untapped, is the engagement of citizen scientists in standardized collection of marine phenology data and contribution of these data to established data flows. Use of metadata with marine phenology related keywords could improve discovery and access to appropriate datasets. When data originators choose to self-publish, publication of research datasets with a digital object identifier, linked to metadata, will also improve subsequent discovery and access. Phenological changes in the marine environment will affect human economics, food systems, and recreation. No one source of data will be sufficient to understand these changes. The collective attention of marine data collectors is needed—whether with an agency, an educational institution, or a citizen scientist group—toward adopting the data management processes and standards needed to ensure availability of sufficient and useable marine data to understand marine phenology.

Accessing non-natural reactivity by irradiating nicotinamide-dependent enzymes with light

NASA Astrophysics Data System (ADS)

Emmanuel, Megan A.; Greenberg, Norman R.; Oblinsky, Daniel G.; Hyster, Todd K.

2016-12-01

Enzymes are ideal for use in asymmetric catalysis by the chemical industry, because their chemical compositions can be tailored to a specific substrate and selectivity pattern while providing efficiencies and selectivities that surpass those of classical synthetic methods. However, enzymes are limited to reactions that are found in nature and, as such, facilitate fewer types of transformation than do other forms of catalysis. Thus, a longstanding challenge in the field of biologically mediated catalysis has been to develop enzymes with new catalytic functions. Here we describe a method for achieving catalytic promiscuity that uses the photoexcited state of nicotinamide co-factors (molecules that assist enzyme-mediated catalysis). Under irradiation with visible light, the nicotinamide-dependent enzyme known as ketoreductase can be transformed from a carbonyl reductase into an initiator of radical species and a chiral source of hydrogen atoms. We demonstrate this new reactivity through a highly enantioselective radical dehalogenation of lactones—a challenging transformation for small-molecule catalysts. Mechanistic experiments support the theory that a radical species acts as an intermediate in this reaction, with NADH and NADPH (the reduced forms of nicotinamide adenine nucleotide and nicotinamide adenine dinucleotide phosphate, respectively) serving as both a photoreductant and the source of hydrogen atoms. To our knowledge, this method represents the first example of photo-induced enzyme promiscuity, and highlights the potential for accessing new reactivity from existing enzymes simply by using the excited states of common biological co-factors. This represents a departure from existing light-driven biocatalytic techniques, which are typically explored in the context of co-factor regeneration.

Access to biologicals in Crohn’s disease in ten European countries

PubMed Central

Péntek, Márta; Lakatos, Peter L; Oorsprong, Talitha; Gulácsi, László; Pavlova, Milena; Groot, Wim; Rencz, Fanni; Brodszky, Valentin; Baji, Petra; Crohn’s Disease Research Group

2017-01-01

AIM To analyze access (availability, affordability and acceptability) to biologicals for Crohn’s disease (CD) in ten European countries and to explore the associations between these dimensions, the uptake of biologicals and economic development. METHODS A questionnaire-based survey combined with desk research was carried out in May 2016. Gastroenterologists from the Czech Republic, France, Germany, Hungary, Latvia, Poland, Romania, Slovakia, Spain and Sweden were invited to participate and provide data on the availability of biologicals/biosimilars, reimbursement criteria, clinical practice and prices, and use of biologicals. An availability score was developed to evaluate the restrictiveness of eligibility and administrative criteria applied in the countries. Affordability was defined as the annual cost of treatment as a share of gross domestic product (GDP) per capita. Correlations with the uptake of biologicals, dimensions of access and GDP per capita were calculated. RESULTS At the time of the survey, infliximab and adalimumab were reimbursed in all ten countries, and vedolizumab was reimbursed in five countries (France, Germany, Latvia, Slovakia, Sweden). Reimbursement criteria were the least strict in Sweden and Germany, and the strictest in Hungary, Poland and Slovakia. Between countries, the annual cost of different biological treatments differed 1.6-3.3-fold. Treatments were the most affordable in Sweden (13%-37% of the GDP per capita) and the least affordable in the Central and Eastern European countries, especially in Hungary (87%-124%) and Romania (141%-277%). Biosimilars made treatments more affordable by driving down the annual costs. The number of patients with CD on biologicals per 100000 population was strongly correlated with GDP per capita (0.91), although substantial differences were found in the uptake among countries with similar economic development. Correlation between the number of patients with CD on biologicals per 100000 population and the availability and affordability was also strong (-0.75, -0.69 respectively). CONCLUSION Substantial inequalities in access to biologicals were largely associated with GDP. To explain differences in access among countries with similar development needs further research on acceptance. PMID:28974896

17 CFR 248.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2014 CFR

2014-04-01

..., or similar form of access number or access code, does not include a number or code in an encrypted... consumer reporting agency, an account number or similar form of access number or access code for a consumer... similar form of access number or access code: (1) To your agent or service provider solely in order to...

Big data in healthcare - the promises, challenges and opportunities from a research perspective: A case study with a model database.

PubMed

Adibuzzaman, Mohammad; DeLaurentis, Poching; Hill, Jennifer; Benneyworth, Brian D

2017-01-01

Recent advances in data collection during routine health care in the form of Electronic Health Records (EHR), medical device data (e.g., infusion pump informatics, physiological monitoring data, and insurance claims data, among others, as well as biological and experimental data, have created tremendous opportunities for biological discoveries for clinical application. However, even with all the advancement in technologies and their promises for discoveries, very few research findings have been translated to clinical knowledge, or more importantly, to clinical practice. In this paper, we identify and present the initial work addressing the relevant challenges in three broad categories: data, accessibility, and translation. These issues are discussed in the context of a widely used detailed database from an intensive care unit, Medical Information Mart for Intensive Care (MIMIC III) database.

BioServices: a common Python package to access biological Web Services programmatically.

PubMed

Cokelaer, Thomas; Pultz, Dennis; Harder, Lea M; Serra-Musach, Jordi; Saez-Rodriguez, Julio

2013-12-15

Web interfaces provide access to numerous biological databases. Many can be accessed to in a programmatic way thanks to Web Services. Building applications that combine several of them would benefit from a single framework. BioServices is a comprehensive Python framework that provides programmatic access to major bioinformatics Web Services (e.g. KEGG, UniProt, BioModels, ChEMBLdb). Wrapping additional Web Services based either on Representational State Transfer or Simple Object Access Protocol/Web Services Description Language technologies is eased by the usage of object-oriented programming. BioServices releases and documentation are available at http://pypi.python.org/pypi/bioservices under a GPL-v3 license.

Do-it-yourself biology: challenges and promises for an open science and technology movement.

PubMed

Landrain, Thomas; Meyer, Morgan; Perez, Ariel Martin; Sussan, Remi

2013-09-01

The do-it-yourself biology (DIYbio) community is emerging as a movement that fosters open access to resources permitting modern molecular biology, and synthetic biology among others. It promises in particular to be a source of cheaper and simpler solutions for environmental monitoring, personal diagnostic and the use of biomaterials. The successful growth of a global community of DIYbio practitioners will depend largely on enabling safe access to state-of-the-art molecular biology tools and resources. In this paper we analyze the rise of DIYbio, its community, its material resources and its applications. We look at the current projects developed for the international genetically engineered machine competition in order to get a sense of what amateur biologists can potentially create in their community laboratories over the coming years. We also show why and how the DIYbio community, in the context of a global governance development, is putting in place a safety/ethical framework for guarantying the pursuit of its activity. And finally we argue that the global spread of DIY biology potentially reconfigures and opens up access to biological information and laboratory equipment and that, therefore, it can foster new practices and transversal collaborations between professional scientists and amateurs.

Superglue from bacteria: unbreakable bridges for protein nanotechnology.

PubMed

Veggiani, Gianluca; Zakeri, Bijan; Howarth, Mark

2014-10-01

Biotechnology is often limited by weak interactions. We suggest that an ideal interaction between proteins would be covalent, specific, require addition of only a peptide tag to the protein of interest, and form under a wide range of conditions. Here we summarize peptide tags that are able to form spontaneous amide bonds, based on harnessing reactions of adhesion proteins from the bacterium Streptococcus pyogenes. These include the irreversible peptide-protein interaction of SpyTag with SpyCatcher, as well as irreversible peptide-peptide interactions via SpyLigase. We describe existing applications, including polymerization to enhance cancer cell capture, assembly of living biomaterial, access to diverse protein shapes, and improved enzyme resilience. We also indicate future opportunities for resisting biological force and extending the scope of protein nanotechnology. Copyright © 2014 Elsevier Ltd. All rights reserved.

Access and benefit sharing: Best practices for the use and exchange of invertebrate biological control agents

USDA-ARS?s Scientific Manuscript database

The Convention on Biological Diversity (CBD) acknowledges the sovereign rights that countries have over their ‘genetic resources’. The Nagoya Protocol that came into force in 2014 provides a framework for implementation of and equitable process by which access to, and sharing of benefits between don...

An editor for pathway drawing and data visualization in the Biopathways Workbench.

PubMed

Byrnes, Robert W; Cotter, Dawn; Maer, Andreia; Li, Joshua; Nadeau, David; Subramaniam, Shankar

2009-10-02

Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface. The Pathway Editor is a program written in the Java programming language that allows de-novo pathway creation and downloading of LIPID MAPS (Lipid Metabolites and Pathways Strategy) and KEGG lipid metabolic pathways, and of measured time-dependent changes to lipid components of metabolism. Accessed through Java Web Start, the program downloads pathways from the LIPID MAPS Pathway database (Pathway) as well as from the LIPID MAPS web server http://www.lipidmaps.org. Data arises from metabolomic (lipidomic), microarray, and protein array experiments performed by the LIPID MAPS consortium of laboratories and is arranged by experiment. Facility is provided to create, connect, and annotate nodes and processes on a drawing panel with reference to database objects and time course data. Node and interaction layout as well as data display may be configured in pathway diagrams as desired. Users may extend diagrams, and may also read and write data and non-lipidomic KEGG pathways to and from files. Pathway diagrams in XML format, containing database identifiers referencing specific compounds and experiments, can be saved to a local file for subsequent use. The program is built upon a library of classes, referred to as the Biopathways Workbench, that convert between different file formats and database objects. An example of this feature is provided in the form of read/construct/write access to models in SBML (Systems Biology Markup Language) contained in the local file system. Inclusion of access to multiple experimental data types and of pathway diagrams within a single interface, automatic updating through connectivity to an online database, and a focus on annotation, including reference to standardized lipid nomenclature as well as common lipid names, supports the view that the Pathway Editor represents a significant, practicable contribution to current pathway modeling tools.

Biological research on a Space Station

NASA Technical Reports Server (NTRS)

Krikorian, A. D.; Johnson, Catherine C.

1990-01-01

A Space Station can provide reliable, long duration access to ug environments for basic and applied biological research. The uniqueness of access to near-weightless environments to probe fundamental questions of significance to gravitational and Space biologists can be exploited from many vantage points. Access to centrifuge facilities that can provide 1 g and hypo-g controls will permit identification of gravity-dependent or primary effects. Understanding secondary effects of the ug environment as well will allow a fuller exploitation of the Space environment.

PathwayAccess: CellDesigner plugins for pathway databases.

PubMed

Van Hemert, John L; Dickerson, Julie A

2010-09-15

CellDesigner provides a user-friendly interface for graphical biochemical pathway description. Many pathway databases are not directly exportable to CellDesigner models. PathwayAccess is an extensible suite of CellDesigner plugins, which connect CellDesigner directly to pathway databases using respective Java application programming interfaces. The process is streamlined for creating new PathwayAccess plugins for specific pathway databases. Three PathwayAccess plugins, MetNetAccess, BioCycAccess and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc and Reactome. PathwayAccess plugins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases and visually integrate pathway data from different databases using standard Systems Biology Markup Language and Systems Biology Graphical Notation. Implemented in Java, PathwayAccess plugins run with CellDesigner version 4.0.1 and were tested on Ubuntu Linux, Windows XP and 7, and MacOSX. Source code, binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv.

Undergraduate students' development of social, cultural, and human capital in a networked research experience

NASA Astrophysics Data System (ADS)

Thompson, Jennifer Jo; Conaway, Evan; Dolan, Erin L.

2016-12-01

Recent calls for reform in undergraduate biology education have emphasized integrating research experiences into the learning experiences of all undergraduates. Contemporary science research increasingly demands collaboration across disciplines and institutions to investigate complex research questions, providing new contexts and models for involving undergraduates in research. In this study, we examined the experiences of undergraduates participating in a multi-institution and interdisciplinary biology research network. Unlike the traditional apprenticeship model of research, in which a student participates in research under the guidance of a single faculty member, students participating in networked research have the opportunity to develop relationships with additional faculty and students working in other areas of the project, at their own and at other institutions. We examined how students in this network develop social ties and to what extent a networked research experience affords opportunities for students to develop social, cultural, and human capital. Most studies of undergraduate involvement in science research have focused on documenting student outcomes rather than elucidating how students gain access to research experiences or how elements of research participation lead to desired student outcomes. By taking a qualitative approach framed by capital theories, we have identified ways that undergraduates utilize and further develop various forms of capital important for success in science research. In our study of the first 16 months of a biology research network, we found that undergraduates drew upon a combination of human, cultural, and social capital to gain access to the network. Within their immediate research groups, students built multidimensional social ties with faculty, peers, and others, yielding social capital that can be drawn upon for information, resources, and support. They reported developing cultural capital in the form of learning to think and work like a scientist—a scientific habitus. They reported developing human capital in the forms of technical, analytical, and communication skills in scientific research. Most of the students had little, direct interaction with network members in other research groups and thus developed little cross-institutional capital. The exception to this trend was at one institution that housed three research groups. Because proximity facilitated shared activities, students across research groups at this institution developed cross-lab ties with faculty and peers through which they developed social, cultural, and human capital. An important long-term concern is whether the capital students have developed will help them access opportunities in science beyond the network. At this point, many undergraduates have had limited opportunities to actually draw on capital beyond the network. Nevertheless, a number of students demonstrated awareness that they had developed resources that they could use in other scientific contexts.

The First Amendment and scientific freedom in the era of bioterrorism.

PubMed

Anton, Brian P

2004-01-01

The events of 9/11 have raised awareness that certain scientific research in the public domain may aid terrorists in their quest to develop biological weapons, and there is a legitimate cause for concern in rare cases. Proposed executive branch responses are consistent in their approach to the problem: restrain the offending research by restricting public access to it in some form or another. This paper examines some of the history of the United States (U.S.) government's restrictions on scientific communication and the protection that the First Amendment affords scientists against such restrictions. It focuses in particular on biological science, which has in recent years come under increased scrutiny due to fears of "bioterrorism." It concludes that science needs to be vigilant against government encroachment, but also needs to become the first line of defense in preventing dissemination of potentially dangerous research data. Should the exercise of prior restraint against biological research become necessary, the guidelines developed at the 2002 Monterey workshop provide a useful framework for determining what biological research might cause "direct, immediate, and irreparable" harm to national security under the New York Times Co. v. United States precedent.

12 CFR 40.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2011 CFR

2011-01-01

... similar form of access number or access code, does not include a number or code in an encrypted form, as... reporting agency, an account number or similar form of access number or access code for a consumer's credit... number or access code: (1) To the bank's agent or service provider solely in order to perform marketing...

12 CFR 40.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2014 CFR

2014-01-01

... similar form of access number or access code, does not include a number or code in an encrypted form, as... reporting agency, an account number or similar form of access number or access code for a consumer's credit... number or access code: (1) To the bank's agent or service provider solely in order to perform marketing...

12 CFR 40.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2012 CFR

2012-01-01

... similar form of access number or access code, does not include a number or code in an encrypted form, as... reporting agency, an account number or similar form of access number or access code for a consumer's credit... number or access code: (1) To the bank's agent or service provider solely in order to perform marketing...

12 CFR 40.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2013 CFR

2013-01-01

... similar form of access number or access code, does not include a number or code in an encrypted form, as... reporting agency, an account number or similar form of access number or access code for a consumer's credit... number or access code: (1) To the bank's agent or service provider solely in order to perform marketing...

Identifying diffusion patterns of research articles on Twitter: A case study of online engagement with open access articles.

PubMed

Alperin, Juan Pablo; Gomez, Charles J; Haustein, Stefanie

2018-03-01

The growing presence of research shared on social media, coupled with the increase in freely available research, invites us to ask whether scientific articles shared on platforms like Twitter diffuse beyond the academic community. We explore a new method for answering this question by identifying 11 articles from two open access biology journals that were shared on Twitter at least 50 times and by analyzing the follower network of users who tweeted each article. We find that diffusion patterns of scientific articles can take very different forms, even when the number of times they are tweeted is similar. Our small case study suggests that most articles are shared within single-connected communities with limited diffusion to the public. The proposed approach and indicators can serve those interested in the public understanding of science, science communication, or research evaluation to identify when research diffuses beyond insular communities.

Availability, health-care costs, and utilization patterns of biologics in Taiwan.

PubMed

Hsieh, Chee-Ruey; Liu, Ya-Ming

2012-01-01

To provide an overview of the use of biologics in Taiwan, including the access to new biologics, the impact of this access on the growth of health-care expenditure, and the utilization patterns. We first conducted a market-level analysis to investigate the availability of global biologics in Taiwan as well as the growth and concentration of aggregate spending on biologics. We then conducted a patient-level analysis to investigate the costs and utilization patterns for selected new biologics. We found that the concentration index is such that the 20 leading biologics in Taiwan account for more than 90% of the total spending on biologics. In our patient-level study on four biologics, the annual cost of treatment per patient ranged from NT$100,000 to NT$400,000. The prevalence rate of the user was between 6.5 and 37.2 per 100,000 of population. The treatment costs were inversely related to the prevalence rate of users. We also found that physicians in larger and public hospitals were more likely to prescribe new biologics to their patients compared with their counterparts practicing in smaller and private hospitals. In addition, we found that physicians were more likely to prescribe biologics to patients with more severe diseases and higher comorbidities. We conclude that public spending on biologics in Taiwan is highly targeted toward about 20 products with higher annual expenditures and growth rates and that the utilization of these biologics is targeted at a small number of patients. In addition, the access to these costly biologics is not uniform among patients in a country with universal coverage for prescription drugs. Copyright © 2012 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

The system spatial-frequency filtering of birefringence images of human blood layers

NASA Astrophysics Data System (ADS)

Ushenko, A. G.; Boychuk, T. M.; Mincer, O. P.; Angelsky, P. O.; Bodnar, N. B.; Oleinichenko, B. P.; Bizer, L. I.

2013-09-01

Among various opticophysical methods [1 - 3] of diagnosing the structure and properties of the optical anisotropic component of various biological objects a specific trend has been singled out - multidimensional laser polarimetry of microscopic images of the biological tissues with the following statistic, correlative and fractal analysis of the coordinate distributions of the azimuths and ellipticity of polarization in approximating of linear birefringence polycrystalline protein networks [4 - 10]. At the same time, in most cases, experimental obtaining of tissue sample is a traumatic biopsy operation. In addition, the mechanisms of transformation of the state of polarization of laser radiation by means of the opticoanisotropic biological structures are more varied (optical dichroism, circular birefringence). Hereat, real polycrystalline networks can be formed by different types, both in size and optical properties of biological crystals. Finally, much more accessible for an experimental investigation are biological fluids such as blood, bile, urine, and others. Thus, further progress of laser polarimetry can be associated with the development of new methods of analysis and processing (selection) of polarization- heterogeneous images of biological tissues and fluids, taking into account a wider set of mechanisms anisotropic mechanisms. Our research is aimed at developing experimental method of the Fourier polarimetry and a spatialfrequency selection for distributions of the azimuth and the ellipticity polarization of blood plasma laser images with a view of diagnosing prostate cancer.

Accommodating those Most at Risk. Responding to a Mismatch in Programme Selection Criteria and Foundation Biology Performance

NASA Astrophysics Data System (ADS)

Kirby, Nicola F.; Dempster, Edith R.

2015-12-01

In South Africa, foundation programmes are a well-established alternative access route to tertiary science study for educationally disadvantaged students. Student access to, and performance in, one such foundation programme has been researched by the authors seeking opportunities to improve student retention. The biology module in particular has been recognised to place students at risk of failing the foundation programme, thereby reducing throughput into mainstream science programmes. This study uses decision tree analysis to provide a detailed description of foundation biology student performance so that points of weakness and opportunities for remedial action may be pinpointed. While students' alternative-entry selection scores have previously been found to most effectively account for performance in the programme as a whole, no similar positive relationship was identified for any subgroup of students in the foundation biology module. Conversely, academic language proficiency in the medium of instruction (English), formerly found to play no role in overall student performance, was revealed as primary in explaining achievement in foundation biology, most adversely affecting students rendered particularly vulnerable by an additional academic and/or socio-economic disadvantage. A pass in the stand-alone foundation academic literacy module did not necessarily correspond to a pass in biology. Compromised by educational disadvantage, compounded by a mismatch in programme selection criteria and inadequate academic literacy support, discipline-specific, fundamental literacy development in the biology curriculum is proposed to enable students towards epistemic access in the module. Pending this intervention, formal access to mainstream study is unlikely for the foundation students most at risk of failure.

Accommodating Those Most at Risk. Responding to a Mismatch in Programme Selection Criteria and Foundation Biology Performance

ERIC Educational Resources Information Center

Kirby, Nicola F.; Dempster, Edith R.

2015-01-01

In South Africa, foundation programmes are a well-established alternative access route to tertiary science study for educationally disadvantaged students. Student access to, and performance in, one such foundation programme has been researched by the authors seeking opportunities to improve student retention. The biology module in particular has…

PIQMIe: a web server for semi-quantitative proteomics data management and analysis

PubMed Central

Kuzniar, Arnold; Kanaar, Roland

2014-01-01

We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement. PMID:24861615

PIQMIe: a web server for semi-quantitative proteomics data management and analysis.

PubMed

Kuzniar, Arnold; Kanaar, Roland

2014-07-01

We present the Proteomics Identifications and Quantitations Data Management and Integration Service or PIQMIe that aids in reliable and scalable data management, analysis and visualization of semi-quantitative mass spectrometry based proteomics experiments. PIQMIe readily integrates peptide and (non-redundant) protein identifications and quantitations from multiple experiments with additional biological information on the protein entries, and makes the linked data available in the form of a light-weight relational database, which enables dedicated data analyses (e.g. in R) and user-driven queries. Using the web interface, users are presented with a concise summary of their proteomics experiments in numerical and graphical forms, as well as with a searchable protein grid and interactive visualization tools to aid in the rapid assessment of the experiments and in the identification of proteins of interest. The web server not only provides data access through a web interface but also supports programmatic access through RESTful web service. The web server is available at http://piqmie.semiqprot-emc.cloudlet.sara.nl or http://www.bioinformatics.nl/piqmie. This website is free and open to all users and there is no login requirement. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Measuring systems of hard to get objects: problems with analysis of measurement results

NASA Astrophysics Data System (ADS)

Gilewska, Grazyna

2005-02-01

The problem accessibility of metrological parameters features of objects appeared in many measurements. Especially if it is biological object which parameters very often determined on the basis of indirect research. Accidental component predominate in forming of measurement results with very limited access to measurement objects. Every measuring process has a lot of conditions limiting its abilities to any way processing (e.g. increase number of measurement repetition to decrease random limiting error). It may be temporal, financial limitations, or in case of biological object, small volume of sample, influence measuring tool and observers on object, or whether fatigue effects e.g. at patient. It's taken listing difficulties into consideration author worked out and checked practical application of methods outlying observation reduction and next innovative methods of elimination measured data with excess variance to decrease of mean standard deviation of measured data, with limited aomunt of data and accepted level of confidence. Elaborated methods wee verified on the basis of measurement results of knee-joint width space got from radiographs. Measurements were carried out by indirectly method on the digital images of radiographs. Results of examination confirmed legitimacy to using of elaborated methodology and measurement procedures. Such methodology has special importance when standard scientific ways didn't bring expectations effects.

NSF-Sponsored Biological and Chemical Oceanography Data Management Office

NASA Astrophysics Data System (ADS)

Allison, M. D.; Chandler, C. L.; Copley, N.; Galvarino, C.; Gegg, S. R.; Glover, D. M.; Groman, R. C.; Wiebe, P. H.; Work, T. T.; Biological; Chemical Oceanography Data Management Office

2010-12-01

Ocean biogeochemistry and marine ecosystem research projects are inherently interdisciplinary and benefit from improved access to well-documented data. Improved data sharing practices are important to the continued exploration of research themes that are a central focus of the ocean science community and are essential to interdisciplinary and international collaborations that address complex, global research themes. In 2006, the National Science Foundation Division of Ocean Sciences (NSF OCE) funded the Biological and Chemical Oceanography Data Management Office (BCO-DMO) to serve the data management requirements of scientific investigators funded by the National Science Foundation’s Biological and Chemical Oceanography Sections. BCO-DMO staff members work with investigators to manage marine biogeochemical, ecological, and oceanographic data and information developed in the course of scientific research. These valuable data sets are documented, stored, disseminated, and protected over short and intermediate time frames. One of the goals of the BCO-DMO is to facilitate regional, national, and international data and information exchange through improved data discovery, access, display, downloading, and interoperability. In May 2010, NSF released a statement to the effect that in October 2010, it is planning to require that all proposals include a data management plan in the form of a two-page supplementary document. The data management plan would be an element of the merit review process. NSF has long been committed to making data from NSF-funded research publicly available and the new policy will strengthen this commitment. BCO-DMO is poised to assist in creating the data management plans and in ultimately serving the data and information resulting from NSF OCE funded research. We will present an overview of the data management system capabilities including: geospatial and text-based data discovery and access systems; recent enhancements to data search tools; data export and download utilities; and strategic use of controlled vocabularies to facilitate data integration and improve interoperability.

CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources.

PubMed

Bleda, Marta; Tarraga, Joaquin; de Maria, Alejandro; Salavert, Francisco; Garcia-Alonso, Luz; Celma, Matilde; Martin, Ainoha; Dopazo, Joaquin; Medina, Ignacio

2012-07-01

During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is far from being optimal. Some of the most common problems are that the information is spread out in many small databases; frequently there are different standards among repositories and some databases are no longer supported or they contain too specific and unconnected information. In addition, data size is increasingly becoming an obstacle when accessing or storing biological data. All these issues make very difficult to extract and integrate information from different sources, to analyze experiments or to access and query this information in a programmatic way. CellBase provides a solution to the growing necessity of integration by easing the access to biological data. CellBase implements a set of RESTful web services that query a centralized database containing the most relevant biological data sources. The database is hosted in our servers and is regularly updated. CellBase documentation can be found at http://docs.bioinfo.cipf.es/projects/cellbase.

Access and benefit sharing (ABS) under the convention on biological diversity (CBD): implications for microbial biological control

USDA-ARS?s Scientific Manuscript database

Researchers and implementers of biological control are confronted with a variety of scientific, regulatory and administrative challenges to their biological control programs. One developing challenge will arise from the implementation of provisions of the Convention on Biological Diversity (CBD) co...

76 FR 30370 - National Institute of General Medical Sciences; Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-25

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

76 FR 30373 - National Institute of General Medical Sciences; Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-25

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

Standard biological parts knowledgebase.

PubMed

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M; Gennari, John H

2011-02-24

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

75 FR 65387 - Agency Information Collection Activities: Proposed Collections; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-22

..., Application for Employer Reporting Internet Access and Form G-440, Report Specifications Sheet. Form BA-12 is... access is obtained, authorized employees may submit reporting forms to the RRB via the Internet. The form.... Title and Purpose of Information Collection. Railroad Service and Compensation Reports/System Access...

Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles.

PubMed

Kafkas, Şenay; Kim, Jee-Hyub; Pi, Xingjun; McEntyre, Johanna R

2015-01-01

In this study, we present an analysis of data citation practices in full text research articles and their corresponding supplementary data files, made available in the Open Access set of articles from Europe PubMed Central. Our aim is to investigate whether supplementary data files should be considered as a source of information for integrating the literature with biomolecular databases. Using text-mining methods to identify and extract a variety of core biological database accession numbers, we found that the supplemental data files contain many more database citations than the body of the article, and that those citations often take the form of a relatively small number of articles citing large collections of accession numbers in text-based files. Moreover, citation of value-added databases derived from submission databases (such as Pfam, UniProt or Ensembl) is common, demonstrating the reuse of these resources as datasets in themselves. All the database accession numbers extracted from the supplementary data are publicly accessible from http://dx.doi.org/10.5281/zenodo.11771. Our study suggests that supplementary data should be considered when linking articles with data, in curation pipelines, and in information retrieval tasks in order to make full use of the entire research article. These observations highlight the need to improve the management of supplemental data in general, in order to make this information more discoverable and useful.

BioSentinel: Enabling CubeSat-Scale Biogical Research Beyond Low Earth Orbit

NASA Technical Reports Server (NTRS)

Sorgenfrei, Matt; Lewis, Brian S.

2014-01-01

The introduction of the Space Launch System will provide NASA with a new means of access to space beyond low Earth orbit (LEO), creating opportunities for scientific research in a range of spacecraft sizes. This presentation describes the preliminary design of the BioSentinel spacecraft, a CubeSat measuring 10cm x 20cm x 30cm, which has been manifested for launch on the maiden voyage of the Space Launch System in 2017. BioSentinel will provide the first direct experimental data from a biological study conducted beyond LEO in over forty years, which in turn will help to pave the way for future human exploration missions. The combination of an advanced biology payload with standard spacecraft bus components required for operation in deep space within a CubeSat form factor poses a unique challenge, and this paper will describe the early design trades under consideration. The baseline spacecraft design calls for the biology payload to occupy four cube-units of volume (denoted 4U), with all spacecraft bus components occupying the remaining 2U.

75 FR 63493 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-15

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

76 FR 37359 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-27

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

76 FR 43334 - National Institute of General Medical Sciences Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-20

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

77 FR 33478 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-06

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862,Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

78 FR 10623 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-14

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

77 FR 59936 - National Institute of General Medical Sciences Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-01

... Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96...

76 FR 44598 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-26

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

76 FR 7573 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-10

... Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96...

76 FR 6803 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-08

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

76 FR 36556 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-22

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

76 FR 62815 - National Institute of General Medical Sciences Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-11

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

78 FR 8549 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-06

... Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96...

76 FR 64957 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-19

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

77 FR 61612 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-10

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

75 FR 56119 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-15

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

75 FR 42757 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-22

... Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96...

76 FR 12980 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-09

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

77 FR 17489 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-26

... Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96...

77 FR 6129 - National Institute of General Medical Sciences Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-07

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

76 FR 10380 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-24

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862,Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

76 FR 32980 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-07

..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

Normal form from biological motion despite impaired ventral stream function.

PubMed

Gilaie-Dotan, S; Bentin, S; Harel, M; Rees, G; Saygin, A P

2011-04-01

We explored the extent to which biological motion perception depends on ventral stream integration by studying LG, an unusual case of developmental visual agnosia. LG has significant ventral stream processing deficits but no discernable structural cortical abnormality. LG's intermediate visual areas and object-sensitive regions exhibit abnormal activation during visual object perception, in contrast to area V5/MT+ which responds normally to visual motion (Gilaie-Dotan, Perry, Bonneh, Malach, & Bentin, 2009). Here, in three studies we used point light displays, which require visual integration, in adaptive threshold experiments to examine LG's ability to detect form from biological and non-biological motion cues. LG's ability to detect and discriminate form from biological motion was similar to healthy controls. In contrast, he was significantly deficient in processing form from non-biological motion. Thus, LG can rely on biological motion cues to perceive human forms, but is considerably impaired in extracting form from non-biological motion. Finally, we found that while LG viewed biological motion, activity in a network of brain regions associated with processing biological motion was functionally correlated with his V5/MT+ activity, indicating that normal inputs from V5/MT+ might suffice to activate his action perception system. These results indicate that processing of biologically moving form can dissociate from other form processing in the ventral pathway. Furthermore, the present results indicate that integrative ventral stream processing is necessary for uncompromised processing of non-biological form from motion. Copyright © 2011 Elsevier Ltd. All rights reserved.

Interactively Open Autonomy Unifies Two Approaches to Function

NASA Astrophysics Data System (ADS)

Collier, John

2004-08-01

Functionality is essential to any form of anticipation beyond simple directedness at an end. In the literature on function in biology, there are two distinct approaches. One, the etiological view, places the origin of function in selection, while the other, the organizational view, individuates function by organizational role. Both approaches have well-known advantages and disadvantages. I propose a reconciliation of the two approaches, based in an interactivist approach to the individuation and stability of organisms. The approach was suggested by Kant in the Critique of Judgment, but since it requires, on his account, the identification a new form of causation, it has not been accessible by analytical techniques. I proceed by construction of the required concept to fit certain design requirements. This construction builds on concepts introduced in my previous four talks to these meetings.

Stretching chimeric DNA: A test for the putative S-form

NASA Astrophysics Data System (ADS)

Whitelam, Stephen; Pronk, Sander; Geissler, Phillip L.

2008-11-01

Double-stranded DNA "overstretches" at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and technological application. Overstretching is thought by some to be a force-induced denaturation and by others to consist of a transition to an elongated, hybridized state called S-DNA. Within a statistical mechanical model, we consider the effect upon overstretching of extreme sequence heterogeneity. "Chimeric" sequences possessing halves of markedly different AT composition elongate under fixed external conditions via distinct, spatially segregated transitions. The corresponding force-extension data vary with pulling rate in a manner that depends qualitatively and strikingly upon whether the hybridized S-form is accessible. This observation implies a test for S-DNA that could be performed in experiment.

75 FR 4101 - Enterprise Income Verification (EIV) System User Access Authorization Form and Rules of Behavior...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-26

... Verification (EIV) System User Access Authorization Form and Rules of Behavior and User Agreement AGENCY... lists the following information: Title of Proposal: Enterprise Income Verification (EIV) System User Access, Authorization Form and Rules Of Behavior and User Agreement. OMB Approval Number: 2577-New. Form...

77 FR 6128 - National Institute of General Medical Sciences Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-07

... Sciences Special Emphasis Panel; Review of application for High- Throughput-Enabled Structural Biology..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

75 FR 71713 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-24

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

77 FR 36563 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-19

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

75 FR 4408 - National Institute Of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-27

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

78 FR 10621 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-14

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

76 FR 67199 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-31

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

77 FR 16248 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-20

... Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

76 FR 35222 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-16

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

77 FR 35989 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-15

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

77 FR 35989 - National Institute of General Medical Sciences Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-15

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

77 FR 35989 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-15

... Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

77 FR 69638 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-20

... Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

78 FR 11658 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-19

... Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

78 FR 59040 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-25

... Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

77 FR 14406 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-09

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

77 FR 38846 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-29

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

77 FR 61613 - National Institute of General Medical Sciences Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-10

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

78 FR 8157 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-05

... Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862,Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

75 FR 43180 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-23

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

77 FR 60444 - National Institute of General Medical Sciences Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-03

... Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

76 FR 14672 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-17

... Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

75 FR 69092 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-10

... Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

75 FR 13557 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-22

... Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

75 FR 7488 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-19

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

77 FR 67385 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-09

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

76 FR 29773 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-23

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

77 FR 39714 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-05

... Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

76 FR 68486 - National Institute of General Medical Sciences Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-04

... Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

75 FR 69090 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-10

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

Data publication with the structural biology data grid supports live analysis

DOE PAGES

Meyer, Peter A.; Socias, Stephanie; Key, Jason; ...

2016-03-07

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of themore » original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. In conclusion, it is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.« less

Data publication with the structural biology data grid supports live analysis

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

Meyer, Peter A.; Socias, Stephanie; Key, Jason

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of themore » original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. In conclusion, it is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.« less

Data publication with the structural biology data grid supports live analysis.

PubMed

Meyer, Peter A; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S; Baxter, Richard H; Blacklow, Stephen C; Boggon, Titus J; Bonvin, Alexandre M J J; Borek, Dominika; Brett, Tom J; Caflisch, Amedeo; Chang, Chung-I; Chazin, Walter J; Corbett, Kevin D; Cosgrove, Michael S; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L; Eck, Michael J; Eichman, Brandt F; Fan, Qing R; Ferré-D'Amaré, Adrian R; Fromme, J Christopher; Garcia, K Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C; Heldwein, Ekaterina E; Jia, Zongchao; Keenan, Robert J; Kruse, Andrew C; Kvansakul, Marc; McLellan, Jason S; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C S; Rapoport, Tom A; Roll-Mecak, Antonina; Rosen, Michael K; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J; Tolia, Niraj H; Tsodikov, Oleg V; Westover, Kenneth D; Wu, Hao; Foster, Ian; Fraser, James S; Maia, Filipe R N C; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercè; Sliz, Piotr

2016-03-07

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.

Data publication with the structural biology data grid supports live analysis

PubMed Central

Meyer, Peter A.; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C.; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S.; Baxter, Richard H.; Blacklow, Stephen C.; Boggon, Titus J.; Bonvin, Alexandre M. J. J.; Borek, Dominika; Brett, Tom J.; Caflisch, Amedeo; Chang, Chung-I; Chazin, Walter J.; Corbett, Kevin D.; Cosgrove, Michael S.; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L.; Eck, Michael J.; Eichman, Brandt F.; Fan, Qing R.; Ferré-D'Amaré, Adrian R.; Christopher Fromme, J.; Garcia, K. Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C.; Heldwein, Ekaterina E.; Jia, Zongchao; Keenan, Robert J.; Kruse, Andrew C.; Kvansakul, Marc; McLellan, Jason S.; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F.; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C. S.; Rapoport, Tom A.; Roll-Mecak, Antonina; Rosen, Michael K.; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U.; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J.; Tolia, Niraj H.; Tsodikov, Oleg V.; Westover, Kenneth D.; Wu, Hao; Foster, Ian; Fraser, James S.; Maia, Filipe R. N C.; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercè; Sliz, Piotr

2016-01-01

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis. PMID:26947396

12 CFR 1016.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2013 CFR

2013-01-01

... encrypted form, as long as you do not provide the recipient with a means to decode the number or code. (2... reporting agency, an account number or similar form of access number or access code for a consumer's credit... similar form of access number or access code: (1) To your agent or service provider solely in order to...

12 CFR 1016.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2014 CFR

2014-01-01

... encrypted form, as long as you do not provide the recipient with a means to decode the number or code. (2... reporting agency, an account number or similar form of access number or access code for a consumer's credit... similar form of access number or access code: (1) To your agent or service provider solely in order to...

12 CFR 216.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2012 CFR

2012-01-01

... code in an encrypted form, as long as you do not provide the recipient with a means to decode the... than to a consumer reporting agency, an account number or similar form of access number or access code... account number or similar form of access number or access code: (1) To your agent or service provider...

16 CFR 313.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2013 CFR

2013-01-01

... encrypted form, as long as you do not provide the recipient with a means to decode the number or code. (2... consumer reporting agency, an account number or similar form of access number or access code for a consumer... similar form of access number or access code: (1) To your agent or service provider solely in order to...

16 CFR 313.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2011 CFR

2011-01-01

... encrypted form, as long as you do not provide the recipient with a means to decode the number or code. (2... consumer reporting agency, an account number or similar form of access number or access code for a consumer... similar form of access number or access code: (1) To your agent or service provider solely in order to...

17 CFR 160.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2013 CFR

2013-04-01

... a number or code in an encrypted form, as long as you do not provide the recipient with a means to... form of access number or access code for a consumer's credit card account, deposit account or... apply if you disclose an account number or similar form of access number or access code: (1) To your...

