Sample records for biological standardization iabs

  1. A Petrologic Study of the IAB Iron Meteorites: Constraints on the Formation of the IAB-Winonaite Parent Body

    NASA Technical Reports Server (NTRS)

    Benedix, G. K.; McCoy, T. J.; Keil, K.; Love, S. G.

    1998-01-01

    We have studied IAB iron meteorites and their silicate-bearing inclusions to elucidate the origin of their parent body. We have divided IAB irons into five categories which best describe the inclusions and other properties of the irons.

  2. Origin of iron meteorite groups IAB and IIICD

    NASA Technical Reports Server (NTRS)

    Wasson, J. T.; Willis, J.; Wai, C. M.; Kracher, A.

    1980-01-01

    Several low Ni-iron meteorites previously classified with group IAB are reclassified with group IIICD because of lower Ge, Ga, W, and Ir concentrations and higher As concentrations. The low Ni extreme of IIICD is now 62 mg/g, and that of IAB is 64 mg/g. It is proposed that the meteorites of both groups formed as individual shock melts on a chondritic parent body. The differences in log element-log Ni slopes of the daughter irons demonstrate that there were detailed differences in the composition and size of phases in the parental material (e.g., more Ni in the sulfides or metal of IAB, or more Ge and Ir in the oxides of IIICD).

  3. Ar-Ar and I-Xe Ages and the Thermal History of IAB Meteorites

    NASA Technical Reports Server (NTRS)

    Bogard, Donald D.; Garrison, Daniel H.; Takeda, Hiroshi

    2005-01-01

    Studies of several samples of the large Caddo County IAB iron meteorite reveal andesitic material, enriched in Si, Na, Al and Ca, which is essentially unique among meteorites. This material is believed to have formed from a chondritic source by partial melting and to have further segregated by grain coarsening. Such an origin implies extended metamorphism of the IAB parent body. New Ar-39- Ar-40 ages for silicate from three different Caddo samples are consistent with a common age of 4.50-4.51 Gyr ago. Less well defined Ar-Ar degassing ages for inclusions from two other IABs, EET8333 and Udei Station, are approx.4.32 Gyr, whereas the age for Campo del Cielo varies considerably over approx.3.23-4.56 Gyr. New I-129-Xe-129 ages for Caddo County and EET8333 are 4557.9+/-0.1 Myr and 4557-4560 Myr, respectively, relative to an age of 4562.3 Myr for Shallowater. Considering all reported Ar-Ar degassing ages for IABs and related winonaites, the range is approx.4.32-4.53 Gyr, but several IABs give similar Ar ages of 4.50-4.52 Gyr. We interpret these older Ar ages to represent cooling after the time of last significant metamorphism on the parent body, and the younger ages to represent later 40Ar diffusion loss. The older Ar-Ar ages for IABs are similar to Sm-Nd and Rb-Sr isochron ages reported in the literature for Caddo County. Considering the possibility that IAB parent body formation was followed by impact disruption, reassembly, and metamorphism (e.g., Benedix et al. 2000), the Ar-Ar ages and IAB cooling rates deduced from Ni concentration profiles in IAB metal (Herpfer et al., 1994) are consistent if the time of the post-assembly metamorphism was as late as approx.4.53 Gyr ago. However, I-Xe ages reported for some IABs define much older ages of approx.4558-4566 Myr, which cannot easily be reconciled with the much younger Ar-Ar and Sm-Nd ages. An explanation for the difference in radiometric ages of IABs may reside in combinations of the following: a) I-Xe ages have very

  4. Metallographic Cooling Rates of IAB Iron Meteorites

    NASA Astrophysics Data System (ADS)

    Meibom, A.; Haack, H.; Jensen, S. K.; Ulff-Moller, F.; Rasmussen, K. L.

    1995-09-01

    Non-metals can play an important role for the diffusion-controlled growth of the Widmanstatten structure in iron meteorites. The presence of P significantly changes the diffusivity and equilibrium concentration of Ni in kamacite and taenite [1,2], and the effects of P have therefore been included in metallographic cooling rate calculations for many years. The presence of C probably increases the diffusivity of Ni in taenite up to a factor of two, which is considerably smaller than the effect of P that increases the Ni diffusivity by up to a factor of 10 [3,1]. On the other hand, C partitions strongly into taenite leaving kamacite essentially C-free (<10 micrograms/g [4]) and significantly reduces the equilibrium Ni-concentration in taenite [5]. Therefore, the effect of C should be included in metallographic cooling rate calculations of C-rich iron meteorites [6]. IAB iron meteorites have much higher bulk C-concentrations than most other iron meteorites and the metallic phases of the IAB irons were probably saturated with C soon after kamacite nucleation commenced. Since C is expected to decrease the solubility of P in taenite [7] we have based our cooling rate estimate of Toluca (IAB) on the Fe-Ni-C system rather than the Fe-Ni-P system. Previous metallographic cooling rates determined for IAB irons, including the effect of P, are low (1-10 degrees C/My [8] and 30-70 degrees C/My [9]). Fractional crystallization of S-rich cores [10, 11] and impact generated melt pools [12] have been proposed as origins of the IAB iron meteorites. Since we expect melt pools near the surface to have cooled significantly faster than the core of a differentiated parent body, the metallographic cooling rates may be used to discriminate between the two models. We have performed thermodynamic calculations on the C-saturated Fe-Ni-C-system at temperatures above 400 degrees C [13]. The results agree with earlier experimental work [5] and indicate that C, to the same degree as P, reduces the

  5. Microstructural and paleomagnetic insight into the cooling history of the IAB parent body

    NASA Astrophysics Data System (ADS)

    Nichols, Claire I. O.; Krakow, Robert; Herrero-Albillos, Julia; Kronast, Florian; Northwood-Smith, Geraint; Harrison, Richard J.

    2018-05-01

    The IABs represent one of only two groups of iron meteorites that did not form by fractional crystallization of liquid Fe-Ni in the core of a differentiated planetesimal. Instead, they are believed to originate from a partially differentiated body that was severely disrupted by one or more impacts during its early history. We present a detailed microstructural and paleomagnetic study of the Odessa and Toluca IAB meteorites, with a view to further constraining the complex history of the IAB parent body. X-ray photoemission electron microscopy and energy dispersive spectroscopy were used to generate high-resolution Ni/Fe maps. The crystallographic architecture of Odessa was analysed using electron backscatter diffraction. Paleomagnetic signals and the magnetic properties of several microstructures were also assessed using X-ray magnetic circular dichroism. Odessa exhibits a complex series of microstructures, requiring an unusual evolution during slow cooling. A conventional Widmanstätten microstructure, consisting of multiple generations of kamacite lamellae surrounded by M-shaped diffusion profiles, developed via continuous precipitation to temperatures below ∼400 °C. Multiple generations of pearlitic plessite nucleated from kamacite/taenite (T > 400 °C) and tetrataenite rim/taenite interfaces (T < 400 °C), via a process of discontinuous precipitation. Rounded rafts of Ni-rich taenite, observed within some regions of pearlitic plessite, are shown to have the same crystallographic orientation as the parental taenite, and a non-standard orientation relationship with the enclosing kamacite. Contrary to current theories, these rafts cannot have formed by coarsening of pre-existing pearlitic plessite. A new bowing mechanism is proposed, whereby rafts of Ni-enriched taenite form between advancing lobes of an irregular reaction front during discontinuous precipitation. Subsequent coarsening leads to the growth of the taenite rafts, and the partial or complete removal

  6. Ar-Ar and I-XE Ages and the Thermal History of IAB Meteorites

    NASA Technical Reports Server (NTRS)

    Bogard, Donald D.; Garrison, Daniel H.; Takeda, Hiroshi

    2006-01-01

    Studies of several samples of the large Caddo County IAB iron meteorite reveal andesitic material, enriched in Si, Na, Al and Ca which is essentially unique among meteorites. This material is believed to have formed from a chondritic source by partial melting and to have further segregated by grain coarsening. Such an origin implies extended metamorphism of the IAB parent body. New Ar-39- Ar-40 ages for silicate from three different Caddo samples are consistent with a common age of 4.50- 4.51 Gyr ago. Less well defined Ar-Ar degassing ages for inclusions from two other IABs, EET8333 and Udei Station, are approx. 4.32 Gyr, whereas the age for Campo del Cielo varies considerably over approx. 3.23-4.56 Gyr. New I-129-Xe-129 ges for Caddo County and EET8333 are 4561.9 plus or minus 0.1 Myr and 4560-4563 Myr, respectively, relative to an age of 4566 Myr for Shallowater. Considering all reported Ar-Ar ages for IABs and related winonaites, the range is approx. 4.32-4.53 Gyr, but several IABs give similar Ar ages of 4.50-4.52 Gyr. We interpret these older ages to represent cooling after the time of last significant metamorphism on the parent body, and the younger ages to represent later 40Ar diffusion loss. These older Ar-Ar ages are similar to Sm-Nd and Rb-Sr isochron ages reported in the literature for Caddo County. Considering the possibility that IAB parent body formation was followed by impact disruption, reassembly, and metamorphism (e.g., Benedix et al. 2000), the time of the postassembly metamorphism may have been as late as approx. 4.53 Gyr ago. However, precise I-Xe ages reported for some IABs define a range of ages of approx. 4560 to approx. 4576 Myr. The older I-Xe ages exceed the oldest precise radiometric ages of meteorites, appear unrealistic, and suggest a bias in the calibration of all I-Xe ages. But even with such a bias, the I-Xe ages of IABs cannot easily be reconciled with the much younger Ar-Ar and Sm-Nd ages and with cooling rates deduced from Ni

  7. Ar-Ar and I-Xe Ages of Caddo County and Thermal History of IAB Iron Meteorites

    NASA Technical Reports Server (NTRS)

    Bogard, Donald D.; Garrison, Daniel H.; Takeda, Hiroshi

    2005-01-01

    Inclusions in IAB iron meteorites include non-chondritic silicate and those with more primitive chondritic silicate composition. Coarse-grained gabbroic material rich in plagioclase and diopside occurs in the Caddo County IAB iron meteorite and represents a new type of chemically differentiated, extra-terrestrial, andesitic silicate. Other parts of Caddo contain mostly andesitic material. Caddo thus exhibits petrologic characteristics of parent body metamorphism of a chondrite-like parent and inhomogeneous segregation of melts. Proposed IAB formation models include parent body partial melting and fractional crystallization or incomplete differentiation due to internal heat sources, and impact/induced melting and mixing. Benedix et al. prefer a hybrid model whereby the IAB parent body largely melted, then underwent collisional breakup, partial mixing of phases, and reassembly. Most reported 129I- Xe-129 ages of IABs are greater than 4.56 Gyr and a few are greater than or = 4.567 Gyr. These oldest ages exceed the 4.567 Gyr Pb-Pb age of Ca, Al-rich inclusions in primitive meteorites,

  8. Carbon Isotopic Heterogeneity of Graphite in the San Juan Mass of the Campo Del Cielo IAB Iron Meteorite

    NASA Technical Reports Server (NTRS)

    Maruoka, T.; Kurat, G.; Zinner, E.; Varela, M. E.; Ametrano, S. J.

    2003-01-01

    The origin of IAB iron meteorites is still a matter of debate. It is generally believed that iron meteorites originated from molten cores in small planetesimals because the fractionation trend of trace elements (e.g., Ir, Ge, Ga, etc. vs. Ni) for most iron meteorites can be more or less explained by fractional crystallization from metal melts. However, this process cannot produce trace element characteristics of the IAB (and other) iron meteorites. To explain these trace element abundance patterns, several models have been proposed. Although most of these models require a high temperature, clear evidence has recently been obtained for a sub-solidus formation of IAB iron meteorites from noble gas analyses. Moreover, heterogeneous distributions of some trace elements in metal and other phases also suggest a low temperature origin of at least some IAB iron meteorites. Here we use the carbon isotopic compositions of graphite to constrain the origin of IAB iron meteorites. Our data confirm a possible low temperature origin of IAB iron meteorites.

  9. The IAB Congress 2016: Is there justice in the bioethics world?

    PubMed

    Gopichandran, Vijayaprasad

    2017-01-01

    This comment contains the reflections of a first-time participant in the 13th International Association of Bioethics Congress (IAB 2016), held from June 14 to 17, 2016, in Edinburgh. At the outset, I would like to make a couple of clarifications. First, the opinions expressed here are my personal reflections and second, I am a physician and public health practitioner by profession and my interest is bioethics. I reflect on the justice implications of the IAB 2016 from the perspective of the challenge of maintaining inclusivity in a multidisciplinary bioethics world.

  10. Working Time and the Volume of Work in Germany: The IAB Concept of Measurement. IAB Labour Market Research Topics.

    ERIC Educational Resources Information Center

    Bach, Hans-Uwe; Koch, Susanne

    The Institut fuer Arbeitsmarkt- und Berufsforschung (IAB) or Institute for Employment Research has developed a detailed working time and volume of work measurement concept in order to more comprehensively assess the demand for labor. The individual components of working time in Germany are obtained from various data sources and combined to form…

  11. Evidence for a Late Reducing Event in IAB-Silicate Inclusions

    NASA Astrophysics Data System (ADS)

    Seckendorff, V. V.; O'Neill, H. St. C.; Zipfel, J.; Palme, H.

    1992-07-01

    Coexisting orthopyroxene (opx) and olivine (ol) in silicate inclusions of IAB-iron meteorites have different Fe/(Fe+Mg) ratios. Ferrosilite (fs) contents of opx are higher than fayalite contents (fa) of ol (e.g., Bunch and Keil 1970). Non-ideal solid solution of fs in opx and/or fa in ol is generally assumed. We reinvestigated the equilibrium Fe-Mg distribution between coexisting ol+opx in the system MgO-FeO-SiO2 (von Seckendorff and O'Neill 1992). Reversal experiments at high- Mg compositions were performed from 900 to 1600 degrees C at 16 and 20 kbar using a barium borosilicate flux. The data could be fitted to a simple thermodynamic model with ol and opx treated as regular solutions and this model was found to describe satisfactorily the literature data extending down to 700 degrees C. For Fe/(Fe+Mg) between 0.05 to 0.15 we find KD^ol-opx close to one from 1600 to 700 degrees C, virtually independent of pressure and temperature. Fig. 1 shows experimental results at the Mg-rich end. Error bars mark 1-sigma standard deviations. Ol is in all cases more Fe-rich than coexisting opx, except for a single run at 1000 degrees C that probably did not reach equilibrium because of slow reaction kinetics. Two calculated distribution curves (1300, 700 degrees C at 16 kbar) lie close together indicating the absence of any significant temperature dependence of the exchange reaction at the Mg- rich end of the system. IAB-silicate inclusions plot outside the range of experimental data (Fig. 1). Although some previous models for Fe-Mg exchange between ol and opx (e.g., Sack 1980) extrapolate to KD<1 at temperatures near 500 degrees C, such models reproduce the experimental data (700 to 1600 degrees C) less well, than our updated model. In addition, temperatures at 500 degrees C are probably too low to allow Fe diffusion in opx. Two pyroxene equilibration temperatures of IAB-silicate inclusions are around 900-1000 degrees C suggesting a similar closure temperature for Fe diffusion

  12. Silicate Inclusions in IAB Irons: Correlations Between Metal Composition and Inclusion Properties, and Inferences for Their Origin

    NASA Astrophysics Data System (ADS)

    Benedix, G. K.; McCoy, T. J.; Keil, K.

    1995-09-01

    IAB irons are the largest group of iron meteorites, exhibit a large range of siderophile element concentrations in their metal, and commonly contain silicate inclusions with roughly chondritic composition. They are closely related to IIICD irons [1,2] and their inclusions resemble winonaites [3]. It has been suggested that IAB's and IIICD's formed in individual impact melt pools [4,2] on a common parent body. However, it has also been suggested that fractional crystallization [5,6] of a S-saturated core could produce the observed siderophile element trends. Metal composition is correlated with silicate inclusion mineralogy in IIICD's [1], indicating reactions between solid silicates and the metallic magma in a core. These trends observed in IIICD's differ from those in IAB's, suggesting different parent bodies. A bi-modal grouping, based primarily on mineralogy and mineral abundances, was suggested for IAB inclusions [7]. However, recent recoveries of several new silicate-bearing IAB's, along with the emergence of new ideas on their origins, prompted a comprehensive study to document more fully the range of inclusions within IAB irons, to examine possible correlations between the compositions of the metallic host and the silicate inclusions, and to elucidate the origin of IAB irons. We are studying troilite-graphite-silicate inclusions in 24 IAB irons with Ni concentrations ranging from 6.6-25.0%. These include Odessa and Copiapo types [7], newly recovered meteorites (e.g., Lueders [8]) and meteorites with extreme Ni contents (e.g., Jenny's Creek, 6.8%; San Cristobal, 25.0% [9]). The inclusions exhibit a range of textures from recrystallized to partial melts (e.g., Caddo County [10]). Rigorous classification [7] is hampered by heterogeneities between group meteorites, between different samples of distinct meteorites, and within individual inclusions. While intergroup heterogeneities make comparisons between the suite of IAB's somewhat difficult, some general trends

  13. Late metal-silicate separation on the IAB parent asteroid: Constraints from combined W and Pt isotopes and thermal modelling

    NASA Astrophysics Data System (ADS)

    Hunt, Alison C.; Cook, David L.; Lichtenberg, Tim; Reger, Philip M.; Ek, Mattias; Golabek, Gregor J.; Schönbächler, Maria

    2018-01-01

    The short-lived 182Hf-182W decay system is a powerful chronometer for constraining the timing of metal-silicate separation and core formation in planetesimals and planets. Neutron capture effects on W isotopes, however, significantly hamper the application of this tool. In order to correct for neutron capture effects, Pt isotopes have emerged as a reliable in-situ neutron dosimeter. This study applies this method to IAB iron meteorites, in order to constrain the timing of metal segregation on the IAB parent body. The ε182W values obtained for the IAB iron meteorites range from -3.61 ± 0.10 to -2.73 ± 0.09. Correlating εiPt with ε182W data yields a pre-neutron capture ε182W of -2.90 ± 0.06. This corresponds to a metal-silicate separation age of 6.0 ± 0.8 Ma after CAI for the IAB parent body, and is interpreted to represent a body-wide melting event. Later, between 10 and 14 Ma after CAI, an impact led to a catastrophic break-up and subsequent reassembly of the parent body. Thermal models of the interior evolution that are consistent with these estimates suggest that the IAB parent body underwent metal-silicate separation as a result of internal heating by short-lived radionuclides and accreted at around 1.4 ± 0.1 Ma after CAIs with a radius of greater than 60 km.

  14. He Who Seeks Shall Find... Or Perhaps Not? Analysis of Firms' Searches for Qualified Personnel, Using Data from the IAB Establishment Panel 2000. IAB Labour Market Research Topics.

    ERIC Educational Resources Information Center

    Kolling, Arnd

    The success of German firms' searches for qualified personnel to fill openings in skilled occupations was examined through a statistical analysis of data from the Institut fur Arbeitsmarkt- und Berufsforschung der Bundesanstalt fur Arbeit's (IAB) establishment panel for 2000. An employer search model was used to explain the current German debate…

  15. Characterizing cosmochemical materials with genetic affinities to the Earth: Genetic and chronological diversity within the IAB iron meteorite complex

    NASA Astrophysics Data System (ADS)

    Worsham, Emily A.; Bermingham, Katherine R.; Walker, Richard J.

    2017-06-01

    The IAB iron meteorite complex consists of a main group (MG) and five chemical subgroups (sLL, sLM, sLH, sHL, and sHH). Here, mass-independent Mo and radiogenic 182W isotope compositions are reported for IAB complex meteorites to evaluate the genetics and chronology, respectively, of the MG and subgroups. Osmium isotopes are used to correct for cosmic ray exposure effects on isotopes of Mo and W. The MG and three subgroups (i.e., sLL, sLM, and sLH), characterized by low Au abundances, have the same Mo isotopic compositions within analytical uncertainty, consistent with a common genetic origin. These meteorites, together with winonaites, are the only cosmochemical materials yet identified with Mo isotopic compositions that are identical to Earth. The Mo isotopic compositions of two subgroups characterized by higher Au abundances (sHL and sHH) are identical to one another within uncertainty, but differ from the low Au subgroups, indicating derivation from genetically distinct materials. The MG has a 182W, post calcium-aluminum inclusion (CAI) formation model age of 3.4 ± 0.7 Ma. One of the low Au subgroups (sLM) is ∼1.7 Ma younger, whereas the high Au subgroups are ∼1.5-3 Ma older. The new Mo-W data, coupled with chemical data, indicate that the MG and the low Au subgroups formed in different impact-generated melts, some of which evidently formed on a chemically disparate, but genetically identical parent body. The high Au subgroups likely formed via core-formation processes on separate, internally-heated parent bodies from other IAB subgroups. The IAB complex meteorites fall on a linear trend defined by 94Mo/96Mo vs. 95Mo/96Mo, along with most other iron meteorite groups. Variation along this line was caused by mixing between at least two nebular components. One component was likely a pure s-process enriched nucleosynthetic carrier, and the other a homogenized nebular component. Sombrerete, currently classified as an sHL iron, has a Mo isotopic composition that

  16. The IAB Iron-Meteorite Complex: A Group, Five Subgroups, Numerous Grouplets, Closely Related, Mainly Formed by Crystal Segregation in Rapidly Cooling Melts

    NASA Technical Reports Server (NTRS)

    Wasson, J. T.; Kallemeyn, G. W.

    2002-01-01

    We present new data or iron meteorites that are members of group IAB or are closely related to this large group, and we have also reevaluated some of our earlier data for these irons. In the past it was not possible to distinguish IAB and IIICD irons on the basis of their positions on element-Ni diagrams. We now find that plotting, the new and revised data yields six sets of compact fields on element-Au diagrams, each set corresponding to a compositional group. The largest set includes the majority (approximately equal to 70) of irons previously designated IA: We christened this set the IAB main group. The remaining five sets we designate subgroups within the IAB complex. Three of these subgroups have Au contents similar to the main group, and form parallel trends in most element-Ni diagrams. The groups originally designated IIIC and IIID are two of these subgroups: they are now well resolved from each other and from the main group. The other low-Au subgroup has Ni contents just above the main group. Two other IAB subgroups have appreciably higher Au contents than the main group and show weaker compositional links to it. We have named these five subgroups on the basis of their Au and Ni contents. The three subgroups having Au contents similar to the main group are the low-Au (L) subgroups the two others the high-Au (H) subgroups. The Ni contents are designated high (H), medium (M), or low (L). Thus the old group IIID is now the sLH subgroup. the old group IIIC is the sLM subgroup. In addition, eight irons assigned to two grouplets plot between sLL and sLM on most element-Au diagrams. A large number (27) of related irons plot outside these compact fields but nonetheless appear to be sufficiently related to also be included in the IAB complex.

  17. 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

  18. 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.

  19. The Sm-Nd systematics of silicate inclusions in iron meteorites: Results from Caddo (IAB)

    NASA Technical Reports Server (NTRS)

    Stewart, Brian W.; Papanastassiou, D. A.; Wasserburg, G. J.

    1993-01-01

    The timing of events leading to the formation of silicate-rich and metal-rich regions in planetesimals remains an important problem in the study of planetary formation and differentiation in the early solar system. The IAB irons are especially important as they are considered to represent a magmatic differentiation series. Iron meteorites present a particular challenge for chronological studies, due to the relative paucity of phases serving as hosts for radioactive parent-daughter nuclides. Recent work using the Re-Os system, following on the pioneering work by Herr et al. and Luck and Allegre, appears promising, but investigators up to now have concentrated on whole rock isochrons. Silicate clasts enclosed within iron meteorites can provide information about the chronology and thermal history of irons. Extensive work on Rb-Sr, K-Ar, and I-Xe has been reported on silicate inclusions in iron meteorites. We report the initial results from our Sm-Nd study of an inclusion with the Caddo IAB iron, the first Sm-Nd isotopic study of a silicate clast embedded within an iron meteorite. Our results include measurements of the standard long-lived Sm-147/Nd-143 (tau = 152 AE) system, as well as the shorter-lived SM-146/Nd-142 (tau = 0.149 AE) system, which has been shown to be very useful in deciphering the history of the early solar system. The Caddo silicate clast was described by Palme et al., who kindly provided us with a major part of the inclusion. The inclusion is coarse-grained consisting predominantly of olivine, clinopyroxene, and plagioclase, with lesser amounts of orthopyroxene, Fe-Ni metal, sulfide, and phosphate. The relatively large grain size (up to 3 mm) and 120 degree grain boundaries suggest extensive metamorphism at high temperatures. Based on study of a thin section, there is evidence for metal invading along grain boundaries in some regions of the inclusion, suggesting that the Fe-Ni metal was molten when the silicate clast was incorporated. Metamorphic

  20. Consistent design schematics for biological systems: standardization of representation in biological engineering

    PubMed Central

    Matsuoka, Yukiko; Ghosh, Samik; Kitano, Hiroaki

    2009-01-01

    The discovery by design paradigm driving research in synthetic biology entails the engineering of de novo biological constructs with well-characterized input–output behaviours and interfaces. The construction of biological circuits requires iterative phases of design, simulation and assembly, leading to the fabrication of a biological device. In order to represent engineered models in a consistent visual format and further simulating them in silico, standardization of representation and model formalism is imperative. In this article, we review different efforts for standardization, particularly standards for graphical visualization and simulation/annotation schemata adopted in systems biology. We identify the importance of integrating the different standardization efforts and provide insights into potential avenues for developing a common framework for model visualization, simulation and sharing across various tools. We envision that such a synergistic approach would lead to the development of global, standardized schemata in biology, empowering deeper understanding of molecular mechanisms as well as engineering of novel biological systems. PMID:19493898

  1. Magnetic and microstructural characterisation of FeNi: Insight into the formation and impact history of the IAB parent body

    NASA Astrophysics Data System (ADS)

    Nichols, C. I. O.; Krakow, R.; Herrero-Albillos, J.; Kronast, F.; Northwood-Smith, G.; Harrison, R. J.

    2017-12-01

    The IABs represent one of only two groups of iron meteorites that did not form by fractional crystallization of liquid Fe-Ni in the core of a differentiated planetesimal. Instead, they are believed to originate from a partially differentiated body that was severely disrupted by one or more impacts during its early history. Paleomagnetic signals from two IABs, Toluca and Odessa, were investigated using X-ray magnetic circular dichroism (XMCD) and X-ray photoemission electron microscopy (X-PEEM) to image the magnetisation of the cloudy zone. The IABs do not appear to have experienced a magnetic field, consistent with the lack of a metallic core on the parent body. We also present a detailed microstructural and magnetic study of the observed FeNi microstructures, characterising their properties using XMCD and X-PEEM. The crystallographic architecture of the microstructures was analysed using electron backscatter diffraction (EBSD). Odessa and Toluca both exhibit a complex series of microstructures, requiring an unusual evolution during slow cooling. A conventional Widmanstätten sequence of kamacite, tetrataenite rim and cloudy zone developed via slow cooling to temperatures below 400 ºC. Subsequent modification of the microstructures resulted in the formation of pearlitic plessite and spheroidized plessite. Compositional and crystallographic analysis suggests that pearlitic and spheroidized plessite formed by impact modification of the cloudy zone and martensite, respectively. This study highlights the importance of characterising microstructures in order to corroborate paleomagnetic observations, as well as improving our understanding of the processes effecting planetary formation and evolution.

  2. The Aggregate National Supply of Job Openings and Firms' Procedures for Filling Positions. IAB Labour Market Research Topics.

    ERIC Educational Resources Information Center

    Magvas, Emil; Spitznagel, Eugen

    Surveys by the Institut fur Arbeitsmarkt- und Berufsforschung (IAB) of German firms' job openings have been combined with job registry data from the Bundesanstalt fur Arbeit on an annual basis since 1989 in order to determine the scope and structure of the aggregate national supply of job openings. The surveys also indicated problems encountered…

  3. 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

  4. Prevalence and development of workplace health promotion in Germany: results of the IAB Establishment Panel 2012.

    PubMed

    Hollederer, Alfons; Wießner, Frank

    2015-10-01

    Based on survey data from the IAB Establishment Panel, the investigation aims to examine the prevalence of workplace health promotion among German establishments and its determinants. The IAB Establishment Panel 2012 comprises interviews with 15,556 establishments of all sizes and industrial sectors in Germany. We first present some descriptive statistics and then analyse the determinants of the prevalence of workplace health promotion by means of a probit regression. In 2012, 27 % of the interviewed establishments reported providing workplace health promotion measures on a voluntary basis. 64 % of all employees do work in establishments with workplace health promotion. From 2002 to 2012, the share of establishments with workplace health promotion increased by 8 % points. The strongest increase was observed in establishments in Western Germany and establishments with work councils. Most popular among the measures of workplace health promotion are employee surveys and analysis of the sickness absence. The vast majority of establishments provide only single measures. The econometric analysis shows that industrial sector, size of establishment, expected problems with human resources and the existence of a work council are important factors for workplace health promotion. Only a minority of establishments are committed to workplace health promotion, while these establishments provide the majority of jobs in Germany. Our analysis displays considerable disparities in terms of prevalence as well as potential for further extensions. This could be taken more into account when discussing innovative approaches of workplace health promotion.

  5. A standard-enabled workflow for synthetic biology.

    PubMed

    Myers, Chris J; Beal, Jacob; Gorochowski, Thomas E; Kuwahara, Hiroyuki; Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Nguyen, Tramy; Oberortner, Ernst; Samineni, Meher; Wipat, Anil; Zhang, Michael; Zundel, Zach

    2017-06-15

    A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  6. 78 FR 57293 - Distribution of Reference Biological Standards and Biological Preparations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-18

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES 42 CFR Part 7 [Docket No. CDC-2013-0013] RIN 0920-AA52 Distribution of Reference Biological Standards and Biological Preparations AGENCY: Centers for Disease Control and Prevention (HHS/CDC), Department of Health and Human Services (HHS). ACTION: Confirmation of...

  7. 78 FR 47319 - Fee Schedule for Reference Biological Standards and Biological Preparations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-05

    ... DEPARTMENT OF HEALTH AND HUMAN SERVICES Centers for Disease Control and Prevention Fee Schedule for Reference Biological Standards and Biological Preparations AGENCY: Centers for Disease Control and Prevention (CDC), Department of Health and Human Services (HHS). ACTION: General notice. SUMMARY: The Centers...

  8. Toward the First Data Acquisition Standard in Synthetic Biology.

    PubMed

    Sainz de Murieta, Iñaki; Bultelle, Matthieu; Kitney, Richard I

    2016-08-19

    This paper describes the development of a new data acquisition standard for synthetic biology. This comprises the creation of a methodology that is designed to capture all the data, metadata, and protocol information associated with biopart characterization experiments. The new standard, called DICOM-SB, is based on the highly successful Digital Imaging and Communications in Medicine (DICOM) standard in medicine. A data model is described which has been specifically developed for synthetic biology. The model is a modular, extensible data model for the experimental process, which can optimize data storage for large amounts of data. DICOM-SB also includes services orientated toward the automatic exchange of data and information between modalities and repositories. DICOM-SB has been developed in the context of systematic design in synthetic biology, which is based on the engineering principles of modularity, standardization, and characterization. The systematic design approach utilizes the design, build, test, and learn design cycle paradigm. DICOM-SB has been designed to be compatible with and complementary to other standards in synthetic biology, including SBOL. In this regard, the software provides effective interoperability. The new standard has been tested by experiments and data exchange between Nanyang Technological University in Singapore and Imperial College London.

  9. The potential of standards-based agriculture biology as an alternative to traditional biology in California

    NASA Astrophysics Data System (ADS)

    Sellu, George Sahr

    schools. Thoron & Meyer (2011) suggested that research into the contribution of integrated science courses toward higher test scores yielded mixed results. This finding may have been due in part to the fact that integrated science courses only incorporate select topics into agriculture education courses. In California, however, agriculture educators have developed standards-based courses such as Agriculture Biology (AgBio) that cover the same content standards as core traditional courses such as traditional biology. Students in both AgBio and traditional biology take the same standardized biology test. This is the first time there has been an opportunity for a fair comparison and a uniform metric for an agriscience course such as AgBio to be directly compared to traditional biology. This study will examine whether there are differences between AgBio and traditional biology with regard to standardized test scores in biology. Furthermore, the study examines differences in perception between teachers and students regarding teaching and learning activities associated with higher achievement in science. The findings of the study could provide a basis for presenting AgBio as a potential alternative to traditional biology. The findings of this study suggest that there are no differences between AgBio and traditional biology students with regard to standardized biology test scores. Additionally, the findings indicate that co-curricular activities in AgBio could contribute higher student achievement in biology. However, further research is required to identify specific activities in AgBio that contribute to higher achievement in science.

  10. Standardization in synthetic biology: an engineering discipline coming of age.

    PubMed

    Decoene, Thomas; De Paepe, Brecht; Maertens, Jo; Coussement, Pieter; Peters, Gert; De Maeseneire, Sofie L; De Mey, Marjan

    2018-08-01

    Leaping DNA read-and-write technologies, and extensive automation and miniaturization are radically transforming the field of biological experimentation by providing the tools that enable the cost-effective high-throughput required to address the enormous complexity of biological systems. However, standardization of the synthetic biology workflow has not kept abreast with dwindling technical and resource constraints, leading, for example, to the collection of multi-level and multi-omics large data sets that end up disconnected or remain under- or even unexploited. In this contribution, we critically evaluate the various efforts, and the (limited) success thereof, in order to introduce standards for defining, designing, assembling, characterizing, and sharing synthetic biology parts. The causes for this success or the lack thereof, as well as possible solutions to overcome these, are discussed. Akin to other engineering disciplines, extensive standardization will undoubtedly speed-up and reduce the cost of bioprocess development. In this respect, further implementation of synthetic biology standards will be crucial for the field in order to redeem its promise, i.e. to enable predictable forward engineering.

  11. Improving Collaboration by Standardization Efforts in Systems Biology

    PubMed Central

    Dräger, Andreas; Palsson, Bernhard Ø.

    2014-01-01

    Collaborative genome-scale reconstruction endeavors of metabolic networks would not be possible without a common, standardized formal representation of these systems. The ability to precisely define biological building blocks together with their dynamic behavior has even been considered a prerequisite for upcoming synthetic biology approaches. Driven by the requirements of such ambitious research goals, standardization itself has become an active field of research on nearly all levels of granularity in biology. In addition to the originally envisaged exchange of computational models and tool interoperability, new standards have been suggested for an unambiguous graphical display of biological phenomena, to annotate, archive, as well as to rank models, and to describe execution and the outcomes of simulation experiments. The spectrum now even covers the interaction of entire neurons in the brain, three-dimensional motions, and the description of pharmacometric studies. Thereby, the mathematical description of systems and approaches for their (repeated) simulation are clearly separated from each other and also from their graphical representation. Minimum information definitions constitute guidelines and common operation protocols in order to ensure reproducibility of findings and a unified knowledge representation. Central database infrastructures have been established that provide the scientific community with persistent links from model annotations to online resources. A rich variety of open-source software tools thrives for all data formats, often supporting a multitude of programing languages. Regular meetings and workshops of developers and users lead to continuous improvement and ongoing development of these standardization efforts. This article gives a brief overview about the current state of the growing number of operation protocols, mark-up languages, graphical descriptions, and fundamental software support with relevance to systems biology. PMID:25538939

  12. Organizing Community-Based Data Standards: Lessons from Developing a Successful Open Standard in Systems Biology

    NASA Astrophysics Data System (ADS)

    Hucka, M.

    2015-09-01

    In common with many fields, including astronomy, a vast number of software tools for computational modeling and simulation are available today in systems biology. This wealth of resources is a boon to researchers, but it also presents interoperability problems. Despite working with different software tools, researchers want to disseminate their work widely as well as reuse and extend the models of other researchers. This situation led in the year 2000 to an effort to create a tool-independent, machine-readable file format for representing models: SBML, the Systems Biology Markup Language. SBML has since become the de facto standard for its purpose. Its success and general approach has inspired and influenced other community-oriented standardization efforts in systems biology. Open standards are essential for the progress of science in all fields, but it is often difficult for academic researchers to organize successful community-based standards. I draw on personal experiences from the development of SBML and summarize some of the lessons learned, in the hope that this may be useful to other groups seeking to develop open standards in a community-oriented fashion.

  13. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

    PubMed

    Galdzicki, Michal; Clancy, Kevin P; Oberortner, Ernst; Pocock, Matthew; Quinn, Jacqueline Y; Rodriguez, Cesar A; Roehner, Nicholas; Wilson, Mandy L; Adam, Laura; Anderson, J Christopher; Bartley, Bryan A; Beal, Jacob; Chandran, Deepak; Chen, Joanna; Densmore, Douglas; Endy, Drew; Grünberg, Raik; Hallinan, Jennifer; Hillson, Nathan J; Johnson, Jeffrey D; Kuchinsky, Allan; Lux, Matthew; Misirli, Goksel; Peccoud, Jean; Plahar, Hector A; Sirin, Evren; Stan, Guy-Bart; Villalobos, Alan; Wipat, Anil; Gennari, John H; Myers, Chris J; Sauro, Herbert M

    2014-06-01

    The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.

  14. Biological standards for the Knowledge-Based BioEconomy: What is at stake.

    PubMed

    de Lorenzo, Víctor; Schmidt, Markus

    2018-01-25

    The contribution of life sciences to the Knowledge-Based Bioeconomy (KBBE) asks for the transition of contemporary, gene-based biotechnology from being a trial-and-error endeavour to becoming an authentic branch of engineering. One requisite to this end is the need for standards to measure and represent accurately biological functions, along with languages for data description and exchange. However, the inherent complexity of biological systems and the lack of quantitative tradition in the field have largely curbed this enterprise. Fortunately, the onset of systems and synthetic biology has emphasized the need for standards not only to manage omics data, but also to increase reproducibility and provide the means of engineering living systems in earnest. Some domains of biotechnology can be easily standardized (e.g. physical composition of DNA sequences, tools for genome editing, languages to encode workflows), while others might be standardized with some dedicated research (e.g. biological metrology, operative systems for bio-programming cells) and finally others will require a considerable effort, e.g. defining the rules that allow functional composition of biological activities. Despite difficulties, these are worthy attempts, as the history of technology shows that those who set/adopt standards gain a competitive advantage over those who do not. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Trace element analysis of extraterrestrial metal samples by inductively coupled plasma mass spectrometry: the standard solutions and digesting acids.

    PubMed

    Wang, Guiqin; Wu, Yangsiqian; Lin, Yangting

    2016-02-28

    Nearly 99% of the total content of extraterrestrial metals is composed of Fe and Ni, but with greatly variable trace element contents. The accuracy obtained in the inductively coupled plasma mass spectrometry (ICP-MS) analysis of solutions of these samples can be significantly influenced by matrix contents, polyatomic ion interference, and the concentrations of external standard solutions. An ICP-MS instrument (X Series 2) was used to determine 30 standard solutions with different concentrations of trace elements, and different matrix contents. Based on these measurements, the matrix effects were determined. Three iron meteorites were dissolved separately in aqua regia and HNO3. Deviations due to variation of matrix contents in the external standard solutions were evaluated and the analysis results of the two digestion methods for iron meteorites were assessed. Our results show obvious deviations due to unmatched matrix contents in the external standard solutions. Furthermore, discrepancy in the measurement of some elements was found between the sample solutions prepared with aqua regia and HNO3, due to loss of chloride during sample preparation and/or incomplete digestion of highly siderophile elements in iron meteorites. An accurate ICP-MS analysis method for extraterrestrial metal samples has been established using external standard solutions with matched matrix contents and digesting the samples with HNO3 and aqua regia. Using the data from this work, the Mundrabilla iron meteorite previously classified as IAB-ung is reclassified as IAB-MG. Copyright © 2016 John Wiley & Sons, Ltd.

  16. Measuring and monitoring biological diversity: Standard methods for mammals

    USGS Publications Warehouse

    Wilson, Don E.; Cole, F. Russell; Nichols, James D.; Rudran, Rasanayagam; Foster, Mercedes S.

    1996-01-01

    Measuring and Monitoring Biological Diversity: Standard Methods for Mammals provides a comprehensive manual for designing and implementing inventories of mammalian biodiversity anywhere in the world and for any group, from rodents to open-country grazers. The book emphasizes formal estimation approaches, which supply data that can be compared across habitats and over time. Beginning with brief natural histories of the twenty-six orders of living mammals, the book details the field techniques—observation, capture, and sign interpretation—appropriate to different species. The contributors provide guidelines for study design, discuss survey planning, describe statistical techniques, and outline methods of translating field data into electronic formats. Extensive appendixes address such issues as the ethical treatment of animals in research, human health concerns, preserving voucher specimens, and assessing age, sex, and reproductive condition in mammals.Useful in both developed and developing countries, this volume and the Biological Diversity Handbook Series as a whole establish essential standards for a key aspect of conservation biology and resource management.

  17. Fish gelatin thin film standards for biological application of PIXE

    NASA Astrophysics Data System (ADS)

    Manuel, Jack E.; Rout, Bibhudutta; Szilasi, Szabolcs Z.; Bohara, Gyanendra; Deaton, James; Luyombya, Henry; Briski, Karen P.; Glass, Gary A.

    2014-08-01

    There exists a critical need to understand the flow and accumulation of metallic ions, both naturally occurring and those introduced to biological systems. In this paper the results of fabricating thin film elemental biological standards containing nearly any combination of trace elements in a protein matrix are presented. Because it is capable of high elemental sensitivity, particle induced X-ray emission spectrometry (PIXE) is an excellent candidate for in situ analysis of biological tissues. Additionally, the utilization of microbeam PIXE allows the determination of elemental concentrations in and around biological cells. However, obtaining elemental reference standards with the same matrix constituents as brain tissue is difficult. An excellent choice for simulating brain-like tissue is Norland® photoengraving glue which is derived from fish skin. Fish glue is water soluble, liquid at room temperature, and resistant to dilute acid. It can also be formed into a thin membrane which dries into a durable, self-supporting film. Elements of interest are introduced to the fish glue in precise volumetric additions of well quantified atomic absorption standard solutions. In this study GeoPIXE analysis package is used to quantify elements intrinsic to the fish glue as well as trace amounts of manganese added to the sample. Elastic (non-Rutherford) backscattered spectroscopy (EBS) and the 1.734 MeV proton-on-carbon 12C(p,p)12C resonance is used for a normalization scheme of the PIXE spectra to account for any discrepancies in X-ray production arising from thickness variation of the prepared standards. It is demonstrated that greater additions of the atomic absorption standard cause a viscosity reduction of the liquid fish glue resulting in thinner films but the film thickness can be monitored by using simultaneous PIXE and EBS proton data acquisition.

  18. A Standards-Based Content Analysis of Selected Biological Science Websites

    ERIC Educational Resources Information Center

    Stewart, Joy E.

    2010-01-01

    The purpose of this study was to analyze the biology content, instructional strategies, and assessment methods of 100 biological science websites that were appropriate for Grade 12 educational purposes. For the analysis of each website, an instrument, developed from the National Science Education Standards (NSES) for Grade 12 Life Science coupled…

  19. Blueprints for green biotech: development and application of standards for plant synthetic biology.

    PubMed

    Patron, Nicola J

    2016-06-15

    Synthetic biology aims to apply engineering principles to the design and modification of biological systems and to the construction of biological parts and devices. The ability to programme cells by providing new instructions written in DNA is a foundational technology of the field. Large-scale de novo DNA synthesis has accelerated synthetic biology by offering custom-made molecules at ever decreasing costs. However, for large fragments and for experiments in which libraries of DNA sequences are assembled in different combinations, assembly in the laboratory is still desirable. Biological assembly standards allow DNA parts, even those from multiple laboratories and experiments, to be assembled together using the same reagents and protocols. The adoption of such standards for plant synthetic biology has been cohesive for the plant science community, facilitating the application of genome editing technologies to plant systems and streamlining progress in large-scale, multi-laboratory bioengineering projects. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  20. Mineralogy, Petrology, Chemistry, and Ar-39 - Ar-40 and Ages of the Caddo County IAB Iron: Evidence for Early Partial Melt Segregation of a Gabbro Area Rich in Plagioclase-Diopside

    NASA Technical Reports Server (NTRS)

    Takeda, Hiroshi; Bogard, Donald D.; Mittlefehldt, David W.; Garrison, Daniel H.

    2000-01-01

    We found coarse-grained gabbroic material rich in plagioclase and diopside in the Caddo County IAB iron meteorite. The polished thin sections studied were made from areas rich in Al and Ca detected by a micro-focus X-ray fluorescence (XRF) mapping technique. The gabbro is not a clast within a breccia, but rather this area is located mainly at silicate-metal boundaries only a few cm away from an area with fine-grained, ultramafic silicate similar to winonaites. Medium-grained orthopyroxene and olivine are found in transitional areas showing no disturbance of their crystalline textures. A vein-like region, starting at the area rich in fine-grained mafic silicate, extends towards the gabbroic area with a gradual increase in abundance of plagioclase and diopside. This texture and our accumulated knowledge of the formation mechanism of IAB/winonaltes meteorites, suggest that the gabbroic materials were formed by inhomogeneous segregation of partial melts of chondritic source materials. Compositional data on two mineralogically distinct samples of the gabbro-rich portion of the inclusion were obtained by INAA. Compared to an average of LAB silicate inclusions or winonaites, the Caddo County gabbro is enriched in the incompatible lithophile elements Na, Ca, Sc, REE and Hf, which is consistent with a melt origin for the gabbro. The cosmogenic space exposure age of Caddo County (511 Ma) is significantly younger than exposure ages of some other IAB meteorites, An 39Ar-40Ar age determination of the gabbroic material indicates a series of upward steps in age from 4.516 Ga to 4.523 Ga, with a few high temperature ages up to 4.54 Ga. The older age could approximate the primary recrystallization age of silicates. The stepped Ar age spectrum may indicate differences in Ar closure temperatures during slow cooling of -2-20'C/Myr in the parent body. Alternatively, the younger Ar-Ar ages may date a shock event which occurred while Caddo County was hot and which also created textures

  1. Standards for plant synthetic biology: a common syntax for exchange of DNA parts.

    PubMed

    Patron, Nicola J; Orzaez, Diego; Marillonnet, Sylvestre; Warzecha, Heribert; Matthewman, Colette; Youles, Mark; Raitskin, Oleg; Leveau, Aymeric; Farré, Gemma; Rogers, Christian; Smith, Alison; Hibberd, Julian; Webb, Alex A R; Locke, James; Schornack, Sebastian; Ajioka, Jim; Baulcombe, David C; Zipfel, Cyril; Kamoun, Sophien; Jones, Jonathan D G; Kuhn, Hannah; Robatzek, Silke; Van Esse, H Peter; Sanders, Dale; Oldroyd, Giles; Martin, Cathie; Field, Rob; O'Connor, Sarah; Fox, Samantha; Wulff, Brande; Miller, Ben; Breakspear, Andy; Radhakrishnan, Guru; Delaux, Pierre-Marc; Loqué, Dominique; Granell, Antonio; Tissier, Alain; Shih, Patrick; Brutnell, Thomas P; Quick, W Paul; Rischer, Heiko; Fraser, Paul D; Aharoni, Asaph; Raines, Christine; South, Paul F; Ané, Jean-Michel; Hamberger, Björn R; Langdale, Jane; Stougaard, Jens; Bouwmeester, Harro; Udvardi, Michael; Murray, James A H; Ntoukakis, Vardis; Schäfer, Patrick; Denby, Katherine; Edwards, Keith J; Osbourn, Anne; Haseloff, Jim

    2015-10-01

    Inventors in the field of mechanical and electronic engineering can access multitudes of components and, thanks to standardization, parts from different manufacturers can be used in combination with each other. The introduction of BioBrick standards for the assembly of characterized DNA sequences was a landmark in microbial engineering, shaping the field of synthetic biology. Here, we describe a standard for Type IIS restriction endonuclease-mediated assembly, defining a common syntax of 12 fusion sites to enable the facile assembly of eukaryotic transcriptional units. This standard has been developed and agreed by representatives and leaders of the international plant science and synthetic biology communities, including inventors, developers and adopters of Type IIS cloning methods. Our vision is of an extensive catalogue of standardized, characterized DNA parts that will accelerate plant bioengineering. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  2. Genetic Diversity of Venezuelan Alphaviruses and Circulation of a Venezuelan Equine Encephalitis Virus Subtype IAB Strain During an Interepizootic Period

    PubMed Central

    Medina, Gladys; Garzaro, Domingo J.; Barrios, Miguel; Auguste, Albert J.; Weaver, Scott C.; Pujol, Flor H.

    2015-01-01

    Several species of alphaviruses have been previously described in the Americas, some of which are associated with encephalitis and others are associated with arthralgia. Venezuelan equine encephalitis virus (VEEV) and eastern equine encephalitis virus (EEEV) are endemic to Venezuela, with the former being responsible for major outbreaks of severe and often fatal disease in animals and humans. The aim of this study was to analyze the genetic diversity of Venezuelan alphaviruses isolated during two decades (1973–1999) of surveillance in northern Venezuela. Phylogenetic analysis indicated the circulation of a VEEV subtype IAB strain 8 years after the last reported outbreak. Thirteen strains within two subclades of South American lineage III of EEEV were also found in Venezuela. Considerable genetic variability was observed among Venezuelan Una virus strains, which were widely distributed among the clades. The first Venezuelan Mayaro sequence was also characterized. PMID:25940191

  3. Genetic diversity of Venezuelan alphaviruses and circulation of a Venezuelan equine encephalitis virus subtype IAB strain during an interepizootic period.

    PubMed

    Medina, Gladys; Garzaro, Domingo J; Barrios, Miguel; Auguste, Albert J; Weaver, Scott C; Pujol, Flor H

    2015-07-01

    Several species of alphaviruses have been previously described in the Americas, some of which are associated with encephalitis and others are associated with arthralgia. Venezuelan equine encephalitis virus (VEEV) and eastern equine encephalitis virus (EEEV) are endemic to Venezuela, with the former being responsible for major outbreaks of severe and often fatal disease in animals and humans. The aim of this study was to analyze the genetic diversity of Venezuelan alphaviruses isolated during two decades (1973-1999) of surveillance in northern Venezuela. Phylogenetic analysis indicated the circulation of a VEEV subtype IAB strain 8 years after the last reported outbreak. Thirteen strains within two subclades of South American lineage III of EEEV were also found in Venezuela. Considerable genetic variability was observed among Venezuelan Una virus strains, which were widely distributed among the clades. The first Venezuelan Mayaro sequence was also characterized. © The American Society of Tropical Medicine and Hygiene.

  4. The Increasing Urgency for Standards in Basic Biological Research

    PubMed Central

    Freedman, Leonard P.; Inglese, James

    2016-01-01

    Research advances build upon the validity and reproducibility of previously published data and findings. Yet irreproducibility in basic biological and preclinical research is pervasive in both academic and commercial settings. Lack of reproducibility has led to invalidated research breakthroughs, retracted papers, and aborted clinical trials. Concerns and requirements for transparent, reproducible, and translatable research are accelerated by the rapid growth of “post-publication peer review,” open access publishing, and data sharing that facilitate the identification of irreproducible data/studies; they are magnified by the explosion of high-throughput technologies, genomics, and other data-intensive disciplines. Collectively, these changes and challenges are decreasing the effectiveness of traditional research quality mechanisms and are contributing to unacceptable—and unsustainable—levels of irreproducibility. The global oncology and basic biological research communities can no longer tolerate or afford widespread irreproducible research. This article discusses (1) how irreproducibility in preclinical research can ultimately be traced to an absence of a unifying life science standards framework, and (2) makes an urgent case for the expanded development and use of consensus-based standards to both enhance reproducibility and drive innovations in cancer research. PMID:25035389

  5. Bioinformatics in high school biology curricula: a study of state science standards.

    PubMed

    Wefer, Stephen H; Sheppard, Keith

    2008-01-01

    The proliferation of bioinformatics in modern biology marks a modern revolution in science that promises to influence science education at all levels. This study analyzed secondary school science standards of 49 U.S. states (Iowa has no science framework) and the District of Columbia for content related to bioinformatics. The bioinformatics content of each state's biology standards was analyzed and categorized into nine areas: Human Genome Project/genomics, forensics, evolution, classification, nucleotide variations, medicine, computer use, agriculture/food technology, and science technology and society/socioscientific issues. Findings indicated a generally low representation of bioinformatics-related content, which varied substantially across the different areas, with Human Genome Project/genomics and computer use being the lowest (8%), and evolution being the highest (64%) among states' science frameworks. This essay concludes with recommendations for reworking/rewording existing standards to facilitate the goal of promoting science literacy among secondary school students.

  6. Bioinformatics in High School Biology Curricula: A Study of State Science Standards

    PubMed Central

    Sheppard, Keith

    2008-01-01

    The proliferation of bioinformatics in modern biology marks a modern revolution in science that promises to influence science education at all levels. This study analyzed secondary school science standards of 49 U.S. states (Iowa has no science framework) and the District of Columbia for content related to bioinformatics. The bioinformatics content of each state's biology standards was analyzed and categorized into nine areas: Human Genome Project/genomics, forensics, evolution, classification, nucleotide variations, medicine, computer use, agriculture/food technology, and science technology and society/socioscientific issues. Findings indicated a generally low representation of bioinformatics-related content, which varied substantially across the different areas, with Human Genome Project/genomics and computer use being the lowest (8%), and evolution being the highest (64%) among states' science frameworks. This essay concludes with recommendations for reworking/rewording existing standards to facilitate the goal of promoting science literacy among secondary school students. PMID:18316818

  7. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017.

    PubMed

    Schreiber, Falk; Bader, Gary D; Gleeson, Padraig; Golebiewski, Martin; Hucka, Michael; Keating, Sarah M; Novère, Nicolas Le; Myers, Chris; Nickerson, David; Sommer, Björn; Waltemath, Dagmar

    2018-03-29

    Standards are essential to the advancement of Systems and Synthetic Biology. COMBINE provides a formal body and a centralised platform to help develop and disseminate relevant standards and related resources. The regular special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards by providing unified, easily citable access. This paper provides an overview of existing COMBINE standards and presents developments of the last year.

  8. Ohio High School Biology Teachers' Views of State Standard for Evolution: Impacts on Practice

    ERIC Educational Resources Information Center

    Borgerding, Lisa A.

    2012-01-01

    High school biology teachers face many challenges as they teach evolution. State standards for evolution may provide support for sound evolution instruction. This study attempts to build upon previous work by investigating teachers' views of evolution standards and their evolution practices in a state where evolution standards have been…

  9. Physical Principles of Development of the State Standard of Biological Cell Polarizability

    NASA Astrophysics Data System (ADS)

    Shuvalov, G. V.; Generalov, K. V.; Generalov, V. M.; Kruchinina, M. V.; Koptev, E. S.; Minin, O. V.; Minin, I. V.

    2018-03-01

    A new state standard of biological cell polarizability based on micron-size latex particles has been developed. As a standard material, it is suggested to use polystyrene. Values of the polarizability calculated for erythrocytes and values of the polarizability of micron-size spherical latex particles measured with measuring-computing complexes agree within the limits of satisfactory relative error. The Standard allows one the unit of polarizability measurements [m3] to be assigned to cells and erythrocytes for the needs of medicine.

  10. A description of the standardized measurement procedures and recommended threshold limit values for biological hazards in Germany.

    PubMed

    Rieger, M A; Lohmeyer, M; Nübling, M; Neuhaus, S; Diefenbach, H; Hofmann, F

    2005-05-01

    On the basis of EU directives 89/391/EEC (to encourage improvements in the safety and health of workers at work) and 2000/54/EC (on the protection of workers from risks related to exposure to biological agents at work), biological hazards at work have to be assessed and preventive measures have to be introduced in all member states of the EU. In Germany, national legislation (Biological Agents Ordinance - BioStoffV and Technical Rules on Biological Agents, TRBA) and recommendations of workers' compensation boards define standardized methods for the assessment of airborne mold, bacteria, and endotoxins. This article describes policies and practices in Germany for measurement of airborne bioaerosols and for interpretation of measurements relative to the standards. As an example, methods and results of measurements in agriculture are shown. The standardized measurement procedures proved suitable for use in livestock buildings. The results of the exploratory measurements in different livestock buildings confirmed the often high concentrations of airborne biological hazards in agriculture that are reported in the literature.

  11. Analysis of a Typical Chinese High School Biology Textbook Using the AAAS Textbook Standards

    ERIC Educational Resources Information Center

    Liang, Ye; Cobern, William W.

    2013-01-01

    The purpose of this study was to evaluate a typical Chinese high school biology textbook using the textbook standards of the American Association for the Advancement of Science (AAAS). The data were composed of three chapters selected from the textbook. Each chapter was analyzed and rated using the AAAS textbook standards. Pearson correlations…

  12. Establishment of the 2nd Korean national biological reference standard for blood coagulation factor VIII:C concentrate.

    PubMed

    Lee, Naery; Seo, Ji Suk; Kim, Jae Ok; Ban, Sang Ja

    2017-05-01

    Since the 1st Korean national biological reference standard for factor (F)VIII concentrate, established in 2001, has shown declining potency, we conducted this study to replace this standard with a 2nd Korean national biological reference standard for blood coagulation FVIII concentrate. The candidate materials for the 2nd standard were prepared in 8000 vials with 10 IU/ml of target potency, according to the approved manufacturing process of blood coagulation Factor VIII:C Monoclonal Antibody-purified, Freeze-dried Human Blood Coagulation Factor VIII:C. Potency was evaluated by one-stage clotting and chromogenic methods and the stability was confirmed to meet the specifications during a period of 73 months. Since the potencies obtained by the two methods differed significantly (P < 0.015), the values were determined separately according to the geometric means (8.9 and 7.4 IU/vial, respectively). The geometric coefficients of interlaboratory variability were 3.4% and 7.6% by the one-stage clotting and chromogenic assays, respectively. Copyright © 2017 International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

  13. Evolution of activities in international biological standardization since the early days of the Health Organisation of the League of Nations.

    PubMed

    Sizaret, P

    1988-01-01

    The main activities in international biological standardization during the 18 years that followed the first international biological standardization meeting in London in 1921 were concerned with expressing the potencies of test preparations in comparison with reference materials. After the Second World War, however, it became clear that the testing of biological substances against international reference materials was only one among several measures for obtaining safe and potent products. The activities in international biological standardization were therefore widened so that, by the strict observance of specific manufacturing and control requirements, it was possible to gain further in safety and efficacy. At the end of 1987, 42 international requirements for biological substances were available and were being used as national requirements, sometimes after minor modification, by the majority of WHO's Member States. This is of utmost importance for the worldwide use of safe and potent biological products, including vaccines.

  14. Bioinformatics in High School Biology Curricula: A Study of State Science Standards

    ERIC Educational Resources Information Center

    Wefer, Stephen H.; Sheppard, Keith

    2008-01-01

    The proliferation of bioinformatics in modern biology marks a modern revolution in science that promises to influence science education at all levels. This study analyzed secondary school science standards of 49 U.S. states (Iowa has no science framework) and the District of Columbia for content related to bioinformatics. The bioinformatics…

  15. Determination of perfluorinated alkyl acid concentrations in biological standard reference materials.

    PubMed

    Reiner, Jessica L; O'Connell, Steven G; Butt, Craig M; Mabury, Scott A; Small, Jeff M; De Silva, Amila O; Muir, Derek C G; Delinsky, Amy D; Strynar, Mark J; Lindstrom, Andrew B; Reagen, William K; Malinsky, Michelle; Schäfer, Sandra; Kwadijk, Christiaan J A F; Schantz, Michele M; Keller, Jennifer M

    2012-11-01

    Standard reference materials (SRMs) are homogeneous, well-characterized materials used to validate measurements and improve the quality of analytical data. The National Institute of Standards and Technology (NIST) has a wide range of SRMs that have mass fraction values assigned for legacy pollutants. These SRMs can also serve as test materials for method development, method validation, and measurement for contaminants of emerging concern. Because inter-laboratory comparison studies have revealed substantial variability of measurements of perfluoroalkyl acids (PFAAs), future analytical measurements will benefit from determination of consensus values for PFAAs in SRMs to provide a means to demonstrate method-specific performance. To that end, NIST, in collaboration with other groups, has been measuring concentrations of PFAAs in a variety of SRMs. Here we report levels of PFAAs and perfluorooctane sulfonamide (PFOSA) determined in four biological SRMs: fish tissue (SRM 1946 Lake Superior Fish Tissue, SRM 1947 Lake Michigan Fish Tissue), bovine liver (SRM 1577c), and mussel tissue (SRM 2974a). We also report concentrations for three in-house quality-control materials: beluga whale liver, pygmy sperm whale liver, and white-sided dolphin liver. Measurements in SRMs show an array of PFAAs, with perfluorooctane sulfonate (PFOS) being the most frequently detected. Reference and information values are reported for PFAAs measured in these biological SRMs.

