Sample records for biological variability

  1. Biological Sampling Variability Study

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    Amidan, Brett G. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Hutchison, Janine R. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)


    There are many sources of variability that exist in the sample collection and analysis process. This paper addresses many, but not all, sources of variability. The main focus of this paper was to better understand and estimate variability due to differences between samplers. Variability between days was also studied, as well as random variability within each sampler. Experiments were performed using multiple surface materials (ceramic and stainless steel), multiple contaminant concentrations (10 spores and 100 spores), and with and without the presence of interfering material. All testing was done with sponge sticks using 10-inch by 10-inch coupons. Bacillus atrophaeus was used as the BA surrogate. Spores were deposited using wet deposition. Grime was coated on the coupons which were planned to include the interfering material (Section 3.3). Samples were prepared and analyzed at PNNL using CDC protocol (Section 3.4) and then cultured and counted. Five samplers were trained so that samples were taken using the same protocol. Each sampler randomly sampled eight coupons each day, four coupons with 10 spores deposited and four coupons with 100 spores deposited. Each day consisted of one material being tested. The clean samples (no interfering materials) were run first, followed by the dirty samples (coated with interfering material). There was a significant difference in recovery efficiency between the coupons with 10 spores deposited (mean of 48.9%) and those with 100 spores deposited (mean of 59.8%). There was no general significant difference between the clean and dirty (containing interfering material) coupons or between the two surface materials; however, there was a significant interaction between concentration amount and presence of interfering material. The recovery efficiency was close to the same for coupons with 10 spores deposited, but for the coupons with 100 spores deposited, the recovery efficiency for the dirty samples was significantly larger (65

  2. Biological variables and prognosis of DCIS. (United States)

    van de Vijver, Marc J


    Based on current knowledge, biological factors that have been investigated in ductal carcinoma in situ (DCIS) include histology of these lesions, the impact of margin status on local recurrence, and several genetic alterations. Optimal integration of these factors in guiding optimal therapy is of great importance, since the incidence of DCIS is rising as a result of population-based mammographic screening. Mastectomy will almost always cure patients with DCIS but represents overtreatment for many. Less extensive treatment options should combine an optimal cosmetic result with the same safety for outcome of disease as mastectomy. To guide such optimal treatment, histological classification is not sufficient and additional biological factors are being investigated for their ability to predict outcome for individual patients with DCIS. In this review, the histological classification of DCIS is described and in addition the emerging knowledge on genetic alterations is summarised. For clinical management of DCIS patients, genetic or other biological factors should be identified that can predict the risk of progression of DCIS to invasive breast cancer and distant metastases. At present, insufficient knowledge on prognostic and predictive factors in DCIS is available. Research in this area is hampered by the difficulties in obtaining DCIS tumour tissue, as the tumour cells grow in the lumen of pre-existing ducts and lobules. As the recurrence rates are relatively low and the most relevant clinical endpoint, distant metastases, is indeed very rare, large numbers of patients (hundreds to a few thousand) need to be studied. Integration of translational studies into clinical trials aimed at optimising the treatment of DCIS are required to achieve this goal.

  3. A comprehensive company database analysis of biological assay variability. (United States)

    Kramer, Christian; Dahl, Göran; Tyrchan, Christian; Ulander, Johan


    Analysis of data from various compounds measured in diverse biological assays is a central part of drug discovery research projects. However, no systematic overview of the variability in biological assays has been published and judgments on assay quality and robustness of data are often based on personal belief and experience within the drug discovery community. To address this we performed a reproducibility analysis of all biological assays at AstraZeneca between 2005 and 2014. We found an average experimental uncertainty of less than a twofold difference and no technologies or assay types had higher variability than others. This work suggests that robust data can be obtained from the most commonly applied biological assays.

  4. Technical variability is greater than biological variability in a microarray experiment but both are outweighed by changes induced by stimulation.

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    Penelope A Bryant

    Full Text Available INTRODUCTION: A central issue in the design of microarray-based analysis of global gene expression is that variability resulting from experimental processes may obscure changes resulting from the effect being investigated. This study quantified the variability in gene expression at each level of a typical in vitro stimulation experiment using human peripheral blood mononuclear cells (PBMC. The primary objective was to determine the magnitude of biological and technical variability relative to the effect being investigated, namely gene expression changes resulting from stimulation with lipopolysaccharide (LPS. METHODS AND RESULTS: Human PBMC were stimulated in vitro with LPS, with replication at 5 levels: 5 subjects each on 2 separate days with technical replication of LPS stimulation, amplification and hybridisation. RNA from samples stimulated with LPS and unstimulated samples were hybridised against common reference RNA on oligonucleotide microarrays. There was a closer correlation in gene expression between replicate hybridisations (0.86-0.93 than between different subjects (0.66-0.78. Deconstruction of the variability at each level of the experimental process showed that technical variability (standard deviation (SD 0.16 was greater than biological variability (SD 0.06, although both were low (SD<0.1 for all individual components. There was variability in gene expression both at baseline and after stimulation with LPS and proportion of cell subsets in PBMC was likely partly responsible for this. However, gene expression changes after stimulation with LPS were much greater than the variability from any source, either individually or combined. CONCLUSIONS: Variability in gene expression was very low and likely to improve further as technical advances are made. The finding that stimulation with LPS has a markedly greater effect on gene expression than the degree of variability provides confidence that microarray-based studies can be used to

  5. Variability for Biological Nitrogen Fixation Capacity in Beans (United States)

    As legumes, common beans have the capacity to form a symbiotic relationship with soil bacteria called rhizobia and fix nitrogen from the atmosphere. Common beans however are considered to be poor nitrogen fixers as compared to other legumes. Identification of genetic variability for N fixation capac...

  6. Estimation of relevant variables on high-dimensional biological patterns using iterated weighted kernel functions.

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    Sergio Rojas-Galeano

    Full Text Available BACKGROUND: The analysis of complex proteomic and genomic profiles involves the identification of significant markers within a set of hundreds or even thousands of variables that represent a high-dimensional problem space. The occurrence of noise, redundancy or combinatorial interactions in the profile makes the selection of relevant variables harder. METHODOLOGY/PRINCIPAL FINDINGS: Here we propose a method to select variables based on estimated relevance to hidden patterns. Our method combines a weighted-kernel discriminant with an iterative stochastic probability estimation algorithm to discover the relevance distribution over the set of variables. We verified the ability of our method to select predefined relevant variables in synthetic proteome-like data and then assessed its performance on biological high-dimensional problems. Experiments were run on serum proteomic datasets of infectious diseases. The resulting variable subsets achieved classification accuracies of 99% on Human African Trypanosomiasis, 91% on Tuberculosis, and 91% on Malaria serum proteomic profiles with fewer than 20% of variables selected. Our method scaled-up to dimensionalities of much higher orders of magnitude as shown with gene expression microarray datasets in which we obtained classification accuracies close to 90% with fewer than 1% of the total number of variables. CONCLUSIONS: Our method consistently found relevant variables attaining high classification accuracies across synthetic and biological datasets. Notably, it yielded very compact subsets compared to the original number of variables, which should simplify downstream biological experimentation.

  7. Combined model of intrinsic and extrinsic variability for computational network design with application to synthetic biology.

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    Tina Toni

    Full Text Available Biological systems are inherently variable, with their dynamics influenced by intrinsic and extrinsic sources. These systems are often only partially characterized, with large uncertainties about specific sources of extrinsic variability and biochemical properties. Moreover, it is not yet well understood how different sources of variability combine and affect biological systems in concert. To successfully design biomedical therapies or synthetic circuits with robust performance, it is crucial to account for uncertainty and effects of variability. Here we introduce an efficient modeling and simulation framework to study systems that are simultaneously subject to multiple sources of variability, and apply it to make design decisions on small genetic networks that play a role of basic design elements of synthetic circuits. Specifically, the framework was used to explore the effect of transcriptional and post-transcriptional autoregulation on fluctuations in protein expression in simple genetic networks. We found that autoregulation could either suppress or increase the output variability, depending on specific noise sources and network parameters. We showed that transcriptional autoregulation was more successful than post-transcriptional in suppressing variability across a wide range of intrinsic and extrinsic magnitudes and sources. We derived the following design principles to guide the design of circuits that best suppress variability: (i high protein cooperativity and low miRNA cooperativity, (ii imperfect complementarity between miRNA and mRNA was preferred to perfect complementarity, and (iii correlated expression of mRNA and miRNA--for example, on the same transcript--was best for suppression of protein variability. Results further showed that correlations in kinetic parameters between cells affected the ability to suppress variability, and that variability in transient states did not necessarily follow the same principles as variability in

  8. Regulation of Spatiotemporal Patterns by Biological Variability: General Principles and Applications to Dictyostelium discoideum.

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    Miriam Grace


    Full Text Available Spatiotemporal patterns often emerge from local interactions in a self-organizing fashion. In biology, the resulting patterns are also subject to the influence of the systematic differences between the system's constituents (biological variability. This regulation of spatiotemporal patterns by biological variability is the topic of our review. We discuss several examples of correlations between cell properties and the self-organized spatiotemporal patterns, together with their relevance for biology. Our guiding, illustrative example will be spiral waves of cAMP in a colony of Dictyostelium discoideum cells. Analogous processes take place in diverse situations (such as cardiac tissue, where spiral waves occur in potentially fatal ventricular fibrillation so a deeper understanding of this additional layer of self-organized pattern formation would be beneficial to a wide range of applications. One of the most striking differences between pattern-forming systems in physics or chemistry and those in biology is the potential importance of variability. In the former, system components are essentially identical with random fluctuations determining the details of the self-organization process and the resulting patterns. In biology, due to variability, the properties of potentially very few cells can have a driving influence on the resulting asymptotic collective state of the colony. Variability is one means of implementing a few-element control on the collective mode. Regulatory architectures, parameters of signaling cascades, and properties of structure formation processes can be "reverse-engineered" from observed spatiotemporal patterns, as different types of regulation and forms of interactions between the constituents can lead to markedly different correlations. The power of this biology-inspired view of pattern formation lies in building a bridge between two scales: the patterns as a collective state of a very large number of cells on the one hand

  9. Biologically variable respiration as a stochastic process in ventilation - a stochastic model study. (United States)

    Min, Kyongyob; Hosoi, Keita; Degami, Masayuki; Kinoshita, Yoshinori


    Based on the fractal bronchial tree, we introduced a function of "asynchronous phasic contractions of lobular bronchiole", which would generate fluctuations in tidal volumes. Stochastic control theory was able to describe a genesis of biological variability in spontaneous respirations using a Schroedinger wave function.

  10. Bayesian model accounting for within-class biological variability in Serial Analysis of Gene Expression (SAGE

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    Brentani Helena


    Full Text Available Abstract Background An important challenge for transcript counting methods such as Serial Analysis of Gene Expression (SAGE, "Digital Northern" or Massively Parallel Signature Sequencing (MPSS, is to carry out statistical analyses that account for the within-class variability, i.e., variability due to the intrinsic biological differences among sampled individuals of the same class, and not only variability due to technical sampling error. Results We introduce a Bayesian model that accounts for the within-class variability by means of mixture distribution. We show that the previously available approaches of aggregation in pools ("pseudo-libraries" and the Beta-Binomial model, are particular cases of the mixture model. We illustrate our method with a brain tumor vs. normal comparison using SAGE data from public databases. We show examples of tags regarded as differentially expressed with high significance if the within-class variability is ignored, but clearly not so significant if one accounts for it. Conclusion Using available information about biological replicates, one can transform a list of candidate transcripts showing differential expression to a more reliable one. Our method is freely available, under GPL/GNU copyleft, through a user friendly web-based on-line tool or as R language scripts at supplemental web-site.

  11. Biological movement variability during the sprint start: performance enhancement or hindrance? (United States)

    Bradshaw, Elizabeth J; Maulder, Peter S; Keogh, Justin W L


    In the current study, we quantified biological movement variability on the start and early acceleration phase of sprinting. Ten male athletes aged 17-23 years (100-m personal best: 10.87 +/- 0.36s) performed four 10-m sprints. Two 250-Hz cameras recorded the sagittal plane action to obtain the two-dimensional kinematics of the block start and initial strides from subsequent manually digitized APAS motion analysis. Infra-red timing lights (80Hz) were used to measure the 10-m sprinting times. The coefficient of variation (CV%) calculation was adjusted to separate biological movement variability (BCV%) from estimates of variability induced by technological error (SEM%) for each individual sprinter and measure. Pearson's product-moment correlation and linear regression analysis were used to establish relationships between measures of BCV% and 10-m sprint start performance (best 10-m time) or 10-m sprint start performance consistency (10-m time BCV%) using SPSS version 12.0. Measurement error markedly inflated traditional measures of movement variability (CV%) by up to 72%. Variability in task outcome measures was considerably lower than that observed in joint rotation velocities. Consistent generation of high horizontal velocity out of the blocks led to more stable and faster starting strides.

  12. An adapted F-test for homogeneity of variability in follow-on biological products. (United States)

    Yang, Jun; Zhang, Nan; Chow, Shein-Chung; Chi, Eric


    In recent years, follow-on biological products (biosimilars) have received much attention from both the biotechnology industry and the regulatory agencies, especially after the passage of the 2010 healthcare reform bill. Unlike the traditional small-molecule drug products, the development of biological products is not only more complicated but also sensitive to small changes (both mean and variation) in procedure/environment during the manufacturing process because of some fundamental differences between drug products and biological products. A small change will have an impact on the quality of the product and consequently the treatment effect. Thus, in addition to the assessment of biosimilarity in average, it was suggested that biosimilarity in variability between biological products should be assessed. In this article, we propose an adapted F-test for homogeneity of variances to assess biosimilarity in variability. We study the performance and concordance of the proposed adapted F-test and compare it with probability-based method by extensive Monte Carlo simulations.

  13. Temporal and spatial variability of soil biological activity at European scale (United States)

    Mallast, Janine; Rühlmann, Jörg


    The CATCH-C project aims to identify and improve the farm-compatibility of Soil Management Practices including to promote productivity, climate change mitigation and soil quality. The focus of this work concentrates on turnover conditions for soil organic matter (SOM). SOM is fundamental for the maintenance of quality and functions of soils while SOM storage is attributed a great importance in terms of climate change mitigation. The turnover conditions depend on soil biological activity characterized by climate and soil properties. Soil biological activity was investigated using two model concepts: a) Re_clim parameter within the ICBM (Introductory Carbon Balance Model) (Andrén & Kätterer 1997) states a climatic factor summarizing soil water storage and soil temperature and its influence on soil biological activity. b) BAT (biological active time) approach derived from model CANDY (CArbon and Nitrogen Dynamic) (Franko & Oelschlägel 1995) expresses the variation of soil moisture, soil temperature and soil aeration as a time scale and an indicator of biological activity for soil organic matter (SOM) turnover. During an earlier stage both model concepts, Re_clim and BAT, were applied based on a monthly data to assess spatial variability of turnover conditions across Europe. This hampers the investigation of temporal variability (e.g. intra-annual). The improved stage integrates daily data of more than 350 weather stations across Europe presented by Klein Tank et al. (2002). All time series data (temperature, precipitation and potential evapotranspiration and soil texture derived from the European Soil Database (JRC 2006)), are used to calculate soil biological activity in the arable layer. The resulting BAT and Re_clim values were spatio-temporal investigated. While "temporal" refers to a long-term trend analysis, "spatial" includes the investigation of soil biological activity variability per environmental zone (ENZ, Metzger et al. 2005 representing similar

  14. Monitoring of airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios. (United States)

    Núñez, Andrés; Amo de Paz, Guillermo; Rastrojo, Alberto; García, Ana M; Alcamí, Antonio; Gutiérrez-Bustillo, A Montserrat; Moreno, Diego A


    The first part of this review ("Monitoring of airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios") describes the current knowledge on the major biological particles present in the air regarding their global distribution, concentrations, ratios and influence of meteorological factors in an attempt to provide a framework for monitoring their biodiversity and variability in such a singular environment as the atmosphere. Viruses, bacteria, fungi, pollen and fragments thereof are the most abundant microscopic biological particles in the air outdoors. Some of them can cause allergy and severe diseases in humans, other animals and plants, with the subsequent economic impact. Despite the harsh conditions, they can be found from land and sea surfaces to beyond the troposphere and have been proposed to play a role also in weather conditions and climate change by acting as nucleation particles and inducing water vapour condensation. In regards to their global distribution, marine environments act mostly as a source for bacteria while continents additionally provide fungal and pollen elements. Within terrestrial environments, their abundances and diversity seem to be influenced by the land-use type (rural, urban, coastal) and their particularities. Temporal variability has been observed for all these organisms, mostly triggered by global changes in temperature, relative humidity, et cetera. Local fluctuations in meteorological factors may also result in pronounced changes in the airbiota. Although biological particles can be transported several hundreds of meters from the original source, and even intercontinentally, the time and final distance travelled are strongly influenced by factors such as wind speed and direction. [Int Microbiol 2016; 19(1):1-1 3].

  15. Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions

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    Werner Mark


    Full Text Available Abstract Background Variations in the influenza Hemagglutinin protein contributes to antigenic drift resulting in decreased efficiency of seasonal influenza vaccines and escape from host immune response. We performed an in silico study to determine characteristics of novel variable and conserved motifs in the Hemagglutinin protein from previously reported H3N2 strains isolated from Hong Kong from 1968–1999 to predict viral motifs involved in significant biological functions. Results 14 MEME blocks were generated and comparative analysis of the MEME blocks identified blocks 1, 2, 3 and 7 to correlate with several biological functions. Analysis of the different Hemagglutinin sequences elucidated that the single block 7 has the highest frequency of amino acid substitution and the highest number of co-mutating pairs. MEME 2 showed intermediate variability and MEME 1 was the most conserved. Interestingly, MEME blocks 2 and 7 had the highest incidence of potential post-translational modifications sites including phosphorylation sites, ASN glycosylation motifs and N-myristylation sites. Similarly, these 2 blocks overlap with previously identified antigenic sites and receptor binding sites. Conclusion Our study identifies motifs in the Hemagglutinin protein with different amino acid substitution frequencies over a 31 years period, and derives relevant functional characteristics by correlation of these motifs with potential post-translational modifications sites, antigenic and receptor binding sites.

  16. Phenotypic evolutionary models in stem cell biology: replacement, quiescence, and variability.

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    Marc Mangel

    Full Text Available Phenotypic evolutionary models have been used with great success in many areas of biology, but thus far have not been applied to the study of stem cells except for investigations of cancer. We develop a framework that allows such modeling techniques to be applied to stem cells more generally. The fundamental modeling structure is the stochastic kinetics of stem cells in their niche and of transit amplifying and fully differentiated cells elsewhere in the organism, with positive and negative feedback. This formulation allows graded signals to be turned into all or nothing responses, and shows the importance of looking beyond the niche for understanding how stem cells behave. Using the deterministic version of this framework, we show how competition between different stem cell lines can be analyzed, and under what circumstances stem cells in a niche will be replaced by other stem cells with different phenotypic characteristics. Using the stochastic version of our framework and state dependent life history theory, we show that the optimal behavior of a focal stem cell will involve long periods of quiescence and that a population of identical stem cells will show great variability in the times at which activity occurs; we compare our results with classic ones on quiescence and variability in the hematopoietic system.

  17. Circulating VEGF as a biological marker in patients with rheumatoid arthritis? Preanalytical and biological variability in healthy persons and in patients

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    Hetland, Merete Lund; Christensen, Ib Jarle; Lottenburger, Tine;


    BACKGROUND: Soluble vascular endothelial growth factor (VEGF) is a promising biomarker in monitoring rheumatoid arthritis (RA), but studies of pre-analytical and biologic variability are few. METHODS: VEGF was measured by ELISA methods in serum and plasma from healthy persons and RA patients. Pre......-analytical factors were investigated. A reference interval for VEGF was established in serum and plasma from 306 healthy persons. Diurnal, day-to-day, week-to-week, long-term variability, and impact of exercise were evaluated. RESULTS: Delayed processing time, room temperature, low centrifugal force....../ml (range: non-detectable to 352); serum: 328 pg/ml (53-1791)) were independent of gender and age. Short- and long-term biologic variability included diurnal variation (sampling should take place after 7 AM) and impact of exercise (increased VEGF immediately after bicycling normalised within 1 hour...

  18. Phytoplankton biomass dynamics and environmental variables around the Rocas Atoll Biological Reserve, South Atlantic

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    Marina Cavalcanti Jales


    Full Text Available Abstract The Rocas Atoll Biological Reserve is located in the Atlantic Ocean, at 3º 51' S and 33º 49' W. It lies 143 nautical miles from the City of Natal, Rio Grande do Norte (Brazil. The purpose of this study was to analyze the hydrology, water masses, currents and chlorophyll a content to determine the dynamics of phytoplankton biomass around the Rocas Atoll. Samples were collected in July 2010 in the area around the Atoll, using the Research Vessel Cruzeiro do Sul of the Brazilian Navy. Two transects were established according to the surface currents, one of which at the southeast of the Atoll (SE and the other at norwest (NW. Three collection points were determined on each of these transects. Samples were collected at different depths (surface and DCM - Deep Chlorophyll Maximum and different times (day and night. According to PCA (Principal Component Analysis, the nutrients analyzed, DIN (dissolved inorganic nitrogen, DIP (dissolved inorganic phosphorus and silicate, were inversely correlated with temperature and dissolved oxygen. Most environmental variables showed a significant increase due to the turbulence on the Northwest transect. There was an increase in the concentration of chlorophyll a and nutrients when the temperature and oxygen in the mixed layer was reduced due to the influence of the SACW (South Atlantic Central Water. Despite the increase observed in some variables such as nutrient salts and chlorophyll a, the temperature in the mixed layer attained a mean value of 23.23 ºC due to the predominance of Tropical Water. The increase of the phytoplankton biomass on the NW transect was, therefore, caused by the "island effect" and not by upwelling.

  19. Chemical Variability and Biological Activities of Essential Oils of Micromeria inodora (Desf.) Benth. from Algeria. (United States)

    Benomari, Fatima Zahra; Djabou, Nassim; Medbouhi, Ali; Khadir, Abdelmounaim; Bendahou, Mourad; Selles, Chaouki; Desjobert, Jean-Marie; Costa, Jean; Muselli, Alain


    The chemical composition of the essential oils isolated from the aerial parts of Micromeria inodora (Desf.) Benth. collected in 24 Algerian localities was investigated from the first time using GC-FID, GC/MS and (13) C-NMR. Altogether, 83 components which accounted for 94.7% of the total oil composition were identified. The main compounds were trans-sesquisabinene hydrate (1; 20.9%), α-terpinyl acetate (2; 19.8%), globulol (3; 4.9%), caryophyllene oxide (4; 4.3%), β-bisabolol (5; 2.9%) and trans-7-epi-sesquisabinene hydrate (6; 2.6%). Comparison with the literature highlighted the originality of the Algerian M. inodora oil and indicated that 1 might be used as taxonomical marker. The study of the chemical variability allowed the discrimination of two main clusters confirming that there is a relation between the essential-oil compositions and the soil nature of the harvest locations. Biological activity of M. inodora essential oil was assessed against fourteen species of microorganisms involved in nosocomial infections using paper disc diffusion and dilution agar assays. The in vitro study demonstrated a good activity against Gram-positive strains such as Staphylococcus aureus, Bacillus cereus, Bacillus subtilis, and Enterococcus faecalis, and moderate activity against Candida albicans. These results might be useful for the future commercial valorization of M. inodora essential oil as a promising source of natural products with potential against various nosocomial community and toxinic infections.