12 CFR 216.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2014 CFR

2014-01-01

... code in an encrypted form, as long as you do not provide the recipient with a means to decode the... than to a consumer reporting agency, an account number or similar form of access number or access code... account number or similar form of access number or access code: (1) To your agent or service provider...

17 CFR 160.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2012 CFR

2012-04-01

... a number or code in an encrypted form, as long as you do not provide the recipient with a means to... form of access number or access code for a consumer's credit card account, deposit account or... apply if you disclose an account number or similar form of access number or access code: (1) To your...

16 CFR 313.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2012 CFR

2012-01-01

... encrypted form, as long as you do not provide the recipient with a means to decode the number or code. (2... consumer reporting agency, an account number or similar form of access number or access code for a consumer... similar form of access number or access code: (1) To your agent or service provider solely in order to...

12 CFR 216.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2013 CFR

2013-01-01

... code in an encrypted form, as long as you do not provide the recipient with a means to decode the... than to a consumer reporting agency, an account number or similar form of access number or access code... account number or similar form of access number or access code: (1) To your agent or service provider...

12 CFR 1016.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2012 CFR

2012-01-01

... encrypted form, as long as you do not provide the recipient with a means to decode the number or code. (2... reporting agency, an account number or similar form of access number or access code for a consumer's credit... similar form of access number or access code: (1) To your agent or service provider solely in order to...

12 CFR 332.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2013 CFR

2013-01-01

... encrypted form, as long as you do not provide the recipient with a means to decode the number or code. (2... consumer reporting agency, an account number or similar form of access number or access code for a consumer... similar form of access number or access code: (1) To your agent or service provider solely in order to...

12 CFR 332.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2011 CFR

2011-01-01

... encrypted form, as long as you do not provide the recipient with a means to decode the number or code. (2... consumer reporting agency, an account number or similar form of access number or access code for a consumer... similar form of access number or access code: (1) To your agent or service provider solely in order to...

12 CFR 332.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2014 CFR

2014-01-01

... encrypted form, as long as you do not provide the recipient with a means to decode the number or code. (2... consumer reporting agency, an account number or similar form of access number or access code for a consumer... similar form of access number or access code: (1) To your agent or service provider solely in order to...

12 CFR 216.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2011 CFR

2011-01-01

... code in an encrypted form, as long as you do not provide the recipient with a means to decode the... than to a consumer reporting agency, an account number or similar form of access number or access code... account number or similar form of access number or access code: (1) To your agent or service provider...

12 CFR 332.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2012 CFR

2012-01-01

... encrypted form, as long as you do not provide the recipient with a means to decode the number or code. (2... consumer reporting agency, an account number or similar form of access number or access code for a consumer... similar form of access number or access code: (1) To your agent or service provider solely in order to...

16 CFR 313.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2014 CFR

2014-01-01

... encrypted form, as long as you do not provide the recipient with a means to decode the number or code. (2... consumer reporting agency, an account number or similar form of access number or access code for a consumer... similar form of access number or access code: (1) To your agent or service provider solely in order to...

17 CFR 160.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2014 CFR

2014-04-01

... a number or code in an encrypted form, as long as you do not provide the recipient with a means to... similar form of access number or access code for a consumer's credit card account, deposit account or... apply if you disclose an account number or similar form of access number or access code: (1) To your...

76 FR 62080 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-06

... Sciences Special Emphasis Panel, Review of Applications for High- Throughput-Enabled Structural Biology... Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

National Biological Information Infrastructure (NBII) | Information Center

Science.gov Websites

National Biological Information Infrastructure (NBII) Contact Information Website: http://www.nbii.gov/ The National Biological Information Infrastructure (NBII) is a broad, collaborative program to provide increased access to data and information on the nation's biological resources. The NBII links diverse, high

Achieving open access to conservation science.

PubMed

Fuller, Richard A; Lee, Jasmine R; Watson, James E M

2014-12-01

Conservation science is a crisis discipline in which the results of scientific enquiry must be made available quickly to those implementing management. We assessed the extent to which scientific research published since the year 2000 in 20 conservation science journals is publicly available. Of the 19,207 papers published, 1,667 (8.68%) are freely downloadable from an official repository. Moreover, only 938 papers (4.88%) meet the standard definition of open access in which material can be freely reused providing attribution to the authors is given. This compares poorly with a comparable set of 20 evolutionary biology journals, where 31.93% of papers are freely downloadable and 7.49% are open access. Seventeen of the 20 conservation journals offer an open access option, but fewer than 5% of the papers are available through open access. The cost of accessing the full body of conservation science runs into tens of thousands of dollars per year for institutional subscribers, and many conservation practitioners cannot access pay-per-view science through their workplace. However, important initiatives such as Research4Life are making science available to organizations in developing countries. We urge authors of conservation science to pay for open access on a per-article basis or to choose publication in open access journals, taking care to ensure the license allows reuse for any purpose providing attribution is given. Currently, it would cost $51 million to make all conservation science published since 2000 freely available by paying the open access fees currently levied to authors. Publishers of conservation journals might consider more cost effective models for open access and conservation-oriented organizations running journals could consider a broader range of options for open access to nonmembers such as sponsorship of open access via membership fees. © 2014 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of the Society for Conservation Biology.

AccessMRS: integrating OpenMRS with smart forms on Android.

PubMed

Fazen, Louis E; Chemwolo, Benjamin T; Songok, Julia J; Ruhl, Laura J; Kipkoech, Carolyne; Green, James M; Ikemeri, Justus E; Christoffersen-Deb, Astrid

2013-01-01

We present a new open-source Android application, AccessMRS, for interfacing with an electronic medical record system (OpenMRS) and loading 'Smart Forms' on a mobile device. AccessMRS functions as a patient-centered interface for viewing OpenMRS data; managing patient information in reminders, task lists, and previous encounters; and launching patient-specific 'Smart Forms' for electronic data collection and dissemination of health information. We present AccessMRS in the context of related software applications we developed to serve Community Health Workers, including AccessInfo, AccessAdmin, AccessMaps, and AccessForms. The specific features and design of AccessMRS are detailed in relationship to the requirements that drove development: the workflows of the Kenyan Ministry of Health Community Health Volunteers (CHVs) supported by the AMPATH Primary Health Care Program. Specifically, AccessMRS was designed to improve the quality of community-based Maternal and Child Health services delivered by CHVs in Kosirai Division. AccessMRS is currently in use by more than 80 CHVs in Kenya and undergoing formal assessment of acceptability, effectiveness, and cost.

How Often Are Drugs Made Available Under the Food and Drug Administration's Expanded Access Process Approved?

PubMed

McKee, Amy E; Markon, André O; Chan-Tack, Kirk M; Lurie, Peter

2017-10-01

In this review of individual patient expanded-access requests to the Center for Drug Evaluation and Research for the period Fiscal Year 2010 to Fiscal Year 2014, we evaluated the number of applications received and the number allowed to proceed. We also evaluated whether drugs and certain biologics obtained under expanded access went on to be approved by the Food and Drug Administration. Finally, we considered concerns that adverse events occurring during expanded access might place sponsors at risk for legal liability. Overall, 98% of individual patient expanded-access requests were allowed to proceed. During the study period, among drugs without a previous approval for any indication or dosage form, 24% of unique drugs (ie, multiple applications for access to the same drug were considered to relate to 1 unique drug), and 20% of expanded-access applications received marketing approval by 1 year after initial submission; 43% and 33%, respectively, were approved by 5 years after initial submission. A search of 3 legal databases and a database of news articles did not appear to identify any product liability cases arising from the use of a product in expanded access. Our analyses seek to give physicians and patients a realistic perspective on the likelihood of a drug's approval as well as certain information regarding the product liability risks for commercial sponsors when providing expanded access to investigational drugs. The US Food and Drug Administration (FDA)'s expanded-access program maintains a careful balance between authorizing patient access to potentially beneficial drugs and protecting them from drugs that may have unknown risks. At the same time, the agency wishes to maintain the integrity of the clinical trials process, ultimately the best way to get safe and effective drugs to patients. © 2017, The American College of Clinical Pharmacology.

pClone: Synthetic Biology Tool Makes Promoter Research Accessible to Beginning Biology Students

ERIC Educational Resources Information Center

Campbell, A. Malcolm; Eckdahl, Todd; Cronk, Brian; Andresen, Corinne; Frederick, Paul; Huckuntod, Samantha; Shinneman, Claire; Wacker, Annie; Yuan, Jason

2014-01-01

The "Vision and Change" report recommended genuine research experiences for undergraduate biology students. Authentic research improves science education, increases the number of scientifically literate citizens, and encourages students to pursue research. Synthetic biology is well suited for undergraduate research and is a growing area…

75 FR 12242 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-15

... Sciences Special Emphasis Panel; NIGMS PSI-Biology Centers for Membrane Proteins. Date: April 9-10, 2010..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

77 FR 15378 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-15

... Sciences Special Emphasis Panel Peer Review of Systems Biology (P50) Grant. Applications Date: April 5..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

76 FR 11801 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-03

... Sciences Special Emphasis Panel, Systems Biology Grant Applications. Date: March 25, 2011. Time: 8 a.m. to... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

Standard Biological Parts Knowledgebase

PubMed Central

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M.; Gennari, John H.

2011-01-01

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate “promoter” parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible. PMID:21390321

Collection overview: ten years of wonderful open access science.

PubMed

Roberts, Roland G; Alfred, Jane

2013-10-01

To mark our tenth Anniversary at PLOS Biology, we are launching a special, celebratory Tenth Anniversary PLOS Biology Collection which showcases 10 specially selected PLOS Biology research articles drawn from a decade of publishing excellent science. It also features newly commissioned articles, including thought-provoking pieces on the Open Access movement (past and present), on article-level metrics, and on the history of the Public Library of Science. Each research article highlighted in the collection is also accompanied by a PLOS Biologue blog post to extend the impact of these remarkable studies to the widest possible audience.

Collection Overview: Ten Years of Wonderful Open Access Science

PubMed Central

Roberts, Roland G.; Alfred, Jane

2013-01-01

To mark our tenth Anniversary at PLOS Biology, we are launching a special, celebratory Tenth Anniversary PLOS Biology Collection which showcases 10 specially selected PLOS Biology research articles drawn from a decade of publishing excellent science. It also features newly commissioned articles, including thought-provoking pieces on the Open Access movement (past and present), on article-level metrics, and on the history of the Public Library of Science. Each research article highlighted in the collection is also accompanied by a PLOS Biologue blog post to extend the impact of these remarkable studies to the widest possible audience. PMID:24167446

The Human Genome Project: Information access, management, and regulation. Final report

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

McInerney, J.D.; Micikas, L.B.

The Human Genome Project is a large, internationally coordinated effort in biological research directed at creating a detailed map of human DNA. This report describes the access of information, management, and regulation of the project. The project led to the development of an instructional module titled The Human Genome Project: Biology, Computers, and Privacy, designed for use in high school biology classes. The module consists of print materials and both Macintosh and Windows versions of related computer software-Appendix A contains a copy of the print materials and discs containing the two versions of the software.

Report of the Interagency biological methods workshop

USGS Publications Warehouse

Gurtz, Martin E.; Muir, Thomas A.

1994-01-01

The U.S. Geological Survey hosted the Interagency Biological Methods Workshop in Reston, Virginia, during June 22-23, 1993. The purposes of the workshop were to (1) promote better communication among Federal agencies that are using or developing biological methods in water-quality assessment programs for streams and rivers, and (2) facilitate the sharing of data and interagency collaboration. The workshop was attended by 45 biologists representing numerous Federal agencies and programs, and a few regional and State programs that were selected to provide additional perspectives. The focus of the workshop was community assessment methods for fish, invertebrates, and algae; physical habitat characterization; and chemical analyses of biological tissues. Charts comparing program objectives, design features, and sampling methods were compiled from materials that were provided by participating agencies prior to the workshop and formed the basis for small workgroup discussions. Participants noted that differences in methods among programs were often necessitated by differences in program objectives. However, participants agreed that where programs have identified similar data needs, the use of common methods is beneficial. Opportunities discussed for improving data compatibility and information sharing included (1) modifying existing methods, (2) adding parameters, (3) improving access to data through shared databases (potentially with common database structures), and (4) future collaborative efforts that range from research on selected protocol questions to followup meetings and continued discussions.

The views of stakeholders on controlled access schemes for high-cost antirheumatic biological medicines in Australia

PubMed Central

Lu, Christine Y; Ritchie, Jan; Williams, Ken; Day, Ric

2007-01-01

Background In Australia, government-subsidised access to high-cost medicines is "targeted" to particular sub-sets of patients under the Pharmaceutical Benefits Scheme to achieve cost-effective use. In order to determine how this access system could be improved, the opinions of key stakeholders on access to biological agents for rheumatoid arthritis were explored. Methods Thirty-six semi-structured interviews were conducted with persons from relevant stakeholder groups. These were transcribed verbatim, and analysed thematically. Results Controlled access to expensive medicines was considered to be equitable and practical; however, there was disagreement as to the method of defining the target patient populations. Other concerns included timeliness of access, excessive bureaucracy, and the need for additional resources to facilitate the scheme. Collaboration between stakeholders was deemed important because it allows more equitable distribution of limited resources. The majority considered that stakeholder consultation should have been broader. Most wanted increased transparency of the decision-making process, ongoing and timely review of access criteria, and an increased provision of information for patients. More structured communication between stakeholders was proposed. Conclusion The Pharmaceutical Benefit Scheme is adapting to meet the changing needs of patients. Provision of subsidised access to high-cost medicines in a manner that is affordable for individuals and society, and that is equitable and efficiently managed is challenging. The views of stakeholders on targeted access to anti-rheumatic biological medicines in Australia acknowledged this challenge and provided a number of suggestions for modifications. These could serve as a basis to inform the debate on how to change the processes and policies so as to improve the scheme. PMID:18096055

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research.

PubMed

Wolstencroft, Katherine; Krebs, Olga; Snoep, Jacky L; Stanford, Natalie J; Bacall, Finn; Golebiewski, Martin; Kuzyakiv, Rostyk; Nguyen, Quyen; Owen, Stuart; Soiland-Reyes, Stian; Straszewski, Jakub; van Niekerk, David D; Williams, Alan R; Malmström, Lars; Rinn, Bernd; Müller, Wolfgang; Goble, Carole

2017-01-04

The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https://fairdomhub.org/) for the Systems Biology community. It is a web-accessible repository for storing and sharing systems biology research assets. It enables researchers to organize, share and publish data, models and protocols, interlink them in the context of the systems biology investigations that produced them, and to interrogate them via API interfaces. By using the FAIRDOMHub, researchers can achieve more effective exchange with geographically distributed collaborators during projects, ensure results are sustained and preserved and generate reproducible publications that adhere to the FAIR guiding principles of data stewardship. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Making metabolism accessible and meaningful: is the definition of a central metabolic dogma within reach?

PubMed

LaRossa, Robert A

2015-04-01

Intermediary metabolism, a dominant research area before the emergence of molecular biology, is attracting renewed interest for fundamental and applied reasons as documented here. Nonetheless, the field may appear to be a thicket precluding entry to all but the most determined. Here we present a metabolic overview that makes this important and fascinating area accessible to a broad range of the molecular biological and biotechnological communities that are being attracted to biological problems crying out for metabolic solutions. This is accomplished by identifying seven key concepts, a so-called metabolic central dogma, that provide a core understanding analogous to the "Central Dogma of Molecular Biology" which focused upon maintenance and flow of genetic information.

Molecular characterization, biological forms and sporozoite rate of Anopheles stephensi in southern Iran

PubMed Central

Chavshin, Ali Reza; Oshaghi, Mohammad Ali; Vatandoost, Hasan; Hanafi-Bojd, Ahmad Ali; Raeisi, Ahmad; Nikpoor, Fatemeh

2014-01-01

Objective To identify the biological forms, sporozoite rate and molecular characterization of the Anopheles stephensi (An. stephensi) in Hormozgan and Sistan-Baluchistan provinces, the most important malarious areas in Iran. Methods Wild live An. stephensi samples were collected from different malarious areas in southern Iran. The biological forms were identified based on number of egg-ridges. Molecular characterization of biological forms was verified by analysis of the mitochondrial cytochrome oxidase subunit I and II (mtDNA-COI/COII). The Plasmodium infection was examined in the wild female specimens by species-specific nested–PCR method. Results Results showed that all three biological forms including mysorensis, intermediate and type are present in the study areas. Molecular investigations revealed no genetic variation between mtDNA COI/COII sequences of the biological forms and no Plasmodium parasites was detected in the collected mosquito samples. Conclusions Presence of three biological forms with identical sequences showed that the known biological forms belong to a single taxon and the various vectorial capacities reported for these forms are more likely corresponded to other epidemiological factors than to the morphotype of the populations. Lack of malaria parasite infection in An. stephensi, the most important vector of malaria, may be partly due to the success and achievement of ongoing active malaria control program in the region. PMID:24144130

Evolving Strategies for the Incorporation of Bioinformatics within the Undergraduate Cell Biology Curriculum

ERIC Educational Resources Information Center

Honts, Jerry E.

2003-01-01

Recent advances in genomics and structural biology have resulted in an unprecedented increase in biological data available from Internet-accessible databases. In order to help students effectively use this vast repository of information, undergraduate biology students at Drake University were introduced to bioinformatics software and databases in…

76 FR 10381 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-24

... Sciences Special Emphasis Panel; Genetics and Cell Biology. Date: March 21-22, 2011. Time: 8 a.m. to 5 p.m..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

Characterising the Phenotypic Diversity of Papilio dardanus Wing Patterns Using an Extensive Museum Collection

PubMed Central

Thompson, Martin J.; Timmermans, Martijn J. T. N.

2014-01-01

The history of 20th Century evolutionary biology can be followed through the study of mimetic butterflies. From the initial findings of discontinuous polymorphism through the debates regarding the evolution of mimicry and the step-size of evolutionary change, to the studies on supergene evolution and molecular characterisation of butterfly genomes, mimetic butterflies have been at the heart of evolutionary thought for over 100 years. During this time, few species have received as much attention and in-depth study as Papilio dardanus. To assist all aspects of mimicry research, we present a complete data-derived overview of the extent of polymorphism within this species. Using historical samples permanently held by the NHM London, we document the extent of phenotypic variation and characterise the diversity present in each of the subspecies and how it varies across Africa. We also demonstrate an association between “imperfect” mimetic forms and the transitional race formed in the area where Eastern and Western African populations meet around Lake Victoria. We present a novel portal for access to this collection, www.mimeticbutterflies.org, allowing remote access to this unique repository. It is hoped that this online resource can act as a nucleus for the sharing and dissemination of other collections databases and imagery connected with mimetic butterflies. PMID:24837717

Disentangling the complexities of how legumes and their symbionts regulate plant nitrogen access and storage

USGS Publications Warehouse

Reed, Sasha C.

2017-01-01

Nitrogen (N) availability strongly influences the structure and function of ecosystems (e.g. Vitousek & Howarth, 1991), but only a relatively small number of microbial groups have the ability to convert the N2 in our atmosphere into biologically available forms.This process, N2 fixation, is the dominant source of new N to the biosphere outside of anthropogenic inputs (Vitousek et al., 2013).Some N2-fixing microorganisms live independently on plant leaves, on decomposing organic material, and in soil (Reed et al.,2011), while others have co-evolved with a few higher plant taxa to form symbioses that fix N2 in root nodules (e.g. Sprent & Raven,1985). The relationship between these legumes and their root nodule symbionts (rhizobia) is one of the most well studied plant –microbe symbioses. Yet, many important questions about the controls, interactions, and implications of legume N2 fixation remain unanswered. In this issue of New Phytologist (pp. 690–699),Wolf, Funk, & Menge elegantly address a fundamental set of questions about N2 fixation in their examination of how herbaceous legumes, their symbionts, and external N availability interact to govern legume access and storage of N.

Quantifying the Effect of DNA Packaging on Gene Expression Level

NASA Astrophysics Data System (ADS)

Kim, Harold

2010-10-01

Gene expression, the process by which the genetic code comes alive in the form of proteins, is one of the most important biological processes in living cells, and begins when transcription factors bind to specific DNA sequences in the promoter region upstream of a gene. The relationship between gene expression output and transcription factor input which is termed the gene regulation function is specific to each promoter, and predicting this gene regulation function from the locations of transcription factor binding sites is one of the challenges in biology. In eukaryotic organisms (for example, animals, plants, fungi etc), DNA is highly compacted into nucleosomes, 147-bp segments of DNA tightly wrapped around histone protein core, and therefore, the accessibility of transcription factor binding sites depends on their locations with respect to nucleosomes - sites inside nucleosomes are less accessible than those outside nucleosomes. To understand how transcription factor binding sites contribute to gene expression in a quantitative manner, we obtain gene regulation functions of promoters with various configurations of transcription factor binding sites by using fluorescent protein reporters to measure transcription factor input and gene expression output in single yeast cells. In this talk, I will show that the affinity of a transcription factor binding site inside and outside the nucleosome controls different aspects of the gene regulation function, and explain this finding based on a mass-action kinetic model that includes competition between nucleosomes and transcription factors.

Recent Advances in Point-of-Access Water Quality Monitoring

NASA Astrophysics Data System (ADS)

Korostynska, O.; Arshak, K.; Velusamy, V.; Arshak, A.; Vaseashta, Ashok

Clean water is one of our most valuable natural resources. In addition to providing safe drinking water it assures functional ecosystems that support fisheries and recreation. Human population growth and its associated increased demands on water pose risks to maintaining acceptable water quality. It is vital to assess source waters and the aquatic systems that receive inputs from industrial waste and sewage treatment plants, storm water systems, and runoff from urban and agricultural lands. Rapid and confident assessments of aquatic resources form the basis for sound environmental management. Current methods engaged in tracing the presence of various bacteria in water employ bulky laboratory equipment and are time consuming. Thus, real-time water quality monitoring is essential for National and International Health and Safety. Environmental water monitoring includes measurements of physical characteristics (e.g. pH, temperature, conductivity), chemical parameters (e.g. oxygen, alkalinity, nitrogen and phosphorus compounds), and abundance of certain biological taxa. Monitoring could also include assays of biological activity such as alkaline phosphatase, tests for toxins such as microcystins and direct measurements of pollutants such as heavy metals or hydrocarbons. Real time detection can significantly reduce the level of damage and also the cost to remedy the problem. This paper presents overview of state-of-the-art methods and devices used for point-of-access water quality monitoring and suggest further developments in this area.

Asymmetric Synthesis of (R)-1-Alkyl Substituted Tetrahydro-ß-carbolines Catalyzed by Strictosidine Synthases.

PubMed

Pressnitz, Desiree; Fischereder, Eva-Maria; Pletz, Jakob; Kofler, Christina; Hammerer, Lucas; Hiebler, Katharina; Lechner, Horst; Richter, Nina; Eger, Elisabeth; Kroutil, Wolfgang

2018-05-31

Stereoselective methods for the synthesis of tetrahydro-ß-carbolines are of significant interest due to the broad spectrum of biological activity of the target molecules. In the plant kingdom strictosidine synthases catalyze the C-C coupling via a Pictet-Spengler reaction of tryptamine and secologanin to exclusively form the (S)-configured tetrahydro-ß-carboline (S)-strictosidine. Investigating the biocatalytic Pictet-Spengler reaction of tryptamine with small-molecular-weight aliphatic aldehydes revealed that the strictosidine synthases gave unexpectedly access to the (R)-configured product. Developing an efficient expression method of the catalyst allowed the preparative transformation of various aldehydes giving the products with up to >98% ee. With this tool in hand a chemoenzymatic two-step synthesis of (R)-harmicine was achieved giving (R)-harmicine in 67% overall yield in optically pure form. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

BCM Search Launcher--an integrated interface to molecular biology data base search and analysis services available on the World Wide Web.

PubMed

Smith, R F; Wiese, B A; Wojzynski, M K; Davison, D B; Worley, K C

1996-05-01

The BCM Search Launcher is an integrated set of World Wide Web (WWW) pages that organize molecular biology-related search and analysis services available on the WWW by function, and provide a single point of entry for related searches. The Protein Sequence Search Page, for example, provides a single sequence entry form for submitting sequences to WWW servers that offer remote access to a variety of different protein sequence search tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, PROSITE, and BLOCKS searches. Other Launch pages provide access to (1) nucleic acid sequence searches, (2) multiple and pair-wise sequence alignments, (3) gene feature searches, (4) protein secondary structure prediction, and (5) miscellaneous sequence utilities (e.g., six-frame translation). The BCM Search Launcher also provides a mechanism to extend the utility of other WWW services by adding supplementary hypertext links to results returned by remote servers. For example, links to the NCBI's Entrez data base and to the Sequence Retrieval System (SRS) are added to search results returned by the NCBI's WWW BLAST server. These links provide easy access to auxiliary information, such as Medline abstracts, that can be extremely helpful when analyzing BLAST data base hits. For new or infrequent users of sequence data base search tools, we have preset the default search parameters to provide the most informative first-pass sequence analysis possible. We have also developed a batch client interface for Unix and Macintosh computers that allows multiple input sequences to be searched automatically as a background task, with the results returned as individual HTML documents directly to the user's system. The BCM Search Launcher and batch client are available on the WWW at URL http:@gc.bcm.tmc.edu:8088/search-launcher.html.

12 CFR 573.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2014 CFR

2014-01-01

... access number or access code, does not include a number or code in an encrypted form, as long as you do... account number or similar form of access number or access code for a consumer's credit card account... or access code: (1) To your agent or service provider solely in order to perform marketing for your...

12 CFR 573.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2012 CFR

2012-01-01

... access number or access code, does not include a number or code in an encrypted form, as long as you do... reporting agency, an account number or similar form of access number or access code for a consumer's credit... number or access code: (1) To your agent or service provider solely in order to perform marketing for...

12 CFR 573.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2011 CFR

2011-01-01

... access number or access code, does not include a number or code in an encrypted form, as long as you do... reporting agency, an account number or similar form of access number or access code for a consumer's credit... number or access code: (1) To your agent or service provider solely in order to perform marketing for...

12 CFR 573.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2013 CFR

2013-01-01

... access number or access code, does not include a number or code in an encrypted form, as long as you do... account number or similar form of access number or access code for a consumer's credit card account... or access code: (1) To your agent or service provider solely in order to perform marketing for your...

[Tissue repositories for research at Sheba Medical Center(SMC].

PubMed

Cohen, Yehudit; Barshack, Iris; Onn, Amir

2013-06-01

Cancer is the number one cause of death in both genders. Breakthroughs in the understanding of cancer biology, the identification of prognostic factors, and the development of new treatments are increasingly dependent on access to human cancer tissues with linked clinicopathological data. Access to human tumor samples and a large investment in translational research are needed to advance this research. The SMC tissue repositories provide researchers with biological materials, which are essential tools for cancer research. SMC tissue repositories for research aim to collect, document and preserve human biospecimens from patients with cancerous diseases. This is in order to provide the highest quality and well annotated biological biospecimens, used as essential tools to achieve the growing demands of scientific research needs. Such repositories are partners in acceLerating biomedical research and medical product development through clinical resources, in order to apply best options to the patients. Following Institutional Review Board approval and signing an Informed Consent Form, the tumor and tumor-free specimens are coLLected by a designated pathologist at the operating room only when there is a sufficient amount of the tumor, in excess of the routine needs. Blood samples are collected prior to the procedure. Other types of specimens collected include ascites fluid, pleural effusion, tissues for Optimal Cutting Temperature [OCT] and primary culture etc. Demographic, clinical, pathologicaL, and follow-up data are collected in a designated database. SMC has already established several organ or disease-specific tissue repositories within different departments. The foundation of tissue repositories requires the concentrated effort of a multidisciplinary team composed of paramedical, medical and scientific professionals. Research projects using these specimens facilitate the development of 'targeted therapy', accelerate basic research aimed at clarifying molecular mechanisms involved in cancer, and support the development of novel diagnostic tools.

The Importance of Transition Metals in the Expanding Network of Microbial Metabolism in the Archean Eon

NASA Astrophysics Data System (ADS)

Moore, E. K.; Jelen, B. I.; Giovannelli, D.; Prabhu, A.; Raanan, H.; Falkowski, P. G.

2017-12-01

Deep time changes in Earth surface redox conditions, particularly due to global oxygenation, has impacted the availability of different metals and substrates that are central in biology. Oxidoreductase proteins are molecular nanomachines responsible for all biological electron transfer processes across the tree of life. These enzymes largely contain transition metals in their active sites. Microbial metabolic pathways form a global network of electron transfer, which expanded throughout the Archean eon. Older metabolisms (sulfur reduction, methanogenesis, anoxygenic photosynthesis) accessed negative redox potentials, while later evolving metabolisms (oxygenic photosynthesis, nitrification/denitrification, aerobic respiration) accessed positive redox potentials. The incorporation of different transition metals facilitated biological innovation and the expansion of the network of microbial metabolism. Network analysis was used to examine the connections between microbial taxa, metabolic pathways, crucial metallocofactors, and substrates in deep time by incorporating biosignatures preserved in the geologic record. Nitrogen fixation and aerobic respiration have the highest level of betweenness among metabolisms in the network, indicating that the oldest metabolisms are not the most central. Fe has by far the highest betweenness among metals. Clustering analysis largely separates High Metal Bacteria (HMB), Low Metal Bacteria (LMB), and Archaea showing that simple un-weighted links between taxa, metabolism, and metals have phylogenetic relevance. On average HMB have the highest betweenness among taxa, followed by Archaea and LMB. There is a correlation between the number of metallocofactors and metabolic pathways in representative bacterial taxa, but Archaea do not follow this trend. In many cases older and more recently evolved metabolisms were clustered together supporting previous findings that proliferation of metabolic pathways is not necessarily chronological.

Accessing Nature’s diversity through metabolic engineering and synthetic biology

PubMed Central

King, Jason R.; Edgar, Steven; Qiao, Kangjian; Stephanopoulos, Gregory

2016-01-01

In this perspective, we highlight recent examples and trends in metabolic engineering and synthetic biology that demonstrate the synthetic potential of enzyme and pathway engineering for natural product discovery. In doing so, we introduce natural paradigms of secondary metabolism whereby simple carbon substrates are combined into complex molecules through “scaffold diversification”, and subsequent “derivatization” of these scaffolds is used to synthesize distinct complex natural products. We provide examples in which modern pathway engineering efforts including combinatorial biosynthesis and biological retrosynthesis can be coupled to directed enzyme evolution and rational enzyme engineering to allow access to the “privileged” chemical space of natural products in industry-proven microbes. Finally, we forecast the potential to produce natural product-like discovery platforms in biological systems that are amenable to single-step discovery, validation, and synthesis for streamlined discovery and production of biologically active agents. PMID:27081481

Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature

PubMed Central

Müller, Hans-Michael; Kenny, Eimear E

2004-01-01

We have developed Textpresso, a new text-mining system for scientific literature whose capabilities go far beyond those of a simple keyword search engine. Textpresso's two major elements are a collection of the full text of scientific articles split into individual sentences, and the implementation of categories of terms for which a database of articles and individual sentences can be searched. The categories are classes of biological concepts (e.g., gene, allele, cell or cell group, phenotype, etc.) and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., biological process, etc.). Together they form a catalog of types of objects and concepts called an ontology. After this ontology is populated with terms, the whole corpus of articles and abstracts is marked up to identify terms of these categories. The current ontology comprises 33 categories of terms. A search engine enables the user to search for one or a combination of these tags and/or keywords within a sentence or document, and as the ontology allows word meaning to be queried, it is possible to formulate semantic queries. Full text access increases recall of biological data types from 45% to 95%. Extraction of particular biological facts, such as gene-gene interactions, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to identify sentences; in searches for two uniquely named genes and an interaction term, the ontology confers a 3-fold increase of search efficiency. Textpresso currently focuses on Caenorhabditis elegans literature, with 3,800 full text articles and 16,000 abstracts. The lexicon of the ontology contains 14,500 entries, each of which includes all versions of a specific word or phrase, and it includes all categories of the Gene Ontology database. Textpresso is a useful curation tool, as well as search engine for researchers, and can readily be extended to other organism-specific corpora of text. Textpresso can be accessed at http://www.textpresso.org or via WormBase at http://www.wormbase.org. PMID:15383839

76 FR 41272 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-13

....375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives, National...

Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research

PubMed Central

Benfey, Philip N.; Bennett, Malcolm; Schiefelbein, John

2010-01-01

Summary Prior to the availability of the genome sequence, the root of Arabidopsis had attracted a small but ardent group of researchers drawn to its accessibility and developmental simplicity. Roots are easily observed when grown on the surface of nutrient agar media, facilitating analysis of responses to stimuli such as gravity and touch. Developmental biologists were attracted to the simple radial organization of primary root tissues, which form a series of concentric cylinders around the central vascular tissue. Equally attractive was the mode of propagation, with stem cells at the tip giving rise to progeny that were confined to cell files. These properties of root development reduced the normal four-dimensional problem of development (three spatial dimensions and time) to a two-dimensional problem, with cell type on the radial axis and developmental time along the longitudinal axis. The availability of the complete Arabidopsis genome sequence has dramatically accelerated traditional genetic research on root biology, and has also enabled entirely new experimental strategies to be applied. Here we review examples of the ways in which availability of the Arabidopsis genome sequence has enhanced progress in understanding root biology. PMID:20409273

Quantification of phenylethylamine and p-tyramine in rat tissues using a new radioenzymatic assay

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

Hamburger, S.A.; Henry, D.P.

Phenylethylamine (PEA) and p-tyramine (p-tym) are biologically active aralkylamines that are found in a number of mammalian tissues, including brain and plasma. The investigation of the biological role of these substances has been hampered by the lack of accessible assay methodology. They have developed a new radioenzymatic assay using barley root tyramine N-methyltransferase and tritiated S-adenosylmethionine. The products formed by the reaction are isolated by TLC. The assay sensitivity was 2.1 and 1.0 pg/tube for PEA and p-tym, respectively. The concentration of PEA and p-tym was determined simultaneously in tissues from Sprague-Dawley rats (280 gm). Plasma PEA and p-tym weremore » 478 +/- 66 and 309 +/- 69 pg/ml, respectively. They conclude that this new procedure is applicable to all tissues examined in that all tissues contain both PEA and p-tym and that these amines are heterogeneously distributed in rat tissues.« less

A virtual tissue bank for primary central nervous system lymphomas in immunocompetent individuals.

PubMed

Ponzoni, Maurilio; Kwee, Ivo; Mazzucchelli, Luca; Ferreri, Andrés J M; Zucca, Emanuele; Doglioni, Claudio; Cavalli, Franco; Bertoni, Francesco

2007-01-01

Primary central nervous system lymphoma (PCNSL) is a rare form of extranodal non-Hodgkin's lymphoma with continuously increasing incidence in both immunosuppressed and immunocompetent individuals. PCNSL is a very aggressive tumor with a poor outcome, and its clinical outcome is much worse than for nodal lymphomas. Differently from lymphomas arising in lymph nodes or in other extranodal sites, the treatment of PCNSL remains very unsatisfactory. Current biologic knowledge of PCNSL is still limited and several fundamental questions remain to be answered. This is mainly due to the paucity of PCNSL material for adequate translational research. With the aim of providing biologic material to investigators interested in PCNSL, we have implemented a virtual tissue bank (VTB) for PCNSL in immunocompetent patients. After registration, the VTB is accessible via any web browser at www.ielsg.org. Only anonymous data are centralized at the website of the International Extranodal Lymphoma Study Group, whilst the pathologic material is maintained at the local pathology institutes. (c) 2007 S. Karger AG, Basel.

Integration, Networking, and Global Biobanking in the Age of New Biology.

PubMed

Karimi-Busheri, Feridoun; Rasouli-Nia, Aghdass

2015-01-01

Scientific revolution is changing the world forever. Many new disciplines and fields have emerged with unlimited possibilities and opportunities. Biobanking is one of many that is benefiting from revolutionary milestones in human genome, post-genomic, and computer and bioinformatics discoveries. The storage, management, and analysis of massive clinical and biological data sets cannot be achieved without a global collaboration and networking. At the same time, biobanking is facing many significant challenges that need to be addressed and solved including dealing with an ever increasing complexity of sample storage and retrieval, data management and integration, and establishing common platforms in a global context. The overall picture of the biobanking of the future, however, is promising. Many population-based biobanks have been formed, and more are under development. It is certain that amazing discoveries will emerge from this large-scale method of preserving and accessing human samples. Signs of a healthy collaboration between industry, academy, and government are encouraging.

Living donor kidney transplantation: "beauty and the beast"!

PubMed

Danovitch, Gabriel M

2013-01-01

The report by Terasaki and colleagues in 1995 that the outcomes of spousal and biologically unrelated transplants were essentially the same as for 1-haplotype matched living related transplants changed the course of clinical transplantation. This article, entitled metaphorically "Beauty and the Beast", describes the dramatic change in the practice of living donor transplantation that followed. In the ensuing two decades, biologically unrelated living donor transplantation became commonplace in the developed world and reached its apotheosis in cross-country living donor paired exchange programs that have made transplantation accessible to many whose donors were deemed "incompatible". Such exchanges can indeed be thought of as a "thing of beauty". Sadly, the same observation was abused to exploit vulnerable donors, and the "beast" in the form of transplant tourism became a feature of transplantation in the developing world. The responsibility of the transplant community to protect the welfare of living donors and their recipients and the key role of trust in the evaluation of living donors is discussed.

Gambling involvement and increased risk of gambling problems.

PubMed

Phillips, James G; Ogeil, Rowan; Chow, Yang-Wai; Blaszczynski, Alex

2013-12-01

The opportunity to gamble has undergone rapid expansion with technology allowing for access to gambling products 24 h a day. This increased online availability challenges governments' abilities to restrict access to gambling. Indeed, the ready access to multiple forms of gambling may potentially contribute to impaired control over urges for problem gamblers. The present study considered whether problem gamblers manifested a tendency to engage in multiple forms of gambling and identified forms of gambling which were more strongly related to problem gambling. In reanalyses of two surveys (Sample 1, N = 464, Sample 2, N = 1141), significant relationships accounting for between 11.3 and 13.5% of the variance were found between the numbers of forms of gambling accessed and degree of problem. Participation in online poker, playing cards and sports wagering were linked to problem gambling. Access to multiple forms of gambling may pose difficulties for the tracking and control of gambling.

77 FR 11562 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-27

... Domestic Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special...

77 FR 33478 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-06

... Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

76 FR 71351 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-17

... Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

77 FR 33471 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-06

... Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

77 FR 10541 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-22

....gov . Catalogue of Federal Domestic Assistanve Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

75 FR 70014 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-16

... Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

75 FR 30410 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-01

... Domestic Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special...

77 FR 10541 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-22

.... 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives, National...

77 FR 14407 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-09

... Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives, National Institutes of Health...

77 FR 31862 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-30

... Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

75 FR 65363 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-22

... Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

77 FR 61612 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-10

... Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

Spread of hatch and delayed feed access affect post hatch performance of female broiler chicks up to day 5.