  16. Measuring the Outcome of At-Risk Students on Biology Standardized Tests When Using Different Instructional Strategies

    NASA Astrophysics Data System (ADS)

    Burns, Dana

    Over the last two decades, online education has become a popular concept in universities as well as K-12 education. This generation of students has grown up using technology and has shown interest in incorporating technology into their learning. The idea of using technology in the classroom to enhance student learning and create higher achievement has become necessary for administrators, teachers, and policymakers. Although online education is a popular topic, there has been minimal research on the effectiveness of online and blended learning strategies compared to the student learning in a traditional K-12 classroom setting. The purpose of this study was to investigate differences in standardized test scores from the Biology End of Course exam when at-risk students completed the course using three different educational models: online format, blended learning, and traditional face-to-face learning. Data was collected from over 1,000 students over a five year time period. Correlation analyzed data from standardized tests scores of eighth grade students was used to define students as "at-risk" for failing high school courses. The results indicated a high correlation between eighth grade standardized test scores and Biology End of Course exam scores. These students were deemed "at-risk" for failing high school courses. Standardized test scores were measured for the at-risk students when those students completed Biology in the different models of learning. Results indicated significant differences existed among the learning models. Students had the highest test scores when completing Biology in the traditional face-to-face model. Further evaluation of subgroup populations indicated statistical differences in learning models for African-American populations, female students, and for male students.

  17. YeastFab: the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae

    PubMed Central

    Guo, Yakun; Dong, Junkai; Zhou, Tong; Auxillos, Jamie; Li, Tianyi; Zhang, Weimin; Wang, Lihui; Shen, Yue; Luo, Yisha; Zheng, Yijing; Lin, Jiwei; Chen, Guo-Qiang; Wu, Qingyu; Cai, Yizhi; Dai, Junbiao

    2015-01-01

    It is a routine task in metabolic engineering to introduce multicomponent pathways into a heterologous host for production of metabolites. However, this process sometimes may take weeks to months due to the lack of standardized genetic tools. Here, we present a method for the design and construction of biological parts based on the native genes and regulatory elements in Saccharomyces cerevisiae. We have developed highly efficient protocols (termed YeastFab Assembly) to synthesize these genetic elements as standardized biological parts, which can be used to assemble transcriptional units in a single-tube reaction. In addition, standardized characterization assays are developed using reporter constructs to calibrate the function of promoters. Furthermore, the assembled transcription units can be either assayed individually or applied to construct multi-gene metabolic pathways, which targets a genomic locus or a receiving plasmid effectively, through a simple in vitro reaction. Finally, using β-carotene biosynthesis pathway as an example, we demonstrate that our method allows us not only to construct and test a metabolic pathway in several days, but also to optimize the production through combinatorial assembly of a pathway using hundreds of regulatory biological parts. PMID:25956650

  18. The Vimos VLT deep survey. Global properties of 20,000 galaxies in the IAB < 22.5 WIDE survey

    NASA Astrophysics Data System (ADS)

    Garilli, B.; Le Fèvre, O.; Guzzo, L.; Maccagni, D.; Le Brun, V.; de la Torre, S.; Meneux, B.; Tresse, L.; Franzetti, P.; Zamorani, G.; Zanichelli, A.; Gregorini, L.; Vergani, D.; Bottini, D.; Scaramella, R.; Scodeggio, M.; Vettolani, G.; Adami, C.; Arnouts, S.; Bardelli, S.; Bolzonella, M.; Cappi, A.; Charlot, S.; Ciliegi, P.; Contini, T.; Foucaud, S.; Gavignaud, I.; Ilbert, O.; Iovino, A.; Lamareille, F.; McCracken, H. J.; Marano, B.; Marinoni, C.; Mazure, A.; Merighi, R.; Paltani, S.; Pellò, R.; Pollo, A.; Pozzetti, L.; Radovich, M.; Zucca, E.; Blaizot, J.; Bongiorno, A.; Cucciati, O.; Mellier, Y.; Moreau, C.; Paioro, L.

    2008-08-01

    The VVDS-Wide survey has been designed to trace the large-scale distribution of galaxies at z ~ 1 on comoving scales reaching ~100~h-1 Mpc, while providing a good control of cosmic variance over areas as large as a few square degrees. This is achieved by measuring redshifts with VIMOS at the ESO VLT to a limiting magnitude IAB = 22.5, targeting four independent fields with sizes of up to 4 deg2 each. We discuss the survey strategy which covers 8.6 deg2 and present the general properties of the current redshift sample. This includes 32 734 spectra in the four regions, covering a total area of 6.1 deg2 with a sampling rate of 22 to 24%. This paper accompanies the public release of the first 18 143 redshifts of the VVDS-Wide survey from the 4 deg2 contiguous area of the F22 field at RA = 22^h. We have devised and tested an objective method to assess the quality of each spectrum, providing a compact figure-of-merit. This is particularly effective in the case of long-lasting spectroscopic surveys with varying observing conditions. Our figure of merit is a measure of the robustness of the redshift measurement and, most importantly, can be used to select galaxies with uniform high-quality spectra to carry out reliable measurements of spectral features. We also use the data available over the four independent regions to directly measure the variance in galaxy counts. We compare it with general predictions from the observed galaxy two-point correlation function at different redshifts and with that measured in mock galaxy surveys built from the Millennium simulation. The purely magnitude-limited VVDS Wide sample includes 19 977 galaxies, 304 type I AGNs, and 9913 stars. The redshift success rate is above 90% independent of magnitude. A cone diagram of the galaxy spatial distribution provides us with the current largest overview of large-scale structure up to z ~ 1, showing a rich texture of over- and under-dense regions. We give the mean N(z) distribution averaged over 6

  19. WHO Expert Committee on Biological Standardization.

    PubMed

    2002-01-01

    This report presents the recommendations of a WHO Expert Committee commissioned to coordinate activities leading to the adoption of international recommendations for the production and quality control of vaccines and other biologicals and the establishment of international biological reference materials. The report starts with a discussion of general issues brought to the attention of the Committee and provides information on issues relevant to international guidelines, recommendations and other matters related to the manufacture and quality control of biologicals. This is followed by information on the status and development of reference materials for bovine spongiform encephalopathy, various antigens, blood products, cytokines, growth factors and endocrinological substances. The second part of the report, of particular interest to manufacturers and national control authorities, contains sets of recommendations for the production and control of poliomyelitis vaccine (oral) and poliomyelitis vaccine (inactivated) and guidelines for the production and control of live attenuated Japanese encephalitis vaccine. Also included are lists of recommendations and guidelines for biological substances used in medicine, and other relevant documents.

  20. Botulinum toxin therapy for treatment of spasticity in multiple sclerosis: review and recommendations of the IAB-Interdisciplinary Working Group for Movement Disorders task force.

    PubMed

    Dressler, Dirk; Bhidayasiri, Roongroj; Bohlega, Saeed; Chahidi, Abderrahmane; Chung, Tae Mo; Ebke, Markus; Jacinto, L Jorge; Kaji, Ryuji; Koçer, Serdar; Kanovsky, Petr; Micheli, Federico; Orlova, Olga; Paus, Sebastian; Pirtosek, Zvezdan; Relja, Maja; Rosales, Raymond L; Sagástegui-Rodríguez, José Alberto; Schoenle, Paul W; Shahidi, Gholam Ali; Timerbaeva, Sofia; Walter, Uwe; Saberi, Fereshte Adib

    2017-01-01

    Botulinum toxin (BT) therapy is an established treatment of spasticity due to stroke. For multiple sclerosis (MS) spasticity this is not the case. IAB-Interdisciplinary Working Group for Movement Disorders formed a task force to explore the use of BT therapy for treatment of MS spasticity. A formalised PubMed literature search produced 55 publications (3 randomised controlled trials, 3 interventional studies, 11 observational studies, 2 case studies, 35 reviews, 1 guideline) all unanimously favouring the use of BT therapy for MS spasticity. There is no reason to believe that BT should be less effective and safe in MS spasticity than it is in stroke spasticity. Recommendations include an update of the current prevalence of MS spasticity and its clinical features according to classifications used in movement disorders. Immunological data on MS patients already treated should be analysed with respect to frequencies of MS relapses and BT antibody formation. Registration authorities should expand registration of BT therapy for spasticity regardless of its aetiology. MS specialists should consider BT therapy for symptomatic treatment of spasticity.

  1. The effect of using graphic organizers in the teaching of standard biology

    NASA Astrophysics Data System (ADS)

    Pepper, Wade Louis, Jr.

    This study was conducted to determine if the use of graphic organizers in the teaching of standard biology would increase student achievement, involvement and quality of activities. The subjects were 10th grade standard biology students in a large southern inner city high school. The study was conducted over a six-week period in an instructional setting using action research as the investigative format. After calculation of the homogeneity between classes, random selection was used to determine the graphic organizer class and the control class. The graphic organizer class was taught unit material through a variety of instructional methods along with the use of teacher generated graphic organizers. The control class was taught the same unit material using the same instructional methods, but without the use of graphic organizers. Data for the study were gathered from in-class written assignments, teacher-generated tests and text-generated tests, and rubric scores of an out-of-class written assignment and project. Also, data were gathered from student reactions, comments, observations and a teacher's research journal. Results were analyzed using descriptive statistics and qualitative interpretation. By comparing statistical results, it was determined that the use of graphic organizers did not make a statistically significant difference in the understanding of biological concepts and retention of factual information. Furthermore, the use of graphic organizers did not make a significant difference in motivating students to fulfill all class assignments with quality efforts and products. However, based upon student reactions and comments along with observations by the researcher, graphic organizers were viewed by the students as a favorable and helpful instructional tool. In lieu of statistical results, student gains from instructional activities using graphic organizers were positive and merit the continuation of their use as an instructional tool.

  2. The use of a single multielement standard for trace analysis in biological materials by external beam PIXE

    NASA Astrophysics Data System (ADS)

    Biswas, S. K.; Khaliquzzaman, M.; Islam, M. M.; Khan, A. H.

    1984-04-01

    The validity of the use of a single multielement standard for mass calibration in thick-target external beam PIXE analysis of biological materials has been investigated. In this study, the NBS orchard leaf, SRM 1571, was used as the basic standard for trace element analysis in other biological materials. Using the present procedure, the concentrations of K, Ca, Mn, Fe, Ni, Cu, Zn, Br, Rb and Sr were determined in several NBS reference materials such as bovine liver, spinach, rice flour, etc., generally in 20 μC irradiations with 2.0 MeV protons. The analytical results are compared with certified values of the NBS as well as with other measurements and the sources of errors are discussed.

  3. Predictive markers of safety and immunogenicity of adjuvanted vaccines.

    PubMed

    Mastelic, Beatris; Garçon, Nathalie; Del Giudice, Giuseppe; Golding, Hana; Gruber, Marion; Neels, Pieter; Fritzell, Bernard

    2013-11-01

    Vaccination represents one of the greatest public health triumphs; in part due to the effect of adjuvants that have been included in vaccine preparations to boost the immune responses through different mechanisms. Although a variety of novel adjuvants have been under development, only a limited number have been approved by regulatory authorities for human vaccines. This report reflects the conclusions of a group of scientists from academia, regulatory agencies and industry who attended a conference on the current state of the art in the adjuvant field. Held at the U.S. Pharmacopeial Convention (USP) in Rockville, Maryland, USA, from 18 to 19 April 2013 and organized by the International Association for Biologicals (IABS), the conference focused particularly on the future development of effective adjuvants and adjuvanted vaccines and on overcoming major hurdles, such as safety and immunogenicity assessment, as well as regulatory scrutiny. More information on the conference output can be found on the IABS website, http://www.iabs.org/. Copyright © 2013. Published by Elsevier Ltd.. All rights reserved.

  4. Interatrial block and interatrial septal thickness in patients with paroxysmal atrial fibrillation undergoing catheter ablation: Long-term follow-up study.

    PubMed

    Gul, Enes E; Pal, Raveen; Caldwell, Jane; Boles, Usama; Hopman, Wilma; Glover, Benedict; Michael, Kevin A; Redfearn, Damian; Simpson, Chris; Abdollah, Hoshiar; Baranchuk, Adrian

    2017-07-01

    Interatrial block (IAB) is a strong predictor of recurrence of atrial fibrillation (AF). IAB is a conduction delay through the Bachman region, which is located in the upper region of the interatrial space. During IAB, the impulse travels from the right atrium to the interatrial septum (IAS) and coronary sinus to finally reach the left atrium in a caudocranial direction. No relation between the presence of IAB and IAS thickness has been established yet. To determine whether a correlation exists between the degree of IAB and the thickness of the IAS and to determine whether IAS thickness predicts AF recurrence. Sixty-two patients with diagnosis of paroxysmal AF undergoing catheter ablation were enrolled. IAB was defined as P-wave duration ≥120 ms. IAS thickness was measured by cardiac computed tomography. Among 62 patients with paroxysmal AF, 45 patients (72%) were diagnosed with IAB. Advanced IAB was diagnosed in 24 patients (39%). Forty-seven patients were male. During a mean follow-up period of 49.8 ± 22 months (range 12-60 months), 32 patients (51%) developed AF recurrence. IAS thickness was similar in patients with and without IAB (4.5 ± 2.0 mm vs. 4.0 ± 1.4 mm; p = .45) and did not predict AF. Left atrial size was significantly enlarged in patients with IAB (40.9 ± 5.7 mm vs. 37.2 ± 4.0 mm; p = .03). Advanced IAB predicted AF recurrence after the ablation (OR: 3.34, CI: 1.12-9.93; p = .03). IAS thickness was not significantly correlated to IAB and did not predict AF recurrence. IAB as previously demonstrated was an independent predictor of AF recurrence. © 2016 Wiley Periodicals, Inc.

  5. Biocoder: A programming language for standardizing and automating biology protocols

    PubMed Central

    2010-01-01

    Background Published descriptions of biology protocols are often ambiguous and incomplete, making them difficult to replicate in other laboratories. However, there is increasing benefit to formalizing the descriptions of protocols, as laboratory automation systems (such as microfluidic chips) are becoming increasingly capable of executing them. Our goal in this paper is to improve both the reproducibility and automation of biology experiments by using a programming language to express the precise series of steps taken. Results We have developed BioCoder, a C++ library that enables biologists to express the exact steps needed to execute a protocol. In addition to being suitable for automation, BioCoder converts the code into a readable, English-language description for use by biologists. We have implemented over 65 protocols in BioCoder; the most complex of these was successfully executed by a biologist in the laboratory using BioCoder as the only reference. We argue that BioCoder exposes and resolves ambiguities in existing protocols, and could provide the software foundations for future automation platforms. BioCoder is freely available for download at http://research.microsoft.com/en-us/um/india/projects/biocoder/. Conclusions BioCoder represents the first practical programming system for standardizing and automating biology protocols. Our vision is to change the way that experimental methods are communicated: rather than publishing a written account of the protocols used, researchers will simply publish the code. Our experience suggests that this practice is tractable and offers many benefits. We invite other researchers to leverage BioCoder to improve the precision and completeness of their protocols, and also to adapt and extend BioCoder to new domains. PMID:21059251

  6. [Bayes' syndrome in cardiac surgery: prevalence of interatrial block in patients younger than 65 years undergoing cardiac surgery and association with postoperative atrial fibrillation].

    PubMed

    García-Izquierdo Jaén, Eusebio; Cobo Rodríguez, Pablo; Solís Solís, Luis; Pham Trung, Chinh; Jiménez Sánchez, Diego; Sánchez García, Manuel; Castro Urda, Victor; Toquero Ramos, Jorge; Fernández Lozano, Ignacio

    2017-11-03

    Interatrial block (IAB) is a well-known entity that is associated with an increased risk of atrial fibrillation (AF). This association is called Bayes' syndrome. The aim of our study was to define the prevalence of IAB among patients younger than 65 years undergoing cardiac surgery and determine whether there is an association between the presence of interatrial conduction delay and postoperative atrial fibrillation (POAF). A total of 207 patients were enrolled. Partial IAB was defined as P-wave>120ms. Advanced IAB was defined as P-wave>120ms+biphasic morphology in the inferior leads. Ocurrence of POAF was assessed and a comparative analysis was conducted between patients that did and did not develop AF. IAB prevalence was 78.3% (partial 66.2%, advanced 12.1%). POAF occurred in 28.5% of all patients, and was more frequent among patients with advanced IAB (44%) compared to 27.7% and 24.4% of POAF among patients with partial IAB and without IAB, respectively. Patients who developed POAF were significantly older, had significantly higher NTproBNP, higher prevalence of atrial enlargement and thyroid disease. After multivariate analysis, advanced IAB was found to be independently associated with POAF. IAB is a frequent finding among patients undergoing cardiac surgery. According to our results, advanced IAB is independently associated with POAF in younger patients (<65 years) undergoing cardiac surgery. Copyright © 2017 Instituto Nacional de Cardiología Ignacio Chávez. Publicado por Masson Doyma México S.A. All rights reserved.

  7. Characterization of the intergenic RNA profile at abdominal-A and Abdominal-B in the Drosophila bithorax complex

    PubMed Central

    Bae, Esther; Calhoun, Vincent C.; Levine, Michael; Lewis, Edward B.; Drewell, Robert A.

    2002-01-01

    The correct spatial expression of two Drosophila bithorax complex (BX-C) genes, abdominal-A (abdA) and Abdominal-B (AbdB), is dependent on the 100-kb intergenic infraabdominal (iab) region. The iab region is known to contain a number of different domains (iab2 through iab8) that harbor cis-regulatory elements responsible for directing expression of abdA and AbdB in the second through eighth abdominal segments. Here, we use in situ hybridization to perform high-resolution mapping of the transcriptional activity in the iab control regions. We show that transcription of the control regions themselves is abundant and precedes activation of the abdA and AbdB genes. As with the homeotic genes of the BX-C, the transcription patterns of the RNAs from the iab control regions demonstrate colinearity with the sequence of the iab regions along the chromosome and the domains in the embryo under the control of the specific iab regions. These observations suggest that the intergenic RNAs may play a role in initiating cis regulation at the BX-C early in development. PMID:12481037

  8. A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

    PubMed

    Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

    2016-06-17

    Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

  9. Fostering Students' Conceptual Knowledge in Biology in the Context of German National Education Standards

    NASA Astrophysics Data System (ADS)

    Förtsch, Christian; Dorfner, Tobias; Baumgartner, Julia; Werner, Sonja; von Kotzebue, Lena; Neuhaus, Birgit J.

    2018-04-01

    The German National Education Standards (NES) for biology were introduced in 2005. The content part of the NES emphasizes fostering conceptual knowledge. However, there are hardly any indications of what such an instructional implementation could look like. We introduce a theoretical framework of an instructional approach to foster students' conceptual knowledge as demanded in the NES (Fostering Conceptual Knowledge) including instructional practices derived from research on single core ideas, general psychological theories, and biology-specific features of instructional quality. First, we aimed to develop a rating manual, which is based on this theoretical framework. Second, we wanted to describe current German biology instruction according to this approach and to quantitatively analyze its effectiveness. And third, we aimed to provide qualitative examples of this approach to triangulate our findings. In a first step, we developed a theoretically devised rating manual to measure Fostering Conceptual Knowledge in videotaped lessons. Data for quantitative analysis included 81 videotaped biology lessons of 28 biology teachers from different German secondary schools. Six hundred forty students completed a questionnaire on their situational interest after each lesson and an achievement test. Results from multilevel modeling showed significant positive effects of Fostering Conceptual Knowledge on students' achievement and situational interest. For qualitative analysis, we contrasted instruction of four teachers, two with high and two with low student achievement and situational interest using the qualitative method of thematic analysis. Qualitative analysis revealed five main characteristics describing Fostering Conceptual Knowledge. Therefore, implementing Fostering Conceptual Knowledge in biology instruction seems promising. Examples of how to implement Fostering Conceptual Knowledge in instruction are shown and discussed.

  10. Synthesis and standardization of biologically synthesized silver nanoparticles

    NASA Astrophysics Data System (ADS)

    Roy, Swarup; Das, Tapan Kumar

    2013-06-01

    The biological silver nanoparticle was synthesized extracellularly by using a fungi Aspergillus foetidus. The live cell filtrate of fungi has been used as reducing agent in the process of nanoparticles synthesis. In 50 ml cell filtrate a volume of AgNO3 stock solution was added to make finally the concentration as 1 mM of AgNO3 and allowed to shake in an incubator for several hrs in dark. The changed color was considered as the primary indication of nanoparticles formation and studies of UV-VIS, DLS, FTIR, AFM, TEM, EDS, Zeta pot. and nitrate reductase assay confirmed the same. It was indicated that stable & 20-40 nm roughly spherical shaped silver nanoparticles was formed. To standardize the nanoparticles biosynthesis different physical parameters like Substrate cone. (0-8 mM), PH-(5-12), Temp.-(5-50°C), incubation time (0-120) hrs and salinity (0.1-1.0 %) were investigated and it was observed that 4 mM AgNO3 conc., PH-9, Temp. -30°C, incubation time 72h and 0.2 % salinity were found to be optimum for the synthesis & stability of the silver nanoparticles.

  11. The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.

    PubMed

    Zheng, Jie; Harris, Marcelline R; Masci, Anna Maria; Lin, Yu; Hero, Alfred; Smith, Barry; He, Yongqun

    2016-09-14

    of Biological and Clinical Statistics (OBCS) is a community-based open source ontology in the domain of biological and clinical statistics. OBCS is a timely ontology that represents statistics-related terms and their relations in a rigorous fashion, facilitates standard data analysis and integration, and supports reproducible biological and clinical research.

  12. Standardizing the atomic description, axis and centre of biological ion channels.

    PubMed

    Kaats, Adrian J; Galiana, Henrietta L; Nadeau, Jay L

    2007-09-15

    A general representation of the atomic co-ordinates of a biological ion channel is obtained from a definition of channel axis and centre. Through rotation and translation of the channel, its centre becomes the origin of the standard co-ordinate system, and the channel axis becomes the system's z-axis. A method for determining the channel axis and centre based on the concepts of mass centre and mass moment of inertia is presented. The method for determining the channel axis can be directly applied to channels that adhere to two specific conditions regarding their geometry and mass distribution. Specific examples are given for Gramicidin A (GA), and the mammalian potassium channel Kv 1.2. For channels that do not adhere to these conditions, minor modifications of these procedures can be applied in determining the channel axis. Specific examples are given for the outer membrane bacterial porin OmpF, and for the staphylococcal pore-forming toxin alpha-hemolysin (alpha HL). The definitions and procedures presented are made in an effort to establish a standard basis for performing, sharing, and comparing computations in a consistent manner.

  13. Expanding biological data standards development processes for US IOOS: visual line transect observing community for mammal, bird, and turtle data

    USGS Publications Warehouse

    Fornwall, M.; Gisiner, R.; Simmons, S. E.; Moustahfid, Hassan; Canonico, G.; Halpin, P.; Goldstein, P.; Fitch, R.; Weise, M.; Cyr, N.; Palka, D.; Price, J.; Collins, D.

    2012-01-01

    The US Integrated Ocean Observing System (IOOS) has recently adopted standards for biological core variables in collaboration with the US Geological Survey/Ocean Biogeographic Information System (USGS/OBIS-USA) and other federal and non-federal partners. In this Community White Paper (CWP) we provide a process to bring into IOOS a rich new source of biological observing data, visual line transect surveys, and to establish quality data standards for visual line transect observations, an important source of at-sea bird, turtle and marine mammal observation data. The processes developed through this exercise will be useful for other similar biogeographic observing efforts, such as passive acoustic point and line transect observations, tagged animal data, and mark-recapture (photo-identification) methods. Furthermore, we suggest that the processes developed through this exercise will serve as a catalyst for broadening involvement by the larger marine biological data community within the goals and processes of IOOS.

  14. Somatic and neuroendocrine responses to standard and biologically salient acoustic startle stimuli in monkeys

    PubMed Central

    Parker, Karen J.; Hyde, Shellie A.; Buckmaster, Christine L.; Tanaka, Serena M.; Brewster, Katharine K.; Schatzberg, Alan F.; Lyons, David M.; Woodward, Steven H.

    2010-01-01

    SUMMARY The startle response, a simple defensive response to a sudden stimulus signaling proximal threat, has been well studied in rodents and humans, but has been rarely examined in monkeys. The first goal of the present studies was to develop a minimally immobilizing startle measurement paradigm and validate its usefulness by testing two core features of the startle response (habituation and graded responsivity) in squirrel monkey subjects. Two different types of startle stimuli were used: standard broad-band noise bursts, and species-specific alarm vocalizations (“yaps”) which are elicited in response to threat in both wild and captive animals. The second goal of the present studies was to test whether yaps produce enhanced startle responsivity due to their increased biological salience compared to simple, non-biologically relevant noise bursts. The third goal of the present studies was to evaluate the hypothalamic pituitary-adrenal (HPA) axis response to startle stimuli, as little is known about the stress-activating role of startle stimuli in any species. These experiments determined that the whole-body startle response in relatively unrestrained squirrel monkeys habituates across repeated stimulus presentations and is proportional to stimulus intensity. In addition, differential habituation was observed across biologically salient vs. standard acoustic startle stimuli. Responses to “yaps” were larger initially but attenuated more rapidly over trials. Responses to “yaps” were also larger in the early subepochs of the response window but then achieved a lower level than responses to noise bursts in the later subepochs. Finally, adrenocorticotropic hormone and cortisol concentrations were significantly elevated above baseline after startle stimuli presentation, though monkeys did not exhibit differential HPA axis responses to the two types of startle stimuli. The development of monkey startle methodology may further enhance the utility of this

  15. The biological standard of living and mortality in Central Italy at the beginning of the 19th century.

    PubMed

    Coppola, Michela

    2013-12-01

    The biological standard of living in Central Italy at the beginning of the 19th century is analyzed using newly collected data on the height of recruits in the army of the Papal States. The results reveal a decline in height for the cohorts born under French rule (1796-1815). Although this trend was common to many parts of Europe, the estimated magnitude of the decline suggests a worsening of the biological standard of living of the working classes in the Papal States even relative to that of other countries. Despite the differences in the economic systems within the Papal States, no significant geographical variation in height has been found: even the most dynamic and advanced regions experienced a dramatic height decline. Mortality also increased during the period under consideration. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. Newly Shaped Intra‐Aortic Balloons Improve the Performance of Counterpulsation at the Semirecumbent Position: An In Vitro Study

    PubMed Central

    Kolyva, Christina; Pepper, John R.

    2016-01-01

    Abstract The major hemodynamic benefits of intra‐aortic balloon pump (IABP) counterpulsation are augmentation in diastolic aortic pressure (P aug) during inflation, and decrease in end‐diastolic aortic pressure (ΔedP) during deflation. When the patient is nursed in the semirecumbent position these benefits are diminished. Attempts to change the shape of the IAB in order to limit or prevent this deterioration have been scarce. The aim of the present study was to investigate the hemodynamic performance of six new IAB shapes, and compare it to that of a traditional cylindrical IAB. A mock circulation system, featuring an artificial left ventricle and an aortic model with 11 branches and physiological resistance and compliance, was used to test one cylindrical and six newly shaped IABs at angles 0, 10, 20, 30, and 40°. Pressure was measured continuously at the aortic root during 1:1 and 1:4 IABP support. Shape 2 was found to consistently achieve, in terms of absolute magnitude, larger ΔedP at angles than the cylindrical IAB. Although ΔedP was gradually diminished with angle, it did so to a lesser degree than the cylindrical IAB; this diminishment was only 53% (with frequency 1:1) and 40% (with frequency 1:4) of that of the cylindrical IAB, when angle increased from 0 to 40°. During inflation Shape 1 displayed a more stable behavior with increasing angle compared to the cylindrical IAB; with an increase in angle from 0 to 40°, diastolic aortic pressure augmentation dropped only by 45% (with frequency 1:1) and by 33% (with frequency 1:4) of the drop reached with the cylindrical IAB. After compensating for differences in nominal IAB volume, Shape 1 generally achieved higher P aug over most angles. Newly shaped IABs could allow for IABP therapy to become more efficient for patients nursed at the semirecumbent position. The findings promote the idea of personalized rather than generalized patient therapy for the achievement of higher IABP therapeutic efficiency

  17. Ethical and methodological standards for laboratory and medical biological rhythm research.

    PubMed

    Portaluppi, Francesco; Touitou, Yvan; Smolensky, Michael H

    2008-11-01

    The main objectives of this article are to update the ethical standards for the conduct of human and animal biological rhythm research and recommend essential elements for quality chronobiological research information, which should be especially useful for new investigators of the rhythms of life. A secondary objective is to provide for those with an interest in the results of chronobiology investigations, but who might be unfamiliar with the field, an introduction to the basic methods and standards of biological rhythm research and time series data analysis. The journal and its editors endorse compliance of all investigators to the principles of the Declaration of Helsinki of the World Medical Association, which relate to the conduct of ethical research on human beings, and the Guide for the Care and Use of Laboratory Animals of the Institute for Laboratory Animal Research of the National Research Council, which relate to the conduct of ethical research on laboratory and other animals. The editors and the readers of the journal expect the authors of submitted manuscripts to have adhered to the ethical standards dictated by local, national, and international laws and regulations in the conduct of investigations and to be unbiased and accurate in reporting never-before-published research findings. Authors of scientific papers are required to disclose all potential conflicts of interest, particularly when the research is funded in part or in full by the medical and pharmaceutical industry, when the authors are stock-holders of the company that manufactures or markets the products under study, or when the authors are a recent or current paid consultant to the involved company. It is the responsibility of the authors of submitted manuscripts to clearly present sufficient detail about the synchronizer schedule of the studied subjects (i.e., the sleep-wake schedule, ambient light-dark cycle, intensity and spectrum of ambient light exposure, seasons when the research was

  18. On the limitations of standard statistical modeling in biological systems: a full Bayesian approach for biology.

    PubMed

    Gomez-Ramirez, Jaime; Sanz, Ricardo

    2013-09-01

    One of the most important scientific challenges today is the quantitative and predictive understanding of biological function. Classical mathematical and computational approaches have been enormously successful in modeling inert matter, but they may be inadequate to address inherent features of biological systems. We address the conceptual and methodological obstacles that lie in the inverse problem in biological systems modeling. We introduce a full Bayesian approach (FBA), a theoretical framework to study biological function, in which probability distributions are conditional on biophysical information that physically resides in the biological system that is studied by the scientist. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Newly Shaped Intra-Aortic Balloons Improve the Performance of Counterpulsation at the Semirecumbent Position: An In Vitro Study.

    PubMed

    Kolyva, Christina; Pepper, John R; Khir, Ashraf W

    2016-08-01

    The major hemodynamic benefits of intra-aortic balloon pump (IABP) counterpulsation are augmentation in diastolic aortic pressure (Paug ) during inflation, and decrease in end-diastolic aortic pressure (ΔedP) during deflation. When the patient is nursed in the semirecumbent position these benefits are diminished. Attempts to change the shape of the IAB in order to limit or prevent this deterioration have been scarce. The aim of the present study was to investigate the hemodynamic performance of six new IAB shapes, and compare it to that of a traditional cylindrical IAB. A mock circulation system, featuring an artificial left ventricle and an aortic model with 11 branches and physiological resistance and compliance, was used to test one cylindrical and six newly shaped IABs at angles 0, 10, 20, 30, and 40°. Pressure was measured continuously at the aortic root during 1:1 and 1:4 IABP support. Shape 2 was found to consistently achieve, in terms of absolute magnitude, larger ΔedP at angles than the cylindrical IAB. Although ΔedP was gradually diminished with angle, it did so to a lesser degree than the cylindrical IAB; this diminishment was only 53% (with frequency 1:1) and 40% (with frequency 1:4) of that of the cylindrical IAB, when angle increased from 0 to 40°. During inflation Shape 1 displayed a more stable behavior with increasing angle compared to the cylindrical IAB; with an increase in angle from 0 to 40°, diastolic aortic pressure augmentation dropped only by 45% (with frequency 1:1) and by 33% (with frequency 1:4) of the drop reached with the cylindrical IAB. After compensating for differences in nominal IAB volume, Shape 1 generally achieved higher Paug over most angles. Newly shaped IABs could allow for IABP therapy to become more efficient for patients nursed at the semirecumbent position. The findings promote the idea of personalized rather than generalized patient therapy for the achievement of higher IABP therapeutic efficiency, with a choice

  20. A generic standard additions based method to determine endogenous analyte concentrations by immunoassays to overcome complex biological matrix interference.

    PubMed

    Pang, Susan; Cowen, Simon

    2017-12-13

    We describe a novel generic method to derive the unknown endogenous concentrations of analyte within complex biological matrices (e.g. serum or plasma) based upon the relationship between the immunoassay signal response of a biological test sample spiked with known analyte concentrations and the log transformed estimated total concentration. If the estimated total analyte concentration is correct, a portion of the sigmoid on a log-log plot is very close to linear, allowing the unknown endogenous concentration to be estimated using a numerical method. This approach obviates conventional relative quantification using an internal standard curve and need for calibrant diluent, and takes into account the individual matrix interference on the immunoassay by spiking the test sample itself. This technique is based on standard additions for chemical analytes. Unknown endogenous analyte concentrations within even 2-fold diluted human plasma may be determined reliably using as few as four reaction wells.

  1. Sustainable agriculture, renewable energy and rural development: An analysis of bio-energy systems used by small farms in China

    NASA Astrophysics Data System (ADS)

    Zhou, Aiming

    Renewable energy needs to be incorporated into the larger picture of sustainable agriculture and rural development if it is to serve the needs of the 3.25 billion human beings whose livelihoods and based on rural economies and ecologies. For rural communities, increasing agriculture production is key to raising income generation and improving social well-being, but this linkage depends also upon not harming natural resources. This dissertation provides an overview of recent Chinese agriculture history, discusses the role of energy in contemporary's China's agriculture and rural development, and introduces a new approach---the integrated agricultural bio-energy (IAB) system---to address the challenge of sustainable agriculture and rural development. IAB is an innovative design and offers a renewable energy solution for improving agricultural productivity, realizing efficient resource management, and enhancing social well-being for rural development. In order to understand how the IAB system can help to achieve sustainable agricultural and rural development in China, a comprehensive evaluation methodology is developed from health, ecological, energy and economic (HE3) perspectives. With data from surveys of 200 small farm households, a detailed study of IAB and conventional agricultural energy (CAE) system applications (in China's Liaoning and Yunnan Province) is conducted. The HE3 impacts of IAB systems in China's rural areas (compared to existing CAE systems) are quantified. The dissertation analyzes the full life-cycle costs and benefits of IAB systems, including their contributions to energy savings, CO2 emissions reduction, agricultural waste reduction, increased rural incomes, better rural health, and improved ecosystem sustainability. The analysis relies upon qualitative and quantitative modeling in order to produce a comprehensive assessment of IAB system impacts. Finally, the dissertation discusses the barriers to greater diffusion of the IAB systems

  2. Biological effects of tritium on fish cells in the concentration range of international drinking water standards.

    PubMed

    Stuart, Marilyne; Festarini, Amy; Schleicher, Krista; Tan, Elizabeth; Kim, Sang Bog; Wen, Kendall; Gawlik, Jilian; Ulsh, Brant

    2016-10-01

    To evaluate whether the current Canadian tritium drinking water limit is protective of aquatic biota, an in vitro study was designed to assess the biological effects of low concentrations of tritium, similar to what would typically be found near a Canadian nuclear power station, and higher concentrations spanning the range of international tritium drinking water standards. Channel catfish peripheral blood B-lymphoblast and fathead minnow testis cells were exposed to 10-100,000 Bq l(-1) of tritium, after which eight molecular and cellular endpoints were assessed. Increased numbers of DNA strand breaks were observed and ATP levels were increased. There were no increases in γH2AX-mediated DNA repair. No differences in cell growth were noted. Exposure to the lowest concentrations of tritium were associated with a modest increase in the viability of fathead minnow testicular cells. Using the micronucleus assay, an adaptive response was observed in catfish B-lymphoblasts. Using molecular endpoints, biological responses to tritium in the range of Canadian and international drinking water standards were observed. At the cellular level, no detrimental effects were noted on growth or cycling, and protective effects were observed as an increase in cell viability and an induced resistance to a large challenge dose.

  3. Intraoperative Active Bleeding in Endoscopic Surgery for Spontaneous Intracerebral Hemorrhage is Predicted by the Spot Sign.

    PubMed

    Miki, Koichi; Yagi, Kenji; Nonaka, Masani; Iwaasa, Mitsutoshi; Abe, Hiroshi; Morishita, Takashi; Arima, Hisatomi; Inoue, Tooru

    2018-05-30

    Endoscopic evacuation of hematoma (EEH) has recently been applied to treat patients with spontaneous intracerebral hemorrhage (sICH). Intraoperative active bleeding (IAB), which is occasionally observed in EEH, might lead to greater blood loss, further brain damage, and more postoperative recurrent hemorrhage. However, no definite predictor of IAB has been established. Because the spot sign is associated with other hemorrhagic complications, we aimed to evaluate whether it predicts IAB. We retrospectively assessed the incidence and risk factors of IAB, including the spot sign, in 127 sICH patients who underwent EEH within 6 hours after computed tomography angiography at our institution between June 2009 and December 2017. The study included 53 women and 74 men with an average age of 66.7 ± 11.8 years. IAB occurred in 40 (31.5%) of the 127 patients, and it was more frequent in patients with the spot sign than in patients without it (14/24 [58.3%] vs. 26/103 [25.2%]; P = 0.003). Multivariable regression analyses suggested that the spot sign was an independent predictor of IAB (odds ratio [OR], 3.02; 95% confidence interval [CI], 1.10-8.30; P = 0.03). In addition, earlier surgery gradually increased the risk of IAB, and surgery within 4 hours of onset was an independent risk factor (OR, 4.34; 95% CI, 1.12-16.9; P = 0.03, referring to postonset 8 hours or more). The spot sign and early surgery were independent predictors of IAB in EEH for sICH. In patients with sICH and spot sign, complete treatment of IAB by electrocoagulation might be important for minimizing surgical complications. Copyright © 2018 Elsevier Inc. All rights reserved.

  4. Second-Degree Interatrial Block in Hemodialysis Patients

    PubMed Central

    Enriquez, Andres; D'Amato, Anna; de Luna, Antoni Bayes; Baranchuk, Adrian

    2015-01-01

    Interatrial conduction delays manifest as a prolonged P-wave duration on surface ECG and the term interatrial block (IAB) has been coined. They are usually fixed, but cases of intermittent IAB have been described, suggesting functional conduction block at the Bachmann bundle region. We report 2 cases of patients on chronic hemodialysis therapy presenting with intermittent IAB. PMID:25755895

  5. The impact of a scheduling change on ninth grade high school performance on biology benchmark exams and the California Standards Test

    NASA Astrophysics Data System (ADS)

    Leonardi, Marcelo

    The primary purpose of this study was to examine the impact of a scheduling change from a trimester 4x4 block schedule to a modified hybrid schedule on student achievement in ninth grade biology courses. This study examined the impact of the scheduling change on student achievement through teacher created benchmark assessments in Genetics, DNA, and Evolution and on the California Standardized Test in Biology. The secondary purpose of this study examined the ninth grade biology teacher perceptions of ninth grade biology student achievement. Using a mixed methods research approach, data was collected both quantitatively and qualitatively as aligned to research questions. Quantitative methods included gathering data from departmental benchmark exams and California Standardized Test in Biology and conducting multiple analysis of covariance and analysis of covariance to determine significance differences. Qualitative methods include journal entries questions and focus group interviews. The results revealed a statistically significant increase in scores on both the DNA and Evolution benchmark exams. DNA and Evolution benchmark exams showed significant improvements from a change in scheduling format. The scheduling change was responsible for 1.5% of the increase in DNA benchmark scores and 2% of the increase in Evolution benchmark scores. The results revealed a statistically significant decrease in scores on the Genetics Benchmark exam as a result of the scheduling change. The scheduling change was responsible for 1% of the decrease in Genetics benchmark scores. The results also revealed a statistically significant increase in scores on the CST Biology exam. The scheduling change was responsible for .7% of the increase in CST Biology scores. Results of the focus group discussions indicated that all teachers preferred the modified hybrid schedule over the trimester schedule and that it improved student achievement.

  6. Chemical and Biological Sensor Standards Study

    DTIC Science & Technology

    2005-01-01

    that is utilized in lieu of Bacillus anthracis in testing biological agent sensors; both are gram positive, spore forming bacteria that have similar...for a given agent dosage is as follows: C = D r 3 f B Tη4π 3 ρ See the table for the variable designation. Using Bacillus anthracis as an example...e.g., genetic similarity, aerosol dynamics, size, shape, etc.) of the agent of interest. For example, Bacillus globigii is a widely used bacterium

  7. Attractiveness of facial averageness and symmetry in non-western cultures: in search of biologically based standards of beauty.

    PubMed

    Rhodes, G; Yoshikawa, S; Clark, A; Lee, K; McKay, R; Akamatsu, S

    2001-01-01

    Averageness and symmetry are attractive in Western faces and are good candidates for biologically based standards of beauty. A hallmark of such standards is that they are shared across cultures. We examined whether facial averageness and symmetry are attractive in non-Western cultures. Increasing the averageness of individual faces, by warping those faces towards an averaged composite of the same race and sex, increased the attractiveness of both Chinese (experiment 1) and Japanese (experiment 2) faces, for Chinese and Japanese participants, respectively. Decreasing averageness by moving the faces away from an average shape decreased attractiveness. We also manipulated the symmetry of Japanese faces by blending each original face with its mirror image to create perfectly symmetric versions. Japanese raters preferred the perfectly symmetric versions to the original faces (experiment 2). These findings show that preferences for facial averageness and symmetry are not restricted to Western cultures, consistent with the view that they are biologically based. Interestingly, it made little difference whether averageness was manipulated by using own-race or other-race averaged composites and there was no preference for own-race averaged composites over other-race or mixed-race composites (experiment 1). We discuss the implications of these results for understanding what makes average faces attractive. We also discuss some limitations of our studies, and consider other lines of converging evidence that may help determine whether preferences for average and symmetric faces are biologically based.

  8. Advanced interatrial block predicts new-onset atrial fibrillation and ischemic stroke in patients with heart failure: The "Bayes' Syndrome-HF" study.

    PubMed

    Escobar-Robledo, Luis Alberto; Bayés-de-Luna, Antoni; Lupón, Josep; Baranchuk, Adrian; Moliner, Pedro; Martínez-Sellés, Manuel; Zamora, Elisabet; de Antonio, Marta; Domingo, Mar; Cediel, Germán; Núñez, Julio; Santiago-Vacas, Evelyn; Bayés-Genís, Antoni

    2018-05-18

    Advanced interatrial block (IAB) is characterized by a prolonged (≥120 ms) and bimodal P wave in the inferior leads. The association between advanced IAB and atrial fibrillation (AF) is known as "Bayes' Syndrome", and there is scarce information about it in heart failure (HF). We examined the prevalence of IAB and whether advanced IAB could predict new-onset AF and/or stroke in HF patients. The prospective observational "Bayes' Syndrome-HF" study included consecutive outpatients with chronic HF. The primary endpoints were new-onset AF, ischemic stroke, and the composite of both. A secondary endpoint included all-cause death alone or in combination with the primary endpoint. Comprehensive multivariable Cox regression analyses were performed. Among 1050 consecutive patients, 536 (51.0%) were in sinus rhythm, 464 with a measurable P wave are the focus of this study. Two-hundred and sixty patients (56.0%) had normal atrial conduction, 95 (20.5%) partial IAB, and 109 (23.5%) advanced IAB. During a mean follow-up of 4.5 ± 2.1 years, 235 patients experienced all-cause death, new-onset AF, or stroke. In multivariable comprehensive Cox regression analyses, advanced IAB was associated with new-onset AF (HR 2.71 [1.61-4.56], P < 0.001), ischemic stroke (HR 3.02 [1.07-8.53], P = 0.04), and the composite of both (HR 2.42 [1.41-4.15], P < 0.001). In patients with HF advanced IAB predicts new-onset AF and ischemic stroke. Future studies must assess whether anticoagulant treatment in Bayes' Syndrome leads to better outcomes in HF. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Advanced interatrial block and ischemic stroke: The Atherosclerosis Risk in Communities Study.

    PubMed

    O'Neal, Wesley T; Kamel, Hooman; Zhang, Zhu-Ming; Chen, Lin Y; Alonso, Alvaro; Soliman, Elsayed Z

    2016-07-26

    Given that recent reports have suggested left atrial disease to be an independent risk factor for ischemic stroke, we sought to examine if advanced interatrial block (aIAB) is an independent stroke risk factor. We examined the association between aIAB and incident ischemic stroke in 14,716 participants (mean age 54 ± 5.8 years; 55% female; 26% black) from the Atherosclerosis Risk in Communities Study (ARIC). Cases of aIAB were identified from digital ECGs recorded during the baseline ARIC visit (1987-1989) and the first 3 follow-up study visits (1990-1992, 1993-1995, and 1996-1998). Adjudicated ischemic stroke events were ascertained through December 31, 2010. There were 266 (1.8%) participants who had evidence of aIAB. Over a median follow-up of 22 years, 916 (6.2%) ischemic stroke events were detected. The incidence rate (per 1,000 person-years) of ischemic stroke among those with aIAB (incidence rate 8.05, 95% confidence interval [CI] 5.7, 11.4) was more than twice the rate in those without aIAB (incidence rate 3.14, 95% CI 2.94, 3.35). In a multivariable Cox regression analysis adjusted for stroke risk factors and potential confounders, aIAB was associated with an increased risk of ischemic stroke (hazard ratio 1.63, 95% CI 1.13, 2.34). The results were consistent across subgroups of participants stratified by age, sex, and race. In the ARIC, aIAB was associated with incident ischemic stroke, which strengthens the hypothesis that left atrial disease should be considered an independent stroke risk factor. © 2016 American Academy of Neurology.

  10. A Strain of Bacillus sphaericus Causes Slower Development of Resistance in Culex quinquefasciatus

    PubMed Central

    Pei, Guofeng; Oliveira, Cláudia M. F.; Yuan, Zhiming; Nielsen-LeRoux, Christina; Silva-Filha, Maria Helena; Yan, Jianpin; Regis, Lêda

    2002-01-01

    Two field-collected Culex quinquefasciatus colonies were subjected to selection pressure by three strains of Bacillus sphaericus, C3-41, 2362, and IAB59, under laboratory conditions. After 13 and 18 generations of exposure to high concentrations of C3-41 and IAB59, a field-collected low-level-resistant colony developed >144,000- and 46.3-fold resistance to strains C3-41 and IAB59, respectively. A field-collected susceptible colony was selected with 2362 and IAB59 for 46 and 12 generations and attained >162,000- and 5.7-fold resistance to the two agents, respectively. The pattern of resistance evolution in mosquitoes depended on continuous selection pressure, and the stronger the selection pressure, the more quickly resistance developed. The resistant colonies obtained after selection with B. sphaericus C3-41 and 2362 showed very high levels of cross-resistance to B. sphaericus 2362 and C3-41, respectively, but they displayed only low-level cross-resistance to IAB59. On the other hand, the IAB59-selected colonies had high cross-resistance to both strains C3-41 and 2362. Additionally, the slower evolution of resistance against strain IAB59 may be explained by the presence of another larvicidal factor. This is in agreement with the nontoxicity of the cloned and purified binary toxin (Bin1) of IAB59 for 2362-resistant larvae. We also verified that all the B. sphaericus-selected colonies showed no cross-resistance to Bacillus thuringiensis subsp. israelensis, suggesting that it would be a promising alternative in managing resistance to B. sphaericus in C. quinquefasciatus larvae. PMID:12039761

  11. A IAB-Complex Iron Meteorite Containing Low-Ca Clinopyroxene: Northwest Africa 468 and its Relationship to Iodranites and Formation by Impact Melting

    NASA Technical Reports Server (NTRS)

    Rubin, Alan E.; Kallemeyn, Gregory W.; Wasson, John T.

    2002-01-01

    Northwest Africa 468 (NWA 468) is a new ungrouped, silicate-rich member of the IAB complex of nonmagmatic iron meteorites. The silicates contain relatively coarse (approximately 300 micron-size) grains of low-Ca clinopyroxene with polysynthetic twinning and inclined extinction. Low-Ca clinopyroxene is indicative of quenching from high temperatures (either from protoenstatite in a few seconds or high-temperature clinoenstatite in a few hours). It seems likely that NWA 468 formed by impact melting followed by rapid cooling to less than or equal to 660 C. After the loss of a metal-sulfide melt from the silicates, sulfide was reintroduced, either from impact-mobilized FeS or as an S2 vapor that combined with metallic Fe to produce FeS. The O-isotopic composition (delta O-17 = -1.39 %) indicates that the precursor material of NWA 468 was a metal-rich (e.g., CR) carbonaceous chondrite. Lodranites are similar in bulk chemical and O-isotopic composition to the silicates in NWA 468; the MAC 88177 lodranite (which also contains low-Ca clinopyroxene) is close in bulk chemical composition. Both NWA 468 and MAC 88177 have relatively low abundances of REE (rare earth elements) and plagiophile elements. Siderophiles in the metal-rich areas of NWA 468 are similar to those in the MAC 88177 whole rock; both samples contain low Ir and relatively high Fe, Cu and Se. Most unweathered lodranites contain approximately 20 - 38 wt. % metallic Fe-Ni. These rocks may have formed in an analogous manner to NWA 468 (i.e., by impact melting of metal-rich carbonaceous-chondrite precursors) but with less separation of metal-rich melts from silicates.

  12. The International Standard for Aureomycin

    PubMed Central

    Humphrey, J. H.; Lightbown, J. W.; Mussett, M. V.; Perry, W. L. M.

    1953-01-01

    In 1950, the Department of Biological Standards, National Institute for Medical Research, London, was authorized by the WHO Expert Committee on Biological Standardization to proceed with the establishment of an International Standard for Aureomycin. A 100-g batch of aureomycin was obtained and was compared with the Standard Preparation of Aureomycin of the United States Food and Drug Administration (FDA) in a collaborative assay in which six laboratories in five countries participated. In all, 30 assays were carried out; 26 of these were done by biological methods, using Sarcina lutea, Bacillus pumilus, Staphylococcus aureus, or Bacillus cereus, and the remaining four by physicochemical methods. The results were subjected to standard methods of analysis, and the overall weighted mean potency (calculated from the biological assays only) was 1.0139, with limits of error of 99.5% to 100.5%. Since the International Standard is 1.39% more potent than the FDA Standard Preparation, it is probable that the latter contains a small amount of inert material; it is also possible that the International Standard itself is not 100% pure. For most practical purposes, however, both preparations may be regarded as substantially pure, and it is considered that to alter the present practice of quoting aureomycin dosage in metric units of weight would be inadvisable. Nevertheless, since the International Standard may not be a pure substance, a unit notation—for use where required in bioassays—is desirable, and the International Unit of Aureomycin has therefore been defined as the activity contained in one microgram of the International Standard. PMID:13141137

  13. Ictal affective symptoms in temporal lobe epilepsy are related to gender and age.

    PubMed

    Toth, Vanda; Fogarasi, Andras; Karadi, Kazmer; Kovacs, Norbert; Ebner, Alois; Janszky, Jozsef

    2010-07-01

    We systematically analyzed the video-recorded and patient-reported, as well as positive and negative ictal affective symptoms (IAS) in temporal lobe epilepsy (TLE). Our aim was to assess (1) frequency, (2) gender effect, (3) lateralizing significance, (4) localizing value, and (5) prognostic significance in epilepsy surgery of IAS in patients with video-registered seizures. We reviewed ictal video recordings of 184 patients (99 women, aged 16-63). All patients had surgery for intractable TLE with video-recorded complex partial seizures (CPS) due to temporal lobe lesions visualized by high-resolution magnetic resonance imaging (MRI). Affective auras (AAs) were categorized into two groups: positive or negative. We registered AAs in 18% of patients: positive in 3%, negative in 15%. We saw ictal affective behavior (IAB) in 22% of patients; 10% had positive, whereas 14% had negative IAB. Two patients had both positive and negative IAB. AAs showed an association with IAB in case of fear expression versus fear auras (p = 0.018). IAB, especially negative IAB, occurred more often in women than in men. Patients with negative IAB were younger than others. We could not demonstrate an association between IAS and the localization, lateralization, or hemispheric dominance. Surgical outcome did not associate with IAS. Patient-reported and video-recorded negative-but not positive-affective signs are related to each other. Video-recorded negative AAs occur more often in women and young patients.

  14. Physical and biological properties of U. S. standard endotoxin EC after exposure to ionizing radiation

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

    Csako, G.; Elin, R.J.; Hochstein, H.D.

    Techniques that reduce the toxicity of bacterial endotoxins are useful for studying the relationship between structure and biological activity. We used ionizing radiation to detoxify a highly refined endotoxin preparation. U.S. standard endotoxin EC. Dose-dependent changes occurred by exposure to /sup 60/Co-radiation in the physical properties and biological activities of the endotoxin. Sodium dodecyl sulfate-polyacrylamide slab gel electrophoresis showed gradual loss of the polysaccharide components (O-side chain and R-core) from the endotoxin molecules. In contrast, although endotoxin revealed a complex absorption pattern in the UV range, radiation treatment failed to modify that pattern. Dose-related destruction of the primary toxic component,more » lipid A, was suggested by the results of activity tests: both the pyrogenicity and limulus reactivity of the endotoxin were destroyed by increasing doses of radiation. The results indicate that the detoxification is probably due to multiple effects of the ionizing radiation on bacterial lipopolysaccharides, and the action involves (i) the destruction of polysaccharide moieties and possibly (ii) the alteration of lipid A component of the endotoxin molecule.« less

  15. P-wave and interatrial block: New predictor for atrial high rate episodes in patients with cardiac implantable electronic devices.

    PubMed

    Rubio Campal, José M; Benezet-Mazuecos, Juan; Iglesias Bravo, José Antonio; Sánchez Borque, Pepa; Miracle Blanco, Ángel; de la Vieja Alarcón, Juan José; Martínez Mariscal, Jaime; Baranchuk, Adrian M; Farré Muncharaz, Jerónimo

    2018-01-12

    The presence of interatrial block (IAB) is associated with the development of atrial fibrillation (AF). The aim of this study was to determine whether P-wave duration and presence of IAB before the implantation of a cardiac implantable electronic device (CIED) are associated with the presence of atrial high rate episodes (AHRE), during long-term follow-up. 380 patients (57% men; 75 ± 10 years) were included. IAB was defined according to the International Consensus Criteria. AHRE was defined as an episode of atrial rate ≥225 beats/min with a minimum duration of 5 minutes. Documented paroxysmal AF before the implantation was present in 24% of the patients; 80% had hypertension and 32% structural heart disease. Mean P-wave duration was 123 ± 23 ms, and 39% of the patients had IAB (32% partial, 7% advanced). After a mean follow-up of 18 ± 12 months, 33% of the patients presented AHRE. Patients with AHRE had a P-wave duration significantly longer (130 ± 24 ms vs 119 ± 21 ms; P < 0.001) and a greater prevalence of IAB (53% vs 32%; P < 0.001). In a multivariate analysis, predictors of AHRE were: IAB (odds ratio [OR] 2.1; 95% confidence interval [CI] [1.3-3.4], P < 0.001) and previous paroxysmal AF (OR 2.6; 95% CI [1.5-4.3], P < 0.001). In patients without previous AF, the presence of IAB was also a significant predictor of AHRE (OR 3.1; 95% CI [1.8-5.5], P < 0.001). IAB is a strong predictor of AHRE in patients with CIED. This finding is independent of the presence of prior paroxysmal AF. © 2018 Wiley Periodicals, Inc.

  16. Synthetic Biology Open Language (SBOL) Version 2.0.0.

    PubMed

    Bartley, Bryan; Beal, Jacob; Clancy, Kevin; Misirli, Goksel; Roehner, Nicholas; Oberortner, Ernst; Pocock, Matthew; Bissell, Michael; Madsen, Curtis; Nguyen, Tramy; Zhang, Zhen; Gennari, John H; Myers, Chris; Wipat, Anil; Sauro, Herbert

    2015-09-04

    Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.0 of SBOL, introducing a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. The standard has been designed to support the explicit and unambiguous description of biological designs by means of a well defined data model. The standard also includes rules and best practices on how to use this data model and populate it with relevant design details. The publication of this specification is intended to make these capabilities more widely accessible to potential developers and users in the synthetic biology community and beyond.

  17. Magnetic Mineralogy of Troilite-Inclusions and their Fe-Ni Host Alloys in IAB Iron Meteorites

    NASA Astrophysics Data System (ADS)

    Kontny, A. M.; Kramar, U.; Luecke, W.

    2011-12-01

    Iron-nickel meteorites often contain isolated, mostly rounded troilite nodules enclosed in a bulk of Fe-Ni alloy. As sulfur has a low solubility in metal, it is excluded from the crystallization of metal during cooling. Therefore troilite nodules are interpreted to be trapped droplets of residual sulfur-enriched melts. Microscopic examinations of the interface (mm-range) between troilite inclusions and Fe-Ni alloy yield clear mineralogical differences compared to the troilite inclusion. Such rims around troilite nodules seem to occur exclusively in Fe-Ni meteorites with slow cooling rates, and therefore might provide interesting clues on segregation, fractional crystallization and reequilibration processes between the Fe-Ni alloy and the sulfide phases. These interfaces however are also highly sensitive to terrestrial weathering. We present microscopic observations in combination with temperature-dependent magnetic susceptibility (k-T curves) in order to identify the magnetic mineralogy of the Morasko (Poland) and Coahuila (Mexico) meteorites, which both geochemically belong to the non-magmatic IAB or IIICD group. In the k-T curves both, rim and troilite nodule are characterized by Curie temperatures (TC) that can be related to magnetite, daubreelite (FeCr2O4), Fe-hydroxide and sometimes cohenite. Therefore the interface seems to be geochemically more similar to the troilite nodule than the Fe-Ni alloy. Optical microscopy in combination with the ferrofluid method revealed complex microstructures of intergrown magnetic (TC = 780-785 °C) and non-magnetic phases in the Fe-Ni alloy, which differ in their Ni-concentration. Towards the rim of the troilite nodule the concentration of magnetic cohenite ((Fe,Ni)3C) and especially schreibersite ((Fe,Ni)3P), which are both intergrown with the metal, increases. Cohenite is easily identified microscopically by a very characteristic stripe-like magnetic domain structure and it shows a TC at about 200 °C. The carbon-rich, dark

  18. [Biogeography: geography or biology?].

    PubMed

    Kafanov, A I

    2009-01-01

    General biogeography is an interdisciplinary science, which combines geographic and biological aspects constituting two distinct research fields: biological geography and geographic biology. These fields differ in the nature of their objects of study, employ different methods and represent Earth sciences and biological sciences, respectively. It is suggested therefore that the classification codes for research fields and the state professional education standard should be revised.

  19. Collaborative study for the establishment of the WHO 3(rd) International Standard for Endotoxin, the Ph. Eur. endotoxin biological reference preparation batch 5 and the USP Reference Standard for Endotoxin Lot H0K354.