  20. Long-term variability and impact on human health of biologically active UV radiation in Moscow (United States)

    Zhdanova, Ekaterina; Chubarova, Natalia


    the developed classification for Moscow. Booth, C.R. and S. Madronich, 1994: Radiation amplification factors: improved formulation accounts for large increases in ultraviolet radiation associated with Antarctic ozone depletion. In: Ultraviolet Radiation in Antarctica: Measurements and Biological Research [Weiler, C.S. and P.A. Penhale (eds.)]. AGU Antarctic Research Series, 62, Washington, DC, USA, 39-42. Chubarova N.Y., 2008: UV variability in Moscow according to long-term UV measurements and reconstruction model. Atmos.Chem.Phys., 8, 3025-3031 Oriowo, M. et al., 2001:, Action spectrum for in vitro UV-induced cataract using whole lenses. Invest.Ophthalmol.&Vis.Sci, 42, 2596-2602. CIE, 1993: Reference Action Spectra for Ultraviolet Induced Erythema and Pigmentation of Different Human skin Types. CIE Research Note, CIE Technical Collection., N.3 CIE, 2006: Action spectrum for the production of previtamin D3 in human skin, Technical report 174, International commission on illumination

  1. Circulating VEGF as a biological marker in patients with rheumatoid arthritis? Preanalytical and biological variability in healthy persons and in patients

    DEFF Research Database (Denmark)

    Hetland, Merete Lund; Christensen, Ib Jarle; Lottenburger, Tine


    -analytical factors were investigated. A reference interval for VEGF was established in serum and plasma from 306 healthy persons. Diurnal, day-to-day, week-to-week, long-term variability, and impact of exercise were evaluated. RESULTS: Delayed processing time, room temperature, low centrifugal force...... and contamination of plasma with cellular elements lead to significant increases in VEGF levels, whereas storage for up to 2 years at -80 degrees C or up to 10 freeze/thaw cycles did not affect VEGF levels. Serum VEGF levels were 7-10 fold higher than plasma VEGF levels. Reference intervals for VEGF (plasma: 45 pg....../ml (range: non-detectable to 352); serum: 328 pg/ml (53-1791)) were independent of gender and age. Short- and long-term biologic variability included diurnal variation (sampling should take place after 7 AM) and impact of exercise (increased VEGF immediately after bicycling normalised within 1 hour...

  2. A muscle stem cell for every muscle: variability of satellite cell biology among different muscle groups

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    Matthew Emerson Randolph


    Full Text Available The human body contains approximately 640 individual skeletal muscles. Despite the fact that all of these muscles are composed of striated muscle tissue, the biology of these muscles and their associated muscle stem cell populations are quite diverse. Skeletal muscles are affected differentially by various muscular dystrophies, such that certain genetic mutations specifically alter muscle function in only a subset of muscles. Additionally, defective muscle stem cells have been implicated in the pathology of some muscular dystrophies. The biology of muscle stem cells varies depending on their embryologic origins and the muscles with which they are associated. Here we review the biology of skeletal muscle stem cell populations of eight different muscle groups. Understanding the biological variation of skeletal muscles and their resident stem cells could provide valuable insight into mechanisms underlying the susceptibility of certain muscles to myopathic disease.

  3. Essential Oil Variability and Biological Activities of Tetraclinis articulata (Vahl) Mast. Wood According to the Extraction Time. (United States)

    Djouahri, Abderrahmane; Saka, Boualem; Boudarene, Lynda; Baaliouamer, Aoumeur


    In the present work, the hydrodistillation (HD) and microwave-assisted hydrodistillation (MAHD) kinetics of essential oil (EO) extracted from Tetraclinis articulata (Vahl) Mast. wood was conducted, in order to assess the impact of extraction time and technique on chemical composition and biological activities. Gas chromatography (GC) and GC/mass spectrometry analyses showed significant differences between the extracted EOs, where each family class or component presents a specific kinetic according to extraction time, technique and especially for the major components: camphene, linalool, cedrol, carvacrol and α-acorenol. Furthermore, our findings showed a high variability for both antioxidant and anti-inflammatory activities, where each activity has a specific effect according to extraction time and technique. The highlighted variability reflects the high impact of extraction time and technique on chemical composition and biological activities, which led to conclude that we should select EOs to be investigated carefully depending on extraction time and technique, in order to isolate the bioactive components or to have the best quality of EO in terms of biological activities and preventive effects in food.

  4. Variability of Biological Degradation of Aromatic Hydrocarbons in an Aerobic Aquifer Determined by Laboratory Batch Experiments

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    Nielsen, Per Henning; Christensen, Thomas Højlund


    The biological aerobic degradation of 7 aromatic hydrocarbons (benzene, toluene, o-xylene, p-dichlorobenzene, o-dichlorobenzene, naphthalene and biphenyl) was studied for 149 days in replicate laboratory batch experiments with groundwater and sediment from 8 localities representing a 15 m × 30 m...

  5. Biological variables for the site survey of surface ecosystems - existing data and survey methods

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    Kylaekorpi, Lasse; Berggren, Jens; Larsson, Mats; Liberg, Maria; Rydgren, Bernt [SwedPower AB, Stockholm (Sweden)


    In the process of selecting a safe and environmentally acceptable location for the deep level repository of nuclear waste, site surveys will be carried out. These site surveys will also include studies of the biota at the site, in order to assure that the chosen site will not conflict with important ecological interests, and to establish a thorough baseline for future impact assessments and monitoring programmes. As a preparation to the site survey programme, a review of the variables that need to be surveyed is conducted. This report contains the review for some of those variables. For each variable, existing data sources and their characteristics are listed. For those variables for which existing data sources are inadequate, suggestions are made for appropriate methods that will enable the establishment of an acceptable baseline. In this report the following variables are reviewed: Fishery, Landscape, Vegetation types, Key biotopes, Species (flora and fauna), Red-listed species (flora and fauna), Biomass (flora and fauna), Water level, water retention time (incl. water body and flow), Nutrients/toxins, Oxygen concentration, Layering, stratification, Light conditions/transparency, Temperature, Sediment transport, (Marine environments are excluded from this review). For a major part of the variables, the existing data coverage is most likely insufficient. Both the temporal and/or the geographical resolution is often limited, which means that complementary surveys must be performed during (or before) the site surveys. It is, however, in general difficult to make exact judgements on the extent of existing data, and also to give suggestions for relevant methods to use in the site surveys. This can be finally decided only when the locations for the sites are decided upon. The relevance of the different variables also depends on the environmental characteristics of the sites. Therefore, we suggest that when the survey sites are selected, an additional review is

  6. Analytical and Biological Variables Influencing Quantitative Hepatitis C Virus (HCV) Measurement in HIV-HCV Coinfection


    Curtis Cooper; Paul MacPherson; William Cameron


    The present review considers issues pertaining to the precision and variability of quantitative hepatitis C virus (HCV) measurement in general, outlines the characteristics of HCV RNA in HIV-HCV coinfection and evaluates those factors which may affect this measure. The clinical relevance of accurate HCV measurement in HIV-HCV coinfection is discussed.

  7. Nonlinear Effects of Nanoparticles: Biological Variability From Hormetic Doses, Small Particle Sizes, and Dynamic Adaptive Interactions


    Bell, Iris R.; Ives, John A.; Wayne B. Jonas


    Researchers are increasingly focused on the nanoscale level of organization where biological processes take place in living systems. Nanoparticles (NPs, e.g., 1–100 nm diameter) are small forms of natural or manufactured source material whose properties differ markedly from those of the respective bulk forms of the “same” material. Certain NPs have diagnostic and therapeutic uses; some NPs exhibit low-dose toxicity; other NPs show ability to stimulate low-dose adaptive responses (hormesis). B...

  8. Chemical Variability and Biological Activities of Volatile Oils from Hyptis suaveolens (L.) Poit.


    Marcelo Polo; Ricardo Marques Montanari; Róbson Ricardo Teixeira; Felipe Terra Martins; Luiz Claudio de Almeida Barbosa


    Hyptis suaveolens (L.) Poit. belongs to the Lamiaceae family and is widely used in folk medicine in various countries. Th e essential oils from H. suaveolens have been extensively investigated and are mainly composed of monoterpenes and sesquiterpenes, although significant diterpene content has been reported in recent studies. The survey of the literature concerning H. suaveolens essential oils revealed a high level of chemical variability in terms of quantity and composition that is c...

  9. Dose Response Association between Physical Activity and Biological, Demographic, and Perceptions of Health Variables

    Directory of Open Access Journals (Sweden)

    Paul D. Loprinzi


    Full Text Available Background: Few population-based studies have examined the association between physical activity (PA and cardiovascular disease risk factors, demographic variables, and perceptions of health status, and we do not have a clear understanding of the dose-response relationship among these variables. Methods: Data from the 2003-2006 National Health and Nutrition Examination Survey was used to examine the dose-response relationship between objectively measured PA and metabolic syndrome (and its individual cardiovascular disease risk factors, demographic variables, and perceptions of health. After exclusions, 5,538 participants 18 years or older were included in the present study, with 2,538 participants providing fasting glucose and 2,527 providing fasting triglyceride data. PA was categorized into deciles. Results: Overall, the health benefits showed a general pattern of increase with each increasing levels of PA. Of the ten PA classifications examined, participants in the highest moderate-to-vigorous physical activity (MVPA category (at least 71 min/day had the lowest odds of developing metabolic syndrome. Conclusion: At a minimum, sedentary adults should strive to meet current PA guidelines (i.e., 150 min/week of MVPA, with additional positive benefits associated with engaging in three times this level of PA.

  10. Chemical Variability and Biological Activities of Volatile Oils from Hyptis suaveolens (L. Poit.

    Directory of Open Access Journals (Sweden)

    Luiz Claudio Barbosa


    Full Text Available Hyptis suaveolens (L. Poit. belongs to the Lamiaceae family and is widely used in folk medicine in various countries. Th e essential oils from H. suaveolens have been extensively investigated and are mainly composed of monoterpenes and sesquiterpenes, although significant diterpene content has been reported in recent studies. The survey of the literature concerning H. suaveolens essential oils revealed a high level of chemical variability in terms of quantity and composition that is commonly observed for volatile oils from other plant species. However, few researchers have dealt with the reasons for such chemical variability. Our research group has been investigating the relationships between growing conditions of the plants and the H. suaveolens (L. Poit. essential oil composition. The results of these investigations have led to some advances in the characterization and knowledge of H. suaveolens chemotypes from Brazil. Nevertheless, since this species presents high level of genetic polymorphism and allows it to adapt to the alterations in environmental features resulting in interpopulational and intrapopulational variability in the volatile oil chemical compositions. Consequently, biochemical assays on the biosynthetic pathway are required in order to detect the molecular mechanisms involved in inducing differential terpenoid biosynthesis within H. suaveolens. These are some of the challenges which require resolution leading to an understanding of the complex secondary metabolism of this species, thereby making possible the volatile oil chemical standardization seeking productivity and phytotherapy.

  11. Chemical variability and biological activities of Brassica rapa var. rapifera parts essential oils depending on geographic variation and extraction technique. (United States)

    Saka, Boualem; Djouahri, Abderrahmane; Djerrad, Zineb; Souhila, Terfi; Aberrane, Sihem; Sabaou, Nasserdine; Baaliouamer, Aoumeur; Boudarene, Lynda


    In the present work, the Brassica rapa var. rapifera parts essential oils and their antioxidant and antimicrobial activities were investigated for the first time depending on geographic origin and extraction technique. GC and GC-MS analyses showed several constituents, including alcohols, aldehydes, esters, ketones, norisoprenoids, terpenic, nitrogen and sulphur compounds, totalizing 38 and 41 compounds in leaves and root essential oils, respectively. Nitrogen compounds were the main volatiles in leaves essential oils and sulphur compounds were the main volatiles in root essential oils. Qualitative and quantitative differences were found among B. rapa var. rapifera parts essential oils collected from different locations and extracted by hydrodistillation (HD) and microwave-assisted hydrodistillation (MAHD) techniques. Furthermore, our findings showed a high variability for both antioxidant and antimicrobial activities. The highlighted variability reflects the high impact of plant part, geographic variation and extraction technique on chemical composition and biological activities, which led to conclude that we should select essential oils to be investigated carefully depending on these factors, in order to isolate the bioactive components or to have the best quality of essential oil in terms of biological activities and preventive effects in food. This article is protected by copyright. All rights reserved.

  12. Rapid evolution of dispersal ability makes biological invasions faster and more variable (United States)

    Ochocki, Brad M.; Miller, Tom E. X.


    Genetic variation in dispersal ability may result in the spatial sorting of alleles during range expansion. Recent theory suggests that spatial sorting can favour the rapid evolution of life history traits at expanding fronts, and therefore modify the ecological dynamics of range expansion. Here we test this prediction by disrupting spatial sorting in replicated invasions of the bean beetle Callosobruchus maculatus across homogeneous experimental landscapes. We show that spatial sorting promotes rapid evolution of dispersal distance, which increases the speed and variability of replicated invasions: after 10 generations of range expansion, invasions subject to spatial sorting spread 8.9% farther and exhibit 41-fold more variable spread dynamics relative to invasions in which spatial sorting is suppressed. Correspondingly, descendants from spatially evolving invasions exhibit greater mean and variance in dispersal distance. Our results reveal an important role for rapid evolution during invasion, even in the absence of environmental filters, and argue for evolutionarily informed forecasts of invasive spread by exotic species or climate change migration by native species. PMID:28128215

  13. A comparison of biologically variable ventilation to recruitment manoeuvres in a porcine model of acute lung injury

    Directory of Open Access Journals (Sweden)

    Rector Edward S


    Full Text Available Abstract Background Biologically variable ventilation (return of physiological variability in rate and tidal volume using a computer-controller was compared to control mode ventilation with and without a recruitment manoeuvre – 40 cm H2O for 40 sec performed hourly; in a porcine oleic acid acute lung injury model. Methods We compared gas exchange, respiratory mechanics, and measured bronchoalveolar fluid for inflammatory cytokines, cell counts and surfactant function. Lung injury was scored by light microscopy. Pigs received mechanical ventilation (FIO2 = 0.3; PEEP 5 cm H2O in control mode until PaO2 decreased to 60 mm Hg with oleic acid infusion (PaO2/FIO2 2O was added after injury. Animals were randomized to one of the 3 modes of ventilation and followed for 5 hr after injury. Results PaO2 and respiratory system compliance was significantly greater with biologically variable ventilation compared to the other 2 groups. Mean and mean peak airway pressures were also lower. There were no differences in cell counts in bronchoalveolar fluid by flow cytometry, or interleukin-8 and -10 levels between groups. Lung injury scoring revealed no difference between groups in the regions examined. No differences in surfactant function were seen between groups by capillary surfactometry. Conclusions In this porcine model of acute lung injury, various indices to measure injury or inflammation did not differ between the 3 approaches to ventilation. However, when using a low tidal volume strategy with moderate levels of PEEP, sustained improvements in arterial oxygen tension and respiratory system compliance were only seen with BVV when compared to CMV or CMV with a recruitment manoeuvre.

  14. Biologic

    CERN Document Server

    Kauffman, L H


    In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers but also extainers ><, entities open to interaction and distinguishing the space that they are not. The boundary algebra of containers and extainers is to biologic what boolean algebra is to classical logic. We show how this formalism encompasses significant parts of the logic of DNA replication, the Dirac formalism for quantum mechanics, formalisms for protein folding and the basic structure of the Temperley Lieb algebra at the foundations of topological invariants of knots and links.

  15. Seasonal Variation of δ13C of Four Tree Species: A Biological Integrator of Environmental Variables

    Institute of Scientific and Technical Information of China (English)

    Hai-Tao LI; Jun XIA; Le XIANG; Tao LIANG; Qi-Jing LIU


    Foliar δ13C values, an indicator of long-term intercellular carbon dioxide concentration and, thus,of long-term water use efficiency (WUE) in plants, were measured for Pinus massoniana Lamb., P. elliottii Engelm., Cunninghamia laceolata (Lamb.) Hook., and Schima superba Gardn. et Champ. in a restored forest ecosystem in the Jiazhu River Basin. Seasonal variation and the relationship between the foliar δ13Cvalues of the four species and environmental factors (monthly total precipitation, monthly average air temperature, relative humidity, atmospheric pressure, and monthly total solar radiation and evaporation)were investigated. The monthly δ13C values and WUE of the four species increased with increasing precipitation, air temperature, solar radiation, and evaporation, whereas δ13C values of the four species decreased with increasing relative humidity and atmospheric pressure. Despite significant differences in δ13C seasonal means for the four species, our results demonstrate a significant convergence in the responses of δ13C values and WUE to seasonal variations in environmental factors among the species investigated and that the δ13C signature for each species gives a strong indication of environmental variables.

  16. Poisson distribution and process as a well-fitting pattern for counting variables in biologic models

    Directory of Open Access Journals (Sweden)

    Lucietta Betti


    with the Poissonness plot proposed by Hoaglin [5]. The goodness-of-fit of Poisson distribution allows to use specific tests, like the global Poisson test (based on a chi-squared statistics and the comparison of two Poisson parameters, based on the statistic z = X1–X2 / (X1+X21/2 which is, for large samples (at least 20 observations approximately standard normally distributed. A very clear review of these tests based on Poisson distribution is given in [6]. This good fit of Poisson distribution suggests that the whole process of germination of wheat seeds may be considered as a non-homogeneous Poisson process, where the germination rate is not constant but changes over time. Keywords: Poisson process, counting variable, goodness-of-fit, wheat germination References [1] L.Betti, M.Brizzi, D.Nani, M.Peruzzi. A pilot statistical study with homeopathic potencies of Arsenicum Album in wheat germination as a simple model. British Homeopathic Journal; 83: 195-201. [2] M.Brizzi, L.Betti (1999, Using statistics for evaluating the effectiveness of homeopathy. Analysis of a large collection of data from simple plant models. III Congresso Nazionale della SIB (Società Italiana di Biometria di Roma, Abstract Book, 74-76. [3] M.Brizzi, D.Nani, L.Betti, M.Peruzzi. Statistical analysis of the effect of high dilutions of Arsenic in a large dataset from a wheat germination model. British Homeopathic Journal, 2000;, 89, 63-67. [4] M.Brizzi, L.Betti (2010, Statistical tools for alternative research in plant experiments. “Metodološki Zvezki – Advances in Methodology and Statistics”, 7, 59-71. [5] D.C.Hoaglin (1980, A Poissonness plot. “The American Statistician”, 34, 146-149. [6] L.Sachs (1984 Applied statistics. A handbook of techniques. Springer Verlag, 186-189.

  17. Spatial variability in the trophic ecology and biology of the deep-sea shrimp Aristaeomorpha foliacea in the Mediterranean Sea (United States)

    Cartes, J. E.; Fanelli, E.; Kapiris, K.; Bayhan, Y. K.; Ligas, A.; López-Pérez, C.; Murenu, M.; Papiol, V.; Rumolo, P.; Scarcella, G.


    The trophic ecology, energy and reproductive states of the deep-water shrimp Aristaeomorpha foliacea, widely distributed along the slopes of the Mediterranean Sea Basins, were analysed in eight areas spread along ca. 3000 km in order to identify patterns in the habitat conditions supporting the species. From W to E the areas were situated between the north side of Eivissa (39°12‧N, 1°20‧E, in the Balearic Basin) and off Mersin, Turkey (36°15‧N, 34°19‧E, in the Levantine Sea). Trends identified mainly as a function of longitude from west to east were: (i) higher δ15N, parallel to δ15N shifts in the top 200 m of the water column for particulate organic N (Pantoja et al., 2002). The δ15N trend indicates that the deep trophic web, i.e. A. foliacea at 400-600 m, reflects the δ15N signal of the photic zone; (ii) a similar significant trend of δ13C, related with exploitation of pelagic versus benthic resources by A. foliacea in each area (i.e. by local variability of terrigenous inputs via submarine canyons). More depleted δ13C was found at mid-longitudes (Tyrrhenian Sea and Sicily Channel) linked to higher consumption of macroplankton prey (Pasiphaea spp., euphausiids and mesopelagic fishes). The feeding intensity (gut fullness, F) and prey diversity (J) of A. foliacea were related, according to generalized linear models, with the temperature and salinity of intermediate waters, variables in turn associated with latitude and longitude. Both F and J were higher in areas with greater shrimp density. The optimal ecological habitat of A. foliacea appears to be located in the Tyrrhenian Sea and the Sicily Channel, where we found the highest F, the greatest trophic diversity and A. foliacea in the best biological condition (i.e. with higher hepato-somatic index, HSI). These are also the areas with the highest densities of A. foliacea. In contrast, in the western Mediterranean Sea (Balearic Basin and the southern Balearic Islands), where A. foliacea has low

  18. Influences of biological variables and geographic location on circulating concentrations of thyroid hormones in wild bottlenose dolphins (Tursiops truncatus). (United States)

    Fair, Patricia A; Montie, Eric; Balthis, Len; Reif, John S; Bossart, Gregory D


    Thyroid hormones (TH) are key regulators of metabolism and development, yet our understanding of the variability in serum TH concentrations in free-ranging marine mammals is limited. Thus, we examined the interrelationships between TH and age, sex, reproductive status, geographic location, and ocean temperatures in wild bottlenose dolphins (Tursiops truncatus). Circulating concentrations of TH (total thyroxine (tT(4)), free T(4) (fT(4)), and total triiodothyronine (tT(3))) were determined in a total of 195 dolphins; 80 from the coastal waters of Charleston, South Carolina (CHS) and 115 from the Indian River Lagoon, Florida (IRL). Age had the most influence on circulating TH concentrations in dolphins at both sites with decreasing concentrations (p<0.0001) observed with increasing age for all TH. No significant differences were found between males and non-reproductive females. Geographic location significantly influenced tT(4) and tT(3) concentrations; CHS dolphins had higher concentrations than IRL animals. These TH differences between CHS and IRL dolphins may be attributed to the colder year-round water temperature that CHS dolphins inhabit compared to IRL dolphins and could constitute an adaptive response to their colder environment. Results from this study highlight the importance of establishing reference values for dolphins in different geographic locations to support valid comparisons. This initial assessment provides a foundation of how biological and environmental variables could affect circulating TH in dolphins, which will help to elucidate the impacts of disease, pollution, and climate change on the thyroid hormone system of aquatic mammals.

  19. Physical and biological forcing of mesoscale variability in the carbonate system of the Ross Sea (Antarctica) during summer 2014 (United States)

    Rivaro, Paola; Ianni, Carmela; Langone, Leonardo; Ori, Carlo; Aulicino, Giuseppe; Cotroneo, Yuri; Saggiomo, Maria; Mangoni, Olga


    Water samples (0-200 m) were collected in a coastal area of the Ross Sea in January 2014 to evaluate the physical and biological forcing on the carbonate system at the mesoscale (distance between stations of 5-10 km). Remote sensing supported the determination of the sampling strategy and helped positioning each sampling station. Total alkalinity, pH, dissolved oxygen, phytoplankton pigments and composition were investigated in combination with measurements of temperature, salinity and current speed. Total inorganic carbon, sea water CO2 partial pressure and the saturation state (Ω) for calcite and aragonite were calculated from the measured total alkalinity and pH. In addition, continuous measurements of atmospheric CO2 concentration were completed. LADCP measurements revealed the presence of a significant change in current speed and direction that corresponded to a clearly defined front characterized by gradients in both temperature and salinity. Phytoplankton biomass was relatively high at all stations and the highest values of chlorophyll-a were found between 20 to 50 m, with the dominant taxonomic group being haptophyceae. The carbonate system properties in surface waters exhibited mesoscale variability with a horizontal length scale of about 10 km. Sea-ice melt, through the input of low salinity water, results in a dilution of the total alkalinity and inorganic carbon, but our observations suggest that phytoplankton activity was the major forcing of the distribution of the carbonate system variables. Higher CO3-, Ω and pH in the surface layer were found where the highest values of chlorophyll-a were observed. The calculated ΔpCO2 pattern follows both MODIS data and in situ chlorophyll-a measurements, and the estimated CO2 fluxes ranged from -0.5 ± 0.4 to -31.0 ± 6.4 mmol m- 2 d- 1. The large range observed in the fluxes is due to both the spatial variability of sea water pCO2 and to the episodic winds experienced.