PubMed

Wang, Y; Li, Y; Willems, E; Willemsen, H; Franssens, L; Koppenol, A; Guo, X; Tona, K; Decuypere, E; Buyse, J; Everaert, N

2014-04-01

It is not rare that newly hatched chicks remain without feed for about 24 to 48 h before they are placed on farms due to a series of logistic operations. Furthermore, the spread in hatching time can also mount up to 30 to 48 h for late v. early hatchers. In other words, the practice is a complex combination of spread of hatch and delayed feed access. The present study was aimed to investigate the combined effects of hatching time with a delay in feed access of 48 h, starting from their hatch-time (biological age). When chicks had access to feed immediately after hatch, late hatchers had a higher feed intake and relative growth rate up to day 5 compared with their early hatched counterparts. Feed deprivation during the first 48 h resulted in retarded early growth rate, which was further aggravated by an impaired feed intake after refeeding. In addition, the differential effects of hatching time on relative growth rate and feed intake observed in immediately fed chicks were eliminated by the 48 h feed delay. The yolk utilization after hatch was faster for the late hatchers up to biological day 2 regardless of the feeding treatments. Hatching muscle glycogen content was higher in the late hatchers compared with that of their early counterparts at hatch and at biological day 2 independent of feeding treatment. Moreover, the liver glycogen content of the late hatchers was also higher at hatch. For the immediately fed chicks, the proportional breast muscle weight of the late hatchers was higher at biological day 2 and 5. For the starved chicks, on the other hand, this effect was only observed after they had access to feed (biological day 5). The different plasma T3 levels at hatch may have contributed to the different post hatch performance. It is concluded that the spread of hatch influenced post hatch performance, especially appetite and growth at least until day 5. Moreover, the delay in feed access interacted with the hatching time and caused adverse effects on the post hatch performance.

Efficient computation of co-transcriptional RNA-ligand interaction dynamics.

PubMed

Wolfinger, Michael T; Flamm, Christoph; Hofacker, Ivo L

2018-05-04

Riboswitches form an abundant class of cis-regulatory RNA elements that mediate gene expression by binding a small metabolite. For synthetic biology applications, they are becoming cheap and accessible systems for selectively triggering transcription or translation of downstream genes. Many riboswitches are kinetically controlled, hence knowledge of their co-transcriptional mechanisms is essential. We present here an efficient implementation for analyzing co-transcriptional RNA-ligand interaction dynamics. This approach allows for the first time to model concentration-dependent metabolite binding/unbinding kinetics. We exemplify this novel approach by means of the recently studied I-A 2 ' -deoxyguanosine (2 ' dG)-sensing riboswitch from Mesoplasma florum. Copyright © 2018 Elsevier Inc. All rights reserved.

Bacillus odysseyi isolate

NASA Technical Reports Server (NTRS)

La Duc, Myron Thomas (Inventor); Venkateswaran, Kasthuri (Inventor)

2007-01-01

The present invention relates to discovery and isolation of a biologically pure culture of a Bacillus odysseyi isolate with high adherence and sterilization resistant properties. B. odysseyi is a round spore forming Bacillus species that produces an exosporium. This novel species has been characterized on the basis of phenotypic traits, 16S rDNA sequence analysis and DNA-DNA hybridization. According to the results of these analyses, this strain belongs to the genus Bacillus and the type strain is 34hs-1.sup.T (=ATCC PTA-4993.sup.T=NRRL B-30641.sup.T=NBRC 100172.sup.T). The GenBank accession number for the 16S rDNA sequence of strain 34hs-1.sup.T is AF526913.

Exchange of natural enemies for biological control: is it a rocky road?-the road in the Euro-Mediterranean region and the South American common market.

PubMed

Coutinot, D; Briano, J; Parra, J R P; de Sá, L A N; Cônsoli, F L

2013-02-01

The access and benefit sharing (ABS) regulations from the Convention on Biological Diversity (CBD) for the use of natural resources became an important issue because the biodiversity of developing countries was heavily accessed and unilaterally exploited by pharmaceutical and seed companies. However, natural enemies used for biological control are living and unmodified genetic resources which cannot be patented and have been treated as resources such as drugs, seeds, or other commercial products. Consequently, the ABS requirements have limited not only the use of natural enemies but also the positive effects that scientifically supported biological control strategies have on the society, the environment, and the economy, reducing problems of pesticide residues, water and soil contamination, and non-target effects. During the last several years, the biological control scientific community has faced new and extremely complicated legislation dictated by a high and diverse number of governmental agencies at different levels, making the access to natural resources for biocontrol purposes a rocky road. Society at large should be aware of how the strict ABS regulations affect the use of natural enemies as biological resources to secure food production, food safety, and global environmental protection. We discuss in here the current difficulties derived from CBD for the exchange of natural enemies taking as example the Euro-Mediterranean region, Argentina, and Brazil to demonstrate how long and diverse are the steps to be followed to obtain the required permits for access and exportation/importation of natural enemies. We then argue that the public visibility of biocontrol strategies should be increased and their benefits highlighted in order to persuade legislators for the development of a less bureaucratic, more expedient, and more centralized regulatory frame, greatly favoring the practice and benefits of biological control. We finally propose a general framework in which ABS issues should be dealt in ways to attend the CBD, but also to make the use of natural resources for the biological control of pests to secure food production and security a possible alternative.

Biological drugs for the treatment of psoriasis in a public health system

PubMed Central

Lopes, Luciane Cruz; Silveira, Miriam Sanches do Nascimento; de Camargo, Iara Alves; Barberato, Silvio; Del Fiol, Fernando de Sá; Osorio-de-Castro, Claudia Garcia Serpa

2014-01-01

OBJECTIVE To analyze the access and utilization profile of biological medications for psoriasis provided by the judicial system in Brazil. METHODS This is a cross-sectional study. We interviewed a total of 203 patients with psoriasis who were on biological medications obtained by the judicial system of the State of Sao Paulo, from 2004 to 2010. Sociodemographics, medical, and political-administrative characteristics were complemented with data obtained from dispensation orders that included biological medications to treat psoriasis and the legal actions involved. The data was analyzed using an electronic data base and shown as simple variable frequencies. The prescriptions contained in the lawsuits were analyzed according to legal provisions. RESULTS A total of 190 lawsuits requesting several biological drugs (adalimumab, efalizumab, etanercept, and infliximab) were analyzed. Patients obtained these medications as a result of injunctions (59.5%) or without having ever demanded biological medication from any health institution (86.2%), i.e., public or private health services. They used the prerogative of free legal aid (72.6%), even though they were represented by private lawyers (91.1%) and treated in private facilities (69.5%). Most of the patients used a biological medication for more than 13 months (66.0%), and some patients were undergoing treatment with this medication when interviewed (44.9%). Approximately one third of the patients discontinued treatment due to worsening of their illness (26.6%), adverse drug reactions (20.5%), lack of efficacy, or because the doctor discontinued this medication (13.8%). None of the analyzed medical prescriptions matched the legal prescribing requirements. Clinical monitoring results showed that 70.3% of the patients had not undergone laboratory examinations (blood work, liver and kidney function tests) for treatment control purposes. CONCLUSIONS The plaintiffs resorted to legal action to get access to biological medications because they were either unaware or had difficulty in accessing them through institutional public health system procedures. Access by means of legal action facilitated long-term use of this type of medication through irregular prescriptions and led to a high rate of adverse drug reactions as well as inappropriate clinical monitoring. PMID:25210824

17 CFR 274.402 - Form ID, uniform application for access codes to file on EDGAR.

Code of Federal Regulations, 2010 CFR

2010-04-01

... for access codes to file on EDGAR. 274.402 Section 274.402 Commodity and Securities Exchanges... Forms for Electronic Filing § 274.402 Form ID, uniform application for access codes to file on EDGAR..., filing agent or training agent to log on to the EDGAR system, submit filings, and change its CCC. (d...

17 CFR 239.63 - Form ID, uniform application for access codes to file on EDGAR.

Code of Federal Regulations, 2011 CFR

2011-04-01

... for access codes to file on EDGAR. 239.63 Section 239.63 Commodity and Securities Exchanges SECURITIES... Statements § 239.63 Form ID, uniform application for access codes to file on EDGAR. Form ID must be filed by... log on to the EDGAR system, submit filings, and change its CCC. (d) Password Modification...

17 CFR 239.63 - Form ID, uniform application for access codes to file on EDGAR.

Code of Federal Regulations, 2010 CFR

2010-04-01

... for access codes to file on EDGAR. 239.63 Section 239.63 Commodity and Securities Exchanges SECURITIES... Statements § 239.63 Form ID, uniform application for access codes to file on EDGAR. Form ID must be filed by... log on to the EDGAR system, submit filings, and change its CCC. (d) Password Modification...

17 CFR 274.402 - Form ID, uniform application for access codes to file on EDGAR.

Code of Federal Regulations, 2011 CFR

2011-04-01

... for access codes to file on EDGAR. 274.402 Section 274.402 Commodity and Securities Exchanges... Forms for Electronic Filing § 274.402 Form ID, uniform application for access codes to file on EDGAR..., filing agent or training agent to log on to the EDGAR system, submit filings, and change its CCC. (d...

WWW.Cell Biology Education: Using the World Wide Web to Develop a New Teaching Topic

ERIC Educational Resources Information Center

Blystone, Robert V.; MacAlpine, Barbara

2005-01-01

"Cell Biology Education" calls attention each quarter to several Web sites of educational interest to the biology community. The Internet provides access to an enormous array of potential teaching materials. In this article, the authors describe one approach for using the World Wide Web to develop a new college biology laboratory exercise. As a…

77 FR 33477 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-06

... Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

76 FR 71350 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-17

... Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

75 FR 71712 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-24

... Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

77 FR 15783 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-16

... Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

78 FR 13364 - National Institute of General Medical Sciences; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-27

... Committee: National Institute of General Medical Sciences Special Emphasis Panel; Systems Biology Grant... Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research... Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

Report on the 5th International Bio-logging Symposium

DTIC Science & Technology

2014-09-30

LONG-TERM GOALS Bio-logging originated in the marine (polar) realm, which explains why marine mammals remain today the main biological models in...Wikelski as the convenor. The Proceedings of BLS5 will be published in two open-access BioMed Central (BMC) journals: Animal Biotelemetry (http

76 FR 13197 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-10

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Develop.m.ental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives, National Institutes of Health, HHS) Dated...

75 FR 28810 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-24

... funding cycle. (Catalogue of Federal Domestic Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research...

75 FR 30408 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-01

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives, National Institutes of Health, HHS) Dated: May 25...

76 FR 67199 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-31

... Research Support; 93.821, Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives, National Institutes of Health, HHS) Dated: October...

78 FR 13362 - National Institute of General Medical Sciences; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-27

... Sciences Special Emphasis Panel Program Projects in Anesthesiology. Date: March 15, 2013. Time: 1:00 p.m..., Cell Biology and Biophysics Research; 93.859, Pharmacology, Physiology, and Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers...

Prediction of phenotypes of missense mutations in human proteins from biological assemblies.

PubMed

Wei, Qiong; Xu, Qifang; Dunbrack, Roland L

2013-02-01

Single nucleotide polymorphisms (SNPs) are the most frequent variation in the human genome. Nonsynonymous SNPs that lead to missense mutations can be neutral or deleterious, and several computational methods have been presented that predict the phenotype of human missense mutations. These methods use sequence-based and structure-based features in various combinations, relying on different statistical distributions of these features for deleterious and neutral mutations. One structure-based feature that has not been studied significantly is the accessible surface area within biologically relevant oligomeric assemblies. These assemblies are different from the crystallographic asymmetric unit for more than half of X-ray crystal structures. We find that mutations in the core of proteins or in the interfaces in biological assemblies are significantly more likely to be disease-associated than those on the surface of the biological assemblies. For structures with more than one protein in the biological assembly (whether the same sequence or different), we find the accessible surface area from biological assemblies provides a statistically significant improvement in prediction over the accessible surface area of monomers from protein crystal structures (P = 6e-5). When adding this information to sequence-based features such as the difference between wildtype and mutant position-specific profile scores, the improvement from biological assemblies is statistically significant but much smaller (P = 0.018). Combining this information with sequence-based features in a support vector machine leads to 82% accuracy on a balanced dataset of 50% disease-associated mutations from SwissVar and 50% neutral mutations from human/primate sequence differences in orthologous proteins. Copyright © 2012 Wiley Periodicals, Inc.

17 CFR 9.11 - Form, contents and delivery of notice of disciplinary or access denial action.

Code of Federal Regulations, 2010 CFR

2010-04-01

... notice of disciplinary or access denial action. 9.11 Section 9.11 Commodity and Securities Exchanges... OTHER ADVERSE ACTIONS Notice and Effective Date of Disciplinary Action or Access Denial Action § 9.11 Form, contents and delivery of notice of disciplinary or access denial action. (a) When required...

Copper-Catalyzed Synthesis of Trifluoroethylarenes from Benzylic Bromodifluoroacetates.

PubMed

Ambler, Brett R; Zhu, Lingui; Altman, Ryan A

2015-08-21

Trifluoroethylarenes are found in a variety of biologically active molecules, and strategies for accessing this substructure are important for developing therapeutic candidates and biological probes. Trifluoroethylarenes can be directly accessed via nucleophilic trifluoromethylation of benzylic electrophiles; however, current catalytic methods do not effectively transform electron-deficient substrates and heterocycles. To address this gap, we report a Cu-catalyzed decarboxylative trifluoromethylation of benzylic bromodifluoroacetates. To account for the tolerance of sensitive functional groups, we propose an inner-sphere mechanism of decarboxylation.

Laying the foundations for a bio-economy

PubMed Central

2008-01-01

Biological technologies are becoming an important part of the economy. Biotechnology already contributes at least 1% of US GDP, with revenues growing as much as 20% annually. The introduction of composable biological parts will enable an engineering discipline similar to the ones that resulted in modern aviation and information technology. As the sophistication of biological engineering increases, it will provide new goods and services at lower costs and higher efficiencies. Broad access to foundational engineering technologies is seen by some as a threat to physical and economic security. However, regulation of access will serve to suppress the innovation required to produce new vaccines and other countermeasures as well as limiting general economic growth. PMID:19003445

Prokaryotic cytoskeletons: protein filaments organizing small cells.

PubMed

Wagstaff, James; Löwe, Jan

2018-04-01

Most, if not all, bacterial and archaeal cells contain at least one protein filament system. Although these filament systems in some cases form structures that are very similar to eukaryotic cytoskeletons, the term 'prokaryotic cytoskeletons' is used to refer to many different kinds of protein filaments. Cytoskeletons achieve their functions through polymerization of protein monomers and the resulting ability to access length scales larger than the size of the monomer. Prokaryotic cytoskeletons are involved in many fundamental aspects of prokaryotic cell biology and have important roles in cell shape determination, cell division and nonchromosomal DNA segregation. Some of the filament-forming proteins have been classified into a small number of conserved protein families, for example, the almost ubiquitous tubulin and actin superfamilies. To understand what makes filaments special and how the cytoskeletons they form enable cells to perform essential functions, the structure and function of cytoskeletal molecules and their filaments have been investigated in diverse bacteria and archaea. In this Review, we bring these data together to highlight the diverse ways that linear protein polymers can be used to organize other molecules and structures in bacteria and archaea.

Memorandum "Open Metadata". Open Access to Documentation Forms and Item Catalogs in Healthcare.

PubMed

Dugas, M; Jöckel, K-H; Friede, T; Gefeller, O; Kieser, M; Marschollek, M; Ammenwerth, E; Röhrig, R; Knaup-Gregori, P; Prokosch, H-U

2015-01-01

At present, most documentation forms and item catalogs in healthcare are not accessible to the public. This applies to assessment forms of routine patient care as well as case report forms (CRFs) of clinical and epidemiological studies. On behalf of the German chairs for Medical Informatics, Biometry and Epidemiology six recommendations to developers and users of documentation forms in healthcare were developed. Open access to medical documentation forms could substantially improve information systems in healthcare and medical research networks. Therefore these forms should be made available to the scientific community, their use should not be unduly restricted, they should be published in a sustainable way using international standards and sources of documentation forms should be referenced in scientific publications.

Image portion identification methods, image parsing methods, image parsing systems, and articles of manufacture

DOEpatents

Lassahn, Gordon D.; Lancaster, Gregory D.; Apel, William A.; Thompson, Vicki S.

2013-01-08

Image portion identification methods, image parsing methods, image parsing systems, and articles of manufacture are described. According to one embodiment, an image portion identification method includes accessing data regarding an image depicting a plurality of biological substrates corresponding to at least one biological sample and indicating presence of at least one biological indicator within the biological sample and, using processing circuitry, automatically identifying a portion of the image depicting one of the biological substrates but not others of the biological substrates.

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems

PubMed Central

Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K.; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C.; Hoeng, Julia

2015-01-01

With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com PMID:25887162

17 CFR 248.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2012 CFR

2012-04-01

... number or access code, does not include a number or code in an encrypted form, as long as you do not... agency, an account number or similar form of access number or access code for a consumer's credit card... number or access code: (1) To your agent or service provider solely in order to perform marketing for...

17 CFR 248.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2013 CFR

2013-04-01

... number or access code, does not include a number or code in an encrypted form, as long as you do not... agency, an account number or similar form of access number or access code for a consumer's credit card... number or access code: (1) To your agent or service provider solely in order to perform marketing for...

17 CFR 248.12 - Limits on sharing account number information for marketing purposes.

Code of Federal Regulations, 2011 CFR

2011-04-01

... number or access code, does not include a number or code in an encrypted form, as long as you do not... agency, an account number or similar form of access number or access code for a consumer's credit card... number or access code: (1) To your agent or service provider solely in order to perform marketing for...

[Role of academic social networks in disseminating the scientific production of researchers in biology/medicine: the example of ResearchGate].

PubMed

Boudry, Christophe; Bouchard, Aline

2017-01-01

Over time, academic social networks are more and more used by researchers, especially thanks to the possibilities of sharing articles they offer. The objective of the present study was to evaluate the proportion, the typology (pre-print, post-print author/publisher) and the legality of the full-text publications deposited by researchers on ResearchGate which is widely used by the medical and biological community, using a sample of 1,500 randomly selected articles in PubMed and published between 2013 and 2015. To compare, the access to the full-text of the 1500 articles via PubMed and PubMed Central has been assessed, putting into evidence the important role ResearchGate plays for providing full-texts of articles in biology/medicine. It also puts academic social networks into perspective in relation to open-access repositories and open access. © 2017 médecine/sciences – Inserm.

Programmable self-assembly of three-dimensional nanostructures from 104 unique components

PubMed Central

Ong, Luvena L.; Hanikel, Nikita; Yaghi, Omar K.; Grun, Casey; Strauss, Maximilian T.; Bron, Patrick; Lai-Kee-Him, Josephine; Schueder, Florian; Wang, Bei; Wang, Pengfei; Kishi, Jocelyn Y.; Myhrvold, Cameron A.; Zhu, Allen; Jungmann, Ralf

2017-01-01

Nucleic acids (DNA and RNA) are widely used to construct nanoscale structures with ever increasing complexity1–14 for possible applications in fields as diverse as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early examples typically containing on the order of 10 unique DNA strands. The introduction of DNA origami4, which uses many staple strands to fold one long scaffold strand into a desired structure, gave access to kilo- to mega-dalton nanostructures containing about 102 unique DNA strands6,7,10,13 . Aiming for even larger DNA origami structures is in principle possible15,16, but faces the challenge of having to manufacture and route an increasingly long scaffold strand. An alternative and in principle more readily scalable approach uses DNA brick assembly8,9, which doesn’t need a scaffold and instead uses hundreds of short DNA brick strands that self-assemble according to specific inter-brick interactions. First-generation bricks used to create 3D structures are 32-nt long with four 8-nt binding domains that directed 102 distinct bricks into well-formed assemblies, but attempts to create larger structures encountered practical challenges and had limited success.9 Here we show that a new generation of DNA bricks with longer binding domains makes it possible to self-assemble 0.1 – 1 giga-dalton three-dimensional nanostructures from 104 unique components, including a 0.5 giga-dalton cuboid containing 30,000 unique bricks and a 1 giga-dalton rotationally symmetric tetramer. We also assemble a cuboid containing 10,000 bricks and 20,000 uniquely addressable ‘nano-voxels’ that serves as a molecular canvas for three-dimensional sculpting, with introduction of sophisticated user-prescribed 3D cavities yielding structures such as letters, a complex helicoid and a teddy bear. We anticipate that, with further optimization, even larger assemblies might be accessible and prove useful as scaffolds or for positioning functional components. PMID:29219968

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

PubMed Central

Aziz, Ramy K.; Devoid, Scott; Disz, Terrence; Edwards, Robert A.; Henry, Christopher S.; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Stevens, Rick L.; Vonstein, Veronika; Xia, Fangfang

2012-01-01

The remarkable advance in sequencing technology and the rising interest in medical and environmental microbiology, biotechnology, and synthetic biology resulted in a deluge of published microbial genomes. Yet, genome annotation, comparison, and modeling remain a major bottleneck to the translation of sequence information into biological knowledge, hence computational analysis tools are continuously being developed for rapid genome annotation and interpretation. Among the earliest, most comprehensive resources for prokaryotic genome analysis, the SEED project, initiated in 2003 as an integration of genomic data and analysis tools, now contains >5,000 complete genomes, a constantly updated set of curated annotations embodied in a large and growing collection of encoded subsystems, a derived set of protein families, and hundreds of genome-scale metabolic models. Until recently, however, maintaining current copies of the SEED code and data at remote locations has been a pressing issue. To allow high-performance remote access to the SEED database, we developed the SEED Servers (http://www.theseed.org/servers): four network-based servers intended to expose the data in the underlying relational database, support basic annotation services, offer programmatic access to the capabilities of the RAST annotation server, and provide access to a growing collection of metabolic models that support flux balance analysis. The SEED servers offer open access to regularly updated data, the ability to annotate prokaryotic genomes, the ability to create metabolic reconstructions and detailed models of metabolism, and access to hundreds of existing metabolic models. This work offers and supports a framework upon which other groups can build independent research efforts. Large integrations of genomic data represent one of the major intellectual resources driving research in biology, and programmatic access to the SEED data will provide significant utility to a broad collection of potential users. PMID:23110173

75 FR 9909 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-04

... Domestic Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and... and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special...

76 FR 67467 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-01

... Federal Domestic Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, CellBiology...,Genetics and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special...

76 FR 10039 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-23

... Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93... Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

77 FR 64813 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-23

... Domestic Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and... and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special...

43 CFR 11.72 - Quantification phase-baseline services determination.

Code of Federal Regulations, 2010 CFR

2010-10-01

... taxonomist or systematic biologist, who has access to a major systematic biology collection for that taxon... time it should be transferred to a major systematic biology collection; or (iii) In the case of a...

77 FR 5816 - National Institute of General Medical Sciences Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-06

... Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93... Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

76 FR 10043 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-23

... Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research... Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

75 FR 42759 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-22

... and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special... Domestic Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and...

75 FR 35820 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-23

... Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives... Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics...

76 FR 35901 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-20

... and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special... Domestic Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and...

75 FR 45647 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-03

... Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives... Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics...

78 FR 72902 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-04

... Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives... Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics...

77 FR 35413 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-13

... Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives... Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics...

77 FR 61612 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-10

... and Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special... Domestic Assistance Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and...

75 FR 56117 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-15

... Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives... Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research...

77 FR 12857 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-02

... Developmental Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives... Program Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research...

Synthetic Biology: Knowledge Accessed by Everyone (Open Sources)

ERIC Educational Resources Information Center

Sánchez Reyes, Patricia Margarita

2016-01-01

Using the principles of biology, along with engineering and with the help of computer, scientists manage to copy. DNA sequences from nature and use them to create new organisms. DNA is created through engineering and computer science managing to create life inside a laboratory. We cannot dismiss the role that synthetic biology could lead in…

76 FR 10038 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-23

... Sciences Special Emphasis Panel, PSI Biology Meeting. Date: March 11, 2011. Time: 1 p.m. to 5 p.m. Agenda... Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93... Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives...

A Problem-Sorting Task Detects Changes in Undergraduate Biological Expertise over a Single Semester

ERIC Educational Resources Information Center

Hoskinson, Anne-Marie; Maher, Jessica Middlemis; Bekkering, Cody; Ebert-May, Diane

2017-01-01

Calls for undergraduate biology reform share similar goals: to produce people who can organize, use, connect, and communicate about biological knowledge. Achieving these goals requires students to gain disciplinary expertise. Experts organize, access, and apply disciplinary knowledge differently than novices, and expertise is measurable. By asking…

Newspaper Coverage of Biological Subissues in the Spotted Owl Debate, 1989-1993.

ERIC Educational Resources Information Center

Furlow, F. Bryant

1994-01-01

Computer archives for 27 U.S. daily newspapers were accessed to evaluate the levels of coverage for 5 biological subissues and 5 ecological concepts in articles on the spotted owl debate. The author identified a correlation between biologist/reporter contact and increased biological subissue and ecological concepts coverage. (LZ)

Developing Information Fluency in Introductory Biology Students in the Context of an Investigative Laboratory

ERIC Educational Resources Information Center

Lindquester, Gary J.; Burks, Romi L.; Jaslow, Carolyn R.

2005-01-01

Students of biology must learn the scientific method for generating information in the field. Concurrently, they should learn how information is reported and accessed. We developed a progressive set of exercises for the undergraduate introductory biology laboratory that combine these objectives. Pre- and postassessments of approximately 100…

Current Developments in Machine Learning Techniques in Biological Data Mining.

PubMed

Dumancas, Gerard G; Adrianto, Indra; Bello, Ghalib; Dozmorov, Mikhail

2017-01-01

This supplement is intended to focus on the use of machine learning techniques to generate meaningful information on biological data. This supplement under Bioinformatics and Biology Insights aims to provide scientists and researchers working in this rapid and evolving field with online, open-access articles authored by leading international experts in this field. Advances in the field of biology have generated massive opportunities to allow the implementation of modern computational and statistical techniques. Machine learning methods in particular, a subfield of computer science, have evolved as an indispensable tool applied to a wide spectrum of bioinformatics applications. Thus, it is broadly used to investigate the underlying mechanisms leading to a specific disease, as well as the biomarker discovery process. With a growth in this specific area of science comes the need to access up-to-date, high-quality scholarly articles that will leverage the knowledge of scientists and researchers in the various applications of machine learning techniques in mining biological data.

Transesophageal NOTES--a critical analysis of relevant problems.

PubMed

Grund, Karl E; Lehmann, Thorsten G

2010-10-01

The transesophageal access route has not become a principal topic in the discussion about NOTES up to now. Analyzing the problems in this new field of surgery, however, the transesophageal route shows high relevance. Here, all possibilities, limitations, and problems of NOTES become obvious. This paper contains a critical analysis of the literature published to date (nine full papers, five abstracts). Nearly all publications represent experimental studies in living pigs. In most cases a submucosal tunnel technique is performed as access route to mediastinum, pleural cavity, and heart. Interventions and operations include simple mediastinoscopies as well as epicardial operations after exposition of the heart. For access and manipulation, conventional flexible endoscopes and instruments are used. Clips, T-bars, or a combination of both achieve the closure. Some studies rely on spontaneous closure of the incision without any suturing or approximation. In such experimental settings, the following results are presented: Access is achieved in 90% of cases, the aim of the operation is met in 92%, technical success in closure is achieved in 90%, healing of incision assessed as good in two of five studies, satisfactory in three of five studies. Mortality, ranging from 6 to 25%, and complication rates were (surprisingly) high. It has to be stressed that analyzing these papers published to date, no adequate attention is paid to basic facts and problems of general and thoracic surgery (e.g. different forms, prevention, diagnosis and therapy of pneumothorax or differentiated forms of ventilation). Relevant differences in the anatomy and physiology of the esophagus and mediastinum between humans and pigs should additionally be taken into account to choose optimal experimental parameters when transferring results to human settings. Moreover, requirements regarding sterility and hygiene in a structure like the mediastinum, which is at high risk from the point of view of infection biology, have not yet been respected. These factors should be taken into account in further studies--as well as clinically relevant disease patterns in humans--to be able to realize possible advantages of this NOTES access in a clinical setting.

Three-dimensional image contrast using biospeckle

NASA Astrophysics Data System (ADS)

Godinho, Robson Pierangeli; Braga, Roberto A., Jr.

2010-09-01

The biospeckle laser (BSL) has been applied in many areas of knowledge and a variety of approaches has been presented to address the best results in biological and non-biological samples, in fast or slow activities, or else in defined flow of materials or in random activities. The methodologies accounted in the literature consider the apparatus used in the image assembling and the way the collected data is processed. The image processing steps presents in turn a variety of procedures with first or second order statistics analysis, and as well with different sizes of data collected. One way to access the biospeckle in defined flow, such as in capillary blood flow in alive animals, was the adoption of the image contrast technique which uses only one image from the illuminated sample. That approach presents some problems related to the resolution of the image, which is reduced during the image contrast processing. In order to help the visualization of the low resolution image formed by the contrast technique, this work presents the three-dimensional procedure as a reliable alternative to enhance the final image. The work based on a parallel processing, with the generation of a virtual map of amplitudes, and maintaining the quasi-online characteristic of the contrast technique. Therefore, it was possible to generate in the same display the observed material, the image contrast result and in addiction the three-dimensional image with adjustable options of rotation. The platform also offers to the user the possibility to access the 3D image offline.

50 CFR 648.53 - Acceptable biological catch (ABC), annual catch limits (ACL), annual catch targets (ACT), DAS...

Code of Federal Regulations, 2011 CFR

2011-10-01

... be implemented as soon as possible after September 30 each year. (v) The Elephant Trunk Access Area shall change to an open area starting in fishing year 2011. For reference, the Elephant Trunk Access... chart depicting the area previously known as the Elephant Trunk Access Area are available from the...

50 CFR 648.53 - Acceptable biological catch (ABC), annual catch limits (ACL), annual catch targets (ACT), DAS...

Code of Federal Regulations, 2012 CFR

2012-10-01

... be implemented as soon as possible after September 30 each year. (v) The Elephant Trunk Access Area shall change to an open area starting in fishing year 2011. For reference, the Elephant Trunk Access... chart depicting the area previously known as the Elephant Trunk Access Area are available from the...

Specifications of Standards in Systems and Synthetic Biology.

PubMed

Schreiber, Falk; Bader, Gary D; Golebiewski, Martin; Hucka, Michael; Kormeier, Benjamin; Le Novère, Nicolas; Myers, Chris; Nickerson, David; Sommer, Björn; Waltemath, Dagmar; Weise, Stephan

2015-09-04

Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic benefits, such as making information exchange, production, and services more efficient. However, novel, innovative areas often either lack proper standards, or documents about standards in these areas are not available from a centralised platform or formal body (such as the International Standardisation Organisation). Systems and synthetic biology is a relatively novel area, and it is only in the last decade that the standardisation of data, information, and models related to systems and synthetic biology has become a community-wide effort. Several open standards have been established and are under continuous development as a community initiative. COMBINE, the ‘COmputational Modeling in BIology’ NEtwork has been established as an umbrella initiative to coordinate and promote the development of the various community standards and formats for computational models. There are yearly two meeting, HARMONY (Hackathons on Resources for Modeling in Biology), Hackathon-type meetings with a focus on development of the support for standards, and COMBINE forums, workshop-style events with oral presentations, discussion, poster, and breakout sessions for further developing the standards. For more information see http://co.mbine.org/. So far the different standards were published and made accessible through the standards’ web- pages or preprint services. The aim of this special issue is to provide a single, easily accessible and citable platform for the publication of standards in systems and synthetic biology. This special issue is intended to serve as a central access point to standards and related initiatives in systems and synthetic biology, it will be published annually to provide an opportunity for standard development groups to communicate updated specifications.

Biomarkers in Sporadic and Familial Alzheimer's Disease.

PubMed

Lista, Simone; O'Bryant, Sid E; Blennow, Kaj; Dubois, Bruno; Hugon, Jacques; Zetterberg, Henrik; Hampel, Harald

2015-01-01

Most forms of Alzheimer's disease (AD) are sporadic (sAD) or inherited in a non-Mendelian fashion, and less than 1% of cases are autosomal-dominant. Forms of sAD do not exhibit familial aggregation and are characterized by complex genetic and environmental interactions. Recently, the expansion of genomic methodologies, in association with substantially larger combined cohorts, has resulted in various genome-wide association studies that have identified several novel genetic associations of AD. Currently, the most effective methods for establishing the diagnosis of AD are defined by multi-modal pathways, starting with clinical and neuropsychological assessment, cerebrospinal fluid (CSF) analysis, and brain-imaging procedures, all of which have significant cost- and access-to-care barriers. Consequently, research efforts have focused on the development and validation of non-invasive and generalizable blood-based biomarkers. Among the modalities conceptualized by the systems biology paradigm and utilized in the "exploratory biomarker discovery arena", proteome analysis has received the most attention. However, metabolomics, lipidomics, transcriptomics, and epigenomics have recently become key modalities in the search for AD biomarkers. Interestingly, biomarker changes for familial AD (fAD), in many but not all cases, seem similar to those for sAD. The integration of neurogenetics with systems biology/physiology-based strategies and high-throughput technologies for molecular profiling is expected to help identify the causes, mechanisms, and biomarkers associated with the various forms of AD. Moreover, in order to hypothesize the dynamic trajectories of biomarkers through disease stages and elucidate the mechanisms of biomarker alterations, updated and more sophisticated theoretical models have been proposed for both sAD and fAD.

Biosimilars for the management of rheumatoid arthritis: economic considerations.

PubMed

Gulácsi, László; Brodszky, Valentin; Baji, Petra; Kim, HoUng; Kim, Su Yeon; Cho, Yu Young; Péntek, Márta

2015-01-01

Biologic drugs have proved highly effective for the treatment of immune-mediated inflammatory diseases such as rheumatoid arthritis (RA). These drugs are often considered cost-effective for well-defined RA patient populations not responding adequately to conventional treatment, but are used first-line relatively rarely, partly due to high costs. Furthermore, not all clinically eligible patients can access biologics even as second-line therapy. Recently, there has been a rise in interest in 'biosimilar' drugs that are highly comparable to the 'reference medicinal product' (RMP) in terms of efficacy and safety but may generally be lower in price. This review summarizes the cost burden of RA and considers the potential role of biosimilars in reducing drug costs and increasing patient access to biologics.

A survey of enabling technologies in synthetic biology

PubMed Central

2013-01-01

Background Realizing constructive applications of synthetic biology requires continued development of enabling technologies as well as policies and practices to ensure these technologies remain accessible for research. Broadly defined, enabling technologies for synthetic biology include any reagent or method that, alone or in combination with associated technologies, provides the means to generate any new research tool or application. Because applications of synthetic biology likely will embody multiple patented inventions, it will be important to create structures for managing intellectual property rights that best promote continued innovation. Monitoring the enabling technologies of synthetic biology will facilitate the systematic investigation of property rights coupled to these technologies and help shape policies and practices that impact the use, regulation, patenting, and licensing of these technologies. Results We conducted a survey among a self-identifying community of practitioners engaged in synthetic biology research to obtain their opinions and experiences with technologies that support the engineering of biological systems. Technologies widely used and considered enabling by survey participants included public and private registries of biological parts, standard methods for physical assembly of DNA constructs, genomic databases, software tools for search, alignment, analysis, and editing of DNA sequences, and commercial services for DNA synthesis and sequencing. Standards and methods supporting measurement, functional composition, and data exchange were less widely used though still considered enabling by a subset of survey participants. Conclusions The set of enabling technologies compiled from this survey provide insight into the many and varied technologies that support innovation in synthetic biology. Many of these technologies are widely accessible for use, either by virtue of being in the public domain or through legal tools such as non-exclusive licensing. Access to some patent protected technologies is less clear and use of these technologies may be subject to restrictions imposed by material transfer agreements or other contract terms. We expect the technologies considered enabling for synthetic biology to change as the field advances. By monitoring the enabling technologies of synthetic biology and addressing the policies and practices that impact their development and use, our hope is that the field will be better able to realize its full potential. PMID:23663447

Form and motion make independent contributions to the response to biological motion in occipitotemporal cortex.

PubMed

Thompson, James C; Baccus, Wendy

2012-01-02

Psychophysical and computational studies have provided evidence that both form and motion cues are used in the perception of biological motion. However, neuroimaging and neurophysiological studies have suggested that the neural processing of actions in temporal cortex might rely on form cues alone. Here we examined the contribution of form and motion to the spatial pattern of response to biological motion in ventral and lateral occipitotemporal cortex, using functional magnetic resonance imaging (fMRI) and multivoxel pattern analysis (MVPA). We found that selectivity to intact versus scrambled biological motion in lateral occipitotemporal cortex was correlated with selectivity for bodies and not for motion. However, this appeared to be due to the fact that subtracting scrambled from intact biological motion removes any contribution of local motion cues. Instead, we found that form and motion made independent contributions to the spatial pattern of responses to biological motion in lateral occipitotemporal regions MT, MST, and the extrastriate body area. The motion contribution was position-dependent, and consistent with the representation of contra- and ipsilateral visual fields in MT and MST. In contrast, only form contributed to the response to biological motion in the fusiform body area, with a bias towards central versus peripheral presentation. These results indicate that the pattern of response to biological motion in ventral and lateral occipitotemporal cortex reflects the linear combination of responses to form and motion. Copyright © 2011 Elsevier Inc. All rights reserved.

Experiences of mobility for people living with rheumatoid arthritis who are receiving biologic drug therapy: implications for podiatry services.

PubMed

Sanders, Lucy; Donovan-Hall, Margaret; Borthwick, Alan; Bowen, Catherine J

2017-01-01

Despite significant advancements in new treatment modalities for rheumatoid arthritis with biological therapies, foot complications remain a disabling and common feature of the disease . In this study the aim was to explore and describe the personal experiences of people with rheumatoid arthritis in receipt of biologic treatments in a bid to understand the impact of this form of medication on their mobility. An interpretative phenomenological analysis (IPA) was undertaken to explore in depth the individual experience of rheumatoid disease through personal accounts of the patient journey spanning both 'before' and 'after' the instigation of biologic therapy. A purposive sampling strategy was adopted and in-depth semi structured interviews used to facilitate rich, detailed interview data exploring the lived experiences of individuals undertaking biological therapy and the changes to mobility experienced as a result. Thematic analysis was employed with an IPA framework to identify key meanings, and report patterns within the data. Five people with rheumatoid arthritis participated in the study. The mean disease duration was 20.2 years (range: 6 -32) and all were being treated with biologic therapies. Four key themes emerged from the data: 1) Life before biologic treatment, depicted in accounts as a negative experience characterised by painful and disabling symptoms and feelings of hopelessness. 2) Life with biologic treatment, often experienced as a life changing transition, restoring function and mobility and offering renewed hope. 3) Sense of self, in which the impact of rheumatoid disease and the subsequent changes arising from biologic therapy reveal a profound impact on feelings of personal identity both pre and post biologic therapy; an effect of footwear on self-image emerges as a dominant sub theme; 4) Unmet footcare needs were evident in the patient narrative, where the unrelenting if diminished impact of foot pain on mobility was viewed in the context of problematic access to foot health services. Whilst the findings from this study mirror those within the existing literature, which report improvements in physical function related to biological therapy, foot problems clearly remained an unremitting feature of life for patients with rheumatoid disease, even when in receipt of biologics.

DB-PABP: a database of polyanion-binding proteins

PubMed Central

Fang, Jianwen; Dong, Yinghua; Salamat-Miller, Nazila; Russell Middaugh, C.

2008-01-01

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references. PMID:17916573

DB-PABP: a database of polyanion-binding proteins.

PubMed

Fang, Jianwen; Dong, Yinghua; Salamat-Miller, Nazila; Middaugh, C Russell

2008-01-01

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references.

PGSB/MIPS PlantsDB Database Framework for the Integration and Analysis of Plant Genome Data.