    PubMed

    Findlay, L; Desai, T; Heath, A; Poole, S; Crivellone, M; Hauck, W; Ambrose, M; Morris, T; Daas, A; Rautmann, G; Buchheit, K H; Spieser, J M; Terao, E

    2015-01-01

    An international collaborative study was organised jointly by the World Health Organization (WHO)/National Institute for Biological Standards and Control (NIBSC), the United States Pharmacopeia (USP) and the European Directorate for the Quality of Medicines & HealthCare (EDQM/Council of Europe) for the establishment of harmonised replacement endotoxin standards for these 3 organisations. Thirty-five laboratories worldwide, including Official Medicines Control Laboratories (OMCLs) and manufacturers enrolled in the study. Three candidate preparations (10/178, 10/190 and 10/196) were produced with the same material and same formulation as the current reference standards with the objective of generating a new (3(rd)) International Standard (IS) with the same potency (10 000 IU/vial) as the current (2(nd)) IS, as well as new European Pharmacopoeia (Ph. Eur.). and USP standards. The suitability of the candidate preparations to act as the reference standard in assays for endotoxin performed according to compendial methods was evaluated. Their potency was calibrated against the WHO 2(nd) IS for Endotoxin (94/580). Gelation and photometric methods produced similar results for each of the candidate preparations. The overall potency estimates for the 3 batches were comparable. Given the intrinsic assay precision, the observed differences between the batches may be considered unimportant for the intended use of these materials. Overall, these results were in line with those generated for the establishment of the current preparations of reference standards. Accelerated degradation testing of vials stored at elevated temperatures supported the long-term stability of the 3 candidate preparations. It was agreed between the 3 organisations that batch 10/178 be shared between WHO and EDQM and that batches 10/190 and 10/196 be allocated to USP, with a common assigned value of 10 000 IU/vial. This value maintains the continuity of the global harmonisation of reference materials and

  20. Biological monitoring and standard setting in the USA: a critical appraisal.

    PubMed

    Rappaport, S M

    1995-05-01

    Occupational exposure limits (OELs) issued in the US by the Occupational Safety and Health Administration (OSHA) require measurements of toxic substances in air rather than in biological samples. Most of OSHA's limits were adopted from the 1968 list of the American Conference of Governmental Industrial Hygienists (ACGIH) Threshold Limit Values (TLVs). Although there are no formal requirements to monitor exposures to these substances, it is implicit in the standards that air sampling will be performed. Of the 13 OELs which OSHA has set de novo, 2 (i.e., those for lead and cadmium) require biomonitoring after air sampling has identified the heavily exposed workers. OSHA appears to value biomonitoring in some circumstances but has apparently not found a consistent rationale for using biomarkers to set and enforce its standards. This paper discusses 2 valuable features of biomarkers which should be exploited by OSHA to further its regulatory agenda. The first relates to controversies associated with dose rate which have come into play in setting short-term exposure limits (STELs) when acute effects do not provide the necessary justification. OSHA has not provided evidence that its STELs are needed to reduce the risks of disease (as in the cases of benzene and ethylene oxide). By investigating the exposure-biomarker relationship, it is possible to determine whether the rate of exposure has any influence on the uptake and elimination of toxic substances and, therefore, whether STELs is needed. This is illustrated with data from 2 studies on styrene exposure. The second feature concerns biomonitoring as the primary means of exposure assessment in situations where the biomarker is accumulated over months or years (as in the cases of lead and cadmium). Using data from the lead-battery industry, it is shown that 'correct' compliance decisions are more likely to arise from evaluation of blood lead measurements than from traditional air monitoring.

  1. Inbreeding Ratio and Genetic Relationships among Strains of the Western Clawed Frog, Xenopus tropicalis

    PubMed Central

    Igawa, Takeshi; Watanabe, Ai; Suzuki, Atsushi; Kashiwagi, Akihiko; Kashiwagi, Keiko; Noble, Anna; Guille, Matt; Simpson, David E.; Horb, Marko E.; Fujii, Tamotsu; Sumida, Masayuki

    2015-01-01

    The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts. PMID:26222540

  2. Intellectual property rights, standards and data exchange in systems biology: Reflections from the IP Expert Meeting at the University of Luxembourg, 8-9 October 2015, ERASysAPP - ERA-Net for Systems Biology Applications.

    PubMed

    van Zimmeren, Esther; Rutz, Berthold; Minssen, Timo

    2016-12-01

    Intellectual property rights (IPRs) have become a key concern for researchers and industry in basically all high-tech sectors. IPRs regularly figure prominently in scientific journals and at scientific conferences and lead to dedicated workshops to increase the awareness and "IPR savviness" of scientists. In 2015, Biotechnology Journal published a report from an expert meeting on "Synthetic Biology & Intellectual Property Rights" organized by the Danish Agency for Science, Technology and Innovation sponsored by the European Research Area Network (ERA-Net) in Synthetic Biology (ERASynBio), in which we provided a number of recommendations for a variety of stakeholders [1]. The current article offers some deeper reflections about the interface between IPRs, standards and data exchange in systems biology (SysBio) resulting from an Expert Meeting funded by another ERA-Net, ERASysAPP. The meeting brought together experts and stakeholders (e.g. scientists, company representatives, officials from public funding organizations) in SysBio from different European countries. Despite the different profiles of the stakeholders at the meeting and the variety of interests, many concerns and opinions were shared. In case particular views were expressed by a specific type of stakeholder, this will be explicitly mentioned in the text. In this article, we explore a number of particularly relevant issues that were discussed at the meeting and offer some recommendations. SysBio involves the study of biological systems at a so-called systems level. This is not a new concept in the life sciences - many former approaches in physiology, enzymology and other scientific disciplines have already taken a systemic view of selected biological subjects. Yet, SysBio has gained strong interest within the past 10 to 15 years. One predominant reason and a critical prerequisite for this success story being that the relevant scientific methodologies and research tools have become far more powerful and

  3. Thermal response of integral abutment bridges with mechanically stabilized earth walls.

    DOT National Transportation Integrated Search

    2013-03-01

    The advantages of integral abutment bridges (IABs) include reduced maintenance costs and increased useful life spans. : However, improved procedures are necessary to account for the impacts of cyclic thermal displacements on IAB components, : includi...

  4. Standard seasons

    NASA Astrophysics Data System (ADS)

    Tuller, Stanton E.

    1990-09-01

    A renewed interest in climatic definitions of the seasons has surfaced in recent years. However, people usually associate biological phenomena and climate with the seasons. Standard seasons, defined as the periods of the year when the climate is within specified bounds, can be delimited in terms of biological phenomena if climatic thresholds are known for the groups of interest. By focusing attention on the time variation they illustrate climatic variation from a different perspective. An example of the type of information provided by standard seasons on the regional scale is given using human thermal standard seasons in the Pacific Basin. The latitudinal control of climate is indicated by the length of the hot and cold seasons. The moderation of maritime climates is seen in the shortness and slower rate of advance and retreat of the hot and cold seasons, and the extended length of the neutral (or spring) season. Standard seasons have widespread application in indicating the times of the year favorable or unfavorable for particular populations or activities. Bioclimatologists can contribute to season definition by expanding the range of information on climate-organism interaction on which seasonal thresholds are based and may find standard seasons useful in presenting the results of many types of investigations.

  5. Synthetic biology: evolution or revolution? A co-founder's perspective.

    PubMed

    Gardner, Timothy S; Hawkins, Kristy

    2013-12-01

    In this article, we relate the story of Synthetic Biology's birth, from the perspective of a co-founder, and consider its original premise--that standardization and abstraction of biological components will unlock the full potential of biological engineering. The standardization ideas of Synthetic Biology emerged in the late 1990s from a convergence of research on cellular computing, and were motivated by an array of applications from tissue regeneration to bio-sensing to mathematical programming. As the definition of Synthetic Biology has grown to be synonymous with Biological Engineering and Biotechnology, the field has lost sight of the fact that its founding premise has not yet been validated. While the value of standardization has been proven in many other engineering disciplines, none of them involve self-replicating systems. The engineering of self-replicating systems will likely benefit from standardization, and also by embracing the forces of evolution that inexorably shape such systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Nature versus design: synthetic biology or how to build a biological non-machine.

    PubMed

    Porcar, M; Peretó, J

    2016-04-18

    The engineering ideal of synthetic biology presupposes that organisms are composed of standard, interchangeable parts with a predictive behaviour. In one word, organisms are literally recognized as machines. Yet living objects are the result of evolutionary processes without any purposiveness, not of a design by external agents. Biological components show massive overlapping and functional degeneracy, standard-free complexity, intrinsic variation and context dependent performances. However, although organisms are not full-fledged machines, synthetic biologists may still be eager for machine-like behaviours from artificially modified biosystems.

  7. Inquiry-based laboratory investigations and student performance on standardized tests in biological science

    NASA Astrophysics Data System (ADS)

    Patke, Usha

    Achievement data from the 3rd International Mathematics and Sciences Study and Program for International Student Assessment in science have indicated that Black students from economically disadvantaged families underachieve at alarming rates in comparison to White and economically advantaged peer groups. The study site was a predominately Black, urban school district experiencing underachievement. The purpose of this correlational study was to examine the relationship between students' use of inquiry-based laboratory investigations and their performance on the Biology End of Course Test, as well as to examine the relationship while partialling out the effects of student gender. Constructivist theory formed the theoretical foundation of the study. Students' perceived levels of experience with inquiry-based laboratory investigations were measured using the Laboratory Program Variable Inventory (LPVI) survey. LPVI scores of 256 students were correlated with test scores and were examined by student gender. The Pearson correlation coefficient revealed a small direct correlation between students' experience in inquiry-based laboratory investigation classes and standardized test scores on the Biology EOCT. A partial correlational analysis indicated that the correlation remained after controlling for gender. This study may prompt a change from teacher-centered to student-centered pedagogy at the local site in order to increase academic achievement for all students. The results of this study may also influence administrators and policy makers to initiate local, state, or nationwide curricular development. A change in curriculum may promote social change as students become more competent, and more able, to succeed in life beyond secondary school.

  8. Soil-structure interaction studies for understanding the behavior of integral abutment bridges.

    DOT National Transportation Integrated Search

    2012-03-01

    Integral Abutment Bridges (IAB) are bridges without any joints within the bridge deck or between the : superstructure and the abutments. An IAB provides many advantages during construction and maintenance of : a bridge. Soil-structure interactions at...

  9. Integral abutment bridges under thermal loading : field monitoring and analysis.

    DOT National Transportation Integrated Search

    2017-08-01

    Integral abutment bridges (IABs) have gained popularity throughout the United States due to their low construction and maintenance costs. Previous research on IABs has been heavily focused on substructure performance, leaving a need for better unders...

  10. Integral abutment bridges under thermal loading : numerical simulations and parametric study.

    DOT National Transportation Integrated Search

    2016-06-01

    Integral abutment bridges (IABs) have become of interest due to their decreased construction and maintenance costs in : comparison to conventional jointed bridges. Most prior IAB research was related to substructure behavior, and, as a result, most :...

  11. Elimination of tumor by CD47/PD-L1 dual-targeting fusion protein that engages innate and adaptive immune responses.

    PubMed

    Liu, Boning; Guo, Huaizu; Xu, Jin; Qin, Ting; Guo, Qingcheng; Gu, Nana; Zhang, Dapeng; Qian, Weizhu; Dai, Jianxin; Hou, Sheng; Wang, Hao; Guo, Yajun

    The host immune system generally serves as a barrier against tumor formation. Programmed death-ligand 1 (PD-L1) is a critical "don't find me" signal to the adaptive immune system, whereas CD47 transmits an anti-phagocytic signal, known as the "don't eat me" signal, to the innate immune system. These and similar immune checkpoints are often overexpressed on human tumors. Thus, dual targeting both innate and adaptive immune checkpoints would likely maximize anti-tumor therapeutic effect and elicit more durable responses. Herein, based on the variable region of atezolizumab and consensus variant 1 (CV1) monomer, we constructed a dual-targeting fusion protein targeting both CD47 and PD-L1 using "Knobs-into-holes" technology, denoted as IAB. It was effective in inducing phagocytosis of tumor cells, stimulating T-cell activation and mediating antibody-dependent cell-mediated cytotoxicity in vitro. No obvious sign of hematological toxicity was observed in mice administered IAB at a dose of 100 mg/kg, and IAB exhibited potent antitumor activity in an immune-competent mouse model of MC38. Additionally, the anti-tumor effect of IAB was impaired by anti-CD8 antibody or clodronate liposomes, which implied that both CD8+ T cells and macrophages were required for the anti-tumor efficacy of IAB and IAB plays an essential role in the engagement of innate and adaptive immune responses. Collectively, these results demonstrate the capacity of an elicited endogenous immune response against tumors and elucidate essential characteristics of synergistic innate and adaptive immune response, and indicate dual blockade of CD47 and PD-L1 by IAB may be a synergistic therapy that activates both innate and adaptive immune response against tumors.

  12. Biological Clocks & Circadian Rhythms

    ERIC Educational Resources Information Center

    Robertson, Laura; Jones, M. Gail

    2009-01-01

    The study of biological clocks and circadian rhythms is an excellent way to address the inquiry strand in the National Science Education Standards (NSES) (NRC 1996). Students can study these everyday phenomena by designing experiments, gathering and analyzing data, and generating new experiments. As students explore biological clocks and circadian…

  13. Influence of Pichia pastoris cellular material on polymerase chain reaction performance as a synthetic biology standard for genome monitoring.

    PubMed

    Templar, Alexander; Woodhouse, Stefan; Keshavarz-Moore, Eli; Nesbeth, Darren N

    2016-08-01

    Advances in synthetic genomics are now well underway in yeasts due to the low cost of synthetic DNA. These new capabilities also bring greater need for quantitating the presence, loss and rearrangement of loci within synthetic yeast genomes. Methods for achieving this will ideally; i) be robust to industrial settings, ii) adhere to a global standard and iii) be sufficiently rapid to enable at-line monitoring during cell growth. The methylotrophic yeast Pichia pastoris (P. pastoris) is increasingly used for industrial production of biotherapeutic proteins so we sought to answer the following questions for this particular yeast species. Is time-consuming DNA purification necessary to obtain accurate end-point polymerase chain reaction (e-pPCR) and quantitative PCR (qPCR) data? Can the novel linear regression of efficiency qPCR method (LRE qPCR), which has properties desirable in a synthetic biology standard, match the accuracy of conventional qPCR? Does cell cultivation scale influence PCR performance? To answer these questions we performed e-pPCR and qPCR in the presence and absence of cellular material disrupted by a mild 30s sonication procedure. The e-pPCR limit of detection (LOD) for a genomic target locus was 50pg (4.91×10(3) copies) of purified genomic DNA (gDNA) but the presence of cellular material reduced this sensitivity sixfold to 300pg gDNA (2.95×10(4) copies). LRE qPCR matched the accuracy of a conventional standard curve qPCR method. The presence of material from bioreactor cultivation of up to OD600=80 did not significantly compromise the accuracy of LRE qPCR. We conclude that a simple and rapid cell disruption step is sufficient to render P. pastoris samples of up to OD600=80 amenable to analysis using LRE qPCR which we propose as a synthetic biology standard. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  14. Biology Curriculum Support Document.

    ERIC Educational Resources Information Center

    North Carolina Dept. of Public Instruction, Raleigh.

    This biology curriculum supplement includes the North Carolina Standard Course of Study Goals, helpful resources, and suggested activities supported by inquiry-based laboratory activities. Contents include a detailed description of content which provides the goals and standards being sough), a materials list for inquiry support labs and…

  15. Calculating life? Duelling discourses in interdisciplinary systems biology.

    PubMed

    Calvert, Jane; Fujimura, Joan H

    2011-06-01

    A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences. Copyright © 2010 Elsevier Ltd. All rights reserved.

  16. Assessing Ecological Impacts of Shrimp and Sewage Effluent: Biological Indicators with Standard Water Quality Analyses

    NASA Astrophysics Data System (ADS)

    Jones, A. B.; O'Donohue, M. J.; Udy, J.; Dennison, W. C.

    2001-01-01

    Despite evidence linking shrimp farming to several cases of environmental degradation, there remains a lack of ecologically meaningful information about the impacts of effluent on receiving waters. The aim of this study was to determine the biological impact of shrimp farm effluent, and to compare and distinguish its impacts from treated sewage effluent. Analyses included standard water quality/sediment parameters, as well as biological indicators including tissue nitrogen (N) content, stable isotope ratio of nitrogen (δ 15N), and amino acid composition of inhabitant seagrasses, mangroves and macroalgae. The study area consisted of two tidal creeks, one receiving effluent from a sewage treatment plant and the other from an intensive shrimp farm. The creeks discharged into the western side of Moreton Bay, a sub-tropical coastal embayment on the east coast of Australia. Characterization of water quality revealed significant differences between the creeks, and with unimpacted eastern Moreton Bay. The sewage creek had higher concentrations of dissolved nutrients (predominantly NO-3/NO-2 and PO3-4, compared to NH+4 in the shrimp creek). In contrast, the shrimp creek was more turbid and had higher phytoplankton productivity. Beyond 750 m from the creek mouths, water quality parameters were indistinguishable from eastern Moreton Bay values. Biological indicators detected significant impacts up to 4 km beyond the creek mouths (reference site). Elevated plant δ 15N values ranged from 10·4-19·6‰ at the site of sewage discharge to 2·9-4·5‰ at the reference site. The free amino acid concentration and composition of seagrass and macroalgae was used to distinguish between the uptake of sewage and shrimp derived N. Proline (seagrass) and serine (macroalgae) were high in sewage impacted plants and glutamine (seagrass) and alanine (macroalgae) were high in plants impacted by shrimp effluent. The δ 15N isotopic signatures and free amino acid composition of inhabitant

  17. Internet addictive behavior in adolescence: a cross-sectional study in seven European countries.

    PubMed

    Tsitsika, Artemis; Janikian, Mari; Schoenmakers, Tim M; Tzavela, Eleni C; Olafsson, Kjartan; Wójcik, Szymon; Macarie, George Florian; Tzavara, Chara; Richardson, Clive

    2014-08-01

    A cross-sectional school-based survey study (N=13,284; 53% females; mean age 15.8±0.7) of 14-17-year-old adolescents was conducted in seven European countries (Greece, Spain, Poland, Germany, Romania, the Netherlands, and Iceland). The aim of the study was to investigate the prevalence of Internet addictive behavior (IAB) and related psychosocial characteristics among adolescents in the participating countries. In the study, we distinguish two problematic groups: adolescents with IAB, characterized by a loss of control over their Internet use, and adolescents "at risk for IAB," showing fewer or weaker symptoms of IAB. The two groups combined form a group of adolescents with dysfunctional Internet behavior (DIB). About 1% of adolescents exhibited IAB and an additional 12.7% were at risk for IAB; thus, in total, 13.9% displayed DIB. The prevalence of DIB was significantly higher among boys than among girls (15.2% vs. 12.7%, p<0.001) and varied widely between countries, from 7.9% in Iceland to 22.8% in Spain. Frequent use of specific online activities (e.g., gambling, social networking, gaming) at least 6 days/week was associated with greater probability of displaying DIB. Multiple logistic regression analysis indicated that DIB was more frequent among adolescents with a lower educational level of the parents, earlier age at first use of the Internet, and greater use of social networking sites and gaming sites. Multiple linear regression analysis showed that externalizing (i.e., behavioral) and internalizing (i.e., emotional) problems were associated with the presence of DIB.

  18. Photometric redshifts for the CFHTLS T0004 deep and wide fields

    NASA Astrophysics Data System (ADS)

    Coupon, J.; Ilbert, O.; Kilbinger, M.; McCracken, H. J.; Mellier, Y.; Arnouts, S.; Bertin, E.; Hudelot, P.; Schultheis, M.; Le Fèvre, O.; Le Brun, V.; Guzzo, L.; Bardelli, S.; Zucca, E.; Bolzonella, M.; Garilli, B.; Zamorani, G.; Zanichelli, A.; Tresse, L.; Aussel, H.

    2009-06-01

    Aims: We compute photometric redshifts in the fourth public release of the Canada-France-Hawaii Telescope Legacy Survey. This unique multi-colour catalogue comprises u^*, g', r', i', z' photometry in four deep fields of 1 deg2 each and 35 deg2 distributed over three wide fields. Methods: We used a template-fitting method to compute photometric redshifts calibrated with a large catalogue of 16 983 high-quality spectroscopic redshifts from the VVDS-F02, VVDS-F22, DEEP2, and the zCOSMOS surveys. The method includes correction of systematic offsets, template adaptation, and the use of priors. We also separated stars from galaxies using both size and colour information. Results: Comparing with galaxy spectroscopic redshifts, we find a photometric redshift dispersion, σΔ z/(1+z_s), of 0.028-0.30 and an outlier rate, |Δ z| ≥ 0.15× (1+z_s), of 3-4% in the deep field at i'_AB < 24. In the wide fields, we find a dispersion of 0.037-0.039 and an outlier rate of 3-4% at i'_AB < 22.5. Beyond i'_AB = 22.5 in the wide fields the number of outliers rises from 5% to 10% at i'_AB < 23 and i'_AB < 24, respectively. For the wide sample the systematic redshift bias stays below 1% to i'_AB < 22.5, whereas we find no significant bias in the deep fields. We investigated the effect of tile-to-tile photometric variations and demonstrated that the accuracy of our photometric redshifts is reduced by at most 21%. Application of our star-galaxy classifier reduced the contamination by stars in our catalogues from 60% to 8% at i'_AB < 22.5 in our field with the highest stellar density while keeping a complete galaxy sample. Our CFHTLS T0004 photometric redshifts are distributed to the community. Our release includes 592891 (i'_AB < 22.5) and 244701 (i'_AB < 24) reliable galaxy photometric redshifts in the wide and deep fields, respectively. Based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and CEA/DAPNIA, at the Canada-France-Hawaii Telescope (CFHT) which is

  19. The Second International Standard for Penicillin*

    PubMed Central

    Humphrey, J. H.; Mussett, M. V.; Perry, W. L. M.

    1953-01-01

    In 1950 the Department of Biological Standards, National Institute for Medical Research, London, was authorized by the WHO Expert Committee on Biological Standardization to prepare the Second International Standard for Penicillin. A single batch of specially recrystallized sodium penicillin G was obtained and 11 laboratories in seven different countries were requested to take part in its collaborative assay. 112 assays were carried out, of which 101 were done by cup-plate methods using either Staphylococcus aureus or Bacillus subtilis. The results were subjected to standard methods of analysis, on the basis of which the authors define the Second International Standard for Penicillin as containing 1,670 International Units (IU) per mg, with limits of error (P = 0.05) of 1,666-1,674 IU/mg. The International Unit is therefore redefined as the activity contained in 0.0005988 mg of the Second International Standard for Penicillin. PMID:13082387

  20. The effect of genetic variation of the serotonin 1B receptor gene on impulsive aggressive behavior and suicide.

    PubMed

    Zouk, Hana; McGirr, Alexander; Lebel, Véronique; Benkelfat, Chawky; Rouleau, Guy; Turecki, Gustavo

    2007-12-05

    Impulsive-aggressive behaviors (IABs) are regarded as possible suicide intermediate phenotypes, mediating the relationship between genes and suicide outcome. In this study, we aimed to investigate the putative relationship between genetic variation at the 5-HT1B receptor gene, which in animal models is involved in impulse-aggression control, IABs, and suicide risk. We investigated the relationship of variation at five 5-HT1B loci and IAB measures in a sample of 696 subjects, including 338 individuals who died by suicide and 358 normal epidemiological controls. We found that variation at the 5-HT1B promoter A-161T locus had a significant effect on levels of IABs, as measured by the Buss-Durkee Hostility Inventory (BDHI). Suicides also differed from controls in distribution of variants at this locus. The A-161T locus, which seems to impact 5-HT1B transcription, could play a role in suicide predisposition by means of mediating impulsive-aggressive behaviors. 2007 Wiley-Liss, Inc.

  1. Reputation-based collaborative network biology.

    PubMed

    Binder, Jean; Boue, Stephanie; Di Fabio, Anselmo; Fields, R Brett; Hayes, William; Hoeng, Julia; Park, Jennifer S; Peitsch, Manuel C

    2015-01-01

    A pilot reputation-based collaborative network biology platform, Bionet, was developed for use in the sbv IMPROVER Network Verification Challenge to verify and enhance previously developed networks describing key aspects of lung biology. Bionet was successful in capturing a more comprehensive view of the biology associated with each network using the collective intelligence and knowledge of the crowd. One key learning point from the pilot was that using a standardized biological knowledge representation language such as BEL is critical to the success of a collaborative network biology platform. Overall, Bionet demonstrated that this approach to collaborative network biology is highly viable. Improving this platform for de novo creation of biological networks and network curation with the suggested enhancements for scalability will serve both academic and industry systems biology communities.

  2. A Test of the Relationship between Reading Ability & Standardized Biology Assessment Scores

    ERIC Educational Resources Information Center

    Allen, Denise A.

    2014-01-01

    Little empirical evidence suggested that independent reading abilities of students enrolled in biology predicted their performance on the Biology I Graduation End-of-Course Assessment (ECA). An archival study was conducted at one Indiana urban public high school in Indianapolis, Indiana, by examining existing educational assessment data to test…

  3. Integrating biological redesign: where synthetic biology came from and where it needs to go.

    PubMed

    Way, Jeffrey C; Collins, James J; Keasling, Jay D; Silver, Pamela A

    2014-03-27

    Synthetic biology seeks to extend approaches from engineering and computation to redesign of biology, with goals such as generating new chemicals, improving human health, and addressing environmental issues. Early on, several guiding principles of synthetic biology were articulated, including design according to specification, separation of design from fabrication, use of standardized biological parts and organisms, and abstraction. We review the utility of these principles over the past decade in light of the field's accomplishments in building complex systems based on microbial transcription and metabolism and describe the progress in mammalian cell engineering. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. An Interactive Attention Board: Improving the Attention of Individuals with Autism and Mental Retardation

    ERIC Educational Resources Information Center

    Sahin, Yasar Guneri; Cimen, Fatih Mehmet

    2011-01-01

    This paper presents a tool named "Interactive Attention Board" (IAB) and an associated software named "Interactive Attention Boards Software" (IABS) for individuals with Mental Retardation and Autism. The proposed system is based on several theories such as perception and learning theories, and it is intended to improve hand-eye coordination and…

  5. Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

    PubMed

    Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

    2015-08-21

    In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

  6. American College Biology and Zoology Course Requirements: A de facto Standardized Curriculum.

    ERIC Educational Resources Information Center

    Heppner, Frank; And Others

    Without a formal mechanism to produce consensus, American colleges generally have come to agree on what constitutes an appropriate set of course requirements for Biology and Zoology majors. This report describes a survey of American four-year colleges and universities offering biology and/or zoology degrees. Questionnaires were sent to 741 biology…

  7. Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks.

    PubMed

    Agapakis, Christina M; Silver, Pamela A

    2009-07-01

    Synthetic biology has been used to describe many biological endeavors over the past thirty years--from designing enzymes and in vitro systems, to manipulating existing metabolisms and gene expression, to creating entirely synthetic replicating life forms. What separates the current incarnation of synthetic biology from the recombinant DNA technology or metabolic engineering of the past is an emphasis on principles from engineering such as modularity, standardization, and rigorously predictive models. As such, synthetic biology represents a new paradigm for learning about and using biological molecules and data, with applications in basic science, biotechnology, and medicine. This review covers the canonical examples as well as some recent advances in synthetic biology in terms of what we know and what we can learn about the networks underlying biology, and how this endeavor may shape our understanding of living systems.

  8. Rabies vaccine standards: comparison of the 5th and 6th WHO international reference standards to the USDA veterinary reference standard.

    PubMed

    Hermann, J; Fry, A; Reising, M; Patterson, P; Siev, D; Gatewood, D

    2012-11-06

    Ensuring rabies vaccines are potent and effective is paramount in preventing transmission of this deadly disease and safeguarding public health. Efficacy of human and veterinary vaccines is ensured by evaluating relative potency estimates of the vaccine compared to a rabies reference standard using the National Institutes of Health (NIH) test. Reference vaccines are based on the International Standard for Rabies Vaccine provided by the World Health Organization (WHO). A comparison study was conducted to determine the relative potency of the 5th WHO, 6th WHO, and United States Department of Agriculture's (USDA) 08-14 reference standards using the NIH test. Results from the study demonstrate that the 6th WHO reference standard is approximately twice as potent as the 5th WHO reference when reconstituted to contain 1 IU per ml. Based on these results, the Center for Veterinary Biologics (CVB) doubled the reconstitution volume of USDA veterinary reference 08-14 from 13 ml to 26 ml, for an initial use dilution of 0.7 IU per ml for use by veterinary biologics manufacturers in the NIH test. This study emphasizes the importance of reference standard calibration for use in the National Institutes of Health test. Published by Elsevier Ltd.

  9. The role of differentiation and standards-based grading in the science learning of struggling and advanced learners in a detracked high school honors biology classroom

    NASA Astrophysics Data System (ADS)

    MacDonald, Michelina Ruth Carter

    The accountability movement in education resulting from the passage of The No Child Left Behind Act of 2001 has brought to light the disparities that exist in student achievement in the United States which play out along racial and socioeconomic lines. Three educational practices hold promise for reducing this achievement gap: differentiated instruction, standards-based assessment, and elimination of academic tracking. The purpose of this practitioner research study was to examine the ways that differentiation and standards-based assessment can support struggling learners and challenge advanced learners in a detracked, honors biology classroom. To gain insight into the role that differentiation and standards-based assessment played in supporting struggling and advanced learners, I used practitioner research to examine the development and implementation of a differentiated, standards-based instructional unit around the conceptual topic of protein synthesis. I collected multiple data pieces for 10 students in the study: two advanced learners, four struggling learners, and four strong learners who struggled in biology. Data analyzed included formative, self-, and summative assessment results; student artifacts; informal and formal student interviews; and, a practitioner reflection journal chronicling critical incidents and actions taken during the development and implementation of this unit and notes from peer debriefing during and following the unit's implementation. As I analyzed the data collected, my four findings fell into two overarching categories related to student grouping. My first three findings reflect what I learned about homogeneous grouping: (1) Pre-assessment based on unit outcomes is not useful for determining groups for tiered instruction; (2) Decisions about differentiation and grouping for differentiation must be made in the act of teaching using formative assessment results; and, (3) Flexible grouping structures are effective for both struggling

  10. Electron microprobe analysis program for biological specimens: BIOMAP

    NASA Technical Reports Server (NTRS)

    Edwards, B. F.

    1972-01-01

    BIOMAP is a Univac 1108 compatible program which facilitates the electron probe microanalysis of biological specimens. Input data are X-ray intensity data from biological samples, the X-ray intensity and composition data from a standard sample and the electron probe operating parameters. Outputs are estimates of the weight percentages of the analyzed elements, the distribution of these estimates for sets of red blood cells and the probabilities for correlation between elemental concentrations. An optional feature statistically estimates the X-ray intensity and residual background of a principal standard relative to a series of standards.

  11. Our Hidden Past: Biology, Part 2

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

    Smith, Ray; Russell, Liane; Mazur, Peter

    In their new home at "The Mouse House" at Y-12, researchers from ORNL's Biology Division conducted studies that led to standards such as dose rate effects that form the basis for current international standards for radiation exposure in humans.

  12. Data Management Rubric for Video Data in Organismal Biology.

    PubMed

    Brainerd, Elizabeth L; Blob, Richard W; Hedrick, Tyson L; Creamer, Andrew T; Müller, Ulrike K

    2017-07-01

    Standards-based data management facilitates data preservation, discoverability, and access for effective data reuse within research groups and across communities of researchers. Data sharing requires community consensus on standards for data management, such as storage and formats for digital data preservation, metadata (i.e., contextual data about the data) that should be recorded and stored, and data access. Video imaging is a valuable tool for measuring time-varying phenotypes in organismal biology, with particular application for research in functional morphology, comparative biomechanics, and animal behavior. The raw data are the videos, but videos alone are not sufficient for scientific analysis. Nearly endless videos of animals can be found on YouTube and elsewhere on the web, but these videos have little value for scientific analysis because essential metadata such as true frame rate, spatial calibration, genus and species, weight, age, etc. of organisms, are generally unknown. We have embarked on a project to build community consensus on video data management and metadata standards for organismal biology research. We collected input from colleagues at early stages, organized an open workshop, "Establishing Standards for Video Data Management," at the Society for Integrative and Comparative Biology meeting in January 2017, and then collected two more rounds of input on revised versions of the standards. The result we present here is a rubric consisting of nine standards for video data management, with three levels within each standard: good, better, and best practices. The nine standards are: (1) data storage; (2) video file formats; (3) metadata linkage; (4) video data and metadata access; (5) contact information and acceptable use; (6) camera settings; (7) organism(s); (8) recording conditions; and (9) subject matter/topic. The first four standards address data preservation and interoperability for sharing, whereas standards 5-9 establish minimum metadata

  13. Measurements of Intra‐Aortic Balloon Wall Movement During Inflation and Deflation: Effects of Angulation

    PubMed Central

    Bruti, Gianpaolo; Kolyva, Christina; Pepper, John R.

    2015-01-01

    Abstract The intra‐aortic balloon pump (IABP) is a ventricular assist device that is used with a broad range of pre‐, intra‐, and postoperative patients undergoing cardiac surgery. Although the clinical efficacy of the IABP is well documented, the question of reduced efficacy when patients are nursed in the semi‐recumbent position remains outstanding. The aim of the present work is therefore to investigate the underlying mechanics responsible for the loss of IABP performance when operated at an angle to the horizontal. Simultaneous recordings of balloon wall movement, providing an estimate of its diameter (D), and fluid pressure were taken at three sites along the intra‐aortic balloon (IAB) at 0 and 45°. Flow rate, used for the calculation of displaced volume, was also recorded distal to the tip of the balloon. An in vitro experimental setup was used, featuring physiological impedances on either side of the IAB ends. IAB inflation at an angle of 45° showed that D increases at the tip of the IAB first, presenting a resistance to the flow displaced away from the tip of the balloon. The duration of inflation decreased by 15.5%, the inflation pressure pulse decreased by 9.6%, and volume decreased by 2.5%. Similarly, changing the position of the balloon from 0 to 45°, the balloon deflation became slower by 35%, deflation pressure pulse decreased by 14.7%, and volume suctioned was decreased by 15.2%. IAB wall movement showed that operating at 45° results in slower deflation compared with 0°. Slow wall movement, and changes in inflation and deflation onsets, result in a decreased volume displacement and pressure pulse generation. Operating the balloon at an angle to the horizontal, which is the preferred nursing position in intensive care units, results in reduced IAB inflation and deflation performance, possibly compromising its clinical benefits. PMID:25959284

  14. 77 FR 36271 - International Energy Agency Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-18

    ... meeting of the Emergency Response Exercise 6 (ERE6) design group, to which certain IAB members will be... meeting of the IEA's Standing Group on Emergency Questions (SEQ) and the IEA's Standing Group on the Oil... IAB at a joint meeting of the IEA's Standing Group on Emergency Questions (SEQ) and the IEA's Standing...

  15. 9 CFR 113.50 - Ingredients 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 Ingredients of biological products... REQUIREMENTS Ingredient Requirements § 113.50 Ingredients of biological products. All ingredients used in a licensed biological product shall meet accepted standards of purity and quality; shall be sufficiently...

  16. BioBrick assembly standards and techniques and associated software tools.

    PubMed

    Røkke, Gunvor; Korvald, Eirin; Pahr, Jarle; Oyås, Ove; Lale, Rahmi

    2014-01-01

    The BioBrick idea was developed to introduce the engineering principles of abstraction and standardization into synthetic biology. BioBricks are DNA sequences that serve a defined biological function and can be readily assembled with any other BioBrick parts to create new BioBricks with novel properties. In order to achieve this, several assembly standards can be used. Which assembly standards a BioBrick is compatible with, depends on the prefix and suffix sequences surrounding the part. In this chapter, five of the most common assembly standards will be described, as well as some of the most used assembly techniques, cloning procedures, and a presentation of the available software tools that can be used for deciding on the best method for assembling of different BioBricks, and searching for BioBrick parts in the Registry of Standard Biological Parts database.

  17. [Biologics - nomenclature and classification].

    PubMed

    Eichbaum, Christine; Haefeli, Walter E

    2011-11-01

    Biological medicines are a heterogeneous group of drugs that are produced by living organisms using genetic or biological technology. Unlike chemically derived small molecules biologics are structurally complex making characterization and manufacturing difficult. Moreover, biological medicines show a great variety concerning their clinical use. To appropriately consider these particularities, there are other standards and guidelines for approval of similar derivatives of biologics, the so-called biosimilars or follow-on biologics. In contrast to a generic medicinal product containing a chemically identical active ingredient, a biosimilar is only expected to be similar to the innovator drug. Nowadays, monoclonal antibodies, fragments of antibodies, and fusion proteins manufactured by recombinant procedures play an important role. They have been used in many specialties for diagnostic and therapeutic purposes and are subject to continuous further development and improvement. Their nomenclature is based on a classification by the WHO which allows drawing conclusions for class of substance, origin, and pharmacological target.

  18. The fusion of biology, computer science, and engineering: towards efficient and successful synthetic biology.

    PubMed

    Linshiz, Gregory; Goldberg, Alex; Konry, Tania; Hillson, Nathan J

    2012-01-01

    Synthetic biology is a nascent field that emerged in earnest only around the turn of the millennium. It aims to engineer new biological systems and impart new biological functionality, often through genetic modifications. The design and construction of new biological systems is a complex, multistep process, requiring multidisciplinary collaborative efforts from "fusion" scientists who have formal training in computer science or engineering, as well as hands-on biological expertise. The public has high expectations for synthetic biology and eagerly anticipates the development of solutions to the major challenges facing humanity. This article discusses laboratory practices and the conduct of research in synthetic biology. It argues that the fusion science approach, which integrates biology with computer science and engineering best practices, including standardization, process optimization, computer-aided design and laboratory automation, miniaturization, and systematic management, will increase the predictability and reproducibility of experiments and lead to breakthroughs in the construction of new biological systems. The article also discusses several successful fusion projects, including the development of software tools for DNA construction design automation, recursive DNA construction, and the development of integrated microfluidics systems.

  19. The Next Generation of Science Standards: Implications for Biology Education

    ERIC Educational Resources Information Center

    Bybee, Rodger W.

    2012-01-01

    The release of A Framework for K-12 Science Education: Practices, Crosscutting Concepts, and Core Ideas (NRC, 2012) provides the basis for the next generation of science standards. This article first describes that foundation for the life sciences; it then presents a draft standard for natural selection and evolution. Finally, there is a…

  20. ASTM lights the way for tissue engineered medical products standards: jump start for combination medical products that restore biological function of human tissues.

    PubMed

    Picciolo, G L; Stocum, D L

    2001-01-01

    Everybody hopes for better health and restoration of impaired bodily function, and now that hope is illuminated by the promise of powerful biological tools that make human cells grow and replace human tissue. ASTM Committee F04 on Medical and Surgical Materials and Devices is taking the lead by defining some of those tools as standards that can be used for the development, production, testing, and regulatory approval of medical products.

  1. Recommendations regarding technical standards for follow-on biologics: comparability, similarity, interchangeability.

    PubMed

    Davis, Gregory C; Beals, John M; Johnson, Craig; Mayer, Mark H; Meiklejohn, Bruce I; Mitlak, Bruce H; Roth, Jody L; Towns, John K; Veenhuizen, Melissa

    2009-07-01

    Policy makers around the world are currently considering the creation of a regulatory pathway for follow-on biologics (FOB), which will have to account for the substantial technical challenges associated with FOB development. These challenges will likely involve more complexity than comparability assessments of process changes made by the same manufacturer. The history of industry-regulator comparability discussions helps explain why the same degree of testing and flexibility now applied to change-control within a manufacturer's own process, at this time, cannot be extrapolated to the observed and possibly unknown differences between two manufacturing processes that are independently developed by different (non-collaborating) parties. This commentary provides recommendations on the technical aspects that should be considered in the creation of an approval pathway for FOB products. In the authors' view, analytical methodology in its current state cannot alone provide full assurance that the FOB is sufficiently similar to the innovator product. Moreover, the FOB manufacturer will not have access to the extensive knowledge accumulated by the innovator manufacturer from early development through marketing. Thus, extensive clinical evaluation will likely be necessary to provide assurance that the FOB is safe and efficacious. If such testing demonstrates the FOB is safe and efficacious per existing regulatory standards, the product should receive marketing approval as a 'similar' product. Since 'similarity' is a fundamentally different determination than establishing interchangeability between the two products, an interchangeability determination must be based on additional testing and market experience to ensure patient safety. Post-marketing surveillance of the FOB should be conducted to ensure that the approved molecule has similar clinical safety and efficacy as the innovator product, prior to any consideration of interchangeability.

  2. Measuring the activity of BioBrick promoters using an in vivo reference standard

    PubMed Central

    Kelly, Jason R; Rubin, Adam J; Davis, Joseph H; Ajo-Franklin, Caroline M; Cumbers, John; Czar, Michael J; de Mora, Kim; Glieberman, Aaron L; Monie, Dileep D; Endy, Drew

    2009-01-01

    Background The engineering of many-component, synthetic biological systems is being made easier by the development of collections of reusable, standard biological parts. However, the complexity of biology makes it difficult to predict the extent to which such efforts will succeed. As a first practical example, the Registry of Standard Biological Parts started at MIT now maintains and distributes thousands of BioBrick™ standard biological parts. However, BioBrick parts are only standardized in terms of how individual parts are physically assembled into multi-component systems, and most parts remain uncharacterized. Standardized tools, techniques, and units of measurement are needed to facilitate the characterization and reuse of parts by independent researchers across many laboratories. Results We found that the absolute activity of BioBrick promoters varies across experimental conditions and measurement instruments. We choose one promoter (BBa_J23101) to serve as an in vivo reference standard for promoter activity. We demonstrated that, by measuring the activity of promoters relative to BBa_J23101, we could reduce variation in reported promoter activity due to differences in test conditions and measurement instruments by ~50%. We defined a Relative Promoter Unit (RPU) in order to report promoter characterization data in compatible units and developed a measurement kit so that researchers might more easily adopt RPU as a standard unit for reporting promoter activity. We distributed a set of test promoters to multiple labs and found good agreement in the reported relative activities of promoters so measured. We also characterized the relative activities of a reference collection of BioBrick promoters in order to further support adoption of RPU-based measurement standards. Conclusion Relative activity measurements based on an in vivoreference standard enables improved measurement of promoter activity given variation in measurement conditions and instruments. These

  3. Where are we in our understanding of the association between narcolepsy and one of the 2009 adjuvanted influenza A (H1N1) vaccines?

    PubMed

    Johansen, K; Brasseur, D; MacDonald, N; Nohynek, H; Vandeputte, J; Wood, D; Neels, P

    2016-07-01

    Evaluating new rare serious vaccine safety signals is difficult and complex work. To further assess the observed increase in narcolepsy cases seen in Europe with the 2009 pandemic H1N1 influenza vaccine, the International Alliance for Biological Standardization (IABS) invited a wide range of experts to a one day meeting in Geneva in October 2015 to present data and to discuss the implications. The presentations covered the following topics: clinical picture of childhood narcolepsy following the 2009 H1N1 pandemic vaccination campaigns; epidemiological studies conducted to assess the risk of narcolepsy, other neurological and immune-related diseases following 2009 pandemic H1N1 influenza vaccine; potential biases influencing the different epidemiological study designs; potential genetic contribution to the development of narcolepsy; potential biological mechanisms for development of narcolepsy in this setting including the role of the virus itself, antigenic differences between the vaccines and differences in AS03-adjuvanted vaccines. The presentations were followed by fulsome roundtable discussions. Members from affected families also attended and made informal comments to round out the day's deliberations. This meeting emphasized the value added in bringing together in a neutral setting a wide range of experts and vaccine producers to discuss such a complex new serious adverse event following immunization. Copyright © 2016.

  4. Biology in Context: Teachers' Professional Development in Learning Communities

    ERIC Educational Resources Information Center

    Elster, Doris

    2009-01-01

    Biology in Context ("bik") is a project that aims to improve biology teaching in lower secondary schools in Germany. Based on a theoretical framework derived from the National Educational Standards, four competence areas should be fostered in biology education: subject knowledge; inquiry acquisition; subject-related communication; and…

  5. Radiological/biological/aerosol removal system

    DOEpatents

    Haslam, Jeffery J

    2015-03-17

    An air filter replacement system for existing buildings, vehicles, arenas, and other enclosed airspaces includes a replacement air filter for replacing a standard air filter. The replacement air filter has dimensions and air flow specifications that allow it to replace the standard air filter. The replacement air filter includes a filter material that removes radiological or biological or aerosol particles.

  6. Nanoparticle-based biologic mimetics

    PubMed Central

    Cliffel, David E.; Turner, Brian N.; Huffman, Brian J.

    2009-01-01

    Centered on solid chemistry foundations, biology and materials science have reached a crossroad where bottom-up designs of new biologically important nanomaterials are a reality. The topics discussed here present the interdisciplinary field of creating biological mimics. Specifically, this discussion focuses on mimics that are developed using various types of metal nanoparticles (particularly gold) through facile synthetic methods. These methods conjugate biologically relevant molecules, e.g., small molecules, peptides, proteins, and carbohydrates, in conformationally favorable orientations on the particle surface. These new products provide stable, safe, and effective substitutes for working with potentially hazardous biologicals for applications such as drug targeting, immunological studies, biosensor development, and biocatalysis. Many standard bioanalytical techniques can be used to characterize and validate the efficacy of these new materials, including quartz crystal microbalance (QCM), surface plasmon resonance (SPR), and enzyme-linked immunosorbent assay (ELISA). Metal nanoparticle–based biomimetics continue to be developed as potential replacements for the native biomolecule in applications of immunoassays and catalysis. PMID:20049778

  7. Graphics processing units in bioinformatics, computational biology and systems biology.

    PubMed

    Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

    2017-09-01

    Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

  8. Data Management Rubric for Video Data in Organismal Biology

    PubMed Central

    Brainerd, Elizabeth L.; Blob, Richard W.; Hedrick, Tyson L.; Creamer, Andrew T.; Müller, Ulrike K.

    2017-01-01

    Synopsis Standards-based data management facilitates data preservation, discoverability, and access for effective data reuse within research groups and across communities of researchers. Data sharing requires community consensus on standards for data management, such as storage and formats for digital data preservation, metadata (i.e., contextual data about the data) that should be recorded and stored, and data access. Video imaging is a valuable tool for measuring time-varying phenotypes in organismal biology, with particular application for research in functional morphology, comparative biomechanics, and animal behavior. The raw data are the videos, but videos alone are not sufficient for scientific analysis. Nearly endless videos of animals can be found on YouTube and elsewhere on the web, but these videos have little value for scientific analysis because essential metadata such as true frame rate, spatial calibration, genus and species, weight, age, etc. of organisms, are generally unknown. We have embarked on a project to build community consensus on video data management and metadata standards for organismal biology research. We collected input from colleagues at early stages, organized an open workshop, “Establishing Standards for Video Data Management,” at the Society for Integrative and Comparative Biology meeting in January 2017, and then collected two more rounds of input on revised versions of the standards. The result we present here is a rubric consisting of nine standards for video data management, with three levels within each standard: good, better, and best practices. The nine standards are: (1) data storage; (2) video file formats; (3) metadata linkage; (4) video data and metadata access; (5) contact information and acceptable use; (6) camera settings; (7) organism(s); (8) recording conditions; and (9) subject matter/topic. The first four standards address data preservation and interoperability for sharing, whereas standards 5–9 establish

  9. Cobalt complexes as internal standards for capillary zone electrophoresis-mass spectrometry studies in biological inorganic chemistry.

    PubMed

    Holtkamp, Hannah U; Morrow, Stuart J; Kubanik, Mario; Hartinger, Christian G

    2017-07-01

    Run-by-run variations are very common in capillary electrophoretic (CE) separations and cause imprecision in both the migration times and the peak areas. This makes peak and kinetic trend identification difficult and error prone. With the aim to identify suitable standards for CE separations which are compatible with the common detectors UV, ESI-MS, and ICP-MS, the Co III complexes [Co(en) 3 ]Cl 3 , [Co(acac) 3 ] and K[Co(EDTA)] were evaluated as internal standards in the reaction of the anticancer drug cisplatin and guanosine 5'-monophosphate as an example of a classical biological inorganic chemistry experiment. These Co III chelate complexes were considered for their stability, accessibility, and the low detection limit for Co in ICP-MS. Furthermore, the Co III complexes are positively and negatively charged as well as neutral, allowing the detection in different areas of the electropherograms. The background electrolytes were chosen to cover a wide pH range. The compatibility to the separation conditions was dependent on the ligands attached to the Co III centers, with only the acetylacetonato (acac) complex being applicable in the pH range 2.8-9.0. Furthermore, because of being charge neutral, this compound could be used as an electroosmotic flow (EOF) marker. In general, employing Co complexes resulted in improved data sets, particularly with regard to the migration times and peak areas, which resulted, for example, in higher linear ranges for the quantification of cisplatin.

  10. Standard Reporting Requirements for Biological Samples in Metabolomics Experiments: Environmental Context

    EPA Science Inventory

    Metabolomic technologies are increasingly being applied to study biological questions in a range of different settings from clinical through to environmental. As with other high-throughput technologies, such as those used in transcriptomics and proteomics, metabolomics continues...

  11. Measurements of Intra-Aortic Balloon Wall Movement During Inflation and Deflation: Effects of Angulation.

    PubMed

    Bruti, Gianpaolo; Kolyva, Christina; Pepper, John R; Khir, Ashraf W

    2015-08-01

    The intra-aortic balloon pump (IABP) is a ventricular assist device that is used with a broad range of pre-, intra-, and postoperative patients undergoing cardiac surgery. Although the clinical efficacy of the IABP is well documented, the question of reduced efficacy when patients are nursed in the semi-recumbent position remains outstanding. The aim of the present work is therefore to investigate the underlying mechanics responsible for the loss of IABP performance when operated at an angle to the horizontal. Simultaneous recordings of balloon wall movement, providing an estimate of its diameter (D), and fluid pressure were taken at three sites along the intra-aortic balloon (IAB) at 0 and 45°. Flow rate, used for the calculation of displaced volume, was also recorded distal to the tip of the balloon. An in vitro experimental setup was used, featuring physiological impedances on either side of the IAB ends. IAB inflation at an angle of 45° showed that D increases at the tip of the IAB first, presenting a resistance to the flow displaced away from the tip of the balloon. The duration of inflation decreased by 15.5%, the inflation pressure pulse decreased by 9.6%, and volume decreased by 2.5%. Similarly, changing the position of the balloon from 0 to 45°, the balloon deflation became slower by 35%, deflation pressure pulse decreased by 14.7%, and volume suctioned was decreased by 15.2%. IAB wall movement showed that operating at 45° results in slower deflation compared with 0°. Slow wall movement, and changes in inflation and deflation onsets, result in a decreased volume displacement and pressure pulse generation. Operating the balloon at an angle to the horizontal, which is the preferred nursing position in intensive care units, results in reduced IAB inflation and deflation performance, possibly compromising its clinical benefits. Copyright © 2015 The Authors. Artificial Organs published by Wiley Periodicals, Inc. on behalf of International Center for

  12. Determination of Perfluorinated Alkyl Acid Concentrations in Biological Standard Reference Materials

    EPA Science Inventory

    Standard reference materials (SRMs) are homogeneous, well-characterized materials used to validate measurements and improve the quality of analytical data. The National Institute of Standards and Technology (NIST) has a wide range of SRMs that have mass fraction values assigned ...

  13. [Synthetic biology and rearrangements of microbial genetic material].

    PubMed

    Liang, Quan-Feng; Wang, Qian; Qi, Qing-Sheng

    2011-10-01

    As an emerging discipline, synthetic biology has shown great scientific values and application prospects. Although there have been many reviews of various aspects on synthetic biology over the last years, this article, for the first time, attempted to discuss the relationship and difference between microbial genetics and synthetic biology. We summarized the recent development of synthetic biology in rearranging microbial genetic materials, including synthesis, design and reduction of genetic materials, standardization of genetic parts and modularization of genetic circuits. The relationship between synthetic biology and microbial genetic engineering was also discussed in the paper.

  14. [Non-conformities management in laboratory of medical biology: application to non-conformities of biological samples during 2009].

    PubMed

    Annaix, Véronique; Rogowski, Julien; Joyau, Mireille; Jaouën, Edtih

    2011-01-01

    The non-conformity management is required for the ISO 15189 standard. The laboratory of medical biology has to carry out suitable acts and procedures to exploit different indicators through the framework of continuous improvement. We particularly study the indicator of biological samples nonconformities and we report 2009 results to the nurses' team managers to find solutions for quality of care to the patient.

  15. Human exposure standards in the frequency range 1 Hz To 100 kHz: the case for adoption of the IEEE standard.

    PubMed

    Patrick Reilly, J

    2014-10-01

    Differences between IEEE C95 Standards (C95.6-2002 and C95.1-2005) in the low-frequency (1 Hz-100 kHz) and the ICNIRP-2010 guidelines appear across the frequency spectrum. Factors accounting for lack of convergence include: differences between the IEEE standards and the ICNIRP guidelines with respect to biological induction models, stated objectives, data trail from experimentally derived thresholds through physical and biological principles, selection and justification of safety/reduction factors, use of probability models, compliance standards for the limbs as distinct from the whole body, defined population categories, strategies for central nervous system protection below 20 Hz, and correspondence of environmental electric field limits with contact currents. This paper discusses these factors and makes the case for adoption of the limits in the IEEE standards.

  16. 21 CFR 640.55 - U.S. Standard preparation.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false U.S. Standard preparation. 640.55 Section 640.55 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS ADDITIONAL STANDARDS FOR HUMAN BLOOD AND BLOOD PRODUCTS Cryoprecipitate § 640.55 U.S. Standard...

  17. 21 CFR 640.55 - U.S. Standard preparation.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 7 2011-04-01 2010-04-01 true U.S. Standard preparation. 640.55 Section 640.55 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS ADDITIONAL STANDARDS FOR HUMAN BLOOD AND BLOOD PRODUCTS Cryoprecipitate § 640.55 U.S. Standard...

  18. On the mechanics of growing thin biological membranes

    NASA Astrophysics Data System (ADS)

    Rausch, Manuel K.; Kuhl, Ellen

    2014-02-01

    Despite their seemingly delicate appearance, thin biological membranes fulfill various crucial roles in the human body and can sustain substantial mechanical loads. Unlike engineering structures, biological membranes are able to grow and adapt to changes in their mechanical environment. Finite element modeling of biological growth holds the potential to better understand the interplay of membrane form and function and to reliably predict the effects of disease or medical intervention. However, standard continuum elements typically fail to represent thin biological membranes efficiently, accurately, and robustly. Moreover, continuum models are typically cumbersome to generate from surface-based medical imaging data. Here we propose a computational model for finite membrane growth using a classical midsurface representation compatible with standard shell elements. By assuming elastic incompressibility and membrane-only growth, the model a priori satisfies the zero-normal stress condition. To demonstrate its modular nature, we implement the membrane growth model into the general-purpose non-linear finite element package Abaqus/Standard using the concept of user subroutines. To probe efficiently and robustness, we simulate selected benchmark examples of growing biological membranes under different loading conditions. To demonstrate the clinical potential, we simulate the functional adaptation of a heart valve leaflet in ischemic cardiomyopathy. We believe that our novel approach will be widely applicable to simulate the adaptive chronic growth of thin biological structures including skin membranes, mucous membranes, fetal membranes, tympanic membranes, corneoscleral membranes, and heart valve membranes. Ultimately, our model can be used to identify diseased states, predict disease evolution, and guide the design of interventional or pharmaceutic therapies to arrest or revert disease progression.

  19. Biological effects from electromagnetic field exposure and public exposure standards.

    PubMed

    Hardell, Lennart; Sage, Cindy

    2008-02-01

    During recent years there has been increasing public concern on potential health risks from power-frequency fields (extremely low frequency electromagnetic fields; ELF) and from radiofrequency/microwave radiation emissions (RF) from wireless communications. Non-thermal (low-intensity) biological effects have not been considered for regulation of microwave exposure, although numerous scientific reports indicate such effects. The BioInitiative Report is based on an international research and public policy initiative to give an overview of what is known of biological effects that occur at low-intensity electromagnetic fields (EMFs) exposure. Health endpoints reported to be associated with ELF and/or RF include childhood leukaemia, brain tumours, genotoxic effects, neurological effects and neurodegenerative diseases, immune system deregulation, allergic and inflammatory responses, breast cancer, miscarriage and some cardiovascular effects. The BioInitiative Report concluded that a reasonable suspicion of risk exists based on clear evidence of bioeffects at environmentally relevant levels, which, with prolonged exposures may reasonably be presumed to result in health impacts. Regarding ELF a new lower public safety limit for habitable space adjacent to all new or upgraded power lines and for all other new constructions should be applied. A new lower limit should also be used for existing habitable space for children and/or women who are pregnant. A precautionary limit should be adopted for outdoor, cumulative RF exposure and for cumulative indoor RF fields with considerably lower limits than existing guidelines, see the BioInitiative Report. The current guidelines for the US and European microwave exposure from mobile phones, for the brain are 1.6 W/Kg and 2 W/Kg, respectively. Since use of mobile phones is associated with an increased risk for brain tumour after 10 years, a new biologically based guideline is warranted. Other health impacts associated with exposure to

  20. Recommendations for designing and conducting veterinary clinical pathology biologic variation studies.

    PubMed

    Freeman, Kathleen P; Baral, Randolph M; Dhand, Navneet K; Nielsen, Søren Saxmose; Jensen, Asger L

    2017-06-01

    The recent creation of a veterinary clinical pathology biologic variation website has highlighted the need to provide recommendations for future studies of biologic variation in animals in order to help standardize and improve the quality of published information and to facilitate review and selection of publications as standard references. The following recommendations are provided in the format and order commonly found in veterinary publications. A checklist is provided to aid in planning, implementing, and evaluating veterinary studies on biologic variation (Appendix S1). These recommendations provide a valuable resource for clinicians, laboratorians, and researchers interested in conducting studies of biologic variation and in determining the quality of studies of biologic variation in veterinary laboratory testing. © 2017 American Society for Veterinary Clinical Pathology.

  1. Synthetic Biology Open Language (SBOL) Version 2.2.0.

    PubMed

    Cox, Robert Sidney; Madsen, Curtis; McLaughlin, James Alastair; Nguyen, Tramy; Roehner, Nicholas; Bartley, Bryan; Beal, Jacob; Bissell, Michael; Choi, Kiri; Clancy, Kevin; Grünberg, Raik; Macklin, Chris; Misirli, Goksel; Oberortner, Ernst; Pocock, Matthew; Samineni, Meher; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Gennari, John H; Myers, Chris; Sauro, Herbert; Wipat, Anil

    2018-04-02

    Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year's JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

  2. Synthetic Biology Open Language (SBOL) Version 2.1.0.

    PubMed

    Beal, Jacob; Cox, Robert Sidney; Grünberg, Raik; McLaughlin, James; Nguyen, Tramy; Bartley, Bryan; Bissell, Michael; Choi, Kiri; Clancy, Kevin; Macklin, Chris; Madsen, Curtis; Misirli, Goksel; Oberortner, Ernst; Pocock, Matthew; Roehner, Nicholas; Samineni, Meher; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Gennari, John H; Myers, Chris; Sauro, Herbert; Wipat, Anil

    2016-09-01

    Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.1 of SBOL that builds upon version 2.0 published in last year's JIB special issue. In particular, SBOL 2.1 includes improved rules for what constitutes a valid SBOL document, new role fields to simplify the expression of sequence features and how components are used in context, and new best practices descriptions to improve the exchange of basic sequence topology information and the description of genetic design provenance, as well as miscellaneous other minor improvements.

  3. Synthetic Biology Open Language (SBOL) Version 2.1.0.

    PubMed

    Beal, Jacob; Cox, Robert Sidney; Grünberg, Raik; McLaughlin, James; Nguyen, Tramy; Bartley, Bryan; Bissell, Michael; Choi, Kiri; Clancy, Kevin; Macklin, Chris; Madsen, Curtis; Misirli, Goksel; Oberortner, Ernst; Pocock, Matthew; Roehner, Nicholas; Samineni, Meher; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Gennari, John; Myers, Chris; Sauro, Herbert; Wipat, Anil

    2016-12-18

    Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.1 of SBOL that builds upon version 2.0 published in last year’s JIB special issue. In particular, SBOL 2.1 includes improved rules for what constitutes a valid SBOL document, new role fields to simplify the expression of sequence features and how components are used in context, and new best practices descriptions to improve the exchange of basic sequence topology information and the description of genetic design provenance, as well as miscellaneous other minor improvements.

  4. Plant Content in the National Science Education Standards

    ERIC Educational Resources Information Center

    Hershey, David R.