  20. Biologic variability in plasma glucose, hemoglobin A1c, and advanced glycation end products associated with diabetes complications. (United States)

    Leslie, R David G; Cohen, Robert M


    Plasma glucose plays a key role in the complications of diabetes mellitus. Hemoglobin A1c (HbA1c) and circulating concentrations of advanced glycation end products (AGEs) are central to diabetes clinical care and pathophysiology. However, there is evidence for variation between individuals in the relationship of plasma glucose to both these measures and to specific complications. The glycation gap (GG) and hemoglobin glycation index represent tools for quantitating the variability in the relationship between plasma glucose and HbA1c useful for identification of underlying mechanisms. Recent evidence demonstrates the heritability of HbA1c, the GG, and AGEs, yet not of glycated serum proteins. There has been tremendous effort devoted to identifying the heritable basis of types 1 and 2 diabetes; however, studies on the heritable contributors to these mediators of glucose effect on complications are only beginning. New evidence for normal biologic variation in the distribution of glucose into the red blood cell (RBC) intracellular compartment and RBC lifespan in people with and without diabetes represent candidates for heritable mechanisms and contributors to the rise in HbA1c with age. Taken as a whole, genetic and mechanistic evidence suggests new potential targets for complications prevention and improvement in complications risk estimation. These observations could help tilt the risk-benefit balance in glycemic control toward a more beneficial outcome.

  1. Is DAS28-CRP with three and four variables interchangeable in individual patients selected for biological treatment in daily clinical practice?

    DEFF Research Database (Denmark)

    Madsen, Ole Rintek


    DAS28 is a widely used composite score for the assessment of disease activity in patients with rheumatoid arthritis (RA) and is often used as a treatment decision tool in the daily clinic. Different versions of DAS28 are available. DAS28-CRP(3) is calculated based on three variables: swollen...... selected for initiating biological treatment. Data were extracted from the Danish registry for biological treatment in rheumatology (DANBIO). Multiple regression analysis was used to assess the predictability of the DAS28 scores by several measures of disease activity. The overall mean DAS28-CRP was 4...

  2. Is DAS28-CRP with three and four variables interchangeable in individual patients selected for biological treatment in daily clinical practice?

    DEFF Research Database (Denmark)

    Madsen, Ole Rintek


    DAS28 is a widely used composite score for the assessment of disease activity in patients with rheumatoid arthritis (RA) and is often used as a treatment decision tool in the daily clinic. Different versions of DAS28 are available. DAS28-CRP(3) is calculated based on three variables: swollen...... and tender joint counts and CRP. DAS28-CRP(4) also includes patient global assessment. Thresholds for low and high disease activity are the same for the two scores. Based on the Bland-Altman method, the interchangeability between DAS28-CRP with three and four variables was examined in 319 RA patients...... selected for initiating biological treatment. Data were extracted from the Danish registry for biological treatment in rheumatology (DANBIO). Multiple regression analysis was used to assess the predictability of the DAS28 scores by several measures of disease activity. The overall mean DAS28-CRP was 4...

  3. Why is there a lack of consensus on molecular subgroups of glioblastoma? Understanding the nature of biological and statistical variability in glioblastoma expression data.

    Directory of Open Access Journals (Sweden)

    Nicholas F Marko

    Full Text Available INTRODUCTION: Gene expression patterns characterizing clinically-relevant molecular subgroups of glioblastoma are difficult to reproduce. We suspect a combination of biological and analytic factors confounds interpretation of glioblastoma expression data. We seek to clarify the nature and relative contributions of these factors, to focus additional investigations, and to improve the accuracy and consistency of translational glioblastoma analyses. METHODS: We analyzed gene expression and clinical data for 340 glioblastomas in The Cancer Genome Atlas (TCGA. We developed a logic model to analyze potential sources of biological, technical, and analytic variability and used standard linear classifiers and linear dimensional reduction algorithms to investigate the nature and relative contributions of each factor. RESULTS: Commonly-described sources of classification error, including individual sample characteristics, batch effects, and analytic and technical noise make measurable but proportionally minor contributions to inconsistent molecular classification. Our analysis suggests that three, previously underappreciated factors may account for a larger fraction of classification errors: inherent non-linear/non-orthogonal relationships among the genes used in conjunction with classification algorithms that assume linearity; skewed data distributions assumed to be Gaussian; and biologic variability (noise among tumors, of which we propose three types. CONCLUSIONS: Our analysis of the TCGA data demonstrates a contributory role for technical factors in molecular classification inconsistencies in glioblastoma but also suggests that biological variability, abnormal data distribution, and non-linear relationships among genes may be responsible for a proportionally larger component of classification error. These findings may have important implications for both glioblastoma research and for translational application of other large-volume biological databases.

  4. Uptake of CO2 in the Pelagic Ocean by the Biological Pump; the Global Flux and the Regional Variability (United States)

    Honjo, S.; Francois, R. H.; Manganini, S. J.; Eglinton, T. I.


    POC (particulate organic carbon) is vertically transported to the oceanic interior by ballasted aggregates, CaCO3 and biogenic opal, with a minor role for lithogenic aerosols through the mesopelagic zone. The diel-migrating zooplankton community is intimately involved with the vertical transport and re-mineralization of POC. Below 1.5-km, the zooplankton ecosystem is minimal, thus the aggregates travel mainly by gravity with little zooplankton influence. We examined the mole fluxes of POC, CaCO3, and biogenic opal Si fluxes retrieved from time-series, bottom tethered sediment traps (TS-trap) at 134 globally distributed pelagic stations at 2 km (m/b) as Fm/bCorg, Fm/bCinorg, and Fm/bSibio. The POC fluxes were normalized to the value at 2 km (m/b). We investigated (1) the geographic contrasts of POC export at m/b and (2) the supply rate of ∑CO2 to the world mesopelagic water column. Fm/bCorg varies from 25 (Pacific Warm Pool) to 605 (divergent Arabian Sea) mmolC m -2 yr-1; Fm/bCinorg varies from >8 (high latitude Polar Oceans) or 15 (Pacific Warm Pool) to 459 (divergent Arabian Sea) mmolC m-2yr-1; and Fm/bSibio, the most spatially/temporally variable flux, ranges from 6 (North Atlantic Drift) to 1118 (Pacific Subarctic Gyre) mmolSi m-2yr-1. The oceanic region exhibiting the highest POC flux over a significantly large region is the area of the North Pacific Boreal Gyres where the average Fm/bCorg = 213, Fm/bCinorg = 126, and Fm/bSibio = 578 mmol m-2yr-1. Fm/bCorg and Fm/bCinorg are particularly high in large upwelling margins, including the divergent Arabian Sea and off Cape Verde. The data set shows the lowest flux over a significant region/basin is Fm/bCorg = 39, whereas the Fm/bCinorg = 69, and Fm/bSibio-2yr-1 in the North Pacific subtropical/tropical gyres; Pan-Atlantic average fluxes are similar except Fm/bSibio fluxes are even lower. Where Corg/Cinorg and Sibio/Cinorg are Ocean,” and where these ratios are ≥1 defines the “Silica Ocean.” The Carbonate

  5. A year in the life of a central California kelp forest: physical and biological insights into biogeochemical variability (United States)

    Koweek, David A.; Nickols, Kerry J.; Leary, Paul R.; Litvin, Steve Y.; Bell, Tom W.; Luthin, Timothy; Lummis, Sarah; Mucciarone, David A.; Dunbar, Robert B.


    Kelp forests are among the world's most productive marine ecosystems, yet little is known about their biogeochemistry. This study presents a 14-month time series (July 2013-August 2014) of surface and benthic dissolved inorganic carbon and total alkalinity measurements, along with accompanying hydrographic measurements, from six locations within a central California kelp forest. We present ranges and patterns of variability in carbonate chemistry, including pH (7.70-8.33), pCO2 (172-952 µatm), and the aragonite saturation state, ΩAr (0.94-3.91). Surface-to-bottom gradients in CO2 system chemistry were as large as the spatial gradients throughout the bottom of the kelp forest. Dissolved inorganic carbon variability was the main driver of the observed CO2 system variability. The majority of spatial variability in the kelp forest can be explained by advection of cold, dense high-CO2 waters into the bottom of the kelp forest, with deeper sites experiencing high-CO2 conditions more frequently. Despite the strong imprint of advection on the biogeochemical variability of the kelp forest, surface waters were undersaturated with CO2 in the spring through fall, indicative of the strong role of photosynthesis on biogeochemical variability. We emphasize the importance of spatially distributed measurements for developing a process-based understanding of kelp forest ecosystem function in a changing climate.

  6. Seasonal and interannual variability of physical and biological dynamics at the shelfbreak front of the Middle Atlantic Bight: nutrient supply mechanisms

    Directory of Open Access Journals (Sweden)

    R. He


    Full Text Available A high-resolution, 3-dimensional coupled biophysical model is used to simulate ocean circulation and ecosystem variations at the shelfbreak front of the Middle Atlantic Bight (MAB. Favorable comparisons between satellite observations and model hindcast solutions from January 2004 to November 2007 indicate the model has intrinsic skills in resolving fundamental physical and biological dynamics at the MAB shelfbreak. Seasonal and interannual variability of ocean physical and biological states and their driving mechanisms are further analyzed. The domain-wide upper water column nutrient content is found to peak in late winter-early spring. Phytoplankton spring bloom starts 1–2 months later, followed by zooplankton bloom in early summer. Our analysis shows the variability of shelfbreak nutrient supply is controlled by local mixing that deepens the mixed layer and injects deep ocean nutrients into the upper water column and alongshore nutrient transport by the shelfbreak jet and associated currents. Nutrient vertical advection associated with the shelfbreak bottom boundary layer convergence is another significant contributor. Spring mean nutrient budget diagnostics along the Nantucket transect are compared between nutrient rich 2004 and nutrient poor 2007. Physical advection and diffusion play the major role in determining strong interannual variations in shelfbreak nutrient content. The biological (source minus sink term is very similar between these two years.

  7. Seasonal variability in biological carbon biomass standing stocks and production in the surface layers of the Bay of Bengal

    Digital Repository Service at National Institute of Oceanography (India)

    Ramaiah, N.; Fernandes, V.; Paul, J.T.; Jyothibabu, R.; Gauns, M.; Jayraj, E.A.

    is leading, apparently, to consequent low BP and, secondary production. Ubiquitous and abundant heterotrophic bacteria are key players in ocean biology and, are important components of marine biomass39. They form food for protozoa, invertebrate larvae...B. The water column microfauna in the size range of 20-200 µm, the microzooplankton, can be called operators of microbial loop in the marine environment. All protozoa, invertebrate larvae, early stages of mesozooplankton <200µm fall in this category...

  8. Pre-analytical and biological variability in circulating interleukin 6 in healthy subjects and patients with rheumatoid arthritis

    DEFF Research Database (Denmark)

    Knudsen, Lene S; Christensen, Ib J; Lottenburger, Tine


    patients. An enzyme-linked immunosorbent assay from R&D was used for determination of serum and plasma IL-6. The IL-6 concentration did not depend on the type of anticoagulant used or the 3-h time delay between sampling and processing or repeated freeze-thaw cycles. The median plasma and serum IL-6 in 318...... in serum IL-6 over a 3-year period (14%, p=0.33). Exercise (cycling) increased serum IL-6 in healthy subjects but not in RA patients. In conclusion, circulating IL-6 is stable regarding sample handling and shows little variation over time. Changes in IL-6 concentrations >60% (2 times the biological...

  9. The response of Carlos Botelho (Lobo, Broa reservoir to the passage of cold fronts as reflected by physical, chemical, and biological variables

    Directory of Open Access Journals (Sweden)

    J. G. Tundisi

    Full Text Available This paper describes and discusses the impacts of the passage of cold fronts on the vertical structure of the Carlos Botelho (Lobo-Broa Reservoir as demonstrated by changes in physical, chemical, and biological variables. The data were obtained with a continuous system measuring 9 variables in vertical profiles in the deepest point of the reservoir (12 m coupled with climatological information and satellite images, during a 32-day period in July and August, 2003. During periods of incidence of cold fronts the reservoir presented vertical mixing. After the dissipation of the cold fronts a period of stability followed with thermal, chemical, and biological (chlorophyll-a stratification. Climatological data obtained during the cold front passage showed lower air temperature, higher wind speed and lower solar radiation. The response of this reservoir can exemplify a generalized process in all shallow reservoirs in the Southeast Brazil and could have several implications for management, particularly in relation to the phytoplankton population dynamics and development of cyanobacterial blooms. Using this as a basis, a predictive model will be developed with the aim of advancing management strategies specially for the drinking water reservoirs of the Metropolitan Region of São Paulo.

  10. Post-glacial variability of sea ice cover, river run-off and biological production in the western Laptev Sea (Arctic Ocean) - A high-resolution biomarker study (United States)

    Hörner, T.; Stein, R.; Fahl, K.; Birgel, D.


    Multi-proxy biomarker measurements were applied on two sediment cores (PS51/154, PS51/159) to reconstruct sea ice cover (IP25), biological production (brassicasterol, dinosterol) and river run-off (campesterol, β-sitosterol) in the western Laptev Sea over the last ∼17 ka with unprecedented temporal resolution. The absence of IP25 from 17.2 to 15.5 ka, in combination with minimum concentration of phytoplankton biomarkers, suggests that the western Laptev Sea shelf was mostly covered with permanent sea ice. Very minor river run-off and restricted biological production occurred during this cold interval. From ∼16 ka until 7.5 ka, a long-term decrease of terrigenous (riverine) organic matter and a coeval increase of marine organic matter reflect the gradual establishment of fully marine conditions in the western Laptev Sea, caused by the onset of the post-glacial transgression. Intensified river run-off and reduced sea ice cover characterized the time interval between 15.2 and 12.9 ka, including the Bølling/Allerød warm period (14.7-12.9 ka). Prominent peaks of the DIP25 Index coinciding with maximum abundances of subpolar foraminifers, are interpreted as pulses of Atlantic water inflow on the western Laptev Sea shelf. After the warm period, a sudden return to severe sea ice conditions with strongest ice-coverage between 11.9 and 11 ka coincided with the Younger Dryas (12.9-11.6 ka). At the onset of the Younger Dryas, a distinct alteration of the ecosystem (reflected in a distinct drop in terrigenous and phytoplankton biomarkers) was detected. During the last 7 ka, the sea ice proxies reflect a cooling of the Laptev Sea spring/summer season. This cooling trend was superimposed by a short-term variability in sea ice coverage, probably representing Bond cycles (1500 ± 500 ka) that are related to solar activity changes. Hence, atmospheric circulation changes were apparently able to affect the sea ice conditions on the Laptev Sea shelf under modern sea level

  11. A coupled physical-biological model of the Northern Gulf of Mexico shelf: model description, validation and analysis of phytoplankton variability

    Directory of Open Access Journals (Sweden)

    K. Fennel


    Full Text Available The Texas-Louisiana shelf in the Northern Gulf of Mexico receives large inputs of nutrients and freshwater from the Mississippi/Atchafalaya River system. The nutrients stimulate high rates of primary production in the river plume, which contributes to the development of a large and recurring hypoxic area in summer, but the mechanistic links between hypoxia and river discharge of freshwater and nutrients are complex as the accumulation and vertical export of organic matter, the establishment and maintenance of vertical stratification, and the microbial degradation of organic matter are controlled by a non-linear interplay of factors. Unraveling these interactions will have to rely on a combination of observations and models. Here we present results from a realistic, 3-dimensional, physical-biological model with focus on a quantification of nutrient-stimulated phytoplankton growth, its variability and the fate of this organic matter. We demonstrate that the model realistically reproduces many features of observed nitrate and phytoplankton dynamics including observed property distributions and rates. We then contrast the environmental factors and phytoplankton source and sink terms characteristic of three model subregions that represent an ecological gradient from eutrophic to oligotrophic conditions. We analyze specifically the reasons behind the counterintuitive observation that primary production in the light-limited plume region near the Mississippi River delta is positively correlated with river nutrient input, and find that, while primary production and phytoplankton biomass are positively correlated with nutrient load, phytoplankton growth rate is not. This suggests that accumulation of biomass in this region is not primarily controlled bottom up by nutrient-stimulation, but top down by systematic differences in the loss processes.

  12. Biological Individuality of Man (United States)


    RECIPIENT’S CAT * LOO NUMBER Biological Individuality of Man 5 TlrPE OF REPORT a PERIOD COVERED Technical « PERFORMING ORO REPORT...Variability 13 A. Background , 13 B. Slatistictl Approaches to Biological Variability 13 C. Genetic Aspects of Biological Variability . 14 III...ioiological determinants of individuality. Only recently, have genetic infaienccs been investigated and the potentialities for future control of bio

  13. Agreement between the DAS28-CRP assessed with 3 and 4 variables in patients with rheumatoid arthritis treated with biological agents in the daily clinic

    DEFF Research Database (Denmark)

    Madsen, Ole Rintek


    The Disease Activity Score-28-C-reactive Protein 4 [DAS28-CRP(4)] composite measure for rheumatoid arthritis (RA) is based on 4 variables: tender and swollen joint counts, CRP, and patient global assessment. DAS28-CRP(3) includes only 3 variables, because patient global assessment has been omitted...

  14. Biological Variability and Impact of Oral Contraceptives on Vitamins B6, B12 and Folate Status in Women of Reproductive Age

    Directory of Open Access Journals (Sweden)

    Samir Samman


    Full Text Available Vitamins B6, B12 and folate play crucial metabolic roles especially during the reproductive years for women. There is limited reporting of within-subject variability of these vitamins. This study aimed to determine the within and between subject variability in serum vitamins B6, B12, folate and erythrocyte folate concentrations in young women; identify factors that contribute to variability; and determine dietary intakes and sources of these vitamins. Data were obtained from the control group of a trial aimed at investigating the effect of iron on the nutritional status of young women (age 25.2 ± 4.2 year; BMI 21.9 ± 2.2 kg/m2. The coefficients of variability within-subject (CVI and between-subject (CVG for serum vitamins B6, B12 and folate, and erythrocyte folate were calculated. Food frequency questionnaires provided dietary data. CVI and CVG were in the range 16.1%–25.7% and 31.7%–62.2%, respectively. Oral contraceptive pill (OCP use was associated (P = 0.042 with lower serum vitamin B12 concentrations. Initial values were 172 ± 16 pmol/L and 318 ± 51 pmol/L for OCP and non-OCP users, respectively; with differences maintained at four time points over 12 weeks. BMI, age, physical activity, alcohol intake and haematological variables did not affect serum or erythrocyte vitamin concentrations. Vitamin B12 intakes were derived from traditional and unexpected sources including commercial energy drinks. Young women using OCP had significantly lower serum vitamin B12 concentrations. This should be considered in clinical decision making and requires further investigation.

  15. Variability and connectivity of plaice populations from the Eastern North Sea to the Baltic Sea, part II. Biological evidence of population mixing

    DEFF Research Database (Denmark)

    Ulrich, Clara; Hansen, Jakob Hemmer; Boje, Jesper


    A multi-disciplinary study was conducted to clarify stock identity and connectivity patterns in the populations of European plaice (Pleuronectes platessa) in the Skagerrak-Kattegat transition area between the Eastern North Sea and the Baltic Sea. Five independent biological studies were carried out...... in parallel. Genetic markers suggested the existence of different genetic populations in the transition area. Growth backcalculation with otoliths resulted in significant although limited differences in growth rates between North Sea and Skagerrak, indicating weak differentiation or important mixing....... Hydrogeographical drift modelling suggested that some North Sea juveniles could settle along the coast line of the Skagerrak and the Kattegat. Tagging data suggested that both juveniles and adult fish from the North Sea perform feeding migrations into Skagerrak in summer/autumn. Finally, survey data suggested...

  16. The influence of biological and technical factors on quantitative analysis of amyloid PET: Points to consider and recommendations for controlling variability in longitudinal data. (United States)

    Schmidt, Mark E; Chiao, Ping; Klein, Gregory; Matthews, Dawn; Thurfjell, Lennart; Cole, Patricia E; Margolin, Richard; Landau, Susan; Foster, Norman L; Mason, N Scott; De Santi, Susan; Suhy, Joyce; Koeppe, Robert A; Jagust, William


    In vivo imaging of amyloid burden with positron emission tomography (PET) provides a means for studying the pathophysiology of Alzheimer's and related diseases. Measurement of subtle changes in amyloid burden requires quantitative analysis of image data. Reliable quantitative analysis of amyloid PET scans acquired at multiple sites and over time requires rigorous standardization of acquisition protocols, subject management, tracer administration, image quality control, and image processing and analysis methods. We review critical points in the acquisition and analysis of amyloid PET, identify ways in which technical factors can contribute to measurement variability, and suggest methods for mitigating these sources of noise. Improved quantitative accuracy could reduce the sample size necessary to detect intervention effects when amyloid PET is used as a treatment end point and allow more reliable interpretation of change in amyloid burden and its relationship to clinical course.

  17. Year-Long Monitoring of Physico-Chemical and Biological Variables Provide a Comparative Baseline of Coral Reef Functioning in the Central Red Sea

    KAUST Repository

    Roik, Anna Krystyna


    Coral reefs in the central Red Sea are sparsely studied and in situ data on physico-chemical and key biotic variables that provide an important comparative baseline are missing. To address this gap, we simultaneously monitored three reefs along a cross-shelf gradient for an entire year over four seasons, collecting data on currents, temperature, salinity, dissolved oxygen (DO), chlorophyll-a, turbidity, inorganic nutrients, sedimentation, bacterial communities of reef water, and bacterial and algal composition of epilithic biofilms. Summer temperature (29–33°C) and salinity (39 PSU) exceeded average global maxima for coral reefs, whereas DO concentration was low (2–4 mg L-1). While temperature and salinity differences were most pronounced between seasons, DO, chlorophyll-a, turbidity, and sedimentation varied most between reefs. Similarly, biotic communities were highly dynamic between reefs and seasons. Differences in bacterial biofilms were driven by four abundant families: Rhodobacteraceae, Flavobacteriaceae, Flammeovirgaceae, and Pseudanabaenaceae. In algal biofilms, green crusts, brown crusts, and crustose coralline algae were most abundant and accounted for most of the variability of the communities. Higher bacterial diversity of biofilms coincided with increased algal cover during spring and summer. By employing multivariate matching, we identified temperature, salinity, DO, and chlorophyll-a as the main contributing physico-chemical drivers of biotic community structures. These parameters are forecast to change most with the progression of ocean warming and increased nutrient input, which suggests an effect on the recruitment of Red Sea benthic communities as a result of climate change and anthropogenic influence. In conclusion, our study provides insight into coral reef functioning in the Red Sea and a comparative baseline to support coral reef studies in the region.

  18. Variability and connectivity of plaice populations from the Eastern North Sea to the Baltic Sea, part II. Biological evidence of population mixing (United States)

    Ulrich, Clara; Hemmer-Hansen, Jakob; Boje, Jesper; Christensen, Asbjørn; Hüssy, Karin; Sun, Hailu; Clausen, Lotte Worsøe


    A multi-disciplinary study was conducted to clarify stock identity and connectivity patterns in the populations of European plaice (Pleuronectes platessa) in the Skagerrak-Kattegat transition area between the Eastern North Sea and the Baltic Sea. Five independent biological studies were carried out in parallel. Genetic markers suggested the existence of different genetic populations in the transition area. Growth backcalculation with otoliths resulted in significant although limited differences in growth rates between North Sea and Skagerrak, indicating weak differentiation or important mixing. Hydrogeographical drift modelling suggested that some North Sea juveniles could settle along the coast line of the Skagerrak and the Kattegat. Tagging data suggested that both juveniles and adult fish from the North Sea perform feeding migrations into Skagerrak in summer/autumn. Finally, survey data suggested that Skagerrak also belongs to the area distribution of North Sea plaice. The outcomes of the individual studies were then combined into an overall synthesis. The existence of some resident components was evidenced, but it was also demonstrated that North Sea plaice migrate for feeding into Skagerrak and might constitute a large share of the catches in this area. The mixing of different populations within a management area has implications for stock assessment and management. Choice must be made to either lump or split the populations, and the feasibility and constraints of both options are discussed. The outcomes of this work have directly influenced the management decisions in 2015.