PubMed

Spannagl, Manuel; Nussbaumer, Thomas; Bader, Kai; Gundlach, Heidrun; Mayer, Klaus F X

2017-01-01

Plant Genome and Systems Biology (PGSB), formerly Munich Institute for Protein Sequences (MIPS) PlantsDB, is a database framework for the integration and analysis of plant genome data, developed and maintained for more than a decade now. Major components of that framework are genome databases and analysis resources focusing on individual (reference) genomes providing flexible and intuitive access to data. Another main focus is the integration of genomes from both model and crop plants to form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny). Data exchange and integrated search functionality with/over many plant genome databases is provided within the transPLANT project.

The logic of automated glycan assembly.

PubMed

Seeberger, Peter H

2015-05-19

Carbohydrates are the most abundant biopolymers on earth and part of every living creature. Glycans are essential as materials for nutrition and for information transfer in biological processes. To date, in few cases a detailed correlation between glycan structure and glycan function has been established. A molecular understanding of glycan function will require pure glycans for biological, immunological, and structural studies. Given the immense structural complexity of glycans found in living organisms and the lack of amplification methods or expression systems, chemical synthesis is the only means to access usable quantities of pure glycan molecules. While the solid-phase synthesis of DNA and peptides has become routine for decades, access to glycans has been technically difficult, time-consuming and confined to a few expert laboratories. In this Account, the development of a comprehensive approach to the automated synthesis of all classes of mammalian glycans, including glycosaminoglycans and glycosylphosphatidyl inositol (GPI) anchors, as well as bacterial and plant carbohydrates is described. A conceptual advance concerning the logic of glycan assembly was required in order to enable automated execution of the synthetic process. Based on the central glycosidic bond forming reaction, a general concept for the protecting groups and leaving groups has been developed. Building blocks that can be procured on large scale, are stable for prolonged periods of time, but upon activation result in high yields and selectivities were identified. A coupling-capping and deprotection cycle was invented that can be executed by an automated synthesis instrument. Straightforward postsynthetic protocols for cleavage from the solid support as well as purification of conjugation-ready oligosaccharides have been established. Introduction of methods to install selectively a wide variety of glycosidic linkages has enabled the rapid assembly of linear and branched oligo- and polysaccharides as large as 30-mers. Fast, reliable access to defined glycans that are ready for conjugation has given rise to glycan arrays, glycan probes, and synthetic glycoconjugate vaccines. While an ever increasing variety of glycans are accessible by automated synthesis, further methodological advances in carbohydrate chemistry are needed to make all possible glycans found in nature. These tools begin to fundamentally impact the medical but also materials aspects of the glycosciences.

Aerospace Medicine and Biology: 1983 cumulative index

NASA Technical Reports Server (NTRS)

1984-01-01

This publication is a cumulative index to the abstracts contained in the Supplements 242 through 253 of Aerospace Medicine and Biology: A Continuing Bibliography. It includes six indexes--subject, personal author, corporate source, contract number, report number, and accession number.

Patient access to reimbursed biological disease-modifying antirheumatic drugs in the European region.

PubMed

Kaló, Zoltán; Vokó, Zoltán; Östör, Andrew; Clifton-Brown, Emma; Vasilescu, Radu; Battersby, Alysia; Gibson, Edward

2017-01-01

Background & Objectives : Biological disease-modifying antirheumatic drugs (bDMARDs) for the treatment of rheumatoid arthritis (RA) are not always accessible to all patients in accordance with international guidelines, partly owing to their high direct costs against a background of restricted healthcare budgets. This study compares the size of RA patient populations with access to reimbursed bDMARDs across 37 European countries, Russia, and Turkey, according to their treatment eligibility defined by European League Against Rheumatism (EULAR) recommendations and national reimbursement criteria. Methods : The size of the RA patient population eligible for bDMARD treatment was estimated in a population model using published RA epidemiological data and clinical criteria defined by 2013 EULAR recommendations along with national reimbursement criteria defined in a survey of the 39 countries in November 2015. Results : According to EULAR recommendations, 32% of the total RA population in the European region is eligible for bDMARD treatment. However, only an average 59% of this EULAR-eligible population remains eligible after applying national reimbursement criteria (from 86% in 'high access' to 13% in 'low-access' countries). Conclusion : Access to reimbursed bDMARDs remains unequal in the European region. As biosimilars of bDMARDs are introduced, changes in reimbursement criteria may increase access to bDMARDs and reduce this inequality.

A general strategy for synthesis of cyclophane-braced peptide macrocycles via palladium-catalysed intramolecular sp3 C-H arylation

NASA Astrophysics Data System (ADS)

Zhang, Xuekai; Lu, Gang; Sun, Meng; Mahankali, Madhu; Ma, Yanfei; Zhang, Mingming; Hua, Wangde; Hu, Yuting; Wang, Qingbing; Chen, Jinghuo; He, Gang; Qi, Xiangbing; Shen, Weijun; Liu, Peng; Chen, Gong

2018-05-01

New methods capable of effecting cyclization, and forming novel three-dimensional structures while maintaining favourable physicochemical properties are needed to facilitate the development of cyclic peptide-based drugs that can engage challenging biological targets, such as protein-protein interactions. Here, we report a highly efficient and generally applicable strategy for constructing new types of peptide macrocycles using palladium-catalysed intramolecular C(sp3)-H arylation reactions. Easily accessible linear peptide precursors of simple and versatile design can be selectively cyclized at the side chains of either aromatic or modified non-aromatic amino acid units to form various cyclophane-braced peptide cycles. This strategy provides a powerful tool to address the long-standing challenge of size- and composition-dependence in peptide macrocyclization, and generates novel peptide macrocycles with uniquely buttressed backbones and distinct loop-type three-dimensional structures. Preliminary cell proliferation screening of the pilot library revealed a potent lead compound with selective cytotoxicity toward proliferative Myc-dependent cancer cell lines.

Enantioselective Brønsted Acid Catalysis as a Tool for the Synthesis of Natural Products and Pharmaceuticals.

PubMed

Merad, Jérémy; Lalli, Claudia; Bernadat, Guillaume; Maury, Julien; Masson, Géraldine

2018-03-15

Synthesis of biologically active molecules (whether at laboratory or industrial scale) remains a highly appealing area of modern organic chemistry. Nowadays, the need to access original bioactive scaffolds goes together with the desire to improve synthetic efficiency, while reducing the environmental footprint of chemical activities. Long neglected in the field of total synthesis, enantioselective organocatalysis has recently emerged as an environmentally friendly and indispensable tool for the construction of relevant bioactive molecules. Notably, enantioselective Brønsted acid catalysis has offered new opportunities in terms of both retrosynthetic disconnections and controlling stereoselectivity. The present report attempts to provide an overview of enantioselective total or formal syntheses designed around Brønsted acid-catalyzed transformations. To demonstrate the versatility of the reactions promoted and the diversity of the accessible motifs, this Minireview draws a systematic parallel between methods and retrosynthetic analysis. The manuscript is organized according to the main reaction types and the nature of newly-formed bonds. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules

PubMed Central

Daina, Antoine; Michielin, Olivier; Zoete, Vincent

2017-01-01

To be effective as a drug, a potent molecule must reach its target in the body in sufficient concentration, and stay there in a bioactive form long enough for the expected biologic events to occur. Drug development involves assessment of absorption, distribution, metabolism and excretion (ADME) increasingly earlier in the discovery process, at a stage when considered compounds are numerous but access to the physical samples is limited. In that context, computer models constitute valid alternatives to experiments. Here, we present the new SwissADME web tool that gives free access to a pool of fast yet robust predictive models for physicochemical properties, pharmacokinetics, drug-likeness and medicinal chemistry friendliness, among which in-house proficient methods such as the BOILED-Egg, iLOGP and Bioavailability Radar. Easy efficient input and interpretation are ensured thanks to a user-friendly interface through the login-free website http://www.swissadme.ch. Specialists, but also nonexpert in cheminformatics or computational chemistry can predict rapidly key parameters for a collection of molecules to support their drug discovery endeavours. PMID:28256516

A metadata template for ocean acidification data

NASA Astrophysics Data System (ADS)

Jiang, L.

2014-12-01

Metadata is structured information that describes, explains, and locates an information resource (e.g., data). It is often coarsely described as data about data, and documents information such as what was measured, by whom, when, where, and how it was sampled, analyzed, with what instruments. Metadata is inherent to ensure the survivability and accessibility of the data into the future. With the rapid expansion of biological response ocean acidification (OA) studies, the lack of a common metadata template to document such type of data has become a significant gap for ocean acidification data management efforts. In this paper, we present a metadata template that can be applied to a broad spectrum of OA studies, including those studying the biological responses of organisms on ocean acidification. The "variable metadata section", which includes the variable name, observation type, whether the variable is a manipulation condition or response variable, and the biological subject on which the variable is studied, forms the core of this metadata template. Additional metadata elements, such as principal investigators, temporal and spatial coverage, platforms for the sampling, data citation are essential components to complete the template. We explain the structure of the template, and define many metadata elements that may be unfamiliar to researchers. For that reason, this paper can serve as a user's manual for the template.

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.

PubMed

Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C; Hoeng, Julia

2015-01-01

With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com © The Author(s) 2015. Published by Oxford University Press.

Can biosimilars help achieve the goals of US health care reform?

PubMed

Boccia, Ralph; Jacobs, Ira; Popovian, Robert; de Lima Lopes, Gilberto

2017-01-01

The US Patient Protection and Affordable Care Act (ACA) aims to expand health care coverage, contain costs, and improve health care quality. Accessibility and affordability of innovative biopharmaceuticals are important to the success of the ACA. As it is substantially more difficult to manufacture them compared with small-molecule drugs, many of which have generic alternatives, biologics may increase drug costs. However, biologics offer demonstrated improvements in patient care that can reduce expensive interventions, thus lowering net health care costs. Biosimilars, which are highly similar to their reference biologics, cost less than the originators, potentially increasing access through reduced prescription drug costs while providing equivalent therapeutic results. This review evaluates 1) the progress made toward enacting health care reform since the passage of the ACA and 2) the role of biosimilars, including the potential impact of expanded biosimilar use on access, health care costs, patient management, and outcomes. Barriers to biosimilar adoption in the USA are noted, including low awareness and financial disincentives relating to reimbursement. The evaluated evidence suggests that the ACA has partly achieved some of its aims; however, the opportunity remains to transform health care to fully achieve reform. Although the future is uncertain, increased use of biosimilars in the US health care system could help achieve expanded access, control costs, and improve the quality of care.

Parents' willingness to pay for biologic treatments in juvenile idiopathic arthritis.

PubMed

Burnett, Heather F; Ungar, Wendy J; Regier, Dean A; Feldman, Brian M; Miller, Fiona A

2014-12-01

Biologic therapies are considered the standard of care for children with the most severe forms of juvenile idiopathic arthritis (JIA). Inconsistent and inadequate drug coverage, however, prevents many children from receiving timely and equitable access to the best treatment. The objective of this study was to evaluate parents' willingness to pay (WTP) for biologic and nonbiologic disease-modifying antirheumatic drugs (DMARDs) used to treat JIA. Utility weights from a discrete choice experiment were used to estimate the WTP for treatment characteristics including child-reported pain, participation in daily activities, side effects, days missed from school, drug treatment, and cost. Conditional logit regression was used to estimate utilities for each attribute level, and expected compensating variation was used to estimate the WTP. Bootstrapping was used to generate 95% confidence intervals for all WTP estimates. Parents had the highest marginal WTP for improved participation in daily activities and pain relief followed by the elimination of side effects of treatment. Parents were willing to pay $2080 (95% confidence interval $698-$4065) more for biologic DMARDs than for nonbiologic DMARDs if the biologic DMARD was more effective. Parents' WTP indicates their preference for treatments that reduce pain and improve daily functioning without side effects by estimating the monetary equivalent of utility for drug treatments in JIA. In addition to evidence of safety and efficacy, assessments of parents' preferences provide a broader perspective to decision makers by helping them understand the aspects of drug treatments in JIA that are most valued by families. Copyright © 2014 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

31 CFR 363.16 - How do I access my account?

Code of Federal Regulations, 2010 CFR

2010-07-01

... SERVICE, DEPARTMENT OF THE TREASURY BUREAU OF THE PUBLIC DEBT REGULATIONS GOVERNING SECURITIES HELD IN TREASURYDIRECT General Provisions Governing Securities Held in TreasuryDirect § 363.16 How do I access my account? You may access your account online using your account number, password, and any other form(s) of...

The molecular biology of prostate cancer: current understanding and clinical implications.

PubMed

Gandhi, Jason; Afridi, Adil; Vatsia, Sohrab; Joshi, Gargi; Joshi, Gunjan; Kaplan, Steven A; Smith, Noel L; Khan, Sardar Ali

2018-04-01

With continuous progress over the past few decades in understanding diagnosis, treatment, and genetics, much has been learned about the prostate cancer-diagnosed genome. A comprehensive MEDLINE® and Google scholar literature search was conducted using keyword variations relating to the genetics of prostate cancer such as chromosomal alterations, androgen receptor, castration-resistant, inheritance, polymorphisms, oncogenes, metastasis, biomarkers, and immunotherapy. Traditionally, androgen receptors (AR) have been the focus of research. Recently, identification of recurrent chromosomal alterations that lead to either multiplication of regions (gain-of-function) or deletion of regions (loss-of-function) has opened the door to greater genetic accessibility. These chromosomal aberrations lead to variation in copy number and gene expression. Some of these chromosomal alterations are inherited, while others undergo somatic mutations during disease progression. Inherited gene mutations that make one susceptible to prostate cancer have been identified with familial-linked studies. Somatic genes that progress tumorigenesis have also been identified. Research on the molecular biology of prostate cancer has characterized these genes into tumor suppressor genes or oncogenes. Additionally, genome-wide assay studies have identified many high-risk single-nucleotide polymorphisms recurrent throughout the prostate cancer-diagnosed genome. Castration-resistant prostate cancer is the most aggressive form of prostate cancer, and its research has elucidated many types of mutations associated with AR itself, including enhanced expression and amplification, point mutations, and alternative splicing. Understanding the molecular biology of prostate cancer has permitted more accurate identification using advanced biomarkers and therapy for aggressive forms using immunotherapy. An age-related disease, prostate cancer commands profound attention. With increasing life expectancy and the continuous pursuit of it, prostate cancer is a powerful obstacle best defeated using targeted therapies specifically designed for the unique molecular profile of the malignancy.

P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net)

PubMed Central

Pillardy, J.

2007-01-01

One of the challenges of high-performance computing (HPC) is user accessibility. At the Cornell University Computational Biology Service Unit, which is also a Microsoft HPC institute, we have developed a computational biology application suite that allows researchers from biological laboratories to submit their jobs to the parallel cluster through an easy-to-use Web interface. Through this system, we are providing users with popular bioinformatics tools including BLAST, HMMER, InterproScan, and MrBayes. The system is flexible and can be easily customized to include other software. It is also scalable; the installation on our servers currently processes approximately 8500 job submissions per year, many of them requiring massively parallel computations. It also has a built-in user management system, which can limit software and/or database access to specified users. TAIR, the major database of the plant model organism Arabidopsis, and SGN, the international tomato genome database, are both using our system for storage and data analysis. The system consists of a Web server running the interface (ASP.NET C#), Microsoft SQL server (ADO.NET), compute cluster running Microsoft Windows, ftp server, and file server. Users can interact with their jobs and data via a Web browser, ftp, or e-mail. The interface is accessible at http://cbsuapps.tc.cornell.edu/.

Biosimilars for the management of inflammatory bowel diseases: economic considerations.

PubMed

Gulacsi, Laszlo; Pentek, Marta; Rencz, Fanni; Brodszky, Valentin; Baji, Petra; Vegh, Zsuzsanna; Gecse, Krisztina B; Danese, Silvio; Peyrin-Biroulet, Laurent; Lakatos, Peter L

2017-04-06

Biological drugs revolutionized the treatment of inflammatory bowel diseases (IBD) such as Crohn's disease and ulcerative colitis. However, not all clinically eligible patients have access to biologicals, due to significant costs and budget impact. Biosimilars are highly comparable to their originator product in terms of clinical efficacy and safety. Biosimilars are priced 15-75% lower than their reference product, which makes them a less costly alternative and is expected to offer better patients access to biologicals. The total projected cost savings are significant. If the achieved budget savings were used to cover more biological therapy, several additional IBD patients could be treated. Currently, the main barriers to the increasing uptake of biosimilars are the few incentives of the key stakeholders, while physicians' and patients' skepticism towards biosimilars seems to be changing. Over the coming years, biosimilars are expected to gain a growing importance in the treatment of IBD, contributing to a better access to treatment, improving population-level health gain and sustainability of health systems. This review summarizes the results of the literature on the economic considerations of biosimilars in IBD and the role of biosimilar infliximab in the treatment of IBD. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Patient's access to healthcare and treatment in rheumatoid arthritis: the views of stakeholders in Portugal.

PubMed

Laires, Pedro A; Mesquita, Rui; Veloso, Luís; Martins, Ana Paula; Cernadas, Rui; Fonseca, João Eurico

2013-09-25

The access to healthcare and treatment by rheumatoid arthritis (RA) patients, particularly to biologics, differs significantly among European countries.We aimed to explore the views and experiences of Portuguese healthcare stakeholders on key barriers which limit the access to treatment, and ultimately to biologics, by RA patients and to find potential solutions (leverage points) to overcome the identified barriers. This was a qualitative research consisting of semi-structured face-to-face interviews with key stakeholders in RA framework. Thirty four individuals from eight groups of stakeholders were interviewed: rural and urban general practitioners (GPs), rheumatologists, hospital managers, hospital pharmacists, budget holders, representatives from the Portuguese Rheumatology Society and the RA Patient Association. Interviews were conducted between May and June 2011. Conventional content analysis with research triangulation was used. The key barriers identified were related to the accessibility to primary healthcare services, difficulties in RA diagnosis among GPs, inefficient referral to secondary healthcare and controlled process of biologics prescription in public hospitals. The leverage points identified included the improvement of epidemiological and clinical knowledge about RA in Portugal, a better understanding of the disease among patients and GPs, the clarification of biologics benefits among budget holders and a raised awareness of the current treatment guidelines. In order to further address the leverage points, the following key initiatives were proposed: optimization of RA national registry; dissemination of information on rheumatic symptoms in primary care facilities and among the general public; increase interaction between rheumatologists and GPs through clinical discussions of successfully treated patients or workshops; broader utilization of disease diagnosis and monitoring tools, such as DAS28, and implementation of hospital-based research to collect real-world data. Most of the key barriers limiting the access to treatment, including biologics, in RA in Portugal are upstream of rheumatology practice. Our findings suggest that future actions should be focused on the primary care level to improve referral to rheumatologists. In addition, the collection of real-world data seems essential to characterise the RA population, to improve disease management and to increase compliance with current treatment guidelines.

The Anopheles stephensi odorant binding protein 1 (AsteObp1) gene: a new molecular marker for biological forms diagnosis.

PubMed

Gholizadeh, S; Firooziyan, S; Ladonni, H; Hajipirloo, H Mohammadzadeh; Djadid, N Dinparast; Hosseini, A; Raz, A

2015-06-01

Anopheles (Cellia) stephensi Liston 1901 is known as an Asian malaria vector. Three biological forms, namely "mysorensis", "intermediate", and "type" have been earlier reported in this species. Nevertheless, the present morphological and molecular information is insufficient to diagnose these forms. During this investigation, An. stephensi biological forms were morphologically identified and sequenced for odorant-binding protein 1 (Obp1) gene. Also, intron I sequences were used to construct phylogenetic trees. Despite nucleotide sequence variation in exon of AsteObp1, nearly 100% identity was observed at the amino acid level among the three biological forms. In order to overcome difficulties in using egg morphology characters, intron I sequences of An. stephensi Obp1 opens new molecular way to the identification of the main Asian malaria vector biological forms. However, multidisciplinary studies are needed to establish the taxonomic status of An. stephensi. Copyright © 2015 Elsevier B.V. All rights reserved.

Limits in the evolution of biological form: a theoretical morphologic perspective.

PubMed

McGhee, George R

2015-12-06

Limits in the evolution of biological form can be empirically demonstrated by using theoretical morphospace analyses, and actual analytic examples are given for univalved ammonoid shell form, bivalved brachiopod shell form and helical bryozoan colony form. Limits in the evolution of form in these animal groups can be shown to be due to functional and developmental constraints on possible evolutionary trajectories in morphospace. Future evolutionary-limit research is needed to analyse the possible existence of temporal constraint in the evolution of biological form on Earth, and in the search for the possible existence of functional alien life forms on Titan and Triton that are developmentally impossible for Earth life.

Post-16 Biology--Some Model Approaches?

ERIC Educational Resources Information Center

Lock, Roger

1997-01-01

Outlines alternative approaches to the teaching of difficult concepts in A-level biology which may help student learning by making abstract ideas more concrete and accessible. Examples include models, posters, and poems for illustrating meiosis, mitosis, genetic mutations, and protein synthesis. (DDR)

Israel Marine Bio-geographic Database (ISRAMAR-BIO)

NASA Astrophysics Data System (ADS)

Greengrass, Eyal; Krivenko, Yevgeniya; Ozer, Tal; Ben Yosef, Dafna; Tom, Moshe; Gertman, Isaac

2015-04-01

The knowledge of the space/time variations of species is the basis for any ecological investigations. While historical observations containing integral concentrations of biological parameters (chlorophyll, abundance, biomass…) are organized partly in ISRAMAR Cast Database, the taxon-specific data collected in Israel has not been sufficiently organized. This has been hindered by the lack of standards, variability of methods and complexity of biological data formalization. The ISRAMAR-BIO DB was developed to store various types of historical and future available information related to marine species observations and related metadata. Currently the DB allows to store biological data acquired by the following sampling devices such as: van veer grab, box corer, sampling bottles, nets (plankton, trawls and fish), quadrates, and cameras. The DB's logical unit is information regarding a specimen (taxa name, barcode, image), related attributes (abundance, size, age, contaminants…), habitat description, sampling device and method, time and space of sampling, responsible organization and scientist, source of information (cruise, project and publication). The following standardization of specimen and attributes naming were implemented: Taxonomy according to World Register of Marine Species (WoRMS: http://www.marinespecies.org). Habitat description according to Coastal and Marine Ecological Classification Standards (CMECS: http://www.cmecscatalog.org) Parameter name; Unit; Device name; Developmental stage; Institution name; Country name; Marine region according to SeaDataNet Vocabularies (http://www.seadatanet.org/Standards-Software/Common-Vocabularies). This system supports two types of data submission procedures, which support the above stated data structure. The first is a downloadable excel file with drop-down fields based on the ISRAMAR-BIO vocabularies. The file is filled and uploaded online by the data contributor. Alternatively, the same dataset can be assembled by filling online forms and then submitted to the DB. Online access to the ISRAMAR-BIO is available through taxon search page, where one can get both biological and geographical data regarding a certain taxon. Further development of the online data access is ongoing. It will include interactive geographical map interface where data may be queried, analyzed and downloaded.

Students' Use of Optional Online Reviews and Its Relationship to Summative Assessment Outcomes in Introductory Biology.

PubMed

Carpenter, Shana K; Rahman, Shuhebur; Lund, Terry J S; Armstrong, Patrick I; Lamm, Monica H; Reason, Robert D; Coffman, Clark R

2017-01-01

Retrieval practice has been shown to produce significant enhancements in student learning of course information, but the extent to which students make use of retrieval to learn information on their own is unclear. In the current study, students in a large introductory biology course were provided with optional online review questions that could be accessed as Test questions (requiring students to answer the questions before receiving feedback) or as Read questions (providing students with the question and correct answer up-front). Students more often chose to access the questions as Test compared with Read, and students who used the Test questions scored significantly higher on subsequent exams compared with students who used Read questions or did not access the questions at all. Following an in-class presentation of superior exam performance following use of the Test questions, student use of Test questions increased significantly for the remainder of the term. These results suggest that practice questions can be an effective tool for enhancing student achievement in biology and that informing students about performance-based outcomes coincides with increased use of retrieval practice. © 2017 S. K. Carpenter et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data

PubMed Central

Westbrook, John D; Feng, Zukang; Persikova, Irina; Sala, Raul; Sen, Sanchayita; Berrisford, John M; Swaminathan, G Jawahar; Oldfield, Thomas J; Gutmanas, Aleksandras; Igarashi, Reiko; Armstrong, David R; Baskaran, Kumaran; Chen, Li; Chen, Minyu; Clark, Alice R; Di Costanzo, Luigi; Dimitropoulos, Dimitris; Gao, Guanghua; Ghosh, Sutapa; Gore, Swanand; Guranovic, Vladimir; Hendrickx, Pieter M S; Hudson, Brian P; Ikegawa, Yasuyo; Kengaku, Yumiko; Lawson, Catherine L; Liang, Yuhe; Mak, Lora; Mukhopadhyay, Abhik; Narayanan, Buvaneswari; Nishiyama, Kayoko; Patwardhan, Ardan; Sahni, Gaurav; Sanz-García, Eduardo; Sato, Junko; Sekharan, Monica R; Shao, Chenghua; Smart, Oliver S; Tan, Lihua; van Ginkel, Glen; Yang, Huanwang; Zhuravleva, Marina A; Markley, John L; Nakamura, Haruki; Kurisu, Genji; Kleywegt, Gerard J; Velankar, Sameer; Berman, Helen M; Burley, Stephen K

2018-01-01

Abstract The Protein Data Bank (PDB) is the single global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands. The worldwide PDB (wwPDB) is the international collaboration that manages the PDB archive according to the FAIR principles: Findability, Accessibility, Interoperability and Reusability. The wwPDB recently developed OneDep, a unified tool for deposition, validation and biocuration of structures of biological macromolecules. All data deposited to the PDB undergo critical review by wwPDB Biocurators. This article outlines the importance of biocuration for structural biology data deposited to the PDB and describes wwPDB biocuration processes and the role of expert Biocurators in sustaining a high-quality archive. Structural data submitted to the PDB are examined for self-consistency, standardized using controlled vocabularies, cross-referenced with other biological data resources and validated for scientific/technical accuracy. We illustrate how biocuration is integral to PDB data archiving, as it facilitates accurate, consistent and comprehensive representation of biological structure data, allowing efficient and effective usage by research scientists, educators, students and the curious public worldwide. Database URL: https://www.wwpdb.org/ PMID:29688351

28 CFR 1100.33 - Access to information and translation services for victims of severe forms of trafficking in...

Code of Federal Regulations, 2012 CFR

2012-07-01

... services for victims of severe forms of trafficking in persons. 1100.33 Section 1100.33 Judicial Administration DEPARTMENT OF JUSTICE AND DEPARTMENT OF STATE TRAFFICKING IN PERSONS Victims of Severe Forms of Trafficking in Persons § 1100.33 Access to information and translation services for victims of severe forms of...

28 CFR 1100.33 - Access to information and translation services for victims of severe forms of trafficking in...

Code of Federal Regulations, 2013 CFR

2013-07-01

... services for victims of severe forms of trafficking in persons. 1100.33 Section 1100.33 Judicial Administration DEPARTMENT OF JUSTICE AND DEPARTMENT OF STATE TRAFFICKING IN PERSONS Victims of Severe Forms of Trafficking in Persons § 1100.33 Access to information and translation services for victims of severe forms of...

28 CFR 1100.33 - Access to information and translation services for victims of severe forms of trafficking in...

Code of Federal Regulations, 2014 CFR

2014-07-01

... services for victims of severe forms of trafficking in persons. 1100.33 Section 1100.33 Judicial Administration DEPARTMENT OF JUSTICE AND DEPARTMENT OF STATE TRAFFICKING IN PERSONS Victims of Severe Forms of Trafficking in Persons § 1100.33 Access to information and translation services for victims of severe forms of...

45 CFR 164.524 - Access of individuals to protected health information.

Code of Federal Regulations, 2010 CFR

2010-10-01

... individual with access to the protected health information in the form or format requested by the individual, if it is readily producible in such form or format; or, if not, in a readable hard copy form or such other form or format as agreed to by the covered entity and the individual. (ii) The covered entity may...

Combining computational models, semantic annotations and simulation experiments in a graph database

PubMed Central

Henkel, Ron; Wolkenhauer, Olaf; Waltemath, Dagmar

2015-01-01

Model repositories such as the BioModels Database, the CellML Model Repository or JWS Online are frequently accessed to retrieve computational models of biological systems. However, their storage concepts support only restricted types of queries and not all data inside the repositories can be retrieved. In this article we present a storage concept that meets this challenge. It grounds on a graph database, reflects the models’ structure, incorporates semantic annotations and simulation descriptions and ultimately connects different types of model-related data. The connections between heterogeneous model-related data and bio-ontologies enable efficient search via biological facts and grant access to new model features. The introduced concept notably improves the access of computational models and associated simulations in a model repository. This has positive effects on tasks such as model search, retrieval, ranking, matching and filtering. Furthermore, our work for the first time enables CellML- and Systems Biology Markup Language-encoded models to be effectively maintained in one database. We show how these models can be linked via annotations and queried. Database URL: https://sems.uni-rostock.de/projects/masymos/ PMID:25754863

Structure of the cleavage-activated prefusion form of the parainfluenza virus 5 fusion protein.

PubMed

Welch, Brett D; Liu, Yuanyuan; Kors, Christopher A; Leser, George P; Jardetzky, Theodore S; Lamb, Robert A

2012-10-09

The paramyxovirus parainfluenza virus 5 (PIV5) enters cells by fusion of the viral envelope with the plasma membrane through the concerted action of the fusion (F) protein and the receptor binding protein hemagglutinin-neuraminidase. The F protein folds initially to form a trimeric metastable prefusion form that is triggered to undergo large-scale irreversible conformational changes to form the trimeric postfusion conformation. It is thought that F refolding couples the energy released with membrane fusion. The F protein is synthesized as a precursor (F0) that must be cleaved by a host protease to form a biologically active molecule, F1,F2. Cleavage of F protein is a prerequisite for fusion and virus infectivity. Cleavage creates a new N terminus on F1 that contains a hydrophobic region, known as the FP, which intercalates target membranes during F protein refolding. The crystal structure of the soluble ectodomain of the uncleaved form of PIV5 F is known; here we report the crystal structure of the cleavage-activated prefusion form of PIV5 F. The structure shows minimal movement of the residues adjacent to the protease cleavage site. Most of the hydrophobic FP residues are buried in the uncleaved F protein, and only F103 at the newly created N terminus becomes more solvent-accessible after cleavage. The conformational freedom of the charged arginine residues that compose the protease recognition site increases on cleavage of F protein.

Structure of the cleavage-activated prefusion form of the parainfluenza virus 5 fusion protein

PubMed Central

Welch, Brett D.; Liu, Yuanyuan; Kors, Christopher A.; Leser, George P.; Jardetzky, Theodore S.; Lamb, Robert A.

2012-01-01

The paramyxovirus parainfluenza virus 5 (PIV5) enters cells by fusion of the viral envelope with the plasma membrane through the concerted action of the fusion (F) protein and the receptor binding protein hemagglutinin-neuraminidase. The F protein folds initially to form a trimeric metastable prefusion form that is triggered to undergo large-scale irreversible conformational changes to form the trimeric postfusion conformation. It is thought that F refolding couples the energy released with membrane fusion. The F protein is synthesized as a precursor (F0) that must be cleaved by a host protease to form a biologically active molecule, F1,F2. Cleavage of F protein is a prerequisite for fusion and virus infectivity. Cleavage creates a new N terminus on F1 that contains a hydrophobic region, known as the FP, which intercalates target membranes during F protein refolding. The crystal structure of the soluble ectodomain of the uncleaved form of PIV5 F is known; here we report the crystal structure of the cleavage-activated prefusion form of PIV5 F. The structure shows minimal movement of the residues adjacent to the protease cleavage site. Most of the hydrophobic FP residues are buried in the uncleaved F protein, and only F103 at the newly created N terminus becomes more solvent-accessible after cleavage. The conformational freedom of the charged arginine residues that compose the protease recognition site increases on cleavage of F protein. PMID:23012473

Protecting Traditional Knowledge Related to Biological Resources: Is Scientific Research Going to Become More Bureaucratized?

PubMed Central

Reddy, Prashant; Lakshmikumaran, Malathi

2015-01-01

For the past several decades, there has been a world debate on the need for protecting traditional knowledge. A global treaty appears to be a distant reality. Of more immediate concern are the steps taken by the global community to protect access to biological resources in the name of protecting traditional knowledge. The Indian experience with implementing the Convention on Biological Diversity has created substantial legal uncertainty in collaborative scientific research between Indians and foreigners apart from bureaucratizing the entire process of scientific research, especially with regard to filing of applications for intellectual property rights. The issue therefore is whether the world needs to better balance the needs of the scientific community with the rights of those who have access to traditional knowledge. PMID:26101205

State-transition diagrams for biologists.

PubMed

Bersini, Hugues; Klatzmann, David; Six, Adrien; Thomas-Vaslin, Véronique

2012-01-01

It is clearly in the tradition of biologists to conceptualize the dynamical evolution of biological systems in terms of state-transitions of biological objects. This paper is mainly concerned with (but obviously not limited too) the immunological branch of biology and shows how the adoption of UML (Unified Modeling Language) state-transition diagrams can ease the modeling, the understanding, the coding, the manipulation or the documentation of population-based immune software model generally defined as a set of ordinary differential equations (ODE), describing the evolution in time of populations of various biological objects. Moreover, that same UML adoption naturally entails a far from negligible representational economy since one graphical item of the diagram might have to be repeated in various places of the mathematical model. First, the main graphical elements of the UML state-transition diagram and how they can be mapped onto a corresponding ODE mathematical model are presented. Then, two already published immune models of thymocyte behavior and time evolution in the thymus, the first one originally conceived as an ODE population-based model whereas the second one as an agent-based one, are refactored and expressed in a state-transition form so as to make them much easier to understand and their respective code easier to access, to modify and run. As an illustrative proof, for any immunologist, it should be possible to understand faithfully enough what the two software models are supposed to reproduce and how they execute with no need to plunge into the Java or Fortran lines.

Telomere Biology—Insights into an Intriguing Phenomenon

PubMed Central

Venkatesan, Shriram; Khaw, Aik Kia; Hande, Manoor Prakash

2017-01-01

Bacteria and viruses possess circular DNA, whereas eukaryotes with typically very large DNA molecules have had to evolve into linear chromosomes to circumvent the problem of supercoiling circular DNA of that size. Consequently, such organisms possess telomeres to cap chromosome ends. Telomeres are essentially tandem repeats of any DNA sequence that are present at the ends of chromosomes. Their biology has been an enigmatic one, involving various molecules interacting dynamically in an evolutionarily well-trimmed fashion. Telomeres range from canonical hexameric repeats in most eukaryotes to unimaginably random retrotransposons, which attach to chromosome ends and reverse-transcribe to DNA in some plants and insects. Telomeres invariably associate with specialised protein complexes that envelop it, also regulating access of the ends to legitimate enzymes involved in telomere metabolism. They also transcribe into repetitive RNA which also seems to be playing significant roles in telomere maintenance. Telomeres thus form the intersection of DNA, protein, and RNA molecules acting in concert to maintain chromosome integrity. Telomere biology is emerging to appear ever more complex than previously envisaged, with the continual discovery of more molecules and interplays at the telomeres. This review also includes a section dedicated to the history of telomere biology, and intends to target the scientific audience new to the field by rendering an understanding of the phenomenon of chromosome end protection at large, with more emphasis on the biology of human telomeres. The review provides an update on the field and mentions the questions that need to be addressed. PMID:28629193

Predicted Arabidopsis Interactome Resource and Gene Set Linkage Analysis: A Transcriptomic Analysis Resource.

PubMed

Yao, Heng; Wang, Xiaoxuan; Chen, Pengcheng; Hai, Ling; Jin, Kang; Yao, Lixia; Mao, Chuanzao; Chen, Xin

2018-05-01

An advanced functional understanding of omics data is important for elucidating the design logic of physiological processes in plants and effectively controlling desired traits in plants. We present the latest versions of the Predicted Arabidopsis Interactome Resource (PAIR) and of the gene set linkage analysis (GSLA) tool, which enable the interpretation of an observed transcriptomic change (differentially expressed genes [DEGs]) in Arabidopsis ( Arabidopsis thaliana ) with respect to its functional impact for biological processes. PAIR version 5.0 integrates functional association data between genes in multiple forms and infers 335,301 putative functional interactions. GSLA relies on this high-confidence inferred functional association network to expand our perception of the functional impacts of an observed transcriptomic change. GSLA then interprets the biological significance of the observed DEGs using established biological concepts (annotation terms), describing not only the DEGs themselves but also their potential functional impacts. This unique analytical capability can help researchers gain deeper insights into their experimental results and highlight prospective directions for further investigation. We demonstrate the utility of GSLA with two case studies in which GSLA uncovered how molecular events may have caused physiological changes through their collective functional influence on biological processes. Furthermore, we showed that typical annotation-enrichment tools were unable to produce similar insights to PAIR/GSLA. The PAIR version 5.0-inferred interactome and GSLA Web tool both can be accessed at http://public.synergylab.cn/pair/. © 2018 American Society of Plant Biologists. All Rights Reserved.

State-Transition Diagrams for Biologists

PubMed Central

Bersini, Hugues; Klatzmann, David; Six, Adrien; Thomas-Vaslin, Véronique

2012-01-01

It is clearly in the tradition of biologists to conceptualize the dynamical evolution of biological systems in terms of state-transitions of biological objects. This paper is mainly concerned with (but obviously not limited too) the immunological branch of biology and shows how the adoption of UML (Unified Modeling Language) state-transition diagrams can ease the modeling, the understanding, the coding, the manipulation or the documentation of population-based immune software model generally defined as a set of ordinary differential equations (ODE), describing the evolution in time of populations of various biological objects. Moreover, that same UML adoption naturally entails a far from negligible representational economy since one graphical item of the diagram might have to be repeated in various places of the mathematical model. First, the main graphical elements of the UML state-transition diagram and how they can be mapped onto a corresponding ODE mathematical model are presented. Then, two already published immune models of thymocyte behavior and time evolution in the thymus, the first one originally conceived as an ODE population-based model whereas the second one as an agent-based one, are refactored and expressed in a state-transition form so as to make them much easier to understand and their respective code easier to access, to modify and run. As an illustrative proof, for any immunologist, it should be possible to understand faithfully enough what the two software models are supposed to reproduce and how they execute with no need to plunge into the Java or Fortran lines. PMID:22844438

PubMed Central

Fernandes, Pedro; Gevaert, Kris; Rothacker, Julie; Saiyed, Taslimarif; Detwiler, Michelle

2012-01-01

This roundtable will feature four international speakers who will discuss national and international collaborative initiatives and outreach efforts in which they participate. They will share how these efforts have facilitated access to cutting-edge technology, fostered new generations of scientists, and ultimately advanced the progression of global scientific research. Open discussion will follow the presentations! Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences, India: experiences in implementing a national high-end core facility organization with the goals of improving regional technology access and enhancing the quality of research for scientists in academia, biotechnology companies, and the biopharmaceutical industry.Monash University Technology Platforms and Broader Victorian and Australian Networks: Australian initiatives to build global research capabilities and identify means to internationally benchmark regional capabilities to ensure delivery of world class infrastructure. Within the context of the current Australian strategic framework, funding considerations will be discussed, along with expectations for partner facilities to collaborate and be fully accessible to academia and industry.Instituto Gulbenkian de Ciencia, Portugal and beyond: Multiple roles of networking in science and extending outreach while consolidating community integration. Discussion will include achievement of community building and integration using concepts of sharing, training, resource availability, and the value and empowerment gained using acquired skills. The role of networking and institutional visibility will also be discussed.PRIME-XS: This EU-funded consortium provides an infrastructure of proteomics technologies to the European research community. The core is formed by six access facilities through which the consortium provides access to their technologies. Twelve partners work together to develop new resources to aid the community including the development of bioinformatic tools to analyze large-scale proteomics data and novel technologies to analyze protein interaction networks, post-translational modifications and more sensitive ways to detect protein and peptide biomarkers in complex samples.