    2005-01-01

    The National Science Education Standards (NSES) provides few resources for teaching about plants. To assure students understand and appreciate plants, the author advocates teaching about plants as a basic biological concept, avoiding animal chauvinism in biology coursework, correcting pseudoscience and anthropomorphisms about plants, and making…

  5. Kepler sheds new and unprecedented light on the variability of a blue supergiant: Gravity waves in the O9.5Iab star HD 188209

    NASA Astrophysics Data System (ADS)

    Aerts, C.; Símon-Díaz, S.; Bloemen, S.; Debosscher, J.; Pápics, P. I.; Bryson, S.; Still, M.; Moravveji, E.; Williamson, M. H.; Grundahl, F.; Fredslund Andersen, M.; Antoci, V.; Pallé, P. L.; Christensen-Dalsgaard, J.; Rogers, T. M.

    2017-06-01

    Stellar evolution models are most uncertain for evolved massive stars. Asteroseismology based on high-precision uninterrupted space photometry has become a new way to test the outcome of stellar evolution theory and was recently applied to a multitude of stars, but not yet to massive evolved supergiants.Our aim is to detect, analyse and interpret the photospheric and wind variability of the O9.5 Iab star HD 188209 from Kepler space photometry and long-term high-resolution spectroscopy. We used Kepler scattered-light photometry obtained by the nominal mission during 1460 d to deduce the photometric variability of this O-type supergiant. In addition, we assembled and analysed high-resolution high signal-to-noise spectroscopy taken with four spectrographs during some 1800 d to interpret the temporal spectroscopic variability of the star. The variability of this blue supergiant derived from the scattered-light space photometry is in full in agreement with the one found in the ground-based spectroscopy. We find significant low-frequency variability that is consistently detected in all spectral lines of HD 188209. The photospheric variability propagates into the wind, where it has similar frequencies but slightly higher amplitudes. The morphology of the frequency spectra derived from the long-term photometry and spectroscopy points towards a spectrum of travelling waves with frequency values in the range expected for an evolved O-type star. Convectively-driven internal gravity waves excited in the stellar interior offer the most plausible explanation of the detected variability. Based on photometric observations made with the NASA Kepler satellite and on spectroscopic observations made with four telescopes: the Nordic Optical Telescope operated by NOTSA and the Mercator Telescope operated by the Flemish Community, both at the Observatorio del Roque de los Muchachos (La Palma, Spain) of the Instituto de Astrofísica de Canarias, the T13 2.0 m Automatic Spectroscopic

  6. H-point standard additions method for simultaneous determination of sulfamethoxazole and trimethoprim in pharmaceutical formulations and biological fluids with simultaneous addition of two analytes

    NASA Astrophysics Data System (ADS)

    Givianrad, M. H.; Saber-Tehrani, M.; Aberoomand-Azar, P.; Mohagheghian, M.

    2011-03-01

    The applicability of H-point standard additions method (HPSAM) to the resolving of overlapping spectra corresponding to the sulfamethoxazole and trimethoprim is verified by UV-vis spectrophotometry. The results show that the H-point standard additions method with simultaneous addition of both analytes is suitable for the simultaneous determination of sulfamethoxazole and trimethoprim in aqueous media. The results of applying the H-point standard additions method showed that the two drugs could be determined simultaneously with the concentration ratios of sulfamethoxazole to trimethoprim varying from 1:18 to 16:1 in the mixed samples. Also, the limits of detections were 0.58 and 0.37 μmol L -1 for sulfamethoxazole and trimethoprim, respectively. In addition the means of the calculated RSD (%) were 1.63 and 2.01 for SMX and TMP, respectively in synthetic mixtures. The proposed method has been successfully applied to the simultaneous determination of sulfamethoxazole and trimethoprim in some synthetic, pharmaceutical formulation and biological fluid samples.

  7. Predicting clinical biological responses to dental materials.

    PubMed

    Wataha, John C

    2012-01-01

    Methods used to measure and predict clinical biological responses to dental materials remain controversial, confusing, and to some extent, unsuccessful. The current paper reviews significant issues surrounding how we assess the biological safety of materials, with a historical summary and critical look at the biocompatibility literature. The review frames these issues from a U.S. perspective to some degree, but emphasizes their global nature and universal importance. The PubMed database and information from the U.S. Food and Drug Administration, International Standards Organization, and American National Standards Institute were searched for prominent literature addressing the definition of biocompatibility, types of biological tests employed, regulatory and standardization issues, and how biological tests are used together to establish the biological safety of materials. The search encompassed articles published in English from approximately 1965-2011. The review does not comprehensively review the literature, but highlights significant issues that confront the field. Years ago, tests for biological safety sought to establish material inertness as the measure of safety, a criterion that is now deemed naive; the definition of biocompatibility has broadened along with the roles for materials in patient oral health care. Controversies persist about how in vitro or animal tests should be used to evaluate the biological safety of materials for clinical use. Controlled clinical trials remain the single best measure of the clinical response to materials, but even these tests have significant limitations and are less useful to identify mechanisms that shape material performance. Practice-based research networks and practitioner databases are emerging as important supplements to controlled clinical trials, but their final utility remains to be determined. Today we ask materials to play increasingly sophisticated structural and therapeutic roles in patient treatment. To

  8. 21 CFR 600.14 - Reporting of biological product deviations by licensed manufacturers.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... this section? (1) You, the manufacturer who holds the biological product license and who had control... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Reporting of biological product deviations by... HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS BIOLOGICAL PRODUCTS: GENERAL Establishment Standards...

  9. Challenges and opportunities in synthetic biology for chemical engineers.

    PubMed

    Luo, Yunzi; Lee, Jung-Kul; Zhao, Huimin

    2013-11-15

    Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement.

  10. BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts.

    PubMed

    Yang, Kun; Stracquadanio, Giovanni; Luo, Jingchuan; Boeke, Jef D; Bader, Joel S

    2016-03-15

    Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder joel.bader@jhu.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

  11. On the mechanics of growing thin biological membranes

    PubMed Central

    Rausch, Manuel K.; Kuhl, Ellen

    2013-01-01

    Despite their seemingly delicate appearance, thin biological membranes fulfill various crucial roles in the human body and can sustain substantial mechanical loads. Unlike engineering structures, biological membranes are able to grow and adapt to changes in their mechanical environment. Finite element modeling of biological growth holds the potential to better understand the interplay of membrane form and function and to reliably predict the effects of disease or medical intervention. However, standard continuum elements typically fail to represent thin biological membranes efficiently, accurately, and robustly. Moreover, continuum models are typically cumbersome to generate from surface-based medical imaging data. Here we propose a computational model for finite membrane growth using a classical midsurface representation compatible with standard shell elements. By assuming elastic incompressibility and membrane-only growth, the model a priori satisfies the zero-normal stress condition. To demonstrate its modular nature, we implement the membrane growth model into the general-purpose non-linear finite element package Abaqus/Standard using the concept of user subroutines. To probe efficiently and robustness, we simulate selected benchmark examples of growing biological membranes under different loading conditions. To demonstrate the clinical potential, we simulate the functional adaptation of a heart valve leaflet in ischemic cardiomyopathy. We believe that our novel approach will be widely applicable to simulate the adaptive chronic growth of thin biological structures including skin membranes, mucous membranes, fetal membranes, tympanic membranes, corneoscleral membranes, and heart valve membranes. Ultimately, our model can be used to identify diseased states, predict disease evolution, and guide the design of interventional or pharmaceutic therapies to arrest or revert disease progression. PMID:24563551

  12. CellML metadata standards, associated tools and repositories

    PubMed Central

    Beard, Daniel A.; Britten, Randall; Cooling, Mike T.; Garny, Alan; Halstead, Matt D.B.; Hunter, Peter J.; Lawson, James; Lloyd, Catherine M.; Marsh, Justin; Miller, Andrew; Nickerson, David P.; Nielsen, Poul M.F.; Nomura, Taishin; Subramanium, Shankar; Wimalaratne, Sarala M.; Yu, Tommy

    2009-01-01

    The development of standards for encoding mathematical models is an important component of model building and model sharing among scientists interested in understanding multi-scale physiological processes. CellML provides such a standard, particularly for models based on biophysical mechanisms, and a substantial number of models are now available in the CellML Model Repository. However, there is an urgent need to extend the current CellML metadata standard to provide biological and biophysical annotation of the models in order to facilitate model sharing, automated model reduction and connection to biological databases. This paper gives a broad overview of a number of new developments on CellML metadata and provides links to further methodological details available from the CellML website. PMID:19380315

  13. The "Next Generation Science Standards" and the Life Sciences

    ERIC Educational Resources Information Center

    Bybee, Rodger W.

    2013-01-01

    Publication of the "Next Generation Science Standards" will be just short of two decades since publication of the "National Science Education Standards" (NRC 1996). In that time, biology and science education communities have advanced, and the new standards will reflect that progress (NRC 1999, 2007, 2009; Kress and Barrett…

  14. Emerging biomedical applications of synthetic biology.

    PubMed

    Weber, Wilfried; Fussenegger, Martin

    2011-11-29

    Synthetic biology aims to create functional devices, systems and organisms with novel and useful functions on the basis of catalogued and standardized biological building blocks. Although they were initially constructed to elucidate the dynamics of simple processes, designed devices now contribute to the understanding of disease mechanisms, provide novel diagnostic tools, enable economic production of therapeutics and allow the design of novel strategies for the treatment of cancer, immune diseases and metabolic disorders, such as diabetes and gout, as well as a range of infectious diseases. In this Review, we cover the impact and potential of synthetic biology for biomedical applications.

  15. NASA Technical Standards Program and Implications for Lessons Learned and Technical Standard Integration

    NASA Technical Reports Server (NTRS)

    Gill, Paul S.; Garcia, Danny; Vaughan, William W.; Parker, Nelson C. (Technical Monitor)

    2002-01-01

    The National Aeronautics and Space Agency consists of fourteen Facilities throughout the United States. They are organized to support the Agency's principal Enterprises: (1) Space Science, (2) Earth Science, (3) Aerospace Technology, (4) Human Exploration and Development of Space, and (5) Biological and Physical Research. Technical Standards are important to the activities of each Enterprise and have been an integral part in the development and operation of NASA Programs and Projects since the Agency was established in 1959. However, for years each Center was responsible for its own standards development and selection of non-NASA technical standards that met the needs of Programs and Projects for which they were responsible. There were few Agencywide applicable Technical Standards, mainly those in area of safety. Department of Defense Standards and Specifications were the foundation and main source for Technical Standards used by the Agency. This process existed until about 1997 when NASA embarked on a Program to convert NASA's Center-developed Technical Standards into Agencywide endorsed NASA Preferred Technical Standards. In addition, action was taken regarding the formal adoption of non-NASA Technical Standards (DOD, SAE, ASTM, ASME, IEEE, etc.) as NASA Preferred Technical Standards.

  16. Challenges and opportunities in synthetic biology for chemical engineers

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

    Luo, YZ; Lee, JK; Zhao, HM

    Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement. (C) 2012 Elsevier Ltd. All rights reserved.

  17. Challenges and opportunities in synthetic biology for chemical engineers

    PubMed Central

    Luo, Yunzi; Lee, Jung-Kul; Zhao, Huimin

    2012-01-01

    Synthetic biology provides numerous great opportunities for chemical engineers in the development of new processes for large-scale production of biofuels, value-added chemicals, and protein therapeutics. However, challenges across all scales abound. In particular, the modularization and standardization of the components in a biological system, so-called biological parts, remain the biggest obstacle in synthetic biology. In this perspective, we will discuss the main challenges and opportunities in the rapidly growing synthetic biology field and the important roles that chemical engineers can play in its advancement. PMID:24222925

  18. Fibrinolysis standards: a review of the current status.

    PubMed

    Thelwell, C

    2010-07-01

    Biological standards are used to calibrate measurements of components of the fibrinolytic system, either for assigning potency values to therapeutic products, or to determine levels in human plasma as an indicator of thrombotic risk. Traditionally WHO International Standards are calibrated in International Units based on consensus values from collaborative studies. The International Unit is defined by the response activity of a given amount of the standard in a bioassay, independent of the method used. Assay validity is based on the assumption that both standard and test preparation contain the same analyte, and the response in an assay is a true function of this analyte. This principle is reflected in the diversity of source materials used to prepare fibrinolysis standards, which has depended on the contemporary preparations they were employed to measure. With advancing recombinant technology, and improved analytical techniques, a reference system based on reference materials and associated reference methods has been recommended for future fibrinolysis standards. Careful consideration and scientific judgement must however be applied when deciding on an approach to develop a new standard, with decisions based on the suitability of a standard to serve its purpose, and not just to satisfy a metrological ideal. 2010 The International Association for Biologicals. Published by Elsevier Ltd. All rights reserved.

  19. Biological aerosol background characterization

    NASA Astrophysics Data System (ADS)

    Blatny, Janet; Fountain, Augustus W., III

    2011-05-01

    To provide useful information during military operations, or as part of other security situations, a biological aerosol detector has to respond within seconds or minutes to an attack by virulent biological agents, and with low false alarms. Within this time frame, measuring virulence of a known microorganism is extremely difficult, especially if the microorganism is of unknown antigenic or nucleic acid properties. Measuring "live" characteristics of an organism directly is not generally an option, yet only viable organisms are potentially infectious. Fluorescence based instruments have been designed to optically determine if aerosol particles have viability characteristics. Still, such commercially available biological aerosol detection equipment needs to be improved for their use in military and civil applications. Air has an endogenous population of microorganisms that may interfere with alarm software technologies. To design robust algorithms, a comprehensive knowledge of the airborne biological background content is essential. For this reason, there is a need to study ambient live bacterial populations in as many locations as possible. Doing so will permit collection of data to define diverse biological characteristics that in turn can be used to fine tune alarm algorithms. To avoid false alarms, improving software technologies for biological detectors is a crucial feature requiring considerations of various parameters that can be applied to suppress alarm triggers. This NATO Task Group will aim for developing reference methods for monitoring biological aerosol characteristics to improve alarm algorithms for biological detection. Additionally, they will focus on developing reference standard methodology for monitoring biological aerosol characteristics to reduce false alarm rates.

  20. A framework for standardizing flight characteristics for separating biology from meteorology in long-range insect transport

    Treesearch

    Gary L. Achtemeier

    1998-01-01

    Once airborne during long-range transport, to what extent is the final destination determined by the biota? It is well known that a biological mechanism initiates flight and another biological mechanism terminates flight. Therefore, efforts to answer the above question should be focused on en route insect behavior. A strategy is proposed to isolate biology...

  1. 21 CFR 610.68 - Exceptions or alternatives to labeling requirements for biological products held by the Strategic...

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... requirements for biological products held by the Strategic National Stockpile. 610.68 Section 610.68 Food and... GENERAL BIOLOGICAL PRODUCTS STANDARDS Labeling Standards § 610.68 Exceptions or alternatives to labeling requirements for biological products held by the Strategic National Stockpile. (a) The appropriate FDA Center...

  2. CORAL REEF BIOLOGICAL CRITERIA: USING THE CLEAN ...

    EPA Pesticide Factsheets

    Coral reefs are declining at unprecedented rates worldwide due to multiple interactive stressors including climate change and land-based sources of pollution. The Clean Water Act (CWA) can be a powerful legal instrument for protecting water resources, including the biological inhabitants of coral reefs. The objective of the CWA is to restore and maintain the chemical, physical and biological integrity of water resources. Coral reef protection and restoration under the Clean Water Act begins with water quality standards - provisions of state or Federal law that consist of a designated use(s) for the waters of the United States and water quality criteria sufficient to protect the uses. Aquatic life use is the designated use that is measured by biological criteria (biocriteria). Biocriteria are expectations set by a jurisdiction for the quality and quantity of living aquatic resources in a defined waterbody. Biocriteria are an important addition to existing management tools for coral reef ecosystems. The Technical Support Document “Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure” will provide a framework to aid States and Territories in their development, adoption, and implementation of coral reef biocriteria in their respective water quality standards. The Technical Support Document “Coral Reef Biological Criteria: Using the Clean Water Act to Protect a National Treasure” will provide a framework for coral re

  3. S-Nitrosothiol measurements in biological systems⋄

    PubMed Central

    Gow, Andrew; Doctor, Allan; Mannick, Joan; Gaston, Benjamin

    2007-01-01

    S-Nitrosothiol (SNO) cysteine modifications are regulated signaling reactions that dramatically affect, and are affected by, protein conformation. The lability of the S-NO bond can make SNO-modified proteins cumbersome to measure accurately. Here, we review methodologies for detecting SNO modifications in biology. There are three caveats. 1) Many assays for biological SNOs are used near the limit of detection: standard curves must be in the biologically relevant concentration range. 2) The assays that are most reliable are those that modify SNO protein or peptide chemistry the least. 3) Each result should be quantitatively validated using more than one assay. Improved assays are needed and are in development. PMID:17379583

  4. H-point standard additions method for simultaneous determination of sulfamethoxazole and trimethoprim in pharmaceutical formulations and biological fluids with simultaneous addition of two analytes.

    PubMed

    Givianrad, M H; Saber-Tehrani, M; Aberoomand-Azar, P; Mohagheghian, M

    2011-03-01

    The applicability of H-point standard additions method (HPSAM) to the resolving of overlapping spectra corresponding to the sulfamethoxazole and trimethoprim is verified by UV-vis spectrophotometry. The results show that the H-point standard additions method with simultaneous addition of both analytes is suitable for the simultaneous determination of sulfamethoxazole and trimethoprim in aqueous media. The results of applying the H-point standard additions method showed that the two drugs could be determined simultaneously with the concentration ratios of sulfamethoxazole to trimethoprim varying from 1:18 to 16:1 in the mixed samples. Also, the limits of detections were 0.58 and 0.37 μmol L(-1) for sulfamethoxazole and trimethoprim, respectively. In addition the means of the calculated RSD (%) were 1.63 and 2.01 for SMX and TMP, respectively in synthetic mixtures. The proposed method has been successfully applied to the simultaneous determination of sulfamethoxazole and trimethoprim in some synthetic, pharmaceutical formulation and biological fluid samples. Copyright © 2011 Elsevier B.V. All rights reserved.

  5. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

    PubMed Central

    Waltemath, Dagmar; Bergmann, Frank T.; Chaouiya, Claudine; Czauderna, Tobias; Gleeson, Padraig; Goble, Carole; Golebiewski, Martin; Hucka, Michael; Juty, Nick; Krebs, Olga; Le Novère, Nicolas; Mi, Huaiyu; Moraru, Ion I.; Myers, Chris J.; Nickerson, David; Olivier, Brett G.; Rodriguez, Nicolas; Schreiber, Falk; Smith, Lucian; Zhang, Fengkai; Bonnet, Eric

    2014-01-01

    The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats in computational systems biology and related fields. This report summarizes the topics and activities of the fourth edition of the annual COMBINE meeting, held in Paris during September 16-20 2013, and attended by a total of 96 people. This edition pioneered a first day devoted to modeling approaches in biology, which attracted a broad audience of scientists thanks to a panel of renowned speakers. During subsequent days, discussions were held on many subjects including the introduction of new features in the various COMBINE standards, new software tools that use the standards, and outreach efforts. Significant emphasis went into work on extensions of the SBML format, and also into community-building. This year’s edition once again demonstrated that the COMBINE community is thriving, and still manages to help coordinate activities between different standards in computational systems biology.

  6. Cycles of Nature. An Introduction to Biological Rhythms.

    ERIC Educational Resources Information Center

    Ahlgren, Andrew; Halberg, Franz

    This book is an outlined for the short study (1- to 2-weeks) of chronobiology, a field of science that explores the relationships between time and biological functions. It develops step-by-step the reasoning that leads to the current scientific understanding of biological rhythms. The unit can be inserted into a standard middle or high school…

  7. Biological control of purple loosestrife in North America

    Treesearch

    Bernd Blossey

    1998-01-01

    In recent years, interest in a biological method to control problem plants in natural areas in the United States has grown. All federal agencies must comply with standards to reduce the use and dependence on chemical control of weeds. But, biological methodologies are not readily available, nor have they been well-endorsed or financially supported. Despite an excellent...

  8. Analysis of the Association Between Electrocardiographic P-wave Characteristics and Atrial Fibrillation in the REGICOR Study.

    PubMed

    Massó-van Roessel, Albert; Escobar-Robledo, Luis Alberto; Dégano, Irene R; Grau, María; Sala, Joan; Ramos, Rafel; Marrugat, Jaume; Bayés de Luna, Antoni; Elosua, Roberto

    2017-10-01

    Atrial fibrillation (AF) is the most common clinically significant cardiac arrhythmia. P-wave duration and interatrial blocks (IAB) have been reported to be associated with AF. Our aim was to determine the individual and combined association of P-wave duration and advanced IAB morphology with AF. We designed an age-, sex-, and survey-matched case-control study nested in a population-based cohort (REGICOR: REgistre GIroní del COR). Two different surveys recruited a total of 9380 participants from 1999 to 2005; all participants were invited to a second examination between 2009 and 2013. For the present study, we selected participants aged 25 to 79 years with follow-up through the end of the study. All electrocardiograms were analyzed by 2 observers to determine P-wave duration and morphology (normal, partial, or advanced IAB). The median follow-up was 7.12 years. Eighty participants presented with AF, had a legible baseline electrocardiogram, and were included in the study, along with 160 controls. P-wave duration and the presence of partial or advanced IAB were associated with AF. When P-wave duration and morphology were considered together, only P-wave duration (≥ 110 milliseconds) showed an independent and strong association with AF. The odds ratio for AF of P-wave duration between 110-119, 120-129 and ≥ 130 milliseconds vs < 110 milliseconds were 5.33; 95%CI, 1.74-16.33, 5.08; 95%CI, 1.73-14.90 and 5.44; 95%CI, 1.95-15.15, respectively. A P-wave longer than 110 milliseconds increases the risk of AF. Advanced IAB morphology did not seem to provide an additional AF risk beyond that of P-wave duration. Copyright © 2017 Sociedad Española de Cardiología. Published by Elsevier España, S.L.U. All rights reserved.

  9. Electrochemiluminescence Assays for Insulin and Glutamic Acid Decarboxylase Autoantibodies Improve Prediction of Type 1 Diabetes Risk

    PubMed Central

    Miao, Dongmei; Steck, Andrea K.; Zhang, Li; Guyer, K. Michelle; Jiang, Ling; Armstrong, Taylor; Muller, Sarah M.; Krischer, Jeffrey; Rewers, Marian

    2015-01-01

    Abstract We recently developed new electrochemiluminescence (ECL) insulin autoantibody (IAA) and glutamic acid decarboxylase 65 autoantibody (GADA) assays that discriminate high-affinity, high-risk diabetes-specific autoantibodies from low-affinity, low-risk islet autoantibodies (iAbs) detected by radioassay (RAD). Here, we report a further validation of the ECL-IAA and -GADA assays in 3,484 TrialNet study participants. The ECL assay and RAD were congruent in those with prediabetes and in subjects with multiple autoantibodies, but only 24% (P<0.0001) of single RAD-IAA-positive and 46% (P<0.0001) of single RAD-GADA-positive were confirmed by the ECL-IAA and -GADA assays, respectively. During a follow-up (mean, 2.4 years), 51% of RAD-IAA-positive and 63% of RAD-GADA-positive subjects not confirmed by ECL became iAb negative, compared with only 17% of RAD-IAA-positive (P<0.0001) and 15% of RAD-GADA-positive (P<0.0001) subjects confirmed by ECL assays. Among subjects with multiple iAbs, diabetes-free survival was significantly shorter if IAA or GADA was positive by ECL and negative by RAD than if IAA or GADA was negative by ECL and positive by RAD (P<0.019 and P<0.0001, respectively). Both positive and negative predictive values in terms of progression to type 1 diabetes mellitus were superior for ECL-IAA and ECL-GADA, compared with RADs. The prevalence of the high-risk human leukocyte antigen-DR3/4, DQB1*0302 genotype was significantly higher in subjects with RAD-IAA or RAD-GADA confirmed by ECL. In conclusion, both ECL-IAA and -GADA are more disease-specific and better able to predict the risk of progression to type 1 diabetes mellitus than the current standard RADs. PMID:25562486

  10. Electrochemiluminescence assays for insulin and glutamic acid decarboxylase autoantibodies improve prediction of type 1 diabetes risk.

    PubMed

    Miao, Dongmei; Steck, Andrea K; Zhang, Li; Guyer, K Michelle; Jiang, Ling; Armstrong, Taylor; Muller, Sarah M; Krischer, Jeffrey; Rewers, Marian; Yu, Liping

    2015-02-01

    We recently developed new electrochemiluminescence (ECL) insulin autoantibody (IAA) and glutamic acid decarboxylase 65 autoantibody (GADA) assays that discriminate high-affinity, high-risk diabetes-specific autoantibodies from low-affinity, low-risk islet autoantibodies (iAbs) detected by radioassay (RAD). Here, we report a further validation of the ECL-IAA and -GADA assays in 3,484 TrialNet study participants. The ECL assay and RAD were congruent in those with prediabetes and in subjects with multiple autoantibodies, but only 24% (P<0.0001) of single RAD-IAA-positive and 46% (P<0.0001) of single RAD-GADA-positive were confirmed by the ECL-IAA and -GADA assays, respectively. During a follow-up (mean, 2.4 years), 51% of RAD-IAA-positive and 63% of RAD-GADA-positive subjects not confirmed by ECL became iAb negative, compared with only 17% of RAD-IAA-positive (P<0.0001) and 15% of RAD-GADA-positive (P<0.0001) subjects confirmed by ECL assays. Among subjects with multiple iAbs, diabetes-free survival was significantly shorter if IAA or GADA was positive by ECL and negative by RAD than if IAA or GADA was negative by ECL and positive by RAD (P<0.019 and P<0.0001, respectively). Both positive and negative predictive values in terms of progression to type 1 diabetes mellitus were superior for ECL-IAA and ECL-GADA, compared with RADs. The prevalence of the high-risk human leukocyte antigen-DR3/4, DQB1*0302 genotype was significantly higher in subjects with RAD-IAA or RAD-GADA confirmed by ECL. In conclusion, both ECL-IAA and -GADA are more disease-specific and better able to predict the risk of progression to type 1 diabetes mellitus than the current standard RADs.

  11. Satisfying Friendship Maintenance Expectations: The Role of Friendship Standards and Biological Sex

    ERIC Educational Resources Information Center

    Hall, Jeffrey A.; Larson, Kiley A.; Watts, Amber

    2011-01-01

    The ideal standards model predicts linear relationship among friendship standards, expectation fulfillment, and relationship satisfaction. Using a diary method, 197 participants reported on expectation fulfillment in interactions with one best, one close, and one casual friend (N = 591) over five days (2,388 interactions). Using multilevel…

  12. Adverse Pregnancy Outcomes Among Women with Prior Spontaneous or Induced Abortions

    PubMed Central

    Makhlouf, Michel A; Clifton, Rebecca G.; Roberts, James M.; Myatt, Leslie; Hauth, John C.; Leveno, Kenneth J.; Varner, Michael W.; Thorp, John M.; Mercer, Brian M.; Peaceman, Alan M.; Ramin, Susan M.; Iams, Jay D.; Sciscione, Anthony; Tolosa, Jorge E.; Sorokin, Yoram

    2014-01-01

    OBJECTIVE To determine whether prior spontaneous (SAB) or induced (IAB) abortions, or the inter-pregnancy interval are associated with subsequent adverse pregnancy outcomes in nulliparous women. METHODS We performed a secondary analysis of data collected from nulliparous women enrolled in a completed trial of vitamins C and E or placebo for preeclampsia prevention. Adjusted odds ratios for maternal and fetal outcomes were determined for nulliparous women with prior SABs and IABs as compared to primigravid participants. RESULTS Compared with primigravidas, women with one prior SAB were at increased risk for perinatal death (OR 1.5; 95% CI 1.1–2.3) in subsequent pregnancies. Two or more SABs were associated with an increased risk for spontaneous preterm birth (OR 2.6, 95% CI 1.7–4.0), preterm PROM (OR 2.9, 95% CI 1.6–5.3) and perinatal death (OR 2.8, 95% CI 1.5–5.3). Women with one previous IAB had higher rates of spontaneous preterm birth (OR 1.4, 95% CI 1.0–1.9) and preterm PROM (OR 2.0, 95% CI 1.4–3.0). An inter-pregnancy interval less than 6 months after SAB was not associated with adverse outcomes. CONCLUSION Nulliparous women with a history of SAB or IAB, especially multiple SABs, are at increased risk for adverse pregnancy outcomes. PMID:24347257

  13. Macromolecules Inquiry: Transformation of a Standard Biochemistry Lab

    ERIC Educational Resources Information Center

    Unsworth, Elizabeth

    2014-01-01

    Identification of macromolecules in food is a standard introductory high school biology lab. The intent of this article is to describe the conversion of this standard cookbook lab into an inquiry investigation. Instead of verifying the macromolecules found in food, students use their knowledge of the macromolecules in food to determine the…

  14. Tadpoles: the Biology of Anuran Larvae

    USGS Publications Warehouse

    McDiarmid, R.W.; Altig, R.

    1999-01-01

    The recent alarming declines in amphibian populations worldwide and the suitability of amphibians for use in answering research questions in disciplines as diverse as molecular systematics, animal behavior, ecology, and evolutionary biology have focused enormous attention on tadpoles. Yet despite this growing interest, relatively little is known about these fascinating creatures. n this invaluable reference, leading experts on tadpole biology relate what we currently know about tadpoles and what we might learn from them in the future. Tadpoles provides detailed summaries of tadpole morphology, development, behavior, ecology, and environmental physiology; explores the evolutionary consequences of the tadpole stage; synthesizes available information on their biodiversity, and presents a standardized terminology and an exhaustive literature review of tadpole biology.

  15. 77 FR 47117 - Chemical, Biological, Radiological, Nuclear (CBRN) Protective Ensemble Standard, Certification...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-07

    ... (at www.justnet.org ) three draft documents related to Chemical, Biological, Radiological, Nuclear... until September 21, 2012. FOR FURTHER INFORMATION CONTACT: For further information, see www.justnet.org , or contact David Otterson by telephone at 301-519-5498 or by email at [email protected]org...

  16. Diffusion of synthetic biology: a challenge to biosafety.

    PubMed

    Schmidt, Markus

    2008-06-01

    One of the main aims of synthetic biology is to make biology easier to engineer. Major efforts in synthetic biology are made to develop a toolbox to design biological systems without having to go through a massive research and technology process. With this "de-skilling" agenda, synthetic biology might finally unleash the full potential of biotechnology and spark a wave of innovation, as more and more people have the necessary skills to engineer biology. But this ultimate domestication of biology could easily lead to unprecedented safety challenges that need to be addressed: more and more people outside the traditional biotechnology community will create self-replicating machines (life) for civil and defence applications, "biohackers" will engineer new life forms at their kitchen table; and illicit substances will be produced synthetically and much cheaper. Such a scenario is a messy and dangerous one, and we need to think about appropriate safety standards now.

  17. ARADISH - Development of a Standardized Plant Growth Chamber for Experiments in Gravitational Biology Using Ground Based Facilities

    NASA Astrophysics Data System (ADS)

    Schüler, Oliver; Krause, Lars; Görög, Mark; Hauslage, Jens; Kesseler, Leona; Böhmer, Maik; Hemmersbach, Ruth

    2016-06-01

    Plant development strongly relies on environmental conditions. Growth of plants in Biological Life Support Systems (BLSS), which are a necessity to allow human survival during long-term space exploration missions, poses a particular problem for plant growth, as in addition to the traditional environmental factors, microgravity (or reduced gravity such as on Moon or Mars) and limited gas exchange hamper plant growth. Studying the effects of reduced gravity on plants requires real or simulated microgravity experiments under highly standardized conditions, in order to avoid the influence of other environmental factors. Analysis of a large number of biological replicates, which is necessary for the detection of subtle phenotypical differences, can so far only be achieved in Ground Based Facilities (GBF). Besides different experimental conditions, the usage of a variety of different plant growth chambers was a major factor that led to a lack of reproducibility and comparability in previous studies. We have developed a flexible and customizable plant growth chamber, called ARAbidopsis DISH (ARADISH), which allows plant growth from seed to seedling, being realized in a hydroponic system or on Agar. By developing a special holder, the ARADISH can be used for experiments with Arabidopsis thaliana or a plant with a similar habitus on common GBF hardware, including 2D clinostats and Random Positioning Machines (RPM). The ARADISH growth chamber has a controlled illumination system of red and blue light emitting diodes (LED), which allows the user to apply defined light conditions. As a proof of concept we tested a prototype in a proteomic experiment in which plants were exposed to simulated microgravity or a 90° stimulus. We optimized the design and performed viability tests after several days of growth in the hardware that underline the utility of ARADISH in microgravity research.

  18. Bovine colostrum as a biologic in clinical medicine: a review. Part I: biotechnological standards, pharmacodynamic and pharmacokinetic characteristics and principles of treatment.

    PubMed

    Struff, W G; Sprotte, G

    2007-04-01

    Mammals supply their newborn before birth, at birth or shortly after birth with antibodies, immunocytes and humoral constituents. This "borrowed immunity" is a form of passive immunization to protect the newborn against environmental pathogens until it establishes its own pathogen recognition and disposal systems. In cows, goats, horses and some other animal species, most immunoglobulins are obtained from the colostrum, the first milk after birth, via the gut but in humans the majority of immunoglobulins, and those of the IgG-class in particular, are acquired from the mother by placental transport in the weeks prior to parturition. It has long been known that the consumption of bovine colostrum by humans has therapeutic effects e.g. in gastrointestinal infections, but only since the second half of the last century has it been possible to prepare stable, standardized preparations of colostrum. These biologics are administered to patients in combination with standard therapies as so-called balanced supportive diets. Investigations with standardized colostrum preparations in animal models of human disease and estimates of bovine IgG activity in the human GI-tract, described in this review, have provided preclinical data supporting the use of bovine colostrum in human diseases. On the other hand, the number of bovine colostrum products with a sufficiently large and reliable database is limited and the precise nature of the therapeutic targets is still being evaluated.

  19. Biology Curriculum Guide. Bulletin 1646.

    ERIC Educational Resources Information Center

    Louisiana State Dept. of Education, Baton Rouge. Div. of Academic Programs.

    This curriculum guide, developed to establish statewide curriculum standards for the Louisiana Competency-based Education Program, contains the minimum competencies and process skills that should be included in a biology course. It consists of: (1) a rationale for an effective science program; (2) a list and description of four major goals of…

  20. Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

    PubMed

    Hucka, M; Finney, A; Bornstein, B J; Keating, S M; Shapiro, B E; Matthews, J; Kovitz, B L; Schilstra, M J; Funahashi, A; Doyle, J C; Kitano, H

    2004-06-01

    Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.

  1. Mammalian synthetic biology for studying the cell

    PubMed Central

    Mathur, Melina; Xiang, Joy S.

    2017-01-01

    Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology. PMID:27932576

  2. Mammalian synthetic biology for studying the cell.

    PubMed

    Mathur, Melina; Xiang, Joy S; Smolke, Christina D

    2017-01-02

    Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology. © 2017 Mathur et al.

  3. 9 CFR 113.113 - Autogenous biologics.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Autogenous biologics. 113.113 Section 113.113 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE VIRUSES, SERUMS, TOXINS, AND ANALOGOUS PRODUCTS; ORGANISMS AND VECTORS STANDARD REQUIREMENTS...

  4. Biologic agents for IBD: practical insights.

    PubMed

    Danese, Silvio; Vuitton, Lucine; Peyrin-Biroulet, Laurent

    2015-09-01

    Six biologic agents are currently approved for the treatment of IBD: four anti-TNF agents (infliximab, adalimumab, golimumab and certolizumab pegol) and two anti-integrin agents (natalizumab and vedolizumab). In Crohn's disease and ulcerative colitis refractory to standard medications, treatment choice among available biologic agents can be challenging. Several parameters should be taken into account to help physicians through the decision-making process, including the comparative effectiveness and long-term safety profile, availability and labelling in the prescriber's country, international guidelines, and cost, as well as patient preferences (such as the route of administration). Herein, we provide practical insights on the use of biologic agents in IBD. The results of head-to-head trials between biologic agents are eagerly awaited to guide decision-making regarding the choice of first-line biologic agents and to determine whether switching within the same drug class or swapping (switching out of the drug class) is preferable after primary or secondary loss of response to the first biologic agent. In the near future, treatment algorithms might evolve with the launch of new drugs (such as ustekinumab, tofacitinib and etrolizumab) and the increased use of biosimilars.

  5. Learning cell biology as a team: a project-based approach to upper-division cell biology.

    PubMed

    Wright, Robin; Boggs, James

    2002-01-01

    To help students develop successful strategies for learning how to learn and communicate complex information in cell biology, we developed a quarter-long cell biology class based on team projects. Each team researches a particular human disease and presents information about the cellular structure or process affected by the disease, the cellular and molecular biology of the disease, and recent research focused on understanding the cellular mechanisms of the disease process. To support effective teamwork and to help students develop collaboration skills useful for their future careers, we provide training in working in small groups. A final poster presentation, held in a public forum, summarizes what students have learned throughout the quarter. Although student satisfaction with the course is similar to that of standard lecture-based classes, a project-based class offers unique benefits to both the student and the instructor.

  6. Introducing Statistical Inference to Biology Students through Bootstrapping and Randomization

    ERIC Educational Resources Information Center

    Lock, Robin H.; Lock, Patti Frazer

    2008-01-01

    Bootstrap methods and randomization tests are increasingly being used as alternatives to standard statistical procedures in biology. They also serve as an effective introduction to the key ideas of statistical inference in introductory courses for biology students. We discuss the use of such simulation based procedures in an integrated curriculum…

  7. Issue-Oriented Science: Using Socioscientific Issues to Engage Biology Students

    ERIC Educational Resources Information Center

    Lenz, Laura; Willcox, Maia K.

    2012-01-01

    In today's global society, with science and technology advancing at a rapid pace, issues about biological topics are common. A typical standards-based high school or general college-level biology classroom naturally lends itself to teaching issue-oriented science. In an issue-oriented classroom, students analyze and discuss personal, societal, and…

  8. Synergistic Synthetic Biology: Units in Concert

    PubMed Central

    Trosset, Jean-Yves; Carbonell, Pablo

    2013-01-01

    Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications. PMID:25022769

  9. Synergistic Synthetic Biology: Units in Concert.

    PubMed

    Trosset, Jean-Yves; Carbonell, Pablo

    2013-01-01

    Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications.

  10. Comparison of human chorionic somatomammotropin (HCS) standards for radioimmunoassay

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

    Cocola, F.; Genazzani, A.R.; Neri, P.

    1973-01-01

    A comparison was made between four commercially available HCS standards for radioimmunoassay, an interim standard from the Division of Biological Standards of the Medical Research Council. and a new preparation from our laboratories. Many differences are found between the various HCS preparations tested, and this may be one reason for the discrepancies found in absolute HCS plasma levels reported by different authors. The new Sclavo preparation seems to be the best, and its use is proposed as a new standard for radioimmunoassay. (auth)

  11. Authentication: A Standard Problem or a Problem of Standards?

    PubMed

    Capes-Davis, Amanda; Neve, Richard M

    2016-06-01

    Reproducibility and transparency in biomedical sciences have been called into question, and scientists have been found wanting as a result. Putting aside deliberate fraud, there is evidence that a major contributor to lack of reproducibility is insufficient quality assurance of reagents used in preclinical research. Cell lines are widely used in biomedical research to understand fundamental biological processes and disease states, yet most researchers do not perform a simple, affordable test to authenticate these key resources. Here, we provide a synopsis of the problems we face and how standards can contribute to an achievable solution.

  12. Impact of Radiation Biology on Fundamental Insights in Biology

    DOE R&D Accomplishments Database

    Setlow, Richard B.

    1982-07-27

    Research supported by OHER [Office of Health and Environmental Research] and its predecessors has as one of its major goals an understanding of the effects of radiation at low doses and dose rates on biological systems, so as to predict their effects on humans. It is not possible to measure such effects directly. They must be predicted from basic knowledge on how radiation affects cellular components such as DNA and membranes and how cells react to such changes. What is the probability of radiation producing human mutations and what are the probabilities of radiation producing cancer? The end results of such studies are radiation exposure standards for workers and for the general population. An extension of these goals is setting standards for exposure to chemicals involved in various energy technologies. This latter problem is much more difficult because chemical dosimetry is a primitive state compared to radiation dosimetry.

  13. [Hygiene and security management in medical biology laboratory].

    PubMed

    Vinner, E; Odou, M F; Fovet, B; Ghnassia, J C

    2013-06-01

    Risk management in Medical Biology Laboratory (MBL) which includes hygiene and waste management, is an integrated process to the whole MBL organisation. It is composed of three stages: risks factors identification, grading and prioritization, and their evaluation in the system. From the legislation and NF EN ISO 15189 standard's requirements viewpoint, prevention and protection actions to implement are described, at premises level, but also at work station environment's one (human resources and equipments) towards biological, chemical, linked to gas, to ionizing or non ionizing radiations and fire riks, in order not to compromise patients safety, employees safety, and quality results. Then, although NF EN 15189 standard only enacts requirements in terms of prevention, curative actions after established blood or chemical exposure accident are defined.

  14. Overview on the standardization in the field of electromagnetic compatibility

    NASA Astrophysics Data System (ADS)

    Goldberg, Georges

    1989-04-01

    Standardization in the domain of electromagnetic compatibility (EMC) is discussed, with specific reference to the standards of the International Electrotechnical Commission, the Comite International Special des Perturbations Radioelectriques, and the Comite Europeen de Normalisation Electrotechnique. EMC fields considered include radiocommunications, telecommunications, biological effects, and data transmission. Standards are presented for such electromagnetic disturbances as low-frequency, high-frequency, conduction, and radiation phenomena.

  15. Evaluation of DoD Biological Safety and Security Implementation

    DTIC Science & Technology

    2016-04-27

    biosecurity policy and directives, plans, orders, and guidance across DoD Component laboratories that were conducting research using biological select ...taken, • ensure that all BSAT laboratories are inspected regularly according to a standardized set of criteria , • coordinate external technical and...Biological Select Agent and Toxins laboratory inspections. Management Comments and Our Response The Under Secretary of Defense for Acquisition

  16. Self-regulating smoking and snacking through physical activity.

    PubMed

    Oh, Hwajung; Taylor, Adrian H

    2014-04-01

    Emotional snacking contributes to weight gain after smoking cessation. Exercise acutely reduces cravings for cigarettes and snack food. This study examined if different exercise intensities acutely reduces snack and cigarette cravings and attentional bias (AB) to video clips of snacks and cigarettes among abstinent smokers. Abstinent smokers (and snackers; N = 23) randomly did 15 mins of moderate and vigorous cycling and a passive control in a cross-over design. Visual initial AB (IAB) and maintained AB (MAB) were assessed pre- and after treatment while watching paired snacking/neutral or smoking/neutral video clips. Desire to snack and smoke were assessed throughout. ANOVAs revealed significant condition × time interactions for initial and maintained AB for smoking [IAB: F(1.58, 34.75) = 3.58, MAB: F(2, 44) = 4.52, p < .05] and snacking [IAB: F(2, 44) = 8.13, MAB: F(2, 44) = 5.08, p < .01]. IAB for both smoking and snacking were lower after moderate and vigorous exercise than the control. MAB was lower only after vigorous exercise. Fully repeated ANOVAs revealed a condition × time interaction for desire to smoke, F(3.31, 72.75) = 12.62, and snack F(4.34, 95.52) = 9.51, p < .001. Cravings were lower after moderate and vigorous exercise, compared with control. Exercise acutely reduces both AB and cravings for cigarettes and snacks and may help self-regulation of smoking and snacking. Vigorous exercise was only more advantageous for reducing MAB.

  17. Adverse pregnancy outcomes among women with prior spontaneous or induced abortions.

    PubMed

    Makhlouf, Michel A; Clifton, Rebecca G; Roberts, James M; Myatt, Leslie; Hauth, John C; Leveno, Kenneth J; Varner, Michael W; Thorp, John M; Mercer, Brian M; Peaceman, Alan M; Ramin, Susan M; Iams, Jay D; Sciscione, Anthony; Tolosa, Jorge E; Sorokin, Yoram

    2014-10-01

    The aim of the article is to determine whether prior spontaneous abortion (SAB) or induced abortion (IAB), or the interpregnancy interval are associated with subsequent adverse pregnancy outcomes in nulliparous women. We performed a secondary analysis of data collected from nulliparous women enrolled in a completed trial of vitamins C and E or placebo for preeclampsia prevention. Adjusted odds ratios (ORs) for maternal and fetal outcomes were determined for nulliparous women with prior SABs and IABs as compared with primigravid participants. Compared with primigravidas, women with one prior SAB were at increased risk for perinatal death (adj. OR, 1.5; 95% CI, 1.1-2.3) in subsequent pregnancies. Two or more SABs were associated with an increased risk for spontaneous preterm birth (PTB) (adj. OR, 2.6, 95% CI, 1.7-4.0), preterm premature rupture of membranes (PROM) (adj. OR, 2.9; 95% CI, 1.6-5.3), and perinatal death (adj. OR, 2.8; 95% CI, 1.5-5.3). Women with one previous IAB had higher rates of spontaneous PTB (adj. OR, 1.4; 95% CI, 1.0-1.9) and preterm PROM (OR, 2.0; 95% CI, 1.4-3.0). An interpregnancy interval less than 6 months after SAB was not associated with adverse outcomes. Nulliparous women with a history of SAB or IAB, especially multiple SABs, are at increased risk for adverse pregnancy outcomes. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  18. News from the Biological Stain Commission No. 11.

    PubMed

    Lyon, H O; Horobin, R W

    2012-01-01

    The 11th issue of News from the Biological Stain Commission (BSC) provides our first impressions of the REACH and ECHA programs. We intend to give a more thorough account of what these important programs actually mean in later editions of News from the Biological Stain Commission. Under the heading of Regulatory Affairs, the Biological Stain Commission's International Affairs Committee presents information from the opening session of the meeting of the International Standards Organization ISO/TC 212 Clinical laboratory testing and in vitro diagnostic test systems held on 2-4 June 2010 in Seoul, Republic of Korea.

  19. Web servicing the biological office.

    PubMed

    Szugat, Martin; Güttler, Daniel; Fundel, Katrin; Sohler, Florian; Zimmer, Ralf

    2005-09-01

    Biologists routinely use Microsoft Office applications for standard analysis tasks. Despite ubiquitous internet resources, information needed for everyday work is often not directly and seamlessly available. Here we describe a very simple and easily extendable mechanism using Web Services to enrich standard MS Office applications with internet resources. We demonstrate its capabilities by providing a Web-based thesaurus for biological objects, which maps names to database identifiers and vice versa via an appropriate synonym list. The client application ProTag makes these features available in MS Office applications using Smart Tags and Add-Ins. http://services.bio.ifi.lmu.de/prothesaurus/

  20. The second international standard for polymyxin B.

    PubMed

    Lightbown, J W; Thomas, A H; Grab, B; Outschoorn, A S

    1973-01-01

    Since supplies of the first International Standard for Polymyxin B were exhausted, it was replaced by a second international standard the potency of which was estimated from the results of a collaborative assay carried out by 5 laboratories in 4 countries. The wide variations in the results probably resulted from difficulties experienced in handling the first international standard. The potency finally agreed upon by the collaborating laboratories, on the basis of the overall mean values obtained after rejection of the most discrepant assays, was 8 403 IU/mg. That value was accepted by the WHO Expert Committee on Biological Standardization (1970), which consequently defined the International Unit of polymyxin B as the activity contained in 0.000119 mg of the second international standard.

  1. The second international standard for polymyxin B*

    PubMed Central

    Lightbown, J. W.; Thomas, A. H.; Grab, B.; Outschoorn, A. S.

    1973-01-01

    Since supplies of the first International Standard for Polymyxin B were exhausted, it was replaced by a second international standard the potency of which was estimated from the results of a collaborative assay carried out by 5 laboratories in 4 countries. The wide variations in the results probably resulted from difficulties experienced in handling the first international standard. The potency finally agreed upon by the collaborating laboratories, on the basis of the overall mean values obtained after rejection of the most discrepant assays, was 8 403 IU/mg. That value was accepted by the WHO Expert Committee on Biological Standardization (1970), which consequently defined the International Unit of polymyxin B as the activity contained in 0.000119 mg of the second international standard. PMID:4350877

  2. [Building confidence in biological products].

    PubMed

    Rosdahl, Nils; Hardy, Anne

    2006-01-01

    During the last decades of the 19th century, discoveries in microbiology paved the way for health programmes as an integral part of social modernisation. Public opinion about the consequences for governmental involvement differed, but in Denmark the state's openness to modern medicine encouraged the establishment of Statens Serum Institut (SSI) in 1902, initially for the production of anti-diphtheritic serum. Under its director, Thorvald Madsen (1870-1957), the SSI soon acquired a reputation for the high quality of its products and its cutting edge research. After qualifying in medicine in 1893, Madsen worked both at the Pasteur Institute and with Paul Ehrlich in Frankfurt. During World War I, he served with the Red Cross, caring for German, Austrian and Russian prisoners of war. He had an extensive and expanding network of international contacts, and he was eminently qualified to assume the elected office of President of the League of Nations' Health Committee. The Committee served as the 'parliamentary body' of the League of Nations Health Organisation (LNHO), and Madsen's hand can be seen in much of the work undertaken by the LNHO. The drive to achieve uniform standards for biological products related directly to his own as well as the SSI's interests and expertise. Undoubtedly, standardization of biological products had an immense importance for their distribution, scientifically, commercially and therapeutically. Madsen was president of the LNHO's Commission on Biological Standardisation from 1924, and during the interwar years, the SSI was heavily involved in establishing standards for biological products such as tuberculin and tetanus antitoxin. Madsen's interests extended to application of prevention technologies, and he utilised the opportunities in Denmark to further their use, notably in the case of tuberculosis. The introduction of the BCG vaccine promised a solution to the TB problem, but the Lübeck disaster generated a widespread reaction against the

  3. Data integration in biological research: an overview.

    PubMed

    Lapatas, Vasileios; Stefanidakis, Michalis; Jimenez, Rafael C; Via, Allegra; Schneider, Maria Victoria

    2015-12-01

    Data sharing, integration and annotation are essential to ensure the reproducibility of the analysis and interpretation of the experimental findings. Often these activities are perceived as a role that bioinformaticians and computer scientists have to take with no or little input from the experimental biologist. On the contrary, biological researchers, being the producers and often the end users of such data, have a big role in enabling biological data integration. The quality and usefulness of data integration depend on the existence and adoption of standards, shared formats, and mechanisms that are suitable for biological researchers to submit and annotate the data, so it can be easily searchable, conveniently linked and consequently used for further biological analysis and discovery. Here, we provide background on what is data integration from a computational science point of view, how it has been applied to biological research, which key aspects contributed to its success and future directions.

  4. Biological reference materials for extracellular vesicle studies.

    PubMed

    Valkonen, S; van der Pol, E; Böing, A; Yuana, Y; Yliperttula, M; Nieuwland, R; Laitinen, S; Siljander, P R M

    2017-02-15

    Extracellular vesicles (EVs) mediate normal physiological homeostasis and pathological processes by facilitating intercellular communication. Research of EVs in basic science and clinical settings requires both methodological standardization and development of reference materials (RM). Here, we show insights and results of biological RM development for EV studies. We used a three-step approach to find and develop a biological RM. First, a literature search was done to find candidates for biological RMs. Second, a questionnaire was sent to EV researchers querying the preferences for RM and their use. Third, a biological RM was selected, developed, characterized, and evaluated. The responses to the survey demonstrated a clear and recognized need for RM optimized for the calibration of EV measurements. Based on the literature, naturally occurring and produced biological RM, such as virus particles and liposomes, were proposed as RM. However, none of these candidate RMs have properties completely matching those of EVs, such as size and refractive index distribution. Therefore, we evaluated the use of nanoerythrosomes (NanoE), vesicles produced from erythrocytes, as a potential biological RM. The strength of NanoE is their resemblance to EVs. Compared to the erythrocyte-derived EVs (eryEVs), NanoE have similar morphology, a similar refractive index (1.37), larger diameter (70% of the NanoE are over 200nm), and increased positive staining for CD235a and lipids (Di-8-ANEPPS) (58% and 67% in NanoE vs. 21% and 45% in eryEVs, respectively). Altogether, our results highlight the general need to develop and validate new RM with similar physical and biochemical properties as EVs to standardize EV measurements between instruments and laboratories. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  5. [Biologic therapy in idiopathic inflammatory myopathy].

    PubMed

    Selva-O'Callaghan, Albert; Ramos Casals, Manel; Grau Junyent, Josep M

    2014-09-15

    The aim of this article is to study the evidence-based knowledge related to the use of biological therapies in patients diagnosed with idiopathic inflammatory myopathy (dermatomyositis, polymyositis and inclusion body myositis). In this review the leading published studies related to the use of biological therapy in patients with myositis are analysed; mainly those with high methodological standards, that means randomized and controlled studies. Methodological drawbacks due to the rarity and heterogeneity of these complex diseases are also addressed. Up to now is not possible to ascertain the biologics as a recommended therapy in patients with myositis, at least based in the current evidence-based knowledge, although it can not be neglected as a therapeutic option in some clinical situations, taking into account the scarce of effective treatments in those patients, especially in refractory myositis. Future studies probably will help to better define the role of biological therapies in patients with idiopathic inflammatory myopathy. Copyright © 2013 Elsevier España, S.L.U. All rights reserved.

  6. Chemical Foundations of Hydrogen Sulfide Biology

    PubMed Central

    Li, Qian; Lancaster, Jack R.

    2013-01-01

    Following nitric oxide (nitrogen monoxide) and carbon monoxide, hydrogen sulfide (or its newer systematic name sulfane, H2S) became the third small molecule that can be both toxic and beneficial depending on the concentration. In spite of its impressive therapeutic potential, the underlying mechanisms for its beneficial effects remain unclear. Any novel mechanism has to obey fundamental chemical principles. H2S chemistry was studied long before its biological relevance was discovered, however, with a few exceptions, these past works have received relatively little attention in the path of exploring the mechanistic conundrum of H2S biological functions. This review calls attention to the basic physical and chemical properties of H2S, focuses on the chemistry between H2S and its three potential biological targets: oxidants, metals and thiol derivatives, discusses the applications of these basics into H2S biology and methodology, and introduces the standard terminology to this youthful field. PMID:23850631

  7. Isotopic studies of metabolic systems by mass spectrometry: using Pascal's triangle to produce biological standards with fully controlled labeling patterns.

    PubMed

    Millard, Pierre; Massou, Stéphane; Portais, Jean-Charles; Létisse, Fabien

    2014-10-21

    Mass spectrometry (MS) is widely used for isotopic studies of metabolism in which detailed information about biochemical processes is obtained from the analysis of isotope incorporation into metabolites. The biological value of such experiments is dependent on the accuracy of the isotopic measurements. Using MS, isotopologue distributions are measured from the quantitative analysis of isotopic clusters. These measurements are prone to various biases, which can occur during the experimental workflow and/or MS analysis. The lack of relevant standards limits investigations of the quality of the measured isotopologue distributions. To meet that need, we developed a complete theoretical and experimental framework for the biological production of metabolites with fully controlled and predictable labeling patterns. This strategy is valid for different isotopes and different types of metabolisms and organisms, and was applied to two model microorganisms, Pichia augusta and Escherichia coli, cultivated on (13)C-labeled methanol and acetate as sole carbon source, respectively. The isotopic composition of the substrates was designed to obtain samples in which the isotopologue distribution of all the metabolites should give the binomial coefficients found in Pascal's triangle. The strategy was validated on a liquid chromatography-tandem mass spectrometry (LC-MS/MS) platform by quantifying the complete isotopologue distributions of different intracellular metabolites, which were in close agreement with predictions. This strategy can be used to evaluate entire experimental workflows (from sampling to data processing) or different analytical platforms in the context of isotope labeling experiments.

  8. The Frontlines of Medicine Project: a proposal for the standardized communication of emergency department data for public health uses including syndromic surveillance for biological and chemical terrorism.

    PubMed

    Barthell, Edward N; Cordell, William H; Moorhead, John C; Handler, Jonathan; Feied, Craig; Smith, Mark S; Cochrane, Dennis G; Felton, Christopher W; Collins, Michael A

    2002-04-01

    The Frontlines of Medicine Project is a collaborative effort of emergency medicine (including emergency medical services and clinical toxicology), public health, emergency government, law enforcement, and informatics. This collaboration proposes to develop a nonproprietary, "open systems" approach for reporting emergency department patient data. The common element is a standard approach to sending messages from individual EDs to regional oversight entities that could then analyze the data received. ED encounter data could be used for various public health initiatives, including syndromic surveillance for chemical and biological terrorism. The interlinking of these regional systems could also permit public health surveillance at a national level based on ED patient encounter data. Advancements in the Internet and Web-based technologies could allow the deployment of these standardized tools in a rapid time frame.

  9. Methods for biological data integration: perspectives and challenges

    PubMed Central

    Gligorijević, Vladimir; Pržulj, Nataša

    2015-01-01

    Rapid technological advances have led to the production of different types of biological data and enabled construction of complex networks with various types of interactions between diverse biological entities. Standard network data analysis methods were shown to be limited in dealing with such heterogeneous networked data and consequently, new methods for integrative data analyses have been proposed. The integrative methods can collectively mine multiple types of biological data and produce more holistic, systems-level biological insights. We survey recent methods for collective mining (integration) of various types of networked biological data. We compare different state-of-the-art methods for data integration and highlight their advantages and disadvantages in addressing important biological problems. We identify the important computational challenges of these methods and provide a general guideline for which methods are suited for specific biological problems, or specific data types. Moreover, we propose that recent non-negative matrix factorization-based approaches may become the integration methodology of choice, as they are well suited and accurate in dealing with heterogeneous data and have many opportunities for further development. PMID:26490630

  10. The Third International Standard for Corticotrophin

    PubMed Central

    Bangham, D. R.; Mussett, M. V.; Stack-Dunne, M. P.

    1962-01-01

    At its meeting in September 1957, the WHO Expert Committee on Biological Standardization agreed with the recommendation of the International Conference on Corticotrophin, held in July 1957, that a new international standard for corticotrophin should be set up, since the Second International Standard was made from crude material and was unsuitable for the assay of the purer preparations of corticotrophin now in general clinical use. In this paper, the authors describe the steps taken to establish the Third International Standard for Corticotrophin, from the preparation and international collaborative assay of the new material to the choice of the ”subcutaneous assay” for deriving the potency. The clinical and pharmacological implications of this choice are discussed. Since the preparation, characterization and exact quantitative assay of standards for corticotrophin are so difficult, several batches of approximately 3500 ampoules were prepared in a similar way from the same material to serve as an international Working Standard. Samples from two batches were included in the collaborative assay and found to have the same potency as the Third Standard. Sufficient ampoules of the Working Standard are available for use as national and laboratory standards. PMID:13966359

  11. 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

  12. Field Markup Language: biological field representation in XML.

    PubMed

    Chang, David; Lovell, Nigel H; Dokos, Socrates

    2007-01-01

    With an ever increasing number of biological models available on the internet, a standardized modeling framework is required to allow information to be accessed or visualized. Based on the Physiome Modeling Framework, the Field Markup Language (FML) is being developed to describe and exchange field information for biological models. In this paper, we describe the basic features of FML, its supporting application framework and its ability to incorporate CellML models to construct tissue-scale biological models. As a typical application example, we present a spatially-heterogeneous cardiac pacemaker model which utilizes both FML and CellML to describe and solve the underlying equations of electrical activation and propagation.

  13. Severe and acute complications of biologics in psoriasis.

    PubMed

    Oussedik, Elias; Patel, Nupur U; Cash, Devin R; Gupta, Angela S; Feldman, Steven R

    2017-12-01

    Biologic therapies have revolutionized the approach to immune-mediated diseases such as psoriasis. Due to their favorable safety profiles and excellent efficacy, biologic agents are considered the gold standard for moderate-to-severe psoriasis. The aim of this paper is to saliently review the severe and acute complications of the Food and Drug Administration (FDA) approved biologic agents for psoriasis. Reviewed agents include tumor necrosis factor alpha inhibitors (etanercept, infliximab, and adalimumab), interleukin 12/23 inhibitors (ustekinumab), and interleukin 17 (IL-17) inhibitors (secukinumab and ixekizumab). While malignancies, serious infections, and major adverse cardiovascular events have been reported, their association with biologic therapy are not hypothesized as causal. However, IL-17 inhibitors appear to cause exacerbations and new cases of inflammatory bowel disease. While more long-term studies are warranted in understanding the biologic's long-term side effect profile, short-term studies have confirmed that the biologics are some of the safest treatment options for psoriasis. Nevertheless, certain populations yield higher risk to acute complications with the biologics than others - physicians must use their judgement and vigilance when monitoring and treating patients undergoing therapy with biological agents.