  19. A coupled physical-biological model of the Northern Gulf of Mexico shelf: model description, validation and analysis of phytoplankton variability

    Directory of Open Access Journals (Sweden)

    K. Fennel


    Full Text Available The Texas-Louisiana shelf in the Northern Gulf of Mexico receives large inputs of nutrients and freshwater from the Mississippi/Atchafalaya River system. The nutrients stimulate high rates of primary production in the river plume, which contributes to the development of a large and recurring hypoxic area in summer. The mechanistic links between hypoxia and river discharge of freshwater and nutrients are complex as the accumulation and vertical export of organic matter, the establishment and maintenance of vertical stratification, and the microbial degradation of organic matter are controlled by a non-linear interplay of factors. We present results from a realistic, 3-dimensional, physical-biological model that includes the processes thought to be of first order importance to hypoxia formation and demonstrate that the model realistically reproduces many features of observed nitrate and phytoplankton dynamics including observed property distributions and rates. We then contrast the environmental factors and phytoplankton source and sink terms characteristic of three model subregions that represent an ecological gradient from eutrophic to oligotrophic conditions. We analyze specifically the reasons behind the counterintuitive observation that primary production in the light-limited plume region near the Mississippi River delta is positively correlated with river nutrient input. We find that, while primary production and phytoplankton biomass are positively correlated with nutrient load, phytoplankton growth rate is not. This suggests that accumulation of biomass in this region is not primarily controlled bottom up by nutrient-stimulation, but top down by systematic differences in the loss processes. We hypothesize that increased retention of river water in high discharge years explains this phenomenon.

  20. Dynamics of suprabenthos-zooplankton communities around the Balearic Islands (western Mediterranean): Influence of environmental variables and effects on the biological cycle of Aristeus antennatus (United States)

    Cartes, J. E.; Madurell, T.; Fanelli, E.; López-Jurado, J. L.

    Dynamics of suprabenthos and zooplankton were analyzed in two areas located in the NW (off Sóller harbour) and S (off Cabrera Archipelago) of Mallorca (Balearic Islands, western Mediterranean) at depths ranging between 135-780 m. Four stations situated respectively at 150 m (shelf-slope break), and at bathyal depths of 350, 650 and 750 m were sampled at bi-monthly intervals during six cruises performed between August 2003 and June 2004. Suprabenthos showed maximum biomass in both areas from late spring to summer (April to August), while minimum biomass was found in autumn (September-November). Though variable, temporal dynamics of zooplankton showed peaks of biomass in late winter and summer (February and June), while minimals occurred in autumn (August-September) and, at bathyal depths, in April. Suprabenthos (abundance; MDS analyses) showed a sample aggregation as a function of depth (3 groups corresponding to the shelf-slope break, upper slope — over 350 m; and the middle, deeper part of the slope — over 650-750 m), without any separation of hauls by season. By contrast, zooplankton samples were separated by season and not by depth. There was evidence of three seasonal groups corresponding to summer (June 2004-August 2003), autumn-winter (September and November 2003, February 2004), and spring (April 2004), being especially well established off Sóller. In general, suprabenthos was significantly correlated with the sediment variables (e.g. total organic matter content (% OM), potential REDOX), whereas zooplankton was almost exclusively dependent on Chl a at the surface, which suggests two different food sources for suprabenthos and zooplankton. The increase of suprabenthos abundance in April-June was paralleled by a sharp increase ( ca. 2.8 times) in the %OM on sediment during the same period, coupled ca. 1-2 months of delay with the peak of surface Chl a recorded in February-March (from satellite imagery data). Suprabenthos biomass was also correlated with

  1. Atribuição de significados biológicos às variáveis da equação logística: uma aplicação do Cálculo nas Ciências Biológicas Attribution of biological meanings to variables of logistic equation: applying Calculus to Biology

    Directory of Open Access Journals (Sweden)

    Lilian Akemi Kato


    Full Text Available Este artigo apresenta, como objetivo principal, uma proposta metodológica para o ensino do Cálculo nos cursos de Ciências Biológicas, que privilegia a atribuição de significados biológicos às variáveis e parâmetros que aparecem nos modelos matemáticos no estudo de dinâmica de populações. Utilizou-se, neste estudo, a equação logística como modelo matemático que caracteriza diversos tipos de crescimento populacional, além de apresentar outras complexidades do fenômeno biológico que podem ser melhor caracterizadas e explicadas por meio dos conceitos matemáticos relacionados ao Cálculo Diferencial. Entende-se que estas relações do Cálculo com as Ciências Biológicas contribuem para a compreensão de fenômenos biológicos complexos que podem ser explicados por equações matemáticas bastante simples.A methodological proposal for the teaching of Calculus in Biology courses is suggested. It would highlight the attribution of biological meanings to variables and parameters in mathematical models within the study of population dynamics. Logistic equations have been used as a mathematical model that characterizes several types of population growth and other complexities of the biological phenomenon which may be better explained through mathematical concepts related to Differential Calculus. Relationship between Calculus and Biology may contribute towards the comprehension of complex biological phenomena that may be explained through simple mathematical equations.

  2. Research on Adaptive Variable Structure Control for Bi-ological Model of Red Tide%赤潮生物种群模型的自适应变结构控制器设计

    Institute of Scientific and Technical Information of China (English)



    【目的】为进一步改进有害藻和有益藻的消长控制模型,更好控制有害藻的发生,避免其所造成的危害。【方法】假设赤潮有害藻密度可测,有益藻密度不可测,在有害藻和有益藻密度模型正则化的基础上,设计神经网络观测器来估计有益藻对应的变量;然后,设计变结构控制使有害藻浓度减少而有益藻浓度增大,最终达到稳定状态。【结果】仿真分析结果显示,有害藻和有益藻持续在稳定的状态。【结论】变结构控制器的设计合理有效。%Objective]In order to overcome the weakness of traditional treatment methods of red tide(including physical method and chemical method),biological treatment technique was ex-plored,where the relationship among creature competition,biological inhibition and biological predation was evaluated.Introducing beneficial creature in the area of red tide could inhibit the eruption of red-tide algae,and reduce the occurrence of red-tide algae and its damage.[Methods]In the paper,we assumed that the density of harmful algae could be measured whereas the den-sity of beneficial algae could not be measured.Based on the regularization of the density model of harmful algae and beneficial algae,neural network viewer was designed to estimate corre-sponding changes of beneficial algae.Then,a variable structure control was designed to reduce the density of harmful algae and increase that of beneficial algae,and finally to reach a steady state.[Results]Simulation results of an example illustrated the effectiveness of the proposed method.[Conclusion]The designed variable structure control is effective.

  3. All biology is computational biology (United States)


    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. PMID:28278152

  4. Ashtekar variables (United States)

    Ashtekar, Abhay


    In the spirit of Scholarpedia, this invited article is addressed to students and younger researchers. It provides the motivation and background material, a summary of the main physical ideas, mathematical structures and results, and an outline of applications of the connection variables for general relativity. These variables underlie both the canonical/Hamiltonian and the spinfoam/path integral approaches in loop quantum gravity.

  5. Biological computation

    CERN Document Server

    Lamm, Ehud


    Introduction and Biological BackgroundBiological ComputationThe Influence of Biology on Mathematics-Historical ExamplesBiological IntroductionModels and Simulations Cellular Automata Biological BackgroundThe Game of Life General Definition of Cellular Automata One-Dimensional AutomataExamples of Cellular AutomataComparison with a Continuous Mathematical Model Computational UniversalitySelf-Replication Pseudo Code Evolutionary ComputationEvolutionary Biology and Evolutionary ComputationGenetic AlgorithmsExample ApplicationsAnalysis of the Behavior of Genetic AlgorithmsLamarckian Evolution Genet

  6. The biology of personality. (United States)

    Mulder, R


    Historically, models of personality have generally postulated, or assumed, a link with biology. This century has witnessed a major revision of these ideas with both behavioural and psychoanalytic theorists emphasising life experiences as being largely responsible for behaviour as adults. Challenges to this assumption of the overwhelming importance of life experiences are reviewed. An extensive body of data now exists suggesting that biology contributes significantly to individual variability. This biological contribution occurs at a relatively low level in the central nervous system, best defined as temperament. Further research has suffered from the lack of a cohesive psychobiological model. Cloninger's tridimensional theory of personality is presented as a model which attempts to bridge the gap between theoretical temperamental traits, neurotransmitter function and clinical psychiatry. It is to be hoped that new theoretical models will be formulated which will focus on the importance of temperamental variables in psychiatric disorders.

  7. Variabilidade biológica de isolados do Citrus leprosis virus (CiLV oriundos de cultivares de laranjeira Biological variability of Citrus leprosis virus (CiLV isolates from sweet orange cultivars

    Directory of Open Access Journals (Sweden)

    Jadier de Oliveira Cunha Junior


    Full Text Available A leprose, causada pelo Citrus leprosis virus (CiLV, é uma das principais doenças presentes em pomares cítricos fluminenses. O objetivo deste trabalho foi comparar o quadro sintomatológico desenvolvido por isolados de CiLV obtidos de cultivares comerciais de laranjeira (Lima, Pêra e Seleta, inoculados mecanicamente em Chenopodium amaranticolor, em três diluições. Após cinco a sete dias da inoculação foram observadas lesões necróticas, com pequeno halo clorótico quando observadas contra a luz. O maior número de lesões, nas três diluições, foi obtido do isolado de 'Seleta', seguido por 'Pêra' e 'Lima'. A melhor diluição utilizada para a observação das lesões foi de 1:10. Os resultados demonstram uma possível variabilidade biológica entre os isolados virais e/ou uma menor ou maior replicação viral, dependendo da cultivar, indicando um possível mecanismo de resistência da planta ao vírus.Citrus leprosis, caused by Citrus leprosis virus (CiLV is one of the major diseases in citrus orchards in the State of Rio de Janeiro. The objective of this study was to compare the development of symptoms on Chenopodium amaranticolor inoculated with CiLV isolates from 'Lima', 'Pera' and 'Seleta' sweet oranges using three different dilutions. Five to seven-days after inoculation, necrotic lesions exhibiting a small chlorotic halo when exposed to the light, were observed. The highest number of lesions developed using the three dilutions was obtained from 'Seleta', an intermediate value from 'Pêra' and the lowest number from 'Lima'. The best dilution for lesions development was 1:10. The results demonstrate a possible biological variability among the virus isolates and/or a lower or higher viral replication, dependent on the cultivar. This indicates a putative mechanism of Citrus resistance to the virus.

  8. [Biological weapons]. (United States)

    Kerwat, K; Becker, S; Wulf, H; Densow, D


    Biological weapons are weapons of mass destruction that use pathogens (bacteria, viruses) or the toxins produced by them to target living organisms or to contaminate non-living substances. In the past, biological warfare has been repeatedly used. Anthrax, plague and smallpox are regarded as the most dangerous biological weapons by various institutions. Nowadays it seems quite unlikely that biological warfare will be employed in any military campaigns. However, the possibility remains that biological weapons may be used in acts of bioterrorism. In addition all diseases caused by biological weapons may also occur naturally or as a result of a laboratory accident. Risk assessment with regard to biological danger often proves to be difficult. In this context, an early identification of a potentially dangerous situation through experts is essential to limit the degree of damage.

  9. Complex variables

    CERN Document Server

    Fisher, Stephen D


    The most important topics in the theory and application of complex variables receive a thorough, coherent treatment in this introductory text. Intended for undergraduates or graduate students in science, mathematics, and engineering, this volume features hundreds of solved examples, exercises, and applications designed to foster a complete understanding of complex variables as well as an appreciation of their mathematical beauty and elegance. Prerequisites are minimal; a three-semester course in calculus will suffice to prepare students for discussions of these topics: the complex plane, basic

  10. Is synthetic biology mechanical biology? (United States)

    Holm, Sune


    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.

  11. Computational biology

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue


    Computation via biological devices has been the subject of close scrutiny since von Neumann’s early work some 60 years ago. In spite of the many relevant works in this field, the notion of programming biological devices seems to be, at best, ill-defined. While many devices are claimed or proved t...

  12. Biological Oceanography (United States)

    Dyhrman, Sonya


    The ocean is arguably the largest habitat on the planet, and it houses an astounding array of life, from microbes to whales. As a testament to this diversity and its importance, the discipline of biological oceanography spans studies of all levels of biological organization, from that of single genes, to organisms, to their population dynamics. Biological oceanography also includes studies on how organisms interact with, and contribute to, essential global processes. Students of biological oceanography are often as comfortable looking at satellite images as they are electron micrographs. This diversity of perspective begins the textbook Biological Oceanography, with cover graphics including a Coastal Zone Color Scanner image representing chlorophyll concentration, an electron micrograph of a dinoflagellate, and a photograph of a copepod. These images instantly capture the reader's attention and illustrate some of the different scales on which budding oceanographers are required to think. Having taught a core graduate course in biological oceanography for many years, Charlie Miller has used his lecture notes as the genesis for this book. The text covers the subject of biological oceanography in a manner that is targeted to introductory graduate students, but it would also be appropriate for advanced undergraduates.

  13. Quantum Biology

    Directory of Open Access Journals (Sweden)

    Alessandro Sergi


    Full Text Available A critical assessment of the recent developmentsof molecular biology is presented.The thesis that they do not lead to a conceptualunderstanding of life and biological systems is defended.Maturana and Varela's concept of autopoiesis is briefly sketchedand its logical circularity avoided by postulatingthe existence of underlying living processes,entailing amplification from the microscopic to the macroscopic scale,with increasing complexity in the passage from one scale to the other.Following such a line of thought, the currently accepted model of condensed matter, which is based on electrostatics and short-ranged forces,is criticized. It is suggested that the correct interpretationof quantum dispersion forces (van der Waals, hydrogen bonding, and so onas quantum coherence effects hints at the necessity of includinglong-ranged forces (or mechanisms for them incondensed matter theories of biological processes.Some quantum effects in biology are reviewedand quantum mechanics is acknowledged as conceptually important to biology since withoutit most (if not all of the biological structuresand signalling processes would not even exist. Moreover, it is suggested that long-rangequantum coherent dynamics, including electron polarization,may be invoked to explain signal amplificationprocess in biological systems in general.

  14. Foldit Biology (United States)


    Report 8/1/2013-7/31/2015 4. TITLE AND SUBTITLE Sa. CONTRACT NUMBER Foldit Biology NOOO 14-13-C-0221 Sb. GRANT NUMBER N/A Sc. PROGRAM ELEMENT...Include area code) Unclassified Unclassified Unclassified (206) 616-2660 Zoran Popović Foldit Biology (Task 1, 2, 3, 4) Final Report...Period Covered by the Report August 1, 2013 – July 31, 2015 Date of Report: July 31, 2015 Project Title: Foldit Biology Contract Number: N00014-13

  15. Complex variables

    CERN Document Server

    Flanigan, Francis J


    A caution to mathematics professors: Complex Variables does not follow conventional outlines of course material. One reviewer noting its originality wrote: ""A standard text is often preferred [to a superior text like this] because the professor knows the order of topics and the problems, and doesn't really have to pay attention to the text. He can go to class without preparation."" Not so here-Dr. Flanigan treats this most important field of contemporary mathematics in a most unusual way. While all the material for an advanced undergraduate or first-year graduate course is covered, discussion

  16. Biological preconcentrator (United States)

    Manginell, Ronald P.; Bunker, Bruce C.; Huber, Dale L.


    A biological preconcentrator comprises a stimulus-responsive active film on a stimulus-producing microfabricated platform. The active film can comprise a thermally switchable polymer film that can be used to selectively absorb and desorb proteins from a protein mixture. The biological microfabricated platform can comprise a thin membrane suspended on a substrate with an integral resistive heater and/or thermoelectric cooler for thermal switching of the active polymer film disposed on the membrane. The active polymer film can comprise hydrogel-like polymers, such as poly(ethylene oxide) or poly(n-isopropylacrylamide), that are tethered to the membrane. The biological preconcentrator can be fabricated with semiconductor materials and technologies.

  17. Biology Notes. (United States)

    School Science Review, 1981


    Outlines a variety of laboratory procedures, techniques, and materials including construction of a survey frame for field biology, a simple tidal system, isolation and applications of plant protoplasts, tropisms, teaching lung structure, and a key to statistical methods for biologists. (DS)

  18. (Biological dosimetry)

    Energy Technology Data Exchange (ETDEWEB)

    Preston, R.J.


    The traveler attended the 1st International Conference on Biological Dosimetry in Madrid, Spain. This conference was organized to provide information to a general audience of biologists, physicists, radiotherapists, industrial hygiene personnel and individuals from related fields on the current ability of cytogenetic analysis to provide estimates of radiation dose in cases of occupational or environmental exposure. There is a growing interest in Spain in biological dosimetry because of the increased use of radiation sources for medical and occupational uses, and with this the anticipated and actual increase in numbers of overexposure. The traveler delivered the introductory lecture on Biological Dosimetry: Mechanistic Concepts'' that was intended to provide a framework by which the more applied lectures could be interpreted in a mechanistic way. A second component of the trip was to provide advice with regard to several recent cases of overexposure that had been or were being assessed by the Radiopathology and Radiotherapy Department of the Hospital General Gregorio Maranon'' in Madrid. The traveler had provided information on several of these, and had analyzed cells from some exposed or purportedly exposed individuals. The members of the biological dosimetry group were referred to individuals at REACTS at Oak Ridge Associated Universities for advice on follow-up treatment.

  19. Marine Biology (United States)

    Dewees, Christopher M.; Hooper, Jon K.


    A variety of informational material for a course in marine biology or oceanology at the secondary level is presented. Among the topics discussed are: food webs and pyramids, planktonic blooms, marine life, plankton nets, food chains, phytoplankton, zooplankton, larval plankton and filter feeders. (BT)

  20. Scaffolded biology. (United States)

    Minelli, Alessandro


    Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development. As scaffold, eventually, we can define any resource used by the biological system, especially in development and reproduction, without incorporating it as happens in the case of resources fueling metabolism. Addressing biological systems as functionally scaffolded systems may help pointing to functional relationships that can impart temporal marking to the developmental process and thus explain its irreversibility; revisiting the boundary between development and metabolism and also regeneration phenomena, by suggesting a conceptual framework within which to investigate phenomena of regular hypermorphic regeneration such as characteristic of deer antlers; fixing a periodization of development in terms of the times at which a scaffolding relationship begins or is terminated; and promoting plant galls to legitimate study objects of developmental biology.

  1. Biology Notes. (United States)

    School Science Review, 1984


    Presents information on the teaching of nutrition (including new information relating to many current O-level syllabi) and part 16 of a reading list for A- and S-level biology. Also includes a note on using earthworms as a source of material for teaching meiosis. (JN)

  2. Heritability and biological explanation. (United States)

    Turkheimer, E


    Modern neuroscientific and genetic technologies have provoked intense disagreement between scientists who envision a future in which biogenetic theories will enrich or even replace psychological theories, and others who consider biogenetic theories exaggerated, dehumanizing, and dangerous. Both sides of the debate about the role of genes and brains in the genesis of human behavior have missed an important point: All human behavior that varies among individuals is partially heritable and correlated with measurable aspects of brains, but the very ubiquity of these findings makes them a poor basis for reformulating scientists' conceptions of human behavior. Materialism requires psychological processes to be physically instantiated, but more crucial for psychology is the occasional empirical discovery of behavioral phenomena that are specific manifestations of low-level biological variables. Heritability and psychobiological association cannot be the basis for establishing whether behavior is genetic or biological, because to do so leads only to the banal tautology that all behavior is ultimately based in the genotype and brain.

  3. A framework for assessing inter-individual variability in pharmacokinetics using virtual human populations and integrating general knowledge of physical chemistry, biology, anatomy, physiology and genetics: A tale of 'bottom-up' vs 'top-down' recognition of covariates. (United States)

    Jamei, Masoud; Dickinson, Gemma L; Rostami-Hodjegan, Amin


    An increasing number of failures in clinical stages of drug development have been related to the effects of candidate drugs in a sub-group of patients rather than the 'average' person. Expectation of extreme effects or lack of therapeutic effects in some subgroups following administration of similar doses requires a full understanding of the issue of variability and the importance of identifying covariates that determine the exposure to the drug candidates in each individual. In any drug development program the earlier these covariates are known the better. An important component of the drive to decrease this failure rate in drug development involves attempts to use physiologically-based pharmacokinetics 'bottom-up' modeling and simulation to optimize molecular features with respect to the absorption, distribution, metabolism and elimination (ADME) processes. The key element of this approach is the separation of information on the system (i.e. human body) from that of the drug (e.g. physicochemical characteristics determining permeability through membranes, partitioning to tissues, binding to plasma proteins or affinities toward certain enzymes and transporter proteins) and the study design (e.g. dose, route and frequency of administration, concomitant drugs and food). In this review, the classical 'top-down' approach in covariate recognition is compared with the 'bottom-up' paradigm. The determinants and sources of inter-individual variability in different stages of drug absorption, distribution, metabolism and excretion are discussed in detail. Further, the commonly known tools for simulating ADME properties are introduced.

  4. Systems biology analysis merging phenotype, metabolomic and genomic data identifies Non-SMC Condensin I Complex, Subunit G (NCAPG and cellular maintenance processes as major contributors to genetic variability in bovine feed efficiency.

    Directory of Open Access Journals (Sweden)

    Philipp Widmann

    Full Text Available Feed efficiency is a paramount factor for livestock economy. Previous studies had indicated a substantial heritability of several feed efficiency traits. In our study, we investigated the genetic background of residual feed intake, a commonly used parameter of feed efficiency, in a cattle resource population generated from crossing dairy and beef cattle. Starting from a whole genome association analysis, we subsequently performed combined phenotype-metabolome-genome analysis taking a systems biology approach by inferring gene networks based on partial correlation and information theory approaches. Our data about biological processes enriched with genes from the feed efficiency network suggest that genetic variation in feed efficiency is driven by genetic modulation of basic processes relevant to general cellular functions. When looking at the predicted upstream regulators from the feed efficiency network, the Tumor Protein P53 (TP53 and Transforming Growth Factor beta 1 (TGFB1 genes stood out regarding significance of overlap and number of target molecules in the data set. These results further support the hypothesis that TP53 is a major upstream regulator for genetic variation of feed efficiency. Furthermore, our data revealed a significant effect of both, the Non-SMC Condensin I Complex, Subunit G (NCAPG I442M (rs109570900 and the Growth /differentiation factor 8 (GDF8 Q204X (rs110344317 loci, on residual feed intake and feed conversion. For both loci, the growth promoting allele at the onset of puberty was associated with a negative, but favorable effect on residual feed intake. The elevated energy demand for increased growth triggered by the NCAPG 442M allele is obviously not fully compensated for by an increased efficiency in converting feed into body tissue. As a consequence, the individuals carrying the NCAPG 442M allele had an additional demand for energy uptake that is reflected by the association of the allele with increased daily

  5. Biologic Influences on Exercise Adherence. (United States)

    Dishman, Rod K.