15. CONSTRUCTION PROGRESS PHOTO SHOWING FORMS GOING UP ON ACCESS ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

15. CONSTRUCTION PROGRESS PHOTO SHOWING FORMS GOING UP ON ACCESS CORRIDOR. INEEL PHOTO NUMBER NRTS-59-336. - Idaho National Engineering Laboratory, Old Waste Calcining Facility, Scoville, Butte County, ID

A comparison of form processing involved in the perception of biological and nonbiological movements

PubMed Central

Thurman, Steven M.; Lu, Hongjing

2016-01-01

Although there is evidence for specialization in the human brain for processing biological motion per se, few studies have directly examined the specialization of form processing in biological motion perception. The current study was designed to systematically compare form processing in perception of biological (human walkers) to nonbiological (rotating squares) stimuli. Dynamic form-based stimuli were constructed with conflicting form cues (position and orientation), such that the objects were perceived to be moving ambiguously in two directions at once. In Experiment 1, we used the classification image technique to examine how local form cues are integrated across space and time in a bottom-up manner. By comparing with a Bayesian observer model that embodies generic principles of form analysis (e.g., template matching) and integrates form information according to cue reliability, we found that human observers employ domain-general processes to recognize both human actions and nonbiological object movements. Experiments 2 and 3 found differential top-down effects of spatial context on perception of biological and nonbiological forms. When a background does not involve social information, observers are biased to perceive foreground object movements in the direction opposite to surrounding motion. However, when a background involves social cues, such as a crowd of similar objects, perception is biased toward the same direction as the crowd for biological walking stimuli, but not for rotating nonbiological stimuli. The model provided an accurate account of top-down modulations by adjusting the prior probabilities associated with the internal templates, demonstrating the power and flexibility of the Bayesian approach for visual form perception. PMID:26746875

BIOPACK: the ground controlled late access biological research facility.

PubMed

van Loon, Jack J W A

2004-03-01

Future Space Shuttle flights shall be characterized by activities necessary to further build the International Space Station, ISS. During these missions limited resources are available to conduct biological experiments in space. The Shuttles' Middeck is a very suitable place to conduct science during the ISS assembly missions or dedicated science missions. The BIOPACK, which flew its first mission during the STS-107, provides a versatile Middeck Locker based research tool for gravitational biology studies. The core facility occupies the space of only two Middeck Lockers. Experiment temperatures are controlled for bacteria, plant, invertebrate and mammalian cultures. Gravity levels and profiles can be set ranging from 0 to 2.0 x g on three independent centrifuges. This provides the experimenter with a 1.0 x g on-board reference and intermediate hypogravity and hypergravity data points to investigate e.g. threshold levels in biological responses. Temperature sensitive items can be stored in the facilities' -10 degrees C and +4 degrees C stowage areas. During STS-107 the facility also included a small glovebox (GBX) and passive temperature controlled units (PTCU). The GBX provides the experimenter with two extra levels of containment for safe sample handling. This biological research facility is a late access (L-10 hrs) laboratory, which, when reaching orbit, could automatically be starting up reducing important experiment lag-time and valuable crew time. The system is completely telecommanded when needed. During flight system parameters like temperatures, centrifuge speeds, experiment commanding or sensor readouts can be monitored and changed when needed. Although ISS provides a wide range of research facilities there is still need for an STS-based late access facility such as the BIOPACK providing experimenters with a very versatile research cabinet for biological experiments under microgravity and in-flight control conditions.

Access to pediatric rheumatology care for Juvenile Idiopathic Arthritis in the United Arab Emirates.

PubMed

Khawaja, Khulood; Al-Maini, Mustafa

2017-05-16

This study looks at access to care for Juvenile Idiopathic Arthritis through pediatric rheumatology in the UAE, as an example of multi-ethnic society. Patients with a diagnosis of Juvenile idiopathic arthritis were identified through the hospital electronic medical records system from January 1st 2011 to December 31st 2014. All residents of the United Arab Emirates hold an Emirates identity card. We divided our patients into two groups: Emirati-Emirates, who are native Emirati children and hold the Emirati nationality, as stated on their Emirates identity card, and who therefore have full, comprehensive access to free medical care; and non-Emirati-Emirates, who represent other nationalities, as stated on their Emirates identity card. The primary objective of this study is to look at access to care for Juvenile idiopathic arthritis through pediatric rheumatology in the two groups. The secondary objective is to look at the effect of having multiple types of healthcare insurance coverage on access to biologics. A retrospective review was carried out. Sixty-six patients with JIA identified: 33 Emirates and 33 non-Emirates. For Emirates, the mean time from onset to first appointment with pediatric rheumatologist and diagnosis is 9 months (range: 1-48), and for non-Emirates is 12.4 months (range: 1-96). Among the Emirates, 10 patients are currently on biologic with methotrexate. Among the non-Emirates, 15 are on biologic with methotrexate. Among the Emirates, 12 are currently in remission while on treatment, as are 10 non-Emirates. Regarding disability, one Emirati patient has blindness secondary to noncompliance while under previous treatment. One Non-Emirati developed joint deformities due to periods of noncompliance and no follow up. Delay in presentation to pediatric rheumatology has been identified as an important factor in our population, which is multi-cultural and multi-ethnic. Type of health care insurance cover did not affect number of patients getting biological therapy once patient seen in the pediatric rheumatology service.

An exploration of student experiences of using biology podcasts in nursing training

PubMed Central

2013-01-01

Background Students regard biological science as one of the most difficult components of the nursing curriculum. However, a good understanding of this area is essential for effective nursing practice. The aim of this study was to explore nursing students’ perceptions of the usefulness of supplementary biology podcasts for their learning. Methods Biological science podcasts (n = 9) were made available to first-year nursing students (n = 189) as supplementary learning tools. On completion of their first year, students were asked to complete a survey which investigated the frequency of their podcast use, reasons for use and their perception of the usefulness of podcasts as a learning tool. 153 of these students participated in the survey study (80.9%). Two focus groups were conducted with students (n = 6) to gain a detailed understanding of student experiences of the usefulness of the podcasts for their learning. Results Survey data demonstrated that most students (71%) accessed at least one podcast. The majority of students who reported accessing podcasts agreed that they were useful as learning tools (83%), revision aids (83%) and that they helped promote understanding of course materials (72%). Focus group participants discussed how they found podcasts especially useful in terms of revision. Students valued being able to repeatedly access the lecture materials, and appreciated having access to podcasts from a range of lecturers. Focus group members discussed the benefits of live recordings, in terms of valuing the information gleaned from questions asked during the lecture sessions, although there were concerns about the level of background noise in live recordings. Lack of awareness of the availability of podcasts was an issue raised by participants in both the survey component and the focus groups and this negatively impacted on podcast use. Conclusions Nursing students found the availability of biology podcasts helpful for their learning. Successful implementation of these tools to support learning requires teaching staff to understand and promote the importance of these tools. PMID:23360078

Gravity Cues Embedded in the Kinematics of Human Motion Are Detected in Form-from-Motion Areas of the Visual System and in Motor-Related Areas

PubMed Central

Cignetti, Fabien; Chabeauti, Pierre-Yves; Menant, Jasmine; Anton, Jean-Luc J. J.; Schmitz, Christina; Vaugoyeau, Marianne; Assaiante, Christine

2017-01-01

The present study investigated the cortical areas engaged in the perception of graviceptive information embedded in biological motion (BM). To this end, functional magnetic resonance imaging was used to assess the cortical areas active during the observation of human movements performed under normogravity and microgravity (parabolic flight). Movements were defined by motion cues alone using point-light displays. We found that gravity modulated the activation of a restricted set of regions of the network subtending BM perception, including form-from-motion areas of the visual system (kinetic occipital region, lingual gyrus, cuneus) and motor-related areas (primary motor and somatosensory cortices). These findings suggest that compliance of observed movements with normal gravity was carried out by mapping them onto the observer’s motor system and by extracting their overall form from local motion of the moving light points. We propose that judgment on graviceptive information embedded in BM can be established based on motor resonance and visual familiarity mechanisms and not necessarily by accessing the internal model of gravitational motion stored in the vestibular cortex. PMID:28861024

Stereoselective Synthesis of Methylene Oxindoles via Palladium(II)-Catalyzed Intramolecular Cross-Coupling of Carbamoyl Chlorides.

PubMed

Le, Christine M; Sperger, Theresa; Fu, Rui; Hou, Xiao; Lim, Yong Hwan; Schoenebeck, Franziska; Lautens, Mark

2016-11-02

We report a highly robust, general and stereoselective method for the synthesis of 3-(chloromethylene)oxindoles from alkyne-tethered carbamoyl chlorides using PdCl 2 (PhCN) 2 as the catalyst. The transformation involves a stereo- and regioselective chloropalladation of an internal alkyne to generate a nucleophilic vinyl Pd II species, which then undergoes an intramolecular cross-coupling with a carbamoyl chloride. The reaction proceeds under mild conditions, is insensitive to the presence of moisture and air, and is readily scalable. The products obtained from this reaction are formed with >95:5 Z:E selectivity in nearly all cases and can be used to access biologically relevant oxindole cores. Through combined experimental and computational studies, we provide insight into stereo- and regioselectivity of the chloropalladation step, as well as the mechanism for the C-C bond forming process. Calculations provide support for a mechanism involving oxidative addition into the carbamoyl chloride bond to generate a high valent Pd IV species, which then undergoes facile C-C reductive elimination to form the final product. Overall, the transformation constitutes a formal Pd II -catalyzed intramolecular alkyne chlorocarbamoylation reaction.

Aerospace Medicine and Biology: A Cumulative Index to the 1985 Issues

NASA Technical Reports Server (NTRS)

1986-01-01

This publication is a cumulative index to the abstracts contained in the Supplements 268 through 279 of Aerospace Medicine and Biology: A Continuing Bibliography. It includes seven indexes - subject, personal author, corporate source, foreign technology, contract number, report number, and accession number.

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 396)

NASA Technical Reports Server (NTRS)

1995-01-01

This publication is a cumulative index to the abstracts contained in the Supplements 385 through 395 of Aerospace Medicine and Biology: A Continuing Bibliography. It includes seven indexes: subject, personal author, corporate source, foreign technology, contract number, report number, and accession number.

Data management and data enrichment for systems biology projects.

PubMed

Wittig, Ulrike; Rey, Maja; Weidemann, Andreas; Müller, Wolfgang

2017-11-10

Collecting, curating, interlinking, and sharing high quality data are central to de.NBI-SysBio, the systems biology data management service center within the de.NBI network (German Network for Bioinformatics Infrastructure). The work of the center is guided by the FAIR principles for scientific data management and stewardship. FAIR stands for the four foundational principles Findability, Accessibility, Interoperability, and Reusability which were established to enhance the ability of machines to automatically find, access, exchange and use data. Within this overview paper we describe three tools (SABIO-RK, Excemplify, SEEK) that exemplify the contribution of de.NBI-SysBio services to FAIR data, models, and experimental methods storage and exchange. The interconnectivity of the tools and the data workflow within systems biology projects will be explained. For many years we are the German partner in the FAIRDOM initiative (http://fair-dom.org) to establish a European data and model management service facility for systems biology. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Balancing Scientific Publication and National Security Concerns: Issues for Congress

DTIC Science & Technology

2003-01-10

because of its potential relevance to biological weapons of mass destruction. Whether the current method of only using classification to limit the...terrorist groups in developing weapons of mass destruction. In 2000, researchers at the Co-operative Research Centre for the Biological Control of Pest...development of chemical, biological , or nuclear weapons is not made accessible to terrorists or countries of proliferation concern. The resolution

Why the Current Insistence on Open Access to Scientific Data? Big Data, Knowledge Production, and the Political Economy of Contemporary Biology

ERIC Educational Resources Information Center

Leonelli, Sabina

2013-01-01

The collection and dissemination of data on human and nonhuman organisms has become a central feature of 21st-century biology and has been endorsed by funding agencies in the United States and Europe as crucial to translating biological research into therapeutic and agricultural innovation. Large molecular data sets, often referred to as "big…

Similar Mutation Rates but Highly Diverse Mutation Spectra in Ascomycete and Basidiomycete Yeasts

DTIC Science & Technology

2016-12-24

Te, and Michael Lynch Department of Biology , Indiana University, Bloomington, IN *Corresponding author: E-mail: longhongan@gmail.com. Accepted...GBE The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access...fungal mutation spectrum. Supplementary Material Supplementary data are available at Genome Biology and Evolution online. Acknowledgments This research

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

Grahn, D.; Wright, B.J.; Carnes, B.A.

A research reactor for exclusive use in experimental radiobiology was designed and built at Argonne National Laboratory in the 1960`s. It was located in a special addition to Building 202, which housed the Division of Biological and Medical Research. Its location assured easy access for all users to the animal facilities, and it was also near the existing gamma-irradiation facilities. The water-cooled, heterogeneous 200-kW(th) reactor, named JANUS, became the focal point for a range of radiobiological studies gathered under the rubic of {open_quotes}the JANUS program{close_quotes}. The program ran from about 1969 to 1992 and included research at all levels ofmore » biological organization, from subcellular to organism. More than a dozen moderate- to large-scale studies with the B6CF{sub 1} mouse were carried out; these focused on the late effects of whole-body exposure to gamma rays or fission neutrons, in matching exposure regimes. In broad terms, these studies collected data on survival and on the pathology observed at death. A deliberate effort was made to establish the cause of death. This archieve describes these late-effects studies and their general findings. The database includes exposure parameters, time of death, and the gross pathology and histopathology in codified form. A series of appendices describes all pathology procedures and codes, treatment or irradiation codes, and the manner in which the data can be accessed in the ORACLE database management system. A series of tables also presents summaries of the individual experiments in terms of radiation quality, sample sizes at entry, mean survival times by sex, and number of gross pathology and histopathology records.« less

Reactome graph database: Efficient access to complex pathway data

PubMed Central

Korninger, Florian; Viteri, Guilherme; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D’Eustachio, Peter

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types. PMID:29377902

Reactome graph database: Efficient access to complex pathway data.

PubMed

Fabregat, Antonio; Korninger, Florian; Viteri, Guilherme; Sidiropoulos, Konstantinos; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types.

State secrets: access to information under the Human Reproductive Technology Act 1991 (WA).

PubMed

Tarrant, Stella

2002-02-01

Many Australian children have a biological father who gave his sperm so that the child's mother could conceive and raise them. Many of these children, and their parent(s), do not know who that biological father is. However, some want to know. The article examines the Western Australian law on access to information about the identity of parties in these arrangements. It is argued that there is an implied right to access identifying information where all parties consent to the exchange of information; that this right has been ignored in official and medical practice and opportunities for good record-keeping missed; and that the current law allows a parent to give consent to the exchange of identifying information on behalf of their child at any time after the child is conceived.

Promoting an active form of learning out-of-class via answering online "study questions" leads to higher than expected exam scores in General Biology.

PubMed

Gibson, Susan I

2015-01-01

A rising need for workers in science, technology, engineering and mathematics (STEM) fields has fueled interest in improving teaching within STEM disciplines. Numerous studies have demonstrated the benefits of active learning approaches on student learning outcomes. However, many of these studies have been conducted in experimental, rather than real-life class, settings. In addition, most of these studies have focused on in-class active learning exercises. This study tested the effects of answering questions outside of class on exam performance for General Biology students at the University of Minnesota. An online database of 1,020 multiple-choice questions covering material from the first half of the course was generated. Students in seven course sections (with an average of ∼265 students per section) were given unlimited access to the online study questions. These students made extensive use of the online questions, with students answering an average of 1,323 questions covering material from the half of the semester for which the questions were available. After students answered a set of questions, they were shown the correct answers for those questions. More specific feedback describing how to arrive at the correct answer was provided for the 73% of the questions for which the correct answers were not deemed to be self-explanatory. The extent to which access to the online study questions improved student learning outcomes was assessed by comparing the performance on exam questions of students in the seven course sections with access to the online study questions with the performance of students in course sections without access to the online study questions. Student performance was analyzed for a total of 89 different exams questions that were not included in the study questions, but that covered the same material covered by the study questions. Each of these 89 questions was used on one to five exams given to students in course sections that had access to the online study questions and on three to 77 exams given to students in sections that lacked such access. Data from over 1,800 students in sections with access to the online study questions show that those students scored a statistically significant average of 6.6% points higher on the exam questions analyzed than students in sections without access to the study questions. This difference was greater than the average amount necessary to raise students' exam grades by one grade (e.g., from a "B-" to a "B"). In addition, there was a higher correlation between number of questions answered and success on exam questions on material related to the study questions than between number of questions answered and success on exam questions on material unrelated to the study questions. The online study question system required substantial effort to set up, but required minimal effort to maintain and was effective in significantly raising average exam scores for even very large course sections.

Standardization and utilization of biobank resources in clinical protein science with examples of emerging applications.

PubMed

Marko-Varga, György; Végvári, Ákos; Welinder, Charlotte; Lindberg, Henrik; Rezeli, Melinda; Edula, Goutham; Svensson, Katrin J; Belting, Mattias; Laurell, Thomas; Fehniger, Thomas E

2012-11-02

Biobanks are a major resource to access and measure biological constituents that can be used to monitor the status of health and disease, both in unique individual samples and within populations. Most "omic" activities rely on access to these collections of stored samples to provide the basis for establishing the ranges and frequencies of expression. Furthermore, information about the relative abundance and form of protein constituents found in stored samples provides an important historical index for comparative studies of inherited, epidemic, and developing disease. Standardizations of sample quality, form, and analysis are an important unmet need and requirement for gaining the full benefit from collected samples. Coupled to this standard is the provision of annotation describing clinical status and metadata of measurements of clinical phenotype that characterizes the sample. Today we have not yet achieved consensus on how to collect, manage, and build biobank archives in order to reach goals where these efforts are translated into value for the patient. Several initiatives (OBBR, ISBER, BBMRI) that disseminate best practice examples for biobanking are expected to play an important role in ensuring the need to preserve the sample integrity of biosamples stored for periods that reach one or several decades. These developments will be of great value and importance to programs such as the Chromosome Human Protein Project (C-HPP) that will associate protein expression in healthy and disease states with genetic foci along of each of the human chromosomes.

Genetically programmed chiral organoborane synthesis

NASA Astrophysics Data System (ADS)

Kan, S. B. Jennifer; Huang, Xiongyi; Gumulya, Yosephine; Chen, Kai; Arnold, Frances H.

2017-12-01

Recent advances in enzyme engineering and design have expanded nature’s catalytic repertoire to functions that are new to biology. However, only a subset of these engineered enzymes can function in living systems. Finding enzymatic pathways that form chemical bonds that are not found in biology is particularly difficult in the cellular environment, as this depends on the discovery not only of new enzyme activities, but also of reagents that are both sufficiently reactive for the desired transformation and stable in vivo. Here we report the discovery, evolution and generalization of a fully genetically encoded platform for producing chiral organoboranes in bacteria. Escherichia coli cells harbouring wild-type cytochrome c from Rhodothermus marinus (Rma cyt c) were found to form carbon-boron bonds in the presence of borane-Lewis base complexes, through carbene insertion into boron-hydrogen bonds. Directed evolution of Rma cyt c in the bacterial catalyst provided access to 16 novel chiral organoboranes. The catalyst is suitable for gram-scale biosynthesis, providing up to 15,300 turnovers, a turnover frequency of 6,100 h-1, a 99:1 enantiomeric ratio and 100% chemoselectivity. The enantiopreference of the biocatalyst could also be tuned to provide either enantiomer of the organoborane products. Evolved in the context of whole-cell catalysts, the proteins were more active in the whole-cell system than in purified forms. This study establishes a DNA-encoded and readily engineered bacterial platform for borylation; engineering can be accomplished at a pace that rivals the development of chemical synthetic methods, with the ability to achieve turnovers that are two orders of magnitude (over 400-fold) greater than those of known chiral catalysts for the same class of transformation. This tunable method for manipulating boron in cells could expand the scope of boron chemistry in living systems.

Biological approaches for addressing the grand challenge of providing access to clean drinking water.

PubMed

Riley, Mark R; Gerba, Charles P; Elimelech, Menachem

2011-03-31

The U.S. National Academy of Engineering (NAE) recently published a document presenting "Grand Challenges for Engineering". This list was proposed by leading engineers and scientists from around the world at the request of the U.S. National Science Foundation (NSF). Fourteen topics were selected for these grand challenges, and at least seven can be addressed using the tools and methods of biological engineering. Here we describe how biological engineers can address the challenge of providing access to clean drinking water. This issue must be addressed in part by removing or inactivating microbial and chemical contaminants in order to properly deliver water safe for human consumption. Despite many advances in technologies this challenge is expanding due to increased pressure on fresh water supplies and to new opportunities for growth of potentially pathogenic organisms.

Biological approaches for addressing the grand challenge of providing access to clean drinking water

PubMed Central

2011-01-01

The U.S. National Academy of Engineering (NAE) recently published a document presenting "Grand Challenges for Engineering". This list was proposed by leading engineers and scientists from around the world at the request of the U.S. National Science Foundation (NSF). Fourteen topics were selected for these grand challenges, and at least seven can be addressed using the tools and methods of biological engineering. Here we describe how biological engineers can address the challenge of providing access to clean drinking water. This issue must be addressed in part by removing or inactivating microbial and chemical contaminants in order to properly deliver water safe for human consumption. Despite many advances in technologies this challenge is expanding due to increased pressure on fresh water supplies and to new opportunities for growth of potentially pathogenic organisms. PMID:21453515

Protecting Traditional Knowledge Related to Biological Resources: Is Scientific Research Going to Become More Bureaucratized?

PubMed

Reddy, Prashant; Lakshmikumaran, Malathi

2015-06-22

For the past several decades, there has been a world debate on the need for protecting traditional knowledge. A global treaty appears to be a distant reality. Of more immediate concern are the steps taken by the global community to protect access to biological resources in the name of protecting traditional knowledge. The Indian experience with implementing the Convention on Biological Diversity has created substantial legal uncertainty in collaborative scientific research between Indians and foreigners apart from bureaucratizing the entire process of scientific research, especially with regard to filing of applications for intellectual property rights. The issue therefore is whether the world needs to better balance the needs of the scientific community with the rights of those who have access to traditional knowledge. Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved.

77 FR 37683 - Proposed Collection; Comment Request; NDAR Data Access Request

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-22

... first where the Principal Investigator (PI) completes the entire NDAR Data Access Request form, and the second where the PI has the Research Assistant begin filling out the form and PI provides the final...

Mucosal melanoma: an update.

PubMed

Ballester Sánchez, R; de Unamuno Bustos, B; Navarro Mira, M; Botella Estrada, R

2015-03-01

Mucosal melanoma is a rare melanoma subtype that differs from the cutaneous form of the tumor in its biology, clinical manifestations, and management. Diagnosis is usually late due to a lack of early or specific signs and the location of lesions in areas that are difficult to access on physical examination. Surgical excision is the treatment of choice for localized disease. The value of sentinel lymph node biopsy and lymphadenectomy is still unclear. Radiotherapy can be used as adjuvant therapy for the control of local disease. c-KIT mutations are more common than in other types of melanoma and this has led to significant advances in the use of imatinib for the treatment of metastatic mucosal melanoma. Copyright © 2014 Elsevier España, S.L.U. and AEDV. All rights reserved.

DNA replication through a chromatin environment.

PubMed

Bellush, James M; Whitehouse, Iestyn

2017-10-05

Compaction of the genome into the nuclear space is achieved by wrapping DNA around octameric assemblies of histone proteins to form nucleosomes, the fundamental repeating unit of chromatin. Aside from providing a means by which to fit larger genomes into the cell, chromatinization of DNA is a crucial means by which the cell regulates access to the genome. While the complex role that chromatin plays in gene transcription has been appreciated for a long time, it is now also apparent that crucial aspects of DNA replication are linked to the biology of chromatin. This review will focus on recent advances in our understanding of how the chromatin environment influences key aspects of DNA replication.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'. © 2017 The Author(s).

Improved Access to NSF Funded Ocean Research Data

NASA Astrophysics Data System (ADS)

Chandler, C. L.; Groman, R. C.; Kinkade, D.; Shepherd, A.; Rauch, S.; Allison, M. D.; Gegg, S. R.; Wiebe, P. H.; Glover, D. M.

2015-12-01

Data from NSF-funded, hypothesis-driven research comprise an essential part of the research results upon which we base our knowledge and improved understanding of the impacts of climate change. Initially funded in 2006, the Biological and Chemical Oceanography Data Management Office (BCO-DMO) works with marine scientists to ensure that data from NSF-funded ocean research programs are fully documented and freely available for future use. BCO-DMO works in partnership with information technology professionals, other marine data repositories and national data archive centers to ensure long-term preservation of these valuable environmental research data. Data contributed to BCO-DMO by the original investigators are enhanced with sufficient discipline-specific documentation and published in a variety of standards-compliant forms designed to enable discovery and support accurate re-use.

Asymmetric 1,2-perfluoroalkyl migration: easy access to enantioenriched α-hydroxy-α-perfluoroalkyl esters.

PubMed

Wang, Pan; Feng, Liang-Wen; Wang, Lijia; Li, Jun-Fang; Liao, Saihu; Tang, Yong

2015-04-15

This study has led to the development of a novel, highly efficient, 1,2-perfluoro-alkyl/-aryl migration process in reactions of hydrate of 1-perfluoro-alkyl/-aryl-1,2-diketones with alcohols, which are promoted by a Zn(II)/bisoxazoline and form α-perfluoro-alkyl/-aryl-substituted α-hydroxy esters. With (-)-8-phenylmenthol as the alcohol, the corresponding menthol esters are generated in high yields with excellent levels of diastereoselectivity. The mechanistic studies show that the benzilic ester-type rearrangement reaction takes place via an unusual 1,2-migration of electron-deficient trifluoromethyl group rather than the phenyl group. The overall process serves as a novel, efficient, and simple approach for the synthesis of highly enantioenriched, biologically relevant α-hydroxy-α-perfluoroalkyl carboxylic acid derivatives.

Aerospace medicine and biology: A cumulative index to a continuing bibliography (supplement 319)

NASA Technical Reports Server (NTRS)

1989-01-01

This publication is a cumulative index to the abstracts contained in Supplements 307 through 318 of Aerospace Medicine and Biology: A Continuing Bibliography. Seven indexes are included -- subject, personal author, corporate source, foreign technology, contract number, report number and accession number.

Aerospace medicine and biology: A cumulative index to a continuing bibliography (supplement 358)

NASA Technical Reports Server (NTRS)

1992-01-01

This publication is a cumulative index to the abstracts contained in Supplements 346 through 357 of Aerospace Medicine and Biology: A Continuing Bibliography. It includes seven indexes: subject, personal author, corporate source, foreign technology, contract number, report number and accession number.

Aerospace medicine and biology: A cumulative index to a continuing bibliography (supplement 345)

NASA Technical Reports Server (NTRS)

1991-01-01

This publication is a cumulative index to the abstracts contained in Supplements 333 through 344 of Aerospace Medicine and Biology: A Continuing Bibliography. Seven indexes are included -- subject, personal author, corporate source, foreign technology, contract number, report number, and accession number.

Aerospace medicine and biology: A cumulative index to the 1986 issues (supplement 293)

NASA Technical Reports Server (NTRS)

1987-01-01

This publication is a cumulative index to the abstracts contained in the Supplements 281 through 292 of Aerospace Medicine and Biology: A Continuing Bibliography. It includes seven indexes - subject, personal author, corporate source, foreign technology, contract number, report number, and accession number.

Aerospace medicine and biology: A cumulative index to a continuing bibliography (supplement 332)

NASA Technical Reports Server (NTRS)

1990-01-01

This publication is a cumulative index to the abstracts contained in Supplements 320 through 331 of Aerospace Medicine and Biology: A Continuing Bibliography. Seven indexes are included -- subject, personal author, corporate source, foreign technology, contract number, report number and accession number.

Aerospace medicine and biology: A cumulative index to a continuing bibliography (supplement 371)

NASA Technical Reports Server (NTRS)

1993-01-01

This publication is a cumulative index to the abstracts contained in Supplements 359 through 370 of Aerospace Medicine and Biology: A Continuing Bibliography. It includes seven indexes: subject, personal author, corporate source, foreign technology, contract number, report number, and accession number.

Aerospace medicine and biology: A cumulative index to a continuing bibliography (supplement 306)

NASA Technical Reports Server (NTRS)

1988-01-01

This publication is a cumulative index to the abstracts contained in the Supplements 294 through 305 of Aerospace Medicine and Biology: A Continuing Bibliography. It includes seven indexes - subject, personal author, corporate source, foreign technology, contract number, report number, and accession number.

Aerospace medicine and biology: A cumulative index to a continuing bibliography (supplement 384)

NASA Technical Reports Server (NTRS)

1994-01-01

This publication is a cumulative index to the abstracts contained in Supplements 372 through 383 of Aerospace Medicine and Biology: A Continuing Bibliography. It includes seven indexes: subject, personal author, corporate source, foreign technology, contract number, report number, and accession number.

Aerospace Medicine and Biology: A continuing bibliography with indexes, supplement 267, January 1985

NASA Technical Reports Server (NTRS)

1985-01-01

This publication is a cumulative index to the abstracts contained in the Supplements 255 through 266 of Aerospace Medicine and Biology: A Continuing Bibliography. It includes seven indexes--subject, personal author, corporate source, foreign technology, contract number, report number, and accession number.

21 CFR 312.310 - Individual patients, including for emergency use.

Code of Federal Regulations, 2010 CFR

2010-04-01

.... 312.310 Section 312.310 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS FOR HUMAN USE INVESTIGATIONAL NEW DRUG APPLICATION Expanded Access to... communications. For investigational biological drug products regulated by the Center for Biologics Evaluation and...

The Economic Impact of Biosimilars on Chronic Immune-Mediated Inflammatory Diseases.

PubMed

Pentek, Marta; Zrubka, Zsombor; Gulacsi, Laszlo

2017-01-01

Biological drugs represent highly effective but costly treatments for chronic immunemediated inflammatory diseases posing substantial burden on health care budgets. Introduction of biosimilars since 2013 has brought forward the potential of market competition, and as a societal benefit, the hope of increased access at a lower cost. We aim to provide a descriptive review on economic aspects and market changes related to the introduction of biosimilar drugs. Our focus is on chronic immune-mediated inflammatory conditions in rheumatology, gastroenterology and dermatology. Based on available literature data, we discuss the determinants of access to biological treatment, summarize the available health economic evidences with special focus on cost-utility and budget impact analyses. Market penetration of biosimilars and their overall impact on biological markets are analyzed. Biosimilar markets are country specific due to differences in the regulatory and reimbursement systems. Cost-utility analyses suggest, that given the lower price of biosimilars, formerly established biological treatment sequence practices and the eligibility criteria for biological treatment deserve reconsideration. Budget impact analyses forecasted significant budget savings in various diagnoses and countries, providing opportunity for the treatment of more patients. Biosimilars may contribute to better patient-access and provide savings to governments. To increase their acceptability, further clinical evidences and real world experiences are needed, as well as education of physicians and patients. The high biosimilar penetration rates in Norway, Denmark and Poland suggest that policies which support interchanging from the reference product may be important drivers of biosimilar uptake. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Gas seal for an in situ oil shale retort and method of forming thermal barrier

DOEpatents

Burton, III, Robert S.

1982-01-01

A gas seal is provided in an access drift excavated in a subterranean formation containing oil shale. The access drift is adjacent an in situ oil shale retort and is in gas communication with the fragmented permeable mass of formation particles containing oil shale formed in the in situ oil shale retort. The mass of formation particles extends into the access drift, forming a rubble pile of formation particles having a face approximately at the angle of repose of fragmented formation. The gas seal includes a temperature barrier which includes a layer of heat insulating material disposed on the face of the rubble pile of formation particles and additionally includes a gas barrier. The gas barrier is a gas-tight bulkhead installed across the access drift at a location in the access drift spaced apart from the temperature barrier.

An Introduction to Programming for Bioscientists: A Python-Based Primer

PubMed Central

Mura, Cameron

2016-01-01

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in molecular biology, biochemistry, and other biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language’s usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a “variable,” the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences. PMID:27271528

An Introduction to Programming for Bioscientists: A Python-Based Primer.

PubMed

Ekmekci, Berk; McAnany, Charles E; Mura, Cameron

2016-06-01

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in molecular biology, biochemistry, and other biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a "variable," the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.

75 FR 62522 - Combined Notice of Filings No. 3

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-12

... filing per 154.203: NAESB EDI Form Filing to be effective 11/1/ 2010. Filed Date: 09/30/2010. Accession....9 EDI Form to be effective 11/1/2010. Filed Date: 09/30/2010. Accession Number: 20100930-5348...

Preservice Biology Teachers' Conceptions about the Tentative Nature of Theories and Models in Biology

ERIC Educational Resources Information Center

Reinisch, Bianca; Krüger, Dirk

2018-01-01

In research on the nature of science, there is a need to investigate the role and status of different scientific knowledge forms. Theories and models are two of the most important knowledge forms within biology and are the focus of this study. During interviews, preservice biology teachers (N = 10) were asked about their understanding of theories…

78 FR 63231 - National Institute of General Medical Sciences; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-23

... Wisconsin Avenue, Bethesda, MD 20814. Contact Person: Nina Sidorova, Ph.D., Scientific Review Officer..., Ph.D., Scientific Review Officer, Office of Scientific Review, National Institute of General Medical... Biological Chemistry Research; 93.862, Genetics and Developmental Biology Research; 93.88, Minority Access to...

MYC RNAi-Pt Combination Nanotherapy for Metastatic Prostate Cancer Treatment

DTIC Science & Technology

2017-10-01

RNAseq data analysis and gene signatures. All trainees also have access to a number of lectures on cancer including our Fall Course on Cancer Biology ...given in the oncology department that meets twice per week and covers major topics related to cancer biology and treatment. Dr. Bieberich holds

MYC RNAi-Pt Combination Nanotherapy for Metastatic Prostate Cancer Treatment

DTIC Science & Technology

2017-10-01

also have access to a number of lectures on cancer including our Fall Course on Cancer Biology given in the oncology department that meets twice per...week and covers major topics related to cancer biology and treatment. Dr. Bieberich holds weekly meetings with his participating students and they are

76 FR 13196 - National Institute of General Medical Sciences; Notice of Closed Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-10

... Nos. 93.375, Minority Biomedical Research Support; 93.821, Cell Biology and Biophysics Research; 93... Biology Research; 93.88, Minority Access to Research Careers; 93.96, Special Minority Initiatives... Sciences Special Emphasis Panel, Research Centers in Trauma, Burn and Perioperative Injury. Date: April 8...

Visualising "Junk" DNA through Bioinformatics

ERIC Educational Resources Information Center

Elwess, Nancy L.; Latourelle, Sandra M.; Cauthorn, Olivia

2005-01-01

One of the hottest areas of science today is the field in which biology, information technology,and computer science are merged into a single discipline called bioinformatics. This field enables the discovery and analysis of biological data, including nucleotide and amino acid sequences that are easily accessed through the use of computers. As…

[Fundamental biological model for trials of wound ballistics].

PubMed

Krajsa, J; Hirt, M

2006-10-01

The aim of our experiment was the testing of effects of common ammunition on usable and slightly accessible biological tissue thereby to create fundamental simple biological model for trials of wounded ballistic. Like objective tissue was elected biological material - pork and beef hind-limbs, pork head, pork bodily cavity. It was discovered that objective tissue is able to react to singles types of shots in all spectrum results namely simple smooth penetration wound as well as splintery fracture in dependence on kind of using ammunition. Pork hind-limb was evaluated like the most suitable biological material for given object.

American Heart Association Principles on the Accessibility and Affordability of Drugs and Biologics: A Presidential Advisory From the American Heart Association.

PubMed

Antman, Elliott M; Creager, Mark A; Houser, Steven R; Warner, John J; Konig, Madeleine

2017-12-12

Net US spending on pharmaceuticals reached $309.5 billion in 2015, an 8.5% increase from the year before, and is expected to reach between $370 and $400 billion by 2020. These current and projected levels have raised serious concerns by policy makers, providers, payers, and patient groups that they are unsustainable and threaten the affordability of and accessibility to much-needed therapies for patients. Two trends related to drugs/biologics and generic drugs/biosimilars underlie this overall increase in spending. First, the market entry prices of innovator pharmaceutical products, or brand drugs and biologics, are at levels that some assessments consider unaffordable to the healthcare system. Second, prices for some established generic drugs such as digoxin and captopril have seen sharp and rapid increases. As an evidence-based patient advocacy organization dedicated to improving the cardiovascular health of all Americans, the American Heart Association has a unique role in advocating for treatments, including medicines that are available, affordable, and accessible to patients. This advisory serves to lay out a set of principles that will guide association engagement in pursuit of this goal. © 2017 American Heart Association, Inc.

Data management strategies for multinational large-scale systems biology projects.

PubMed

Wruck, Wasco; Peuker, Martin; Regenbrecht, Christian R A

2014-01-01

Good accessibility of publicly funded research data is essential to secure an open scientific system and eventually becomes mandatory [Wellcome Trust will Penalise Scientists Who Don't Embrace Open Access. The Guardian 2012]. By the use of high-throughput methods in many research areas from physics to systems biology, large data collections are increasingly important as raw material for research. Here, we present strategies worked out by international and national institutions targeting open access to publicly funded research data via incentives or obligations to share data. Funding organizations such as the British Wellcome Trust therefore have developed data sharing policies and request commitment to data management and sharing in grant applications. Increased citation rates are a profound argument for sharing publication data. Pre-publication sharing might be rewarded by a data citation credit system via digital object identifiers (DOIs) which have initially been in use for data objects. Besides policies and incentives, good practice in data management is indispensable. However, appropriate systems for data management of large-scale projects for example in systems biology are hard to find. Here, we give an overview of a selection of open-source data management systems proved to be employed successfully in large-scale projects.

Animals as Mobile Biological Sensors for Forest Fire Detection.

PubMed

Sahin, Yasar Guneri

2007-12-04

This paper proposes a mobile biological sensor system that can assist in earlydetection of forest fires one of the most dreaded natural disasters on the earth. The main ideapresented in this paper is to utilize animals with sensors as Mobile Biological Sensors(MBS). The devices used in this system are animals which are native animals living inforests, sensors (thermo and radiation sensors with GPS features) that measure thetemperature and transmit the location of the MBS, access points for wireless communicationand a central computer system which classifies of animal actions. The system offers twodifferent methods, firstly: access points continuously receive data about animals' locationusing GPS at certain time intervals and the gathered data is then classified and checked tosee if there is a sudden movement (panic) of the animal groups: this method is called animalbehavior classification (ABC). The second method can be defined as thermal detection(TD): the access points get the temperature values from the MBS devices and send the datato a central computer to check for instant changes in the temperatures. This system may beused for many purposes other than fire detection, namely animal tracking, poachingprevention and detecting instantaneous animal death.