  14. Specific immunotherapy and biological treatments for occupational allergy.

    PubMed

    Moscato, Gianna; Pala, Gianni; Sastre, Joaquin

    2014-12-01

    Occupational allergy represents a substantial health, social, and financial burden for the society. Its management is a complex task that, in selected cases, may also include allergen-specific immunotherapy. The purpose of this article is to review clinical data on allergen immunotherapy and biological treatments applied to occupational allergy in 2013. Immunotherapy in occupational allergic diseases has been scarcely used, and only for a few sensitizers, such as latex, flour, and Hymenoptera venom, partly due to the lack of standardized extracts. The recent use of the molecular diagnosis can improve the indication and selection of suitable allergens for preparing new standardized and powerful extracts for immunotherapy. Some recent reports suggest a beneficial role of treatment with omalizumab in workers with occupational asthma who continue to be exposed to the causal agent. Although scarce, available data suggest that immunotherapy and biological treatments may allow allergic workers to continue their work activity, but further studies are needed to standardize extracts and to evaluate the cost-effectiveness of these treatments, when exposure at the workplace cannot be avoided.

  15. Interlaboratory studies and initiatives developing standards for proteomics

    PubMed Central

    Ivanov, Alexander R.; Colangelo, Christopher M.; Dufresne, Craig P.; Friedman, David B.; Lilley, Kathryn S.; Mechtler, Karl; Phinney, Brett S.; Rose, Kristie L.; Rudnick, Paul A.; Searle, Brian C.; Shaffer, Scott A.; Weintraub, Susan T.

    2013-01-01

    Proteomics is a rapidly transforming interdisciplinary field of research that embraces a diverse set of analytical approaches to tackle problems in fundamental and applied biology. This view-point article highlights the benefits of interlaboratory studies and standardization initiatives to enable investigators to address many of the challenges found in proteomics research. Among these initiatives, we discuss our efforts on a comprehensive performance standard for characterizing PTMs by MS that was recently developed by the Association of Biomolecular Resource Facilities (ABRF) Proteomics Standards Research Group (sPRG). PMID:23319436

  16. A glossary for avian conservation biology

    Treesearch

    Rolf R. Koford; John B. Dunning; Christine A. Ribic; Deborah M. Finch

    1994-01-01

    This glossary provides standard definitions for many of the terms used in avian conservation biology. We compiled these definitions to assist communication among researchers, managers, and others involved in the Neotropical Migratory Bird Conservation Program, also known as Partners in Flight. We used existing glossaries and recent literature to prepare this glossary....

  17. Internal Rb-Sr Age and Initial Sr-87/Sr-86 of a Silicate Inclusion from the Campo Del Cielo Iron Meteorite

    NASA Technical Reports Server (NTRS)

    Liu, Y.; Nyquist, L.; Wiesmann, H.; Shih, C.; Schwandt, C.; Takeda, H.

    2003-01-01

    The largest group of iron meteorites, IAB, is distinguished by the presence of diverse silicate inclusions. In principle, Rb-Sr and Sm-Nd radiometric dating of these silicate inclusions by internal isochron techniques can determine both the times of melting and parent/daughter ratios in the precursor materials via initial Sr-87/Sr-86 and Nd-143/Nd-144 ratios. The Sr-87/Sr-86 and Nd-143/Nd-144 ratios could distinguish chondritic precursors from already differentiated silicates. We reported Rb-Sr and Sm-Nd internal ischron ages of 4.52+/-0.03 Ga and 4.50+/-0.04 Ga, respectively, for plagioclase-diopside-rich material in the Caddo County IAB iron meteorite. These results are essentially identical to literature values of its Ar-Ar age of 4.520+/-0.005 Ga and its Sm-Nd age of 4.53+/-0.02 Ga. The purpose of this study is to evaluate the formation and evolution of silicate inclusions in IAB iron meteorites by determination of their initial Sr-87/Sr-86 ratios combined with higher-resolution chronology and mineralogical and geochemical studies.

  18. Quantitative Analysis of the Trends Exhibited by the Three Interdisciplinary Biological Sciences: Biophysics, Bioinformatics, and Systems Biology.

    PubMed

    Kang, Jonghoon; Park, Seyeon; Venkat, Aarya; Gopinath, Adarsh

    2015-12-01

    New interdisciplinary biological sciences like bioinformatics, biophysics, and systems biology have become increasingly relevant in modern science. Many papers have suggested the importance of adding these subjects, particularly bioinformatics, to an undergraduate curriculum; however, most of their assertions have relied on qualitative arguments. In this paper, we will show our metadata analysis of a scientific literature database (PubMed) that quantitatively describes the importance of the subjects of bioinformatics, systems biology, and biophysics as compared with a well-established interdisciplinary subject, biochemistry. Specifically, we found that the development of each subject assessed by its publication volume was well described by a set of simple nonlinear equations, allowing us to characterize them quantitatively. Bioinformatics, which had the highest ratio of publications produced, was predicted to grow between 77% and 93% by 2025 according to the model. Due to the large number of publications produced in bioinformatics, which nearly matches the number published in biochemistry, it can be inferred that bioinformatics is almost equal in significance to biochemistry. Based on our analysis, we suggest that bioinformatics be added to the standard biology undergraduate curriculum. Adding this course to an undergraduate curriculum will better prepare students for future research in biology.

  19. Progressive Education Standards: A Neuroscience Framework

    ERIC Educational Resources Information Center

    O'Grady, Patty

    2011-01-01

    This paper proposes a coherent and unique set of 12 standards, adopting a neuroscience framework for biologically based on school reform. This model of educational principles and practices aligns with the long-standing principles and practices of the Progressive Education Movement in the United States and the emerging principles of neuroscience.…

  20. All biology is computational biology.

    PubMed

    Markowetz, Florian

    2017-03-01

    Here, I argue that computational thinking and techniques are so central to the quest of understanding life that today all biology is computational biology. Computational biology brings order into our understanding of life, it makes biological concepts rigorous and testable, and it provides a reference map that holds together individual insights. The next modern synthesis in biology will be driven by mathematical, statistical, and computational methods being absorbed into mainstream biological training, turning biology into a quantitative science.

  1. Prospective iterative trial of proteasome inhibitor-based desensitization.

    PubMed

    Woodle, E S; Shields, A R; Ejaz, N S; Sadaka, B; Girnita, A; Walsh, R C; Alloway, R R; Brailey, P; Cardi, M A; Abu Jawdeh, B G; Roy-Chaudhury, P; Govil, A; Mogilishetty, G

    2015-01-01

    A prospective iterative trial of proteasome inhibitor (PI)-based therapy for reducing HLA antibody (Ab) levels was conducted in five phases differing in bortezomib dosing density and plasmapheresis timing. Phases included 1 or 2 bortezomib cycles (1.3 mg/m(2) × 6-8 doses), one rituximab dose and plasmapheresis. HLA Abs were measured by solid phase and flow cytometry (FCM) assays. Immunodominant Ab (iAb) was defined as highest HLA Ab level. Forty-four patients received 52 desensitization courses (7 patients enrolled in multiple phases): Phase 1 (n = 20), Phase 2 (n = 12), Phase 3 (n = 10), Phase 4 (n = 5), Phase 5 (n = 5). iAb reductions were observed in 38 of 44 (86%) patients and persisted up to 10 months. In Phase 1, a 51.5% iAb reduction was observed at 28 days with bortezomib alone. iAb reductions increased with higher bortezomib dosing densities and included class I, II, and public antigens (HLA DRβ3, HLA DRβ4 and HLA DRβ5). FCM median channel shifts decreased in 11/11 (100%) patients by a mean of 103 ± 54 mean channel shifts (log scale). Nineteen out of 44 patients (43.2%) were transplanted with low acute rejection rates (18.8%) and de novo DSA formation (12.5%). In conclusion, PI-based desensitization consistently and durably reduces HLA Ab levels providing an alternative to intravenous immune globulin-based desensitization. © Copyright 2014 The American Society of Transplantation and the American Society of Transplant Surgeons.

  2. Global multiplicity of dietary standards for trace elements.

    PubMed

    Freeland-Graves, Jeanne H; Lee, Jane J

    2012-06-01

    Consistent guidelines across the world for dietary standards of trace elements remain elusive. Harmonization of dietary standards has been suggested by international agencies to facilitate consistency in food and nutrition policies and international trade. Yet significant barriers exist to standardize recommendations on a global basis, such as vast differences in geography, food availability and transport; cultural, social and economic constraints, and biological diversity. Simple commonality is precluded further by the variety of terminologies among countries and regions related to diet. Certain unions have created numerous nutritional descriptive categories for standards, while other large countries are limited to only a few. This paper will explore the global multiplicity of dietary standards and efforts for harmonization. Copyright © 2012 Elsevier GmbH. All rights reserved.

  3. Standardization of allergen products: 2. Detailed characterization of GMP-produced recombinant Phl p 5.0109 as European Pharmacopoeia reference standard.

    PubMed

    Himly, M; Nandy, A; Kahlert, H; Thilker, M; Steiner, M; Briza, P; Neubauer, A; Klysner, S; van Ree, R; Buchheit, K-H; Vieths, S; Ferreira, F

    2016-04-01

    The Biological Standardization Programme of the European Directorate for Quality of Medicines and Healthcare (EDQM) aims at the establishment of well-characterized reference standards based on recombinant allergens and validated assays for the quantification of major allergen content. The objective of this study was to examine the detailed physicochemical and immunological characterization of recombinant Phl p 5.0109, the second available allergen reference standard. Recombinant Phl p 5.0109 PP5ar06007 was produced under GMP conditions and analyzed by an array of physicochemical and immunological methods for identity, quantity, homogeneity, and folding stability in bulk solution, as well as thermal denaturation, aggregation state, and biological activity when formulated for long-time storage. PP5ar06007 revealed as a highly homogeneous, monomeric, well-folded preparation of rPhl p 5.0109, as documented by mass spectrometry, SDS-PAGE, isoelectric focusing, size-exclusion chromatography with light scattering, circular dichroism, and infrared spectroscopy. Upon storage at +4°C, PP5ar06007 retained the monomeric state for at least 2 months. A protein quantity of 1.56 ± 0.03 mg/ml was determined by amino acid analysis in PP5ar06007, and its biological activity was shown to be comparable to natural Phl p 5 in terms of basophil activation and T-cell reactivity. Recombinant Phl p 5.0109 PP5ar06007 was characterized extensively at the physicochemical and immunological level. It revealed to be a highly stable, monomeric, and immunologically equivalent of its natural counterpart. PP5ar06007 is now available as European Pharmacopoeia allergen reference standard for grass pollen products. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  4. SBRML: a markup language for associating systems biology data with models.

    PubMed

    Dada, Joseph O; Spasić, Irena; Paton, Norman W; Mendes, Pedro

    2010-04-01

    Research in systems biology is carried out through a combination of experiments and models. Several data standards have been adopted for representing models (Systems Biology Markup Language) and various types of relevant experimental data (such as FuGE and those of the Proteomics Standards Initiative). However, until now, there has been no standard way to associate a model and its entities to the corresponding datasets, or vice versa. Such a standard would provide a means to represent computational simulation results as well as to frame experimental data in the context of a particular model. Target applications include model-driven data analysis, parameter estimation, and sharing and archiving model simulations. We propose the Systems Biology Results Markup Language (SBRML), an XML-based language that associates a model with several datasets. Each dataset is represented as a series of values associated with model variables, and their corresponding parameter values. SBRML provides a flexible way of indexing the results to model parameter values, which supports both spreadsheet-like data and multidimensional data cubes. We present and discuss several examples of SBRML usage in applications such as enzyme kinetics, microarray gene expression and various types of simulation results. The XML Schema file for SBRML is available at http://www.comp-sys-bio.org/SBRML under the Academic Free License (AFL) v3.0.

  5. A methodology to annotate systems biology markup language models with the synthetic biology open language.

    PubMed

    Roehner, Nicholas; Myers, Chris J

    2014-02-21

    Recently, we have begun to witness the potential of synthetic biology, noted here in the form of bacteria and yeast that have been genetically engineered to produce biofuels, manufacture drug precursors, and even invade tumor cells. The success of these projects, however, has often failed in translation and application to new projects, a problem exacerbated by a lack of engineering standards that combine descriptions of the structure and function of DNA. To address this need, this paper describes a methodology to connect the systems biology markup language (SBML) to the synthetic biology open language (SBOL), existing standards that describe biochemical models and DNA components, respectively. Our methodology involves first annotating SBML model elements such as species and reactions with SBOL DNA components. A graph is then constructed from the model, with vertices corresponding to elements within the model and edges corresponding to the cause-and-effect relationships between these elements. Lastly, the graph is traversed to assemble the annotating DNA components into a composite DNA component, which is used to annotate the model itself and can be referenced by other composite models and DNA components. In this way, our methodology can be used to build up a hierarchical library of models annotated with DNA components. Such a library is a useful input to any future genetic technology mapping algorithm that would automate the process of composing DNA components to satisfy a behavioral specification. Our methodology for SBML-to-SBOL annotation is implemented in the latest version of our genetic design automation (GDA) software tool, iBioSim.

  6. 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).

  7. 42 CFR 493.1423 - Standard; Testing personnel qualifications.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ..., or bachelor's degree in a chemical, physical, biological or clinical laboratory science, or medical... stability and storage; (F) The skills required to implement the quality control policies and procedures of... HUMAN SERVICES (CONTINUED) STANDARDS AND CERTIFICATION LABORATORY REQUIREMENTS Personnel for Nonwaived...

  8. [Important issues of biological safety].

    PubMed

    Onishchenko, G G

    2007-01-01

    The problem of biological security raises alarm due to the real growth of biological threats. Biological security includes a wide scope of problems, the solution of which becomes a part of national security as a necessary condition for the constant development of the country. A number of pathogens, such as human immunodeficiency virus, exotic Ebola and Lassa viruses causing hemorrhagic fever,rotaviruses causing acute intestinal diseases, etc. were first discovered in the last century. Terrorist actions committed in the USA in 2001 using the anthrax pathogen made the problem of biological danger even more important. In Russian Federation, biological threats are counteracted through the united state policy being a part of general state security policy. The biological Security legislation of Russian Federation is chiefly based on the 1992 Federal Law on Security. On the basis of cumulated experience, the President of Russia ratified Basics of Russian Federation's State Policy for Chemical and Biological Security for the Period through 2010 and Beyond on 4 December, 2003. The document determines the main directions and stages of the state development in the area of chemical and biological security. The Federal target program Russian Federation's National Program for Chemical and Biological Security is being developed, and its development is to be completed soon in order to perfect the national system for biological security and fulfill Basics of Russian Federation's State Policy for Chemical and Biological Security for the Period through 2010 and Beyond, ratified by the President. The new global strategy for control over infectious diseases, presented in the materials of Saint Petersburg summit of the Group of Eight, as well as the substantive part of its elements in Sanitary International Standards, are to a large degree an acknowledgement of the Russian Federation's experience and the algorithm for fighting extremely dangerous infections. This Russia's experience has

  9. Creating biological nanomaterials using synthetic biology.

    PubMed

    Rice, MaryJoe K; Ruder, Warren C

    2014-02-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

  10. 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

  11. Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI)

    PubMed Central

    Amberg, Alexander; Barrett, Dave; Beale, Michael H.; Beger, Richard; Daykin, Clare A.; Fan, Teresa W.-M.; Fiehn, Oliver; Goodacre, Royston; Griffin, Julian L.; Hankemeier, Thomas; Hardy, Nigel; Harnly, James; Higashi, Richard; Kopka, Joachim; Lane, Andrew N.; Lindon, John C.; Marriott, Philip; Nicholls, Andrew W.; Reily, Michael D.; Thaden, John J.; Viant, Mark R.

    2013-01-01

    There is a general consensus that supports the need for standardized reporting of metadata or information describing large-scale metabolomics and other functional genomics data sets. Reporting of standard metadata provides a biological and empirical context for the data, facilitates experimental replication, and enables the re-interrogation and comparison of data by others. Accordingly, the Metabolomics Standards Initiative is building a general consensus concerning the minimum reporting standards for metabolomics experiments of which the Chemical Analysis Working Group (CAWG) is a member of this community effort. This article proposes the minimum reporting standards related to the chemical analysis aspects of metabolomics experiments including: sample preparation, experimental analysis, quality control, metabolite identification, and data pre-processing. These minimum standards currently focus mostly upon mass spectrometry and nuclear magnetic resonance spectroscopy due to the popularity of these techniques in metabolomics. However, additional input concerning other techniques is welcomed and can be provided via the CAWG on-line discussion forum at http://msi-workgroups.sourceforge.net/ or http://Msi-workgroups-feedback@lists.sourceforge.net. Further, community input related to this document can also be provided via this electronic forum. PMID:24039616

  12. Space Synthetic Biology Project

    NASA Technical Reports Server (NTRS)

    Howard, David; Roman, Monsi; Mansell, James (Matt)

    2015-01-01

    Synthetic biology is an effort to make genetic engineering more useful by standardizing sections of genetic code. By standardizing genetic components, biological engineering will become much more similar to traditional fields of engineering, in which well-defined components and subsystems are readily available in markets. Specifications of the behavior of those components and subsystems can be used to model a system which incorporates them. Then, the behavior of the novel system can be simulated and optimized. Finally, the components and subsystems can be purchased and assembled to create the optimized system, which most often will exhibit behavior similar to that indicated by the model. The Space Synthetic Biology project began in 2012 as a multi-Center effort. The purpose of this project was to harness Synthetic Biology principals to enable NASA's missions. A central target for application was to Environmental Control & Life Support (ECLS). Engineers from NASA Marshall Space Flight Center's (MSFC's) ECLS Systems Development Branch (ES62) were brought into the project to contribute expertise in operational ECLS systems. Project lead scientists chose to pursue the development of bioelectrochemical technologies to spacecraft life support. Therefore, the ECLS element of the project became essentially an effort to develop a bioelectrochemical ECLS subsystem. Bioelectrochemical systems exploit the ability of many microorganisms to drive their metabolisms by direct or indirect utilization of electrical potential gradients. Whereas many microorganisms are capable of deriving the energy required for the processes of interest (such as carbon dioxide (CO2) fixation) from sunlight, it is believed that subsystems utilizing electrotrophs will exhibit smaller mass, volume, and power requirements than those that derive their energy from sunlight. In the first 2 years of the project, MSFC personnel conducted modeling, simulation, and conceptual design efforts to assist the

  13. Silk-polypyrrole biocompatible actuator performance under biologically relevant conditions

    NASA Astrophysics Data System (ADS)

    Hagler, Jo'elen; Peterson, Ben; Murphy, Amanda; Leger, Janelle

    Biocompatible actuators that are capable of controlled movement and can function under biologically relevant conditions are of significant interest in biomedical fields. Previously, we have demonstrated that a composite material of silk biopolymer and the conducting polymer polypyrrole (PPy) can be formed into a bilayer device that can bend under applied voltage. Further, these silk-PPy composites can generate forces comparable to human muscle (>0.1 MPa) making them ideal candidates for interfacing with biological tissues. Here silk-PPy composite films are tested for performance under biologically relevant conditions including exposure to a complex protein serum and biologically relevant temperatures. Free-end bending actuation performance, current response, force generation and, mass degradation were investigated . Preliminary results show that when exposed to proteins and biologically relevant temperatures, these silk-PPy composites show minimal degradation and are able to generate forces and conduct currents comparable to devices tested under standard conditions. NSF.

  14. cPath: open source software for collecting, storing, and querying biological pathways

    PubMed Central

    Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

    2006-01-01

    Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. Results We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling. PMID:17101041

  15. cPath: open source software for collecting, storing, and querying biological pathways.

    PubMed

    Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

    2006-11-13

    Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.

  16. 9 CFR 113.51 - Requirements for primary cells used for production of biologics.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 9 Animals and Animal Products 1 2012-01-01 2012-01-01 false Requirements for primary cells used... VECTORS STANDARD REQUIREMENTS Ingredient Requirements § 113.51 Requirements for primary cells used for production of biologics. Primary cells used to prepare biological products shall be derived from normal...

  17. 9 CFR 113.51 - Requirements for primary cells used for production of biologics.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 9 Animals and Animal Products 1 2011-01-01 2011-01-01 false Requirements for primary cells used... VECTORS STANDARD REQUIREMENTS Ingredient Requirements § 113.51 Requirements for primary cells used for production of biologics. Primary cells used to prepare biological products shall be derived from normal...

  18. 9 CFR 113.51 - Requirements for primary cells used for production of biologics.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 9 Animals and Animal Products 1 2014-01-01 2014-01-01 false Requirements for primary cells used... VECTORS STANDARD REQUIREMENTS Ingredient Requirements § 113.51 Requirements for primary cells used for production of biologics. Primary cells used to prepare biological products shall be derived from normal...

  19. 9 CFR 113.51 - Requirements for primary cells used for production of biologics.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 9 Animals and Animal Products 1 2013-01-01 2013-01-01 false Requirements for primary cells used... VECTORS STANDARD REQUIREMENTS Ingredient Requirements § 113.51 Requirements for primary cells used for production of biologics. Primary cells used to prepare biological products shall be derived from normal...

  20. 9 CFR 113.51 - Requirements for primary cells used for production of biologics.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Requirements for primary cells used... VECTORS STANDARD REQUIREMENTS Ingredient Requirements § 113.51 Requirements for primary cells used for production of biologics. Primary cells used to prepare biological products shall be derived from normal...

  1. [Research strategies in standard decoction of medicinal slices].

    PubMed

    Chen, Shi-Lin; Liu, An; Li, Qi; Toru, Sugita; Zhu, Guang-Wei; Sun, Yi; Dai, Yun-Tao; Zhang, Jun; Zhang, Tie-Jun; Takehisa, Tomoda; Liu, Chang-Xiao

    2016-04-01

    This paper discusses the research situation of the standard decoction of medicinal slices at home and abroad. Combined with the experimental data, the author proposes that the standard decoction of medicinal slices is made of single herb using standard process which should be guided by the theory of traditional Chinese medicine, based on clinical practice and referred to modern extraction method with a standard process. And the author also proposes the principles of establishing the specification of process parameters and quality standards and established the basis of drug efficacy material and biological reference. As a standard material and standard system, the standard decoction of medicinal slices can provide standards for clinical medication, standardize the use of the new type of medicinal slices especially for dispensing granules, which were widely used in clinical. It can ensure the accuracy of drugs and consistency of dose, and to solve current supervision difficulties. Moreover the study of standard decoction of medicinal slices will provide the research on dispensing granules, traditional Chinese medicine prescription standard decoction and couplet medicines standard decoction a useful reference. Copyright© by the Chinese Pharmaceutical Association.

  2. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE).

    PubMed

    Le Novère, Nicolas; Hucka, Michael; Anwar, Nadia; Bader, Gary D; Demir, Emek; Moodie, Stuart; Sorokin, Anatoly

    2011-11-30

    The Computational Modeling in Biology Network (COMBINE), is an initiative to coordinate the development of the various community standards and formats in computational systems biology and related fields. This report summarizes the activities pursued at the first annual COMBINE meeting held in Edinburgh on October 6-9 2010 and the first HARMONY hackathon, held in New York on April 18-22 2011. The first of those meetings hosted 81 attendees. Discussions covered both official COMBINE standards-(BioPAX, SBGN and SBML), as well as emerging efforts and interoperability between different formats. The second meeting, oriented towards software developers, welcomed 59 participants and witnessed many technical discussions, development of improved standards support in community software systems and conversion between the standards. Both meetings were resounding successes and showed that the field is now mature enough to develop representation formats and related standards in a coordinated manner.

  3. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)

    PubMed Central

    Le Novère, Nicolas; Hucka, Michael; Anwar, Nadia; Bader, Gary D; Demir, Emek; Moodie, Stuart; Sorokin, Anatoly

    2011-01-01

    The Computational Modeling in Biology Network (COMBINE), is an initiative to coordinate the development of the various community standards and formats in computational systems biology and related fields. This report summarizes the activities pursued at the first annual COMBINE meeting held in Edinburgh on October 6-9 2010 and the first HARMONY hackathon, held in New York on April 18-22 2011. The first of those meetings hosted 81 attendees. Discussions covered both official COMBINE standards-(BioPAX, SBGN and SBML), as well as emerging efforts and interoperability between different formats. The second meeting, oriented towards software developers, welcomed 59 participants and witnessed many technical discussions, development of improved standards support in community software systems and conversion between the standards. Both meetings were resounding successes and showed that the field is now mature enough to develop representation formats and related standards in a coordinated manner. PMID:22180826

  4. The archiving and dissemination of biological structure data.

    PubMed

    Berman, Helen M; Burley, Stephen K; Kleywegt, Gerard J; Markley, John L; Nakamura, Haruki; Velankar, Sameer

    2016-10-01

    The global Protein Data Bank (PDB) was the first open-access digital archive in biology. The history and evolution of the PDB are described, together with the ways in which molecular structural biology data and information are collected, curated, validated, archived, and disseminated by the members of the Worldwide Protein Data Bank organization (wwPDB; http://wwpdb.org). Particular emphasis is placed on the role of community in establishing the standards and policies by which the PDB archive is managed day-to-day. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  5. Immunogenicity of biologic therapies: causes and consequences.

    PubMed

    Boehncke, Wolf-Henning; Brembilla, Nicolo Costantino

    2018-04-25

    Antibodies or fusion proteins termed biologics allow the targeted therapy of diseases. Many of these agents have proven superior efficacy and safety to conventional therapies, and subsequently revolutionized the management of numerous chronic diseases. Repetitive administration of these protein-based therapeutics to immunocompetent patients elicit immune responses in the form of Anti Drug Antibodies (ADAs), which in turn impact their pharmacological properties and may trigger adverse events. Areas covered: Structural characteristics determining the immunogenicity of biologics are reviewed along with strategies to minimize it. Next, the different types of treatment-emerging ADAs, their potential clinical implications, and assays to detect them are addressed. Emphasis is put on the review of data on the immunogenicity of different types of biologics across numerous indications. Finally, practical considerations are discussed on how to manage patients with issues around the immunogenicity of their biologic treatment. Expert commentary: Immunogenicity is a clinically relevant criterion when selecting a biologic. Besides intrinsic properties of the agent (namely its structure), its respective mode of action, dosing regimen, comedication, and the indication treated must be considered. ADA detection assays need to be standardized to improve comparability of available data and to allow clinical decision-making.

  6. BioBlocks: Programming Protocols in Biology Made Easier.

    PubMed

    Gupta, Vishal; Irimia, Jesús; Pau, Iván; Rodríguez-Patón, Alfonso

    2017-07-21

    The methods to execute biological experiments are evolving. Affordable fluid handling robots and on-demand biology enterprises are making automating entire experiments a reality. Automation offers the benefit of high-throughput experimentation, rapid prototyping, and improved reproducibility of results. However, learning to automate and codify experiments is a difficult task as it requires programming expertise. Here, we present a web-based visual development environment called BioBlocks for describing experimental protocols in biology. It is based on Google's Blockly and Scratch, and requires little or no experience in computer programming to automate the execution of experiments. The experiments can be specified, saved, modified, and shared between multiple users in an easy manner. BioBlocks is open-source and can be customized to execute protocols on local robotic platforms or remotely, that is, in the cloud. It aims to serve as a de facto open standard for programming protocols in Biology.

  7. Student Conceptions about Energy in Biological Contexts

    ERIC Educational Resources Information Center

    Opitz, Sebastian T.; Blankenstein, Andreas; Harms, Ute

    2017-01-01

    The concept of energy serves biologists as a powerful analytical model to describe phenomena that occurs in the natural world. Due to the concept's relevance, educational standards of different countries identify energy as a core idea for the teaching and learning of biology and other science subjects. However, previous research on students'…

  8. Third International Standard for Posterior Pituitary

    PubMed Central

    Bangham, D. R.; Mussett, Marjorie V.

    1958-01-01

    In October 1955, stocks of the Second International Standard for Posterior Pituitary were running low and the Department of Biological Standards of the National Institute for Medical Research, London, was asked to proceed with the arrangements for an international collaborative assay of material for the Third Standard. A single 142-g batch of posterior-pituitary-lobe powder was obtained and distributed in ampoules, in approximately 30-mg quantities. Samples were sent to 19 laboratories in 10 countries. In all, 185 assays were carried out, 122 for oxytocic activity, 53 for vasopressor activity and 10 for antidiuretic activity. On the basis of the results, which were analysed statistically at the National Institute for Medical Research, it was agreed that the potency of the Third Standard (re-named International Standard for Oxytocic, Vasopressor and Antidiuretic Substances in 1956, in view of the recent synthesis of oxytocin and vasopressin) should be expressed as 2.0 International Units per milligram. The International Unit therefore remains unchanged as 0.5 mg of the dry powder. PMID:13585079

  9. Protocol for Standardizing High-to-Moderate Abundance Protein Biomarker Assessments Through an MRM-with-Standard-Peptides Quantitative Approach.

    PubMed

    Percy, Andrew J; Yang, Juncong; Chambers, Andrew G; Mohammed, Yassene; Miliotis, Tasso; Borchers, Christoph H

    2016-01-01

    Quantitative mass spectrometry (MS)-based approaches are emerging as a core technology for addressing health-related queries in systems biology and in the biomedical and clinical fields. In several 'omics disciplines (proteomics included), an approach centered on selected or multiple reaction monitoring (SRM or MRM)-MS with stable isotope-labeled standards (SIS), at the protein or peptide level, has emerged as the most precise technique for quantifying and screening putative analytes in biological samples. To enable the widespread use of MRM-based protein quantitation for disease biomarker assessment studies and its ultimate acceptance for clinical analysis, the technique must be standardized to facilitate precise and accurate protein quantitation. To that end, we have developed a number of kits for assessing method/platform performance, as well as for screening proposed candidate protein biomarkers in various human biofluids. Collectively, these kits utilize a bottom-up LC-MS methodology with SIS peptides as internal standards and quantify proteins using regression analysis of standard curves. This chapter details the methodology used to quantify 192 plasma proteins of high-to-moderate abundance (covers a 6 order of magnitude range from 31 mg/mL for albumin to 18 ng/mL for peroxidredoxin-2), and a 21-protein subset thereof. We also describe the application of this method to patient samples for biomarker discovery and verification studies. Additionally, we introduce our recently developed Qualis-SIS software, which is used to expedite the analysis and assessment of protein quantitation data in control and patient samples.

  10. Ultrasound: biological effects and industrial hygiene concerns.

    PubMed

    Wiernicki, C; Karoly, W J

    1985-09-01

    Due to the increased use of high intensity ultrasonic devices, there is now a greater risk of worker exposure to ultrasonic radiation than there was in the past. Exposure to high power ultrasound may produce adverse biological effects. High power ultrasound, characterized by high intensity outputs at frequencies of 20-100 kHz, has a wide range of applications throughout industry. Future applications may involve equipment with higher energy outputs. Contact ultrasound, i.e., no airspace between the energy source and the biological tissue, is significantly more hazardous than exposure to airborne ultrasound because air transmits less than one percent of the energy. This paper discusses biological effects associated with overexposure to ultrasound, exposure standards proposed for airborne and contact ultrasound, industrial hygiene controls that can be employed to minimize exposure, and the instrumentation that is required for evaluating exposures.

  11. Medical examiners, coroners, and biologic terrorism: a guidebook for surveillance and case management.

    PubMed

    Nolte, Kurt B; Hanzlick, Randy L; Payne, Daniel C; Kroger, Andrew T; Oliver, William R; Baker, Andrew M; McGowan, Dennis E; DeJong, Joyce L; Bell, Micahel R; Guarner, Jeannette; Shieh, Wun-Ju; Zaki, Sherif R

    2004-06-11

    Medical examiners and coroners (ME/Cs) are essential public health partners for terrorism preparedness and response. These medicolegal investigators support both public health and public safety functions and investigate deaths that are sudden, suspicious, violent, unattended, and unexplained. Medicolegal autopsies are essential for making organism-specific diagnoses in deaths caused by biologic terrorism. This report has been created to 1) help public health officials understand the role of ME/Cs in biologic terrorism surveillance and response efforts and 2) provide ME/Cs with the detailed information required to build capacity for biologic terrorism preparedness in a public health context. This report provides background information regarding biologic terrorism, possible biologic agents, and the consequent clinicopathologic diseases, autopsy procedures, and diagnostic tests as well as a description of biosafety risks and standards for autopsy precautions. ME/Cs' vital role in terrorism surveillance requires consistent standards for collecting, analyzing, and disseminating data. Familiarity with the operational, jurisdictional, and evidentiary concerns involving biologic terrorism-related death investigation is critical to both ME/Cs and public health authorities. Managing terrorism-associated fatalities can be expensive and can overwhelm the existing capacity of ME/Cs. This report describes federal resources for funding and reimbursement for ME/C preparedness and response activities and the limited support capacity of the federal Disaster Mortuary Operational Response Team. Standards for communication are critical in responding to any emergency situation. This report, which is a joint collaboration between CDC and the National Association of Medical Examiners (NAME), describes the relationship between ME/Cs and public health departments, emergency management agencies, emergency operations centers, and the Incident Command System.

  12. Evaluation of Roadmap to Achieve Energy Delivery Systems Cybersecurity

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

    Chavez, Adrian R.

    The Department of Energy/Office of Electricity Delivery and Energy Reliability (DOE/OE) Cybersecurity for Energy Delivery Systems (CEDS) program is currently evaluating the Roadmap to Achieve Energy Delivery Systems Cybersecurity document that sets a vision and outlines a set of milestones. The milestones are divided into five strategic focus areas that include: 1. Build a Culture of Security; 2. Assess and Monitor Risk; 3. Develop and Implement New Protective Measures to Reduce Risk; 4. Manage Incidents; and 5. Sustain Security Improvements. The most current version of the roadmap was last updated in September of 2016. Sandia National Laboratories (SNL) has beenmore » tasked with revisiting the roadmap to update the current state of energy delivery systems cybersecurity protections. SNL is currently working with previous and current partners to provide feedback on which of the roadmap milestones have been met and to identify any preexisting or new gaps that are not addressed by the roadmap. The specific focus areas SNL was asked to evaluate are: 1. Develop and Implement New Protective Measures to Reduce Risk and 2. Sustain Security Improvements. SNL has formed an Industry Advisory Board (IAB) to assist in answering these questions. The IAB consists of previous partners on past CEDS funded efforts as well as new collaborators that have unique insights into the current state of cybersecurity within energy delivery systems. The IAB includes asset owners, utilities and vendors of control systems. SNL will continue to maintain regular communications with the IAB to provide various perspectives on potential future updates to further improve the breadth of cybersecurity coverage of the roadmap.« less

  13. A transformative model for undergraduate quantitative biology education.

    PubMed

    Usher, David C; Driscoll, Tobin A; Dhurjati, Prasad; Pelesko, John A; Rossi, Louis F; Schleiniger, Gilberto; Pusecker, Kathleen; White, Harold B

    2010-01-01

    The BIO2010 report recommended that students in the life sciences receive a more rigorous education in mathematics and physical sciences. The University of Delaware approached this problem by (1) developing a bio-calculus section of a standard calculus course, (2) embedding quantitative activities into existing biology courses, and (3) creating a new interdisciplinary major, quantitative biology, designed for students interested in solving complex biological problems using advanced mathematical approaches. To develop the bio-calculus sections, the Department of Mathematical Sciences revised its three-semester calculus sequence to include differential equations in the first semester and, rather than using examples traditionally drawn from application domains that are most relevant to engineers, drew models and examples heavily from the life sciences. The curriculum of the B.S. degree in Quantitative Biology was designed to provide students with a solid foundation in biology, chemistry, and mathematics, with an emphasis on preparation for research careers in life sciences. Students in the program take core courses from biology, chemistry, and physics, though mathematics, as the cornerstone of all quantitative sciences, is given particular prominence. Seminars and a capstone course stress how the interplay of mathematics and biology can be used to explain complex biological systems. To initiate these academic changes required the identification of barriers and the implementation of solutions.

  14. A Transformative Model for Undergraduate Quantitative Biology Education

    PubMed Central

    Driscoll, Tobin A.; Dhurjati, Prasad; Pelesko, John A.; Rossi, Louis F.; Schleiniger, Gilberto; Pusecker, Kathleen; White, Harold B.

    2010-01-01

    The BIO2010 report recommended that students in the life sciences receive a more rigorous education in mathematics and physical sciences. The University of Delaware approached this problem by (1) developing a bio-calculus section of a standard calculus course, (2) embedding quantitative activities into existing biology courses, and (3) creating a new interdisciplinary major, quantitative biology, designed for students interested in solving complex biological problems using advanced mathematical approaches. To develop the bio-calculus sections, the Department of Mathematical Sciences revised its three-semester calculus sequence to include differential equations in the first semester and, rather than using examples traditionally drawn from application domains that are most relevant to engineers, drew models and examples heavily from the life sciences. The curriculum of the B.S. degree in Quantitative Biology was designed to provide students with a solid foundation in biology, chemistry, and mathematics, with an emphasis on preparation for research careers in life sciences. Students in the program take core courses from biology, chemistry, and physics, though mathematics, as the cornerstone of all quantitative sciences, is given particular prominence. Seminars and a capstone course stress how the interplay of mathematics and biology can be used to explain complex biological systems. To initiate these academic changes required the identification of barriers and the implementation of solutions. PMID:20810949

  15. Biologic variability of cardiac troponin I in healthy dogs and dogs with different stages of myxomatous mitral valve disease using standard and high-sensitivity immunoassays.

    PubMed

    Winter, Randolph L; Saunders, Ashley B; Gordon, Sonya G; Miller, Matthew W; Fosgate, Geoffrey T; Suchodolski, Jan S; Steiner, Jörg M

    2017-06-01

    Biologic variability (BV) is one aspect of interpreting changes in biomarker concentrations known to be clinically important in people with cardiac disease, but it has not been adequately addressed in dogs so far. The purpose of the study was to determine BV of cardiac troponin I (cTnI) in healthy dogs and dogs with 3 stages of myxomatous mitral valve disease (MMVD). Healthy dogs and dogs with 3 stages of MMVD were prospectively assigned to groups based on comprehensive clinical evaluation using current guidelines. Concentrations of cTnI were measured hourly, daily, and weekly using standard and high-sensitivity immunoassays. Within- (CV I ) and between-subject (CV G ) coefficients of variability, percent reference change value (RCV), and index of individuality (IoI) were calculated. All 10 healthy dogs and 76/112 (68%) of samples from 28 MMVD dogs had cTnI concentrations below the limit of detection (LOD) using a standard sensitivity immunoassay. Only 49/160 (31%) of healthy dog samples and no MMVD samples had cTnI below the high-sensitivity immunoassay LOD. Data analysis for the high-sensitivity immunoassay revealed CV I of 48.1%, CV G of 60.1%, RCV of 134.0%, and IoI of 0.804 in healthy dogs. In MMVD dogs, CV I was 39.6%, CV G was 80.7%, RCV was 110%, and IoI was 0.494. Of all MMVD dogs, those with Stage B2 had the lowest RCV of 91%. Biologic variability affects cTnI concentrations in healthy dogs and dogs with MMVD. Consideration of BV may be clinically relevant when monitoring individual changes in cTnI values, using high-sensitivity immunoassays. © 2017 American Society for Veterinary Clinical Pathology.

  16. Synthetic biology: new engineering rules for an emerging discipline

    PubMed Central

    Andrianantoandro, Ernesto; Basu, Subhayu; Karig, David K; Weiss, Ron

    2006-01-01

    Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development. PMID:16738572

  17. Synthetic biology: new engineering rules for an emerging discipline.

    PubMed

    Andrianantoandro, Ernesto; Basu, Subhayu; Karig, David K; Weiss, Ron

    2006-01-01

    Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development.

  18. Safety Identifying of Integral Abutment Bridges under Seismic and Thermal Loads

    PubMed Central

    Easazadeh Far, Narges; Barghian, Majid

    2014-01-01

    Integral abutment bridges (IABs) have many advantages over conventional bridges in terms of strength and maintenance cost. Due to the integrity of these structures uniform thermal and seismic loads are known important ones on the structure performance. Although all bridge design codes consider temperature and earthquake loads separately in their load combinations for conventional bridges, the thermal load is an “always on” load and, during the occurrence of an earthquake, these two important loads act on bridge simultaneously. Evaluating the safety level of IABs under combination of these loads becomes important. In this paper, the safety of IABs—designed by AASHTO LRFD bridge design code—under combination of thermal and seismic loads is studied. To fulfill this aim, first the target reliability indexes under seismic load have been calculated. Then, these analyses for the same bridge under combination of thermal and seismic loads have been repeated and the obtained reliability indexes are compared with target indexes. It is shown that, for an IAB designed by AASHTO LRFD, the indexes have been reduced under combined effects. So, the target level of safety during its design life is not provided and the code's load combination should be changed. PMID:25405232

  19. Making United States Integrated Ocean Observing System (U.S. IOOS) inclusive of marine biological resources

    USGS Publications Warehouse

    Moustahfid, H.; Potemra, J.; Goldstein, P.; Mendelssohn, R.; Desrochers, A.

    2011-01-01

    An important Data Management and Communication (DMAC) goal is to enable a multi-disciplinary view of the ocean environment by facilitating discovery and integration of data from various sources, projects and scientific domains. United States Integrated Ocean Observing System (U.S. IOOS) DMAC functional requirements are based upon guidelines for standardized data access services, data formats, metadata, controlled vocabularies, and other conventions. So far, the data integration effort has focused on geophysical U.S. IOOS core variables such as temperature, salinity, ocean currents, etc. The IOOS Biological Observations Project is addressing the DMAC requirements that pertain to biological observations standards and interoperability applicable to U.S. IOOS and to various observing systems. Biological observations are highly heterogeneous and the variety of formats, logical structures, and sampling methods create significant challenges. Here we describe an informatics framework for biological observing data (e.g. species presence/absence and abundance data) that will expand information content and reconcile standards for the representation and integration of these biological observations for users to maximize the value of these observing data. We further propose that the approach described can be applied to other datasets generated in scientific observing surveys and will provide a vehicle for wider dissemination of biological observing data. We propose to employ data definition conventions that are well understood in U.S. IOOS and to combine these with ratified terminologies, policies and guidelines. ?? 2011 MTS.

  20. [Numerical simulation and operation optimization of biological filter].

    PubMed

    Zou, Zong-Sen; Shi, Han-Chang; Chen, Xiang-Qiang; Xie, Xiao-Qing

    2014-12-01

    BioWin software and two sensitivity analysis methods were used to simulate the Denitrification Biological Filter (DNBF) + Biological Aerated Filter (BAF) process in Yuandang Wastewater Treatment Plant. Based on the BioWin model of DNBF + BAF process, the operation data of September 2013 were used for sensitivity analysis and model calibration, and the operation data of October 2013 were used for model validation. The results indicated that the calibrated model could accurately simulate practical DNBF + BAF processes, and the most sensitive parameters were the parameters related to biofilm, OHOs and aeration. After the validation and calibration of model, it was used for process optimization with simulating operation results under different conditions. The results showed that, the best operation condition for discharge standard B was: reflux ratio = 50%, ceasing methanol addition, influent C/N = 4.43; while the best operation condition for discharge standard A was: reflux ratio = 50%, influent COD = 155 mg x L(-1) after methanol addition, influent C/N = 5.10.

  1. Dissecting Redox Biology Using Fluorescent Protein Sensors.

    PubMed

    Schwarzländer, Markus; Dick, Tobias P; Meyer, Andreas J; Morgan, Bruce

    2016-05-01

    Fluorescent protein sensors have revitalized the field of redox biology by revolutionizing the study of redox processes in living cells and organisms. Within one decade, a set of fundamental new insights has been gained, driven by the rapid technical development of in vivo redox sensing. Redox-sensitive yellow and green fluorescent protein variants (rxYFP and roGFPs) have been the central players. Although widely used as an established standard tool, important questions remain surrounding their meaningful use in vivo. We review the growing range of thiol redox sensor variants and their application in different cells, tissues, and organisms. We highlight five key findings where in vivo sensing has been instrumental in changing our understanding of redox biology, critically assess the interpretation of in vivo redox data, and discuss technical and biological limitations of current redox sensors and sensing approaches. We explore how novel sensor variants may further add to the current momentum toward a novel mechanistic and integrated understanding of redox biology in vivo. Antioxid. Redox Signal. 24, 680-712.

  2. Electric and Magnetic Manipulation of Biological Systems

    NASA Astrophysics Data System (ADS)

    Lee, H.; Hunt, T. P.; Liu, Y.; Ham, D.; Westervelt, R. M.

    2005-06-01

    New types of biological cell manipulation systems, a micropost matrix, a microelectromagnet matrix, and a microcoil array, were developed. The micropost matrix consists of post-shaped electrodes embedded in an insulating layer. With a separate ac voltage applied to each electrode, the micropost matrix generates dielectrophoretic force to trap and move individual biological cells. The microelectromagnet matrix consists of two arrays of straight wires aligned perpendicular to each other, that are covered with insulating layers. By independently controlling the current in each wire, the microelectromagnet matrix creates versatile magnetic fields to manipulate individual biological cells attached to magnetic beads. The microcoil array is a set of coils implemented in a foundry using a standard silicon fabrication technology. Current sources to the coils, and control circuits are integrated on a single chip, making the device self-contained. Versatile manipulation of biological cells was demonstrated using these devices by generating optimized electric or magnetic field patterns. A single yeast cell was trapped and positioned with microscopic resolution, and multiple yeast cells were trapped and independently moved along the separate paths for cell-sorting.

  3. Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

    PubMed

    Sorokin, Anatoly; Le Novère, Nicolas; Luna, Augustin; Czauderna, Tobias; Demir, Emek; Haw, Robin; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Villéger, Alice

    2015-09-04

    The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

  4. An Implementation-Focused Bio/Algorithmic Workflow for Synthetic Biology.

    PubMed

    Goñi-Moreno, Angel; Carcajona, Marta; Kim, Juhyun; Martínez-García, Esteban; Amos, Martyn; de Lorenzo, Víctor

    2016-10-21

    As synthetic biology moves away from trial and error and embraces more formal processes, workflows have emerged that cover the roadmap from conceptualization of a genetic device to its construction and measurement. This latter aspect (i.e., characterization and measurement of synthetic genetic constructs) has received relatively little attention to date, but it is crucial for their outcome. An end-to-end use case for engineering a simple synthetic device is presented, which is supported by information standards and computational methods and focuses on such characterization/measurement. This workflow captures the main stages of genetic device design and description and offers standardized tools for both population-based measurement and single-cell analysis. To this end, three separate aspects are addressed. First, the specific vector features are discussed. Although device/circuit design has been successfully automated, important structural information is usually overlooked, as in the case of plasmid vectors. The use of the Standard European Vector Architecture (SEVA) is advocated for selecting the optimal carrier of a design and its thorough description in order to unequivocally correlate digital definitions and molecular devices. A digital version of this plasmid format was developed with the Synthetic Biology Open Language (SBOL) along with a software tool that allows users to embed genetic parts in vector cargoes. This enables annotation of a mathematical model of the device's kinetic reactions formatted with the Systems Biology Markup Language (SBML). From that point onward, the experimental results and their in silico counterparts proceed alongside, with constant feedback to preserve consistency between them. A second aspect involves a framework for the calibration of fluorescence-based measurements. One of the most challenging endeavors in standardization, metrology, is tackled by reinterpreting the experimental output in light of simulation results, allowing

  5. DeviceEditor visual biological CAD canvas

    PubMed Central

    2012-01-01

    Background Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. Results We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs. PMID:22373390

  6. Biological Criteria for Protection of U.S. Coral Reefs.

    EPA Science Inventory

    Coral reef ecosystems are threatened by natural stressors, human activities, and natural stressors exacerbated by human activities. Under the U.S. Clean Water Act, States and Territories may guard against anthropogenic threats by adopting water quality standards based on biologic...

  7. Biological Criteria for Protection of U.S. Coral Reefs

    EPA Science Inventory

    Coral reef ecosystems are threatened by natural stressors, human activities, and natural stressors exacerbated by human activities. Under the U.S. Clean Water Act, States and Territories may guard against anthropogenic threats by adopting water quality standards based on biologic...

  8. Aerospace Medicine and Biology: A Continuing Bibliography. Supplement 476

    NASA Technical Reports Server (NTRS)

    1998-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP-1998-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract.

  9. Teaching strategies and student achievement in high school block scheduled biology classes

    NASA Astrophysics Data System (ADS)

    Louden, Cynthia Knapp

    The objectives of this study included determining whether teachers in block or traditionally scheduled biology classes (1) implement inquiry-based instruction more often or with different methods, (2) understand the concept of inquiry-based instruction as it is described in the National Science Standards, (3) have classes with significantly different student achievement, and (4) believe that their school schedule facilitates their use of inquiry-based instruction in the classroom. Biology teachers in block and non-block scheduled classes were interviewed, surveyed, and observed to determine the degree to which they implement inquiry-based instructional practices in their classrooms. State biology exams were used to indicate student achievement. Teachers in block scheduled and traditional classes used inquiry-based instruction with nearly the same frequency. Approximately 30% of all teachers do not understand the concept of inquiry-based instruction as described by the National Science Standards. No significant achievement differences between block and traditionally scheduled biology classes were found using ANCOVA analyses and a nonequivalent control-group quasi-experimental design. Using the same analysis techniques, significant achievement differences were found between biology classes with teachers who used inquiry-based instruction frequently and infrequently. Teachers in block schedules believed that their schedules facilitated inquiry-based instruction more than teachers in traditional schedules.

  10. Data Integration and Mining for Synthetic Biology Design.

    PubMed

    Mısırlı, Göksel; Hallinan, Jennifer; Pocock, Matthew; Lord, Phillip; McLaughlin, James Alastair; Sauro, Herbert; Wipat, Anil

    2016-10-21

    One aim of synthetic biologists is to create novel and predictable biological systems from simpler modular parts. This approach is currently hampered by a lack of well-defined and characterized parts and devices. However, there is a wealth of existing biological information, which can be used to identify and characterize biological parts, and their design constraints in the literature and numerous biological databases. However, this information is spread among these databases in many different formats. New computational approaches are required to make this information available in an integrated format that is more amenable to data mining. A tried and tested approach to this problem is to map disparate data sources into a single data set, with common syntax and semantics, to produce a data warehouse or knowledge base. Ontologies have been used extensively in the life sciences, providing this common syntax and semantics as a model for a given biological domain, in a fashion that is amenable to computational analysis and reasoning. Here, we present an ontology for applications in synthetic biology design, SyBiOnt, which facilitates the modeling of information about biological parts and their relationships. SyBiOnt was used to create the SyBiOntKB knowledge base, incorporating and building upon existing life sciences ontologies and standards. The reasoning capabilities of ontologies were then applied to automate the mining of biological parts from this knowledge base. We propose that this approach will be useful to speed up synthetic biology design and ultimately help facilitate the automation of the biological engineering life cycle.

  11. The International Standard for Oxytetracycline

    PubMed Central

    Humphrey, J. H.; Lightbown, J. W.; Mussett, M. V.; Perry, W. L. M.

    1955-01-01

    The first attempt to set up an international standard for oxytetracycline, using oxytetracycline hydrochloride, failed because of difficulties in obtaining a preparation whose moisture content was uniform after distribution into ampoules. A preparation of dihydrate of oxytetracycline base was obtained instead, and was compared in an international collaborative assay with a sample of oxytetracycline hydrochloride, which was the current working standard of Chas. Pfizer & Co., Inc., USA. The results of the collaborative assay showed that the potency of the dihydrate was uniform, and that it was a suitable preparation for use as the International Standard. Evidence was obtained, however, that the reference preparation at the time of examination was less potent than had been originally supposed, and that it was hydrated. The potency of the proposed international standard was recalculated after allowance for water in the reference preparation, and the resulting biological potency agreed well with that to be expected on the basis of the physicochemical properties of the preparation. It was agreed, therefore, that the recalculated values should be used, and the preparation of oxytetracycline base dihydrate used in the collaborative assay is established as the International Standard for Oxytetracycline with a potency of 900 International Units per mg. PMID:13284563

  12. A comparison of Massachusetts and Texas high school biology teachers' attitudes towards the teaching of evolution

    NASA Astrophysics Data System (ADS)

    Howarth, Richard T.

    Darwin's theory of evolution by natural selection is considered to be the unifying theory for all life sciences (American Association for the Advancement of Science, AAAS, 1990; National Academy of Sciences, 1998; National Research Council, NRC, 1996; National Science Teachers Association, NSTA, 2010a) and as such, the biology topic has been established as a central learning standard by the National Science Education Science Standards (NSES, 2005). The purpose of this study was to compare how Massachusetts and Texas high school biology teachers' attitudes toward the teaching of evolution differ as compared to other biology topics. Texas and Massachusetts are two states that exemplify standards based education yet differ dramatically in their histories surrounding the topic of evolution. A survey was conducted among 217 Massachusetts and 139 Texas in-service high school biology teachers to help provide a sense of the phenomena surrounding biology teachers in respect to how their attitudes towards the teaching of evolution are shaped. Additionally, an open-ended question was asked to help contextualize the results of the survey between teachers of these two states. The findings in this study suggest that community appears to be a powerful persuasive message and socialization experience that shapes the development of attitudes towards evolution for some educators, especially when it is highly intertwined with religion. For biology teachers in the state of Texas, the synergistic result of this relationship has resulted in statistically significant differences in regards to attitudes towards evolution as compared to teachers in Massachusetts. These findings yield implications regarding scientific literacy, student learning, assessment, the quality of science instruction, curriculum, undergraduate biology programs, and the needs of biology teachers in terms of professional development.

  13. Aerospace medicine and biology: A continuing bibliography with indexes, supplement

    NASA Technical Reports Server (NTRS)

    1972-01-01

    Subject coverage concentrates on the biological, physiological, psychological, and environmental effects to which man is subjected during and following simulated or actual flight in the earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Each entry consists of a standard citation accompanied by its abstract.

  14. Link between the dielectric properties of mesomorphic and biological materials

    NASA Astrophysics Data System (ADS)

    Szwajczak, Elzbieta; Szymanski, Aleksander B.

    2002-06-01

    An application of liquid crystalline materials as a model materials for the use in dielectric spectroscopy of the artificial biological materials and the tissues is discussed. It is shown that an application of the standard electrochemical concepts may break in the case of liquid crystalline materials as well as biological materials. The presence of space charge regions as well as electrical non- linearities of the sample may suggest some special possibility of the time domain technique application.

  15. Removing the tree-ring width biological trend using expected basal area increment

    Treesearch

    Franco Biondi; Fares Qeadan

    2008-01-01

    One of the main elements of dendrochronological standardization is the removal of the biological trend, i.e., the progressive decline of ring width along a cross-sectional radius that is mostly caused by the corresponding increase in stem diameter over time. A very common option for removing this biological trend is to fit a modified negative exponential curve to the...

  16. A Transformative Model for Undergraduate Quantitative Biology Education

    ERIC Educational Resources Information Center

    Usher, David C.; Driscoll, Tobin A.; Dhurjati, Prasad; Pelesko, John A.; Rossi, Louis F.; Schleiniger, Gilberto; Pusecker, Kathleen; White, Harold B.

    2010-01-01

    The "BIO2010" report recommended that students in the life sciences receive a more rigorous education in mathematics and physical sciences. The University of Delaware approached this problem by (1) developing a bio-calculus section of a standard calculus course, (2) embedding quantitative activities into existing biology courses, and (3)…

  17. Creationism in the Biology Classroom: What Do Teachers Teach & How Do They Teach It?

    ERIC Educational Resources Information Center

    Moore, Randy

    2008-01-01

    Approximately one-fourth of biology teachers in public schools include creationism in their biology courses. Most of these teachers 1) present creationism as a scientific alternative to evolution, and 2) present only the biblical (i.e., Christian) story of creation. State science-education standards, position statements from professional…

  18. The International Standard for Anti-Brucella abortus Serum

    PubMed Central

    Stableforth, A. W.

    1954-01-01

    In field trials on the eradication of brucellosis from dairy herds in Great Britain, which began in 1933, a serum standard of reference was used for the examination of agglutinating suspensions prepared in different laboratories. In 1937, the Office International des Epizooties (OIE) adopted this standard and made recommendations for its use internationally. These recommendations were revised by OIE in 1948, by the Third Inter-American Congress on Brucellosis and by the Joint FAO/WHO Expert Panel on Brucellosis in 1950, and again by the latter body in 1952. A new batch equivalent in potency to the original standard was established by the WHO Expert Committee on Biological Standardization in 1952 as the International Standard for Anti-Brucella abortus Serum. The International Standard, or a national standard of equivalent potency, ensures comparability of the titres obtained in different countries by different methods, and the results of such comparisons can be expressed in a simple manner by describing the titres in terms of International Units of Brucella antibody. PMID:13199656

  19. Altitude exposure in sports: the Athlete Biological Passport standpoint.

    PubMed

    Sanchis-Gomar, Fabian; Pareja-Galeano, Helios; Brioche, Thomas; Martinez-Bello, Vladimir; Lippi, Giuseppe

    2014-03-01

    The Athlete Biological Passport (ABP) is principally founded on monitoring an athlete's biological variables over time, to identify abnormal biases on a longitudinal basis. Several factors are known to influence the results of these markers. However, the manner in which the altitude factor is taken into account still needs to be standardized. Causal relationships between haematological variables should be correctly integrated into ABP software. In particular, modifications of haematological parameters during and after exposure to different altitudes/hypoxic protocols need to be properly included within detection models. Copyright © 2013 John Wiley & Sons, Ltd.

  20. Evolution Acceptance and Epistemological Beliefs of College Biology Students

    ERIC Educational Resources Information Center

    Borgerding, Lisa A.; Deniz, Hasan; Anderson, Elizabeth Shevock

    2017-01-01

    Evolutionary theory is central to biology, and scientifically accurate evolution instruction is promoted within national and state standards documents. Previous literature has identified students' epistemological beliefs as potential predictors of evolution acceptance. The present work seeks to explore more directly how student views of evolution…

  1. Toward Contactless Biology: Acoustophoretic DNA Transfection

    NASA Astrophysics Data System (ADS)

    Vasileiou, Thomas; Foresti, Daniele; Bayram, Adem; Poulikakos, Dimos; Ferrari, Aldo

    2016-02-01

    Acoustophoresis revolutionized the field of container-less manipulation of liquids and solids by enabling mixing procedures which avoid contamination and loss of reagents due to the contact with the support. While its applications to chemistry and engineering are straightforward, additional developments are needed to obtain reliable biological protocols in a contactless environment. Here, we provide a first, fundamental step towards biological reactions in air by demonstrating the acoustophoretic DNA transfection of mammalian cells. We developed an original acoustophoretic design capable of levitating, moving and mixing biological suspensions of living mammalians cells and of DNA plasmids. The precise and sequential delivery of the mixed solutions into tissue culture plates is actuated by a novel mechanism based on the controlled actuation of the acoustophoretic force. The viability of the contactless procedure is tested using a cellular model sensitive to small perturbation of neuronal differentiation pathways. Additionally, the efficiency of the transfection procedure is compared to standard, container-based methods for both single and double DNA transfection and for different cell types including adherent growing HeLa cancer cells, and low adhesion neuron-like PC12 cells. In all, this work provides a proof of principle which paves the way to the development of high-throughput acoustophoretic biological reactors.

  2. Toward Contactless Biology: Acoustophoretic DNA Transfection.

    PubMed

    Vasileiou, Thomas; Foresti, Daniele; Bayram, Adem; Poulikakos, Dimos; Ferrari, Aldo

    2016-02-01

    Acoustophoresis revolutionized the field of container-less manipulation of liquids and solids by enabling mixing procedures which avoid contamination and loss of reagents due to the contact with the support. While its applications to chemistry and engineering are straightforward, additional developments are needed to obtain reliable biological protocols in a contactless environment. Here, we provide a first, fundamental step towards biological reactions in air by demonstrating the acoustophoretic DNA transfection of mammalian cells. We developed an original acoustophoretic design capable of levitating, moving and mixing biological suspensions of living mammalians cells and of DNA plasmids. The precise and sequential delivery of the mixed solutions into tissue culture plates is actuated by a novel mechanism based on the controlled actuation of the acoustophoretic force. The viability of the contactless procedure is tested using a cellular model sensitive to small perturbation of neuronal differentiation pathways. Additionally, the efficiency of the transfection procedure is compared to standard, container-based methods for both single and double DNA transfection and for different cell types including adherent growing HeLa cancer cells, and low adhesion neuron-like PC12 cells. In all, this work provides a proof of principle which paves the way to the development of high-throughput acoustophoretic biological reactors.