    Diagnostic profiles of 362 male participants in an exercise program were analyzed to determine the biological variables between exercise adherence and symptoms of coronary disease. Findings indicated that individuals with lower metabolic capacity tended to adhere longer, to be less fit, were leaner, and began with more symptoms related to coronary…

  6. Mesoscopic biology

    Indian Academy of Sciences (India)

    G V Shivashankar


    In this paper we present a qualitative outlook of mesoscopic biology where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy. Novel biomolecular machines, governed by coded information at the level of DNA and proteins, operate at these length scales in biological systems. In recent years advances in technology have led to the study of some of the design principles of these machines; in particular at the level of an individual molecule. For example, the forces that operate in molecular interactions, the stochasticity involved in these interactions and their spatio-temporal dynamics are beginning to be explored. Understanding such design principles is opening new possibilities in mesoscopic physics with potential applications.

  7. Marine biology

    Energy Technology Data Exchange (ETDEWEB)

    Thurman, H.V.; Webber, H.H.


    This book discusses both taxonomic and ecological topics on marine biology. Full coverage of marine organisms of all five kingdoms is provided, along with interesting and thorough discussion of all major marine habitats. Organization into six major parts allows flexibility. It also provides insight into important topics such as disposal of nuclear waste at sea, the idea that life began on the ocean floor, and how whales, krill, and people interact. A full-color photo chapter reviews questions, and exercises. The contents are: an overview marine biology: fundamental concepts/investigating life in the ocean; the physical ocean, the ocean floor, the nature of water, the nature and motion of ocean water; general ecology, conditions for life in the sea, biological productivity and energy transfer; marine organisms; monera, protista, mycota and metaphyta; the smaller marine animals, the large animals marine habitats, the intertidal zone/benthos of the continental shelf, the photic zone, the deep ocean, the ocean under stress, marine pollution, appendix a: the metric system and conversion factors/ appendix b: prefixes and suffixes/ appendix c: taxonomic classification of common marine organisms, and glossary, and index.

  8. Atmospheric variables as driving variables of agricultural and forest ecosystems

    Directory of Open Access Journals (Sweden)

    Luigi Mariani

    Full Text Available Atmospheric variables, which represent meteorology if seen in their instantaneous behavior or climatology if seen in their long time behavior, can be considered among the main driving variables of agricultural and forest ecosystems. In other words meteo-climatic variables determine productivity and quality and territorial specificity of agroforestry productions. On the base of this premise some significant examples are shown in order to describe how different modeling approaches (empirical and mechanistic can improve our degree of description of phenomena and the rationality of our approach to management of agro-ecosystem. The need of strict linkage among agrometeorology and other physical and biological sciences referred to agro-forestry ecosystems is also discussed.

  9. Biological Databases

    Directory of Open Access Journals (Sweden)

    Kaviena Baskaran


    Full Text Available Biology has entered a new era in distributing information based on database and this collection of database become primary in publishing information. This data publishing is done through Internet Gopher where information resources easy and affordable offered by powerful research tools. The more important thing now is the development of high quality and professionally operated electronic data publishing sites. To enhance the service and appropriate editorial and policies for electronic data publishing has been established and editors of article shoulder the responsibility.

  10. Variability control: key to regulatory compliance and sustainability goals. (United States)

    Englande, A J; Eckenfelder, W W; Jin, G


    The focus of this paper is on variability concerns in wastewater treatment and approaches to control unacceptable fluctuations in effluent quality. Areas considered include: factors contributing to variability in both waste loads and process technology performance; variability assessment; control of variability employing the process best management practice (BMP); design/operation of biological waste treatment technologies for variability reduction; and modelling to enhance process control.

  11. Biological biomaterials

    Energy Technology Data Exchange (ETDEWEB)

    Jorge-Herrero, E. [Servicio de Cirugia Experimental. Clinica Puerta de Hierro, Madrid (Spain)


    There are a number of situations in which substances of biological origin are employed as biomaterials. Most of them are macromolecules derived from isolated connective tissue or the connective tissue itself in membrane form, in both cases, the tissue can be used in its natural form or be chemically treated. In other cases, certain blood vessels can be chemically pretreated and used as vascular prostheses. Proteins such as albumin, collagen and fibrinogen are employed to coat vascular prostheses. Certain polysaccharides have also been tested for use in controlled drug release systems. Likewise, a number of tissues, such as dura mater, bovine pericardium, procine valves and human valves, are used in the preparation of cardiac prostheses. We also use veins from animals or humans in arterial replacement. In none of these cases are the tissues employed dissimilar to the native tissues as they have been chemically modified, becoming a new bio material with different physical and biochemical properties. In short, we find that natural products are being utilized as biomaterials and must be considered as such; thus, it is necessary to study both their chemicobiological and physicomechanical properties. In the present report, we review the current applications, problems and future prospects of some of these biological biomaterials. (Author) 84 refs.

  12. Structural Biology Fact Sheet (United States)

    ... Home > Science Education > Structural Biology Fact Sheet Structural Biology Fact Sheet Tagline (Optional) Middle/Main Content Area What is structural biology? Structural biology is a field of science focused ...

  13. Simulating Biological and Non-Biological Motion (United States)

    Bruzzo, Angela; Gesierich, Benno; Wohlschlager, Andreas


    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…

  14. A Brief Introduction to Chinese Biological Biological

    Institute of Scientific and Technical Information of China (English)


    Chinese Biological Abstracts sponsored by the Library, the Shanghai Institutes for Biological Sciences, the Biological Documentation and Information Network, all of the Chinese Academy of Sciences, commenced publication in 1987 and was initiated to provide access to the Chinese information in the field of biology.

  15. Cell biology perspectives in phage biology. (United States)

    Ansaldi, Mireille


    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.

  16. Wireless-accessible sensor populations for monitoring biological variables

    NARCIS (Netherlands)

    Mazzu, Marco; Scalvini, Simonetta; Giordano, A.; Frumento, E.; Wells, Hannah; Lokhorst, C.; Glisenti, Fulvio


    The current health-care infrastructure is generally considered to be inadequate to meet the needs of an increasingly older population. We have investigated the feasibility of a passive in-home monitoring system based on wireless accessible sensor populations (WASP). In an EU-funded project we have i

  17. Single-molecule dynamics at variable temperatures

    NARCIS (Netherlands)

    Zondervan, Rob


    Single-molecule optics has evolved from a specialized variety of optical spectroscopy at low temperatures into a versatile tool to address questions in physics, chemistry, biology, and materials science. In this thesis, the potential of single-molecule (and ensemble) optical microscopy at variable t

  18. Bio-inspired variable structural color materials. (United States)

    Zhao, Yuanjin; Xie, Zhuoying; Gu, Hongcheng; Zhu, Cun; Gu, Zhongze


    Natural structural color materials, especially those that can undergo reversible changes, are attracting increasing interest in a wide variety of research fields. Inspired by the natural creatures, many elaborately nanostructured photonic materials with variable structural colors were developed. These materials have found important applications in switches, display devices, sensors, and so on. In this critical review, we will provide up-to-date research concerning the natural and bio-inspired photonic materials with variable structural colors. After introducing the variable structural colors in natural creatures, we will focus on the studies of artificial variable structural color photonic materials, including their bio-inspired designs, fabrications and applications. The prospects for the future development of these fantastic variable structural color materials will also be presented. We believe this review will promote the communications among biology, bionics, chemistry, optical physics, and material science (196 references).

  19. Biological warfare agents. (United States)

    Pohanka, Miroslav; Kuca, Kamil


    Biological warfare agents are a group of pathogens and toxins of biological origin that can be potentially misused for military or criminal purposes. The present review attempts to summarize necessary knowledge about biological warfare agents. The historical aspects, examples of applications of these agents such as anthrax letters, biological weapons impact, a summary of biological warfare agents and epidemiology of infections are described. The last section tries to estimate future trends in research on biological warfare agents.

  20. Intraspecific chromosome variability

    Directory of Open Access Journals (Sweden)

    N Dubinin


    Full Text Available (Editorial preface. The publication is presented in order to remind us of one of dramatic pages of the history of genetics. It re-opens for the contemporary reader a comprehensive work marking the priority change from plant cytogenetics to animal cytogenetics led by wide population studies which were conducted on Drosophila polytene chromosomes. The year of the publication (1937 became the point of irretrievable branching between the directions of Old World and New World genetics connected with the problems of chromosome variability and its significance for the evolution of the species. The famous book of T. Dobzhansky (1937 was published by Columbia University in the US under the title “Genetics and the origin of species”, and in the shadow of this American ‘skybuilding’ all other works grew dim. It is remarkable that both Dobzhansky and Dubinin come to similar conclusions about the role of chromosomes in speciation. This is not surprising given that they both might be considered as representatives of the Russian genetic school, by their birth and education. Interestingly, Dobzhansky had never referred to the full paper of Dubinin et al. (1937, though a previous short communication in Nature (1936 was included together with all former papers on the related subject. In full, the volume of the original publication printed in the Biological Journal in Moscow comprised 47 pages, in that number 41 pages of the Russian text accompanied by 16 Figs, a table and reference list, and, above all, 6 pages of the English summary. This final part in English is now reproduced in the authors’ version with the only addition being the reference list in the originally printed form.

  1. Variability as an Operant? (United States)

    Holth, Per


    A series of experiments on operant variability by Neuringer and colleagues (e.g., Neuringer, 1986, 2002; Page & Neuringer, 1985) have been repeatedly cited as showing that behavioral variability can be reinforced by making reinforcement contingent on it. They showed that the degree of variability in pigeons' eight-peck sequences, as measured by U…

  2. Biological conversion system (United States)

    Scott, C.D.

    A system for bioconversion of organic material comprises a primary bioreactor column wherein a biological active agent (zymomonas mobilis) converts the organic material (sugar) to a product (alcohol), a rejuvenator column wherein the biological activity of said biological active agent is enhanced, and means for circulating said biological active agent between said primary bioreactor column and said rejuvenator column.

  3. Network biology methods integrating biological data for translational science. (United States)

    Bebek, Gurkan; Koyutürk, Mehmet; Price, Nathan D; Chance, Mark R


    The explosion of biomedical data, both on the genomic and proteomic side as well as clinical data, will require complex integration and analysis to provide new molecular variables to better understand the molecular basis of phenotype. Currently, much data exist in silos and is not analyzed in frameworks where all data are brought to bear in the development of biomarkers and novel functional targets. This is beginning to change. Network biology approaches, which emphasize the interactions between genes, proteins and metabolites provide a framework for data integration such that genome, proteome, metabolome and other -omics data can be jointly analyzed to understand and predict disease phenotypes. In this review, recent advances in network biology approaches and results are identified. A common theme is the potential for network analysis to provide multiplexed and functionally connected biomarkers for analyzing the molecular basis of disease, thus changing our approaches to analyzing and modeling genome- and proteome-wide data.

  4. Synthetic biology: insights into biological computation. (United States)

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


    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

  5. Translational environmental biology: cell biology informing conservation. (United States)

    Traylor-Knowles, Nikki; Palumbi, Stephen R


    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.

  6. Biología poblacional de huirales submareales de Macrocystis integrifolia y Lessonia trabeculata (Laminariales, Phaeophyceae en un ecosistema de surgencia del norte de Chile: variabilidad interanual y El Niño 1997-1998 Population biology of the subtidal kelps Macrocystis integrifolia and Lessonia trabeculata (Laminariales, Phaeophyceae in an upwelling ecosystem of northern Chile: interannual variability and El Niño 1997-1998

    Directory of Open Access Journals (Sweden)



    of L. trabeculata, although drifting kelp rafts and "seed banks" of microscopic dormant stages may provide supplementary recruitment. In the temperate SE Pacific, oceanographic events that act on different spatial-temporal scales plus low frequency biological processes (changes in grazer abundance, which act on local scales, produce inter-annual variability in the long-term dymanics of kelp populations. Furthermore, the interactive effects between centers of permanent upwelling and the oscillating temporal periodicity of oceanographic events that produce positive (El Niño and negative (La Niña thermal anomalies modify the spatial arrangement of subtidal kelp populations on a latitudinal gradientEste trabajo describe la biología poblacional de Macrocystis integrifolia y Lessonia trabeculata durante y después de El Niño 1997-1998, en un área de surgencia costera permanente en el norte de Chile. Los patrones de distribución espacio-temporales de esporofitos adultos y juveniles de ambos huiros fueron evaluados estacionalmente entre 1996 y 2003. Ambos huiros conforman un ensamble que se distribuye entre 2-15 m de profundidad con patrones disjuntos a lo largo del gradiente batimétrico, y con dos morfos de L. trabeculata que dependen de la presencia o ausencia de M. integrifolia. Durante El Niño 1997-1998, los patrones espacio-temporales de abundancia del ensamble de huiros son mantenidos por la continuidad de los procesos de surgencia costera que amortiguan y moderan el calentamiento superficial del mar y la disminución de nutrientes. En este contexto, después de un evento El Niño las localidades asociadas a áreas con surgencia permanente pueden funcionar como áreas "fuentes" productora de propágulos reproductivos incrementando la tasa de recolonización en áreas "sumideros" adyacentes donde se produjo extinción local de huiros. Durante La Niña 1998-2000, la intensificación de los procesos de surgencia incrementa la entrada de nutrientes hacia h

  7. Computational Systems Chemical Biology


    Oprea, Tudor I.; Elebeoba E. May; Leitão, Andrei; Tropsha, Alexander


    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007).

  8. The semantics of biological forms. (United States)

    Albertazzi, Liliana; Canal, Luisa; Dadam, James; Micciolo, Rocco


    This study analyses how certain qualitative perceptual appearances of biological forms are correlated with expressions of natural language. Making use of the Osgood semantic differential, we presented the subjects with 32 drawings of biological forms and a list of 10 pairs of connotative adjectives to be put in correlations with them merely by subjective judgments. The principal components analysis made it possible to group the semantics of forms according to two distinct axes of variability: harmony and dynamicity. Specifically, the nonspiculed, nonholed, and flat forms were perceived as harmonic and static; the rounded ones were harmonic and dynamic. The elongated forms were somewhat disharmonious and somewhat static. The results suggest the existence in the general population of a correspondence between perceptual and semantic processes, and of a nonsymbolic relation between visual forms and their adjectival expressions in natural language.

  9. Variability of Blazars

    Indian Academy of Sciences (India)

    J. H. Fan; Y. Liu; Y. Li; Q. F. Zhang; J. Tao; O. Kurtanidze


    Variability is one of the characteristics of blazars. The rapid variability is superposed on the long term variation. In this work, the variability on different time scales, such as intra-day (IDV), short-term (STV) and long-term (LTV) variations are presented for some sources. We also presented our own observations of some selected objects, for which the historical data were compiled for periodicity analysis using several methods. The parameters of the binary black hole system OJ 287 are determined.

  10. Brainstem response and state-trait variables (United States)

    Gilliland, Kirby


    A series of investigations are summarized from a personality research program that have relevance for mental state estimation. Of particular concern are those personality variables that are believed to have either a biological or perceptual basis and their relationship to human task performance and psychophysiology. These variables are among the most robust personality measures and include such dimensions as extraversion-introversion, sensation seeking, and impulsiveness. These dimensions also have the most distinct link to performance and psychophysiology. Through the course of many of these investigations two issues have emerged repeatedly: these personality dimensions appear to mediate mental state, and mental state appears to influence measures of performance or psychophysiology.

  11. The nebular variables

    CERN Document Server

    Glasby, John S


    The Nebular Variables focuses on the nebular variables and their characteristics. Discussions are organized by type of nebular variable, namely, RW Aurigae stars, T Orionis stars, T Tauri stars, and peculiar nebular objects. Topics range from light variations of the stars to their spectroscopic and physical characteristics, spatial distribution, interaction with nebulosity, and evolutionary features. This volume is divided into four sections and consists of 25 chapters, the first of which provides general information on nebular variables, including their stellar associations and their classifi

  12. Does biological relatedness affect child survival?

    Directory of Open Access Journals (Sweden)


    Full Text Available Objective: We studied child survival in Rakai, Uganda where many children are fostered out or orphaned. Methods: Biological relatedness is measured as the average of the Wright's coefficients between each household member and the child. Instrumental variables for fostering include proportion of adult males in household, age and gender of household head. Control variables include SES, religion, polygyny, household size, child age, child birth size, and child HIV status. Results: Presence of both parents in the household increased the odds of survival by 28%. After controlling for the endogeneity of child placement decisions in a multivariate model we found that lower biological relatedness of a child was associated with statistically significant reductions in child survival. The effects of biological relatedness on child survival tend to be stronger for both HIV- and HIV+ children of HIV+ mothers. Conclusions: Reductions in the numbers of close relatives caring for children of HIV+ mothers reduce child survival.

  13. Resetting Biological Clocks (United States)

    Winfree, Arthur T.


    Reports on experiments conducted on two biological clocks, in organisms in the plant and animal kingdoms, which indicate that biological oscillation can be arrested by a single stimulus of a definite strength delivered at the proper time. (GS)

  14. Biology is simple. (United States)

    Newman, Tim


    This paper explores the potential for simplicity to reveal new biological understanding. Borrowing selectively from physics thinking, and contrasting with Crick's reductionist philosophy, the author argues that greater emphasis on simplicity is necessary to advance biology and its applications.

  15. Biology of Blood (United States)

    ... here for the Professional Version Home Blood Disorders Biology of Blood Overview of Blood Resources In This ... Version. DOCTORS: Click here for the Professional Version Biology of Blood Overview of Blood Components of Blood ...

  16. Variable volume combustor

    Energy Technology Data Exchange (ETDEWEB)

    Ostebee, Heath Michael; Ziminsky, Willy Steve; Johnson, Thomas Edward; Keener, Christopher Paul


    The present application provides a variable volume combustor for use with a gas turbine engine. The variable volume combustor may include a liner, a number of micro-mixer fuel nozzles positioned within the liner, and a linear actuator so as to maneuver the micro-mixer fuel nozzles axially along the liner.



    Rozet, Eric; de Tullio, Pascal; Hubert, Philippe; Govaerts., B.


    Due to the huge amount of information available in NMR spectra obtained from the analysis of metabolomic experiments, multivariate analysis such as Principal Component Analysis (PCA) are required to understand the influence of treatments over the metabolites [1]. However, many experiments in metabolomics studies have more complexes variability structures than simply comparing several treatments: they may include time effects, biological effects such as diet or hormonal status, and other bloc...

  18. Designing synthetic biology. (United States)

    Agapakis, Christina M


    Synthetic biology is frequently defined as the application of engineering design principles to biology. Such principles are intended to streamline the practice of biological engineering, to shorten the time required to design, build, and test synthetic gene networks. This streamlining of iterative design cycles can facilitate the future construction of biological systems for a range of applications in the production of fuels, foods, materials, and medicines. The promise of these potential applications as well as the emphasis on design has prompted critical reflection on synthetic biology from design theorists and practicing designers from many fields, who can bring valuable perspectives to the discipline. While interdisciplinary connections between biologists and engineers have built synthetic biology via the science and the technology of biology, interdisciplinary collaboration with artists, designers, and social theorists can provide insight on the connections between technology and society. Such collaborations can open up new avenues and new principles for research and design, as well as shed new light on the challenging context-dependence-both biological and social-that face living technologies at many scales. This review is inspired by the session titled "Design and Synthetic Biology: Connecting People and Technology" at Synthetic Biology 6.0 and covers a range of literature on design practice in synthetic biology and beyond. Critical engagement with how design is used to shape the discipline opens up new possibilities for how we might design the future of synthetic biology.




  20. Biology Myth-Killers (United States)

    Lampert, Evan


    "Biology Myth-Killers" is an activity designed to identify and correct common misconceptions for high school and college introductory biology courses. Students identify common myths, which double as biology misconceptions, and use appropriate sources to share the "truth" about the myths. This learner-centered activity is a fun…

  1. Distinguishability of Biological Material Using Ultraviolet Multi-Spectral Fluorescence

    Energy Technology Data Exchange (ETDEWEB)

    Gray, P.C.; Heinen, R.J.; Rigdon, L.D.; Rosenthal, S.E.; Shokair, I.R.; Siragusa, G.R.; Tisone, G.C.; Wagner, J.S.


    Recent interest in the detection and analysis of biological samples by spectroscopic methods has led to questions concerning the degree of distinguishability and biological variability of the ultraviolet (W) fluorescent spectra from such complex samples. We show that the degree of distinguishability of such spectra is readily determined numerically.

  2. Breeding biology and nestling development of the Grasshopper Buzzard

    NARCIS (Netherlands)

    Buij, R.; Kortekaas, K.; Folkertsma, I.; van der Velde, M.; Komdeur, J.; de Iongh, H. H.; Monadjem, A.


    Research into the effect of environmental variables on reproductive success of tropical raptors is often constrained by the lack of information on breeding biology. We provide the first detailed information of the breeding biology and nestling development of the Grasshopper Buzzard Butastur rufipenn

  3. Time lags in biological models

    CERN Document Server

    MacDonald, Norman


    In many biological models it is necessary to allow the rates of change of the variables to depend on the past history, rather than only the current values, of the variables. The models may require discrete lags, with the use of delay-differential equations, or distributed lags, with the use of integro-differential equations. In these lecture notes I discuss the reasons for including lags, especially distributed lags, in biological models. These reasons may be inherent in the system studied, or may be the result of simplifying assumptions made in the model used. I examine some of the techniques available for studying the solution of the equations. A large proportion of the material presented relates to a special method that can be applied to a particular class of distributed lags. This method uses an extended set of ordinary differential equations. I examine the local stability of equilibrium points, and the existence and frequency of periodic solutions. I discuss the qualitative effects of lags, and how these...

  4. Dynamical Systems and Control Theory Inspired by Molecular Biology (United States)


    in both bacterial and eukaryotic signaling pathways. A common theme in the systems biology literature is that certain systems whose output variables...AFRL-OSR-VA-TR-2014-0282 DYNAMICAL SYSTEMS AND CONTROL THEORY INSPIRED BY MOLECULAR BIOLOGY Eduardo Sontag RUTGERS THE STATE UNIVERSITY OF NEW JERSEY...Standard Form 298 (Re . 8-98) v Prescribed by ANSI Std. Z39.18 DYNAMICAL SYSTEMS AND CONTROL THEORY INSPIRED BY MOLECULAR BIOLOGY AFOSR FA9550-11-1-0247

  5. Eternity Variables to Simulate Specifications

    NARCIS (Netherlands)

    Hesselink, WH; Boiten, EA; Moller, B


    Simulation of specifications is introduced as a unification and generalization of refinement mappings, history variables, forward simulations, prophecy variables, and backward simulations. Eternity variables are introduced as a more powerful alternative for prophecy variables and backward simulation

  6. Computational systems chemical biology. (United States)

    Oprea, Tudor I; May, Elebeoba E; Leitão, Andrei; Tropsha, Alexander


    There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology (SCB) (Nat Chem Biol 3: 447-450, 2007).The overarching goal of computational SCB is to develop tools for integrated chemical-biological data acquisition, filtering and processing, by taking into account relevant information related to interactions between proteins and small molecules, possible metabolic transformations of small molecules, as well as associated information related to genes, networks, small molecules, and, where applicable, mutants and variants of those proteins. There is yet an unmet need to develop an integrated in silico pharmacology/systems biology continuum that embeds drug-target-clinical outcome (DTCO) triplets, a capability that is vital to the future of chemical biology, pharmacology, and systems biology. Through the development of the SCB approach, scientists will be able to start addressing, in an integrated simulation environment, questions that make the best use of our ever-growing chemical and biological data repositories at the system-wide level. This chapter reviews some of the major research concepts and describes key components that constitute the emerging area of computational systems chemical biology.

  7. Quantum biological information theory

    CERN Document Server

    Djordjevic, Ivan B


    This book is a self-contained, tutorial-based introduction to quantum information theory and quantum biology. It serves as a single-source reference to the topic for researchers in bioengineering, communications engineering, electrical engineering, applied mathematics, biology, computer science, and physics. The book provides all the essential principles of the quantum biological information theory required to describe the quantum information transfer from DNA to proteins, the sources of genetic noise and genetic errors as well as their effects. Integrates quantum information and quantum biology concepts; Assumes only knowledge of basic concepts of vector algebra at undergraduate level; Provides a thorough introduction to basic concepts of quantum information processing, quantum information theory, and quantum biology; Includes in-depth discussion of the quantum biological channel modelling, quantum biological channel capacity calculation, quantum models of aging, quantum models of evolution, quantum models o...