Animals as Mobile Biological Sensors for Forest Fire Detection

PubMed Central

2007-01-01

This paper proposes a mobile biological sensor system that can assist in early detection of forest fires one of the most dreaded natural disasters on the earth. The main idea presented in this paper is to utilize animals with sensors as Mobile Biological Sensors (MBS). The devices used in this system are animals which are native animals living in forests, sensors (thermo and radiation sensors with GPS features) that measure the temperature and transmit the location of the MBS, access points for wireless communication and a central computer system which classifies of animal actions. The system offers two different methods, firstly: access points continuously receive data about animals' location using GPS at certain time intervals and the gathered data is then classified and checked to see if there is a sudden movement (panic) of the animal groups: this method is called animal behavior classification (ABC). The second method can be defined as thermal detection (TD): the access points get the temperature values from the MBS devices and send the data to a central computer to check for instant changes in the temperatures. This system may be used for many purposes other than fire detection, namely animal tracking, poaching prevention and detecting instantaneous animal death. PMID:28903281

Students’ Use of Optional Online Reviews and Its Relationship to Summative Assessment Outcomes in Introductory Biology

PubMed Central

Carpenter, Shana K.; Rahman, Shuhebur; Lund, Terry J. S.; Armstrong, Patrick I.; Lamm, Monica H.; Reason, Robert D.; Coffman, Clark R.

2017-01-01

Retrieval practice has been shown to produce significant enhancements in student learning of course information, but the extent to which students make use of retrieval to learn information on their own is unclear. In the current study, students in a large introductory biology course were provided with optional online review questions that could be accessed as Test questions (requiring students to answer the questions before receiving feedback) or as Read questions (providing students with the question and correct answer up-front). Students more often chose to access the questions as Test compared with Read, and students who used the Test questions scored significantly higher on subsequent exams compared with students who used Read questions or did not access the questions at all. Following an in-class presentation of superior exam performance following use of the Test questions, student use of Test questions increased significantly for the remainder of the term. These results suggest that practice questions can be an effective tool for enhancing student achievement in biology and that informing students about performance-based outcomes coincides with increased use of retrieval practice. PMID:28408408

Data management strategies for multinational large-scale systems biology projects

PubMed Central

Peuker, Martin; Regenbrecht, Christian R.A.

2014-01-01

Good accessibility of publicly funded research data is essential to secure an open scientific system and eventually becomes mandatory [Wellcome Trust will Penalise Scientists Who Don’t Embrace Open Access. The Guardian 2012]. By the use of high-throughput methods in many research areas from physics to systems biology, large data collections are increasingly important as raw material for research. Here, we present strategies worked out by international and national institutions targeting open access to publicly funded research data via incentives or obligations to share data. Funding organizations such as the British Wellcome Trust therefore have developed data sharing policies and request commitment to data management and sharing in grant applications. Increased citation rates are a profound argument for sharing publication data. Pre-publication sharing might be rewarded by a data citation credit system via digital object identifiers (DOIs) which have initially been in use for data objects. Besides policies and incentives, good practice in data management is indispensable. However, appropriate systems for data management of large-scale projects for example in systems biology are hard to find. Here, we give an overview of a selection of open-source data management systems proved to be employed successfully in large-scale projects. PMID:23047157

pClone: Synthetic Biology Tool Makes Promoter Research Accessible to Beginning Biology Students

PubMed Central

Eckdahl, Todd; Cronk, Brian; Andresen, Corinne; Frederick, Paul; Huckuntod, Samantha; Shinneman, Claire; Wacker, Annie; Yuan, Jason

2014-01-01

The Vision and Change report recommended genuine research experiences for undergraduate biology students. Authentic research improves science education, increases the number of scientifically literate citizens, and encourages students to pursue research. Synthetic biology is well suited for undergraduate research and is a growing area of science. We developed a laboratory module called pClone that empowers students to use advances in molecular cloning methods to discover new promoters for use by synthetic biologists. Our educational goals are consistent with Vision and Change and emphasize core concepts and competencies. pClone is a family of three plasmids that students use to clone a new transcriptional promoter or mutate a canonical promoter and measure promoter activity in Escherichia coli. We also developed the Registry of Functional Promoters, an open-access database of student promoter research results. Using pre- and posttests, we measured significant learning gains among students using pClone in introductory biology and genetics classes. Student posttest scores were significantly better than scores of students who did not use pClone. pClone is an easy and affordable mechanism for large-enrollment labs to meet the high standards of Vision and Change. PMID:26086659

Extension of research data repository system to support direct compute access to biomedical datasets: enhancing Dataverse to support large datasets

PubMed Central

McKinney, Bill; Meyer, Peter A.; Crosas, Mercè; Sliz, Piotr

2016-01-01

Access to experimental X-ray diffraction image data is important for validation and reproduction of macromolecular models and indispensable for the development of structural biology processing methods. In response to the evolving needs of the structural biology community, we recently established a diffraction data publication system, the Structural Biology Data Grid (SBDG, data.sbgrid.org), to preserve primary experimental datasets supporting scientific publications. All datasets published through the SBDG are freely available to the research community under a public domain dedication license, with metadata compliant with the DataCite Schema (schema.datacite.org). A proof-of-concept study demonstrated community interest and utility. Publication of large datasets is a challenge shared by several fields, and the SBDG has begun collaborating with the Institute for Quantitative Social Science at Harvard University to extend the Dataverse (dataverse.org) open-source data repository system to structural biology datasets. Several extensions are necessary to support the size and metadata requirements for structural biology datasets. In this paper, we describe one such extension—functionality supporting preservation of filesystem structure within Dataverse—which is essential for both in-place computation and supporting non-http data transfers. PMID:27862010

The genotype-phenotype map of an evolving digital organism.

PubMed

Fortuna, Miguel A; Zaman, Luis; Ofria, Charles; Wagner, Andreas

2017-02-01

To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable.

The genotype-phenotype map of an evolving digital organism

PubMed Central

Zaman, Luis; Wagner, Andreas

2017-01-01

To understand how evolving systems bring forth novel and useful phenotypes, it is essential to understand the relationship between genotypic and phenotypic change. Artificial evolving systems can help us understand whether the genotype-phenotype maps of natural evolving systems are highly unusual, and it may help create evolvable artificial systems. Here we characterize the genotype-phenotype map of digital organisms in Avida, a platform for digital evolution. We consider digital organisms from a vast space of 10141 genotypes (instruction sequences), which can form 512 different phenotypes. These phenotypes are distinguished by different Boolean logic functions they can compute, as well as by the complexity of these functions. We observe several properties with parallels in natural systems, such as connected genotype networks and asymmetric phenotypic transitions. The likely common cause is robustness to genotypic change. We describe an intriguing tension between phenotypic complexity and evolvability that may have implications for biological evolution. On the one hand, genotypic change is more likely to yield novel phenotypes in more complex organisms. On the other hand, the total number of novel phenotypes reachable through genotypic change is highest for organisms with simple phenotypes. Artificial evolving systems can help us study aspects of biological evolvability that are not accessible in vastly more complex natural systems. They can also help identify properties, such as robustness, that are required for both human-designed artificial systems and synthetic biological systems to be evolvable. PMID:28241039

Organic Haze as a Biosignature in Anoxic Earth-Like Atmospheres

NASA Technical Reports Server (NTRS)

Arney, Giada; Domagal-Goldman, Shawn D.; Meadows, Victoria S.

2017-01-01

Early Earth may have hosted a biologically mediated global organic haze during the Archean eon (3.8-2.5 billion years ago). This haze would have significantly impacted multiple aspects of our planet, including its potential for habitability and its spectral appearance. Here, we model worlds with Archean-like levels of carbon dioxide orbiting the ancient Sun and anM4Vdwarf (GJ 876) and show that organic haze formation requires methane fluxes consistent with estimated Earth-like biological production rates. On planets with high fluxes of biogenic organic sulfur gases (CS2, OCS, CH3SH, and CH3SCH3), photochemistry involving these gases can drive haze formation at lower CH4/CO2 ratios than methane photochemistry alone. For a planet orbiting the Sun, at 30x the modern organic sulfur gas flux, haze forms at a CH4/CO2 ratio 20% lower than at 1x the modern organic sulfur flux. For a planet orbiting the M4V star, the impact of organic sulfur gases is more pronounced: at 1x the modern Earth organic sulfur flux, a substantial haze forms at CH4/CO2 approx. 0.2, but at 30x the organic sulfur flux, the CH4/CO2 ratio needed to form haze decreases by a full order of magnitude. Detection of haze at an anomalously low CH4/ CO2 ratio could suggest the influence of these biogenic sulfur gases and therefore imply biological activity on an exoplanet. When these organic sulfur gases are not readily detectable in the spectrum of an Earth-like exoplanet, the thick organic haze they can help produce creates a very strong absorption feature at UV-blue wavelengths detectable in reflected light at a spectral resolution as low as 10. In direct imaging, constraining CH4 and CO2 concentrations will require higher spectral resolution, and R > 170 is needed to accurately resolve the structure of the CO2 feature at 1.57 microns, likely the most accessible CO2 feature on an Archean-like exoplanet.

Organic Haze as a Biosignature in Anoxic Earth-like Atmospheres

PubMed Central

Domagal-Goldman, Shawn D.; Meadows, Victoria S.

2018-01-01

Abstract Early Earth may have hosted a biologically mediated global organic haze during the Archean eon (3.8–2.5 billion years ago). This haze would have significantly impacted multiple aspects of our planet, including its potential for habitability and its spectral appearance. Here, we model worlds with Archean-like levels of carbon dioxide orbiting the ancient Sun and an M4V dwarf (GJ 876) and show that organic haze formation requires methane fluxes consistent with estimated Earth-like biological production rates. On planets with high fluxes of biogenic organic sulfur gases (CS2, OCS, CH3SH, and CH3SCH3), photochemistry involving these gases can drive haze formation at lower CH4/CO2 ratios than methane photochemistry alone. For a planet orbiting the Sun, at 30× the modern organic sulfur gas flux, haze forms at a CH4/CO2 ratio 20% lower than at 1× the modern organic sulfur flux. For a planet orbiting the M4V star, the impact of organic sulfur gases is more pronounced: at 1× the modern Earth organic sulfur flux, a substantial haze forms at CH4/CO2 ∼ 0.2, but at 30× the organic sulfur flux, the CH4/CO2 ratio needed to form haze decreases by a full order of magnitude. Detection of haze at an anomalously low CH4/CO2 ratio could suggest the influence of these biogenic sulfur gases and therefore imply biological activity on an exoplanet. When these organic sulfur gases are not readily detectable in the spectrum of an Earth-like exoplanet, the thick organic haze they can help produce creates a very strong absorption feature at UV-blue wavelengths detectable in reflected light at a spectral resolution as low as 10. In direct imaging, constraining CH4 and CO2 concentrations will require higher spectral resolution, and R > 170 is needed to accurately resolve the structure of the CO2 feature at 1.57 μm, likely the most accessible CO2 feature on an Archean-like exoplanet. Key Words: Organic haze—Organic sulfur gases—Biosignatures—Archean Earth. Astrobiology 18, 311–329. PMID:29189040

Organic Haze as a Biosignature in Anoxic Earth-like Atmospheres.

PubMed

Arney, Giada; Domagal-Goldman, Shawn D; Meadows, Victoria S

2018-03-01

Early Earth may have hosted a biologically mediated global organic haze during the Archean eon (3.8-2.5 billion years ago). This haze would have significantly impacted multiple aspects of our planet, including its potential for habitability and its spectral appearance. Here, we model worlds with Archean-like levels of carbon dioxide orbiting the ancient Sun and an M4V dwarf (GJ 876) and show that organic haze formation requires methane fluxes consistent with estimated Earth-like biological production rates. On planets with high fluxes of biogenic organic sulfur gases (CS 2 , OCS, CH 3 SH, and CH 3 SCH 3 ), photochemistry involving these gases can drive haze formation at lower CH 4 /CO 2 ratios than methane photochemistry alone. For a planet orbiting the Sun, at 30× the modern organic sulfur gas flux, haze forms at a CH 4 /CO 2 ratio 20% lower than at 1× the modern organic sulfur flux. For a planet orbiting the M4V star, the impact of organic sulfur gases is more pronounced: at 1× the modern Earth organic sulfur flux, a substantial haze forms at CH 4 /CO 2 ∼ 0.2, but at 30× the organic sulfur flux, the CH 4 /CO 2 ratio needed to form haze decreases by a full order of magnitude. Detection of haze at an anomalously low CH 4 /CO 2 ratio could suggest the influence of these biogenic sulfur gases and therefore imply biological activity on an exoplanet. When these organic sulfur gases are not readily detectable in the spectrum of an Earth-like exoplanet, the thick organic haze they can help produce creates a very strong absorption feature at UV-blue wavelengths detectable in reflected light at a spectral resolution as low as 10. In direct imaging, constraining CH 4 and CO 2 concentrations will require higher spectral resolution, and R > 170 is needed to accurately resolve the structure of the CO 2 feature at 1.57 μm, likely the most accessible CO 2 feature on an Archean-like exoplanet. Key Words: Organic haze-Organic sulfur gases-Biosignatures-Archean Earth. Astrobiology 18, 311-329.

NDEx - The Network Data Exchange | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

NDEx is an online commons where scientists can upload, share, and publicly distribute biological networks and pathway models. The NDEx Project maintains a web-accessible public server, a documentation website, provides seamless connectivity to Cytoscape as well as programmatic access using a variety of languages including Python and Java.

Characteristics of Open Access Journals in Six Subject Areas

ERIC Educational Resources Information Center

Walters, William H.; Linvill, Anne C.

2011-01-01

We examine the characteristics of 663 Open Access (OA) journals in biology, computer science, economics, history, medicine, and psychology, then compare the OA journals with impact factors to comparable subscription journals. There is great variation in the size of OA journals; the largest publishes more than 2,700 articles per year, but half…

Flow chemistry kinetic studies reveal reaction conditions for ready access to unsymmetrical trehalose analogues.

PubMed

Patel, Mitul K; Davis, Benjamin G

2010-10-07

Monofunctionalization of trehalose, a widely-found symmetric plant disaccharide, was studied in a microreactor to give valuable kinetic insights that have allowed improvements in desymmetrization yields and the development of a reaction sequence for large scale monofunctionalizations that allow access to probes of trehalose's biological function.

Technology-Enhanced Research in the Science Classroom.

ERIC Educational Resources Information Center

Francis, Joseph W.

1997-01-01

Describes a project where students use the Internet as a research tool. Discusses using e-mail to access molecular biology databases and identify proteins using amino acid sequences, obtaining complete amino acid sequences using the world wide web, using telnet to access library resources on the Internet, and various stages of protein analysis…

Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components

NASA Astrophysics Data System (ADS)

Ong, Luvena L.; Hanikel, Nikita; Yaghi, Omar K.; Grun, Casey; Strauss, Maximilian T.; Bron, Patrick; Lai-Kee-Him, Josephine; Schueder, Florian; Wang, Bei; Wang, Pengfei; Kishi, Jocelyn Y.; Myhrvold, Cameron; Zhu, Allen; Jungmann, Ralf; Bellot, Gaetan; Ke, Yonggang; Yin, Peng

2017-12-01

Nucleic acids (DNA and RNA) are widely used to construct nanometre-scale structures with ever increasing complexity, with possible application in fields such as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early kilodalton-scale examples containing typically tens of unique DNA strands. The introduction of DNA origami, which uses many staple strands to fold one long scaffold strand into a desired structure, has provided access to megadalton-scale nanostructures that contain hundreds of unique DNA strands. Even larger DNA origami structures are possible, but manufacturing and manipulating an increasingly long scaffold strand remains a challenge. An alternative and more readily scalable approach involves the assembly of DNA bricks, which each consist of four short binding domains arranged so that the bricks can interlock. This approach does not require a scaffold; instead, the short DNA brick strands self-assemble according to specific inter-brick interactions. First-generation bricks used to create three-dimensional structures are 32 nucleotides long, consisting of four eight-nucleotide binding domains. Protocols have been designed to direct the assembly of hundreds of distinct bricks into well formed structures, but attempts to create larger structures have encountered practical challenges and had limited success. Here we show that DNA bricks with longer, 13-nucleotide binding domains make it possible to self-assemble 0.1-1-gigadalton, three-dimensional nanostructures from tens of thousands of unique components, including a 0.5-gigadalton cuboid containing about 30,000 unique bricks and a 1-gigadalton rotationally symmetric tetramer. We also assembled a cuboid that contains around 10,000 bricks and about 20,000 uniquely addressable, 13-base-pair ‘voxels’ that serves as a molecular canvas for three-dimensional sculpting. Complex, user-prescribed, three-dimensional cavities can be produced within this molecular canvas, enabling the creation of shapes such as letters, a helicoid and a teddy bear. We anticipate that with further optimization of structure design, strand synthesis and assembly procedure even larger structures could be accessible, which could be useful for applications such as positioning functional components.

SWS: accessing SRS sites contents through Web Services.

PubMed

Romano, Paolo; Marra, Domenico

2008-03-26

Web Services and Workflow Management Systems can support creation and deployment of network systems, able to automate data analysis and retrieval processes in biomedical research. Web Services have been implemented at bioinformatics centres and workflow systems have been proposed for biological data analysis. New databanks are often developed by taking into account these technologies, but many existing databases do not allow a programmatic access. Only a fraction of available databanks can thus be queried through programmatic interfaces. SRS is a well know indexing and search engine for biomedical databanks offering public access to many databanks and analysis tools. Unfortunately, these data are not easily and efficiently accessible through Web Services. We have developed 'SRS by WS' (SWS), a tool that makes information available in SRS sites accessible through Web Services. Information on known sites is maintained in a database, srsdb. SWS consists in a suite of WS that can query both srsdb, for information on sites and databases, and SRS sites. SWS returns results in a text-only format and can be accessed through a WSDL compliant client. SWS enables interoperability between workflow systems and SRS implementations, by also managing access to alternative sites, in order to cope with network and maintenance problems, and selecting the most up-to-date among available systems. Development and implementation of Web Services, allowing to make a programmatic access to an exhaustive set of biomedical databases can significantly improve automation of in-silico analysis. SWS supports this activity by making biological databanks that are managed in public SRS sites available through a programmatic interface.

[The hyperiricosuria as an indicator of derangement of biologic functions of endoecology and adaptation, biologic reactions of excretion, inflammation and arterial tension].

PubMed

Titov, V N; Oshchepkova, E V; Dmitriev, V A; Gushchina, O V; Shiriaeva, Iu K; Iashin, A Ia

2012-04-01

During millions years in all animals allantoine (oxidized by uricase uric acid) was catabolite of purines and ascorbic acid was an acceptor of active forms of oxygen. The proximal tubules of nephron reabsorbed the trace amounts of uric acid Then during phylogenesis the primates had a mutation of ascorbic acid gen minus. Later on occurred a second spontaneous mutation and uricase gen minus and uric acid became catabolites of purines. In absence of ascorbic acid synthesis ions of urates became a major capturers of active forms of oxygen and all uric acid as before underwent the reabsorption. Later the carriers were formed which began in epithelium of proximal tubules to secrete all uric acid into urine. At every incident of "littering" of intercellular medium with endogenic flogogens (impairment of biologic function of endoecology) under compensatory development of biologic reaction of inflammation the need in inactivation of active forms of oxygen increases. Hence later on in phylogenesis one more stage was formed--post secretory reabsorption of uric acid In the biologic reaction of inflammation epithelium of proximal tubules initiates retentional hyperiricosuria. The general antioxidant activity of human blood plasma in 60% is presented by urates' ions. The excretion of uric acid includes 4 stages: filtration, full reabsorption, secretion and post secretory reabsorption. In phylogenesis these stages formed in sequence. The mild hyperiricosuria is most frequently considered as a non-specific indicator of activation of biologic reaction of inflammation. The productive hyperiricosuria develops more infrequently under surplus of meat food and cytolysis syndrome (intensification of cell loss in vivo). Under concentration of uric acid more than 400 mkmol/l part of urates circulates in intercellular medium in the form of crystals. The microcrystals of uric acid (biologic "litter") initiate the syndrome of systemic inflammatory response as an endogenic flogogen--initiator of inflammation. The uric acid in the form of ion-capturers of active forms of oxygen is involved into in the formation of syndrome of compensatory anti-inflammatory defense. It may be assumed that simultaneously with post-secretory reabsorption of ions of urates in proximal tubules of nephron occurs intensification of philogenetically late post-secretory reabsorption of ions of sodium and activation of of biologic reaction of hydrodynamic and hydraulic pressure in local pool of intravascular medium i.e. arterial tension. The uric acid simultaneously participates in realization of biologic function of endoecology and adaptation, biologic reactions of excretion, inflammation and arterial tension.

Fluorescence correlation spectroscopy: novel variations of an established technique.

PubMed

Haustein, Elke; Schwille, Petra

2007-01-01

Fluorescence correlation spectroscopy (FCS) is one of the major biophysical techniques used for unraveling molecular interactions in vitro and in vivo. It allows minimally invasive study of dynamic processes in biological specimens with extremely high temporal and spatial resolution. By recording and correlating the fluorescence fluctuations of single labeled molecules through the exciting laser beam, FCS gives information on molecular mobility and photophysical and photochemical reactions. By using dual-color fluorescence cross-correlation, highly specific binding studies can be performed. These have been extended to four reaction partners accessible by multicolor applications. Alternative detection schemes shift accessible time frames to slower processes (e.g., scanning FCS) or higher concentrations (e.g., TIR-FCS). Despite its long tradition, FCS is by no means dated. Rather, it has proven to be a highly versatile technique that can easily be adapted to solve specific biological questions, and it continues to find exciting applications in biology and medicine.

CHOmine: an integrated data warehouse for CHO systems biology and modeling

PubMed Central

Hanscho, Michael; Ruckerbauer, David E.; Zanghellini, Jürgen; Borth, Nicole

2017-01-01

Abstract The last decade has seen a surge in published genome-scale information for Chinese hamster ovary (CHO) cells, which are the main production vehicles for therapeutic proteins. While a single access point is available at www.CHOgenome.org, the primary data is distributed over several databases at different institutions. Currently research is frequently hampered by a plethora of gene names and IDs that vary between published draft genomes and databases making systems biology analyses cumbersome and elaborate. Here we present CHOmine, an integrative data warehouse connecting data from various databases and links to other ones. Furthermore, we introduce CHOmodel, a web based resource that provides access to recently published CHO cell line specific metabolic reconstructions. Both resources allow to query CHO relevant data, find interconnections between different types of data and thus provides a simple, standardized entry point to the world of CHO systems biology. Database URL: http://www.chogenome.org PMID:28605771

Barriers to accessing biologic treatment for rheumatoid arthritis in Greece: the unseen impact of the fiscal crisis--the Health Outcomes Patient Environment (HOPE) study.

PubMed

Souliotis, Kyriakos; Papageorgiou, Manto; Politi, Anastasia; Ioakeimidis, Dimitrios; Sidiropoulos, Prodromos

2014-01-01

The latest regulatory change in the distribution system of biologic disease-modifying, antirheumatic drugs limited their sale only through the designated pharmacies of the National Organization for Healthcare Services Provision (EOPYY) or the National Health System (NHS) hospitals, adding to the complexity of access to effective treatment for rheumatoid arthritis (RA) in Greece. The aim of this paper was to assess the barriers to access RA treatment, by recording patients', rheumatologists' and EOPYY pharmacists' experiences. One twenty-three patients, 12 rheumatologists and 27 pharmacists from Athens and other urban areas in Greece participated in the study. Three types of standardized questionnaires were used to elicit information from each group of respondents using the method of personal interview for patients and the method of postal survey for doctors and pharmacists. During the last year, 26% of patients encountered problems in accessing their rheumatologist and 49% of patients experienced difficulties in accessing their medication. Ninety-two percent of rheumatologists and 96% of pharmacists confirmed that patients experience difficulties in accessing RA medication. The most commonly reported reasons for reduced access to medical treatment were travel difficulties and long distance from doctor's clinic, as well as delays in booking an appointment. The most frequently reported barriers to access pharmaceutical treatment were difficulties in the prescription process, distance from EOPYY pharmacies and medicine shortages in NHS hospitals. The study showed that RA patients are facing increased barriers to access timely and effective treatment. Redesign of the current system of distribution ensuring the operation of additional points of sale is deemed necessary.

DSSTOX WEBSITE LAUNCH: IMPROVING PUBLIC ACCESS ...

EPA Pesticide Factsheets

DSSTox Website Launch: Improving Public Access to Databases for Building Structure-Toxicity Prediction ModelsAnn M. RichardUS Environmental Protection Agency, Research Triangle Park, NC, USADistributed: Decentralized set of standardized, field-delimited databases, each separatelyauthored and maintained, that are able to accommodate diverse toxicity data content;Structure-Searchable: Standard format (SDF) structure-data files that can be readily imported into available chemical relational databases and structure-searched;Tox: Toxicity data as it exists in widely disparate forms in current public databases, spanning diverse toxicity endpoints, test systems, levels of biological content, degrees of summarization, and information content.INTRODUCTIONThe economic and social pressures to reduce the need for animal testing and to better anticipate the potential for human and eco-toxicity of environmental, industrial, or pharmaceutical chemicals are as pressing today as at any time prior. However, the goal of predicting chemical toxicity in its many manifestations, the `T' in 'ADMET' (adsorption, distribution, metabolism, elimination, toxicity), remains one of the most difficult and largely unmet challenges in a chemical screening paradigm [1]. It is widely acknowledged that the single greatest hurdle to improving structure-activity relationship (SAR) toxicity prediction capabilities, in both the pharmaceutical and environmental regulation arenas, is the lack of suffici

A Federated Network for Translational Cancer Research Using Clinical Data and Biospecimens

PubMed Central

Becich, Michael J.; Bollag, Roni J.; Chavan, Girish; Corrigan, Julia; Dhir, Rajiv; Feldman, Michael D.; Gaudioso, Carmelo; Legowski, Elizabeth; Maihle, Nita J.; Mitchell, Kevin; Murphy, Monica; Sakthivel, Mayur; Tseytlin, Eugene; Weaver, JoEllen

2015-01-01

Advances in cancer research and personalized medicine will require significant new bridging infrastructures, including more robust biorepositories that link human tissue to clinical phenotypes and outcomes. In order to meet that challenge, four cancer centers formed the TIES Cancer Research Network, a federated network that facilitates data and biospecimen sharing among member institutions. Member sites can access pathology data that is de-identified and processed with the TIES natural language processing system, which creates a repository of rich phenotype data linked to clinical biospecimens. TIES incorporates multiple security and privacy best practices that, combined with legal agreements, network policies and procedures, enable regulatory compliance. The TIES Cancer Research Network now provides integrated access to investigators at all member institutions, where multiple investigator-driven pilot projects are underway. Examples of federated search across the network illustrate the potential impact on translational research, particularly for studies involving rare cancers, rare phenotypes, and specific biologic behaviors. The network satisfies several key desiderata including local control of data and credentialing, inclusion of rich phenotype information, and applicability to diverse research objectives. The TIES Cancer Research Network presents a model for a national data and biospecimen network. PMID:26670560

Exploring the Diffusion of Molecular Oxygen in the Red Fluorescent Protein mCherry Using Explicit Oxygen Molecular Dynamics Simulations

PubMed Central

Regmi, Chola K.; Bhandari, Yuba R.; Gerstman, Bernard S.; Chapagain, Prem P.

2013-01-01

The development of fluorescent proteins (FPs) has revolutionized cell biology research. The monomeric variants of red fluorescent proteins (RFPs), known as mFruits, have been especially valuable for tagging and tracking cellular processes in vivo. Determining oxygen diffusion pathways in FPs can be important for improving photostability and for understanding maturation of the chromophore. We use molecular dynamics (MD) calculations to investigate the diffusion of molecular oxygen in one of the most useful monomeric RFPs, mCherry. We describe a pathway that allows oxygen molecules to enter from the solvent and travel through the protein barrel to the chromophore. We calculate the free-energy of an oxygen molecule at points along the path. The pathway contains several oxygen hosting pockets, which are identified by the amino acid residues that form the pocket. We also investigate an RFP variant known to be significantly less photostable than mCherry and find much easier oxygen access in this variant. The results provide a better understanding of the mechanism of molecular oxygen access into the fully folded mCherry protein barrel and provide insight into the photobleaching process in these proteins. PMID:23363049

Integration of microbial biopesticides in greenhouse floriculture: The Canadian experience.

PubMed

Brownbridge, Michael; Buitenhuis, Rose

2017-11-28

Historically, greenhouse floriculture has relied on synthetic insecticides to meet its pest control needs. But, growers are increasingly faced with the loss or failure of synthetic chemical pesticides, declining access to new chemistries, stricter environmental/health and safety regulations, and the need to produce plants in a manner that meets the 'sustainability' demands of a consumer driven market. In Canada, reports of thrips resistance to spinosad (Success™) within 6-12 months of its registration prompted a radical change in pest management philosophy and approach. Faced with a lack of registered chemical alternatives, growers turned to biological control out of necessity. Biological control now forms the foundation for pest management programs in Canadian floriculture greenhouses. Success in a biocontrol program is rarely achieved through the use of a single agent, though. Rather, it is realized through the concurrent use of biological, cultural and other strategies within an integrated plant production system. Microbial insecticides can play a critical supporting role in biologically-based integrated pest management (IPM) programs. They have unique modes of action and are active against a range of challenging pests. As commercial microbial insecticides have come to market, research to generate efficacy data has assisted their registration in Canada, and the development and adaptation of integrated programs has promoted uptake by floriculture growers. This review documents some of the work done to integrate microbial insecticides into chrysanthemum and poinsettia production systems, outlines current use practices, and identifies opportunities to improve efficacy in Canadian floriculture crops. Copyright © 2017 Elsevier Inc. All rights reserved.

Expression of Resistance in Amaranthus spp. (Caryophyllales: Amaranthaceae): Effects of Selected Accessions on the Behaviour and Biology of the Amaranth Leaf-Webber, Spoladea recurvalis (Lepidoptera: Crambidae).

PubMed

Othim, Stephen T O; Ramasamy, Srinivasan; Kahuthia-Gathu, Ruth; Dubois, Thomas; Ekesi, Sunday; Fiaboe, Komi K M

2018-06-08

Spoladea recurvalis F. is a major pest moth of amaranth ( Amaranthus spp.) flowers worldwide, with a potential of causing complete foliage loss under severe outbreaks. Chemical insecticides are uneconomical for resource-poor farmers and pose health and environmental risks. Host plant resistance (HPR) to insects is an effective, economical and environmentally friendly alternative that is poorly understood and largely unexploited among traditional leafy vegetables. A total of 35 amaranth accessions were evaluated for the expression of their antixenotic and antibiotic traits against S. recurvalis , focusing on their effects on the biology of the pest in comparison with a susceptible accession. The accession VI036227 was found to be highly resistant against the pest, exhibiting exemplary antibiosis by causing 100% larval mortality within the first 36 h, despite not being deterrent for oviposition. The accessions VI048076, VI056563 and VI047555-B demonstrated moderate resistance against the pest for specific parameters including low oviposition, moderate early stage larval mortality and reduced adult longevity. Total mortality and weight gain in these three accessions were, however, not significantly different from the susceptible control. Higher numbers of eggs were laid in no-choice compared to choice situations. The implications of these findings in the management of S. recurvalis on amaranths are discussed.

Database Resources of the BIG Data Center in 2018

PubMed Central

Xu, Xingjian; Hao, Lili; Zhu, Junwei; Tang, Bixia; Zhou, Qing; Song, Fuhai; Chen, Tingting; Zhang, Sisi; Dong, Lili; Lan, Li; Wang, Yanqing; Sang, Jian; Hao, Lili; Liang, Fang; Cao, Jiabao; Liu, Fang; Liu, Lin; Wang, Fan; Ma, Yingke; Xu, Xingjian; Zhang, Lijuan; Chen, Meili; Tian, Dongmei; Li, Cuiping; Dong, Lili; Du, Zhenglin; Yuan, Na; Zeng, Jingyao; Zhang, Zhewen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Zou, Dong; Song, Shuhui; Sang, Jian; Xia, Lin; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Xiao, Jingfa; Zou, Dong; Wang, Fan; Hao, Lili; Liang, Fang; Li, Mengwei; Sun, Shixiang; Zou, Dong; Li, Rujiao; Yu, Chunlei; Wang, Guangyu; Sang, Jian; Liu, Lin; Li, Mengwei; Li, Man; Niu, Guangyi; Cao, Jiabao; Sun, Shixiang; Xia, Lin; Yin, Hongyan; Zou, Dong; Xu, Xingjian; Ma, Lina; Chen, Huanxin; Sun, Yubin; Yu, Lei; Zhai, Shuang; Sun, Mingyuan; Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Song, Shuhui; Hao, Lili; Li, Rujiao; Ma, Lina; Sang, Jian; Wang, Yanqing; Tang, Bixia; Zou, Dong; Wang, Fan

2018-01-01

Abstract The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. PMID:29036542

A Radical Pathway for Organic Phosphorylation during Schreibersite Corrosion with Implications for the Origin of Life

NASA Technical Reports Server (NTRS)

Pasek, Matthew A.; Dworkin, Jason P.; Lauretta, Dante S.

2007-01-01

Phosphorylated compounds (e.g. DNA, RNA, phospholipids, and many coenzymes) are critical to biochemistry. Thus, their origin is of prime interest to origin of life studies. The corrosion of the meteoritic mineral schreibersite ((Fe,Ni)3P) may have significantly contributed to the origin of phosphorylated biomolecules. Corrosion of synthetic schreibersite in a variety of solutions was analyzed by nuclear magnetic resonance spectroscopy, mass spectrometry, and electron paramagnetic resonance spectroscopy. These methods suggest a radical reaction pathway for the corrosion of schreibersite to form phosphite radicals (raised dot PO3 sup 2-)) aqueous solution. These radicals can form activated polyphosphates and can phosphorylate organic compounds such as acetate (3% yield). Phosphonates (O3P-C) are found in the organic P inventory of the carbonaceous meteorite Murchison. While phosphonates are rare in biochemistry, the ubiquity of corroding iron meteorites on the early Earth could have provided an accessible source of organophosphorous for the origin of life allowing the invention of the organophosphates in modern biology as a product of early evolution.

Synthesis and conformational analysis of linear homo- and heterooligomers from novel 2-C-branched sugar amino acids (SAAs).

PubMed

Tian, Guang-Zong; Hu, Jing; Zhang, Heng-Xi; Rademacher, Christoph; Zou, Xiao-Peng; Zheng, Hong-Ning; Xu, Fei; Wang, Xiao-Li; Linker, Torsten; Yin, Jian

2018-04-26

Sugar amino acids (SAAs), as biologically interesting structures bearing both amino and carboxylic acid functional groups represent an important class of multifunctional building blocks. In this study, we develop an easy access to novel SAAs in only three steps starting from nitro compounds in high yields in analytically pure form, easily available by ceric (IV) mediated radical additions. Such novel SAAs have been applied in the assembly of total nine carbopeptoids with the form of linear homo- and heterooligomers for the structural investigations employing circular dichroism (CD) spectroscopy, which suggest that the carbopeptoids emerge a well-extended, left (or right)-handed conformation similar to polyproline II (PPII) helices. NMR studies also clearly demonstrated the presence of ordered secondary structural elements. 2D-ROESY spectra were acquired to identify i+1 NH ↔  i C 1 H, i C 2 H correlations which support the conformational analysis of tetramers by CD spectroscopy. These findings provide interesting information of SAAs and their oligomers as potential scaffolds for discovering new drugs and materials.

Life beyond the limits of knowledge: crystalline life in the popular science of Desiderius Papp (1895-1993).

PubMed

Brandstetter, Thomas

2012-10-01

The aim of this article is to show how, and in which context, astrobiological reasoning was employed before the establishment of astrobiology as a scientific discipline. By way of an example, I will discuss a popular science book published in 1931 by the Hungarian journalist Desiderius Papp. The author claims that this book represents an innovation in astrobiological reasoning, as it draws on contemporary biological research to conduct thought experiments, thereby coming up with concrete forms of possible extraterrestrial life. One of the most interesting of these forms was crystalline life. After a short overview on the history of this concept, this article will show how Papp drew on recent research by Otto Lehmann on liquid crystals to convey the idea that life may be based on other elements than carbon. The author concludes by arguing that popular science did not only make specialist knowledge accessible to a general public but also served to probe the limits of knowledge and point toward the situatedness of established categories and definitions.

Genetic divergence among Psidium accessions based on single nucleotide polymorphisms developed for Eucalyptus.

PubMed

Costa, S R; Santos, C A F

2017-05-04

The goal of this study was to analyze the genetic divergence among Psidium species accessions based on SNPs developed for Eucalyptus. Fifty-three Psidium accessions, including 47 P. guajava, were genotyped with EUCHIP60K. The dendrogram similarity ranged from 0.58 to 1.00, with a cophenetic value of 0.97. Five groups were identified at dendrogram cut point of 0.7: the first with 44 guava accessions, the second with 1 guava accession, the third with 3 P. guineense accessions, the forth with 2 guava accessions, and the fifth with 3 P. cattleianum accessions. The Bayesian analyses suggested seven subpopulations, with formation of two additional groups with guava accessions. Primers designed with Eucalyptus SNP sequences resulted in reliable Psidium amplicons on 6% polyacrylamide gels. In general, the SNP dendrogram agreed with biological genus structure, since different species were not grouped, indicating that transferability among Myrtaceae genus was possible and reliable.

The AAS Working Group on Accessibility and Disability (WGAD) Year 1 Highlights and Database Access

NASA Astrophysics Data System (ADS)

Knierman, Karen A.; Diaz Merced, Wanda; Aarnio, Alicia; Garcia, Beatriz; Monkiewicz, Jacqueline A.; Murphy, Nicholas Arnold

2017-06-01

The AAS Working Group on Accessibility and Disability (WGAD) was formed in January of 2016 with the express purpose of seeking equity of opportunity and building inclusive practices for disabled astronomers at all educational and career stages. In this presentation, we will provide a summary of current activities, focusing on developing best practices for accessibility with respect to astronomical databases, publications, and meetings. Due to the reliance of space sciences on databases, it is important to have user centered design systems for data retrieval. The cognitive overload that may be experienced by users of current databases may be mitigated by use of multi-modal interfaces such as xSonify. Such interfaces would be in parallel or outside the original database and would not require additional software efforts from the original database. WGAD is partnering with the IAU Commission C1 WG Astronomy for Equity and Inclusion to develop such accessibility tools for databases and methods for user testing. To collect data on astronomical conference and meeting accessibility considerations, WGAD solicited feedback from January AAS attendees via a web form. These data, together with upcoming input from the community and analysis of accessibility documents of similar conferences, will be used to create a meeting accessibility document. Additionally, we will update the progress of journal access guidelines and our social media presence via Twitter. We recommend that astronomical journals form committees to evaluate the accessibility of their publications by performing user-centered usability studies.

32 CFR Appendix E to Part 197 - Form Letter-Conditions Governing Access to Official Records for Historical Research Purposes

Code of Federal Regulations, 2010 CFR

2010-07-01

... 32 National Defense 2 2010-07-01 2010-07-01 false Form Letter-Conditions Governing Access to Official Records for Historical Research Purposes E Appendix E to Part 197 National Defense Department of... THE FILES OF THE OFFICE OF THE SECRETARY OF DEFENSE (OSD) Pt. 197, App. E Appendix E to Part 197—Form...

Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork.