  3. Toward Contactless Biology: Acoustophoretic DNA Transfection

    PubMed Central

    Vasileiou, Thomas; Foresti, Daniele; Bayram, Adem; Poulikakos, Dimos; Ferrari, Aldo

    2016-01-01

    Acoustophoresis revolutionized the field of container-less manipulation of liquids and solids by enabling mixing procedures which avoid contamination and loss of reagents due to the contact with the support. While its applications to chemistry and engineering are straightforward, additional developments are needed to obtain reliable biological protocols in a contactless environment. Here, we provide a first, fundamental step towards biological reactions in air by demonstrating the acoustophoretic DNA transfection of mammalian cells. We developed an original acoustophoretic design capable of levitating, moving and mixing biological suspensions of living mammalians cells and of DNA plasmids. The precise and sequential delivery of the mixed solutions into tissue culture plates is actuated by a novel mechanism based on the controlled actuation of the acoustophoretic force. The viability of the contactless procedure is tested using a cellular model sensitive to small perturbation of neuronal differentiation pathways. Additionally, the efficiency of the transfection procedure is compared to standard, container-based methods for both single and double DNA transfection and for different cell types including adherent growing HeLa cancer cells, and low adhesion neuron-like PC12 cells. In all, this work provides a proof of principle which paves the way to the development of high-throughput acoustophoretic biological reactors. PMID:26828312

  4. Monitoring biological diversity: strategies, tools, limitations, and challenges.

    Treesearch

    Erik A. Beever

    2006-01-01

    Monitoring is an assessment of the spatial and temporal variability in one or more ecosystem properties, and is an essential component of adaptive management. Monitoring can help determine whether mandated environmental standards are being met and can provide an early-warning system of ecological change. Development of a strategy for monitoring biological diversity...

  5. Physical Growth, Biological Age, and Nutritional Transitions of Adolescents Living at Moderate Altitudes in Peru.

    PubMed

    Cossio-Bolaños, Marco; Campos, Rossana Gómez; Andruske, Cynthia Lee; Flores, Antonio Viveros; Luarte-Rocha, Cristian; Olivares, Pedro R; Garcia-Rubio, Javier; de Arruda, Miguel

    2015-09-25

    Peru is experiencing a stage of nutritional transition where the principal characteristics are typical of countries undergoing development. The objectives of this study were the following: (a) compare physical growth patterns with an international standard; (b) determine biological age; and (c) analyze the double nutritional burden of adolescents living at a moderate altitude in Peru. Weight, standing height, and sitting height were measured in 551 adolescents of both sexes (12.0 to 17.9 years old) from an urban area of Arequipa, Peru (2328 m). Physical growth was compared with the international standard of the CDC-2000. Biological age was determined by using a non-invasive transversal technique based on years from age at peak height velocity (APHV). Nutritional state was determined by means of weight for age and height for age. Z scores were calculated using international standards from the CDC-2000. Body weight for both sexes was similar to the CDC-2000 international standards. At all ages, the girls' height (p < 0.05) was below the standards. However, the boys' height (p < 0.05) was less at ages, 15, 16, and 17. Biological age showed up in girls at age 12.7 years and for boys at 15.2 years. Stunted growth (8.7% boys and 18.0% girls) and over weight (11.3% boys and 8.8% girls) occurred in both groups. A relationship existed in both sexes between the categories of weight for the age and stunted growth by sex. Adolescents living at a moderate altitude exhibited stunted linear growth and biological maturation. Furthermore, adolescents of both sexes showed the presence of the double nutritional burden (stunted growth and excessive weight).

  6. Knowledge base and functionality of concepts of some Filipino biology teachers in five biology topics

    NASA Astrophysics Data System (ADS)

    Barquilla, Manuel B.

    2018-01-01

    This mixed research, is a snapshot of some Filipino Biology teachers' knowledge structure and how their concepts of the five topics in Biology (Photosynthesis, Cellular Respiration, human reproductive system, Mendelian genetics and NonMendelian genetics) functions and develops inside a biology classroom. The study focuses on the six biology teachers and a total of 222 students in their respective classes. Of the Six (6) teachers, three (3) are under the Science curriculum and the other three (3) are under regular curriculum in both public and private schools in Iligan city and Lanao del Norte, Philippines. The study utilized classroom discourses, concept maps, interpretative case-study method, bracketing method, and concept analysis for qualitative part; the quantitative part uses a nonparametric statistical tool, Kendall's tau Coefficient for determining relationship and congruency while measures of central tendencies and dispersion (mean, and standard deviation) for concept maps scores interpretation. Knowledge Base of Biology teachers were evaluated by experts in field of specialization having a doctorate program (e.g. PhD in Genetics) and PhD Biology candidates. The data collection entailed seven (7) months immersion: one (1) month for preliminary phase for the researcher to gain teachers' and students' confidence and the succeeding six (6) months for main observation and data collection. The evaluation of teachers' knowledge base by experts indicated that teachers' knowledge of (65%) is lower than the minimum (75%) recommended by ABD-el-Khalick and Boujaoude (1997). Thus, the experts believe that content knowledge of the teachers is hardly adequate for their teaching assignment. Moreover, the teachers in this study do not systematically use reallife situation to apply the concepts they teach. They can identify concepts too abstract for their student; however, they seldom use innovative ways to bring the discussion to their students' level of readiness and

  7. Standardized Analytical Methods for Environmental Restoration Following Homeland Security Events

    USDA-ARS?s Scientific Manuscript database

    Methodology was formulated for use in the event of a terrorist attack using a variety of chemical, radioactive, biological, and toxic agents. Standardized analysis procedures were determined for use should these events occur. This publication is annually updated....

  8. International Standard Payload Rack volume

    NASA Technical Reports Server (NTRS)

    2001-01-01

    Outer dimensions of the International Standard Payload Rack (ISPR) that will be used on the International Space Station (ISS) sets the envelope for scientists designing hardware for experiments in biological and physical sciences aboard ISS. The ISPR includes attachments to ISS utilities (electrical power, heating and cooling, data, fluids, vacuum, etc.) through standoffs that hold the racks in place in the lab modules. Usage will range from facilities that take entire racks to specialized drawers occupying a portion of a rack.

  9. Recent advances in synthetic biology of cyanobacteria.

    PubMed

    Sengupta, Annesha; Pakrasi, Himadri B; Wangikar, Pramod P

    2018-05-09

    Cyanobacteria are attractive hosts that can be engineered for the photosynthetic production of fuels, fine chemicals, and proteins from CO 2 . Moreover, the responsiveness of these photoautotrophs towards different environmental signals, such as light, CO 2 , diurnal cycle, and metals make them potential hosts for the development of biosensors. However, engineering these hosts proves to be a challenging and lengthy process. Synthetic biology can make the process of biological engineering more predictable through the use of standardized biological parts that are well characterized and tools to assemble them. While significant progress has been made with model heterotrophic organisms, many of the parts and tools are not portable in cyanobacteria. Therefore, efforts are underway to develop and characterize parts derived from cyanobacteria. In this review, we discuss the reported parts and tools with the objective to develop cyanobacteria as cell factories or biosensors. We also discuss the issues related to characterization, tunability, portability, and the need to develop enabling technologies to engineer this "green" chassis.

  10. Effect of genomic drift of influenza PCR tests.

    PubMed

    Stellrecht, Kathleen A; Nattanmai, Seela M; Butt, Jumshan; Maceira, Vincente P; Espino, Alvin A; Castro, Allan J; Landes, Allen; Dresser, Nicolas; Butt, Shafiq A

    2017-08-01

    Nucleic acid amplification assays have become the method of choice for influenza (Flu) testing due to superior accuracy and faster turnaround time. Although assays are designed to detect highly conserved genomic targets, mutations can influence test sensitivity. Most of the circulating viruses in the United States during the 2014-2015 season were associated with significant genetic drift; however, the effect on testing was unknown. We compared the performance of Prodesse ProFlu+/ProFAST+ (PFlu/PFAST), FilmArray Respiratory Panel (RP), cobas ® Influenza A/B test (cIAB), and Xpert ® Flu (Xpt) in a retrospective analysis of consecutive nasopharyngeal specimens received for a two-week period during the winter of 2015. Furthermore, limits of detection (LOD) were determined with six isolates of Flu. Of the 275 specimens, 63 were positive for FluA by PFAST, 60 were positive by RP, 58 were positive by cIAB and 52 were positive by Xpt. Only a subset of 135 specimens was tested by PFlu, of which 32 were positive. The sensitivity/specificity for PFAST, RP, cIAB, Xpt and PFlu was 100/99.1%, 96.7/99.5%, 91.8/99.1%, 85.2%/100%, and 75.6%/98.9%, respectively. LOD analyses demonstrated assay performance variations were strain associated. Specifically, PFlu's and cIAB's LODs were higher with A/Texas/50/2012-like and A/Switzerland/9715293/2013-like strains, while Xpt's highest LOD was with the Swiss strain. Strain-associated assay performance variation is known to occur with other Flu test methods; hence, it is not surprising that such variation would be observed with molecular tests. Careful monitoring and reporting for strain-associated variances are warranted for all test methods. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Functional Dissection of the Blocking and Bypass Activities of the Fab-8 Boundary in the Drosophila Bithorax Complex.

    PubMed

    Kyrchanova, Olga; Mogila, Vladic; Wolle, Daniel; Deshpande, Girish; Parshikov, Alexander; Cléard, Fabienne; Karch, Francois; Schedl, Paul; Georgiev, Pavel

    2016-07-01

    Functionally autonomous regulatory domains direct the parasegment-specific expression of the Drosophila Bithorax complex (BX-C) homeotic genes. Autonomy is conferred by boundary/insulator elements that separate each regulatory domain from its neighbors. For six of the nine parasegment (PS) regulatory domains in the complex, at least one boundary is located between the domain and its target homeotic gene. Consequently, BX-C boundaries must not only block adventitious interactions between neighboring regulatory domains, but also be permissive (bypass) for regulatory interactions between the domains and their gene targets. To elucidate how the BX-C boundaries combine these two contradictory activities, we have used a boundary replacement strategy. We show that a 337 bp fragment spanning the Fab-8 boundary nuclease hypersensitive site and lacking all but 83 bp of the 625 bp Fab-8 PTS (promoter targeting sequence) fully rescues a Fab-7 deletion. It blocks crosstalk between the iab-6 and iab-7 regulatory domains, and has bypass activity that enables the two downstream domains, iab-5 and iab-6, to regulate Abdominal-B (Abd-B) transcription in spite of two intervening boundary elements. Fab-8 has two dCTCF sites and we show that they are necessary both for blocking and bypass activity. However, CTCF sites on their own are not sufficient for bypass. While multimerized dCTCF (or Su(Hw)) sites have blocking activity, they fail to support bypass. Moreover, this bypass defect is not rescued by the full length PTS. Finally, we show that orientation is critical for the proper functioning the Fab-8 replacement. Though the inverted Fab-8 boundary still blocks crosstalk, it disrupts the topology of the Abd-B regulatory domains and does not support bypass. Importantly, altering the orientation of the Fab-8 dCTCF sites is not sufficient to disrupt bypass, indicating that orientation dependence is conferred by other factors.

  12. Functional Dissection of the Blocking and Bypass Activities of the Fab-8 Boundary in the Drosophila Bithorax Complex

    PubMed Central

    Wolle, Daniel; Deshpande, Girish; Parshikov, Alexander; Cléard, Fabienne; Karch, Francois; Schedl, Paul; Georgiev, Pavel

    2016-01-01

    Functionally autonomous regulatory domains direct the parasegment-specific expression of the Drosophila Bithorax complex (BX-C) homeotic genes. Autonomy is conferred by boundary/insulator elements that separate each regulatory domain from its neighbors. For six of the nine parasegment (PS) regulatory domains in the complex, at least one boundary is located between the domain and its target homeotic gene. Consequently, BX-C boundaries must not only block adventitious interactions between neighboring regulatory domains, but also be permissive (bypass) for regulatory interactions between the domains and their gene targets. To elucidate how the BX-C boundaries combine these two contradictory activities, we have used a boundary replacement strategy. We show that a 337 bp fragment spanning the Fab-8 boundary nuclease hypersensitive site and lacking all but 83 bp of the 625 bp Fab-8 PTS (promoter targeting sequence) fully rescues a Fab-7 deletion. It blocks crosstalk between the iab-6 and iab-7 regulatory domains, and has bypass activity that enables the two downstream domains, iab-5 and iab-6, to regulate Abdominal-B (Abd-B) transcription in spite of two intervening boundary elements. Fab-8 has two dCTCF sites and we show that they are necessary both for blocking and bypass activity. However, CTCF sites on their own are not sufficient for bypass. While multimerized dCTCF (or Su(Hw)) sites have blocking activity, they fail to support bypass. Moreover, this bypass defect is not rescued by the full length PTS. Finally, we show that orientation is critical for the proper functioning the Fab-8 replacement. Though the inverted Fab-8 boundary still blocks crosstalk, it disrupts the topology of the Abd-B regulatory domains and does not support bypass. Importantly, altering the orientation of the Fab-8 dCTCF sites is not sufficient to disrupt bypass, indicating that orientation dependence is conferred by other factors. PMID:27428541

  13. Cell biology perspectives in phage biology.

    PubMed

    Ansaldi, Mireille

    2012-01-01

    Cellular biology has long been restricted to large cellular organisms. However, as the resolution of microscopic methods increased, it became possible to study smaller cells, in particular bacterial cells. Bacteriophage biology is one aspect of bacterial cell biology that has recently gained insight from cell biology. Despite their small size, bacteriophages could be successfully labeled and their cycle studied in the host cells. This review aims to put together, although non-extensively, several cell biology studies that recently pushed the elucidation of key mechanisms in phage biology, such as the lysis-lysogeny decision in temperate phages or genome replication and transcription, one step further.

  14. Building Better Scientists through Cross-Disciplinary Collaboration in Synthetic Biology: A Report from the Genome Consortium for Active Teaching Workshop 2010

    ERIC Educational Resources Information Center

    Wolyniak, Michael J.; Alvarez, Consuelo J.; Chandrasekaran, Vidya; Grana, Theresa M.; Holgado, Andrea; Jones, Christopher J.; Morris, Robert W.; Pereira, Anil L.; Stamm, Joyce; Washington, Talitha M.; Yang, Yixin

    2010-01-01

    Synthetic biology is the application of engineering and mathematical principles to develop novel biological devices and circuits. What separates synthetic biology from traditional molecular biology is the development of standardized interchangeable DNA "parts," just as advances in engineering in the nineteenth century brought about standardized…

  15. Biological sequence compression algorithms.

    PubMed

    Matsumoto, T; Sadakane, K; Imai, H

    2000-01-01

    Today, more and more DNA sequences are becoming available. The information about DNA sequences are stored in molecular biology databases. The size and importance of these databases will be bigger and bigger in the future, therefore this information must be stored or communicated efficiently. Furthermore, sequence compression can be used to define similarities between biological sequences. The standard compression algorithms such as gzip or compress cannot compress DNA sequences, but only expand them in size. On the other hand, CTW (Context Tree Weighting Method) can compress DNA sequences less than two bits per symbol. These algorithms do not use special structures of biological sequences. Two characteristic structures of DNA sequences are known. One is called palindromes or reverse complements and the other structure is approximate repeats. Several specific algorithms for DNA sequences that use these structures can compress them less than two bits per symbol. In this paper, we improve the CTW so that characteristic structures of DNA sequences are available. Before encoding the next symbol, the algorithm searches an approximate repeat and palindrome using hash and dynamic programming. If there is a palindrome or an approximate repeat with enough length then our algorithm represents it with length and distance. By using this preprocessing, a new program achieves a little higher compression ratio than that of existing DNA-oriented compression algorithms. We also describe new compression algorithm for protein sequences.

  16. Simulating Biological and Non-Biological Motion

    ERIC Educational Resources Information Center

    Bruzzo, Angela; Gesierich, Benno; Wohlschlager, Andreas

    2008-01-01

    It is widely accepted that the brain processes biological and non-biological movements in distinct neural circuits. Biological motion, in contrast to non-biological motion, refers to active movements of living beings. Aim of our experiment was to investigate the mechanisms underlying mental simulation of these two movement types. Subjects had to…

  17. Development of data representation standards by the human proteome organization proteomics standards initiative

    PubMed Central

    Albar, Juan Pablo; Binz, Pierre-Alain; Eisenacher, Martin; Jones, Andrew R; Mayer, Gerhard; Omenn, Gilbert S; Orchard, Sandra; Vizcaíno, Juan Antonio; Hermjakob, Henning

    2015-01-01

    Objective To describe the goals of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization, the methods that the PSI has employed to create data standards, the resulting output of the PSI, lessons learned from the PSI’s evolution, and future directions and synergies for the group. Materials and Methods The PSI has 5 categories of deliverables that have guided the group. These are minimum information guidelines, data formats, controlled vocabularies, resources and software tools, and dissemination activities. These deliverables are produced via the leadership and working group organization of the initiative, driven by frequent workshops and ongoing communication within the working groups. Official standards are subjected to a rigorous document process that includes several levels of peer review prior to release. Results We have produced and published minimum information guidelines describing what information should be provided when making data public, either via public repositories or other means. The PSI has produced a series of standard formats covering mass spectrometer input, mass spectrometer output, results of informatics analysis (both qualitative and quantitative analyses), reports of molecular interaction data, and gel electrophoresis analyses. We have produced controlled vocabularies that ensure that concepts are uniformly annotated in the formats and engaged in extensive software development and dissemination efforts so that the standards can efficiently be used by the community. Conclusion In its first dozen years of operation, the PSI has produced many standards that have accelerated the field of proteomics by facilitating data exchange and deposition to data repositories. We look to the future to continue developing standards for new proteomics technologies and workflows and mechanisms for integration with other omics data types. Our products facilitate the translation of genomics and proteomics findings to clinical and

  18. Is synthetic biology mechanical biology?

    PubMed

    Holm, Sune

    2015-12-01

    A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

  19. Immunotherapy safety: a prospective multi-centric monitoring study of biologically standardized therapeutic vaccines for allergic diseases.

    PubMed

    Moreno, C; Cuesta-Herranz, J; Fernández-Távora, L; Alvarez-Cuesta, E

    2004-04-01

    The fear of side-effects has led to strict regulations preventing a more widespread use of specific immunotherapy (SIT) in some countries, in spite of the low risk of systemic reactions (SRs) reported in well-controlled studies. The goal of the study was to carry out a prospective and multi-centric trial to evaluate the safety, risk factors and compliance degree of commercially available SIT. The study was carried out in 14 allergy departments from Spain. Four-hundred and eighty-eight patients with rhinitis and/or asthma were submitted to treatment with biologically standardized allergen extracts commercially available. They were administered following the European Academy of Allergy and Clinical Immunology guidelines. Four hundred and twenty-three patients (86.7%) completed the treatment and remained under control at the end of the trial. Out of 17,526 administered doses, 17,368 doses (99.1%) were not associated with a reaction. Eighteen patients (3.7%) experienced 53 (0.3% of the doses) SRs. All immediate SRs were mild or moderate and responded well to ordinary treatment measures. There were no fatal reactions, anaphylactic shock or life-threatening reactions. A higher ratio of SRs was found among asthmatic and dust mite allergic patients, although multi-variable logistic analysis did not demonstrate any risk factor associated with SRs. There was also a subgroup of patients at risk for recurrent reactions, and therefore 40% of SRs had been avoided if the maximal number of SRs had been previously limited to only three SRs. This multi-centric study showed that SIT was a safe treatment with a very good compliance. Future guidelines of SIT should limit the maximal number of SRs.

  20. Synthetic biology: insights into biological computation.

    PubMed

    Manzoni, Romilde; Urrios, Arturo; Velazquez-Garcia, Silvia; de Nadal, Eulàlia; Posas, Francesc

    2016-04-18

    Organisms have evolved a broad array of complex signaling mechanisms that allow them to survive in a wide range of environmental conditions. They are able to sense external inputs and produce an output response by computing the information. Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology. In this context, biocomputation is the branch of synthetic biology aimed at implementing artificial computational devices using engineered biological motifs as building blocks. Biocomputational devices are defined as biological systems that are able to integrate inputs and return outputs following pre-determined rules. Over the last decade the number of available synthetic engineered devices has increased exponentially; simple and complex circuits have been built in bacteria, yeast and mammalian cells. These devices can manage and store information, take decisions based on past and present inputs, and even convert a transient signal into a sustained response. The field is experiencing a fast growth and every day it is easier to implement more complex biological functions. This is mainly due to advances in in vitro DNA synthesis, new genome editing tools, novel molecular cloning techniques, continuously growing part libraries as well as other technological advances. This allows that digital computation can now be engineered and implemented in biological systems. Simple logic gates can be implemented and connected to perform novel desired functions or to better understand and redesign biological processes. Synthetic biological digital circuits could lead to new therapeutic approaches, as well as new and efficient ways to produce complex molecules such as antibiotics, bioplastics or biofuels. Biological computation not only provides possible biomedical and

  1. [Standards in Medical Informatics: Fundamentals and Applications].

    PubMed

    Suárez-Obando, Fernando; Camacho Sánchez, Jhon

    2013-09-01

    The use of computers in medical practice has enabled novel forms of communication to be developed in health care. The optimization of communication processes is achieved through the use of standards to harmonize the exchange of information and provide a common language for all those involved. This article describes the concept of a standard applied to medical informatics and its importance in the development of various applications, such as computational representation of medical knowledge, disease classification and coding systems, medical literature searches and integration of biological and clinical sciences. Copyright © 2013 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

  2. Personal Constructions of Biological Concepts--The Repertory Grid Approach

    ERIC Educational Resources Information Center

    McCloughlin, Thomas J. J.; Matthews, Philip S. C.

    2017-01-01

    This work discusses repertory grid analysis as a tool for investigating the structures of students' representations of biological concepts. Repertory grid analysis provides the researcher with a variety of techniques that are not associated with standard methods of concept mapping for investigating conceptual structures. It can provide valuable…

  3. GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules.

    PubMed

    Sarrion-Perdigones, Alejandro; Falconi, Erica Elvira; Zandalinas, Sara I; Juárez, Paloma; Fernández-del-Carmen, Asun; Granell, Antonio; Orzaez, Diego

    2011-01-01

    Synthetic Biology requires efficient and versatile DNA assembly systems to facilitate the building of new genetic modules/pathways from basic DNA parts in a standardized way. Here we present GoldenBraid (GB), a standardized assembly system based on type IIS restriction enzymes that allows the indefinite growth of reusable gene modules made of standardized DNA pieces. The GB system consists of a set of four destination plasmids (pDGBs) designed to incorporate multipartite assemblies made of standard DNA parts and to combine them binarily to build increasingly complex multigene constructs. The relative position of type IIS restriction sites inside pDGB vectors introduces a double loop ("braid") topology in the cloning strategy that allows the indefinite growth of composite parts through the succession of iterative assembling steps, while the overall simplicity of the system is maintained. We propose the use of GoldenBraid as an assembly standard for Plant Synthetic Biology. For this purpose we have GB-adapted a set of binary plasmids for A. tumefaciens-mediated plant transformation. Fast GB-engineering of several multigene T-DNAs, including two alternative modules made of five reusable devices each, and comprising a total of 19 basic parts are also described.

  4. Aerospace Medicine and Biology: A Continuing Bibliography With Indexes. Supplement 486

    NASA Technical Reports Server (NTRS)

    1999-01-01

    In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract.

  5. Aerospace medicine and biology: A continuing bibliography with indexes, supplement 97

    NASA Technical Reports Server (NTRS)

    1972-01-01

    Subject coverage concentrates on the biological, physiological, psychological, and environmental effects to which man is subjected during and following simulated or actual flight in the earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Each entry consists of a standard citation accompanied by its abstract.

  6. Aerospace medicine and biology: A continuing bibliography with indexes (supplement 94)

    NASA Technical Reports Server (NTRS)

    1971-01-01

    Subject coverage concentrates on the biological, physiological, psychological, and environmental effects to which man is subjected during and following simulated or actual flight in the earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Each entry consists of a standard citation accompanied by its abstract.

  7. Aerospace medicine and biology: A continuing bibliography with indexes, supplement 96

    NASA Technical Reports Server (NTRS)

    1971-01-01

    Subject coverage concentrates on the biological, physiological, psychological, and environmental effects to which man is subjected during and following simulated or actual flight in the earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Each entry consists of a standard citation accompanied by its abstract.

  8. Aerospace medicine and biology: A continuing bibliography with indexes (supplement 100)

    NASA Technical Reports Server (NTRS)

    1972-01-01

    Subject coverage concentrates on the biological, physiological, psychological, and environmental effects to which man is subjected during and following simulated or actual flight in the earth's atmosphere or in interplanetary space. Reference describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Each entry consists of a standard citation accompanied by its abstract.

  9. Elemental Analysis in Biological Matrices Using ICP-MS.

    PubMed

    Hansen, Matthew N; Clogston, Jeffrey D

    2018-01-01

    The increasing exploration of metallic nanoparticles for use as cancer therapeutic agents necessitates a sensitive technique to track the clearance and distribution of the material once introduced into a living system. Inductively coupled plasma mass spectrometry (ICP-MS) provides a sensitive and selective tool for tracking the distribution of metal components from these nanotherapeutics. This chapter presents a standardized method for processing biological matrices, ensuring complete homogenization of tissues, and outlines the preparation of appropriate standards and controls. The method described herein utilized gold nanoparticle-treated samples; however, the method can easily be applied to the analysis of other metals.

  10. Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants

    PubMed Central

    Hill, Camilla Beate; Czauderna, Tobias; Klapperstück, Matthias; Roessner, Ute; Schreiber, Falk

    2015-01-01

    Life on earth depends on dynamic chemical transformations that enable cellular functions, including electron transfer reactions, as well as synthesis and degradation of biomolecules. Biochemical reactions are coordinated in metabolic pathways that interact in a complex way to allow adequate regulation. Biotechnology, food, biofuel, agricultural, and pharmaceutical industries are highly interested in metabolic engineering as an enabling technology of synthetic biology to exploit cells for the controlled production of metabolites of interest. These approaches have only recently been extended to plants due to their greater metabolic complexity (such as primary and secondary metabolism) and highly compartmentalized cellular structures and functions (including plant-specific organelles) compared with bacteria and other microorganisms. Technological advances in analytical instrumentation in combination with advances in data analysis and modeling have opened up new approaches to engineer plant metabolic pathways and allow the impact of modifications to be predicted more accurately. In this article, we review challenges in the integration and analysis of large-scale metabolic data, present an overview of current bioinformatics methods for the modeling and visualization of metabolic networks, and discuss approaches for interfacing bioinformatics approaches with metabolic models of cellular processes and flux distributions in order to predict phenotypes derived from specific genetic modifications or subjected to different environmental conditions. PMID:26557642

  11. Indices of polarimetric purity for biological tissues inspection

    NASA Astrophysics Data System (ADS)

    Van Eeckhout, Albert; Lizana, Angel; Garcia-Caurel, Enric; Gil, José J.; Sansa, Adrià; Rodríguez, Carla; Estévez, Irene; González, Emilio; Escalera, Juan C.; Moreno, Ignacio; Campos, Juan

    2018-02-01

    We highlight the interest of using the Indices of Polarimetric Purity (IPPs) for the biological tissue inspection. These are three polarimetric metrics focused on the study of the depolarizing behaviour of the sample. The IPPs have been recently proposed in the literature and provide different and synthetized information than the commonly used depolarizing indices, as depolarization index (PΔ) or depolarization power (Δ). Compared with the standard polarimetric images of biological samples, IPPs enhance the contrast between different tissues of the sample and show differences between similar tissues which are not observed using the other standard techniques. Moreover, they present further physical information related to the depolarization mechanisms inherent to different tissues. In addition, the algorithm does not require advanced calculations (as in the case of polar decompositions), being the indices of polarimetric purity fast and easy to implement. We also propose a pseudo-coloured image method which encodes the sample information as a function of the different indices weights. These images allow us to customize the visualization of samples and to highlight certain of their constitutive structures. The interest and potential of the IPP approach are experimentally illustrated throughout the manuscript by comparing polarimetric images of different ex-vivo samples obtained with standard polarimetric methods with those obtained from the IPPs analysis. Enhanced contrast and retrieval of new information are experimentally obtained from the different IPP based images.

  12. CURRICULUM GUIDES IN BIOLOGY--LIFE SCIENCE, BIOLOGY--GENERAL, AND BIOLOGY--ADVANCED PLACEMENT.

    ERIC Educational Resources Information Center

    WESNER, GORDON E.; AND OTHERS

    "BIOLOGY--LIFE SCIENCE" IS GEARED TO STUDENTS OF AVERAGE ABILITY, "BIOLOGY--GENERAL" IS OFFERED FOR THOSE WHO HAVE COMPLETED "BIOLOGY--GENERAL" IN GRADES 10 OR 11 AND WHO WISH TO PURSUE COLLEGE LEVEL STUDY WHILE IN GRADE 12. THE NONTECHNICAL "BIOLOGY--LIFE SCIENCE" HAS OUTLINED UNITS IN ORGANIZING FOOD,…

  13. Physical Growth, Biological Age, and Nutritional Transitions of Adolescents Living at Moderate Altitudes in Peru

    PubMed Central

    Cossio-Bolaños, Marco; Gómez Campos, Rossana; Andruske, Cynthia Lee; Flores, Antonio Viveros; Luarte-Rocha, Cristian; Olivares, Pedro R.; Garcia-Rubio, Javier; de Arruda, Miguel

    2015-01-01

    Background: Peru is experiencing a stage of nutritional transition where the principal characteristics are typical of countries undergoing development. Objectives: The objectives of this study were the following: (a) compare physical growth patterns with an international standard; (b) determine biological age; and (c) analyze the double nutritional burden of adolescents living at a moderate altitude in Peru. Design: Weight, standing height, and sitting height were measured in 551 adolescents of both sexes (12.0 to 17.9 years old) from an urban area of Arequipa, Peru (2328 m). Physical growth was compared with the international standard of the CDC-2000. Biological age was determined by using a non-invasive transversal technique based on years from age at peak height velocity (APHV). Nutritional state was determined by means of weight for age and height for age. Z scores were calculated using international standards from the CDC-2000. Results: Body weight for both sexes was similar to the CDC-2000 international standards. At all ages, the girls’ height (p < 0.05) was below the standards. However, the boys’ height (p < 0.05) was less at ages, 15, 16, and 17. Biological age showed up in girls at age 12.7 years and for boys at 15.2 years. Stunted growth (8.7% boys and 18.0% girls) and over weight (11.3% boys and 8.8% girls) occurred in both groups. A relationship existed in both sexes between the categories of weight for the age and stunted growth by sex. Conclusions: Adolescents living at a moderate altitude exhibited stunted linear growth and biological maturation. Furthermore, adolescents of both sexes showed the presence of the double nutritional burden (stunted growth and excessive weight). PMID:26404334

  14. Cross-platform comparison of nucleic acid hybridization: toward quantitative reference standards.

    PubMed

    Halvorsen, Ken; Agris, Paul F

    2014-11-15

    Measuring interactions between biological molecules is vitally important to both basic and applied research as well as development of pharmaceuticals. Although a wide and growing range of techniques is available to measure various kinetic and thermodynamic properties of interacting biomolecules, it can be difficult to compare data across techniques of different laboratories and personnel or even across different instruments using the same technique. Here we evaluate relevant biological interactions based on complementary DNA and RNA oligonucleotides that could be used as reference standards for many experimental systems. We measured thermodynamics of duplex formation using isothermal titration calorimetry, differential scanning calorimetry, and ultraviolet-visible (UV-vis) monitored denaturation/renaturation. These standards can be used to validate results, compare data from disparate techniques, act as a teaching tool for laboratory classes, or potentially to calibrate instruments. The RNA and DNA standards have many attractive features, including low cost, high purity, easily measurable concentrations, and minimal handling concerns, making them ideal for use as a reference material. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Standards for the Ph.D. Degree in the Molecular Biosciences.

    ERIC Educational Resources Information Center

    Vella, F.; de Meis, Leopoldo; Mehler, Alan H.; Rombauts, Wilfried; White, Harold B., III; Wood, E. J.

    2000-01-01

    Argues that the barriers between the traditional biosciences have disappeared while interdisciplinarity has become commonplace. Presents the suggested standards for Ph.D. degrees in biochemistry and molecular biology recommended by the Committee on Education of the International Union of Biochemistry. (Author/CCM)

  16. Developmental biology, the stem cell of biological disciplines.

    PubMed

    Gilbert, Scott F

    2017-12-01

    Developmental biology (including embryology) is proposed as "the stem cell of biological disciplines." Genetics, cell biology, oncology, immunology, evolutionary mechanisms, neurobiology, and systems biology each has its ancestry in developmental biology. Moreover, developmental biology continues to roll on, budding off more disciplines, while retaining its own identity. While its descendant disciplines differentiate into sciences with a restricted set of paradigms, examples, and techniques, developmental biology remains vigorous, pluripotent, and relatively undifferentiated. In many disciplines, especially in evolutionary biology and oncology, the developmental perspective is being reasserted as an important research program.

  17. 21 CFR 601.20 - Biologics licenses; issuance and conditions.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Biologics licenses; issuance and conditions. 601.20 Section 601.20 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES... examination of the product and upon a determination that the product complies with the standards established...

  18. Relations between Intuitive Biological Thinking and Biological Misconceptions in Biology Majors and Nonmajors

    PubMed Central

    Coley, John D.; Tanner, Kimberly

    2015-01-01

    Research and theory development in cognitive psychology and science education research remain largely isolated. Biology education researchers have documented persistent scientifically inaccurate ideas, often termed misconceptions, among biology students across biological domains. In parallel, cognitive and developmental psychologists have described intuitive conceptual systems—teleological, essentialist, and anthropocentric thinking—that humans use to reason about biology. We hypothesize that seemingly unrelated biological misconceptions may have common origins in these intuitive ways of knowing, termed cognitive construals. We presented 137 undergraduate biology majors and nonmajors with six biological misconceptions. They indicated their agreement with each statement, and explained their rationale for their response. Results indicate frequent agreement with misconceptions, and frequent use of construal-based reasoning among both biology majors and nonmajors in their written explanations. Moreover, results also show associations between specific construals and the misconceptions hypothesized to arise from those construals. Strikingly, such associations were stronger among biology majors than nonmajors. These results demonstrate important linkages between intuitive ways of thinking and misconceptions in discipline-based reasoning, and raise questions about the origins, persistence, and generality of relations between intuitive reasoning and biological misconceptions. PMID:25713093

  19. The risk of serious infection with biologics in treating patients with rheumatoid arthritis: A Systematic Review and Meta-analysis

    PubMed Central

    Singh, Jasvinder A.; Cameron, Chris; Noorbaloochi, Shahrzad; Cullis, Tyler; Tucker, Matthew; Christensen, Robin; Ghogomu, Elizabeth Tanjong; Coyle, Doug; Clifford, Tammy; Tugwell, Peter; Wells, George A.

    2015-01-01

    Background Serious infections are a major concern for patients considering treatmentsfor rheumatoid arthritis (RA). Evidence is inconsistent on whether biologicsare associated with an increased risk of serious infection compared to traditional disease-modifying anti-rheumatic drugs (DMARDs). Methods A systematic literature search was undertaken using MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials, and www.clinicaltrials.gov from inception through February 11, 2014. Search terms included biologics, rheumatoid arthritis and their synonyms. Trials were eligible for inclusion if they included any of the biologics and reported serious infections. The risk of bias was assessed using the Cochrane Risk of Bias Tool. We conducted a Bayesian network meta-analysis,using a binomial likelihood model, of published trials to assess the risk of serious infections of biologics in RA patients, compared to traditional DMARDs. Findings The systematic review identified 106 trials that included RA patients on biologic and reported on serious infections. Compared to traditional DMARDs, standard-dose biologic (odds ratio [OR],1.31; 95% credible interval [CrI], 1.09 to 1.58) andhigh-dose biologic (OR, 1.90; 95% Crl, 1.50 to 2.39) were associated with an increased risk of serious infections, while low-dose biologics (OR, 0.93; 95% CrI, 0.65 to 1.33) were not. The risk was lower in patients who are methotrexate naïve compared withtraditional DMARD- or anti-TNF-biologic-experienced. The absolute increase in the number of serious infectionsper 1000 patients treated each year compared to traditional DMARDs ranged from 6 for standard-dose biologic to 55 for combination biologic therapy. Interpretation Standard-dose and high-dose biologics (with/without traditional DMARDs) are associated with an increase in serious infections compared to traditional DMARDs in RA, while low-dose biologics are not.Clinicians should discuss the balance between benefit and harm with the individual

  20. Creating Cost-Effective DNA Size Standards for Use in Teaching and Research Laboratories

    ERIC Educational Resources Information Center

    Shultz, Jeff

    2011-01-01

    I have devised a method with which a molecular size standard can be readily manufactured using Lambda DNA and PCR. This method allows the production of specific sized DNA fragments and is easily performed in a standard molecular biology laboratory. The material required to create these markers can also be used to provide a highly robust and…

  1. An improved Pearson's correlation proximity-based hierarchical clustering for mining biological association between genes.

    PubMed

    Booma, P M; Prabhakaran, S; Dhanalakshmi, R

    2014-01-01

    Microarray gene expression datasets has concerned great awareness among molecular biologist, statisticians, and computer scientists. Data mining that extracts the hidden and usual information from datasets fails to identify the most significant biological associations between genes. A search made with heuristic for standard biological process measures only the gene expression level, threshold, and response time. Heuristic search identifies and mines the best biological solution, but the association process was not efficiently addressed. To monitor higher rate of expression levels between genes, a hierarchical clustering model was proposed, where the biological association between genes is measured simultaneously using proximity measure of improved Pearson's correlation (PCPHC). Additionally, the Seed Augment algorithm adopts average linkage methods on rows and columns in order to expand a seed PCPHC model into a maximal global PCPHC (GL-PCPHC) model and to identify association between the clusters. Moreover, a GL-PCPHC applies pattern growing method to mine the PCPHC patterns. Compared to existing gene expression analysis, the PCPHC model achieves better performance. Experimental evaluations are conducted for GL-PCPHC model with standard benchmark gene expression datasets extracted from UCI repository and GenBank database in terms of execution time, size of pattern, significance level, biological association efficiency, and pattern quality.

  2. An Improved Pearson's Correlation Proximity-Based Hierarchical Clustering for Mining Biological Association between Genes

    PubMed Central

    Booma, P. M.; Prabhakaran, S.; Dhanalakshmi, R.

    2014-01-01

    Microarray gene expression datasets has concerned great awareness among molecular biologist, statisticians, and computer scientists. Data mining that extracts the hidden and usual information from datasets fails to identify the most significant biological associations between genes. A search made with heuristic for standard biological process measures only the gene expression level, threshold, and response time. Heuristic search identifies and mines the best biological solution, but the association process was not efficiently addressed. To monitor higher rate of expression levels between genes, a hierarchical clustering model was proposed, where the biological association between genes is measured simultaneously using proximity measure of improved Pearson's correlation (PCPHC). Additionally, the Seed Augment algorithm adopts average linkage methods on rows and columns in order to expand a seed PCPHC model into a maximal global PCPHC (GL-PCPHC) model and to identify association between the clusters. Moreover, a GL-PCPHC applies pattern growing method to mine the PCPHC patterns. Compared to existing gene expression analysis, the PCPHC model achieves better performance. Experimental evaluations are conducted for GL-PCPHC model with standard benchmark gene expression datasets extracted from UCI repository and GenBank database in terms of execution time, size of pattern, significance level, biological association efficiency, and pattern quality. PMID:25136661

  3. Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

    PubMed

    Moodie, Stuart; Le Novère, Nicolas; Demir, Emek; Mi, Huaiyu; Villéger, Alice

    2015-09-04

    The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Process Description language represents biological entities and processes between these entities within a network. SBGN PD focuses on the mechanistic description and temporal dependencies of biological interactions and transformations. The nodes (elements) are split into entity nodes describing, e.g., metabolites, proteins, genes and complexes, and process nodes describing, e.g., reactions and associations. The edges (connections) provide descriptions of relationships (or influences) between the nodes, such as consumption, production, stimulation and inhibition. Among all three languages of SBGN, PD is the closest to metabolic and regulatory pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

  4. Relations between intuitive biological thinking and biological misconceptions in biology majors and nonmajors.

    PubMed

    Coley, John D; Tanner, Kimberly

    2015-03-02

    Research and theory development in cognitive psychology and science education research remain largely isolated. Biology education researchers have documented persistent scientifically inaccurate ideas, often termed misconceptions, among biology students across biological domains. In parallel, cognitive and developmental psychologists have described intuitive conceptual systems--teleological, essentialist, and anthropocentric thinking--that humans use to reason about biology. We hypothesize that seemingly unrelated biological misconceptions may have common origins in these intuitive ways of knowing, termed cognitive construals. We presented 137 undergraduate biology majors and nonmajors with six biological misconceptions. They indicated their agreement with each statement, and explained their rationale for their response. Results indicate frequent agreement with misconceptions, and frequent use of construal-based reasoning among both biology majors and nonmajors in their written explanations. Moreover, results also show associations between specific construals and the misconceptions hypothesized to arise from those construals. Strikingly, such associations were stronger among biology majors than nonmajors. These results demonstrate important linkages between intuitive ways of thinking and misconceptions in discipline-based reasoning, and raise questions about the origins, persistence, and generality of relations between intuitive reasoning and biological misconceptions. © 2015 J. D. Coley and K. Tanner. CBE—Life Sciences Education © 2015 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).

  5. Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance*

    PubMed Central

    Paulovich, Amanda G.; Billheimer, Dean; Ham, Amy-Joan L.; Vega-Montoto, Lorenzo; Rudnick, Paul A.; Tabb, David L.; Wang, Pei; Blackman, Ronald K.; Bunk, David M.; Cardasis, Helene L.; Clauser, Karl R.; Kinsinger, Christopher R.; Schilling, Birgit; Tegeler, Tony J.; Variyath, Asokan Mulayath; Wang, Mu; Whiteaker, Jeffrey R.; Zimmerman, Lisa J.; Fenyo, David; Carr, Steven A.; Fisher, Susan J.; Gibson, Bradford W.; Mesri, Mehdi; Neubert, Thomas A.; Regnier, Fred E.; Rodriguez, Henry; Spiegelman, Cliff; Stein, Stephen E.; Tempst, Paul; Liebler, Daniel C.

    2010-01-01

    Optimal performance of LC-MS/MS platforms is critical to generating high quality proteomics data. Although individual laboratories have developed quality control samples, there is no widely available performance standard of biological complexity (and associated reference data sets) for benchmarking of platform performance for analysis of complex biological proteomes across different laboratories in the community. Individual preparations of the yeast Saccharomyces cerevisiae proteome have been used extensively by laboratories in the proteomics community to characterize LC-MS platform performance. The yeast proteome is uniquely attractive as a performance standard because it is the most extensively characterized complex biological proteome and the only one associated with several large scale studies estimating the abundance of all detectable proteins. In this study, we describe a standard operating protocol for large scale production of the yeast performance standard and offer aliquots to the community through the National Institute of Standards and Technology where the yeast proteome is under development as a certified reference material to meet the long term needs of the community. Using a series of metrics that characterize LC-MS performance, we provide a reference data set demonstrating typical performance of commonly used ion trap instrument platforms in expert laboratories; the results provide a basis for laboratories to benchmark their own performance, to improve upon current methods, and to evaluate new technologies. Additionally, we demonstrate how the yeast reference, spiked with human proteins, can be used to benchmark the power of proteomics platforms for detection of differentially expressed proteins at different levels of concentration in a complex matrix, thereby providing a metric to evaluate and minimize preanalytical and analytical variation in comparative proteomics experiments. PMID:19858499

  6. Synthetic biology R&D risks: Social-institutional contexts matter!

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

    Wolfe, Amy K.; Bjornstad, David J.; Shumpert, Barry L.

    Social and institutional analyses currently are missing from considerations of synthetic biology R&D-related biosafety, which instead have bioethics, governance, or technical orientations. Social and institutional context shapes standard practice. Here, analyzing context helps identify circumstances that create, amplify, or diminish risk, thereby revealing new opportunities for avoiding or managing those risks.

  7. Synthetic biology R&D risks: Social-institutional contexts matter!

    DOE PAGES

    Wolfe, Amy K.; Bjornstad, David J.; Shumpert, Barry L.; ...

    2016-02-15

    Social and institutional analyses currently are missing from considerations of synthetic biology R&D-related biosafety, which instead have bioethics, governance, or technical orientations. Social and institutional context shapes standard practice. Here, analyzing context helps identify circumstances that create, amplify, or diminish risk, thereby revealing new opportunities for avoiding or managing those risks.

  8. Automated GC-MS analysis of free amino acids in biological fluids.

    PubMed

    Kaspar, Hannelore; Dettmer, Katja; Gronwald, Wolfram; Oefner, Peter J

    2008-07-15

    A gas chromatography-mass spectrometry (GC-MS) method was developed for the quantitative analysis of free amino acids as their propyl chloroformate derivatives in biological fluids. Derivatization with propyl chloroformate is carried out directly in the biological samples without prior protein precipitation or solid-phase extraction of the amino acids, thereby allowing automation of the entire procedure, including addition of reagents, extraction and injection into the GC-MS. The total analysis time was 30 min and 30 amino acids could be reliably quantified using 19 stable isotope-labeled amino acids as internal standards. Limits of detection (LOD) and lower limits of quantification (LLOQ) were in the range of 0.03-12 microM and 0.3-30 microM, respectively. The method was validated using a certified amino acid standard and reference plasma, and its applicability to different biological fluids was shown. Intra-day precision for the analysis of human urine, blood plasma, and cell culture medium was 2.0-8.8%, 0.9-8.3%, and 2.0-14.3%, respectively, while the inter-day precision for human urine was 1.5-14.1%.

  9. Biology in Bloom: Implementing Bloom's Taxonomy to Enhance Student Learning in Biology

    PubMed Central

    Dirks, Clarissa; Wenderoth, Mary Pat

    2008-01-01

    We developed the Blooming Biology Tool (BBT), an assessment tool based on Bloom's Taxonomy, to assist science faculty in better aligning their assessments with their teaching activities and to help students enhance their study skills and metacognition. The work presented here shows how assessment tools, such as the BBT, can be used to guide and enhance teaching and student learning in a discipline-specific manner in postsecondary education. The BBT was first designed and extensively tested for a study in which we ranked almost 600 science questions from college life science exams and standardized tests. The BBT was then implemented in three different collegiate settings. Implementation of the BBT helped us to adjust our teaching to better enhance our students' current mastery of the material, design questions at higher cognitive skills levels, and assist students in studying for college-level exams and in writing study questions at higher levels of Bloom's Taxonomy. From this work we also created a suite of complementary tools that can assist biology faculty in creating classroom materials and exams at the appropriate level of Bloom's Taxonomy and students to successfully develop and answer questions that require higher-order cognitive skills. PMID:19047424

  10. Promoting microbiology education through the iGEM synthetic biology competition.

    PubMed

    Kelwick, Richard; Bowater, Laura; Yeoman, Kay H; Bowater, Richard P

    2015-08-01

    Synthetic biology has developed rapidly in the 21st century. It covers a range of scientific disciplines that incorporate principles from engineering to take advantage of and improve biological systems, often applied to specific problems. Methods important in this subject area include the systematic design and testing of biological systems and, here, we describe how synthetic biology projects frequently develop microbiology skills and education. Synthetic biology research has huge potential in biotechnology and medicine, which brings important ethical and moral issues to address, offering learning opportunities about the wider impact of microbiological research. Synthetic biology projects have developed into wide-ranging training and educational experiences through iGEM, the International Genetically Engineered Machines competition. Elements of the competition are judged against specific criteria and teams can win medals and prizes across several categories. Collaboration is an important element of iGEM, and all DNA constructs synthesized by iGEM teams are made available to all researchers through the Registry for Standard Biological Parts. An overview of microbiological developments in the iGEM competition is provided. This review is targeted at educators that focus on microbiology and synthetic biology, but will also be of value to undergraduate and postgraduate students with an interest in this exciting subject area. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  11. Biological Properties and Therapeutic Applications of Propolis.

    PubMed

    Sforcin, José M

    2016-06-01

    Propolis is a resinous material collected by bees from bud and exudates of the plants, mixed with bee enzymes, pollen and wax. In this review, the biological properties of propolis and some therapeutic applications are discussed. The same biological activities have been investigated until today, using samples from different geographic regions. Thus, the study of the biological properties of a given sample should always be associated with its chemical composition and botanical source, representing a particular sample of a given geographic area, exploring its biological potential and the role of its constituents. Efforts have been carried out to explain propolis' mechanisms of action in vivo and in vitro, but the majority of propolis' targets and actions are still unclear. The number of formulations containing propolis and patents have increased, although propolis extracts have been used deliberately with different recommendations, not always mentioning the chemical composition, vegetal source and the methods of extraction. Clinical studies will help to obtain criterious recommendations in view of the expected outcomes. Further investigation should explore the effects of common compounds found in the samples from all over the world in an attempt to standardize the research on propolis and to obtain new drugs. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  12. The Biological Macromolecule Crystallization Database and NASA Protein Crystal Growth Archive

    PubMed Central

    Gilliland, Gary L.; Tung, Michael; Ladner, Jane

    1996-01-01

    The NIST/NASA/CARB Biological Macromolecule Crystallization Database (BMCD), NIST Standard Reference Database 21, contains crystal data and crystallization conditions for biological macromolecules. The database entries include data abstracted from published crystallographic reports. Each entry consists of information describing the biological macromolecule crystallized and crystal data and the crystallization conditions for each crystal form. The BMCD serves as the NASA Protein Crystal Growth Archive in that it contains protocols and results of crystallization experiments undertaken in microgravity (space). These database entries report the results, whether successful or not, from NASA-sponsored protein crystal growth experiments in microgravity and from microgravity crystallization studies sponsored by other international organizations. The BMCD was designed as a tool to assist x-ray crystallographers in the development of protocols to crystallize biological macromolecules, those that have previously been crystallized, and those that have not been crystallized. PMID:11542472

  13. Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 498

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP-1999-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract.

  14. Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 482

    NASA Technical Reports Server (NTRS)

    1999-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP-1999-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract.

  15. Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 489

    NASA Technical Reports Server (NTRS)

    1999-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP-1999-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract.

  16. Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 478

    NASA Technical Reports Server (NTRS)

    1998-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP-1998-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract.

  17. Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 477

    NASA Technical Reports Server (NTRS)

    1998-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP-1998-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract.

  18. Subattomole sensitivity in biological accelerator mass spectrometry.

    PubMed

    Salehpour, Mehran; Possnert, Göran; Bryhni, Helge

    2008-05-15

    The Uppsala University 5 MV Pelletron tandem accelerator has been used to study (14)C-labeled biological samples utilizing accelerator mass spectrometry (AMS) technology. We have adapted a sample preparation method for small biological samples down to a few tens of micrograms of carbon, involving among others, miniaturizing of the graphitization reactor. Standard AMS requires about 1 mg of carbon with a limit of quantitation of about 10 amol. Results are presented for a range of small sample sizes with concentrations down to below 1 pM of a pharmaceutical substance in human blood. It is shown that (14)C-labeled molecular markers can be routinely measured from the femtomole range down to a few hundred zeptomole (10 (-21) mol), without the use of any additional separation methods.

  19. Ventral aspect of the visual form pathway is not critical for the perception of biological motion

    PubMed Central

    Gilaie-Dotan, Sharon; Saygin, Ayse Pinar; Lorenzi, Lauren J.; Rees, Geraint; Behrmann, Marlene

    2015-01-01

    Identifying the movements of those around us is fundamental for many daily activities, such as recognizing actions, detecting predators, and interacting with others socially. A key question concerns the neurobiological substrates underlying biological motion perception. Although the ventral “form” visual cortex is standardly activated by biologically moving stimuli, whether these activations are functionally critical for biological motion perception or are epiphenomenal remains unknown. To address this question, we examined whether focal damage to regions of the ventral visual cortex, resulting in significant deficits in form perception, adversely affects biological motion perception. Six patients with damage to the ventral cortex were tested with sensitive point-light display paradigms. All patients were able to recognize unmasked point-light displays and their perceptual thresholds were not significantly different from those of three different control groups, one of which comprised brain-damaged patients with spared ventral cortex (n > 50). Importantly, these six patients performed significantly better than patients with damage to regions critical for biological motion perception. To assess the necessary contribution of different regions in the ventral pathway to biological motion perception, we complement the behavioral findings with a fine-grained comparison between the lesion location and extent, and the cortical regions standardly implicated in biological motion processing. This analysis revealed that the ventral aspects of the form pathway (e.g., fusiform regions, ventral extrastriate body area) are not critical for biological motion perception. We hypothesize that the role of these ventral regions is to provide enhanced multiview/posture representations of the moving person rather than to represent biological motion perception per se. PMID:25583504

  20. GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules

    PubMed Central

    Sarrion-Perdigones, Alejandro; Falconi, Erica Elvira; Zandalinas, Sara I.; Juárez, Paloma; Fernández-del-Carmen, Asun; Granell, Antonio; Orzaez, Diego

    2011-01-01

    Synthetic Biology requires efficient and versatile DNA assembly systems to facilitate the building of new genetic modules/pathways from basic DNA parts in a standardized way. Here we present GoldenBraid (GB), a standardized assembly system based on type IIS restriction enzymes that allows the indefinite growth of reusable gene modules made of standardized DNA pieces. The GB system consists of a set of four destination plasmids (pDGBs) designed to incorporate multipartite assemblies made of standard DNA parts and to combine them binarily to build increasingly complex multigene constructs. The relative position of type IIS restriction sites inside pDGB vectors introduces a double loop (“braid”) topology in the cloning strategy that allows the indefinite growth of composite parts through the succession of iterative assembling steps, while the overall simplicity of the system is maintained. We propose the use of GoldenBraid as an assembly standard for Plant Synthetic Biology. For this purpose we have GB-adapted a set of binary plasmids for A. tumefaciens-mediated plant transformation. Fast GB-engineering of several multigene T-DNAs, including two alternative modules made of five reusable devices each, and comprising a total of 19 basic parts are also described. PMID:21750718

  1. Establishing a national biological laboratory safety and security monitoring program.

    PubMed

    Blaine, James W

    2012-12-01

    The growing concern over the potential use of biological agents as weapons and the continuing work of the Biological Weapons Convention has promoted an interest in establishing national biological laboratory biosafety and biosecurity monitoring programs. The challenges and issues that should be considered by governments, or organizations, embarking on the creation of a biological laboratory biosafety and biosecurity monitoring program are discussed in this article. The discussion focuses on the following questions: Is there critical infrastructure support available? What should be the program focus? Who should be monitored? Who should do the monitoring? How extensive should the monitoring be? What standards and requirements should be used? What are the consequences if a laboratory does not meet the requirements or is not willing to comply? Would the program achieve the results intended? What are the program costs? The success of a monitoring program can depend on how the government, or organization, responds to these questions.

  2. Quantitative computational models of molecular self-assembly in systems biology

    PubMed Central

    Thomas, Marcus; Schwartz, Russell

    2017-01-01

    Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally. PMID:28535149

  3. Quantitative computational models of molecular self-assembly in systems biology.

    PubMed

    Thomas, Marcus; Schwartz, Russell

    2017-05-23

    Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

  4. Ontology- and graph-based similarity assessment in biological networks.

    PubMed

    Wang, Haiying; Zheng, Huiru; Azuaje, Francisco

    2010-10-15

    A standard systems-based approach to biomarker and drug target discovery consists of placing putative biomarkers in the context of a network of biological interactions, followed by different 'guilt-by-association' analyses. The latter is typically done based on network structural features. Here, an alternative analysis approach in which the networks are analyzed on a 'semantic similarity' space is reported. Such information is extracted from ontology-based functional annotations. We present SimTrek, a Cytoscape plugin for ontology-based similarity assessment in biological networks. http://rosalind.infj.ulst.ac.uk/SimTrek.html francisco.azuaje@crp-sante.lu Supplementary data are available at Bioinformatics online.

  5. Viscoelastic characterization of soft biological materials

    NASA Astrophysics Data System (ADS)

    Nayar, Vinod Timothy

    elastic material. The effects of sample stiffness were evaluated by testing both the quasi-static and dynamic mechanical properties of different concentration agar samples, ranging from 0.5% to 5.0%. The dynamic nanoindentation protocol showed some sensitivity to sample stiffness, but characterization remained consistently applicable to soft biological materials. Comparative experiments were performed on both 0.5% and 5.0% agar as well as porcine eye tissue samples using published dynamic macrocompression standards. By comparing these new tests to those obtained with nanoindentation, the effects due to length-scale, stiffness, size, viscoelastic, and methodological conditions are evaluated. Both testing methodologies can be adapted for the environmental and mounting conditions, but the limitations of standardized macro-scale tests are explored. The factors affecting mechanical characterization of soft and thin viscoelastic biological materials are researched and a comprehensive protocol is presented. This work produces material mechanical properties for use in improving future medical implant designs on a wide variety of biological tissue and materials.

  6. TH-A-BRD-01: Radiation Biology for Radiation Therapy Physicists

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

    Orton, C; Borras, C; Carlson, D

    Mechanisms by which radiation kills cells and ways cell damage can be repaired will be reviewed. The radiobiological parameters of dose, fractionation, delivery time, dose rate, and LET will be discussed. The linear-quadratic model for cell survival for high and low dose rate treatments and the effect of repopulation will be presented and discussed. The rationale for various radiotherapy techniques such as conventional fractionation, hyperfractionation, hypofractionation, and low and high dose rate brachytherapy, including permanent implants, will be presented. The radiobiological principles underlying radiation protection guidelines and the different radiation dosimetry terms used in radiation biology and in radiation protectionmore » will be reviewed. Human data on radiation induced cancer, including increases in the risk of second cancers following radiation therapy, as well as data on radiation induced tissue reactions, such as cardiovascular effects, for follow up times up to 20–40 years, published by ICRP, NCRP and BEIR Committees, will be examined. The latest risk estimates per unit dose will be presented. Their adoption in recent radiation protection standards and guidelines and their impact on patient and workers safety in radiotherapy will be discussed. Biologically-guided radiotherapy (BGRT) provides a systematic method to derive prescription doses that integrate patient-specific information about tumor and normal tissue biology. Treatment individualization based on patient-specific biology requires the identification of biological objective functions to facilitate the design and comparison of competing treatment modalities. Biological objectives provide a more direct approach to plan optimization instead of relying solely on dose-based surrogates and can incorporate factors that alter radiation response, such as DNA repair, tumor hypoxia, and relative biological effectiveness. We review concepts motivating biological objectives and provide examples

  7. The biological standard of living in pre-modern Korea: Determinants of height of militia recruits during the Chosŏn dynasty.

    PubMed

    Jun, Seong Ho; Lewis, James B; Schwekendiek, Daniel

    2017-02-01

    This paper extends the research on the biological standard of living in the Korean peninsula back to pre-modern times. Drawing on militia rosters of the Chosŏn Dynasty from the sixteenth to eighteenth centuries, we tentatively conclude that the final height of Korean men during this period was 166cm and thus slightly above that of modern North Korean men (165cm). On the other hand, the average height of modern South Korean men is 172cm, 6cm more than what we tentatively estimate for pre-modern Korean men. Regression analysis of the height of pre-modern Korean men finds that un-free Koreans ("slaves") were significantly shorter by about 0.6-0.7cm than commoners, whereas the average height of recruits suffering from smallpox did not differ significantly from that of other recruits. Moreover, regional, as opposed to birth-dummy, variables account, and to a significant degree, for most of the differences in height. Whether or not this is a result of socioeconomic differences across provinces or a result of other regionally-varying factors remains an open question. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. The Mouse Tumor Biology Database: A Comprehensive Resource for Mouse Models of Human Cancer.