  8. Matricially free random variables

    CERN Document Server

    Lenczewski, Romuald


    We show that the operatorial framework developed by Voiculescu for free random variables can be extended to arrays of random variables whose multiplication imitates matricial multiplication. The associated notion of independence, called matricial freeness, can be viewed as a generalization of both freeness and monotone independence. At the same time, the sums of matricially free random variables, called random pseudomatrices, are closely related to Gaussian random matrices. The main results presented in this paper concern the standard and tracial central limit theorems for random pseudomatrices and the corresponding limit distributions which can be viewed as matricial generalizations of semicirle laws.

  9. Variable Attitude Test Stand (United States)

    Federal Laboratory Consortium — The Variable Attitude Test Stand designed and built for testing of the V-22 tilt rotor aircraft propulsion system, is used to evaluate the effect of aircraft flight...

  10. The Princeton Variability Survey

    CERN Document Server

    Blake, C


    The Princeton Variability Survey (PVS) is a robotic survey which makes use of readily available, ``off-the-shelf'' type hardware products, in conjunction with a powerful set of commercial software products, in order to monitor and discover variable objects in the night sky. The main goal of the PVS has been to devise an automated telescope and data reduction system, requiring only moderate technical and financial resources to assemble, which may be easily replicated by the dedicated amateur, a student group, or a professional and used to study and discover a variety of variable objects, such as stars. This paper describes the hardware and software components of the PVS device, as well as observational results from the initial season of the PVS, including the discovery of a new bright variable star.

  11. Calculus of one variable

    CERN Document Server

    Grossman, Stanley I


    Calculus of One Variable, Second Edition presents the essential topics in the study of the techniques and theorems of calculus.The book provides a comprehensive introduction to calculus. It contains examples, exercises, the history and development of calculus, and various applications. Some of the topics discussed in the text include the concept of limits, one-variable theory, the derivatives of all six trigonometric functions, exponential and logarithmic functions, and infinite series.This textbook is intended for use by college students.

  12. Software Testing Requires Variability

    DEFF Research Database (Denmark)

    Christensen, Henrik Bærbak


    Software variability is the ability of a software system or artefact to be changed, customized or configured for use in a particular context. Variability in software systems is important from a number of perspectives. Some perspectives rightly receive much attention due to their direct economic...... impact in software production. As is also apparent from the call for papers these perspectives focus on qualities such as reuse, adaptability, and maintainability....

  13. Standard biological parts knowledgebase. (United States)

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


    We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology ( 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 ( 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.

  14. Standard biological parts knowledgebase.

    Directory of Open Access Journals (Sweden)

    Michal Galdzicki

    Full Text Available We have created the Knowledgebase of Standard Biological Parts (SBPkb as a publically accessible Semantic Web resource for synthetic biology ( 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 ( 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.

  15. The Fractal Simulation Of Biological Shapes (United States)

    Pickover, Clifford A.


    This paper provides a light introduction to simple graphics techniques for visualizing a large class of biological shapes generated from recursive algorithms. In order to capture some of the structural richness inherent in organisms, the algorithms produce not only extreme variability but also a high level of organization. The material primarily comes from previous published works of the author. For a general background on fractal methods in mathematics and science, see Mandelbrot's famous book. For research on the fractal characterization of other biological structures, such as the lung's bronchial tree and the surfaces of protein molecules.

  16. Plant synthetic biology. (United States)

    Liu, Wusheng; Stewart, C Neal


    Plant synthetic biology is an emerging field that combines engineering principles with plant biology toward the design and production of new devices. This emerging field should play an important role in future agriculture for traditional crop improvement, but also in enabling novel bioproduction in plants. In this review we discuss the design cycles of synthetic biology as well as key engineering principles, genetic parts, and computational tools that can be utilized in plant synthetic biology. Some pioneering examples are offered as a demonstration of how synthetic biology can be used to modify plants for specific purposes. These include synthetic sensors, synthetic metabolic pathways, and synthetic genomes. We also speculate about the future of synthetic biology of plants.

  17. Branching processes in biology

    CERN Document Server

    Kimmel, Marek


    This book provides a theoretical background of branching processes and discusses their biological applications. Branching processes are a well-developed and powerful set of tools in the field of applied probability. The range of applications considered includes molecular biology, cellular biology, human evolution and medicine. The branching processes discussed include Galton-Watson, Markov, Bellman-Harris, Multitype, and General Processes. As an aid to understanding specific examples, two introductory chapters, and two glossaries are included that provide background material in mathematics and in biology. The book will be of interest to scientists who work in quantitative modeling of biological systems, particularly probabilists, mathematical biologists, biostatisticians, cell biologists, molecular biologists, and bioinformaticians. The authors are a mathematician and cell biologist who have collaborated for more than a decade in the field of branching processes in biology for this new edition. This second ex...

  18. Classifying TDSS Stellar Variables (United States)

    Amaro, Rachael Christina; Green, Paul J.; TDSS Collaboration


    The Time Domain Spectroscopic Survey (TDSS), a subprogram of SDSS-IV eBOSS, obtains classification/discovery spectra of point-source photometric variables selected from PanSTARRS and SDSS multi-color light curves regardless of object color or lightcurve shape. Tens of thousands of TDSS spectra are already available and have been spectroscopically classified both via pipeline and by visual inspection. About half of these spectra are quasars, half are stars. Our goal is to classify the stars with their correct variability types. We do this by acquiring public multi-epoch light curves for brighter stars (rprogram for analyzing astronomical time-series data, to constrain variable type both for broad statistics relevant to future surveys like the Transiting Exoplanet Survey Satellite (TESS) and the Large Synoptic Survey Telescope (LSST), and to find the inevitable exotic oddballs that warrant further follow-up. Specifically, the Lomb-Scargle Periodogram and the Box-Least Squares Method are being implemented and tested against their known variable classifications and parameters in the Catalina Surveys Periodic Variable Star Catalog. Variable star classifications include RR Lyr, close eclipsing binaries, CVs, pulsating white dwarfs, and other exotic systems. The key difference between our catalog and others is that along with the light curves, we will be using TDSS spectra to help in the classification of variable type, as spectra are rich with information allowing estimation of physical parameters like temperature, metallicity, gravity, etc. This work was supported by the SDSS Research Experience for Undergraduates program, which is funded by a grant from Sloan Foundation to the Astrophysical Research Consortium.

  19. Chemical Biology is.....



    Chemical Biology is a relatively new field, and as such is not yet simply or succinctly defined. It includes such a wide range of fundamental problems that this commentary could only include just a few snapshots of potential areas of interest. Overarching themes and selected recent successes and ideas in chemical biology are described to illustrate broadly the scope of the field, but should not be taken as exhaustive. The Chemical Biology Section of Chemistry Central Journal is pleased to rec...

  20. Biological detector and method

    Energy Technology Data Exchange (ETDEWEB)

    Sillerud, Laurel; Alam, Todd M.; McDowell, Andrew F.


    A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

  1. Biological detector and method (United States)

    Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F


    A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

  2. Biological detector and method (United States)

    Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F


    A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

  3. Chemical space and biology. (United States)

    Dobson, Christopher M


    Chemical space--which encompasses all possible small organic molecules, including those present in biological systems--is vast. So vast, in fact, that so far only a tiny fraction of it has been explored. Nevertheless, these explorations have greatly enhanced our understanding of biology, and have led to the development of many of today's drugs. The discovery of new bioactive molecules, facilitated by a deeper understanding of the nature of the regions of chemical space that are relevant to biology, will advance our knowledge of biological processes and lead to new strategies to treat disease.

  4. Polythiophenes in biological applications. (United States)

    Sista, Prakash; Ghosh, Koushik; Martinez, Jennifer S; Rocha, Reginaldo C


    Polythiophene and its derivatives have shown tremendous potential for interfacing electrically conducting polymers with biological applications. These semiconducting organic polymers are relatively soft, conduct electrons and ions, have low cytotoxicity, and can undergo facile chemical modifications. In addition, the reduction in electrical impedance of electrodes coated with polythiophenes may prove to be invaluable for a stable and permanent connection between devices and biological tissues. This review article focuses on the synthesis and some key applications of polythiophenes in multidisciplinary areas at the interface with biology. These polymers have shown tremendous potential in biological applications such as diagnostics, therapy, drug delivery, imaging, implant devices and artificial organs.

  5. Mathematical models in biology bringing mathematics to life

    CERN Document Server

    Ferraro, Maria; Guarracino, Mario


    This book presents an exciting collection of contributions based on the workshop “Bringing Maths to Life” held October 27-29, 2014 in Naples, Italy.  The state-of-the art research in biology and the statistical and analytical challenges facing huge masses of data collection are treated in this Work. Specific topics explored in depth surround the sessions and special invited sessions of the workshop and include genetic variability via differential expression, molecular dynamics and modeling, complex biological systems viewed from quantitative models, and microscopy images processing, to name several. In depth discussions of the mathematical analysis required to extract insights from complex bodies of biological datasets, to aid development in the field novel algorithms, methods and software tools for genetic variability, molecular dynamics, and complex biological systems are presented in this book. Researchers and graduate students in biology, life science, and mathematics/statistics will find the content...

  6. Deconstructed Transverse Mass Variables

    CERN Document Server

    Ismail, Ahmed; Virzi, Joseph S; Walker, Devin G E


    Traditional searches for R-parity conserving natural supersymmetry (SUSY) require large transverse mass and missing energy cuts to separate the signal from large backgrounds. SUSY models with compressed spectra inherently produce signal events with small amounts of missing energy that are hard to explore. We use this difficulty to motivate the construction of "deconstructed" transverse mass variables which are designed preserve information on both the norm and direction of the missing momentum. We demonstrate the effectiveness of these variables in searches for the pair production of supersymmetric top-quark partners which subsequently decay into a final state with an isolated lepton, jets and missing energy. We show that the use of deconstructed transverse mass variables extends the accessible compressed spectra parameter space beyond the region probed by traditional methods. The parameter space can further be expanded to neutralino masses that are larger than the difference between the stop and top masses. ...

  7. Gaia and Variable Stars

    CERN Document Server

    Udalski, A; Skowron, D M; Skowron, J; Pietrukowicz, P; Mróz, P; Poleski, R; Szymański, M K; Kozłowski, S; Wyrzykowski, Ł; Ulaczyk, K; Pawlak, M


    We present a comparison of the Gaia DR1 samples of pulsating variable stars - Cepheids and RR Lyrae type - with the OGLE Collection of Variable Stars aiming at the characterization of the Gaia mission performance in the stellar variability domain. Out of 575 Cepheids and 2322 RR Lyrae candidates from the Gaia DR1 samples located in the OGLE footprint in the sky, 559 Cepheids and 2302 RR Lyrae stars are genuine pulsators of these types. The number of misclassified stars is low indicating reliable performance of the Gaia data pipeline. The completeness of the Gaia DR1 samples of Cepheids and RR Lyrae stars is at the level of 60-75% as compared to the OGLE Collection dataset. This level of completeness is moderate and may limit the applicability of the Gaia data in many projects.

  8. Validation and Variability

    DEFF Research Database (Denmark)

    Carusi, Annamaria


    as inter-subject variability. This need is simultaneously social and epistemic: social as systems biologists attempt to engage with the interests and concerns of clinicians and others in applied medical research; epistemic as they attempt to develop new strategies to cope with variability in the validation...... and experimentally inclined modellers on one hand, and attempts to forge new collaborations with medical scientists on the other. Apart from the scientific interest of the population of models approach for tackling variability, the trial also offers a good illustration of the epistemology of experiment......-facing modelling. I claim that it shows the extent to which experiment-facing modelling and validation require the establishment of criteria for comparing models and experiments that enable them to be linked together. These 'grounds of comparability' are the broad framework in which validation experiments...

  9. Correlated neural variability in persistent state networks. (United States)

    Polk, Amber; Litwin-Kumar, Ashok; Doiron, Brent


    Neural activity that persists long after stimulus presentation is a biological correlate of short-term memory. Variability in spiking activity causes persistent states to drift over time, ultimately degrading memory. Models of short-term memory often assume that the input fluctuations to neural populations are independent across cells, a feature that attenuates population-level variability and stabilizes persistent activity. However, this assumption is at odds with experimental recordings from pairs of cortical neurons showing that both the input currents and output spike trains are correlated. It remains unclear how correlated variability affects the stability of persistent activity and the performance of cognitive tasks that it supports. We consider the stochastic long-timescale attractor dynamics of pairs of mutually inhibitory populations of spiking neurons. In these networks, persistent activity was less variable when correlated variability was globally distributed across both populations compared with the case when correlations were locally distributed only within each population. Using a reduced firing rate model with a continuum of persistent states, we show that, when input fluctuations are correlated across both populations, they drive firing rate fluctuations orthogonal to the persistent state attractor, thereby causing minimal stochastic drift. Using these insights, we establish that distributing correlated fluctuations globally as opposed to locally improves network's performance on a two-interval, delayed response discrimination task. Our work shows that the correlation structure of input fluctuations to a network is an important factor when determining long-timescale, persistent population spiking activity.

  10. An appraisal of biological responses and network of environmental interactions in non-mining and mining impacted coastal waters

    Digital Repository Service at National Institute of Oceanography (India)

    Fernandes, C.E.G.; Malik, A; Jineesh, V.K.; Fernandes, S.O.; Das, A; Pandey, S.S.; Kanolkar, G.; Sujith, P.P.; Velip, D.; Shaikh, S.; Helekar, S.; Gonsalves, M.J.B.D.; Nair, S.; LokaBharathi, P.A

    iron brought from the hinterlands. We hypothesize that there could be a shift in biological response along with changes in network of interactions between environmental and biological variables in these mining and non-mining impacted regions, lying 160...

  11. Variable selection through CART

    CERN Document Server

    Sauvé, Marie


    This paper deals with variable selection in the regression and binary classification frameworks. It proposes an automatic and exhaustive procedure which relies on the use of the CART algorithm and on model selection via penalization. This work, of theoretical nature, aims at determining adequate penalties, i.e. penalties which allow to get oracle type inequalities justifying the performance of the proposed procedure. Since the exhaustive procedure can not be executed when the number of variables is too big, a more practical procedure is also proposed and still theoretically validated. A simulation study completes the theoretical results.

  12. Terrestrial Carbon Cycle Variability (United States)

    Baldocchi, Dennis; Ryu, Youngryel; Keenan, Trevor


    A growing literature is reporting on how the terrestrial carbon cycle is experiencing year-to-year variability because of climate anomalies and trends caused by global change. As CO 2 concentration records in the atmosphere exceed 50 years and as satellite records reach over 30 years in length, we are becoming better able to address carbon cycle variability and trends. Here we review how variable the carbon cycle is, how large the trends in its gross and net fluxes are, and how well the signal can be separated from noise. We explore mechanisms that explain year-to-year variability and trends by deconstructing the global carbon budget. The CO 2 concentration record is detecting a significant increase in the seasonal amplitude between 1958 and now. Inferential methods provide a variety of explanations for this result, but a conclusive attribution remains elusive. Scientists have reported that this trend is a consequence of the greening of the biosphere, stronger northern latitude photosynthesis, more photosynthesis by semi-arid ecosystems, agriculture and the green revolution, tropical temperature anomalies, or increased winter respiration. At the global scale, variability in the terrestrial carbon cycle can be due to changes in constituent fluxes, gross primary productivity, plant respiration and heterotrophic (microbial) respiration, and losses due to fire, land use change, soil erosion, or harvesting. It remains controversial whether or not there is a significant trend in global primary productivity (due to rising CO 2, temperature, nitrogen deposition, changing land use, and preponderance of wet and dry regions). The degree to which year-to-year variability in temperature and precipitation anomalies affect global primary productivity also remains uncertain. For perspective, interannual variability in global gross primary productivity is relatively small (on the order of 2 Pg-C y -1) with respect to a large and uncertain background (123 +/- 4 Pg-C y -1), and

  13. Applied complex variables

    CERN Document Server

    Dettman, John W


    Analytic function theory is a traditional subject going back to Cauchy and Riemann in the 19th century. Once the exclusive province of advanced mathematics students, its applications have proven vital to today's physicists and engineers. In this highly regarded work, Professor John W. Dettman offers a clear, well-organized overview of the subject and various applications - making the often-perplexing study of analytic functions of complex variables more accessible to a wider audience. The first half of Applied Complex Variables, designed for sequential study, is a step-by-step treatment of fun

  14. Complex variables I essentials

    CERN Document Server

    Solomon, Alan D


    REA's Essentials provide quick and easy access to critical information in a variety of different fields, ranging from the most basic to the most advanced. As its name implies, these concise, comprehensive study guides summarize the essentials of the field covered. Essentials are helpful when preparing for exams, doing homework and will remain a lasting reference source for students, teachers, and professionals. Complex Variables I includes functions of a complex variable, elementary complex functions, integrals of complex functions in the complex plane, sequences and series, and poles and r

  15. Biology Library Workbook. (United States)

    Miller, Constance; And Others

    A library skills workbook provides college biology students with an introduction to biological library resources. Divided into two sections, the first contains explanations of the various steps in the library research process. The second consists of exercises keyed to the explanatory chapters of the first section. (RAA)

  16. Homosexuality, biology, and ideology. (United States)

    Haumann, G


    This paper critically examines the complex relationships and interdependencies between biological theories on homosexuality and sociosexual ideologies. It challenges the privileged status of biology as the ultimate authority on homosexuality. This status is based on the belief that biology is a value-free science. On the contrary, this essay shows how unacknowledged assumptions and culturally bound patterns of thinking about sexuality taint biological research. Sociosexual ideologies are defined as principles that organize the ways we express our sexualities and the way we theorize about them in biology. The following ideologies are identified: (1) sexuality-as-heterosexuality, (2) sexuality-as-reproduction, (3) sexual dualism (male vs. female), and (4) the view the homosexuality is a sexual inversion. The process by which these ideologies are incorporated into biology is two-fold: (1) as a projective act from society onto nature and (2) as a reflective act from nature back into society. It is further argued that biological knowledge of homosexuality resulting from that process can be used for diverse political interests. Finally, it is proposed that since biological theories on homosexuality are inseparable from the context of their paradigmatic origin, it is possible that new theories could be derived from new ideologies.

  17. Psoriasis : implications of biologics

    NARCIS (Netherlands)

    Lecluse, L.L.A.


    Since the end of 2004 several specific immunomodulating therapies: ‘biologic response modifiers’ or ‘biologics’ have been registered for moderate to severe psoriasis in Europe. This thesis is considering the implications of the introduction of the biologics for psoriasis patients, focusing on safety

  18. Biological Macromolecule Crystallization Database (United States)

    SRD 21 Biological Macromolecule Crystallization Database (Web, free access)   The Biological Macromolecule Crystallization Database and NASA Archive for Protein Crystal Growth Data (BMCD) contains the conditions reported for the crystallization of proteins and nucleic acids used in X-ray structure determinations and archives the results of microgravity macromolecule crystallization studies.

  19. Experimenting with Mathematical Biology (United States)

    Sanft, Rebecca; Walter, Anne


    St. Olaf College recently added a Mathematical Biology concentration to its curriculum. The core course, Mathematics of Biology, was redesigned to include a wet laboratory. The lab classes required students to collect data and implement the essential modeling techniques of formulation, implementation, validation, and analysis. The four labs…

  20. Introduction to systems biology

    NARCIS (Netherlands)

    Bruggeman, F.J.; Hornberg, J.J.; Boogerd, F.C.; Westerhoff, H.V.; Boogerd, F.C.; Bruggeman, F.J.; Hofmeyr, J.H.S.; Westerhoff, H.V.


    The developments in the molecular biosciences have made possible a shift to combined molecular and system-level approaches to biological research under the name of Systems Biology. It integrates many types of molecular knowledge, which can best be achieved by the synergistic use of models and experi

  1. Quantification of variability in trichome patterns

    Directory of Open Access Journals (Sweden)

    Bettina eGreese


    Full Text Available While pattern formation is studied in various areas of biology, little is known about the intrinsic noise leading to variations between individual realizations of the pattern. One prominent example for de novo pattern formation in plants is the patterning of trichomes on Arabidopsis leaves, which involves genetic regulation and cell-to-cell communication. These processes are potentially variable due to , e.g., the abundance of cell components or environmental conditions. To elevate the understanding of the regulatory processes underlying the pattern formation it is crucial to quantitatively analyze the variability in naturally occurring patterns. Here, we review recent approaches towards characterization of noise on trichome initiation. We present methods for the quantification of spatial patterns, which are the basis for data-driven mathematical modeling and enable the analysis of noise from different sources. Besides the insight gained on trichome formation, the examination of observed trichome patterns also shows that highly regulated biological processes can be substantially affected by variability.

  2. Frontiers in mathematical biology

    CERN Document Server


    Volume 100, which is the final volume of the LNBM series serves to commemorate the acievements in two decades of this influential collection of books in mathematical biology. The contributions, by the leading mathematical biologists, survey the state of the art in the subject, and offer speculative, philosophical and critical analyses of the key issues confronting the field. The papers address fundamental issues in cell and molecular biology, organismal biology, evolutionary biology, population ecology, community and ecosystem ecology, and applied biology, plus the explicit and implicit mathematical challenges. Cross-cuttting issues involve the problem of variation among units in nonlinear systems, and the related problems of the interactions among phenomena across scales of space, time and organizational complexity.

  3. Space biology research development (United States)

    Bonting, Sjoerd L.


    The purpose of the Search for Extraterrestrial Intelligence (SETI) Institute is to conduct and promote research related activities regarding the search for extraterrestrial life, particularly intelligent life. Such research encompasses the broad discipline of 'Life in the Universe', including all scientific and technological aspects of astronomy and the planetary sciences, chemical evolution, the origin of life, biological evolution, and cultural evolution. The primary purpose was to provide funding for the Principal Investigator to collaborate with the personnel of the SETI Institute and the NASA-Ames Research center in order to plan and develop space biology research on and in connection with Space Station Freedom; to promote cooperation with the international partners in the space station; to conduct a study on the use of biosensors in space biology research and life support system operation; and to promote space biology research through the initiation of an annual publication 'Advances in Space Biology and Medicine'.

  4. Optics of Biological Particles

    CERN Document Server

    Hoekstra, Alfons; Videen, Gorden


    This book covers the optics of single biological particles, both theory and experiment, with emphasis on Elastic Light Scattering and Fluorescence. It deals with the optics of bacteria (bio-aerosols), marine particles (selected phytoplankton communities) and red and white blood cells. Moreover, there are dedicated chapters on a general theory for scattering by a cell, and modelling and simulation of scattering by inhomogeneous biological cells. Finally, one chapter is dedicated to astro-biological signatures, discussing the possibilities for detecting non-terrestrial biological material. The volume has up-to-date discussions on new experimental and numerical techniques, and many examples of applications of these techniques in real-life systems, as used to detect and characterize e.g. biological warfare agents or human blood cells.

  5. Biological sample collector (United States)

    Murphy, Gloria A.


    A biological sample collector is adapted to a collect several biological samples in a plurality of filter wells. A biological sample collector may comprise a manifold plate for mounting a filter plate thereon, the filter plate having a plurality of filter wells therein; a hollow slider for engaging and positioning a tube that slides therethrough; and a slide case within which the hollow slider travels to allow the tube to be aligned with a selected filter well of the plurality of filter wells, wherein when the tube is aligned with the selected filter well, the tube is pushed through the hollow slider and into the selected filter well to sealingly engage the selected filter well and to allow the tube to deposit a biological sample onto a filter in the bottom of the selected filter well. The biological sample collector may be portable.