PubMed

Druka, Arnis; Druka, Ilze; Centeno, Arthur G; Li, Hongqiang; Sun, Zhaohui; Thomas, William T B; Bonar, Nicola; Steffenson, Brian J; Ullrich, Steven E; Kleinhofs, Andris; Wise, Roger P; Close, Timothy J; Potokina, Elena; Luo, Zewei; Wagner, Carola; Schweizer, Günther F; Marshall, David F; Kearsey, Michael J; Williams, Robert W; Waugh, Robbie

2008-11-18

A typical genetical genomics experiment results in four separate data sets; genotype, gene expression, higher-order phenotypic data and metadata that describe the protocols, processing and the array platform. Used in concert, these data sets provide the opportunity to perform genetic analysis at a systems level. Their predictive power is largely determined by the gene expression dataset where tens of millions of data points can be generated using currently available mRNA profiling technologies. Such large, multidimensional data sets often have value beyond that extracted during their initial analysis and interpretation, particularly if conducted on widely distributed reference genetic materials. Besides quality and scale, access to the data is of primary importance as accessibility potentially allows the extraction of considerable added value from the same primary dataset by the wider research community. Although the number of genetical genomics experiments in different plant species is rapidly increasing, none to date has been presented in a form that allows quick and efficient on-line testing for possible associations between genes, loci and traits of interest by an entire research community. Using a reference population of 150 recombinant doubled haploid barley lines we generated novel phenotypic, mRNA abundance and SNP-based genotyping data sets, added them to a considerable volume of legacy trait data and entered them into the GeneNetwork http://www.genenetwork.org. GeneNetwork is a unified on-line analytical environment that enables the user to test genetic hypotheses about how component traits, such as mRNA abundance, may interact to condition more complex biological phenotypes (higher-order traits). Here we describe these barley data sets and demonstrate some of the functionalities GeneNetwork provides as an easily accessible and integrated analytical environment for exploring them. By integrating barley genotypic, phenotypic and mRNA abundance data sets directly within GeneNetwork's analytical environment we provide simple web access to the data for the research community. In this environment, a combination of correlation analysis and linkage mapping provides the potential to identify and substantiate gene targets for saturation mapping and positional cloning. By integrating datasets from an unsequenced crop plant (barley) in a database that has been designed for an animal model species (mouse) with a well established genome sequence, we prove the importance of the concept and practice of modular development and interoperability of software engineering for biological data sets.

45 CFR Appendix A to Part 84 - Analysis of Final Regulation

Code of Federal Regulations, 2010 CFR

2010-10-01

... 84 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION NONDISCRIMINATION ON... decide that it would be cost-efficient for one college to offer biology, the second physics, and the... which one college undertook to make its biology lab accessible, another its physics lab, and a third its...

The Annotated Bibliography and Citation Behavior: Enhancing Student Scholarship in an Undergraduate Biology Course

ERIC Educational Resources Information Center

Flaspohler, Molly R.; Rux, Erika M.; Flaspohler, John A.

2007-01-01

Contemporary undergraduates in the biological sciences have unprecedented access to scientific information. Although many of these students may be savvy technologists, studies from the field of library and information science consistently show that undergraduates often struggle to locate, evaluate, and use high-quality, reputable sources of…

What Trends Do Turkish Biology Education Studies Indicate?

ERIC Educational Resources Information Center

Topsakal, Unsal Umdu; Calik, Muammer; Cavus, Ragip

2012-01-01

The aim of this study is to determine what trends Turkish biology education studies indicate. To achieve this aim, the researchers examined online databases of the Higher Education Council and open access archives of graduate theses in web sites of Turkish universities. Finally, totally 138 graduate theses were elicited to analyze in regard to…

An Evaluation of Web Enhanced Instruction in College Level Biology Courses

ERIC Educational Resources Information Center

Keasar, Tamar; Baruch, Rachel; Grobgeld-Dahan, Esther

2005-01-01

Websites that accompany science courses typically aim to provide easy access to learning materials, and to facilitate student-instructor communication. We tested whether these aims were achieved in two web enhanced, lower division undergraduate biology courses in an Israeli college. We collected data on the students' attitudes through pre- and…

BioModels.net Web Services, a free and integrated toolkit for computational modelling software.

PubMed

Li, Chen; Courtot, Mélanie; Le Novère, Nicolas; Laibe, Camille

2010-05-01

Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. BioModels.net defines agreed-upon standards for model curation. A fundamental one, MIRIAM (Minimum Information Requested in the Annotation of Models), standardises the annotation and curation process of quantitative models in biology. To support this standard, MIRIAM Resources maintains a set of standard data types for annotating models, and provides services for manipulating these annotations. Furthermore, BioModels.net creates controlled vocabularies, such as SBO (Systems Biology Ontology) which strictly indexes, defines and links terms used in Systems Biology. Finally, BioModels Database provides a free, centralised, publicly accessible database for storing, searching and retrieving curated and annotated computational models. Each resource provides a web interface to submit, search, retrieve and display its data. In addition, the BioModels.net team provides a set of Web Services which allows the community to programmatically access the resources. A user is then able to perform remote queries, such as retrieving a model and resolving all its MIRIAM Annotations, as well as getting the details about the associated SBO terms. These web services use established standards. Communications rely on SOAP (Simple Object Access Protocol) messages and the available queries are described in a WSDL (Web Services Description Language) file. Several libraries are provided in order to simplify the development of client software. BioModels.net Web Services make one step further for the researchers to simulate and understand the entirety of a biological system, by allowing them to retrieve biological models in their own tool, combine queries in workflows and efficiently analyse models.

NBII-SAIN Data Management Toolkit

USGS Publications Warehouse

Burley, Thomas E.; Peine, John D.

2009-01-01

The Strategic Plan for the U.S. Geological Survey Biological Informatics Program (2005-2009) recognizes the need for effective data management: Though the Federal government invests more than $600 million per year in biological data collection, it is difficult to address these issues because of limited accessibility and lack of standards for data and information...variable quality, sources, methods, and formats (for example observations in the field, museum specimens, and satellite images) present additional challenges. This is further complicated by the fast-moving target of emerging and changing technologies such as GPS and GIS. Even though these technologies offer new solutions, they also create new informatics challenges (Ruggiero and others, 2005). The USGS National Biological Information Infrastructure program, hereafter referred to as NBII, is charged with the mission to improve the way data and information are gathered, documented, stored, and accessed. The central objective of this project is a direct reflection of the purpose of NBII as described by John Mosesso, Program Manager of the U.S. Geological Survey-Biological Informatics Program-GAP Analysis: At the outset, the reason for bringing about NBII was that there were significant amounts of data and information scattered all over the U.S., not accessible, in incompatible formats, and that NBII was tasked with addressing this problem...NBII's focus is to pull data together that truly matters to someone or communities. Essentially, the core questions are: 1) what are the issues, 2) where is the data, and 3) how can we make it usable and accessible (John Mosesso, U.S. Geological Survey, oral commun., 2006). Redundancy in data collection can be a major issue when multiple stakeholders are involved with a common effort. In 2001 the U.S. General Accounting Office (USGAO) estimated that about 50 percent of the Federal government's geospatial data at the time was redundant. In addition, approximately 80 percent of the cost of a spatial information system is associated with spatial data collection and management (U.S. General Accounting Office, 2003). These figures indicate that the resources (time, personnel, money) of many agencies and organizations could be used more efficiently and effectively. Dedicated and conscientious data management coordination and documentation is critical for reducing such redundancy. Substantial cost savings and increased efficiency are direct results of a pro-active data management approach. In addition, details of projects as well as data and information are frequently lost as a result of real-world occurrences such as the passing of time, job turnover, and equipment changes and failure. A standardized, well documented database allows resource managers to identify issues, analyze options, and ultimately make better decisions in the context of adaptive management (National Land and Water Resources Audit and the Australia New Zealand Land Information Council on behalf of the Australian National Government, 2003). Many environmentally focused, scientific, or natural resource management organizations collect and create both spatial and non-spatial data in some form. Data management appropriate for those data will be contingent upon the project goal(s) and objectives and thus will vary on a case-by-case basis. This project and the resulting Data Management Toolkit, hereafter referred to as the Toolkit, is therefore not intended to be comprehensive in terms of addressing all of the data management needs of all projects that contain biological, geospatial, and other types of data. The Toolkit emphasizes the idea of connecting a project's data and the related management needs to the defined project goals and objectives from the outset. In that context, the Toolkit presents and describes the fundamental components of sound data and information management that are common to projects involving biological, geospatial, and other related data

Remarks on Height-Diameter Modeling

Treesearch

Lei Yuancai; Bernard R. Parresol

2001-01-01

Height-diameter model forms in earlier published papers are examined. The selection criteria used in height-diameter model forms are not reasonable when considering tree biological growth pattern. During model selection, forms for height-diameter relationships should include consideration of both data-related and reasonable biological criteria, not just data-related...

Data Discovery, Exploration, Integration and Delivery - a practical experience

NASA Astrophysics Data System (ADS)

Kirsch, Peter; Barnes, Tim; Breen, Paul

2010-05-01

To fully address the questions and issues arising within Earth Systems Science; the discovery, exploration, integration, delivery and sharing of data, metadata and services across potentially many disciplines and areas of expertise is fundamental. British Antarctic Survey (BAS) collects, manages and curates data across many fields of the geophysical and biological sciences (including upper atmospheric physics, atmospheric chemistry, meteorology, glaciology, oceanography, Polar ecology and biology). BAS, through its Polar Data Centre has an interest to construct and deliver a user-friendly, informative, and administratively low overhead interface onto these data holdings. Designing effective interfaces and frameworks onto the heterogeneous datasets described above is non-trivial. We will discuss some of our approaches and implementations; particularly those addressing the following issues: How to aid and guide the user to accurate discovery of data? Many portals do not inform users clearly enough about the datasets they actually hold. As a result the search interface by which a user is meant to discover information is often inadequate and assumes prior knowledge (for example, that the dataset you are looking for actually exists; that a particular event, campaign, research cruise took place; and that you have a specialist knowledge of the terminology in a particular field), assumptions that cannot be made in multi-disciplinary topic areas. How easily is provenance, quality, and metadata information displayed and accessed? Once informed through the portal that data is available it is often extremely difficult to assess its provenance and quality information and broader documentation (including field reports, notebooks and software repositories). We shall demonstrate some simple methodologies. Can the user access summary data or visualizations of the dataset? It may be that the user is interested in some event, feature or threshold within the dataset; mechanisms need to be provided to allow a user to browse the data (or at least a summary of the data in the most appropriate form be it a plot, table, video etc) prior to making the decision to download or request data. A framework should be flexible enough to allow several methods of visualization. Can datasets be compared and or integrated? By allowing the inclusion of open, 3rd party, standards compliant utilities (e.g. Open Geo-Spatial Consortium WxS clients) into the framework, the utility of a data access system can be made more valuable. Is accessing the actual data straightforward? The process of accessing the data should follow naturally from the data discovery and browsing stages. The user should be made aware of terms and conditions of access. Access restrictions (if applicable) and security should be made as unobtrusive as possible. How is user feedback and comment monitored and acted upon? In general these systems exist to serve science communities, appropriate notice and acknowledgement of their needs and requirements must be taken into account when designing and developing these systems if they are to be of continued use in the future.

Genome Science: A Video Tour of the Washington University Genome Sequencing Center for High School and Undergraduate Students

PubMed Central

2005-01-01

Sequencing of the human genome has ushered in a new era of biology. The technologies developed to facilitate the sequencing of the human genome are now being applied to the sequencing of other genomes. In 2004, a partnership was formed between Washington University School of Medicine Genome Sequencing Center's Outreach Program and Washington University Department of Biology Science Outreach to create a video tour depicting the processes involved in large-scale sequencing. “Sequencing a Genome: Inside the Washington University Genome Sequencing Center” is a tour of the laboratory that follows the steps in the sequencing pipeline, interspersed with animated explanations of the scientific procedures used at the facility. Accompanying interviews with the staff illustrate different entry levels for a career in genome science. This video project serves as an example of how research and academic institutions can provide teachers and students with access and exposure to innovative technologies at the forefront of biomedical research. Initial feedback on the video from undergraduate students, high school teachers, and high school students provides suggestions for use of this video in a classroom setting to supplement present curricula. PMID:16341256

The Pathway of Oligomeric DNA Melting Investigated by Molecular Dynamics Simulations

PubMed Central

Wong, Ka-Yiu; Pettitt, B. Montgomery

2008-01-01

Details of the reaction coordinate for DNA melting are fundamental to much of biology and biotechnology. Recently, it has been shown experimentally that there are at least three states involved. To clarify the reaction mechanism of the melting transition of DNA, we perform 100-ns molecular dynamics simulations of a homo-oligomeric, 12-basepair DNA duplex, d(A12)·d(T12), with explicit salt water at 400 K. Analysis of the trajectory reveals the various biochemically important processes that occur on different timescales. Peeling (including fraying from the ends), searching for Watson-Crick complements, and dissociation are recognizable processes. However, we find that basepair searching for Watson-Crick complements along a strand is not mechanistically tied to or directly accessible from the dissociation steps of strand melting. A three-step melting mechanism is proposed where the untwisting of the duplex is determined to be the major component of the reaction coordinate at the barrier. Though the observations are limited to the characteristics of the system being studied, they provide important insight into the mechanism of melting of other more biologically relevant forms of DNA, which will certainly differ in details from those here. PMID:18952784

Physics of metabolic organization

NASA Astrophysics Data System (ADS)

Jusup, Marko; Sousa, Tânia; Domingos, Tiago; Labinac, Velimir; Marn, Nina; Wang, Zhen; Klanjšček, Tin

2017-03-01

We review the most comprehensive metabolic theory of life existing to date. A special focus is given to the thermodynamic roots of this theory and to implications that the laws of physics-such as the conservation of mass and energy-have on all life. Both the theoretical foundations and biological applications are covered. Hitherto, the foundations were more accessible to physicists or mathematicians, and the applications to biologists, causing a dichotomy in what always should have been a single body of work. To bridge the gap between the two aspects of the same theory, we (i) adhere to the theoretical formalism, (ii) try to minimize the amount of information that a reader needs to process, but also (iii) invoke examples from biology to motivate the introduction of new concepts and to justify the assumptions made, and (iv) show how the careful formalism of the general theory enables modular, self-consistent extensions that capture important features of the species and the problem in question. Perhaps the most difficult among the introduced concepts, the utilization (or mobilization) energy flow, is given particular attention in the form of an original and considerably simplified derivation. Specific examples illustrate a range of possible applications-from energy budgets of individual organisms, to population dynamics, to ecotoxicology.

Poultry genetic resource conservation using primordial germ cells

PubMed Central

NAKAMURA, Yoshiaki

2016-01-01

The majority of poultry genetic resources are maintained in situ in living populations. However, in situ conservation of poultry genetic resources always carries the risk of loss owing to pathogen outbreaks, genetic problems, breeding cessation, or natural disasters. Cryobanking of germplasm in birds has been limited to the use of semen, preventing conservation of the W chromosome and mitochondrial DNA. A further challenge is posed by the structure of avian eggs, which restricts the cryopreservation of ova and fertilized embryos, a technique widely used for mammalian species. By using a unique biological property and accessibility of avian primordial germ cells (PGCs), precursor cells for gametes, which temporally circulate in the vasculature during early development, an avian PGC transplantation technique has been established. To date, several techniques for PGC manipulation including purification, cryopreservation, depletion, and long-term culture have been developed in chickens. PGC transplantation combined with recent advanced PGC manipulation techniques have enabled ex situ conservation of poultry genetic resources in their complete form. Here, the updated technologies for avian PGC manipulation are introduced, and then the concept of a poultry PGC-bank is proposed by considering the biological properties of avian PGCs. PMID:27210834

Molecular imprinting at walls of silica nanotubes for TNT recognition.

PubMed

Xie, Chenggen; Liu, Bianhua; Wang, Zhenyang; Gao, Daming; Guan, Guijian; Zhang, Zhongping

2008-01-15

This paper reports the molecular imprinting at the walls of highly uniform silica nanotubes for the recognition of 2,4,6-trinitrotoluene (TNT). It has been demonstrated that TNT templates were efficiently imprinted into the matrix of silica through the strong acid-base pairing interaction between TNT and 3-aminopropyltriethoxysilane (APTS). TNT-imprinted silica nanotubes were synthesized by the gelation reaction between APTS and tetraethylorthosilicate (TEOS), selectively occurring at the porous walls of APTS-modified alumina membranes. The removal of the original TNT templates leaves the imprinted cavities with covalently anchored amine groups at the cavity walls. A high density of recognition sites with molecular selectivity to the TNT analyte was created at the wall of silica nanotubes. Furthermore, most of these recognition sites are situated at the inside and outside surfaces of tubular walls and in the proximity of the two surfaces due to the ultrathin wall thickness of only 15 nm, providing a better site accessibility and lower mass-transfer resistance. Therefore, greater capacity and faster kinetics of uptaking target species were achieved. The silica nanotube reported herein is an ideal form of material for imprinting various organic or biological molecules toward applications in chemical/biological sensors and bioassay.

The structural diversity of artificial genetic polymers

PubMed Central

Anosova, Irina; Kowal, Ewa A.; Dunn, Matthew R.; Chaput, John C.; Van Horn, Wade D.; Egli, Martin

2016-01-01

Synthetic genetics is a subdiscipline of synthetic biology that aims to develop artificial genetic polymers (also referred to as xeno-nucleic acids or XNAs) that can replicate in vitro and eventually in model cellular organisms. This field of science combines organic chemistry with polymerase engineering to create alternative forms of DNA that can store genetic information and evolve in response to external stimuli. Practitioners of synthetic genetics postulate that XNA could be used to safeguard synthetic biology organisms by storing genetic information in orthogonal chromosomes. XNA polymers are also under active investigation as a source of nuclease resistant affinity reagents (aptamers) and catalysts (xenozymes) with practical applications in disease diagnosis and treatment. In this review, we provide a structural perspective on known antiparallel duplex structures in which at least one strand of the Watson–Crick duplex is composed entirely of XNA. Currently, only a handful of XNA structures have been archived in the Protein Data Bank as compared to the more than 100 000 structures that are now available. Given the growing interest in xenobiology projects, we chose to compare the structural features of XNA polymers and discuss their potential to access new regions of nucleic acid fold space. PMID:26673703

ADAM: analysis of discrete models of biological systems using computer algebra.

PubMed

Hinkelmann, Franziska; Brandon, Madison; Guang, Bonny; McNeill, Rustin; Blekherman, Grigoriy; Veliz-Cuba, Alan; Laubenbacher, Reinhard

2011-07-20

Many biological systems are modeled qualitatively with discrete models, such as probabilistic Boolean networks, logical models, Petri nets, and agent-based models, to gain a better understanding of them. The computational complexity to analyze the complete dynamics of these models grows exponentially in the number of variables, which impedes working with complex models. There exist software tools to analyze discrete models, but they either lack the algorithmic functionality to analyze complex models deterministically or they are inaccessible to many users as they require understanding the underlying algorithm and implementation, do not have a graphical user interface, or are hard to install. Efficient analysis methods that are accessible to modelers and easy to use are needed. We propose a method for efficiently identifying attractors and introduce the web-based tool Analysis of Dynamic Algebraic Models (ADAM), which provides this and other analysis methods for discrete models. ADAM converts several discrete model types automatically into polynomial dynamical systems and analyzes their dynamics using tools from computer algebra. Specifically, we propose a method to identify attractors of a discrete model that is equivalent to solving a system of polynomial equations, a long-studied problem in computer algebra. Based on extensive experimentation with both discrete models arising in systems biology and randomly generated networks, we found that the algebraic algorithms presented in this manuscript are fast for systems with the structure maintained by most biological systems, namely sparseness and robustness. For a large set of published complex discrete models, ADAM identified the attractors in less than one second. Discrete modeling techniques are a useful tool for analyzing complex biological systems and there is a need in the biological community for accessible efficient analysis tools. ADAM provides analysis methods based on mathematical algorithms as a web-based tool for several different input formats, and it makes analysis of complex models accessible to a larger community, as it is platform independent as a web-service and does not require understanding of the underlying mathematics.

[Intellectual property rights in Costa Rica in the light of the Biodiversity Convention].

PubMed

Salazar, R; Cabrera, J A

1996-04-01

This report analyzes intellectual property rights and acquisition of biological samples in light of the Biological Diversity Convention, with emphasis on Costa Rica. It examines the legal framework which exists for the protection of biological resources in this country, especially evaluating the law regarding protection of biota, which was approved in 1992. This includes information regarding access to genetic resources, and regulation for the aforementioned law. It examines the Biological Diversity Convention which was signed at the Rio Summit in 1992, whose objectives and goals, above all, emphasize the subject of distribution of benefits to be derived from the utilization of biological resources.

A dedicated database system for handling multi-level data in systems biology.

PubMed

Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

2014-01-01

Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging. To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a yeast data repository was implemented as an integrated database environment which is operated by the database system. Two applications were implemented to demonstrate extensibility and utilization of the system. Both illustrate how the user can access the database via the web query function and implemented scripts. These scripts are specific for two sample cases: 1) Detecting the pheromone pathway in protein interaction networks; and 2) Finding metabolic reactions regulated by Snf1 kinase. In this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered in systems biology. Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions. The two sample cases on the yeast integrated data clearly demonstrate the value of a sole database environment for systems biology research.

Engagement of Gay Men and Other Men Who Have Sex with Men (MSM) in the Response to HIV: A Critical Step in Achieving an AIDS-Free Generation.

PubMed

Stahlman, Shauna; Beyrer, Chris; Sullivan, Patrick S; Mayer, Kenneth H; Baral, Stefan D

2016-12-01

Men who have sex with men (MSM) continue to be at elevated risk for HIV acquisition and transmission secondary to biological and behavioral characteristics, social and sexual network characteristics, community environmental factors, and structural factors. HIV incidence rates remain high among MSM in both low- and high-income settings, and in both concentrated and more generalized HIV epidemic settings. While data quality tends to be poorer, the best estimates collectively suggest that MSM have up to 20 times the odds of living with HIV as compared to other reproductive aged adults across low- and middle-income countries. Recent prevention strategies to lower biological HIV transmission and acquisition risks, including the early use of antiretrovirals to decrease infectiousness for those living with HIV, and pre-exposure prophylaxis for those at significant risk of HIV acquisition, have demonstrated the potential to change the trajectory of the HIV epidemics among MSM. However, the coverage and effectiveness of these approaches is limited by structural factors including the punitive legal frameworks and institutional discrimination that contribute to limited uptake, challenges to adherence, and suboptimal health-seeking behaviors among MSM. More intensive efforts will be required to reach MSM who do not currently have access to relevant and effective prevention and treatment services or elect not to access these services given enacted and/or perceived stigma. Respect for human rights, including efforts to aggressively confront and combat the forms of stigma that are preventing us from achieving an AIDS-Free generation, are needed for all people including gay men and other MSM.

Platelet lysate enhances synovial fluid multipotential stromal cells functions: Implications for therapeutic use.

PubMed

Altaie, Ala; Baboolal, Thomas G; Wall, Owen; Jones, Elena; McGonagle, Dennis

2018-03-01

Although intra-articular injection of platelet products is increasingly used for joint regenerative approaches, there are few data on their biological effects on joint-resident multipotential stromal cells (MSCs), which are directly exposed to the effects of these therapeutic strategies. Therefore, this study investigated the effect of platelet lysate (PL) on synovial fluid-derived MSCs (SF-MSCs), which in vivo have direct access to sites of cartilage injury. SF-MSCs were obtained during knee arthroscopic procedures (N = 7). Colony forming unit-fibroblast (CFU-F), flow-cytometric phenotyping, carboxyfluorescein succinimidyl ester-based immunomodulation for T-cell and trilineage differentiation assays were performed using PL and compared with standard conditions. PL-enhanced SF-MSC (PL-MSC) proliferation as CFU-F colonies was 1.4-fold larger, and growing cultures had shorter population-doubling times. PL-MSCs and fetal calf serum (FCS)-MSCs had the same immunophenotype and similar immunomodulation activities. In chondrogenic and osteogenic differentiation assays, PL-MSCs produced 10% more sulfated-glycosaminoglycan (sGAG) and 45% less Ca ++ compared with FCS-MSCs, respectively. Replacing chondrogenic medium transforming growth factor-β3 with 20% or 50% PL further increased sGAG production of PL-MSCs by 69% and 95%, respectively, compared with complete chondrogenic medium. Also, Dulbecco's Modified Eagle's Medium high glucose (HG-DMEM) plus 50% PL induced more chondrogenesis compared with HG-DMEM plus 10% FCS and was comparable to complete chondrogenic medium. This is the first study to assess SF-MSC responses to PL and provides biological support to the hypothesis that PL may be capable of modulating multiple functional aspects of joint resident MSCs with direct access to injured cartilage. Copyright © 2017 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites.

PubMed

Li, Li; Crabtree, Jonathan; Fischer, Steve; Pinney, Deborah; Stoeckert, Christian J; Sibley, L David; Roos, David S

2004-01-01

ApiEST-DB (http://www.cbil.upenn.edu/paradbs-servlet/) provides integrated access to publicly available EST data from protozoan parasites in the phylum Apicomplexa. The database currently incorporates a total of nearly 100,000 ESTs from several parasite species of clinical and/or veterinary interest, including Eimeria tenella, Neospora caninum, Plasmodium falciparum, Sarcocystis neurona and Toxoplasma gondii. To facilitate analysis of these data, EST sequences were clustered and assembled to form consensus sequences for each organism, and these assemblies were then subjected to automated annotation via similarity searches against protein and domain databases. The underlying relational database infrastructure, Genomics Unified Schema (GUS), enables complex biologically based queries, facilitating validation of gene models, identification of alternative splicing, detection of single nucleotide polymorphisms, identification of stage-specific genes and recognition of phylogenetically conserved and phylogenetically restricted sequences.

Ultrasmall nanoparticles induce ferroptosis in nutrient-deprived cancer cells and suppress tumour growth

NASA Astrophysics Data System (ADS)

Kim, Sung Eun; Zhang, Li; Ma, Kai; Riegman, Michelle; Chen, Feng; Ingold, Irina; Conrad, Marcus; Turker, Melik Ziya; Gao, Minghui; Jiang, Xuejun; Monette, Sebastien; Pauliah, Mohan; Gonen, Mithat; Zanzonico, Pat; Quinn, Thomas; Wiesner, Ulrich; Bradbury, Michelle S.; Overholtzer, Michael

2016-11-01

The design of cancer-targeting particles with precisely tuned physicochemical properties may enhance the delivery of therapeutics and access to pharmacological targets. However, a molecular-level understanding of the interactions driving the fate of nanomedicine in biological systems remains elusive. Here, we show that ultrasmall (<10 nm in diameter) poly(ethylene glycol)-coated silica nanoparticles, functionalized with melanoma-targeting peptides, can induce a form of programmed cell death known as ferroptosis in starved cancer cells and cancer-bearing mice. Tumour xenografts in mice intravenously injected with nanoparticles using a high-dose multiple injection scheme exhibit reduced growth or regression, in a manner that is reversed by the pharmacological inhibitor of ferroptosis, liproxstatin-1. These data demonstrate that ferroptosis can be targeted by ultrasmall silica nanoparticles and may have therapeutic potential.

Formation of droplet interface bilayers in a Teflon tube

NASA Astrophysics Data System (ADS)

Walsh, Edmond; Feuerborn, Alexander; Cook, Peter R.

2016-09-01

Droplet-interface bilayers (DIBs) have applications in disciplines ranging from biology to computing. We present a method for forming them manually using a Teflon tube attached to a syringe pump; this method is simple enough it should be accessible to those without expertise in microfluidics. It exploits the properties of interfaces between three immiscible liquids, and uses fluid flow through the tube to pack together drops coated with lipid monolayers to create bilayers at points of contact. It is used to create functional nanopores in DIBs composed of phosphocholine using the protein α-hemolysin (αHL), to demonstrate osmotically-driven mass transfer of fluid across surfactant-based DIBs, and to create arrays of DIBs. The approach is scalable, and thousands of DIBs can be prepared using a robot in one hour; therefore, it is feasible to use it for high throughput applications.

High-performance web services for querying gene and variant annotation.

PubMed

Xin, Jiwen; Mark, Adam; Afrasiabi, Cyrus; Tsueng, Ginger; Juchler, Moritz; Gopal, Nikhil; Stupp, Gregory S; Putman, Timothy E; Ainscough, Benjamin J; Griffith, Obi L; Torkamani, Ali; Whetzel, Patricia L; Mungall, Christopher J; Mooney, Sean D; Su, Andrew I; Wu, Chunlei

2016-05-06

Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe MyGene.info and MyVariant.info, high-performance web services for querying gene and variant annotation information. These web services are currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model for organizing and querying biological annotation information. MyGene.info and MyVariant.info are provided as high-performance web services, accessible at http://mygene.info and http://myvariant.info . Both are offered free of charge to the research community.

Promoting an active form of learning out-of-class via answering online “study questions” leads to higher than expected exam scores in General Biology

PubMed Central

2015-01-01

A rising need for workers in science, technology, engineering and mathematics (STEM) fields has fueled interest in improving teaching within STEM disciplines. Numerous studies have demonstrated the benefits of active learning approaches on student learning outcomes. However, many of these studies have been conducted in experimental, rather than real-life class, settings. In addition, most of these studies have focused on in-class active learning exercises. This study tested the effects of answering questions outside of class on exam performance for General Biology students at the University of Minnesota. An online database of 1,020 multiple-choice questions covering material from the first half of the course was generated. Students in seven course sections (with an average of ∼265 students per section) were given unlimited access to the online study questions. These students made extensive use of the online questions, with students answering an average of 1,323 questions covering material from the half of the semester for which the questions were available. After students answered a set of questions, they were shown the correct answers for those questions. More specific feedback describing how to arrive at the correct answer was provided for the 73% of the questions for which the correct answers were not deemed to be self-explanatory. The extent to which access to the online study questions improved student learning outcomes was assessed by comparing the performance on exam questions of students in the seven course sections with access to the online study questions with the performance of students in course sections without access to the online study questions. Student performance was analyzed for a total of 89 different exams questions that were not included in the study questions, but that covered the same material covered by the study questions. Each of these 89 questions was used on one to five exams given to students in course sections that had access to the online study questions and on three to 77 exams given to students in sections that lacked such access. Data from over 1,800 students in sections with access to the online study questions show that those students scored a statistically significant average of 6.6% points higher on the exam questions analyzed than students in sections without access to the study questions. This difference was greater than the average amount necessary to raise students’ exam grades by one grade (e.g., from a “B-” to a “B”). In addition, there was a higher correlation between number of questions answered and success on exam questions on material related to the study questions than between number of questions answered and success on exam questions on material unrelated to the study questions. The online study question system required substantial effort to set up, but required minimal effort to maintain and was effective in significantly raising average exam scores for even very large course sections. PMID:26500828

32 CFR Appendix A to Part 651 - References

Code of Federal Regulations, 2014 CFR

2014-07-01

... publications and forms are accessible from a variety of sources through the use of electronic media or paper products. In most cases, electronic publications and forms that are associated with military organizations can be accessed at various address or web sites on the Internet. Since electronic addresses can...

32 CFR Appendix A to Part 651 - References

Code of Federal Regulations, 2012 CFR

2012-07-01

... publications and forms are accessible from a variety of sources through the use of electronic media or paper products. In most cases, electronic publications and forms that are associated with military organizations can be accessed at various address or web sites on the Internet. Since electronic addresses can...

32 CFR Appendix A to Part 651 - References

Code of Federal Regulations, 2013 CFR

2013-07-01

... publications and forms are accessible from a variety of sources through the use of electronic media or paper products. In most cases, electronic publications and forms that are associated with military organizations can be accessed at various address or web sites on the Internet. Since electronic addresses can...

36 CFR 7.82 - Apostle Islands National Lakeshore.

Code of Federal Regulations, 2012 CFR

2012-07-01

... the purpose of providing access for legal forms of: (i) Ice fishing; (ii) Hunting and trapping; (iii... authorized solely for the purpose of providing access for legal forms of: (i) Ice fishing; (ii) Hunting and... park headquarters. (d) Ice augers and power engines. (1) Ice auger means a portable gasoline or...

36 CFR 7.82 - Apostle Islands National Lakeshore.

Code of Federal Regulations, 2010 CFR

2010-07-01

... the purpose of providing access for legal forms of: (i) Ice fishing; (ii) Hunting and trapping; (iii... authorized solely for the purpose of providing access for legal forms of: (i) Ice fishing; (ii) Hunting and... park headquarters. (d) Ice augers and power engines. (1) Ice auger means a portable gasoline or...

36 CFR 7.82 - Apostle Islands National Lakeshore.

Code of Federal Regulations, 2011 CFR

2011-07-01

... the purpose of providing access for legal forms of: (i) Ice fishing; (ii) Hunting and trapping; (iii... authorized solely for the purpose of providing access for legal forms of: (i) Ice fishing; (ii) Hunting and... park headquarters. (d) Ice augers and power engines. (1) Ice auger means a portable gasoline or...

36 CFR 7.82 - Apostle Islands National Lakeshore.

Code of Federal Regulations, 2013 CFR

2013-07-01

... the purpose of providing access for legal forms of: (i) Ice fishing; (ii) Hunting and trapping; (iii... authorized solely for the purpose of providing access for legal forms of: (i) Ice fishing; (ii) Hunting and... park headquarters. (d) Ice augers and power engines. (1) Ice auger means a portable gasoline or...

36 CFR 7.82 - Apostle Islands National Lakeshore.

Code of Federal Regulations, 2014 CFR

2014-07-01

... the purpose of providing access for legal forms of: (i) Ice fishing; (ii) Hunting and trapping; (iii... authorized solely for the purpose of providing access for legal forms of: (i) Ice fishing; (ii) Hunting and... park headquarters. (d) Ice augers and power engines. (1) Ice auger means a portable gasoline or...

Learner Attention to Form in ACCESS Task-Based Interaction

ERIC Educational Resources Information Center

Dao, Phung; Iwashita, Noriko; Gatbonton, Elizabeth

2017-01-01

This study explored the potential effects of communicative tasks developed using a reformulation of a task-based language teaching called Automatization in Communicative Contexts of Essential Speech Sequences (ACCESS) that includes automatization of language elements as one of its goals on learner attention to form in task-based interaction. The…

The Role of Genome Accessibility in Transcription Factor Binding in Bacteria.

PubMed

Gomes, Antonio L C; Wang, Harris H

2016-04-01

ChIP-seq enables genome-scale identification of regulatory regions that govern gene expression. However, the biological insights generated from ChIP-seq analysis have been limited to predictions of binding sites and cooperative interactions. Furthermore, ChIP-seq data often poorly correlate with in vitro measurements or predicted motifs, highlighting that binding affinity alone is insufficient to explain transcription factor (TF)-binding in vivo. One possibility is that binding sites are not equally accessible across the genome. A more comprehensive biophysical representation of TF-binding is required to improve our ability to understand, predict, and alter gene expression. Here, we show that genome accessibility is a key parameter that impacts TF-binding in bacteria. We developed a thermodynamic model that parameterizes ChIP-seq coverage in terms of genome accessibility and binding affinity. The role of genome accessibility is validated using a large-scale ChIP-seq dataset of the M. tuberculosis regulatory network. We find that accounting for genome accessibility led to a model that explains 63% of the ChIP-seq profile variance, while a model based in motif score alone explains only 35% of the variance. Moreover, our framework enables de novo ChIP-seq peak prediction and is useful for inferring TF-binding peaks in new experimental conditions by reducing the need for additional experiments. We observe that the genome is more accessible in intergenic regions, and that increased accessibility is positively correlated with gene expression and anti-correlated with distance to the origin of replication. Our biophysically motivated model provides a more comprehensive description of TF-binding in vivo from first principles towards a better representation of gene regulation in silico, with promising applications in systems biology.

Extension of research data repository system to support direct compute access to biomedical datasets: enhancing Dataverse to support large datasets.

PubMed

McKinney, Bill; Meyer, Peter A; Crosas, Mercè; Sliz, Piotr

2017-01-01

Access to experimental X-ray diffraction image data is important for validation and reproduction of macromolecular models and indispensable for the development of structural biology processing methods. In response to the evolving needs of the structural biology community, we recently established a diffraction data publication system, the Structural Biology Data Grid (SBDG, data.sbgrid.org), to preserve primary experimental datasets supporting scientific publications. All datasets published through the SBDG are freely available to the research community under a public domain dedication license, with metadata compliant with the DataCite Schema (schema.datacite.org). A proof-of-concept study demonstrated community interest and utility. Publication of large datasets is a challenge shared by several fields, and the SBDG has begun collaborating with the Institute for Quantitative Social Science at Harvard University to extend the Dataverse (dataverse.org) open-source data repository system to structural biology datasets. Several extensions are necessary to support the size and metadata requirements for structural biology datasets. In this paper, we describe one such extension-functionality supporting preservation of file system structure within Dataverse-which is essential for both in-place computation and supporting non-HTTP data transfers. © 2016 New York Academy of Sciences.

Biosimilars for psoriasis: worldwide overview of regulatory guidelines, uptake and implications for dermatology clinical practice.

PubMed

Cohen, A D; Wu, J J; Puig, L; Chimenti, S; Vender, R; Rajagopalan, M; Romiti, R; de la Cruz, C; Skov, L; Zachariae, C; Young, H S; Foley, P; van der Walt, J M; Naldi, L; Prens, E P; Blauvelt, A

2017-12-01

The introduction of biological drugs for the treatment of patients with psoriasis has revolutionized treatment paradigms and enabled numerous patients to achieve disease control with an acceptable safety profile. However, the high cost of biologics limits access to these medications for the majority of patients worldwide. In recent years, the introduction of biosimilars for inflammatory diseases has become a fast evolving field. The future use of biosimilars offers the potential for decreased cost and increased access to biologics for patients with psoriasis. For approval of biosimilars, different regulatory agencies use highly variable methods for definition, production, approval, marketing and postmarketing surveillance. Due to potential interchangeability between biologics and biosimilars, traceability and pharmacovigilance are required to collect accurate data about adverse events in patients with psoriasis; spontaneous reporting, registries and use of 'big data' should facilitate this process on a global basis. The current article describes biosimilar regulatory guidelines and examples of biosimilar uptake in clinical practice in several countries around the world. As it is apparent that biological therapy treatment decisions may become more physician independent, the International Psoriasis Council recommends that dermatologists should take an active role in the development of biosimilar prescribing policies with their respective healthcare settings and government agencies. © 2017 British Association of Dermatologists.

The Arabidopsis Information Resource: Making and Mining the ‘Gold Standard’ Annotated Reference Plant Genome

PubMed Central

Berardini, Tanya Z.; Reiser, Leonore; Li, Donghui; Mezheritsky, Yarik; Muller, Robert; Strait, Emily; Huala, Eva

2015-01-01

The Arabidopsis Information Resource (TAIR) is a continuously updated, online database of genetic and molecular biology data for the model plant Arabidopsis thaliana that provides a global research community with centralized access to data for over 30,000 Arabidopsis genes. TAIR’s biocurators systematically extract, organize, and interconnect experimental data from the literature along with computational predictions, community submissions, and high throughput datasets to present a high quality and comprehensive picture of Arabidopsis gene function. TAIR provides tools for data visualization and analysis, and enables ordering of seed and DNA stocks, protein chips and other experimental resources. TAIR actively engages with its users who contribute expertise and data that augments the work of the curatorial staff. TAIR’s focus in an extensive and evolving ecosystem of online resources for plant biology is on the critically important role of extracting experimentally-based research findings from the literature and making that information computationally accessible. In response to the loss of government grant funding, the TAIR team founded a nonprofit entity, Phoenix Bioinformatics, with the aim of developing sustainable funding models for biological databases, using TAIR as a test case. Phoenix has successfully transitioned TAIR to subscription-based funding while still keeping its data relatively open and accessible. PMID:26201819

Selective access and editing in a database

NASA Technical Reports Server (NTRS)

Maluf, David A. (Inventor); Gawdiak, Yuri O. (Inventor)

2010-01-01

Method and system for providing selective access to different portions of a database by different subgroups of database users. Where N users are involved, up to 2.sup.N-1 distinguishable access subgroups in a group space can be formed, where no two access subgroups have the same members. Two or more members of a given access subgroup can edit, substantially simultaneously, a document accessible to each member.