    PubMed

    Krupke, Debra M; Begley, Dale A; Sundberg, John P; Richardson, Joel E; Neuhauser, Steven B; Bult, Carol J

    2017-11-01

    Research using laboratory mice has led to fundamental insights into the molecular genetic processes that govern cancer initiation, progression, and treatment response. Although thousands of scientific articles have been published about mouse models of human cancer, collating information and data for a specific model is hampered by the fact that many authors do not adhere to existing annotation standards when describing models. The interpretation of experimental results in mouse models can also be confounded when researchers do not factor in the effect of genetic background on tumor biology. The Mouse Tumor Biology (MTB) database is an expertly curated, comprehensive compendium of mouse models of human cancer. Through the enforcement of nomenclature and related annotation standards, MTB supports aggregation of data about a cancer model from diverse sources and assessment of how genetic background of a mouse strain influences the biological properties of a specific tumor type and model utility. Cancer Res; 77(21); e67-70. ©2017 AACR . ©2017 American Association for Cancer Research.

  9. Risk of serious infection in biological treatment of patients with rheumatoid arthritis: a systematic review and meta-analysis.

    PubMed

    Singh, Jasvinder A; Cameron, Chris; Noorbaloochi, Shahrzad; Cullis, Tyler; Tucker, Matthew; Christensen, Robin; Ghogomu, Elizabeth Tanjong; Coyle, Doug; Clifford, Tammy; Tugwell, Peter; Wells, George A

    2015-07-18

    Serious infections are a major concern for patients considering treatments for rheumatoid arthritis. Evidence is inconsistent as to whether biological drugs are associated with an increased risk of serious infection compared with traditional disease-modifying antirheumatic drugs (DMARDs). We did a systematic review and meta-analysis of serious infections in patients treated with biological drugs compared with those treated with traditional DMARDs. We did a systematic literature search with Medline, Embase, Cochrane Central Register of Controlled Trials, and ClinicalTrials.gov from their inception to Feb 11, 2014. Search terms included "biologics", "rheumatoid arthritis" and their synonyms. Trials were eligible for inclusion if they included any of the approved biological drugs and reported serious infections. We assessed the risk of bias with the Cochrane Risk of Bias Tool. We did a Bayesian network meta-analysis of published trials using a binomial likelihood model to assess the risk of serious infections in patients with rheumatoid arthritis who were treated with biological drugs, compared with those treated with traditional DMARDs. The odds ratio (OR) of serious infection was the primary measure of treatment effect and calculated 95% credible intervals using Markov Chain Monte Carlo methods. The systematic review identified 106 trials that reported serious infections and included patients with rheumatoid arthritis who received biological drugs. Compared with traditional DMARDs, standard-dose biological drugs (OR 1.31, 95% credible interval [CrI] 1.09-1.58) and high-dose biological drugs (1.90, 1.50-2.39) were associated with an increased risk of serious infections, although low-dose biological drugs (0.93, 0.65-1.33) were not. The risk was lower in patients who were methotrexate naive compared with traditional DMARD-experienced or anti-tumour necrosis factor biological drug-experienced patients. The absolute increase in the number of serious infections per 1000

  10. Physical, chemical, and biological data for selected streams in Chester County, Pennsylvania, 1969-80

    USGS Publications Warehouse

    Moore, C.R.

    1989-01-01

    This report presents physical, chemical, and biological data collected at 50 sampling sites on selected streams in Chester County, Pennsylvania from 1969 to 1980. The physical data consist of air and water temperature, stream discharge, suspended sediment, pH, specific conductance, and dissolved oxygen. The chemical data consist of laboratory determinations of total nutrients, major ions, and trace metals. The biological data consist of total coliform, fecal coliform, and fecal streptococcus bacteriological analyses, and benthicmacroinvertebrate population analyses. Brillouin's diversity index, maximum diversity, minimum diversity, and evenness for each sample, and median and mean Brilloiuin's diversity index, standard deviation, and standard error of the mean were calculated for the benthic-macroinvertebrate data for each site.

  11. Genome Scale Modeling in Systems Biology: Algorithms and Resources

    PubMed Central

    Najafi, Ali; Bidkhori, Gholamreza; Bozorgmehr, Joseph H.; Koch, Ina; Masoudi-Nejad, Ali

    2014-01-01

    In recent years, in silico studies and trial simulations have complemented experimental procedures. A model is a description of a system, and a system is any collection of interrelated objects; an object, moreover, is some elemental unit upon which observations can be made but whose internal structure either does not exist or is ignored. Therefore, any network analysis approach is critical for successful quantitative modeling of biological systems. This review highlights some of most popular and important modeling algorithms, tools, and emerging standards for representing, simulating and analyzing cellular networks in five sections. Also, we try to show these concepts by means of simple example and proper images and graphs. Overall, systems biology aims for a holistic description and understanding of biological processes by an integration of analytical experimental approaches along with synthetic computational models. In fact, biological networks have been developed as a platform for integrating information from high to low-throughput experiments for the analysis of biological systems. We provide an overview of all processes used in modeling and simulating biological networks in such a way that they can become easily understandable for researchers with both biological and mathematical backgrounds. Consequently, given the complexity of generated experimental data and cellular networks, it is no surprise that researchers have turned to computer simulation and the development of more theory-based approaches to augment and assist in the development of a fully quantitative understanding of cellular dynamics. PMID:24822031

  12. Replacement of the International Standard for Tetanus Antitoxin and the Use of the Standard in the Flocculation Test

    PubMed Central

    Spaun, J.; Lyng, J.

    1970-01-01

    Since 1935 the International Unit for Tetanus Antitoxin has been defined as the activity contained in a certain weight of the first International Standard for Tetanus Antitoxin. As stocks of this standard had become depleted, 11 laboratories in 8 countries were requested to participate in a collaborative assay of a preparation proposed as a replacement. The assay results were analysed and presented to the WHO Expert Committee on Biological Standardization in 1969 which established the preparation studied as the second International Standard for Tetanus Antitoxin and defined the International Unit for Tetanus Antitoxin as the activity contained in 0.03384 mg of the second International Standard for Tetanus Antitoxin. This definition would ensure the continuity of the size of this international unit. The analysis of the collaborative studies also showed that the second International Standard for Tetanus Antitoxin has suitable properties for use in the flocculation test for the determination of the antigen content of tetanus toxoids in Lf values. The designation Lf-equivalent is described and the problems relating to the use of this term for the expression of results of in vitro assays are analysed in relation to the use of international units for expressing results of in vivo assays. As the second International Standard for Tetanus Antitoxin has an in vivo/in vitro ratio of 1.4, the Lf-equivalent of this antitoxin is 1.4 times less than its unitage. PMID:5310949

  13. BioPAX – A community standard for pathway data sharing

    PubMed Central

    Demir, Emek; Cary, Michael P.; Paley, Suzanne; Fukuda, Ken; Lemer, Christian; Vastrik, Imre; Wu, Guanming; D’Eustachio, Peter; Schaefer, Carl; Luciano, Joanne; Schacherer, Frank; Martinez-Flores, Irma; Hu, Zhenjun; Jimenez-Jacinto, Veronica; Joshi-Tope, Geeta; Kandasamy, Kumaran; Lopez-Fuentes, Alejandra C.; Mi, Huaiyu; Pichler, Elgar; Rodchenkov, Igor; Splendiani, Andrea; Tkachev, Sasha; Zucker, Jeremy; Gopinath, Gopal; Rajasimha, Harsha; Ramakrishnan, Ranjani; Shah, Imran; Syed, Mustafa; Anwar, Nadia; Babur, Ozgun; Blinov, Michael; Brauner, Erik; Corwin, Dan; Donaldson, Sylva; Gibbons, Frank; Goldberg, Robert; Hornbeck, Peter; Luna, Augustin; Murray-Rust, Peter; Neumann, Eric; Reubenacker, Oliver; Samwald, Matthias; van Iersel, Martijn; Wimalaratne, Sarala; Allen, Keith; Braun, Burk; Whirl-Carrillo, Michelle; Dahlquist, Kam; Finney, Andrew; Gillespie, Marc; Glass, Elizabeth; Gong, Li; Haw, Robin; Honig, Michael; Hubaut, Olivier; Kane, David; Krupa, Shiva; Kutmon, Martina; Leonard, Julie; Marks, Debbie; Merberg, David; Petri, Victoria; Pico, Alex; Ravenscroft, Dean; Ren, Liya; Shah, Nigam; Sunshine, Margot; Tang, Rebecca; Whaley, Ryan; Letovksy, Stan; Buetow, Kenneth H.; Rzhetsky, Andrey; Schachter, Vincent; Sobral, Bruno S.; Dogrusoz, Ugur; McWeeney, Shannon; Aladjem, Mirit; Birney, Ewan; Collado-Vides, Julio; Goto, Susumu; Hucka, Michael; Le Novère, Nicolas; Maltsev, Natalia; Pandey, Akhilesh; Thomas, Paul; Wingender, Edgar; Karp, Peter D.; Sander, Chris; Bader, Gary D.

    2010-01-01

    BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data (http://www.biopax.org). Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery. PMID:20829833

  14. The Main Biological Hazards in Animal Biosafety Level 2 Facilities and Strategies for Control.

    PubMed

    Li, Xiao Yan; Xue, Kang Ning; Jiang, Jin Sheng; Lu, Xuan Cheng

    2016-04-01

    Concern about the biological hazards involved in microbiological research, especially research involving laboratory animals, has increased in recent years. Working in an animal biosafety level 2 facility (ABSL-2), commonly used for research on infectious diseases, poses various biological hazards. Here, the regulations and standards related to laboratory biosafety in China are introduced, the potential biological hazards present in ABSL-2 facilities are analyzed, and a series of strategies to control the hazards are presented. Copyright © 2016 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

  15. Piquing Student Interest with Pharmacology: An Interdisciplinary Program Helps High School Students Learn Biology and Chemistry Principles

    ERIC Educational Resources Information Center

    Halpin, Myra J.; Hoeffler, Leanne; Schwartz-Bloom, Rochelle D.

    2005-01-01

    To help students learn science concepts, Pharmacology Education Partnership (PEP)--a science education program that incorporates relevant topics related to drugs and drug abuse into standard biology and chemistry curricula was developed. The interdisciplinary PEP curriculum provides six modules to teach biology and chemistry principles within the…

  16. Water Quality Standards for Coral Reef Protection | Science ...

    EPA Pesticide Factsheets

    The U.S. Clean Water Act provides a legal framework to protect coastal biological resources such as coral reefs, mangrove forests, and seagrass meadows from the damaging effects of human activities. Even though many resources are protected under this authority, water quality standards have not been effectively applied to coral reefs. The Environmental Protection Agency is promoting biocriteria and other water quality standards through collaborative development of bioassessment procedures, indicators and monitoring strategies. To support regulatory action, bioassessment indicators must be biologically meaningful, relevant to management, responsive to human disturbance, and relatively immune to natural variability. A rapid bioassessment protocol for reef-building stony corals was developed and tested for regulatory applicability. Preliminary testing in the Florida Keys found indicators had sufficient precision and provided information relevant to coral reef management. Sensitivity to human disturbance was demonstrated in the U.S. Virgin Islands for five of eight indicators tested. Once established, monitoring programs using these indicators can provide valuable, long-term records of coral condition and regulatory compliance. Development of a rapid bioassement protocol for reef-building stony corals was tested for regulatory applicability.

  17. Pyrolysis-gas chromatography/mass spectrometry analyses of biological particulates collected during recent space shuttle missions

    NASA Technical Reports Server (NTRS)

    Matney, M. L.; Limero, T. F.; James, J. T.

    1994-01-01

    Biological particulates collected on air filters during shuttle missions (STS-40 and STS-42) were identified using pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS). A method was developed for identifying the atmospheric particles and their sources through the analysis of standard materials and the selection of "marker" compounds specific to the particle type. Pyrolysis spectra of biological standards were compared with those of airborne particles collected during two space shuttle missions; marker compounds present in the shuttle particle spectra were matched with those of the standards to identify the source of particles. Particles of 0,5--1-mm diameter and weighing as little as 40 micrograms could be identified using this technique. The Py-GC/MS method identified rat food and soilless plant-growth media as two sources of particles collected from the shuttle atmosphere during flight.

  18. Genesis of IIICD Iron Meteorites: Evidence From Silicate Inclusions

    NASA Astrophysics Data System (ADS)

    McCoy, T. J.; Keil, K.; Scott, E. R. D.; Haack, H.

    1992-07-01

    The IAB and IIICD iron meteorite groups exhibit much larger ranges in siderophile concentrations than other groups and commonly contain silicate inclusions. Extensive studies of metal in both groups and silicates in IAB irons have led to a variety of ideas to explain the genesis of these groups. Wasson et al. (1980) envision each meteorite forming in a separate impact melt pool. Kracher (1982, 1985) suggested that the siderophile trends might result from fractional crystallization of both metal and troilite in a S-saturated magma. A role for oxidation-reduction in these groups has been proposed by Scott and Bild (1974). Similarities in siderophile elemental trends indicate that IIICD metal has a similar origin, although data on silicate inclusions in IIICD irons are scarce (Ramdohr, 1973; Scott and Bild, 1974; Kracher and Kurat, 1977; Prinz et al., 1982; Clayton et al., 1983). We report the first detailed study of silicate inclusions in IIICD iron meteorites in an attempt to elucidate their history. We have studied the only silicate-bearing IIICD irons - Carlton, Dayton, and the recently reported Maltahohe. Silicate-graphite-phosphate inclusions comprise at most a few percent of the bulk meteorite, and silicates comprise <25 vol% of the inclusion. Silicate mineralogy and chemistry vary systematically with increasing M content of the metal. Maltahohe (10.7 wt% Ni) and Carlton (13.0%) contain olivine, pyroxene, and plagioclase, whereas Dayton (17.0%) contains pyroxene, plagioclase, and SiO2. Pyroxene becomes more FeO-rich from Maltahohe (FS(sub)7.8) to Carlton (Fs(sub)9.7) to Dayton (Fs(sub)11.6). Inverse FeO zoning in silicates and lower Fa than Fs indicate reduction in all three meteorites. Plagioclase compositions in IIICD (An(sub)1.1-4.9) are lower than IAB (An(sub)9.2-2l.5) and uncorrelated with Ni content. The abundances of associated phases also vary. Graphite comprises ~25 vol% of Maltahohe silicate inclusions, but only a few percent in Carlton, and is absent

  19. Biologic Approaches for the Treatment of Partial Tears of the Anterior Cruciate Ligament

    PubMed Central

    Dallo, Ignacio; Chahla, Jorge; Mitchell, Justin J.; Pascual-Garrido, Cecilia; Feagin, John A.; LaPrade, Robert F.

    2017-01-01

    Background: Anterior cruciate ligament reconstruction (ACLR) has been established as the gold standard for treatment of complete ruptures of the anterior cruciate ligament (ACL) in active, symptomatic individuals. In contrast, treatment of partial tears of the ACL remains controversial. Biologically augmented ACL-repair techniques are expanding in an attempt to regenerate and improve healing and outcomes of both the native ACL and the reconstructed graft tissue. Purpose: To review the biologic treatment options for partial tears of the ACL. Study Design: Review. Methods: A literature review was performed that included searches of PubMed, Medline, and Cochrane databases using the following keywords: partial tear of the ACL, ACL repair, bone marrow concentrate, growth factors/healing enhancement, platelet-rich plasma (PRP), stem cell therapy. Results: The use of novel biologic ACL repair techniques, including growth factors, PRP, stem cells, and bioscaffolds, have been reported to result in promising preclinical and short-term clinical outcomes. Conclusion: The potential benefits of these biological augmentation approaches for partial ACL tears are improved healing, better proprioception, and a faster return to sport and activities of daily living when compared with standard reconstruction procedures. However, long-term studies with larger cohorts of patients and with technique validation are necessary to assess the real effect of these approaches. PMID:28210653

  20. Network-based drug discovery by integrating systems biology and computational technologies

    PubMed Central

    Leung, Elaine L.; Cao, Zhi-Wei; Jiang, Zhi-Hong; Zhou, Hua

    2013-01-01

    Network-based intervention has been a trend of curing systemic diseases, but it relies on regimen optimization and valid multi-target actions of the drugs. The complex multi-component nature of medicinal herbs may serve as valuable resources for network-based multi-target drug discovery due to its potential treatment effects by synergy. Recently, robustness of multiple systems biology platforms shows powerful to uncover molecular mechanisms and connections between the drugs and their targeting dynamic network. However, optimization methods of drug combination are insufficient, owning to lacking of tighter integration across multiple ‘-omics’ databases. The newly developed algorithm- or network-based computational models can tightly integrate ‘-omics’ databases and optimize combinational regimens of drug development, which encourage using medicinal herbs to develop into new wave of network-based multi-target drugs. However, challenges on further integration across the databases of medicinal herbs with multiple system biology platforms for multi-target drug optimization remain to the uncertain reliability of individual data sets, width and depth and degree of standardization of herbal medicine. Standardization of the methodology and terminology of multiple system biology and herbal database would facilitate the integration. Enhance public accessible databases and the number of research using system biology platform on herbal medicine would be helpful. Further integration across various ‘-omics’ platforms and computational tools would accelerate development of network-based drug discovery and network medicine. PMID:22877768

  1. Biological effectiveness of neutrons: Research needs

    NASA Astrophysics Data System (ADS)

    Casarett, G. W.; Braby, L. A.; Broerse, J. J.; Elkind, M. M.; Goodhead, D. T.; Oleinick, N. L.

    1994-02-01

    The goal of this report was to provide a conceptual plan for a research program that would provide a basis for determining more precisely the biological effectiveness of neutron radiation with emphasis on endpoints relevant to the protection of human health. This report presents the findings of the experts for seven particular categories of scientific information on neutron biological effectiveness. Chapter 2 examines the radiobiological mechanisms underlying the assumptions used to estimate human risk from neutrons and other radiations. Chapter 3 discusses the qualitative and quantitative models used to organize and evaluate experimental observations and to provide extrapolations where direct observations cannot be made. Chapter 4 discusses the physical principles governing the interaction of radiation with biological systems and the importance of accurate dosimetry in evaluating radiation risk and reducing the uncertainty in the biological data. Chapter 5 deals with the chemical and molecular changes underlying cellular responses and the LET dependence of these changes. Chapter 6, in turn, discusses those cellular and genetic changes which lead to mutation or neoplastic transformation. Chapters 7 and 8 examine deterministic and stochastic effects, respectively, and the data required for the prediction of such effects at different organizational levels and for the extrapolation from experimental results in animals to risks for man. Gaps and uncertainties in this data are examined relative to data required for establishing radiation protection standards for neutrons and procedures for the effective and safe use of neutron and other high-LET radiation therapy.

  2. News from the Biological Stain Commission No. 5.

    PubMed

    Lyon, H O; Dapson, R W

    2009-06-01

    In this fifth issue of News from the Biological Stain Commission (BSC), under the heading of Regulatory Affairs, the BSC's International Affairs Committee provides more information from the meeting of the International Standards Organization ISO/TC 212 Committee that took place on June 2-4, 2008 at Vancouver, Canada. In addition, we give an update on the current situation regarding the supplies of hematoxylin.

  3. [Supervision, administration and standard research related to tissue engineered medical products].

    PubMed

    Xi, Ting-fei; Chen, Liang; Zhao, Peng

    2003-11-01

    Tissue engineering advance in supplying the reparative and reconstructive medicine with promising tissue engineered medical products(TEMPs) and the new therapy alternative. The related supervision and administration of TEMPs is being developed and the standard research of TEMPs is also in progress. The Food and Drug Administration(FDA) of the United States has treated TEMPs as combined products and supervised them according to the level of risk to patients. Lately, FDA has determined that the Center for Devices and Radiological Health (CDRH) should take charge of examination and approval of TEMPs, with the cooperation of the Center for Biological Evaluations and Research(CBER). The regulatory controls have been established respectively in European Union and Japan. In China, TEMPs are identified as medical devices combined with cells. The Department of Medical Device of the State Food and Drug Administration (SFDA) is responsible for the examination and approval of TEMPs, and National Institute for the Control of Pharmaceutical & Biological Products(NICPBP) is responsible for evaluation tests. The standards of TEMPs are formulated mainly by the American Society of Testing Materials(ASTM) and International Standardization Organization(ISO).

  4. Towards BioDBcore: a community-defined information specification for biological databases

    PubMed Central

    Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K.; Bateman, Alex; Blake, Judith A.; Bult, Carol J.; Cherry, J. Michael; Chisholm, Rex L.; Cochrane, Guy; Cook, Charles E.; Eppig, Janan T.; Galperin, Michael Y.; Gentleman, Robert; Goble, Carole A.; Gojobori, Takashi; Hancock, John M.; Howe, Douglas G.; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E.; Mizrachi, Ilene Karsch; Orchard, Sandra; Ouellette, B. F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin Wee; Tatusova, Tatiana; Whetzel, Patricia L.; White, Owen; Yamasaki, Chisato

    2011-01-01

    The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21097465

  5. Towards BioDBcore: a community-defined information specification for biological databases

    PubMed Central

    Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K.; Bateman, Alex; Blake, Judith A.; Bult, Carol J.; Cherry, J. Michael; Chisholm, Rex L.; Cochrane, Guy; Cook, Charles E.; Eppig, Janan T.; Galperin, Michael Y.; Gentleman, Robert; Goble, Carole A.; Gojobori, Takashi; Hancock, John M.; Howe, Douglas G.; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E.; Karsch Mizrachi, Ilene; Orchard, Sandra; Ouellette, B.F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin W.; Tatusova, Tatiana; Whetzel, Patricia L.; White, Owen; Yamasaki, Chisato

    2011-01-01

    The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources; and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21205783

  6. Assessment of compatibility among Armillaria cepistipes, A. sinapina, and North American biological species X and XI, using culture morphology and molecular biology

    Treesearch

    Mark T. Banik; Harold H. Burdsall

    1998-01-01

    Ten single-spore isolates each of Armillaria sinapina, A. cepistipes, and North American biological species (NABS)X and XI were paired in all combinations. A second set of ten single-spore isolates of each species was likewise paired. Each pairing was duplicated for a total of 3280 pairs. Using the standard morphological criteria (e.g., fluffy, crustose) to assess the...

  7. Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 488

    NASA Technical Reports Server (NTRS)

    1999-01-01

    This report lists reports, articles and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract.

  8. Nonlinear dimensionality reduction methods for synthetic biology biobricks' visualization.

    PubMed

    Yang, Jiaoyun; Wang, Haipeng; Ding, Huitong; An, Ning; Alterovitz, Gil

    2017-01-19

    Visualizing data by dimensionality reduction is an important strategy in Bioinformatics, which could help to discover hidden data properties and detect data quality issues, e.g. data noise, inappropriately labeled data, etc. As crowdsourcing-based synthetic biology databases face similar data quality issues, we propose to visualize biobricks to tackle them. However, existing dimensionality reduction methods could not be directly applied on biobricks datasets. Hereby, we use normalized edit distance to enhance dimensionality reduction methods, including Isomap and Laplacian Eigenmaps. By extracting biobricks from synthetic biology database Registry of Standard Biological Parts, six combinations of various types of biobricks are tested. The visualization graphs illustrate discriminated biobricks and inappropriately labeled biobricks. Clustering algorithm K-means is adopted to quantify the reduction results. The average clustering accuracy for Isomap and Laplacian Eigenmaps are 0.857 and 0.844, respectively. Besides, Laplacian Eigenmaps is 5 times faster than Isomap, and its visualization graph is more concentrated to discriminate biobricks. By combining normalized edit distance with Isomap and Laplacian Eigenmaps, synthetic biology biobircks are successfully visualized in two dimensional space. Various types of biobricks could be discriminated and inappropriately labeled biobricks could be determined, which could help to assess crowdsourcing-based synthetic biology databases' quality, and make biobricks selection.

  9. Growing wheat in Biosphere 2 under elevated CO2: observations and modeling

    NASA Technical Reports Server (NTRS)

    Tubiello, F. N.; Mahato, T.; Morton, T.; Druitt, J. W.; Volk, T.; Marino, B. D.

    1999-01-01

    Spring wheat (Triticum aestivum L., cv. Yecora Rojo) was grown in the intensive agricultural biome (IAB) of Biosphere 2 during the l995-l996 winter/spring season. Environmental conditions were characterized by a day/night temperature regime of 27/17 degrees C, relative humidity (RH) levels around 45%, mean atmospheric CO2 concentration of 450 ppmv, and natural light conditions with mean intensities about half of outside levels. Weekly samples of above-ground plant matter were collected throughout the growing season and phenological events recorded. A computer model, CERES-Wheat, previously tested under both field and controlled conditions, was used to simulate the observed crop growth and to help in data analysis. We found that CERES-Wheat simulated the data collected at Biosphere 2 to within 10% of observed, thus suggesting that wheat growth inside the IAB was comparable to that documented in other environments. The model predicts phenological stages and final dry matter (DM) production within l0% of the observed data. Measured DM production rates, normalized for light absorbed by the crop. suggested photosynthetic efficiencies intermediate between those observed under optimal field conditions and those recorded in NASA-Controlled Ecological Life-Support Systems (CELSS). We suggest that such a difference can be explained primarily in terms of low light levels inside the IAB, with additional effects due to elevated CO2 concentrations and diffuse light fractions.

  10. Polarimetric imaging of biological tissues based on the indices of polarimetric purity.

    PubMed

    Van Eeckhout, Albert; Lizana, Angel; Garcia-Caurel, Enric; Gil, José J; Sansa, Adrià; Rodríguez, Carla; Estévez, Irene; González, Emilio; Escalera, Juan C; Moreno, Ignacio; Campos, Juan

    2018-04-01

    We highlight the interest of using the indices of polarimetric purity (IPPs) to the inspection of biological tissues. The IPPs were recently proposed in the literature and they result in a further synthetization of the depolarizing properties of samples. Compared with standard polarimetric images of biological samples, IPP-based images lead to larger image contrast of some biological structures and to a further physical interpretation of the depolarizing mechanisms inherent to the samples. In addition, unlike other methods, their calculation do not require advanced algebraic operations (as is the case of polar decompositions), and they result in 3 indicators of easy implementation. We also propose a pseudo-colored encoding of the IPP information that leads to an improved visualization of samples. This last technique opens the possibility of tailored adjustment of tissues contrast by using customized pseudo-colored images. The potential of the IPP approach is experimentally highlighted along the manuscript by studying 3 different ex-vivo samples. A significant image contrast enhancement is obtained by using the IPP-based methods, compared to standard polarimetric images. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Relations between Intuitive Biological Thinking and Biological Misconceptions in Biology Majors and Nonmajors

    ERIC Educational Resources Information Center

    Coley, John D.; Tanner, Kimberly

    2015-01-01

    Research and theory development in cognitive psychology and science education research remain largely isolated. Biology education researchers have documented persistent scientifically inaccurate ideas, often termed "misconceptions," among biology students across biological domains. In parallel, cognitive and developmental psychologists…

  12. Radiation Standards: The Last Word or at Least a Definitive One

    ERIC Educational Resources Information Center

    Gillette, Robert

    1972-01-01

    Discusses the report of the National Academy of Science Committee on the Biological Effects of Ionizing Radiation, with particular reference to the possibilities for lowering maximum permissible standards for exposure to man-made radiation. The excessive use of diagnostic X-rays is considered. (AL)

  13. The navigation of biological hyperspace

    NASA Astrophysics Data System (ADS)

    Conway Morris, Simon

    2003-04-01

    A recurrent argument against the reality of biological evolution is the claim that there is insufficient time for the emergence of biological complexity. Such a view is a staple of creation "scientists", but even cosmologists and biochemists have been overheard murmuring similar sentiments. Certainly the stock response, that the scientific evidence for evolution is overwhelming, must be made. However, it is also the case that whilst the efficacity of natural selection is not in dispute, it is context-free and fails to explain the specificities of life. This observation is usually greeted with a Gallic shrug: "Yes, the biosphere is very rich, but so what?" Indeed, the standard scientific response is that evolution is dogged by contingent happenstance, with the implication that a given complexity, say intelligence, is an evolutionary fluke. This, however, is inconsistent with the ubiquity of evolutionary convergence. Here I outline the argument for such convergence providing a "road-map" of possibilities that arguably has universal applications and as importantly points to a much deeper structure to life.

  14. Biological safety cabinetry.

    PubMed Central

    Kruse, R H; Puckett, W H; Richardson, J H

    1991-01-01

    The biological safety cabinet is the one piece of laboratory and pharmacy equipment that provides protection for personnel, the product, and the environment. Through the history of laboratory-acquired infections from the earliest published case to the emergence of hepatitis B and AIDS, the need for health care worker protection is described. A brief description with design, construction, function, and production capabilities is provided for class I and class III safety cabinets. The development of the high-efficiency particulate air filter provided the impetus for clean room technology, from which evolved the class II laminar flow biological safety cabinet. The clean room concept was advanced when the horizontal airflow clean bench was manufactured; it became popular in pharmacies for preparing intravenous solutions because the product was protected. However, as with infectious microorganisms and laboratory workers, individual sensitization to antibiotics and the advent of hazardous antineoplastic agents changed the thinking of pharmacists and nurses, and they began to use the class II safety cabinet to prevent adverse personnel reactions to the drugs. How the class II safety cabinet became the mainstay in laboratories and pharmacies is described, and insight is provided into the formulation of National Sanitation Foundation standard number 49 and its revisions. The working operations of a class II cabinet are described, as are the variations of the four types with regard to design, function, air velocity profiles, and the use of toxins. The main certification procedures are explained, with examples of improper or incorrect certifications. The required levels of containment for microorganisms are given. Instructions for decontaminating the class II biological safety cabinet of infectious agents are provided; unfortunately, there is no method for decontaminating the cabinet of antineoplastic agents. Images PMID:2070345

  15. Synthetic Biology: Putting Synthesis into Biology

    PubMed Central

    Liang, Jing; Luo, Yunzi; Zhao, Huimin

    2010-01-01

    The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways, and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself – encompassing many branches of science, and across many scales of application. New DNA synthesis and assembly techniques have made routine the customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery – a self-replicating organism – is being pursued at this moment. It is the purpose of this review to dissect and organize these various components of synthetic biology into a coherent picture. PMID:21064036

  16. Biological satellite scientific devices

    NASA Astrophysics Data System (ADS)

    Perepech, B. L.; Rumiantsev, V. P.; Galkin, V. M.; Shakhvorostov, S. V.; Rvachev, S. S.

    1991-02-01

    The paper describes the NA SBS 9 systems developed for the ninth Cosmos-2044 biological test mission. The NA SBS 9 life support systems designed for monkeys and rats follow standard design of BIOS-Vivarium and BIOS-Primate units. The main features of NA SBS 9 include the use of a recently developed HF physiological data recorder Skat-3; the incorporation into BIOS-Primate of two units intended for biorhythmic studies (the BBI-Zh system for studying beetles and the VITALOG developed by NASA for studies on monkeys); and a new version of BIOS-Primate system incorporating a capacitance-link and an inductance-link temperature transmitters and a brain tissue oxygen tension control channel.

  17. Source Identification of Human Biological Materials and Its Prospect in Forensic Science.

    PubMed

    Zou, K N; Gui, C; Gao, Y; Yang, F; Zhou, H G

    2016-06-01

    Source identification of human biological materials in crime scene plays an important role in reconstructing the crime process. Searching specific genetic markers to identify the source of different human biological materials is the emphasis and difficulty of the research work of legal medical experts in recent years. This paper reviews the genetic markers which are used for identifying the source of human biological materials and studied widely, such as DNA methylation, mRNA, microRNA, microflora and protein, etc. By comparing the principles and methods of source identification of human biological materials using different kinds of genetic markers, different source of human biological material owns suitable marker types and can be identified by detecting single genetic marker or combined multiple genetic markers. Though there is no uniform standard and method for identifying the source of human biological materials in forensic laboratories at present, the research and development of a series of mature and reliable methods for distinguishing different human biological materials play the role as forensic evidence which will be the future development direction. Copyright© by the Editorial Department of Journal of Forensic Medicine.

  18. Re-thinking organisms: The impact of databases on model organism biology.

    PubMed

    Leonelli, Sabina; Ankeny, Rachel A

    2012-03-01

    Community databases have become crucial to the collection, ordering and retrieval of data gathered on model organisms, as well as to the ways in which these data are interpreted and used across a range of research contexts. This paper analyses the impact of community databases on research practices in model organism biology by focusing on the history and current use of four community databases: FlyBase, Mouse Genome Informatics, WormBase and The Arabidopsis Information Resource. We discuss the standards used by the curators of these databases for what counts as reliable evidence, acceptable terminology, appropriate experimental set-ups and adequate materials (e.g., specimens). On the one hand, these choices are informed by the collaborative research ethos characterising most model organism communities. On the other hand, the deployment of these standards in databases reinforces this ethos and gives it concrete and precise instantiations by shaping the skills, practices, values and background knowledge required of the database users. We conclude that the increasing reliance on community databases as vehicles to circulate data is having a major impact on how researchers conduct and communicate their research, which affects how they understand the biology of model organisms and its relation to the biology of other species. Copyright © 2011 Elsevier Ltd. All rights reserved.

  19. Alignment between High School Biology Curriculum Standard and the Standardised Tests of Four Provinces in China

    ERIC Educational Resources Information Center

    Lu, Qun; Liu, Enshan

    2012-01-01

    With the development and implementation of new curriculum standards, the field tests of education reform in senior high schools began in 2004 in four pilot provinces in mainland China. After five years of the reform, it is necessary to know how and to what extent the curriculum standard guides test classroom instruction. The present study was…

  20. Designing and encoding models for synthetic biology.

    PubMed

    Endler, Lukas; Rodriguez, Nicolas; Juty, Nick; Chelliah, Vijayalakshmi; Laibe, Camille; Li, Chen; Le Novère, Nicolas

    2009-08-06

    A key component of any synthetic biology effort is the use of quantitative models. These models and their corresponding simulations allow optimization of a system design, as well as guiding their subsequent analysis. Once a domain mostly reserved for experts, dynamical modelling of gene regulatory and reaction networks has been an area of growth over the last decade. There has been a concomitant increase in the number of software tools and standards, thereby facilitating model exchange and reuse. We give here an overview of the model creation and analysis processes as well as some software tools in common use. Using markup language to encode the model and associated annotation, we describe the mining of components, their integration in relational models, formularization and parametrization. Evaluation of simulation results and validation of the model close the systems biology 'loop'.

  1. Familial transmission of venous thromboembolism: a cohort study of 80 214 Swedish adoptees linked to their biological and adoptive parents.

    PubMed

    Zöller, Bengt; Li, Xinjun; Sundquist, Jan; Sundquist, Kristina

    2014-06-01

    Venous thromboembolism (VTE) clusters in families, but the familial risk of VTE has not been determined among adoptees. The aim was to disentangle the contributions of genetic and environmental factors to the familial transmission of VTE. The Swedish Multi-Generation Register was used to follow all Swedish-born adoptees born from 1932 to 2004 (n=80,214) between January 1, 1964, and December 31, 2010, for VTE. The risk of VTE was estimated in adoptees with ≥1 biological parent with VTE compared with adoptees without a biological parent with VTE. The risk of VTE was also estimated in adoptees with ≥1 adoptive parent with VTE compared with adoptees without an adoptive parent with VTE. Adoptees with ≥1 biological parent with VTE (n=137) were more likely to have VTE than adoptees without a biological parent with VTE (standardized incidence ratio) 1.51 (95% confidence interval, 1.27-1.79). The standardized incidence ratio for VTE was highest for adoptees with a biological parent diagnosed with VTE before the age of 50 years (standardized incidence ratio=2.03, 1.24-3.14). In contrast, adoptees with ≥1 adoptive parent with VTE (n=156) were not at increased risk of VTE (standardized incidence ratio=1.07, 0.91-1.25). These novel findings suggest that genetic factors make a stronger contribution to the familial transmission of VTE from parents to offspring than family environmental factors. © 2014 American Heart Association, Inc.

  2. Collaborative study for the calibration of a replacement International Standard for Tetanus Toxoid Adsorbed.

    PubMed

    Tierney, Rob; Stickings, Paul; Hockley, Jason; Rigsby, Peter; Iwaki, Masaaki; Sesardic, Dorothea

    2011-11-01

    We present the results of a collaborative study for the establishment of a replacement International Standard (IS) for Tetanus Toxoid Adsorbed. Two candidate preparations were included in the study, one of which was established as the 4th IS for Tetanus Toxoid Adsorbed at the WHO Expert Committee on Biological Standardization meeting in October 2010. This preparation was found to have a unitage of 490 IU/ampoule, based on calibration in guinea pig challenge assays. Results from mouse challenge assays suggest that the relative performance of two candidate preparations may differ significantly between guinea pigs and mice. The authors note that the number of laboratories that performed guinea pig challenge assays, which are used to calibrate and assign IU, is much lower than in previous collaborative studies and this may have implications for calibration of replacement standards in the future. The issue of assigning separate units to the IS for guinea pig and mouse assays is discussed. The study also assessed performance of the replacement standard in serological assays which are used as alternative procedures to challenge assays for tetanus potency testing. Results suggest that the replacement standard is suitable for use as the reference vaccine in serological assays. Copyright © 2011 The International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

  3. SU-E-J-12: An Image-Guided Soft Robotic Patient Positioning System for Maskless Head-And-Neck Cancer Radiotherapy: A Proof-Of-Concept Study

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

    Ogunmolu, O; Gans, N; Jiang, S

    Purpose: We propose a surface-image-guided soft robotic patient positioning system for maskless head-and-neck radiotherapy. The ultimate goal of this project is to utilize a soft robot to realize non-rigid patient positioning and real-time motion compensation. In this proof-of-concept study, we design a position-based visual servoing control system for an air-bladder-based soft robot and investigate its performance in controlling the flexion/extension cranial motion on a mannequin head phantom. Methods: The current system consists of Microsoft Kinect depth camera, an inflatable air bladder (IAB), pressured air source, pneumatic valve actuators, custom-built current regulators, and a National Instruments myRIO microcontroller. The performance ofmore » the designed system was evaluated on a mannequin head, with a ball joint fixed below its neck to simulate torso-induced head motion along flexion/extension direction. The IAB is placed beneath the mannequin head. The Kinect camera captures images of the mannequin head, extracts the face, and measures the position of the head relative to the camera. This distance is sent to the myRIO, which runs control algorithms and sends actuation commands to the valves, inflating and deflating the IAB to induce head motion. Results: For a step input, i.e. regulation of the head to a constant displacement, the maximum error was a 6% overshoot, which the system then reduces to 0% steady-state error. In this initial investigation, the settling time to reach the regulated position was approximately 8 seconds, with 2 seconds of delay between the command start of motion due to capacitance of the pneumatics, for a total of 10 seconds to regulate the error. Conclusion: The surface image-guided soft robotic patient positioning system can achieve accurate mannequin head flexion/extension motion. Given this promising initial Result, the extension of the current one-dimensional soft robot control to multiple IABs for non-rigid positioning

  4. A systematic approach to infer biological relevance and biases of gene network structures.

    PubMed

    Antonov, Alexey V; Tetko, Igor V; Mewes, Hans W

    2006-01-10

    The development of high-throughput technologies has generated the need for bioinformatics approaches to assess the biological relevance of gene networks. Although several tools have been proposed for analysing the enrichment of functional categories in a set of genes, none of them is suitable for evaluating the biological relevance of the gene network. We propose a procedure and develop a web-based resource (BIOREL) to estimate the functional bias (biological relevance) of any given genetic network by integrating different sources of biological information. The weights of the edges in the network may be either binary or continuous. These essential features make our web tool unique among many similar services. BIOREL provides standardized estimations of the network biases extracted from independent data. By the analyses of real data we demonstrate that the potential application of BIOREL ranges from various benchmarking purposes to systematic analysis of the network biology.

  5. Determination of metallothionein in biological fluids using enzyme-linked immunoassay with commercial antibody.

    PubMed

    Milnerowicz, Halina; Bizoń, Anna

    2010-01-01

    Metallothionein (MT) is a low molecular weight cysteine-rich protein with a number of roles in the pro/antioxidant balance and homeostasis of essential metals, such as zinc and copper, and in the detoxification of heavy metals, such as cadmium and mercury. Until now, detection of metallothionein in biological fluids remained difficult because of a lack of a broadly reactive commercial test. Meaningful comparison of the values of metallothionein concentrations reported by different authors using their specific isolation procedures and different conditions of enzyme-linked immunoassay is difficult due to the absence of a reference material for metallothionein. Therefore in the present study, we describe a quantitative assay for metallothionein in biological fluids such as plasma and urine performed by a direct enzyme-linked immunoassay using a commercially available monoclonal mouse anti-metallothionein clone E9 antibody and commercial standards of metallothionein from rabbit liver and a custom preparation of metallothionein from human liver. The sensitivity of the assay for the standard containing two isoforms MT-I and MT-II from human liver was 140 pg/well. The reactivity of the commercial standards and standards containing two isoforms MT-I and MT-II isolated from human liver in our laboratory with a commercial monoclonal mouse anti-metallothionein clone E9 antibody were similar. This suggests that the described ELISA test can be useful for determination of metallothionein concentration in biological fluids. The concentrations of metallothionein in human plasma, erythrocyte lysate and in urine of smoking and non-smoking healthy volunteers are reported. Tobacco smoking increases the extracellular metallothionein concentration (plasma and urine) but does not affect the intracellular concentration (erythrocyte lysate).

  6. Biological Evolution and the History of the Earth Are Foundations of Science

    NASA Astrophysics Data System (ADS)

    2008-01-01

    AGU affirms the central importance of including scientific theories of Earth history and biological evolution in science education. Within the scientific community, the theory of biological evolution is not controversial, nor have ``alternative explanations'' been found. This is why no competing theories are required by the U.S. National Science Education Standards. Explanations of natural phenomena that appeal to the supernatural or are based on religious doctrine-and therefore cannot be tested through scientific inquiry-are not scientific, and have no place in the science classroom.

  7. Quantum Information Biology: From Information Interpretation of Quantum Mechanics to Applications in Molecular Biology and Cognitive Psychology

    NASA Astrophysics Data System (ADS)

    Asano, Masanari; Basieva, Irina; Khrennikov, Andrei; Ohya, Masanori; Tanaka, Yoshiharu; Yamato, Ichiro

    2015-10-01

    We discuss foundational issues of quantum information biology (QIB)—one of the most successful applications of the quantum formalism outside of physics. QIB provides a multi-scale model of information processing in bio-systems: from proteins and cells to cognitive and social systems. This theory has to be sharply distinguished from "traditional quantum biophysics". The latter is about quantum bio-physical processes, e.g., in cells or brains. QIB models the dynamics of information states of bio-systems. We argue that the information interpretation of quantum mechanics (its various forms were elaborated by Zeilinger and Brukner, Fuchs and Mermin, and D' Ariano) is the most natural interpretation of QIB. Biologically QIB is based on two principles: (a) adaptivity; (b) openness (bio-systems are fundamentally open). These principles are mathematically represented in the framework of a novel formalism— quantum adaptive dynamics which, in particular, contains the standard theory of open quantum systems.

  8. Teaching cell and molecular biology for gender equity.

    PubMed

    Sible, Jill C; Wilhelm, Dayna E; Lederman, Muriel

    2006-01-01

    Science, technology, engineering, and math (STEM) fields, including cell biology, are characterized by the "leaky pipeline" syndrome in which, over time, women leave the discipline. The pipeline itself and the pond into which it empties may not be neutral. Explicating invisible norms, attitudes, and practices by integrating social studies of science into science education may be the necessary first step in helping female students persist in STEM disciplines. In 2003 and 2004, a sophomore Cell and Molecular Biology course at Virginia Tech (Blacksburg, VA) was taught integrating social studies of science with standard material. The course was successfully implemented, teaching students factual content while increasing awareness of the cultures of science and their self-confidence in engaging with the subject. Course evaluation data indicated that females in particular perceived greater gains in logical thinking and problem-solving abilities than females in a traditional cell biology course. Consistent with K-12 studies, males in this class were likely to view scientists as male only, whereas females viewed scientists as male and female. This pilot project demonstrates that social studies can be integrated successfully in a cell biology course. Longitudinal studies of this cohort of students will indicate whether this approach contributes to the retention of women in the field.

  9. Biological monitoring results for cadmium exposed workers.

    PubMed

    McDiarmid, M A; Freeman, C S; Grossman, E A; Martonik, J

    1996-11-01

    As part of a settlement agreement with the Occupational Safety and Health Administration (OSHA) involving exposure to cadmium (Cd), a battery production facility provided medical surveillance data to OSHA for review. Measurements of cadmium in blood, cadmium in urine, and beta 2-microglobulin in urine were obtained for more than 100 workers over an 18-month period. Some airborne Cd exposure data were also made available. Two subpopulations of this cohort were of primary interest in evaluating compliance with the medical surveillance provisions of the Cadmium Standard. These were a group of 16 workers medically removed from cadmium exposure due to elevations in some biological parameter, and a group of platemakers. Platemaking had presented a particularly high exposure opportunity and had recently undergone engineering interventions to minimize exposure. The effect on three biological monitoring parameters of medical removal protection in the first group and engineering controls in platemakers is reported. Results reveal that both medical removal from cadmium exposures and exposure abatement through the use of engineering and work practice controls generally result in declines in biological monitoring parameters of exposed workers. Implications for the success of interventions are discussed.

  10. [Biosafety provision on handling pathogenic biological agents on the concept of biorisk assessment and management].

    PubMed

    Dobrokhotskiĭ, O N; Kolombet, L V

    2010-01-01

    The paper shows it urgent to realize the concept of biological risk assessment and management on handling pathogenic biological agents (PBA). It gives a number of objective reasons that impede development of a methodology to assess laboratory biological risks. A concept of continuous improvement (a process approach) is proposed for use as a biorisk management tool for biosafety assurance when handling PBA. It is demonstrated that development of international cooperation urgently requires that national concepts and standards be harmonized with international regulatory documents on biosafety assurance on handling PBA.

  11. Guidelines for Managing Suspected Chemical and Biological Agent Incidents in Rail Tunnel Systems

    DOT National Transportation Integrated Search

    2002-03-01

    These emergency management guidelines are designed to help transit managers (1) prepare and implement standard operating procedures (SOPs) for handling potential and actual chemical or biological agent attacks in their rail tunnel system and (2) unde...

  12. MARK-AGE standard operating procedures (SOPs): A successful effort.

    PubMed

    Moreno-Villanueva, María; Capri, Miriam; Breusing, Nicolle; Siepelmeyer, Anne; Sevini, Federica; Ghezzo, Alessandro; de Craen, Anton J M; Hervonen, Antti; Hurme, Mikko; Schön, Christiane; Grune, Tilman; Franceschi, Claudio; Bürkle, Alexander

    2015-11-01

    Within the MARK-AGE project, a population study (3337 subjects) was conducted to identify a set of biomarkers of ageing which, as a combination of parameters with appropriate weighting, would measure biological age better than any single marker. The MARK-AGE project involves 14 European countries and a total of 26 research centres. In such a study, standard operating procedures (SOPs) are an essential task, which are binding for all MARK-AGE Beneficiaries. The SOPs cover all aspects of subject's recruitment, collection, shipment and distribution of biological samples (blood and its components, buccal mucosa cells or BMC and urine) as well as the anthropometric measurements and questionnaires. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  13. Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 490

    NASA Technical Reports Server (NTRS)

    1999-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP-1999-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract. Two indexes-subject and author are included after the abstract section.

  14. Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 487

    NASA Technical Reports Server (NTRS)

    1999-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP-1999-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract. Two indexes-subject and author are included after the abstract section.

  15. Aerospace Medicine and Biology: A Continuing Bibliography With Indexes. Supplement 502

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP-2000-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract. Two indexes-subject and author are included after the abstract section.

  16. It's not about you: a simple proposition for improving biology education.

    PubMed

    Wright, Robin

    2014-10-01

    THE Genetics Society of America's Elizabeth W. Jones Award for Excellence in Education recognizes significant and sustained impact on genetics education. Consistent with her philosophy of linking research and education, the 2014 Awardee Robin Wright includes undergraduate students in all of her research. She seeks to teach how to think like and to actually be a biologist, working in teams and looking at real-world problems. She emphasizes a learner-centered model of classroom work that promotes and enhances lifelong skills, and has transformed biology education at the University of Minnesota through several efforts including developing the interactive, stimulating Foundations of Biology course sequence, encouraging active learning and open-ended research; supporting the construction of Active Learning Classrooms; and establishing Student Learning Outcomes, standards that measure biology education. She serves as founding editor-in-chief of CourseSource, focusing national effort to collect learner-centered, outcomes-based teaching resources in undergraduate biology. Copyright © 2014 by the Genetics Society of America.

  17. Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 504

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP-2000-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract. Two indexes- subject and author are included after the abstract section.

  18. Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 494

    NASA Technical Reports Server (NTRS)

    1999-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract. The NASA CASI price code table, addresses of organizations, and document availability information are included before the abstract section. Two indexes--subject and author are included after the abstract section.

  19. Advances in the Biology and Chemistry of Sialic Acids

    PubMed Central

    Chen, Xi; Varki, Ajit

    2010-01-01

    Sialic acids are a subset of nonulosonic acids, which are nine-carbon alpha-keto aldonic acids. Natural existing sialic acid-containing structures are presented in different sialic acid forms, various sialyl linkages, and on diverse underlying glycans. They play important roles in biological, pathological, and immunological processes. Sialobiology has been a challenging and yet attractive research area. Recent advances in chemical and chemoenzymatic synthesis as well as large-scale E. coli cell-based production have provided a large library of sialoside standards and derivatives in amounts sufficient for structure-activity relationship studies. Sialoglycan microarrays provide an efficient platform for quick identification of preferred ligands for sialic acid-binding proteins. Future research on sialic acid will continue to be at the interface of chemistry and biology. Research efforts will not only lead to a better understanding of the biological and pathological importance of sialic acids and their diversity, but could also lead to the development of therapeutics. PMID:20020717

  20. The Biological and Toxicological Activity of Gases and Vapors

    PubMed Central

    Sánchez-Moreno, Ricardo; Gil-Lostes, Javier; Acree, William E.; Cometto-Muñiz, J. Enrique; Cain, William S.

    2010-01-01

    A large amount of data on the biological and toxicological activity of gases and vapors has been collected from the literature. Processes include sensory irritation thresholds, the Alarie mouse test, inhalation anesthesia, etc. It is shown that a single equation using only five descriptors (properties of the gases and vapors) plus a set of indicator variables for the given processes can correlate 643 biological and non-lethal toxicological activities of ‘non-reactive’ compounds with a standard deviation of 0.36 log unit. The equation is scaled to sensory irritation thresholds obtained by the procedure of Cometto-Muñiz, and Cain, and provides a general equation for the prediction of sensory irritation thresholds in man. It is suggested that differences in biological/toxicological activity arise primarily from transport from the gas phase to a receptor phase or area, except for odor detection thresholds where interaction with a receptor(s) is important. PMID:19913608

  1. BioMOL: a computer-assisted biological modeling tool for complex chemical mixtures and biological processes at the molecular level.

    PubMed Central

    Klein, Michael T; Hou, Gang; Quann, Richard J; Wei, Wei; Liao, Kai H; Yang, Raymond S H; Campain, Julie A; Mazurek, Monica A; Broadbelt, Linda J

    2002-01-01

    A chemical engineering approach for the rigorous construction, solution, and optimization of detailed kinetic models for biological processes is described. This modeling capability addresses the required technical components of detailed kinetic modeling, namely, the modeling of reactant structure and composition, the building of the reaction network, the organization of model parameters, the solution of the kinetic model, and the optimization of the model. Even though this modeling approach has enjoyed successful application in the petroleum industry, its application to biomedical research has just begun. We propose to expand the horizons on classic pharmacokinetics and physiologically based pharmacokinetics (PBPK), where human or animal bodies were often described by a few compartments, by integrating PBPK with reaction network modeling described in this article. If one draws a parallel between an oil refinery, where the application of this modeling approach has been very successful, and a human body, the individual processing units in the oil refinery may be considered equivalent to the vital organs of the human body. Even though the cell or organ may be much more complicated, the complex biochemical reaction networks in each organ may be similarly modeled and linked in much the same way as the modeling of the entire oil refinery through linkage of the individual processing units. The integrated chemical engineering software package described in this article, BioMOL, denotes the biological application of molecular-oriented lumping. BioMOL can build a detailed model in 1-1,000 CPU sec using standard desktop hardware. The models solve and optimize using standard and widely available hardware and software and can be presented in the context of a user-friendly interface. We believe this is an engineering tool with great promise in its application to complex biological reaction networks. PMID:12634134

  2. Reference Standardization for Mass Spectrometry and High-resolution Metabolomics Applications to Exposome Research

    PubMed Central

    Go, Young-Mi; Walker, Douglas I.; Liang, Yongliang; Uppal, Karan; Soltow, Quinlyn A.; Tran, ViLinh; Strobel, Frederick; Quyyumi, Arshed A.; Ziegler, Thomas R.; Pennell, Kurt D.; Miller, Gary W.; Jones, Dean P.

    2015-01-01

    The exposome is the cumulative measure of environmental influences and associated biological responses throughout the lifespan, including exposures from the environment, diet, behavior, and endogenous processes. A major challenge for exposome research lies in the development of robust and affordable analytic procedures to measure the broad range of exposures and associated biologic impacts occurring over a lifetime. Biomonitoring is an established approach to evaluate internal body burden of environmental exposures, but use of biomonitoring for exposome research is often limited by the high costs associated with quantification of individual chemicals. High-resolution metabolomics (HRM) uses ultra-high resolution mass spectrometry with minimal sample preparation to support high-throughput relative quantification of thousands of environmental, dietary, and microbial chemicals. HRM also measures metabolites in most endogenous metabolic pathways, thereby providing simultaneous measurement of biologic responses to environmental exposures. The present research examined quantification strategies to enhance the usefulness of HRM data for cumulative exposome research. The results provide a simple reference standardization protocol in which individual chemical concentrations in unknown samples are estimated by comparison to a concurrently analyzed, pooled reference sample with known chemical concentrations. The approach was tested using blinded analyses of amino acids in human samples and was found to be comparable to independent laboratory results based on surrogate standardization or internal standardization. Quantification was reproducible over a 13-month period and extrapolated to thousands of chemicals. The results show that reference standardization protocol provides an effective strategy that will enhance data collection for cumulative exposome research. In principle, the approach can be extended to other types of mass spectrometry and other analytical methods. PMID

  3. Monitoring biological diversity: strategies, tools, limitations, and challenges

    USGS Publications Warehouse

    Beever, E.A.

    2006-01-01

    Monitoring is an assessment of the spatial and temporal variability in one or more ecosystem properties, and is an essential component of adaptive management. Monitoring can help determine whether mandated environmental standards are being met and can provide an early-warning system of ecological change. Development of a strategy for monitoring biological diversity will likely be most successful when based upon clearly articulated goals and objectives and may be enhanced by including several key steps in the process. Ideally, monitoring of biological diversity will measure not only composition, but also structure and function at the spatial and temporal scales of interest. Although biodiversity monitoring has several key limitations as well as numerous theoretical and practical challenges, many tools and strategies are available to address or overcome such challenges; I summarize several of these. Due to the diversity of spatio-temporal scales and comprehensiveness encompassed by existing definitions of biological diversity, an effective monitoring design will reflect the desired sampling domain of interest and its key stressors, available funding, legal requirements, and organizational goals.

  4. QconCATs: design and expression of concatenated protein standards for multiplexed protein quantification.

    PubMed

    Simpson, Deborah M; Beynon, Robert J

    2012-09-01

    Systems biology requires knowledge of the absolute amounts of proteins in order to model biological processes and simulate the effects of changes in specific model parameters. Quantification concatamers (QconCATs) are established as a method to provide multiplexed absolute peptide standards for a set of target proteins in isotope dilution standard experiments. Two or more quantotypic peptides representing each of the target proteins are concatenated into a designer gene that is metabolically labelled with stable isotopes in Escherichia coli or other cellular or cell-free systems. Co-digestion of a known amount of QconCAT with the target proteins generates a set of labelled reference peptide standards for the unlabelled analyte counterparts, and by using an appropriate mass spectrometry platform, comparison of the intensities of the peptide ratios delivers absolute quantification of the encoded peptides and in turn the target proteins for which they are surrogates. In this review, we discuss the criteria and difficulties associated with surrogate peptide selection and provide examples in the design of QconCATs for quantification of the proteins of the nuclear factor κB pathway.

  5. INDEX OF PUBLICATIONS ON BIOLOGICAL EFFECTS OF ELECTROMAGNETIC RADIATION (0-100 GHZ)

    EPA Science Inventory

    Considerable research effort has been made into the biological effects of electro-magnetic radiation over the frequency range of 0-100 GHz. This work intensified since 1966 when occupational exposure guidelines were made by American Standards Institute - C95.9. During this period...

  6. An introduction to microbiome analysis for human biology applications.

    PubMed

    Amato, Katherine R

    2017-01-01

    Research examining the gut microbiota is currently exploding, and results are providing new perspectives on human biology. Factors such as host diet and physiology influence the composition and function of the gut microbiota, which in turn affects human nutrition, health, and behavior via interactions with metabolism, the immune system, and the brain. These findings represent an exciting new twist on familiar topics, and as a result, gut microbiome research is likely to provide insight into unresolved biological mechanisms driving human health. However, much remains to be learned about the broader ecological and evolutionary contexts within which gut microbes and humans are affecting each other. Here, I outline the procedures for generating data describing the gut microbiota with the goal of facilitating the wider integration of microbiome analyses into studies of human biology. I describe the steps involved in sample collection, DNA extraction, PCR amplification, high-throughput sequencing, and bioinformatics. While this review serves only as an introduction to these topics, it provides sufficient resources for researchers interested in launching new microbiome initiatives. As knowledge of these methods spreads, microbiome analysis should become a standard tool in the arsenal of human biology research. © 2016 Wiley Periodicals, Inc.

  7. Automatic document classification of biological literature

    PubMed Central

    Chen, David; Müller, Hans-Michael; Sternberg, Paul W

    2006-01-01

    Background Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature. Results We present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. Conclusion We have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. PMID:16893465

  8. PathJam: a new service for integrating biological pathway information.

    PubMed

    Glez-Peña, Daniel; Reboiro-Jato, Miguel; Domínguez, Rubén; Gómez-López, Gonzalo; Pisano, David G; Fdez-Riverola, Florentino

    2010-10-28

    Biological pathways are crucial to much of the scientific research today including the study of specific biological processes related with human diseases. PathJam is a new comprehensive and freely accessible web-server application integrating scattered human pathway annotation from several public sources. The tool has been designed for both (i) being intuitive for wet-lab users providing statistical enrichment analysis of pathway annotations and (ii) giving support to the development of new integrative pathway applications. PathJam’s unique features and advantages include interactive graphs linking pathways and genes of interest, downloadable results in fully compatible formats, GSEA compatible output files and a standardized RESTful API.

  9. EPR spectroscopy of complex biological iron-sulfur systems.

    PubMed

    Hagen, Wilfred R

    2018-02-21

    From the very first discovery of biological iron-sulfur clusters with EPR, the spectroscopy has been used to study not only purified proteins but also complex systems such as respiratory complexes, membrane particles and, later, whole cells. In recent times, the emphasis of iron-sulfur biochemistry has moved from characterization of individual proteins to the systems biology of iron-sulfur biosynthesis, regulation, degradation, and implications for human health. Although this move would suggest a blossoming of System-EPR as a specific, non-invasive monitor of Fe/S (dys)homeostasis in whole cells, a review of the literature reveals limited success possibly due to technical difficulties in adherence to EPR spectroscopic and biochemical standards. In an attempt to boost application of System-EPR the required boundary conditions and their practical applications are explicitly and comprehensively formulated.

  10. Elements of Morphology: Standard Terminology for the External Genitalia

    PubMed Central

    Hennekam, Raoul C.M.; Allanson, Judith E.; Biesecker, Leslie G.; Carey, John C.; Opitz, John M.; Vilain, Eric

    2015-01-01

    An international group of clinicians working in the field of dysmorphology has initiated the standardization of terms used to describe human morphology. The goals are to standardize these terms and reach consensus regarding their definitions. In this way, we will increase the utility of descriptions of the human phenotype and facilitate reliable comparisons of findings among patients. Discussions with other workers in dysmorphology and related fields, such as developmental biology and molecular genetics, will becomemore precise. Here we introduce the anatomy of the male and female genitalia, and define and illustrate the terms that describe the major characteristics of these body regions. PMID:23650202

  11. 7th Annual Systems Biology Symposium: Systems Biology and Engineering

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

    Galitski, Timothy P.