  6. Biofilm diatom community structure: Influence of temporal and substratum variability

    Digital Repository Service at National Institute of Oceanography (India)

    Patil, J.S.; Anil, A.C.

    -chemical and biological properties. Of these, physical variability, driven primarily by external forces is fundamental. Wind- and weather-driven events cause physical changes and disruptions. These events lead to variability in temperature, irradiance, precipitation, run... in the microphyto- benthic community of this study area (Mitabavkar & Anil, 2002). They frequently resuspend into the surface waters through physical processes such as waves, tides and currents (de Jonge, 1995; de Jonge & van Beusekom, 1995) and thereby influence...

  7. Modeling, estimation and identification of stochastic systems with latent variables


    Bottegal, Giulio


    The main topic of this thesis is the analysis of static and dynamic models in which some variables, although directly influencing the behavior of certain observables, are not accessible to measurements. These models find applications in many branches of science and engineering, such as control systems, communications, natural and biological sciences and econometrics. It is well-known that models with unaccessible - or latent - variables, usually suffer from a lack of uniqueness of representat...

  8. Spatial Variability of Rainfall

    DEFF Research Database (Denmark)

    Jensen, N.E.; Pedersen, Lisbeth


    As a part of a Local Area Weather Radar (LAWR) calibration exercise 15 km south of Århus, Denmark, the variability in accumulated rainfall within a single radar pixel (500 by 500 m) was measured using nine high-resolution rain gauges. The measured values indicate up to a 100% variation between...

  9. Variability and component composition

    NARCIS (Netherlands)

    Storm, T. van der


    In component-based product populations, feature models have to be described at the component level to be able to benefit from a product family approach. As a consequence, composition of components becomes very complex. We describe how component-level variability can be managed in the face of compone

  10. Variable gravity research facility (United States)

    Allan, Sean; Ancheta, Stan; Beine, Donna; Cink, Brian; Eagon, Mark; Eckstein, Brett; Luhman, Dan; Mccowan, Daniel; Nations, James; Nordtvedt, Todd


    Spin and despin requirements; sequence of activities required to assemble the Variable Gravity Research Facility (VGRF); power systems technology; life support; thermal control systems; emergencies; communication systems; space station applications; experimental activities; computer modeling and simulation of tether vibration; cost analysis; configuration of the crew compartments; and tether lengths and rotation speeds are discussed.

  11. Variability in GPS sources

    NARCIS (Netherlands)

    Jauncey, DL; King, EA; Bignall, HE; Lovell, JEJ; Kedziora-Chudczer, L; Tzioumis, AK; Tingay, SJ; Macquart, JP; McCulloch, PM


    Flux density monitoring data at 2.3 and 8.4 GHz is presented for a sample of 33 southern hemisphere GPS sources, drawn from the 2.7 GHz Parkes survey. This monitoring data, together with VLBI monitoring data, shows that a small fraction of these sources, similar to10%, vary. Their variability falls

  12. Variable speed generators

    CERN Document Server

    Boldea, Ion


    With the deregulation of electrical energy production and distribution, says Boldea (Polytechnical Institute, Timisoara, Romania) producers are looking for ways to tailor their electricity for different markets. Variable-speed electric generators are serving that purpose, up to the 400 megavolt ampere unit size, in Japan since 1996 and Germany sinc

  13. BISAC Variable Format. (United States)

    Information Technology and Libraries, 1983


    Presents revision of Book Industry Systems Advisory Committee (BISAC) format designed specifically for electronic transmission of purchase orders for monograph or series titles combining fixed and variable length data fields which was approved in January 1983. Special characters, sample address descriptions, summary of fixed records, glossary, and…

  14. Several real variables

    CERN Document Server

    Kantorovitz, Shmuel


    This undergraduate textbook is based on lectures given by the author on the differential and integral calculus of functions of several real variables. The book has a modern approach and includes topics such as: •The p-norms on vector space and their equivalence •The Weierstrass and Stone-Weierstrass approximation theorems •The differential as a linear functional; Jacobians, Hessians, and Taylor's theorem in several variables •The Implicit Function Theorem for a system of equations, proved via Banach’s Fixed Point Theorem •Applications to Ordinary Differential Equations •Line integrals and an introduction to surface integrals This book features numerous examples, detailed proofs, as well as exercises at the end of sections. Many of the exercises have detailed solutions, making the book suitable for self-study. Several Real Variables will be useful for undergraduate students in mathematics who have completed first courses in linear algebra and analysis of one real variable.

  15. Variable polarity arc welding (United States)

    Bayless, E. O., Jr.


    Technological advances generate within themselves dissatisfactions that lead to further advances in a process. A series of advances in welding technology which culminated in the Variable Polarity Plasma Arc (VPPA) Welding Process and an advance instituted to overcome the latest dissatisfactions with the process: automated VPPA welding are described briefly.

  16. Integration i flere variable

    DEFF Research Database (Denmark)

    Markvorsen, Steen


    -integralerne. Undervejs introduceres \\texttt{Integrator8}. Det er en pakke med Maple procedurer, som er udviklet specielt med henblik på eksempelbaseret visuel læring af de indledende integrationsbegreber og deres mangfoldige anvendelser. Vi giver eksempler på, hvordan integration i flere variable anvendes til beregning...

  17. Variable rate irrigation (United States)

    Systems are available to producers to make variable-rate applications of defoliants, fertilizer, lime, pesticides, plant growth regulators, and seed. These systems could potentially offer cost savings to a producer; however, the full potential of the benefits and savings cannot be realized if water ...

  18. Lake Ontario: Nearshore Variability (United States)

    We conducted a high-resolution survey with towed electronic instrumentation along the Lake Ontario nearshore (720 km) at a 20 meter contour. The survey was conducted September 6-10, 2008 with a shorter 300 km survey conducted August 14-15 for comparing of temporal variability. ...

  19. Structured population models in biology and epidemiology

    CERN Document Server

    Ruan, Shigui


    This book consists of six chapters written by leading researchers in mathematical biology. These chapters present recent and important developments in the study of structured population models in biology and epidemiology. Topics include population models structured by age, size, and spatial position; size-structured models for metapopulations, macroparasitc diseases, and prion proliferation; models for transmission of microparasites between host populations living on non-coincident spatial domains; spatiotemporal patterns of disease spread; method of aggregation of variables in population dynamics; and biofilm models. It is suitable as a textbook for a mathematical biology course or a summer school at the advanced undergraduate and graduate level. It can also serve as a reference book for researchers looking for either interesting and specific problems to work on or useful techniques and discussions of some particular problems.

  20. Variability of single trial brain activation predicts fluctuations in reaction time. (United States)

    Bender, Stephan; Banaschewski, Tobias; Roessner, Veit; Klein, Christoph; Rietschel, Marcella; Feige, Bernd; Brandeis, Daniel; Laucht, Manfred


    Brain activation stability is crucial to understanding attention lapses. EEG methods could provide excellent markers to assess neuronal response variability with respect to temporal (intertrial coherence) and spatial variability (topographic consistency) as well as variations in activation intensity (low frequency variability of single trial global field power). We calculated intertrial coherence, topographic consistency and low frequency amplitude variability during target P300 in a continuous performance test in 263 15-year-olds from a cohort with psychosocial and biological risk factors. Topographic consistency and low frequency amplitude variability predicted reaction time fluctuations (RTSD) in a linear model. Higher RTSD was only associated with higher psychosocial adversity in the presence of the homozygous 6R-10R dopamine transporter haplotype. We propose that topographic variability of single trial P300 reflects noise as well as variability in evoked cortical activation patterns. Dopaminergic neuromodulation interacted with environmental and biological risk factors to predict behavioural reaction time variability.

  1. Short timescale variability in the Faint Sky Variability Survey

    NARCIS (Netherlands)

    Morales-Rueda, L.; Groot, P.J.; Augusteijn, T.; Nelemans, G.; Vreeswijk, P.M.; Besselaar, E.J.M. van den


    We present the V-band variability analysis of the point sources in the Faint Sky Variability Survey on time-scales from 24 min to tens of days. We find that about one per cent of the point sources down to V = 24 are variables. We discuss the variability-detection probabilities for each field dependi

  2. Managing biological diversity (United States)

    Samson, Fred B.; Knopf, Fritz L.


    Biological diversity is the variety of life and accompanying ecological processes (Off. Technol. Assess. 1987, Wilcove and Samson 1987, Keystone 1991). Conservation of biological diversity is a major environmental issue (Wilson 1988, Counc. Environ. Quality 1991). The health and future of the earth's ecological systems (Lubchenco et al. 1991), global climate change (Botkin 1990), and an ever-increasing rate in loss of species, communities, and ecological systems (Myers 1990) are among issues drawing biological diversity to the mainstream of conservation worldwide (Int. Union Conserv. Nat. and Nat. Resour. [IUCN] et al. 1991). The legal mandate for conserving biological diversity is now in place (Carlson 1988, Doremus 1991). More than 19 federal laws govern the use of biological resources in the United States (Rein 1991). The proposed National Biological Diversity Conservation and Environmental Research Act (H.R. 585 and S.58) notes the need for a national biological diversity policy, would create a national center for biological diversity research, and recommends a federal interagency strategy for ecosystem conservation. There are, however, hard choices ahead for the conservation of biological diversity, and biologists are grappling with how to set priorities in research and management (Roberts 1988). We sense disillusion among field biologists and managers relative to how to operationally approach the seemingly overwhelming charge of conserving biological diversity. Biologists also need to respond to critics like Hunt (1991) who suggest a tree farm has more biological diversity than an equal area of old-growth forest. At present, science has played only a minor role in the conservation of biological diversity (Weston 1992) with no unified approach available to evaluate strategies and programs that address the quality and quantity of biological diversity (Murphy 1990, Erwin 1992). Although actions to conserve biological diversity need to be clearly defined by

  3. Biological and Chemical Security

    Energy Technology Data Exchange (ETDEWEB)

    Fitch, P J


    The LLNL Chemical & Biological National Security Program (CBNP) provides science, technology and integrated systems for chemical and biological security. Our approach is to develop and field advanced strategies that dramatically improve the nation's capabilities to prevent, prepare for, detect, and respond to terrorist use of chemical or biological weapons. Recent events show the importance of civilian defense against terrorism. The 1995 nerve gas attack in Tokyo's subway served to catalyze and focus the early LLNL program on civilian counter terrorism. In the same year, LLNL began CBNP using Laboratory-Directed R&D investments and a focus on biodetection. The Nunn-Lugar-Domenici Defense Against Weapons of Mass Destruction Act, passed in 1996, initiated a number of U.S. nonproliferation and counter-terrorism programs including the DOE (now NNSA) Chemical and Biological Nonproliferation Program (also known as CBNP). In 2002, the Department of Homeland Security was formed. The NNSA CBNP and many of the LLNL CBNP activities are being transferred as the new Department becomes operational. LLNL has a long history in national security including nonproliferation of weapons of mass destruction. In biology, LLNL had a key role in starting and implementing the Human Genome Project and, more recently, the Microbial Genome Program. LLNL has over 1,000 scientists and engineers with relevant expertise in biology, chemistry, decontamination, instrumentation, microtechnologies, atmospheric modeling, and field experimentation. Over 150 LLNL scientists and engineers work full time on chemical and biological national security projects.

  4. On Complex Random Variables

    Directory of Open Access Journals (Sweden)

    Anwer Khurshid


    Full Text Available Normal 0 false false false EN-US X-NONE X-NONE In this paper, it is shown that a complex multivariate random variable  is a complex multivariate normal random variable of dimensionality if and only if all nondegenerate complex linear combinations of  have a complex univariate normal distribution. The characteristic function of  has been derived, and simpler forms of some theorems have been given using this characterization theorem without assuming that the variance-covariance matrix of the vector  is Hermitian positive definite. Marginal distributions of  have been given. In addition, a complex multivariate t-distribution has been defined and the density derived. A characterization of the complex multivariate t-distribution is given. A few possible uses of this distribution have been suggested.

  5. [Socioeconomic variables and fertility]. (United States)

    Arguello, O


    While making comparative analyses of data collected by the World Fertility Survey regarding Latin America, a group of investigators of CELADE (Centro Latinoamericano de Demografia) realized that the selection of economic variables for the study of fertility had serious limitations. Such limitations did not allow the elaboration of a theory which took into account the complicated process of fertility, in all its socioeconomic, cultural, and psychological manifestations. Thus, this paper intends to lay the theoretical basis for the selection of all relevant variables, distinguishing, for example, the average fertility of women according to area of residence, place of early socialization, migrant status, social status, occupation of husband, level of instruction, occupation, and all changes in occupational activities of women in fertile age.

  6. Documentation of TRU biological transport model (BIOTRAN)

    Energy Technology Data Exchange (ETDEWEB)

    Gallegos, A.F.; Garcia, B.J.; Sutton, C.M.


    Inclusive of Appendices, this document describes the purpose, rationale, construction, and operation of a biological transport model (BIOTRAN). This model is used to predict the flow of transuranic elements (TRU) through specified plant and animal environments using biomass as a vector. The appendices are: (A) Flows of moisture, biomass, and TRU; (B) Intermediate variables affecting flows; (C) Mnemonic equivalents (code) for variables; (D) Variable library (code); (E) BIOTRAN code (Fortran); (F) Plants simulated; (G) BIOTRAN code documentation; (H) Operating instructions for BIOTRAN code. The main text is presented with a specific format which uses a minimum of space, yet is adequate for tracking most relationships from their first appearance to their formulation in the code. Because relationships are treated individually in this manner, and rely heavily on Appendix material for understanding, it is advised that the reader familiarize himself with these materials before proceeding with the main text.

  7. Complex variable HVPT

    Energy Technology Data Exchange (ETDEWEB)

    Killingbeck, John P [Mathematics Department, University of Hull, Hull HU6 7RX (United Kingdom); Grosjean, Alain [Laboratoire d' Astrophysique de l' Observatoire de Besancon (CNRS, UPRES-A 6091), 41 bis Avenue de l' Observatoire, BP 1615, 25010 Besancon Cedex (France); Jolicard, Georges [Laboratoire d' Astrophysique de l' Observatoire de Besancon (CNRS, UPRES-A 6091), 41 bis Avenue de l' Observatoire, BP 1615, 25010 Besancon Cedex (France)


    Complex variable hypervirial perturbation theory is applied to the case of oscillator and Coulomb potentials perturbed by a single term potential of the form Vx{sup n} or Vr{sup n}, respectively. The trial calculations reported show that this approach can produce accurate complex energies for resonant states via a simple and speedy calculation and can also be useful in studies of PT symmetry and tunnelling resonance effects. (addendum)

  8. Flaring variability of Microquasars

    CERN Document Server

    Trushkin, Sergei A; Nizhelskij, Nikolaj A


    We discuss flaring variability of radio emission of microquasars, measured in monitoring programs with the RATAN-600 radio telescope. We carried out a multi-frequency (1-30 GHz) daily monitoring of the radio flux variability of the microquasars SS433, GRS1915+105, and Cyg X-3 during the recent sets in 2005-2007. A lot of bright short-time flares were detected from GRS 1915+105 and they could be associated with active X-ray events. In January 2006 we detected a drop down of the quiescent fluxes from Cyg X-3 (from 100 to $\\sim$20 mJy), then the 1 Jy-flare was detected on 2 February 2006 after 18 days of quenched radio emission. The daily spectra of the flare in the maximum were flat from 2 to 110 GHz, using the quasi-simultaneous observations at 110 GHz with the RT45m telescope and the NMA millimeter array of NRO in Japan. Several bright radio flaring events (1-15 Jy) followed during the continuing state of very variable and intensive 1-12 keV X-ray emission ($\\sim$0.5 Crab), which was monitored in the RXTE ASM...

  9. Thermodynamics of Biological Processes (United States)

    Garcia, Hernan G.; Kondev, Jane; Orme, Nigel; Theriot, Julie A.; Phillips, Rob


    There is a long and rich tradition of using ideas from both equilibrium thermodynamics and its microscopic partner theory of equilibrium statistical mechanics. In this chapter, we provide some background on the origins of the seemingly unreasonable effectiveness of ideas from both thermodynamics and statistical mechanics in biology. After making a description of these foundational issues, we turn to a series of case studies primarily focused on binding that are intended to illustrate the broad biological reach of equilibrium thinking in biology. These case studies include ligand-gated ion channels, thermodynamic models of transcription, and recent applications to the problem of bacterial chemotaxis. As part of the description of these case studies, we explore a number of different uses of the famed Monod–Wyman–Changeux (MWC) model as a generic tool for providing a mathematical characterization of two-state systems. These case studies should provide a template for tailoring equilibrium ideas to other problems of biological interest. PMID:21333788

  10. Hammond Bay Biological Station (United States)

    Federal Laboratory Consortium — Hammond Bay Biological Station (HBBS), located near Millersburg, Michigan, is a field station of the USGS Great Lakes Science Center (GLSC). HBBS was established by...

  11. Enhanced Biological Sampling Data (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This is a database of a variety of biological, reproductive, and energetic data collected from fish on the continental shelf in the northwest Atlantic Ocean. Species...

  12. Chemistry and biology data (United States)

    U.S. Environmental Protection Agency — Chemical monitoring data and biological data from field collected samples. This dataset is associated with the following publication: Biales , A., D. Denton , D....

  13. Laboratory of Biological Modeling (United States)

    Federal Laboratory Consortium — The Laboratory of Biological Modeling is defined by both its methodologies and its areas of application. We use mathematical modeling in many forms and apply it to...

  14. Laboratory of Biological Modeling (United States)

    Federal Laboratory Consortium — The Laboratory of Biological Modeling is defined by both its methodologies and its areas of application. We use mathematical modeling in many forms and apply it to a...

  15. Precision Measurement in Biology (United States)

    Quake, Stephen

    Is biology a quantitative science like physics? I will discuss the role of precision measurement in both physics and biology, and argue that in fact both fields can be tied together by the use and consequences of precision measurement. The elementary quanta of biology are twofold: the macromolecule and the cell. Cells are the fundamental unit of life, and macromolecules are the fundamental elements of the cell. I will describe how precision measurements have been used to explore the basic properties of these quanta, and more generally how the quest for higher precision almost inevitably leads to the development of new technologies, which in turn catalyze further scientific discovery. In the 21st century, there are no remaining experimental barriers to biology becoming a truly quantitative and mathematical science.

  16. Biological satellite Kosmos-936 (United States)

    Vedeshin, L. A.


    A description is given of physiological experiments performed on the biological satellite Kosmos-936. Other experiments to determine the electrostatic and dielectric responses to the effects of cosmic radiation are discussed.

  17. Fishery Biology Database (AGDBS) (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Basic biological data are the foundation on which all assessments of fisheries resources are built. These include parameters such as the size and age composition of...

  18. Large Pelagics Biological Survey (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Large Pelagics Biological Survey (LPBS) collects additional length and weight information and body parts such as otoliths, caudal vertebrae, dorsal spines, and...

  19. Vibrations, Quanta and Biology

    CERN Document Server

    Huelga, S F


    Quantum biology is an emerging field of research that concerns itself with the experimental and theoretical exploration of non-trivial quantum phenomena in biological systems. In this tutorial overview we aim to bring out fundamental assumptions and questions in the field, identify basic design principles and develop a key underlying theme -- the dynamics of quantum dynamical networks in the presence of an environment and the fruitful interplay that the two may enter. At the hand of three biological phenomena whose understanding is held to require quantum mechanical processes, namely excitation and charge transfer in photosynthetic complexes, magneto-reception in birds and the olfactory sense, we demonstrate that this underlying theme encompasses them all, thus suggesting its wider relevance as an archetypical framework for quantum biology.

  20. Mechanical Biological Treatment

    DEFF Research Database (Denmark)

    Bilitewski, B-; Oros, Christiane; Christensen, Thomas Højlund


    or residual waste (after some recyclables removed at the source). The concept was originally to reduce the amount of waste going to landfill, but MBT technologies are today also seen as plants recovering fuel as well as material fractions. As the name suggests the technology combines mechanical treatment......The basic processes and technologies of composting and anaerobic digestion, as described in the previous chapters, are usually used for specific or source-separated organic waste flows. However, in the 1990s mechanical biological waste treatment technologies (MBT) were developed for unsorted...... technologies (screens, sieves, magnets, etc.) with biological technologies (composting, anaerobic digestion). Two main technologies are available: Mechanical biological pretreatment (MBP), which first removes an RDF fraction and then biologically treats the remaining waste before most of it is landfilled...

  1. Multiscale Biological Materials

    DEFF Research Database (Denmark)

    Frølich, Simon

    example of biological design. We investigated the architecture of A. simplex and found that an advanced hierarchical biomineralized structure acts as the interface between soft musculature and a stiff substrate, thus securing underwater attachment. In bone, the mechanical properties of the material......, and the nanoscale response of bone in compression. Lastly, a framework for the investigation of biological design principles has been developed. The framework combines parametric modeling, multi-material 3D-printing, and direct mechanical testing to efficiently screen large parameter spaces of biological design. We......Materials formed by organisms, also known as biological materials, exhibit outstanding structural properties. The range of materials formed in nature is remarkable and their functions include support, protection, motion, sensing, storage, and maintenance of physiological homeostasis. These complex...

  2. [Systems biology of cancer]. (United States)

    Barillot, Emmanuel; Calzone, Laurence; Zinovyev, Andrei


    Cancer Systems Biology is now accepted and recognized as a promising field both in biological and clinical research. It relies on a rigorous formalization of regulation networks into precise and unambiguous languages. It provides both detailed and modular views of the complex biological system of interest (which in cancer research is typically an interaction network governing essential cellular events such as proliferation, differentiation, cell death...) in order to facilitate the interpretation of molecular profiles of tumors. The translation of these networks into mathematical models allows prediction of the evolution of the system in time and under certain perturbations. As a result, it can not only propose specific target points for pharmaceutical purposes, but also anticipate the evolution of tumors as well as their classifications. These characteristics emphasize the important role of Systems Biology of Cancer in the future of biomedical research.

  3. Insecticides and Biological Control (United States)

    Furness, G. O.


    Use of insecticides has been questioned due to their harmful effects on edible items. Biological control of insects along with other effective practices for checking spread of parasites on crops are discussed. (PS)

  4. Nestedness across biological scales (United States)

    Marquitti, Flavia M. D.; Raimundo, Rafael L. G.; Sebastián-González, Esther; Coltri, Patricia P.; Perez, S. Ivan; Brandt, Débora Y. C.; Nunes, Kelly; Daura-Jorge, Fábio G.; Floeter, Sergio R.; Guimarães, Paulo R.


    Biological networks pervade nature. They describe systems throughout all levels of biological organization, from molecules regulating metabolism to species interactions that shape ecosystem dynamics. The network thinking revealed recurrent organizational patterns in complex biological systems, such as the formation of semi-independent groups of connected elements (modularity) and non-random distributions of interactions among elements. Other structural patterns, such as nestedness, have been primarily assessed in ecological networks formed by two non-overlapping sets of elements; information on its occurrence on other levels of organization is lacking. Nestedness occurs when interactions of less connected elements form proper subsets of the interactions of more connected elements. Only recently these properties began to be appreciated in one-mode networks (where all elements can interact) which describe a much wider variety of biological phenomena. Here, we compute nestedness in a diverse collection of one-mode networked systems from six different levels of biological organization depicting gene and protein interactions, complex phenotypes, animal societies, metapopulations, food webs and vertebrate metacommunities. Our findings suggest that nestedness emerge independently of interaction type or biological scale and reveal that disparate systems can share nested organization features characterized by inclusive subsets of interacting elements with decreasing connectedness. We primarily explore the implications of a nested structure for each of these studied systems, then theorize on how nested networks are assembled. We hypothesize that nestedness emerges across scales due to processes that, although system-dependent, may share a general compromise between two features: specificity (the number of interactions the elements of the system can have) and affinity (how these elements can be connected to each other). Our findings suggesting occurrence of nestedness

  5. Biological Parameters of Impact (United States)


    zone between no effect and gross injury or death . For example, the pilot who survives an aircraft crash, but who is injured or unconscious so that he...Biological effects were limited to one incidence of bradycardia (116 t36 t and three instances of premature ventricular contractions. However. subjeCtiY" I...R.F.Chandler INTRODUCTION -Investigation of the biological effects of abrupt acceleration (impact) was stimulated by the advent of technical advances

  6. Systems cell biology. (United States)

    Mast, Fred D; Ratushny, Alexander V; Aitchison, John D


    Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology.