Host range determination of Colletotrichum gloeosporioides f. sp. salsolae, a biological control agent of tumbleweed: from BLUPs to biomass loss

USDA-ARS?s Scientific Manuscript database

Host range tests were conducted with Colletotrichum gloeosporioides f. sp. salsolae (CGS) in quarantine to determine whether the fungus is safe to release in N. America for biological control of tumbleweed (Salsola tragus L., Chenopodiaceae). Ninety-two accessions were analyzed from 19 families and...

A Biological Brain in a Cultural Classroom: Applying Biological Research to Classroom Management.

ERIC Educational Resources Information Center

Sylwester, Robert

This book applies the latest in brain research and learning theory to classroom management. The concepts of psychoneurophysiology are made readily accessible. The book offers creative data gathering activities to help students manage their own behavior and to help teachers learn how their own behavior impacts the classroom environment. The seven…

The Accessibility of Academic Vocabulary to Spanish Speaking High School Biology Students

ERIC Educational Resources Information Center

Reed, Deborah K.; Medina, Luis A.; Martinez, Norma A.; Veleta, Lorena G.

2013-01-01

One recommendation for better preparing English language learners (ELLs) for scientific fields is to capitalize on Spanish speakers' knowledge of cognates. However, little is known about the presence of cognates in high school biology content. This study examined the linguistic basis of 968 terms co-occurring in at least one of four textbooks…

48 CFR 3053.303 - Agency forms.

Code of Federal Regulations, 2010 CFR

2010-10-01

... section illustrates agency-specified forms. To access these forms go to: http://www.dhs.gov (under “Business, Acquisition Information”) or https://dhsonline.dhs.gov/portal/jhtml/general/forms.jhtml. Form...

48 CFR 3053.303 - Agency forms.

Code of Federal Regulations, 2011 CFR

2011-10-01

... section illustrates agency-specified forms. To access these forms go to: http://www.dhs.gov (under “Business, Acquisition Information”) or https://dhsonline.dhs.gov/portal/jhtml/general/forms.jhtml. Form...

48 CFR 3053.303 - Agency forms.

Code of Federal Regulations, 2012 CFR

2012-10-01

... section illustrates agency-specified forms. To access these forms go to: http://www.dhs.gov (under “Business, Acquisition Information”) or https://dhsonline.dhs.gov/portal/jhtml/general/forms.jhtml. Form...

48 CFR 3053.303 - Agency forms.

Code of Federal Regulations, 2014 CFR

2014-10-01

... section illustrates agency-specified forms. To access these forms go to: http://www.dhs.gov (under “Business, Acquisition Information”) or https://dhsonline.dhs.gov/portal/jhtml/general/forms.jhtml. Form...

48 CFR 3053.303 - Agency forms.

Code of Federal Regulations, 2013 CFR

2013-10-01

... section illustrates agency-specified forms. To access these forms go to: http://www.dhs.gov (under “Business, Acquisition Information”) or https://dhsonline.dhs.gov/portal/jhtml/general/forms.jhtml. Form...

9 CFR 114.4 - Identification of biological products.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Identification of biological products... REQUIREMENTS FOR BIOLOGICAL PRODUCTS § 114.4 Identification of biological products. Suitable tags or labels of... biological products, all component parts to be combined to form a biological product, all biological products...

The Use of Textbooks for Advanced-Level GCE Courses in Physics, Chemistry and Biology by Sixth-Form Students.

ERIC Educational Resources Information Center

Newton, D. P.

1984-01-01

A survey of sixth-form students to determine the level of A-level textbook use in physics, chemistry, and biology in English schools found that texts are used primarily after the lesson, at the student's discretion, and with great variations between students. Biology texts were used most, and physics texts used least. (MBR)

The Effects of 3D Computer Simulation on Biology Students' Achievement and Memory Retention

ERIC Educational Resources Information Center

Elangovan, Tavasuria; Ismail, Zurida

2014-01-01

A quasi experimental study was conducted for six weeks to determine the effectiveness of two different 3D computer simulation based teaching methods, that is, realistic simulation and non-realistic simulation on Form Four Biology students' achievement and memory retention in Perak, Malaysia. A sample of 136 Form Four Biology students in Perak,…

Crystal structure of a macrophage migration inhibitory factor from Giardia lamblia

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

Buchko, Garry W.; Abendroth, Jan; Robinson, Howard

2013-06-15

Macrophage migration inhibitory factor (MIF) is a eukaryotic cytokine that affects a broad spectrum of immune responses and its activation/inactivation is associated with numerous diseases. During protozoan infections MIF is not only expressed by the host, but, has also been observed to be expressed by some parasites and released into the host. To better understand the biological role of parasitic MIF proteins, the crystal structure of the MIF protein from Giardia lamblia (Gl-MIF), the etiological agent responsible for giardiasis, has been determined at 2.30 Å resolution. The 114-residue protein adopts an α/β fold consisting of a four-stranded β-sheet with twomore » anti-parallel α-helices packed against a face of the β-sheet. An additional short β-strand aligns anti-parallel to β4 of the β-sheet in the adjacent protein unit to help stabilize a trimer, the biologically relevant unit observed in all solved MIF crystal structures to date, and form a discontinuous β-barrel. The structure of Gl-MIF is compared to the MIF structures from humans (Hs-MIF) and three Plasmodium species (falciparum, berghei, and yoelii). The structure of all five MIF proteins are generally similar with the exception of a channel that runs through the center of each trimer complex. Relative to Hs-MIF, there are differences in solvent accessibility and electrostatic potential distribution in the channel of Gl-MIF and the Plasmodium-MIFs due primarily to two “gate-keeper” residues in the parasitic MIFs. For the Plasmodium MIFs the gate-keeper residues are at positions 44 (Y==>R) and 100 (V==>D) and for Gl-MIF it is at position 100 (V==>R). If these gate-keeper residues have a biological function and contribute to the progression of parasitemia they may also form the basis for structure-based drug design targeting parasitic MIF proteins.« less

sequence of Gl-MIF and the other Crystal structure of a macrophage migration inhibitory factor from Giardia lamblia

PubMed Central

Abendroth, Jan; Robinson, Howard; Zhang, Yanfeng; Hewitt, Stephen N.; Edwards, Thomas E.; Van Voorhis, Wesley C.; Myler, Peter J.

2013-01-01

Macrophage migration inhibitory factor (MIF) is a eukaryotic cytokine that affects a broad spectrum of immune responses and its activation/inactivation is associated with numerous diseases. During protozoan infections MIF is not only expressed by the host, but, has also been observed to be expressed by some parasites and released into the host. To better understand the biological role of parasitic MIF proteins, the crystal structure of the MIF protein from Giardia lamblia (Gl-MIF), the etiological agent responsible for giardiasis, has been determined at 2.30 Å resolution. The 114-residue protein adopts an α/β fold consisting of a four-stranded β-sheet with two anti-parallel α-helices packed against a face of the β-sheet. An additional short β-strand aligns anti-parallel to β4 of the β-sheet in the adjacent protein unit to help stabilize a trimer, the biologically relevant unit observed in all solved MIF crystal structures to date, and form a discontinuous β-barrel. The structure of Gl-MIF is compared to the MIF structures from humans (Hs-MIF) and three Plasmodium species (falciparum, berghei, and yoelii). The structure of all five MIF proteins are generally similar with the exception of a channel that runs through the center of each trimer complex. Relative to Hs-MIF, there are differences in solvent accessibility and electrostatic potential distribution in the channel of Gl-MIF and the Plasmodium-MIFs due primarily to two “gate-keeper” residues in the parasitic MIFs. For the Plasmodium MIFs the gate-keeper residues are at positions 44 (Y⇒R) and 100 (V⇒D) and for Gl-MIF it is at position 100 (V⇒R). If these gate-keeper residues have a biological function and contribute to the progression of parasitemia they may also form the basis for structure-based drug design targeting parasitic MIF proteins. PMID:23709284

Classifying Life, Reconstructing History and Teaching Diversity: Philosophical Issues in the Teaching of Biological Systematics and Biodiversity

NASA Astrophysics Data System (ADS)

Reydon, Thomas A. C.

2013-02-01

Classification is a central endeavor in every scientific field of work. Classification in biology, however, is distinct from classification in other fields of science in a number of ways. Thus, understanding how biological classification works is an important element in understanding the nature of biological science. In the present paper, I discuss a number of philosophical issues that are characteristic for classification in biological science, paying special attention to questions related to science education. My aims are (1) to provide science educators and others concerned with the teaching of biology with an accessible overview of the philosophy of biological classification and (2) to show how knowledge of the philosophy of classification can play an important role in science teaching.

Hot gas path component cooling system having a particle collection chamber

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

Miranda, Carlos Miguel; Lacy, Benjamin Paul

A cooling system for a hot gas path component includes a substrate having an outer surface and an inner surface. The inner surface defines at least one interior space. A passage is formed in the substrate between the outer surface and the inner surface. An access passage is formed in the substrate and extends from the outer surface to the inner space. The access passage is formed at a first acute angle to the passage and includes a particle collection chamber. The access passage is configured to channel a cooling fluid to the passage. Furthermore, the passage is configured tomore » channel the cooling fluid therethrough to cool the substrate.« less

Biological Research in Support of Project MILES.

DTIC Science & Technology

1981-07-01

E S BEATRICE UNCLASSIFIED LAIR - 9 6 N too INSTITUTE REPORT NO. 96’ 0 BIOLOGICAL RESEARCH IN SUPPORT OF PROJECT MILES DA Via . LUND, aS BRUCE E...ACCESSION NO. 3’ R ENTS CATALOG NUMBER LAIR Drp-Nr96 _ _ _ _ _ _ S5T, F EnI r~,.. VERED Biological Research in Support of Project MILES )n. Anual .je 7...experiments at other agencies did not confirm the LAIR observation of retinal clouding. The ocular effects were studied of lasers operating at infrared

Quantitative biology of single neurons

PubMed Central

Eberwine, James; Lovatt, Ditte; Buckley, Peter; Dueck, Hannah; Francis, Chantal; Kim, Tae Kyung; Lee, Jaehee; Lee, Miler; Miyashiro, Kevin; Morris, Jacqueline; Peritz, Tiina; Schochet, Terri; Spaethling, Jennifer; Sul, Jai-Yoon; Kim, Junhyong

2012-01-01

The building blocks of complex biological systems are single cells. Fundamental insights gained from single-cell analysis promise to provide the framework for understanding normal biological systems development as well as the limits on systems/cellular ability to respond to disease. The interplay of cells to create functional systems is not well understood. Until recently, the study of single cells has concentrated primarily on morphological and physiological characterization. With the application of new highly sensitive molecular and genomic technologies, the quantitative biochemistry of single cells is now accessible. PMID:22915636

Synthetic biology between technoscience and thing knowledge.

PubMed

Gelfert, Axel

2013-06-01

Synthetic biology presents a challenge to traditional accounts of biology: Whereas traditional biology emphasizes the evolvability, variability, and heterogeneity of living organisms, synthetic biology envisions a future of homogeneous, humanly engineered biological systems that may be combined in modular fashion. The present paper approaches this challenge from the perspective of the epistemology of technoscience. In particular, it is argued that synthetic-biological artifacts lend themselves to an analysis in terms of what has been called 'thing knowledge'. As such, they should neither be regarded as the simple outcome of applying theoretical knowledge and engineering principles to specific technological problems, nor should they be treated as mere sources of new evidence in the general pursuit of scientific understanding. Instead, synthetic-biological artifacts should be viewed as partly autonomous research objects which, qua their material-biological constitution, embody knowledge about the natural world-knowledge that, in turn, can be accessed via continuous experimental interrogation. Copyright © 2013 Elsevier Ltd. All rights reserved.

14 CFR 153.5 - Aviation safety inspector airport access.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 14 Aeronautics and Space 3 2010-01-01 2010-01-01 false Aviation safety inspector airport access... TRANSPORTATION (CONTINUED) AIRPORTS AIRPORT OPERATIONS Aviation Safety Inspector Access § 153.5 Aviation safety... must grant Aviation Safety Inspectors bearing FAA Form 110A free and uninterrupted access to public-use...

Two-Year Community: Using Formative Assessment to Improve Microscope Skills among Urban Community College General Biology I Lab Students

ERIC Educational Resources Information Center

Keller, Charles

2017-01-01

Community colleges serve the noble mission of making higher education accessible to a broader spectrum of society than traditional 4-year institutions. A side effect of this broad access is a lower level of student preparedness for success in science, technology, engineering, and mathematics (STEM) courses. This work describes our efforts to…

Bryophytes for Beginners: The Usability of a Printed Dichotomous Key versus a Multi-Access Computer-Based Key for Bryophyte Identification

ERIC Educational Resources Information Center

Stagg, Bethan C.; Donkin, Maria E.; Smith, Alison M.

2015-01-01

Bryophytes are a rewarding study group in field biology and the UK bryophyte flora has international importance to biodiversity conservation. We designed an identification key to common woodland moss species and compared the usability of two formats, web-based multi-access and printed dichotomous key, with undergraduate students. The rate of…

Peptoid nanosheets exhibit a new secondary-structure motif.

PubMed

Mannige, Ranjan V; Haxton, Thomas K; Proulx, Caroline; Robertson, Ellen J; Battigelli, Alessia; Butterfoss, Glenn L; Zuckermann, Ronald N; Whitelam, Stephen

2015-10-15

A promising route to the synthesis of protein-mimetic materials that are capable of complex functions, such as molecular recognition and catalysis, is provided by sequence-defined peptoid polymers--structural relatives of biologically occurring polypeptides. Peptoids, which are relatively non-toxic and resistant to degradation, can fold into defined structures through a combination of sequence-dependent interactions. However, the range of possible structures that are accessible to peptoids and other biological mimetics is unknown, and our ability to design protein-like architectures from these polymer classes is limited. Here we use molecular-dynamics simulations, together with scattering and microscopy data, to determine the atomic-resolution structure of the recently discovered peptoid nanosheet, an ordered supramolecular assembly that extends macroscopically in only two dimensions. Our simulations show that nanosheets are structurally and dynamically heterogeneous, can be formed only from peptoids of certain lengths, and are potentially porous to water and ions. Moreover, their formation is enabled by the peptoids' adoption of a secondary structure that is not seen in the natural world. This structure, a zigzag pattern that we call a Σ('sigma')-strand, results from the ability of adjacent backbone monomers to adopt opposed rotational states, thereby allowing the backbone to remain linear and untwisted. Linear backbones tiled in a brick-like way form an extended two-dimensional nanostructure, the Σ-sheet. The binary rotational-state motif of the Σ-strand is not seen in regular protein structures, which are usually built from one type of rotational state. We also show that the concept of building regular structures from multiple rotational states can be generalized beyond the peptoid nanosheet system.

Database Resources of the BIG Data Center in 2018.

PubMed

2018-01-04

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The growing role of biologics and biosimilars in the United States: Perspectives from the APhA Biologics and Biosimilars Stakeholder Conference.

PubMed

Crespi-Lofton, Judy; Skelton, Jann B

The American Pharmacists Association (APhA) convened the Biologics and Biosimilars Stakeholder Conference on November 30, 2016, in Washington DC. The objectives of the Conference were to determine the key issues and challenges within the marketplace for biologics, follow-on biologics (FOBs), and biosimilars, identify potential roles and responsibilities of pharmacists regarding biologic and biosimilar medications, and identify actions or activities that pharmacists may take to optimize the safe and cost-effective use of biologics and biosimilars. National thought leaders and stakeholder representatives, including individuals from the Food and Drug Administration, Centers for Medicare and Medicaid Services, a private third-party payer, manufacturers, and several national organizations of health care professionals, participated in the conference. Information shared by this group was supplemented with relevant legal and regulatory information and published literature. Biologics play a valuable role in the treatment of numerous health conditions, but their associated costs, which tend to be greater than those of small-molecule drugs, place a burden on the health care system. Biosimilars (both noninterchangeable and interchangeable) are highly similar copies of the originator biologic and offer the potential to reduce costs and improve patient access to biological products by increasing treatment options and creating a more competitive market. Despite the potential benefits of biosimilars, certain factors may limit their uptake. The conference participants explored issues that different stakeholders think influence the use of biologics, including biosimilars, in the United States. Barriers included technology, prescriber-pharmacist communication, legislation and regulations, limited patient and health care practitioner knowledge of biological products, patient and health care practitioner perceptions of biosimilars, and evolving science or lack of long-term data. After participants identified issues, they discussed strategies to address these concerns, including the need to enhance the education of pharmacists, prescribers, and patients regarding biologic products, including biosimilars and FOBs; the passage of state laws and regulations that do not impede the use of biosimilars, including interchangeable biosimilars; the use of product-specific tracking information in electronic health records and surveillance systems; bidirectional communication among pharmacists, prescribers, and other members of the care team to support pharmacovigilance and the maintenance of accurate patient records; and the development of evidence-based third-party payer policies. Patient access to safe and cost-effective treatments is an important goal for the health care system. As the availability and use of biosimilars, including those determined to be interchangeable, increases, their potential to lower costs and improve patient access to treatment grows. However, the extent of such growth is, in part, dependent on various stakeholders' decisions to provide, pay for, or use these products in a safe and thoughtful manner. Ongoing stakeholder collaboration, educational activities, and review of current government or payer policies are required to optimize the uptake of biological products, including biosimilars. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Synthetic biology to access and expand nature’s chemical diversity

PubMed Central

Smanski, Michael J.; Zhou, Hui; Claesen, Jan; Shen, Ben; Fischbach, Michael; Voigt, Christopher A.

2016-01-01

Bacterial genomes encode the biosynthetic potential to produce hundreds of thousands of complex molecules with diverse applications, from medicine to agriculture and materials. Economically accessing the potential encoded within sequenced genomes promises to reinvigorate waning drug discovery pipelines and provide novel routes to intricate chemicals. This is a tremendous undertaking, as the pathways often comprise dozens of genes spanning as much as 100+ kiliobases of DNA, are controlled by complex regulatory networks, and the most interesting molecules are made by non-model organisms. Advances in synthetic biology address these issues, including DNA construction technologies, genetic parts for precision expression control, synthetic regulatory circuits, computer aided design, and multiplexed genome engineering. Collectively, these technologies are moving towards an era when chemicals can be accessed en mass based on sequence information alone. This will enable the harnessing of metagenomic data and massive strain banks for high-throughput molecular discovery and, ultimately, the ability to forward design pathways to complex chemicals not found in nature. PMID:26876034

Imaging and the new biology: What's wrong with this picture?

NASA Astrophysics Data System (ADS)

Vannier, Michael W.

2004-05-01

The Human Genome has been defined, giving us one part of the equation that stems from the central dogma of molecular biology. Despite this awesome scientific achievement, the correspondence between genomics and imaging is weak, since we cannot predict an organism's phenotype from even perfect knowledge of its genetic complement. Biological knowledge comes in several forms, and the genome is perhaps the best known and most completely understood type. Imaging creates another form of biological information, providing the ability to study morphology, growth and development, metabolic processes, and diseases in vitro and in vivo at many levels of scale. The principal challenge in biomedical imaging for the future lies in the need to reconcile the data provided by one or multiple modalities with other forms of biological knowledge, most importantly the genome, proteome, physiome, and other "-ome's." To date, the imaging science community has not set a high priority on the unification of their results with genomics, proteomics, and physiological functions in most published work. Images are relatively isolated from other forms of biological data, impairing our ability to conceive and address many fundamental questions in research and clinical practice. This presentation will explain the challenge of biological knowledge integration in basic research and clinical applications from the standpoint of imaging and image processing. The impediments to progress, isolation of the imaging community, and mainstream of new and future biological science will be identified, so the critical and immediate need for change can be highlighted.

Lexical Access in Early Stages of Visual Word Processing: A Single-Trial Correlational MEG Study of Heteronym Recognition

ERIC Educational Resources Information Center

Solomyak, Olla; Marantz, Alec

2009-01-01

We present an MEG study of heteronym recognition, aiming to distinguish between two theories of lexical access: the "early access" theory, which entails that lexical access occurs at early (pre 200 ms) stages of processing, and the "late access" theory, which interprets this early activity as orthographic word-form identification rather than…

Investigation of transient forms of sulfur during biological treatment of spent caustic.

PubMed

Kalantari, Hamed; Nosrati, Mohsen; Shojaosadati, Seyed Abbas; Shavandi, Mahmoud

2018-06-01

In the present study, the production of various transient forms of sulfur during biological oxidation of sulfidic spent caustics under haloalkaline conditions in a stirred tank bioreactor is investigated. Also, the effects of abiotic aeration (chemical oxidation), dissolved oxygen (DO) concentration and sodium concentration on forms of sulfur during biological treatment are demonstrated. Thioalkalivibrio versutus strain was used for sulfide oxidation in spent caustic (SC). The aeration had an important effect on sulfide oxidation and its final products. At DO concentrations above 2 mg l -1 , majority of sulfide was oxidized to sulfate. Maximum sulfide removal efficiency (%R) and yield of sulfate production [Formula: see text] was obtained in Na + concentration ranging from 0.6 to 2 M. Abiotic aeration, which is the most important factor of production of thiosulfate, resulted in the formation of an undesired product-polysulfide. However, abiotic aeration can be used as a pretreatment to biological treatment. In the bioreactor the removal efficiency was obtained as 82.7% and various forms of sulfur such as polysulfide, biosulfur, thiosulfate and sulfate was observed during biological treatment of SC.

Impaired visual recognition of biological motion in schizophrenia.

PubMed

Kim, Jejoong; Doop, Mikisha L; Blake, Randolph; Park, Sohee

2005-09-15

Motion perception deficits have been suggested to be an important feature of schizophrenia but the behavioral consequences of such deficits are unknown. Biological motion refers to the movements generated by living beings. The human visual system rapidly and effortlessly detects and extracts socially relevant information from biological motion. A deficit in biological motion perception may have significant consequences for detecting and interpreting social information. Schizophrenia patients and matched healthy controls were tested on two visual tasks: recognition of human activity portrayed in point-light animations (biological motion task) and a perceptual control task involving detection of a grouped figure against the background noise (global-form task). Both tasks required detection of a global form against background noise but only the biological motion task required the extraction of motion-related information. Schizophrenia patients performed as well as the controls in the global-form task, but were significantly impaired on the biological motion task. In addition, deficits in biological motion perception correlated with impaired social functioning as measured by the Zigler social competence scale [Zigler, E., Levine, J. (1981). Premorbid competence in schizophrenia: what is being measured? Journal of Consulting and Clinical Psychology, 49, 96-105.]. The deficit in biological motion processing, which may be related to the previously documented deficit in global motion processing, could contribute to abnormal social functioning in schizophrenia.

[THE FAILURE MODES AND EFFECTS ANALYSIS FACILITATES A SAFE, TIME AND MONEY SAVING OPEN ACCESS COLONOSCOPY SERVICE].

PubMed

Gingold-Belfer, Rachel; Niv, Yaron; Horev, Nehama; Gross, Shuli; Sahar, Nadav; Dickman, Ram

2017-04-01

Failure modes and effects analysis (FMEA) is used for the identification of potential risks in health care processes. We used a specific FMEA - based form for direct referral for colonoscopy and assessed it for procedurerelated perforations. Ten experts in endoscopy evaluated and computed the entire referral process, modes of preparation for the endoscopic procedure, the endoscopic procedure itself and the discharge process. We used FMEA assessing for likelihood of occurrence, detection and severity and calculated the risk profile number (RPN) for each of the above points. According to the highest RPN results we designed a specific open access referral form and then compared the occurrence of colonic perforations (between 2010 and 2013) in patients who were referred through the open access arm (Group 1) to those who had a prior clinical consultation (non-open access, Group 2). Our experts in endoscopy (5 physicians and 5 nurses) identified 3 categories of failure modes that, on average, reached the highest RPNs. We identified 9,558 colonoscopies in group 1, and 12,567 in group 2. Perforations were identified in three patients from the open access group (1:3186, 0.03%) and in 10 from group 2 (1:1256, 0.07%) (p = 0.024). Direct referral for colonoscopy saved 9,558 pre-procedure consultations and the sum of $850,000. The FMEA tool-based specific referral form facilitates a safe, time and money saving open access colonoscopy service. Our form may be adopted by other gastroenterological clinics in Israel.

A theory of biological relativity: no privileged level of causation.

PubMed

Noble, Denis

2012-02-06

Must higher level biological processes always be derivable from lower level data and mechanisms, as assumed by the idea that an organism is completely defined by its genome? Or are higher level properties necessarily also causes of lower level behaviour, involving actions and interactions both ways? This article uses modelling of the heart, and its experimental basis, to show that downward causation is necessary and that this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes. These insights are then generalized. A priori, there is no privileged level of causation. The relations between this form of 'biological relativity' and forms of relativity in physics are discussed. Biological relativity can be seen as an extension of the relativity principle by avoiding the assumption that there is a privileged scale at which biological functions are determined.

A theory of biological relativity: no privileged level of causation

PubMed Central

Noble, Denis

2012-01-01

Must higher level biological processes always be derivable from lower level data and mechanisms, as assumed by the idea that an organism is completely defined by its genome? Or are higher level properties necessarily also causes of lower level behaviour, involving actions and interactions both ways? This article uses modelling of the heart, and its experimental basis, to show that downward causation is necessary and that this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes. These insights are then generalized. A priori, there is no privileged level of causation. The relations between this form of ‘biological relativity’ and forms of relativity in physics are discussed. Biological relativity can be seen as an extension of the relativity principle by avoiding the assumption that there is a privileged scale at which biological functions are determined. PMID:23386960

Current status and future directions of Lévy walk research

PubMed Central

2018-01-01

ABSTRACT Lévy walks are a mathematical construction useful for describing random patterns of movement with bizarre fractal properties that seem to have no place in biology. Nonetheless, movement patterns resembling Lévy walks have been observed at scales ranging from the microscopic to the ecological. They have been seen in the molecular machinery operating within cells during intracellular trafficking, in the movement patterns of T cells within the brain, in DNA, in some molluscs, insects, fish, birds and mammals, in the airborne flights of spores and seeds, and in the collective movements of some animal groups. Lévy walks are also evident in trace fossils (ichnofossils) – the preserved form of tracks made by organisms that occupied ancient sea beds about 252-66 million years ago. And they are utilised by algae that originated around two billion years ago, and still exist today. In September of 2017, leading researchers from across the life sciences, along with mathematicians and physicists, got together at a Company of Biologists' Workshop to discuss the origins and biological significance of these movement patterns. In this Review the essence of the technical and sometimes heated discussions is distilled and made accessible for all. In just a few pages, the reader is taken from a gentle introduction to the frontiers of a very active field of scientific enquiry. What emerges is a fascinating story of a truly inter-disciplinary scientific endeavour that is seeking to better understand movement patterns occurring across all biological scales. PMID:29326297

Allelic database and accession divergence of a Brazilian mango collection based on microsatellite markers.

PubMed

Dos Santos Ribeiro, I C N; Lima Neto, F P; Santos, C A F

2012-12-19

Allelic patterns and genetic distances were examined in a collection of 103 foreign and Brazilian mango (Mangifera indica) accessions in order to develop a reference database to support cultivar protection and breeding programs. An UPGMA dendrogram was generated using Jaccard's coefficients from a distance matrix based on 50 alleles of 12 microsatellite loci. The base pair number was estimated by the method of inverse mobility. The cophenetic correlation was 0.8. The accessions had a coefficient of similarity from 30 to 100%, which reflects high genetic variability. Three groups were observed in the UPGMA dendrogram; the first group was formed predominantly by foreign accessions, the second group was formed by Brazilian accessions, and the Dashehari accession was isolated from the others. The 50 microsatellite alleles did not separate all 103 accessions, indicating that there are duplicates in this mango collection. These 12 microsatellites need to be validated in order to establish a reliable set to identify mango cultivars.

BioMart Central Portal: an open database network for the biological community

PubMed Central

Guberman, Jonathan M.; Ai, J.; Arnaiz, O.; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J.; Di Génova, A.; Forbes, Simon; Fujisawa, T.; Gadaleta, E.; Goodstein, D. M.; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S.; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R.; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J.; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S.; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B.; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J.; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D. T.; Wong-Erasmus, Marie; Yao, L.; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

2011-01-01

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities. Database URL: http://central.biomart.org. PMID:21930507

BioMart Central Portal: an open database network for the biological community.

PubMed

Guberman, Jonathan M; Ai, J; Arnaiz, O; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J; Di Génova, A; Forbes, Simon; Fujisawa, T; Gadaleta, E; Goodstein, D M; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D T; Wong-Erasmus, Marie; Yao, L; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

2011-01-01

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.

Recombinant protein expression for structural biology in HEK 293F suspension cells: a novel and accessible approach.

PubMed

Portolano, Nicola; Watson, Peter J; Fairall, Louise; Millard, Christopher J; Milano, Charles P; Song, Yun; Cowley, Shaun M; Schwabe, John W R

2014-10-16

The expression and purification of large amounts of recombinant protein complexes is an essential requirement for structural biology studies. For over two decades, prokaryotic expression systems such as E. coli have dominated the scientific literature over costly and less efficient eukaryotic cell lines. Despite the clear advantage in terms of yields and costs of expressing recombinant proteins in bacteria, the absence of specific co-factors, chaperones and post-translational modifications may cause loss of function, mis-folding and can disrupt protein-protein interactions of certain eukaryotic multi-subunit complexes, surface receptors and secreted proteins. The use of mammalian cell expression systems can address these drawbacks since they provide a eukaryotic expression environment. However, low protein yields and high costs of such methods have until recently limited their use for structural biology. Here we describe a simple and accessible method for expressing and purifying milligram quantities of protein by performing transient transfections of suspension grown HEK (Human Embryonic Kidney) 293 F cells.

Summary of the International Conference on Arabidopsis Research 2011, June 22-25, 2011

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

Meyers, Blake C

2012-07-15

This project provided participant support for the gathering of plant biologists at the International Conferences on Arabidopsis Research (ICAR) in 2011. Arabidopsis thaliana, the reference flowering plant, has been intensely studied over the last 20 years and has proven to be an ideal model for studying nearly all aspects of plant biology. The success of this research field has been greatly facilitated by the openness and collegiality of the community fostered through multiple international forums including the ICAR. Advances in basic and applied plant biology are featured at the meeting, which is the primary gathering point for this strongly integratedmore » international community. The ICAR convenes plant researchers, allows discussion and dissemination of the latest research in plant biology, and facilitates dialog among those that may be separated by geography, career stage, and culture. This project focused on facilitating access by early career scientists that have reduced access to attend major meetings.« less

CHOmine: an integrated data warehouse for CHO systems biology and modeling.

PubMed

Gerstl, Matthias P; Hanscho, Michael; Ruckerbauer, David E; Zanghellini, Jürgen; Borth, Nicole

2017-01-01

The last decade has seen a surge in published genome-scale information for Chinese hamster ovary (CHO) cells, which are the main production vehicles for therapeutic proteins. While a single access point is available at www.CHOgenome.org, the primary data is distributed over several databases at different institutions. Currently research is frequently hampered by a plethora of gene names and IDs that vary between published draft genomes and databases making systems biology analyses cumbersome and elaborate. Here we present CHOmine, an integrative data warehouse connecting data from various databases and links to other ones. Furthermore, we introduce CHOmodel, a web based resource that provides access to recently published CHO cell line specific metabolic reconstructions. Both resources allow to query CHO relevant data, find interconnections between different types of data and thus provides a simple, standardized entry point to the world of CHO systems biology. http://www.chogenome.org. © The Author(s) 2017. Published by Oxford University Press.

Open access chemical probes for epigenetic targets

PubMed Central

Brown, Peter J; Müller, Susanne

2015-01-01

Background High attrition rates in drug discovery call for new approaches to improve target validation. Academia is filling gaps, but often lacks the experience and resources of the pharmaceutical industry resulting in poorly characterized tool compounds. Discussion The SGC has established an open access chemical probe consortium, currently encompassing ten pharmaceutical companies. One of its mandates is to create well-characterized inhibitors (chemical probes) for epigenetic targets to enable new biology and target validation for drug development. Conclusion Epigenetic probe compounds have proven to be very valuable and have not only spurred a plethora of novel biological findings, but also provided starting points for clinical trials. These probes have proven to be critical complementation to traditional genetic targeting strategies and provided sometimes surprising results. PMID:26397018

The European Bioinformatics Institute's data resources 2014.

PubMed

Brooksbank, Catherine; Bergman, Mary Todd; Apweiler, Rolf; Birney, Ewan; Thornton, Janet

2014-01-01

Molecular Biology has been at the heart of the 'big data' revolution from its very beginning, and the need for access to biological data is a common thread running from the 1965 publication of Dayhoff's 'Atlas of Protein Sequence and Structure' through the Human Genome Project in the late 1990s and early 2000s to today's population-scale sequencing initiatives. The European Bioinformatics Institute (EMBL-EBI; http://www.ebi.ac.uk) is one of three organizations worldwide that provides free access to comprehensive, integrated molecular data sets. Here, we summarize the principles underpinning the development of these public resources and provide an overview of EMBL-EBI's database collection to complement the reviews of individual databases provided elsewhere in this issue.

pClone: Synthetic Biology Tool Makes Promoter Research Accessible to Beginning Biology Students.

PubMed

Campbell, A Malcolm; Eckdahl, Todd; Cronk, Brian; Andresen, Corinne; Frederick, Paul; Huckuntod, Samantha; Shinneman, Claire; Wacker, Annie; Yuan, Jason

2014-01-01

The Vision and Change report recommended genuine research experiences for undergraduate biology students. Authentic research improves science education, increases the number of scientifically literate citizens, and encourages students to pursue research. Synthetic biology is well suited for undergraduate research and is a growing area of science. We developed a laboratory module called pClone that empowers students to use advances in molecular cloning methods to discover new promoters for use by synthetic biologists. Our educational goals are consistent with Vision and Change and emphasize core concepts and competencies. pClone is a family of three plasmids that students use to clone a new transcriptional promoter or mutate a canonical promoter and measure promoter activity in Escherichia coli. We also developed the Registry of Functional Promoters, an open-access database of student promoter research results. Using pre- and posttests, we measured significant learning gains among students using pClone in introductory biology and genetics classes. Student posttest scores were significantly better than scores of students who did not use pClone. pClone is an easy and affordable mechanism for large-enrollment labs to meet the high standards of Vision and Change. © 2014 A. M. Campbell et al. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Parallel Systems Laboratory: Access, Allocation, and Control

DTIC Science & Technology

1992-06-30

boog Eae...4d READ ISTRUCTIONSREPORT DOCUMENTATIO PAGE BEFOR COMPLETNG FORM I. REPORT NUMNER 2. GOVT ACCESSION NO 3- RECIPINT’S CATALOG NUMR9 . TITLE (an...a summary of the salient results of this research in capsule form which is followed by an extensive list of publications, dissertations and theses...because it provides the asymptotic use of currently wasted cycles. To do so, we examine a distribution of w(u It) in a very simple form and for

LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2.

PubMed

Cannon, Robert C; Gleeson, Padraig; Crook, Sharon; Ganapathy, Gautham; Marin, Boris; Piasini, Eugenio; Silver, R Angus

2014-01-01

Computational models are increasingly important for studying complex neurophysiological systems. As scientific tools, it is essential that such models can be reproduced and critically evaluated by a range of scientists. However, published models are currently implemented using a diverse set of modeling approaches, simulation tools, and computer languages making them inaccessible and difficult to reproduce. Models also typically contain concepts that are tightly linked to domain-specific simulators, or depend on knowledge that is described exclusively in text-based documentation. To address these issues we have developed a compact, hierarchical, XML-based language called LEMS (Low Entropy Model Specification), that can define the structure and dynamics of a wide range of biological models in a fully machine readable format. We describe how LEMS underpins the latest version of NeuroML and show that this framework can define models of ion channels, synapses, neurons and networks. Unit handling, often a source of error when reusing models, is built into the core of the language by specifying physical quantities in models in terms of the base dimensions. We show how LEMS, together with the open source Java and Python based libraries we have developed, facilitates the generation of scripts for multiple neuronal simulators and provides a route for simulator free code generation. We establish that LEMS can be used to define models from systems biology and map them to neuroscience-domain specific simulators, enabling models to be shared between these traditionally separate disciplines. LEMS and NeuroML 2 provide a new, comprehensive framework for defining computational models of neuronal and other biological systems in a machine readable format, making them more reproducible and increasing the transparency and accessibility of their underlying structure and properties.

LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2

PubMed Central

Cannon, Robert C.; Gleeson, Padraig; Crook, Sharon; Ganapathy, Gautham; Marin, Boris; Piasini, Eugenio; Silver, R. Angus

2014-01-01

Computational models are increasingly important for studying complex neurophysiological systems. As scientific tools, it is essential that such models can be reproduced and critically evaluated by a range of scientists. However, published models are currently implemented using a diverse set of modeling approaches, simulation tools, and computer languages making them inaccessible and difficult to reproduce. Models also typically contain concepts that are tightly linked to domain-specific simulators, or depend on knowledge that is described exclusively in text-based documentation. To address these issues we have developed a compact, hierarchical, XML-based language called LEMS (Low Entropy Model Specification), that can define the structure and dynamics of a wide range of biological models in a fully machine readable format. We describe how LEMS underpins the latest version of NeuroML and show that this framework can define models of ion channels, synapses, neurons and networks. Unit handling, often a source of error when reusing models, is built into the core of the language by specifying physical quantities in models in terms of the base dimensions. We show how LEMS, together with the open source Java and Python based libraries we have developed, facilitates the generation of scripts for multiple neuronal simulators and provides a route for simulator free code generation. We establish that LEMS can be used to define models from systems biology and map them to neuroscience-domain specific simulators, enabling models to be shared between these traditionally separate disciplines. LEMS and NeuroML 2 provide a new, comprehensive framework for defining computational models of neuronal and other biological systems in a machine readable format, making them more reproducible and increasing the transparency and accessibility of their underlying structure and properties. PMID:25309419

Fulfillment of Koch’s postulates and partial host range of Septoria lepidii Desm., a fungal pathogen for potential biological control of hoary cress (Lepidium spp.)

USDA-ARS?s Scientific Manuscript database

We have fulfilled Koch’s postulates and conducted host range tests with Septoria lepidii Desm. on five geographical accessions of hoary cress. Host range results showed the fungus specific to Lepidium spp. and damaging to hoary cress. This fungus is potentially an important biological control agent ...

A Web-Accessible Protein Structure Prediction Pipeline

DTIC Science & Technology

2009-06-01

Abstract Proteins are the molecular basis of nearly all structural, catalytic, sensory, and regulatory functions in living organisms. The biological...sensory, and regulatory functions in living organisms. The structure of a protein is essential in understanding its function at the molecular level...Characterizing sequence-structure and structure-function relationships have been the goals of molecular biology for more than three decades