    2008-04-01

    Systems biology recognizes the complex multi-scale organization of biological systems, from molecules to ecosystems. The International Symposium on Systems Biology has been hosted by the Institute for Systems Biology in Seattle, Washington, since 2002. The annual two-day event gathers the most influential researchers transforming biology into an integrative discipline investingating complex systems. Engineering and application of new technology is a central element of systems biology. Genome-scale, or very small-scale, biological questions drive the enigneering of new technologies, which enable new modes of experimentation and computational analysis, leading to new biological insights and questions. Concepts and analytical methods in engineering aremore » now finding direct applications in biology. Therefore, the 2008 Symposium, funded in partnership with the Department of Energy, featured global leaders in "Systems Biology and Engineering."« less

  12. 75 FR 67711 - International Energy Agency Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-03

    ... DEPARTMENT OF ENERGY International Energy Agency Meetings AGENCY: Department of Energy. ACTION: Notice of meetings. SUMMARY: The Industry Advisory Board (IAB) to the International Energy Agency (IEA... Security Programs, Department of Energy, 1000 [[Page 67712

  13. Building biological foundries for next-generation synthetic biology.

    PubMed

    Chao, Ran; Yuan, YongBo; Zhao, HuiMin

    2015-07-01

    Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries.

  14. Marine molecular biology: an emerging field of biological sciences.

    PubMed

    Thakur, Narsinh L; Jain, Roopesh; Natalio, Filipe; Hamer, Bojan; Thakur, Archana N; Müller, Werner E G

    2008-01-01

    An appreciation of the potential applications of molecular biology is of growing importance in many areas of life sciences, including marine biology. During the past two decades, the development of sophisticated molecular technologies and instruments for biomedical research has resulted in significant advances in the biological sciences. However, the value of molecular techniques for addressing problems in marine biology has only recently begun to be cherished. It has been proven that the exploitation of molecular biological techniques will allow difficult research questions about marine organisms and ocean processes to be addressed. Marine molecular biology is a discipline, which strives to define and solve the problems regarding the sustainable exploration of marine life for human health and welfare, through the cooperation between scientists working in marine biology, molecular biology, microbiology and chemistry disciplines. Several success stories of the applications of molecular techniques in the field of marine biology are guiding further research in this area. In this review different molecular techniques are discussed, which have application in marine microbiology, marine invertebrate biology, marine ecology, marine natural products, material sciences, fisheries, conservation and bio-invasion etc. In summary, if marine biologists and molecular biologists continue to work towards strong partnership during the next decade and recognize intellectual and technological advantages and benefits of such partnership, an exciting new frontier of marine molecular biology will emerge in the future.

  15. Biologically Based Restorative Management of Tooth Wear

    PubMed Central

    Kelleher, Martin G. D.; Bomfim, Deborah I.; Austin, Rupert S.

    2012-01-01

    The prevalence and severity of tooth wear is increasing in industrialised nations. Yet, there is no high-level evidence to support or refute any therapeutic intervention. In the absence of such evidence, many currently prevailing management strategies for tooth wear may be failing in their duty of care to first and foremost improve the oral health of patients with this disease. This paper promotes biologically sound approaches to the management of tooth wear on the basis of current best evidence of the aetiology and clinical features of this disease. The relative risks and benefits of the varying approaches to managing tooth wear are discussed with reference to long-term follow-up studies. Using reference to ethical standards such as “The Daughter Test”, this paper presents case reports of patients with moderate-to-severe levels of tooth wear managed in line with these biologically sound principles. PMID:22315608

  16. Preference for point-light human biological motion in newborns: contribution of translational displacement.

    PubMed

    Bidet-Ildei, Christel; Kitromilides, Elenitsa; Orliaguet, Jean-Pierre; Pavlova, Marina; Gentaz, Edouard

    2014-01-01

    In human newborns, spontaneous visual preference for biological motion is reported to occur at birth, but the factors underpinning this preference are still in debate. Using a standard visual preferential looking paradigm, 4 experiments were carried out in 3-day-old human newborns to assess the influence of translational displacement on perception of human locomotion. Experiment 1 shows that human newborns prefer a point-light walker display representing human locomotion as if on a treadmill over random motion. However, no preference for biological movement is observed in Experiment 2 when both biological and random motion displays are presented with translational displacement. Experiments 3 and 4 show that newborns exhibit preference for translated biological motion (Experiment 3) and random motion (Experiment 4) displays over the same configurations moving without translation. These findings reveal that human newborns have a preference for the translational component of movement independently of the presence of biological kinematics. The outcome suggests that translation constitutes the first step in development of visual preference for biological motion. PsycINFO Database Record (c) 2014 APA, all rights reserved.

  17. Converting differential-equation models of biological systems to membrane computing.

    PubMed

    Muniyandi, Ravie Chandren; Zin, Abdullah Mohd; Sanders, J W

    2013-12-01

    This paper presents a method to convert the deterministic, continuous representation of a biological system by ordinary differential equations into a non-deterministic, discrete membrane computation. The dynamics of the membrane computation is governed by rewrite rules operating at certain rates. That has the advantage of applying accurately to small systems, and to expressing rates of change that are determined locally, by region, but not necessary globally. Such spatial information augments the standard differentiable approach to provide a more realistic model. A biological case study of the ligand-receptor network of protein TGF-β is used to validate the effectiveness of the conversion method. It demonstrates the sense in which the behaviours and properties of the system are better preserved in the membrane computing model, suggesting that the proposed conversion method may prove useful for biological systems in particular. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  18. Initiatives in biological research in Indian psychiatry

    PubMed Central

    Shrivatava, Amresh

    2010-01-01

    Biological psychiatry is an exploratory science for mental health. These biological changes provide some explicit insight into the complex area of ‘brain-mind and behavior’. One major achievement of research in biological field is the finding to explain how biological factors cause changes in behavior. In India, we have a clear history of initiatives in research from a biological perspective, which goes back to 1958. In the last 61 years, this field has seen significant evolution, precision and effective utilization of contemporary technological advances. It is a matter of great pride to see that in spite of difficult times in terms of challenges of practice and services, administration, resource, funding and manpower the zest for research was very forthcoming. There was neither dedicated time nor any funding for conducting research. It came from the intellectual insight of our fore fathers in the field of mental health to gradually grow to the state of strategic education in research, training in research, international research collaborations and setting up of internationally accredited centers. During difficult economic conditions in the past, the hypothesis tested and conclusions derived have not been so important. It is more important how it was done, how it was made possible and how robust traditions were established. Almost an entire spectrum of biological research has been touched upon by Indian researchers. Some of these are electroconvulsive therapy, biological markers, neurocognition, neuroimaging, neuroendocrine, neurochemistry, electrophysiology and genetics. A lot has been published given the limited space in the Indian Journal of Psychiatry and other medical journals published in India. A large body of biological research conducted on Indian patients has also been published in International literature (which I prefer to call non-Indian journals). Newer research questions in biological psychiatry, keeping with trend of international standards are

  19. Thermal behavior of IDOT integral abutment bridges and proposed design modifications.

    DOT National Transportation Integrated Search

    2013-05-01

    The Illinois Department of Transportation (IDOT) has increasingly constructed integral abutment bridges (IABs) : over the past few decades, similar to those in many other states. Because the length and skew limitations : currently employed by IDOT ha...

  20. Preapproval and postapproval availability of published comparative efficacy research on biological agents.

    PubMed

    Thomas, Rachel Hutchins; Freeman, Maisha Kelly; Hughes, Peter J

    2013-07-15

    Preapproval and postapproval availability of published comparative efficacy studies on biological agents approved between 2000 and 2010 was investigated. Approval packages published on the Food and Drug Administration (FDA) website were examined for all biological agents approved between 2000 and 2010 to determine if comparative efficacy studies were available at the time of FDA approval. The availability of comparative efficacy studies published subsequent to approval was determined by searching PubMed for randomized, active-controlled experimental or observational study designs that measured efficacy as the primary endpoint and were relevant to the original FDA-approved indication. From 2000 to 2010, 107 biological agents were approved by FDA. Of the biological agents with alternative treatments, 54.6% had comparative efficacy data available at the time of approval. Although standard-reviewed biological agents were more likely to have comparative efficacy trials included in the FDA approval packages than priority-reviewed biological agents, statistically significant differences are unlikely. Subsequent to approval, 58.1% of biological agents had at least one published comparative efficacy trial, representing a 3.5% absolute increase in the availability of comparative efficacy studies since the time of approval. Vaccines and biological agents in the hematologic diseases, oncology, and miscellaneous diseases classes had fewer published postapproval comparative efficacy studies per agent compared with the overall group of biological agents. Nearly half of all biological agents approved for marketing between 2000 and 2010 lacked publicly accessible, active-controlled efficacy studies at the time of drug approval; a slightly greater proportion of biological agents had comparative efficacy data published subsequent to their approval.

  1. Interacting domain-specific languages with biological problem solving environments

    NASA Astrophysics Data System (ADS)

    Cickovski, Trevor M.

    Iteratively developing a biological model and verifying results with lab observations has become standard practice in computational biology. This process is currently facilitated by biological Problem Solving Environments (PSEs), multi-tiered and modular software frameworks which traditionally consist of two layers: a computational layer written in a high level language using design patterns, and a user interface layer which hides its details. Although PSEs have proven effective, they still enforce some communication overhead between biologists refining their models through repeated comparison with experimental observations in vitro or in vivo, and programmers actually implementing model extensions and modifications within the computational layer. I illustrate the use of biological Domain-Specific Languages (DSLs) as a middle-level PSE tier to ameliorate this problem by providing experimentalists with the ability to iteratively test and develop their models using a higher degree of expressive power compared to a graphical interface, while saving the requirement of general purpose programming knowledge. I develop two radically different biological DSLs: XML-based BIOLOGO will model biological morphogenesis using a cell-centered stochastic cellular automaton and translate into C++ modules for an object-oriented PSE C OMPUCELL3D, and MDLab will provide a set of high-level Python libraries for running molecular dynamics simulations, using wrapped functionality from the C++ PSE PROTOMOL. I describe each language in detail, including its its roles within the larger PSE and its expressibility in terms of representable phenomena, and a discussion of observations from users of the languages. Moreover I will use these studies to draw general conclusions about biological DSL development, including dependencies upon the goals of the corresponding PSE, strategies, and tradeoffs.

  2. Computational intelligence approaches for pattern discovery in biological systems.

    PubMed

    Fogel, Gary B

    2008-07-01

    Biology, chemistry and medicine are faced by tremendous challenges caused by an overwhelming amount of data and the need for rapid interpretation. Computational intelligence (CI) approaches such as artificial neural networks, fuzzy systems and evolutionary computation are being used with increasing frequency to contend with this problem, in light of noise, non-linearity and temporal dynamics in the data. Such methods can be used to develop robust models of processes either on their own or in combination with standard statistical approaches. This is especially true for database mining, where modeling is a key component of scientific understanding. This review provides an introduction to current CI methods, their application to biological problems, and concludes with a commentary about the anticipated impact of these approaches in bioinformatics.

  3. Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

    PubMed

    Mi, Huaiyu; Schreiber, Falk; Moodie, Stuart; Czauderna, Tobias; Demir, Emek; Haw, Robin; Luna, Augustin; Le Novère, Nicolas; Sorokin, Anatoly; Villéger, Alice

    2015-09-04

    The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Activity Flow language represents the influences of activities among various entities within a network. Unlike SBGN PD and ER that focus on the entities and their relationships with others, SBGN AF puts the emphasis on the functions (or activities) performed by the entities, and their effects to the functions of the same or other entities. The nodes (elements) describe the biological activities of the entities, such as protein kinase activity, binding activity or receptor activity, which can be easily mapped to Gene Ontology molecular function terms. The edges (connections) provide descriptions of relationships (or influences) between the activities, e.g., positive influence and negative influence. Among all three languages of SBGN, AF is the closest to signaling pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

  4. Standards for the Protection of Skin Barrier Function.

    PubMed

    Giménez-Arnau, Ana

    2016-01-01

    The skin is a vital organ, and through our skin we are in close contact with the entire environment. If we lose our skin we lose our life. The barrier function of the skin is mainly driven by the sophisticated epidermis in close relationship with the dermis. The epidermal epithelium is a mechanically, chemically, biologically and immunologically active barrier submitted to continuous turnover. The barrier function of the skin needs to be protected and restored. Its own physiology allows its recovery, but many times this is not sufficient. This chapter is focused on the standards to restore, treat and prevent barrier function disruption. These standards were developed from a scientific, academic and clinical point of view. There is a lack of standardized administrative recommendations. Still, there is a walk to do that will help to reduce the social and economic burden of diseases characterized by an abnormal skin barrier function. © 2016 S. Karger AG, Basel.

  5. Academic Preparation in Biology and Advocacy for Teaching Evolution: Biology versus Non-Biology Teachers

    ERIC Educational Resources Information Center

    Nehm, Ross H.; Kim, Sun Young; Sheppard, Keith

    2009-01-01

    Despite considerable focus on evolution knowledge-belief relationships, little research has targeted populations with strong content backgrounds, such as undergraduate degrees in biology. This study (1) measured precertified biology and non-biology teachers' (n = 167) knowledge of evolution and the nature of science; (2) quantified teacher…

  6. A cumulative index to a continuing bibliography on aerospace medicine and biology, January 1972

    NASA Technical Reports Server (NTRS)

    1972-01-01

    Subject coverage concentrates on the biological, physiological, psychological, and environmental effects to which man is subjected during and following simulated or actual flight in the earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Each entry consists of a standard citation accompanied by its abstract.

  7. [Biologics and mycobacterial diseases].

    PubMed

    Tsuyuguchi, Kazunari; Matsumoto, Tomoshige

    2013-03-01

    developing TB. Lastly, Dr. Matsumoto stressed the risk of discontinuing TNF-alpha inhibitor during treatment for tuberculosis. He showed from his clinical experience that TNF-alpha inhibitor can be safely used in active TB patient receiving effective antituberculosis chemotherapy and it is even more effective for prevention of paradoxical response. Active discussion was done about the four topics, including the matter beyond present guidelines. We hope these discussions will form the basis for the establishment of new guideline for the management of mycobacterial disease when using immunosuppressive agents including biologics. 1. The risk of developing tuberculosis (TB) and situations of screening for TB risk at administration of biologics-the case of rheumatoid arthritis: Shigeto TOHMA (Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital) We calculated the standardized incidence ratio (SIR) of TB from the clinical data on National Database of Rheumatic Diseases by iR-net in Japan (NinJa) and compared with the SIR of TB from the data of the post-marketing surveillances of five biologics. Among 43584 patient-years, forty patients developed TB. The SIR of TB in NinJa was 4.34 (95%CI: 3.00-5.69). According to the post-marketing surveillances of 5 biologics, the SIR of TB were 3.62-34.4. The incidence of TB in patients with RA was higher than general population in Japan, and was increased more by some biologics. We have to recognize the risk of TB when we start biologics therapy to patients with RA. Although the frequency of implementation of QuantiFERON test (QFT) had gradually increased, it was still limited to 41%. In order to predict the risk of developing TB and to prevent TB, it might be better to check all RA patients by QFT at time time of biologics administration. 2. Biologics and nontuberculous mycobacterial diseases: Hitoshi TOKUDA (Social Insurance Central General Hospital) Several topics about the

  8. Reference Standardization for Mass Spectrometry and High-resolution Metabolomics Applications to Exposome Research.

    PubMed

    Go, Young-Mi; Walker, Douglas I; Liang, Yongliang; Uppal, Karan; Soltow, Quinlyn A; Tran, ViLinh; Strobel, Frederick; Quyyumi, Arshed A; Ziegler, Thomas R; Pennell, Kurt D; Miller, Gary W; Jones, Dean P

    2015-12-01

    The exposome is the cumulative measure of environmental influences and associated biological responses throughout the lifespan, including exposures from the environment, diet, behavior, and endogenous processes. A major challenge for exposome research lies in the development of robust and affordable analytic procedures to measure the broad range of exposures and associated biologic impacts occurring over a lifetime. Biomonitoring is an established approach to evaluate internal body burden of environmental exposures, but use of biomonitoring for exposome research is often limited by the high costs associated with quantification of individual chemicals. High-resolution metabolomics (HRM) uses ultra-high resolution mass spectrometry with minimal sample preparation to support high-throughput relative quantification of thousands of environmental, dietary, and microbial chemicals. HRM also measures metabolites in most endogenous metabolic pathways, thereby providing simultaneous measurement of biologic responses to environmental exposures. The present research examined quantification strategies to enhance the usefulness of HRM data for cumulative exposome research. The results provide a simple reference standardization protocol in which individual chemical concentrations in unknown samples are estimated by comparison to a concurrently analyzed, pooled reference sample with known chemical concentrations. The approach was tested using blinded analyses of amino acids in human samples and was found to be comparable to independent laboratory results based on surrogate standardization or internal standardization. Quantification was reproducible over a 13-month period and extrapolated to thousands of chemicals. The results show that reference standardization protocol provides an effective strategy that will enhance data collection for cumulative exposome research. In principle, the approach can be extended to other types of mass spectrometry and other analytical methods. © The

  9. ESTABLISH AND STANDARDIZE METHODOLOGY FOR ...

    EPA Pesticide Factsheets

    Research is conducted to develop and standardize methods to detect and measure occurrence of human enteric viruses that cause waterborne disease. The viruses of concern include the emerging pathogens--hepatitis E virus and group B rotaviruses. Also of concern are the coxsackieviruses and echoviruses--two members of the Office of Water's Contaminant Candidate List (CCL). Under this task, indicators of fecal pollution are also being evaluated as to their importance in evaluating microbial water quality. Another focus of the research is to address the standardization, evaluation and promulgation of detection methods for bacterial viruses. Develop sensitive techniques to detect and identify emerging human waterborne pathogenic viruses and viruses on the CCL.Determine effectiveness of viral indicators to measure microbial quality in water matrices.Support activities: (a) culture and distribution of mammalian cells for Agency and scientific community research needs, (b) provide operator expertise for research requiring confocal and electron microscopy, (c) glassware cleaning, sterilization and biological waste disposal for the Cincinnati EPA facility, (d) operation of infectious pathogenic suite, (e) maintenance of walk-in constant temperature rooms and (f) provide Giardia cysts.

  10. Investigating How German Biology Teachers Use Three-Dimensional Physical Models in Classroom Instruction: a Video Study

    NASA Astrophysics Data System (ADS)

    Werner, Sonja; Förtsch, Christian; Boone, William; von Kotzebue, Lena; Neuhaus, Birgit J.

    2017-07-01

    To obtain a general understanding of science, model use as part of National Education Standards is important for instruction. Model use can be characterized by three aspects: (1) the characteristics of the model, (2) the integration of the model into instruction, and (3) the use of models to foster scientific reasoning. However, there were no empirical results describing the implementation of National Education Standards in science instruction concerning the use of models. Therefore, the present study investigated the implementation of different aspects of model use in German biology instruction. Two biology lessons on the topic neurobiology in grade nine of 32 biology teachers were videotaped (N = 64 videos). These lessons were analysed using an event-based coding manual according to three aspects of model described above. Rasch analysis of the coded categories was conducted and showed reliable measurement. In the first analysis, we identified 68 lessons where a total of 112 different models were used. The in-depth analysis showed that special aspects of an elaborate model use according to several categories of scientific reasoning were rarely implemented in biology instruction. A critical reflection of the used model (N = 25 models; 22.3%) and models to demonstrate scientific reasoning (N = 26 models; 23.2%) were seldom observed. Our findings suggest that pre-service biology teacher education and professional development initiatives in Germany have to focus on both aspects.

  11. Evaluating children's conservation biology learning at the zoo.

    PubMed

    Jensen, Eric

    2014-08-01

    Millions of children visit zoos every year with parents or schools to encounter wildlife firsthand. Public conservation education is a requirement for membership in professional zoo associations. However, in recent years zoos have been criticized for failing to educate the public on conservation issues and related biological concepts, such as animal adaptation to habitats. I used matched pre- and postvisit mixed methods questionnaires to investigate the educational value of zoo visits for children aged 7-15 years. The questionnaires gathered qualitative data from these individuals, including zoo-related thoughts and an annotated drawing of a habitat. A content analysis of these qualitative data produced the quantitative data reported in this article. I evaluated the relative learning outcomes of educator-guided and unguided zoo visits at London Zoo, both in terms of learning about conservation biology (measured by annotated drawings) and changing attitudes toward wildlife conservation (measured using thought-listing data). Forty-one percent of educator-guided visits and 34% of unguided visits resulted in conservation biology-related learning. Negative changes in children's understanding of animals and their habitats were more prevalent in unguided zoo visits. Overall, my results show the potential educational value of visiting zoos for children. However, they also suggest that zoos' standard unguided interpretive materials are insufficient for achieving the best outcomes for visiting children. These results support a theoretical model of conservation biology learning that frames conservation educators as toolmakers who develop conceptual resources to enhance children's understanding of science. © 2014 Society for Conservation Biology.

  12. High Standards or a High Standard of Standardness?

    ERIC Educational Resources Information Center

    McWilliam, Erica

    2010-01-01

    This paper explores the difference between "high standards" and a "high standard of standardness" of professional service provision in teacher-librarianship. That is to say, it explores the difference between a demonstrated deep commitment to 21st century learning ("high standards") and demonstrated compliance with a pre-determined checklist of…

  13. The phytotronist and the phenotype: plant physiology, Big Science, and a Cold War biology of the whole plant.

    PubMed

    Munns, David P D

    2015-04-01

    This paper describes how, from the early twentieth century, and especially in the early Cold War era, the plant physiologists considered their discipline ideally suited among all the plant sciences to study and explain biological functions and processes, and ranked their discipline among the dominant forms of the biological sciences. At their apex in the late-1960s, the plant physiologists laid claim to having discovered nothing less than the "basic laws of physiology." This paper unwraps that claim, showing that it emerged from the construction of monumental big science laboratories known as phytotrons that gave control over the growing environment. Control meant that plant physiologists claimed to be able to produce a standard phenotype valid for experimental biology. Invoking the standards of the physical sciences, the plant physiologists heralded basic biological science from the phytotronic produced phenotype. In the context of the Cold War era, the ability to pursue basic science represented the highest pinnacle of standing within the scientific community. More broadly, I suggest that by recovering the history of an underappreciated discipline, plant physiology, and by establishing the centrality of the story of the plant sciences in the history of biology can historians understand the massive changes wrought to biology by the conceptual emergence of the molecular understanding of life, the dominance of the discipline of molecular biology, and the rise of biotechnology in the 1980s. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Quality assurance of chemical ingredient classification for the National Drug File - Reference Terminology.

    PubMed

    Zheng, Ling; Yumak, Hasan; Chen, Ling; Ochs, Christopher; Geller, James; Kapusnik-Uner, Joan; Perl, Yehoshua

    2017-09-01

    The National Drug File - Reference Terminology (NDF-RT) is a large and complex drug terminology consisting of several classification hierarchies on top of an extensive collection of drug concepts. These hierarchies provide important information about clinical drugs, e.g., their chemical ingredients, mechanisms of action, dosage form and physiological effects. Within NDF-RT such information is represented using tens of thousands of roles connecting drugs to classifications. In previous studies, we have introduced various kinds of Abstraction Networks to summarize the content and structure of terminologies in order to facilitate their visual comprehension, and support quality assurance of terminologies. However, these previous kinds of Abstraction Networks are not appropriate for summarizing the NDF-RT classification hierarchies, due to its unique structure. In this paper, we present the novel Ingredient Abstraction Network (IAbN) to summarize, visualize and support the audit of NDF-RT's Chemical Ingredients hierarchy and its associated drugs. A common theme in our quality assurance framework is to use characterizations of sets of concepts, revealed by the Abstraction Network structure, to capture concepts, the modeling of which is more complex than for other concepts. For the IAbN, we characterize drug ingredient concepts as more complex if they belong to IAbN groups with multiple parent groups. We show that such concepts have a statistically significantly higher rate of errors than a control sample and identify two especially common patterns of errors. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Semantic Web meets Integrative Biology: a survey.

    PubMed

    Chen, Huajun; Yu, Tong; Chen, Jake Y

    2013-01-01

    Integrative Biology (IB) uses experimental or computational quantitative technologies to characterize biological systems at the molecular, cellular, tissue and population levels. IB typically involves the integration of the data, knowledge and capabilities across disciplinary boundaries in order to solve complex problems. We identify a series of bioinformatics problems posed by interdisciplinary integration: (i) data integration that interconnects structured data across related biomedical domains; (ii) ontology integration that brings jargons, terminologies and taxonomies from various disciplines into a unified network of ontologies; (iii) knowledge integration that integrates disparate knowledge elements from multiple sources; (iv) service integration that build applications out of services provided by different vendors. We argue that IB can benefit significantly from the integration solutions enabled by Semantic Web (SW) technologies. The SW enables scientists to share content beyond the boundaries of applications and websites, resulting into a web of data that is meaningful and understandable to any computers. In this review, we provide insight into how SW technologies can be used to build open, standardized and interoperable solutions for interdisciplinary integration on a global basis. We present a rich set of case studies in system biology, integrative neuroscience, bio-pharmaceutics and translational medicine, to highlight the technical features and benefits of SW applications in IB.

  16. The Global Genome Biodiversity Network (GGBN) Data Standard specification

    PubMed Central

    Droege, G.; Barker, K.; Seberg, O.; Coddington, J.; Benson, E.; Berendsohn, W. G.; Bunk, B.; Butler, C.; Cawsey, E. M.; Deck, J.; Döring, M.; Flemons, P.; Gemeinholzer, B.; Güntsch, A.; Hollowell, T.; Kelbert, P.; Kostadinov, I.; Kottmann, R.; Lawlor, R. T.; Lyal, C.; Mackenzie-Dodds, J.; Meyer, C.; Mulcahy, D.; Nussbeck, S. Y.; O'Tuama, É.; Orrell, T.; Petersen, G.; Robertson, T.; Söhngen, C.; Whitacre, J.; Wieczorek, J.; Yilmaz, P.; Zetzsche, H.; Zhang, Y.; Zhou, X.

    2016-01-01

    Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today’s ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard. Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard PMID:27694206

  17. The Global Genome Biodiversity Network (GGBN) Data Standard specification.

    PubMed

    Droege, G; Barker, K; Seberg, O; Coddington, J; Benson, E; Berendsohn, W G; Bunk, B; Butler, C; Cawsey, E M; Deck, J; Döring, M; Flemons, P; Gemeinholzer, B; Güntsch, A; Hollowell, T; Kelbert, P; Kostadinov, I; Kottmann, R; Lawlor, R T; Lyal, C; Mackenzie-Dodds, J; Meyer, C; Mulcahy, D; Nussbeck, S Y; O'Tuama, É; Orrell, T; Petersen, G; Robertson, T; Söhngen, C; Whitacre, J; Wieczorek, J; Yilmaz, P; Zetzsche, H; Zhang, Y; Zhou, X

    2016-01-01

    Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today's ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard.Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard. © The Author(s) 2016. Published by Oxford University Press.

  18. Biological Agents

    MedlinePlus

    ... E-Tools Safety and Health Topics / Biological Agents Biological Agents This page requires that javascript be enabled ... 202) 693-2300 if additional assistance is required. Biological Agents Menu Overview In Focus: Ebola Frederick A. ...

  19. [Analysis of varieties and standards of Leguminosae plants used in Tibetan medicine].

    PubMed

    Cao, Lan; Du, Xiao-lang; Zhong, Wei-hong; Zhong, Wei-jin; He, Jun-wei; Mu, Ze-jing; Zhong, Guo-yue

    2015-12-01

    In this paper, the domestic varieties and quality standard of Leguminosae medicinal plants used in Tibetan medicine were analyzed. The results showed that there were 36 genera and 142 species (including varieties), as well as 64 medicinal materials varieties of Leguminosae plants were recorded in relevant literatures. In relevant Tibetan standards and literatures, there are great differences in varieties, sources, used parts, and efficacy of medicinal plants. Among them, about 38.0% (including 54 species) of the endemic plants, about 25.4% (including 36 species) of the original plants have medicinal standard legal records, except 9 kinds of traditional Chinese medicine general quality standard more fairly completed, the most varieties have only description about characters, identification, etc. Therefore it is necessary to reinforce study for the herbal textual, resources and the use present situation, chemical components and biological activity, quality standard, medicinal terms specification, to promote establishment of quality standard system for variety-terminologies-sources of Tibetan medicinal plants.

  20. "I'm Not the Science Type": Effect of an Inquiry Biology Content Course on Preservice Elementary Teachers' Intentions about Teaching Science

    ERIC Educational Resources Information Center

    Weld, Jeffrey; Funk, Lucas

    2005-01-01

    Inquiry Into Life Science is a content biology course expressly for the fulfillment of the General Education life science laboratory course requirement of elementary education majors at this university. The course is modeled on the Teaching Standards and Content Standards of the National Science Education Standards [National Research Council.…

  1. Quantitative biology: where modern biology meets physical sciences.

    PubMed

    Shekhar, Shashank; Zhu, Lian; Mazutis, Linas; Sgro, Allyson E; Fai, Thomas G; Podolski, Marija

    2014-11-05

    Quantitative methods and approaches have been playing an increasingly important role in cell biology in recent years. They involve making accurate measurements to test a predefined hypothesis in order to compare experimental data with predictions generated by theoretical models, an approach that has benefited physicists for decades. Building quantitative models in experimental biology not only has led to discoveries of counterintuitive phenomena but has also opened up novel research directions. To make the biological sciences more quantitative, we believe a two-pronged approach needs to be taken. First, graduate training needs to be revamped to ensure biology students are adequately trained in physical and mathematical sciences and vice versa. Second, students of both the biological and the physical sciences need to be provided adequate opportunities for hands-on engagement with the methods and approaches necessary to be able to work at the intersection of the biological and physical sciences. We present the annual Physiology Course organized at the Marine Biological Laboratory (Woods Hole, MA) as a case study for a hands-on training program that gives young scientists the opportunity not only to acquire the tools of quantitative biology but also to develop the necessary thought processes that will enable them to bridge the gap between these disciplines. © 2014 Shekhar, Zhu, Mazutis, Sgro, Fai, and Podolski. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication 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).

  2. GoldenBraid 2.0: a comprehensive DNA assembly framework for plant synthetic biology.

    PubMed

    Sarrion-Perdigones, Alejandro; Vazquez-Vilar, Marta; Palací, Jorge; Castelijns, Bas; Forment, Javier; Ziarsolo, Peio; Blanca, José; Granell, Antonio; Orzaez, Diego

    2013-07-01

    Plant synthetic biology aims to apply engineering principles to plant genetic design. One strategic requirement of plant synthetic biology is the adoption of common standardized technologies that facilitate the construction of increasingly complex multigene structures at the DNA level while enabling the exchange of genetic building blocks among plant bioengineers. Here, we describe GoldenBraid 2.0 (GB2.0), a comprehensive technological framework that aims to foster the exchange of standard DNA parts for plant synthetic biology. GB2.0 relies on the use of type IIS restriction enzymes for DNA assembly and proposes a modular cloning schema with positional notation that resembles the grammar of natural languages. Apart from providing an optimized cloning strategy that generates fully exchangeable genetic elements for multigene engineering, the GB2.0 toolkit offers an evergrowing open collection of DNA parts, including a group of functionally tested, premade genetic modules to build frequently used modules like constitutive and inducible expression cassettes, endogenous gene silencing and protein-protein interaction tools, etc. Use of the GB2.0 framework is facilitated by a number of Web resources that include a publicly available database, tutorials, and a software package that provides in silico simulations and laboratory protocols for GB2.0 part domestication and multigene engineering. In short, GB2.0 provides a framework to exchange both information and physical DNA elements among bioengineers to help implement plant synthetic biology projects.

  3. The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs.

    PubMed

    Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Pocock, Matthew; Flanagan, Keith; Hallinan, Jennifer; Wipat, Anil

    2016-06-17

    Recently, synthetic biologists have developed the Synthetic Biology Open Language (SBOL), a data exchange standard for descriptions of genetic parts, devices, modules, and systems. The goals of this standard are to allow scientists to exchange designs of biological parts and systems, to facilitate the storage of genetic designs in repositories, and to facilitate the description of genetic designs in publications. In order to achieve these goals, the development of an infrastructure to store, retrieve, and exchange SBOL data is necessary. To address this problem, we have developed the SBOL Stack, a Resource Description Framework (RDF) database specifically designed for the storage, integration, and publication of SBOL data. This database allows users to define a library of synthetic parts and designs as a service, to share SBOL data with collaborators, and to store designs of biological systems locally. The database also allows external data sources to be integrated by mapping them to the SBOL data model. The SBOL Stack includes two Web interfaces: the SBOL Stack API and SynBioHub. While the former is designed for developers, the latter allows users to upload new SBOL biological designs, download SBOL documents, search by keyword, and visualize SBOL data. Since the SBOL Stack is based on semantic Web technology, the inherent distributed querying functionality of RDF databases can be used to allow different SBOL stack databases to be queried simultaneously, and therefore, data can be shared between different institutes, centers, or other users.

  4. A practical workflow for making anatomical atlases for biological research.

    PubMed

    Wan, Yong; Lewis, A Kelsey; Colasanto, Mary; van Langeveld, Mark; Kardon, Gabrielle; Hansen, Charles

    2012-01-01

    The anatomical atlas has been at the intersection of science and art for centuries. These atlases are essential to biological research, but high-quality atlases are often scarce. Recent advances in imaging technology have made high-quality 3D atlases possible. However, until now there has been a lack of practical workflows using standard tools to generate atlases from images of biological samples. With certain adaptations, CG artists' workflow and tools, traditionally used in the film industry, are practical for building high-quality biological atlases. Researchers have developed a workflow for generating a 3D anatomical atlas using accessible artists' tools. They used this workflow to build a mouse limb atlas for studying the musculoskeletal system's development. This research aims to raise the awareness of using artists' tools in scientific research and promote interdisciplinary collaborations between artists and scientists. This video (http://youtu.be/g61C-nia9ms) demonstrates a workflow for creating an anatomical atlas.

  5. INAA Application for Trace Element Determination in Biological Reference Material

    NASA Astrophysics Data System (ADS)

    Atmodjo, D. P. D.; Kurniawati, S.; Lestiani, D. D.; Adventini, N.

    2017-06-01

    Trace element determination in biological samples is often used in the study of health and toxicology. Determination change to its essentiality and toxicity of trace element require an accurate determination method, which implies that a good Quality Control (QC) procedure should be performed. In this study, QC for trace element determination in biological samples was applied by analyzing the Standard Reference Material (SRM) Bovine muscle 8414 NIST using Instrumental Neutron Activation Analysis (INAA). Three selected trace element such as Fe, Zn, and Se were determined. Accuracy of the elements showed as %recovery and precision as %coefficient of variance (%CV). The result showed that %recovery of Fe, Zn, and Se were in the range between 99.4-107%, 92.7-103%, and 91.9-112%, respectively, whereas %CV were 2.92, 3.70, and 5.37%, respectively. These results showed that INAA method is precise and accurate for trace element determination in biological matrices.

  6. Curriculum and course materials for a forensic DNA biology course.

    PubMed

    Elkins, Kelly M

    2014-01-01

    The Forensic Science Education Programs Accreditation Commission (FEPAC) requires accredited programs offer a "coherent curriculum" to ensure each student gains a "thorough grounding of the natural…sciences." Part of this curriculum includes completion of a minimum of 15 semester-hours forensic science coursework, nine of which can involve a class in forensic DNA biology. Departments that have obtained or are pursuing FEPAC accreditation can meet this requirement by offering a stand-alone forensic DNA biology course; however, materials necessary to instruct students are often homegrown and not standardized; in addition, until recently, the community lacked commercially available books, lab manuals, and teaching materials, and many of the best pedagogical resources were scattered across various peer-reviewed journals. The curriculum discussed below is an attempt to synthesize this disparate information, and although certainly not the only acceptable methodology, the below discussion represents "a way" for synthesizing and aggregating this information into a cohesive, comprehensive whole. Copyright © 2013 by The International Union of Biochemistry and Molecular Biology.

  7. Biological characterization of a novel in vitro cell irradiator

    PubMed Central

    Fowler, Tyler L.; Fisher, Michael M.; Bailey, Alison M.; Bednarz, Bryan P.

    2017-01-01

    To evaluate the overall robustness of a novel cellular irradiator we performed a series of well-characterized, dose-responsive assays to assess the consequences of DNA damage. We used a previously described novel irradiation system and a traditional 137Cs source to irradiate a cell line. The generation of reactive oxygen species was assessed using chloromethyl-H2DCFDA dye, the induction of DNA DSBs was observed using the comet assay, and the initiation of DNA break repair was assessed through γH2AX image cytometry. A high correlation between physical absorbed dose and biologic dose was seen for the production of intracellular reactive oxygen species, physical DNA double strand breaks, and modulation of the cellular double stand break pathway. The results compared favorably to irradiation with a traditional 137Cs source. The rapid, straightforward tests described form a reasonable approach for biologic characterization of novel irradiators. These additional testing metrics go beyond standard physics testing such as Monte Carlo simulation and thermo-luminescent dosimeter evaluation to confirm that a novel irradiator can produce the desired dose effects in vitro. Further, assessment of these biological metrics confirms that the physical handling of the cells during the irradiation process results in biologic effects that scale appropriately with dose. PMID:29232400

  8. Recommendations for accreditation of laboratories in molecular biology of hematologic malignancies.

    PubMed

    Flandrin-Gresta, Pascale; Cornillet, Pascale; Hayette, Sandrine; Gachard, Nathalie; Tondeur, Sylvie; Mauté, Carole; Cayuela, Jean-Michel

    2015-01-01

    Over recent years, the development of molecular biology techniques has improved the hematological diseases diagnostic and follow-up. Consequently, these techniques are largely used in the biological screening of these diseases; therefore the Hemato-oncology molecular diagnostics laboratories must be actively involved in the accreditation process according the ISO 15189 standard. The French group of molecular biologists (GBMHM) provides requirements for the implementation of quality assurance for the medical molecular laboratories. This guideline states the recommendations for the pre-analytical, analytical (methods validation procedures, quality controls, reagents), and post-analytical conditions. In addition, herein we state a strategy for the internal quality control management. These recommendations will be regularly updated.

  9. GlycoRDF: an ontology to standardize glycomics data in RDF.

    PubMed

    Ranzinger, Rene; Aoki-Kinoshita, Kiyoko F; Campbell, Matthew P; Kawano, Shin; Lütteke, Thomas; Okuda, Shujiro; Shinmachi, Daisuke; Shikanai, Toshihide; Sawaki, Hiromichi; Toukach, Philip; Matsubara, Masaaki; Yamada, Issaku; Narimatsu, Hisashi

    2015-03-15

    Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/). © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 485

    NASA Technical Reports Server (NTRS)

    1999-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP-1999-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract. The NASA CASI price code table, addresses of organizations, and document availability information are included before the abstract section. Two indexes-subject and author are included after the abstract section.

  11. Aerospace Medicine and Biology: A Continuing Bibliography With Indexes. Supplement 506

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP#2000-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract. The NASA CASI price code table, addresses of organizations, and document availability information are included before the abstract section. Two indexes- subject and author are included after the abstract section.

  12. Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 496

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP#2000-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth#s atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract. The NASA CASI price code table, addresses of organizations, and document availability information are included before the abstract section. Two indexes#subject and author are included after the abstract section.

  13. Aerospace Medicine and Biology: A Continuing Bibliography With Indexes. Supplement 499

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP#1999-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth#s atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract. The NASA CASI price code table, addresses of organizations, and document availability information are included before the abstract section. Two indexes-subject and author are included after the abstract section.

  14. Perception of Science Standards' Effectiveness and Their Implementation by Science Teachers

    NASA Astrophysics Data System (ADS)

    Klieger, Aviva; Yakobovitch, Anat

    2011-06-01

    The introduction of standards into the education system poses numerous challenges and difficulties. As with any change, plans should be made for teachers to understand and implement the standards. This study examined science teachers' perceptions of the effectiveness of the standards for teaching and learning, and the extent and ease/difficulty of implementing science standards in different grades. The research used a mixed methods approach, combining qualitative and quantitative research methods. The research tools were questionnaires that were administered to elementary school science teachers. The majority of the teachers perceived the standards in science as effective for teaching and learning and only a small minority viewed them as restricting their pedagogical autonomy. Differences were found in the extent of implementation of the different standards and between different grades. The teachers perceived a different degree of difficulty in the implementation of the different standards. The standards experienced as easiest to implement were in the field of biology and materials, whereas the standards in earth sciences and the universe and technology were most difficult to implement, and are also those evaluated by the teachers as being implemented to the least extent. Exposure of teachers' perceptions on the effectiveness of standards and the implementation of the standards may aid policymakers in future planning of teachers' professional development for the implementation of standards.

  15. Petrology, Mineralogy, and Trace Element Geochemistry of Yuanyang

    NASA Astrophysics Data System (ADS)

    Wang, H. Y.; Xu, W. B.

    2016-09-01

    Yuanyang was found in Yunnan in 2010. Yuanyang has a rusted surface, and there are also some corroded materials inside. The major phases in Yuanyang are kamacite (Ni 4.88-6.21 wt%) and taenite (Ni 26.13-50.27 wt%). The minor ones are schreibersite, sphalerite, and carlsbergite. Yuanyang is a coarse octahedrite with a high content of kamacite (80 vol%). No silicate inclusions are found in Yuanyang. The instrumental neutron activation analysis (INAA) of Yuanyang reveals that it is a low-Ni (7 wt%) and low-Au (1.565 ppm) iron. Yuanyang is an IAB-MG iron. The Ir content (1.00 ppm) of Yuanyang is relatively low compared to other IAB-MG irons. This is probably due to the partial melting of Ir-rich phase in its parent body during an impact event.

  16. 7 CFR 205.203 - Soil fertility and crop nutrient management practice standard.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 3 2014-01-01 2014-01-01 false Soil fertility and crop nutrient management practice... Requirements § 205.203 Soil fertility and crop nutrient management practice standard. (a) The producer must..., and biological condition of soil and minimize soil erosion. (b) The producer must manage crop...

  17. 7 CFR 205.203 - Soil fertility and crop nutrient management practice standard.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 3 2013-01-01 2013-01-01 false Soil fertility and crop nutrient management practice... Requirements § 205.203 Soil fertility and crop nutrient management practice standard. (a) The producer must..., and biological condition of soil and minimize soil erosion. (b) The producer must manage crop...

  18. 7 CFR 205.203 - Soil fertility and crop nutrient management practice standard.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 3 2012-01-01 2012-01-01 false Soil fertility and crop nutrient management practice... Requirements § 205.203 Soil fertility and crop nutrient management practice standard. (a) The producer must..., and biological condition of soil and minimize soil erosion. (b) The producer must manage crop...

  19. 7 CFR 205.203 - Soil fertility and crop nutrient management practice standard.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 3 2011-01-01 2011-01-01 false Soil fertility and crop nutrient management practice... Requirements § 205.203 Soil fertility and crop nutrient management practice standard. (a) The producer must..., and biological condition of soil and minimize soil erosion. (b) The producer must manage crop...

  20. [Research progress on breeding standard of medicinal animals and discussion on several key problems].

    PubMed

    Zhou, Yi-Quan; Qu, Xian-You; Yang, Guang; Li, Jun-de; Su, Yan; Li, Ying

    2016-12-01

    Medicinal animal breeding standards is regarded as the law to normalize relevant production that can guarantee the quality of traditional Chinese medicine of animal category. The article summarized the medicinal animal resources in our country and the present condition of medicinal animal breeding standards. It considered the current animal breeding standards system was in adequate, not only the quantity of breeding standards, the standard content and index were also uncomprehensive, which is not conducive to the scientific and orderly development and utilization of medicinal animal resources. The article pointed out that the development of the basic standards, environmental control, feed quality, raising management, inspection and quarantine should be included into the medicinal animal breeding standards, and the medicinal animal breeding standards content framework was introduced. Meanwhile, animal welfare, biological safety and file management should be concerned during the process of research. Hope the article has good reference value to medicinal animal breeding standards establishment and production management. Copyright© by the Chinese Pharmaceutical Association.

  1. The Relationships Between Epistemic Beliefs in Biology and Approaches to Learning Biology Among Biology-Major University Students in Taiwan

    NASA Astrophysics Data System (ADS)

    Lin, Yi-Chun; Liang, Jyh-Chong; Tsai, Chin-Chung

    2012-12-01

    The aim of this study was to investigate the relationships between students' epistemic beliefs in biology and their approaches to learning biology. To this end, two instruments, the epistemic beliefs in biology and the approaches to learning biology surveys, were developed and administered to 520 university biology students, respectively. By and large, it was found that the students reflected "mixed" motives in biology learning, while those who had more sophisticated epistemic beliefs tended to employ deep strategies. In addition, the results of paired t tests revealed that the female students were more likely to possess beliefs about biological knowledge residing in external authorities, to believe in a right answer, and to utilize rote learning as a learning strategy. Moreover, compared to juniors and seniors, freshmen and sophomores tended to hold less mature views on all factors of epistemic beliefs regarding biology. Another comparison indicated that theoretical biology students (e.g. students majoring in the Department of Biology) tended to have more mature beliefs in learning biology and more advanced strategies for biology learning than those students studying applied biology (e.g. in the Department of Biotechnology). Stepwise regression analysis, in general, indicated that students who valued the role of experiments and justify epistemic assumptions and knowledge claims based on evidence were more oriented towards having mixed motives and utilizing deep strategies to learn biology. In contrast, students who believed in the certainty of biological knowledge were more likely to adopt rote learning strategies and to aim to qualify in biology.

  2. Request for Travel Funds for Systems Radiation Biology Workshop

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

    Barcellos-Hoff, Mary Helen

    The 3rd International Systems Radiation Biology Workshop brought together the major European, US and Japanese research programs on radiation risk as well as selected experts representing systems biological approaches to discuss how the new methodologies could be best exploited for low dose research. A significant part of the workshop was devoted to discussions organised as breakout group sessions. To facilitate discussions number of participants was limited to 60 persons. To achieve the goals of this symposium in this international conference, support from DOE is vital. Hence, this proposal requested support in the amount of $15,000 to cover the travel expensesmore » of international experts and radiation biology scientists from the United States. This supporting mechanism was clearly identified to the selected US participants as a conference support award from the DOE (See attached PDF). The workshop was an outstanding opportunity to strengthen interactions between leading experts in the emerging areas of radiation sciences, and will also provide opportunities for younger scientists to meet with experts and discuss their results. This workshop was designed to endorse active engagement in international collaboration. A major objective of this conference was to effectively communicate research results, in order to ensure that current thinking reflects sound science of radiation biology. Further, this international event addressed the use and success of scientific initiatives in radiation biology for policymakers, standard-setters, and the general public.« less

  3. ASTM International Workshop on Standards & Measurements for Tissue Engineering Scaffolds

    PubMed Central

    Simon, Carl G.; Yaszemski, Michael J.; Ratcliffe, Anthony; Tomlins, Paul; Luginbuehl, Reto; Tesk, John A.

    2016-01-01

    The “Workshop on Standards & Measurements for Tissue Engineering Scaffolds” was held on May 21, 2013 in Indianapolis, IN and was sponsored by the ASTM International (ASTM). The purpose of the workshop was to identify the highest priority items for future standards work for scaffolds used in the development and manufacture of tissue engineered medical products (TEMPs). Eighteen speakers and 78 attendees met to assess current scaffold standards and to prioritize needs for future standards. A key finding was that the ASTM TEMPs subcommittees (F04.41-46) have many active “guide” documents for educational purposes, but that few standard “test methods” or “practices” have been published. Overwhelmingly, the most clearly identified need was standards for measuring the structure of scaffolds, followed by standards for biological characterization, including in vitro testing, animal models and cell-material interactions. The third most pressing need was to develop standards for assessing the mechanical properties of scaffolds. Additional needs included standards for assessing scaffold degradation, clinical outcomes with scaffolds, effects of sterilization on scaffolds, scaffold composition and drug release from scaffolds. Discussions also highlighted the need for additional scaffold reference materials and the need to use them for measurement traceability. Finally, dialogue emphasized the needs to promote the use of standards in scaffold fabrication, characterization, and commercialization and to assess the use and impact of standards in the TEMPs community. Many scaffold standard needs have been identified and focus should now turn to generating these standards to support the use of scaffolds in TEMPs. PMID:25220952

  4. The Secret Lives of Cepheids: Searching for Evolutionary Changes Using Photoelectric Photometry

    NASA Astrophysics Data System (ADS)

    Toce, Michael; Guinan, Edward F.; Engle, Scott G.; Wasatonic, Richard P.

    2016-01-01

    Classical Cepheids are pulsating, yellow supergiants and one of the most important classes of variable stars. They have a direct linear relationship between their period and luminosity and thus serve as crucial "standard candles" for determining the cosmic distance scale and measuring the Hubble Constant. Also, Cepheids play a fundamental role in the calibration of Type Ia supernovae, indicating that the expansion of the Universe is accelerating, and also infer the existence of dark energy. Studies of changes in their pulsation periods and amplitudes reveal evolutionary changes too subtle to detect directly, and understanding these various characteristics of Cepheids is critical to their use as high-precision standard candles. To this end, the Villanova Secret Lives of Cepheids (SLiC) program was created as a comprehensive study of Cepheid behavior, evolution, pulsations, atmospheres, heating dynamics, shocks and winds. As part of the SLiC program, ground-based photometry is being carried out of small sample of bright Cepheids. The observations are being made using the 14-inch reflector telescope at Villanova Campus Observatory. Mounted on the telescope is a SBIG photoelectric photometer equipped with standard Johnson UBVRI filters. Photometry is being carried out of the following stars along with their spectral type, period, and visual mag: X Cyg (F7Ib, ~16.39d, 6.47mag), DT Cyg (F7.5Ib, ~2.5d, 5.82mag), S Sge (G5Ibv, ~8.38d, 5.36mag), FF Aql (F6Ib, ~4.47d, 5.38mag), Eta Aql (F6Iab, ~7.18d,3.80mag), and Delta Cep (F5Iab, ~5.37d, 3.75mag). The primary scientific objectives are to obtain light curves to investigate possible evolutionary changes from small variations in luminosity, light amplitude and pulsation period. Special emphasis was placed on the classical Cepheid X Cyg due to recent changes in pulsation period, shown by Szabados via a phase jump in X Cyg's O-C (observed - calculated). X Cyg holds priority in our observations as we attempt to affirm or deny

  5. Biological Concepts. Student Manual. Biological Treatment Process Control.

    ERIC Educational Resources Information Center

    Carnegie, John W.

    This manual contains the textual material for a three-lesson unit which introduces students to the basic concepts applicable to all biological treatment systems. The general topic areas addressed in the lessons are: (1) the microorganisms found in biological systems; (2) the factors that affect the growth and health of biological systems; and (3)…

  6. 3D topography of biologic tissue by multiview imaging and structured light illumination

    NASA Astrophysics Data System (ADS)

    Liu, Peng; Zhang, Shiwu; Xu, Ronald

    2014-02-01

    Obtaining three-dimensional (3D) information of biologic tissue is important in many medical applications. This paper presents two methods for reconstructing 3D topography of biologic tissue: multiview imaging and structured light illumination. For each method, the working principle is introduced, followed by experimental validation on a diabetic foot model. To compare the performance characteristics of these two imaging methods, a coordinate measuring machine (CMM) is used as a standard control. The wound surface topography of the diabetic foot model is measured by multiview imaging and structured light illumination methods respectively and compared with the CMM measurements. The comparison results show that the structured light illumination method is a promising technique for 3D topographic imaging of biologic tissue.

  7. Experimental study of biological effects of leads and aluminum following oral administration.

    PubMed Central

    Krasovskiĭ, G N; Vasukovich, L Y; Chariev, O G

    1979-01-01

    A wide spectrum of the biological effects of lead and aluminum ions is noted during short-term and long-term oral administration to laboratory animals. The general toxic and gonadotoxic effects of these metals during a short-term experiment appeared to be identical, and the correlation of these effects was preserved during chronic experiments. Lead (0.03 mg/l.) and aluminum (0.5 mg/l.) concentrations in water may be dangerous to the health of the population, and hygienic standards are recommended for inclusion in the standard for drinking water quality. PMID:446457

  8. The value of closed-circuit rebreathers for biological research

    USGS Publications Warehouse

    Pyle, Richrad L.; Lobel, Phillip S.; Tomoleoni, Joseph

    2016-01-01

    Closed-circuit rebreathers have been used for underwater biological research since the late 1960s, but have only started to gain broader application within scientific diving organizations within the past two decades. Rebreathers offer certain specific advantages for such research, especially for research involving behavior and surveys that depend on unobtrusive observers or for a stealthy approach to wildlife for capture and tagging, research that benefits from extended durations underwater, and operations requiring access to relatively deep (>50 m) environments (especially in remote locations). Although many institutions have been slow to adopt rebreather technology within their diving programs, recent developments in rebreather technology that improve safety, standardize training requirements, and reduce costs of equipment and maintenance, will likely result in a trend of increasing utilization of rebreathers for underwater biological research.

  9. Positioning Genomics in Biology Education: Content Mapping of Undergraduate Biology Textbooks†

    PubMed Central

    Wernick, Naomi L. B.; Ndung’u, Eric; Haughton, Dominique; Ledley, Fred D.

    2014-01-01

    Biological thought increasingly recognizes the centrality of the genome in constituting and regulating processes ranging from cellular systems to ecology and evolution. In this paper, we ask whether genomics is similarly positioned as a core concept in the instructional sequence for undergraduate biology. Using quantitative methods, we analyzed the order in which core biological concepts were introduced in textbooks for first-year general and human biology. Statistical analysis was performed using self-organizing map algorithms and conventional methods to identify clusters of terms and their relative position in the books. General biology textbooks for both majors and nonmajors introduced genome-related content after text related to cell biology and biological chemistry, but before content describing higher-order biological processes. However, human biology textbooks most often introduced genomic content near the end of the books. These results suggest that genomics is not yet positioned as a core concept in commonly used textbooks for first-year biology and raises questions about whether such textbooks, or courses based on the outline of these textbooks, provide an appropriate foundation for understanding contemporary biological science. PMID:25574293

  10. Positioning genomics in biology education: content mapping of undergraduate biology textbooks.

    PubMed

    Wernick, Naomi L B; Ndung'u, Eric; Haughton, Dominique; Ledley, Fred D

    2014-12-01

    Biological thought increasingly recognizes the centrality of the genome in constituting and regulating processes ranging from cellular systems to ecology and evolution. In this paper, we ask whether genomics is similarly positioned as a core concept in the instructional sequence for undergraduate biology. Using quantitative methods, we analyzed the order in which core biological concepts were introduced in textbooks for first-year general and human biology. Statistical analysis was performed using self-organizing map algorithms and conventional methods to identify clusters of terms and their relative position in the books. General biology textbooks for both majors and nonmajors introduced genome-related content after text related to cell biology and biological chemistry, but before content describing higher-order biological processes. However, human biology textbooks most often introduced genomic content near the end of the books. These results suggest that genomics is not yet positioned as a core concept in commonly used textbooks for first-year biology and raises questions about whether such textbooks, or courses based on the outline of these textbooks, provide an appropriate foundation for understanding contemporary biological science.

  11. Biological Systems, Energy Sources, and Biology Teaching. Biology and Human Welfare.

    ERIC Educational Resources Information Center

    Tribe, Michael; Pritchard, Alan J.

    This five-chapter document (part of a series on biology and human welfare) focuses on biological systems as energy sources and on the teaching of this subject area. Chapter 1 discusses various topics related to energy and ecology, including biomass, photosynthesis and world energy balances, energy flow through ecosystems, and others. Chapter 2…

  12. SUPERNUMERARY RIBS IN DEVELOPMENTAL TOXICITY BIOASSAYS AND IN HUMAN POPULATIONS: INCIDENCE AND BIOLOGICAL SIGNIFICANCE

    EPA Science Inventory

    Abstract
    Supernumerary or accessory ribs (SNR), either lumbar (LSNR) or cervical (CSNR) are a common finding in standard developmental toxicology bioassays. The biological significance of these anomalies within the regulatory arena has been problematic and the subject of some...

  13. Translational environmental biology: cell biology informing conservation.

    PubMed

    Traylor-Knowles, Nikki; Palumbi, Stephen R

    2014-05-01

    Typically, findings from cell biology have been beneficial for preventing human disease. However, translational applications from cell biology can also be applied to conservation efforts, such as protecting coral reefs. Recent efforts to understand the cell biological mechanisms maintaining coral health such as innate immunity and acclimatization have prompted new developments in conservation. Similar to biomedicine, we urge that future efforts should focus on better frameworks for biomarker development to protect coral reefs. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology.

    PubMed

    Moore, Simon J; Lai, Hung-En; Kelwick, Richard J R; Chee, Soo Mei; Bell, David J; Polizzi, Karen Marie; Freemont, Paul S

    2016-10-21

    Golden Gate cloning is a prominent DNA assembly tool in synthetic biology for the assembly of plasmid constructs often used in combinatorial pathway optimization, with a number of assembly kits developed specifically for yeast and plant-based expression. However, its use for synthetic biology in commonly used bacterial systems such as Escherichia coli has surprisingly been overlooked. Here, we introduce EcoFlex a simplified modular package of DNA parts for a variety of applications in E. coli, cell-free protein synthesis, protein purification and hierarchical assembly of transcription units based on the MoClo assembly standard. The kit features a library of constitutive promoters, T7 expression, RBS strength variants, synthetic terminators, protein purification tags and fluorescence proteins. We validate EcoFlex by assembling a 68-part containing (20 genes) plasmid (31 kb), characterize in vivo and in vitro library parts, and perform combinatorial pathway assembly, using pooled libraries of either fluorescent proteins or the biosynthetic genes for the antimicrobial pigment violacein as a proof-of-concept. To minimize pathway screening, we also introduce a secondary module design site to simplify MoClo pathway optimization. In summary, EcoFlex provides a standardized and multifunctional kit for a variety of applications in E. coli synthetic biology.

  15. Informing Biological Design by Integration of Systems and Synthetic Biology

    PubMed Central

    Smolke, Christina D.; Silver, Pamela A.

    2011-01-01

    Synthetic biology aims to make the engineering of biology faster and more predictable. In contrast, systems biology focuses on the interaction of myriad components and how these give rise to the dynamic and complex behavior of biological systems. Here, we examine the synergies between these two fields. PMID:21414477

  16. Integral abutment bridge for Louisiana's soft and stiff soils.

    DOT National Transportation Integrated Search

    2016-03-01

    Integral abutment bridges (IABs) have been designed and constructed in a few US states in the past few : decades. The initial purpose of building such bridges was to eliminate the expansion joints and resolve the : joint-induced problems. Although IA...

  17. 78 FR 16665 - International Energy Agency Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-18

    ... DEPARTMENT OF ENERGY International Energy Agency Meetings AGENCY: Department of Energy. ACTION: Notice of meetings. SUMMARY: The Industry Advisory Board (IAB) to the International Energy Agency (IEA..., Department of Energy, 1000 Independence Avenue SW., Washington, DC 20585, 202-586- 3417. SUPPLEMENTARY...

  18. 76 FR 35869 - International Energy Agency meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-20

    ... DEPARTMENT OF ENERGY International Energy Agency meetings AGENCY: Department of Energy, DOE. ACTION: Notice of meetings. SUMMARY: The Industry Advisory Board (IAB) to the International Energy Agency..., Department of Energy, 1000 Independence Avenue, SW., Washington, DC 20585, 202-586-3417. SUPPLEMENTARY...

  19. 78 FR 36542 - International Energy Agency Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-18

    ... DEPARTMENT OF ENERGY International Energy Agency Meetings AGENCY: Department of Energy. ACTION: Notice of meetings. SUMMARY: The Industry Advisory Board (IAB) to the International Energy Agency (IEA.... Clark, Assistant General Counsel for International and National Security Programs, Department of Energy...

  20. 76 FR 14003 - International Energy Agency Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-15

    ... DEPARTMENT OF ENERGY International Energy Agency Meetings AGENCY: Department of Energy. ACTION: Notice of meetings. SUMMARY: The Industry Advisory Board (IAB) to the International Energy Agency (IEA... National Security Programs, Department of Energy, 1000 Independence Avenue, SW., Washington, DC 20585, 202...