  7. Processes Understanding of Decadal Climate Variability (United States)

    Prömmel, Kerstin; Cubasch, Ulrich


    The realistic representation of decadal climate variability in the models is essential for the quality of decadal climate predictions. Therefore, the understanding of those processes leading to decadal climate variability needs to be improved. Several of these processes are already included in climate models but their importance has not yet completely been clarified. The simulation of other processes requires sometimes a higher resolution of the model or an extension by additional subsystems. This is addressed within one module of the German research program "MiKlip II - Decadal Climate Predictions" ( with a focus on the following processes. Stratospheric processes and their impact on the troposphere are analysed regarding the climate response to aerosol perturbations caused by volcanic eruptions and the stratospheric decadal variability due to solar forcing, climate change and ozone recovery. To account for the interaction between changing ozone concentrations and climate a computationally efficient ozone chemistry module is developed and implemented in the MiKlip prediction system. The ocean variability and air-sea interaction are analysed with a special focus on the reduction of the North Atlantic cold bias. In addition, the predictability of the oceanic carbon uptake with a special emphasis on the underlying mechanism is investigated. This addresses a combination of physical, biological and chemical processes.

  8. FDA 101: Regulating Biological Products (United States)

    ... Products For Consumers Home For Consumers Consumer Updates FDA 101: Regulating Biological Products Share Tweet Linkedin Pin ... field. back to top What biological products does FDA regulate? The Center for Biologics Evaluation and Research ( ...

  9. Translational applications of evaluating physiologic variability in human endotoxemia. (United States)

    Scheff, Jeremy D; Mavroudis, Panteleimon D; Calvano, Steve E; Androulakis, Ioannis P


    Dysregulation of the inflammatory response is a critical component of many clinically challenging disorders such as sepsis. Inflammation is a biological process designed to lead to healing and recovery, ultimately restoring homeostasis; however, the failure to fully achieve those beneficial results can leave a patient in a dangerous persistent inflammatory state. One of the primary challenges in developing novel therapies in this area is that inflammation is comprised of a complex network of interacting pathways. Here, we discuss our approaches towards addressing this problem through computational systems biology, with a particular focus on how the presence of biological rhythms and the disruption of these rhythms in inflammation may be applied in a translational context. By leveraging the information content embedded in physiologic variability, ranging in scale from oscillations in autonomic activity driving short-term heart rate variability to circadian rhythms in immunomodulatory hormones, there is significant potential to gain insight into the underlying physiology.

  10. Breeding biology and nestling development of the Grasshopper Buzzard


    Buij, R.; Kortekaas, K.; Folkertsma, I.; Van Der Velde, M.; Komdeur, J.; H. H. de Iongh; A. Monadjem


    Research into the effect of environmental variables on reproductive success of tropical raptors is often constrained by the lack of information on breeding biology. We provide the first detailed information of the breeding biology and nestling development of the Grasshopper Buzzard Butastur rufipennis, an Afrotropical migratory raptor threatened by extensive land transformation in its breeding range. Breeding coincided with the transition from the dry to the wet season. The mean incubation pe...

  11. Spectral Variability of FSRQs

    Indian Academy of Sciences (India)

    Minfeng Gu; Y. L. Ai


    The optical variability of 29 flat spectrum radio quasars in SDSS Stripe 82 region are investigated by using DR7 released multi-epoch data. All FSRQs show variations with overall amplitude ranging from 0.24 mag to 3.46 mag in different sources. About half of FSRQs show a bluer-when-brighter trend, which is commonly observed for blazars. However, only one source shows a redder-when-brighter trend, which implies it is rare in FSRQs. In this source, the thermal emission may be responsible for the spectral behaviour.

  12. Complex variables II essentials

    CERN Document Server

    Solomon, Alan D


    REA's Essentials provide quick and easy access to critical information in a variety of different fields, ranging from the most basic to the most advanced. As its name implies, these concise, comprehensive study guides summarize the essentials of the field covered. Essentials are helpful when preparing for exams, doing homework and will remain a lasting reference source for students, teachers, and professionals. Complex Variables II includes elementary mappings and Mobius transformation, mappings by general functions, conformal mappings and harmonic functions, applying complex functions to a

  13. Variable leak gas source (United States)

    Henderson, Timothy M.; Wuttke, Gilbert H.


    A variable leak gas source and a method for obtaining the same which includes filling a quantity of hollow glass micro-spheres with a gas, storing said quantity in a confined chamber having a controllable outlet, heating said chamber above room temperature, and controlling the temperature of said chamber to control the quantity of gas passing out of said controllable outlet. Individual gas filled spheres may be utilized for calibration purposes by breaking a sphere having a known quantity of a known gas to calibrate a gas detection apparatus.

  14. Jets with Variable R

    CERN Document Server

    Krohn, David; Wang, Lian-Tao


    We introduce a new class of jet algorithms designed to return conical jets with a variable Delta R radius. A specific example, in which Delta R scales as 1/pT, proves particularly useful in capturing the kinematic features of a wide variety of hard scattering processes. We implement this Delta R scaling in a sequential recombination algorithm and test it by reconstructing resonance masses and kinematic endpoints. These test cases show 10-20% improvements in signal efficiency compared to fixed Delta R algorithms. We also comment on cuts useful in reducing continuum jet backgrounds.

  15. Thermal biology of Phymaturus lizards: evolutionary constraints or lack of environmental variation? (United States)

    Cruz, Felix B; Belver, Luciana; Acosta, Juan C; Villavicencio, Héctor J; Blanco, Graciela; Cánovas, Maria G


    Several aspects of the biology of Phymaturus lizards including their herbivorous diet, specialized microhabitat use, and viviparous reproductive mode are highly conserved within the group. Here, we explore two aspects of Phymaturus thermal biology and test for the co-evolution among aspects of the thermal biology in these lizards, such as thermal preferenda and critical temperatures. Secondly, we explore correlations among variation in thermal biology with elevation and latitude. To do so, we used phylogenetically based comparative analyses (PCM) together with conventional statistics. Our results show that thermal biology for Phymaturus is conservative and our data do not suggest the co-evolution of thermal variables. Moreover, we detected low levels of variation in the thermal parameters studied, and no clear relationships between climatic and thermal variables. As a significant association between climatic and thermal variables could be demonstrated for a set of syntopic Liolaemus lizards, we suggest that thermal biology in Phymaturus lizards may be evolutionarily or ecologically constrained.

  16. Ecological perspectives on synthetic biology: insights from microbial population biology (United States)

    Escalante, Ana E.; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael


    The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems. PMID

  17. A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

    NARCIS (Netherlands)

    H.M.J. Sontrop; P.D. Moerland; R. van den Ham; M.J.T. Reinders; W.F.J. Verhaegh


    Background: Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for

  18. Stochastic Methods in Biology

    CERN Document Server

    Kallianpur, Gopinath; Hida, Takeyuki


    The use of probabilistic methods in the biological sciences has been so well established by now that mathematical biology is regarded by many as a distinct dis­ cipline with its own repertoire of techniques. The purpose of the Workshop on sto­ chastic methods in biology held at Nagoya University during the week of July 8-12, 1985, was to enable biologists and probabilists from Japan and the U. S. to discuss the latest developments in their respective fields and to exchange ideas on the ap­ plicability of the more recent developments in stochastic process theory to problems in biology. Eighteen papers were presented at the Workshop and have been grouped under the following headings: I. Population genetics (five papers) II. Measure valued diffusion processes related to population genetics (three papers) III. Neurophysiology (two papers) IV. Fluctuation in living cells (two papers) V. Mathematical methods related to other problems in biology, epidemiology, population dynamics, etc. (six papers) An important f...

  19. Biological warfare agents

    Directory of Open Access Journals (Sweden)

    Duraipandian Thavaselvam


    Full Text Available The recent bioterrorist attacks using anthrax spores have emphasized the need to detect and decontaminate critical facilities in the shortest possible time. There has been a remarkable progress in the detection, protection and decontamination of biological warfare agents as many instrumentation platforms and detection methodologies are developed and commissioned. Even then the threat of biological warfare agents and their use in bioterrorist attacks still remain a leading cause of global concern. Furthermore in the past decade there have been threats due to the emerging new diseases and also the re-emergence of old diseases and development of antimicrobial resistance and spread to new geographical regions. The preparedness against these agents need complete knowledge about the disease, better research and training facilities, diagnostic facilities and improved public health system. This review on the biological warfare agents will provide information on the biological warfare agents, their mode of transmission and spread and also the detection systems available to detect them. In addition the current information on the availability of commercially available and developing technologies against biological warfare agents has also been discussed. The risk that arise due to the use of these agents in warfare or bioterrorism related scenario can be mitigated with the availability of improved detection technologies.

  20. Information Complexity and Biology (United States)

    Bagnoli, Franco; Bignone, Franco A.; Cecconi, Fabio; Politi, Antonio

    Kolmogorov contributed directly to Biology in essentially three problems: the analysis of population dynamics (Lotka-Volterra equations), the reaction-diffusion formulation of gene spreading (FKPP equation), and some discussions about Mendel's laws. However, the widely recognized importance of his contribution arises from his work on algorithmic complexity. In fact, the limited direct intervention in Biology reflects the generally slow growth of interest of mathematicians towards biological issues. From the early work of Vito Volterra on species competition, to the slow growth of dynamical systems theory, contributions to the study of matter and the physiology of the nervous system, the first 50-60 years have witnessed important contributions, but as scattered pieces apparently uncorrelated, and in branches often far away from Biology. Up to the 40' it is hard to see the initial loose build up of a convergence, for those theories that will become mainstream research by the end of the century, and connected by the study of biological systems per-se.

  1. Chatter Prediction for Variable Pitch and Variable Helix Milling

    Directory of Open Access Journals (Sweden)

    Yong Wang


    Full Text Available Regenerative chatter is a self-excited vibration that can occur during milling, which shortens the lifetime of the tool and results in unacceptable surface quality. In this paper, an improved semidiscretization method for modeling and simulation with variable pitch and variable helix milling is proposed. Because the delay between each flute varies along the axial depth of the tool in milling, the cutting tool is discrete into some axial layers to simplify calculation. A comparison of the predicted and observed performance of variable pitch and variable helix against uniform pitch and uniform helix milling is presented. It is shown that variable pitch and variable helix milling can obtain larger stable cutting area than uniform pitch and uniform helix milling. Thus, it is concluded that variable pitch and variable helix milling are an effective way for suppressing chatter.

  2. Interest in biology. Part I: A multidimensional construct (United States)

    Gardner, Paul L.; Tamir, Pinchas

    Interest in a school subject (e.g., biology) is conceptualized in terms of three components: topics, activities, and motives, each of which has several dimensions. In this study, seven instruments were developed and administered to grade-10 biology students in Israel. Factor analysis provided support for the conceptualization which underlies the development of the instruments. Topic dimensions included biochemical processes, nonhuman organisms, human biology, personal hygiene, and practical applications; the activity dimensions were experiential learning, reception learning, writing/summarizing and group discussion; motives included environmental issues, moral issues, examination success, personal independence, problem solving, and four career dimensions (research, high-status professions, lower-status careers, woodsy-birdsy careers). In an analysis described in Part II of this paper, the students were classified into four groups on the basis of their grade-11 subject enrollment intentions: H (high-level biology), L (low-level biology), P (physical science), and N (no science). Zero-order and multiple correlations were found between interest and other variables and membership/nonmembership of the four groups. Students in Group H were characterized by higher achievement in year-10 biology, higher levels of enjoyment of biology, career orientations towards research or high-status biology-based professions, greater interest in various biology topics, especially reproduction/cell division/genetics, and a greater tendency to regard the Bagrut (grade-12) examination as interesting. Students in Group N displayed lower levels of interest in various topics (especially the microscope, plants, and reproduction), were less motivated to solve problems, had poorer grades in biology (and chemistry), were less likely to perceive biology as useful, were less likely to regard the Bagrut examination as fair, and were less likely to be interested in social modes of learning. There

  3. Variable optofluidic slit aperture

    Institute of Scientific and Technical Information of China (English)

    Stefan Schuhladen; Kaustubh Banerjee; Moritz Stürmer; Philipp Müller; Ulrike Wallrabe; Hans Zappe


    The shape of liquid interfaces can be precisely controlled using electrowetting,an actuation mechanism which has been widely used for tunable optofluidic micro-optical components such as lenses or irises.We have expanded the considerable flexibility inherent in electrowetting actuation to realize a variable optofluidic slit,a tunable and reconfigurable two-dimensional aperture with no mechanically moving parts.This optofluidic slit is formed by precisely controlled movement of the liquid interfaces of two highly opaque ink droplets.The 1.5 mm long slit aperture,with controllably variable discrete widths down to 45 μm,may be scanned across a length of 1.5 mm with switching times between adjacent slit positions of less than 120 ms.In addition,for a fixed slit aperture position,the width may be tuned to a minimum of 3 μm with high uniformity and linearity over the entire slit length.This compact,purely fluidic device offers an electrically controlled aperture tuning range not achievable with extant mechanical alternatives of a similar size.

  4. Suspended graphene variable capacitor (United States)

    AbdelGhany, M.; Mahvash, F.; Mukhopadhyay, M.; Favron, A.; Martel, R.; Siaj, M.; Szkopek, T.


    Electromechanical variable capacitors, or varactors, find a wide range of applications including sensing applications and the tuning of electrical circuit resonance. We demonstrate a nano-electromechanical graphene varactor, a variable capacitor wherein the capacitance is tuned by voltage controlled deflection of a dense array of suspended graphene membranes. The low flexural rigidity of graphene monolayers is exploited to achieve low actuation voltage and high tunable capacitance density in an ultra-thin structure. Large arrays comprising thousands of suspensions were fabricated to give a tunable capacitance of over 10 pF mm-2. This capacitance density suggests that graphene offers a potential solution to the challenge of reducing the size of micro-electromechanical systems (MEMS). A capacitance tuning of 55% was achieved with a 10 V actuating voltage, exceeding the 50% tuning limit of Hookean parallel plate pull-in without the use of complex mechanical schemes that occupy substrate area. Capacitor behavior was investigated experimentally, and described by a simple theoretical model. Mechanical properties of the graphene membranes were measured independently using atomic force microscopy. We present a comparison of state-of-the-art MEMS and graphene varactors. The quality factor of graphene varactors is limited by graphene sheet resistance, pull-in voltage can be improved with more aggressive scaling, while the power handling and cycling stability of graphene varactors remains unknown.

  5. Solar Irradiance Variability

    CERN Document Server

    Solanki, Sami K


    The Sun has long been considered a constant star, to the extent that its total irradiance was termed the solar constant. It required radiometers in space to detect the small variations in solar irradiance on timescales of the solar rotation and the solar cycle. A part of the difficulty is that there are no other constant natural daytime sources to which the Sun's brightness can be compared. The discovery of solar irradiance variability rekindled a long-running discussion on how strongly the Sun affects our climate. A non-negligible influence is suggested by correlation studies between solar variability and climate indicators. The mechanism for solar irradiance variations that fits the observations best is that magnetic features at the solar surface, i.e. sunspots, faculae and the magnetic network, are responsible for almost all variations (although on short timescales convection and p-mode oscillations also contribute). In spite of significant progress important questions are still open. Thus there is a debat...

  6. Modeling Shared Variables in VHDL

    DEFF Research Database (Denmark)

    Madsen, Jan; Brage, Jens P.


    A set of concurrent processes communicating through shared variables is an often used model for hardware systems. This paper presents three modeling techniques for representing such shared variables in VHDL, depending on the acceptable constraints on accesses to the variables. Also a set of guide......A set of concurrent processes communicating through shared variables is an often used model for hardware systems. This paper presents three modeling techniques for representing such shared variables in VHDL, depending on the acceptable constraints on accesses to the variables. Also a set...

  7. Fostering synergy between cell biology and systems biology



    In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules; predicting mechanisms and identifying generalizable themes; generating hypotheses...

  8. Informing biological design by integration of systems and synthetic biology. (United States)

    Smolke, Christina D; Silver, Pamela A


    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.

  9. Biological applications of nanobiotechnology. (United States)

    de Morais, Michele Greque; Martins, Vilásia Guimarães; Steffens, Daniela; Pranke, Patricia; da Costa, Jorge Alberto Vieira


    Nanotechnology is a multidisciplinary field that covers a vast and diverse array of devices derived from engineering, physics, chemistry, and biology. Nanotechnology has opened up by rapid advances in science and technology, creating new opportunities for advances in the fields of medicine, electronics, foods, and the environment. Nanoscale structures and materials (nanoparticles, nanowires, nanofibers, nanotubes) have been explored in many biological applications (biosensing, biological separation, molecular imaging, anticancer therapy) because their novel properties and functions differ drastically from their bulk counterparts. Their high volume/surface ratio, improved solubility, and multifunctionality open many new possibilities. The objective of this review is to describe the potential benefits and impacts of the nanobiotechnology in different areas.

  10. Epigenetics: Biology's Quantum Mechanics

    Directory of Open Access Journals (Sweden)

    Richard A Jorgensen


    Full Text Available The perspective presented here is that modern genetics is at a similar stage of development as were early formulations of quantum mechanics theory in the 1920's and that in 2010 we are at the dawn of a new revolution in genetics that promises to enrich and deepen our understanding of the gene and the genome. The interrelationships and interdependence of two views of the gene - the molecular biological view and the epigenetic view - are explored, and it is argued that the classical molecular biological view is incomplete without incorporation of the epigenetic perspective and that in a sense the molecular biological view has been evolving to include the epigenetic view. Intriguingly, this evolution of the molecular view toward the broader and more inclusive epigenetic view of the gene has an intriguing, if not precise, parallel in the evolution of concepts of atomic physics from Newtonian mechanics to quantum mechanics that are interesting to consider.

  11. Epigenetics: Biology's Quantum Mechanics. (United States)

    Jorgensen, Richard A


    The perspective presented here is that modern genetics is at a similar stage of development as were early formulations of quantum mechanics theory in the 1920s and that in 2010 we are at the dawn of a new revolution in genetics that promises to enrich and deepen our understanding of the gene and the genome. The interrelationships and interdependence of two views of the gene - the molecular biological view and the epigenetic view - are explored, and it is argued that the classical molecular biological view is incomplete without incorporation of the epigenetic perspective and that in a sense the molecular biological view has been evolving to include the epigenetic view. Intriguingly, this evolution of the molecular view toward the broader and more inclusive epigenetic view of the gene has an intriguing, if not precise, parallel in the evolution of concepts of atomic physics from Newtonian mechanics to quantum mechanics that are interesting to consider.

  12. Nutritional Systems Biology

    DEFF Research Database (Denmark)

    Jensen, Kasper

    sites of diet on the disease pathway. We propose a framework for interrogating the critical targets in colon cancer process and identifying plant-based dietary interventions as important modifiers using a systems chemical biology approach. The fifth chapter of the thesis is on discovering of novel anti...... number of thoroughly selected targets. Our need for fundamental understanding of the building blocks of the complex biological systems had been the main reason for the reductionist approach that was mainly applied in the past to elucidate these systems. Nowadays, it is widely recognized that systems...... components with biological systems and their connection to health and disease. The database will be enriched with predicted interactions between food components and protein targets, based on their structural and pharmacophore similarity with known small molecule ligands. Further to this, the associations...

  13. [Biologics in SLE]. (United States)

    Karonitsch, Thomas; Aringer, Martin


    Biologics have become indispensable in the last decade in the treatment of the more common rheumatic diseases. For treating systemic lupus erythematodes (SLE), B-cell depletion, albeit off-label, has been a well-accepted strategy in severe and refractory disease. Unexpectedly, however, the results of the first randomized controlled rituximab trials in SLE were negative. New trials with improved study protocols are ongoing, which should resolve this issue. In 2012, with the approval of belimumab, SLE finally entered the era of approved biological therapies. The anti-Blys/BAFF antibody belimumab showed prevention of SLE flares, glucocorticoid sparing, and significant improvement in the quality of life of SLE patients, in part by drastically reducing immune complex mediated fatigue. Positive reports on further targeting approaches give hope that additional biological agents will be available for SLE therapy soon.

  14. Biological therapy of psoriasis

    Directory of Open Access Journals (Sweden)

    Sivamani Raja


    Full Text Available The treatment of psoriasis has undergone a revolution with the advent of biologic therapies, including infliximab, etanercept, adalimumab, efalizumab, and alefacept. These medications are designed to target specific components of the immune system and are a major technological advancement over traditional immunosuppressive medications. These usually being well tolerated are being found useful in a growing number of immune-mediated diseases, psoriasis being just one example. The newest biologic, ustekinumab, is directed against the p40 subunit of the IL-12 and IL-23 cytokines. It has provided a new avenue of therapy for an array of T-cell-mediated diseases. Biologics are generally safe; however, there has been concern over the risk of lymphoma with use of these agents. All anti-TNF-α agents have been associated with a variety of serious and "routine" opportunistic infections.

  15. Biological Soft Robotics. (United States)

    Feinberg, Adam W


    In nature, nanometer-scale molecular motors are used to generate force within cells for diverse processes from transcription and transport to muscle contraction. This adaptability and scalability across wide temporal, spatial, and force regimes have spurred the development of biological soft robotic systems that seek to mimic and extend these capabilities. This review describes how molecular motors are hierarchically organized into larger-scale structures in order to provide a basic understanding of how these systems work in nature and the complexity and functionality we hope to replicate in biological soft robotics. These span the subcellular scale to macroscale, and this article focuses on the integration of biological components with synthetic materials, coupled with bioinspired robotic design. Key examples include nanoscale molecular motor-powered actuators, microscale bacteria-controlled devices, and macroscale muscle-powered robots that grasp, walk, and swim. Finally, the current challenges and future opportunities in the field are addressed.

  16. Biological therapy and dentistry (United States)

    Radfar, Lida; Ahmadabadi, Roshanak E; Masood, Farah; Scofield, R Hal


    In recent years, a new class of drugs has revolutionized the treatment of autoimmune, allergic, infectious and many more diseases. These drugs are classified into three groups, cytokines, monoclonal antibodies and fusion proteins. Biological drugs have less side effects compared to conventional drugs, and may target special damaged cells, but not all the cells. There may be side effects such as infection, hypersensitivity, hematological disorders, cancer, hepatotoxicity and neurological disorders, but there is not enough evidence or long term studies of the mechanism of action and side effects of these drugs. Patients on biological therapy may need some special consideration in dentistry. This paper is a review regarding the classification, mechanism of action and side effects of these drugs, and dental consideration for patients on biological therapy. PMID:26372436

  17. 7th Annual Systems Biology Symposium: Systems Biology and Engineering

    Energy Technology Data Exchange (ETDEWEB)

    Galitski, Timothy P.


    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 are 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."

  18. [Cybernetics and biology]. (United States)

    Vasil'ev, G F


    Owing to methodical disadvantages, the theory of control still lacks the potential for the analysis of biological systems. To get the full benefit of the method in addition to the algorithmic model of control (as of today the only used model in the theory of control) a parametric model of control is offered to employ. The reasoning for it is explained. The approach suggested provides the possibility to use all potential of the modern theory of control for the analysis of biological systems. The cybernetic approach is shown taking a system of the rise of glucose concentration in blood as an example.

  19. PAC research in biology

    Energy Technology Data Exchange (ETDEWEB)

    Chain, C. Y., E-mail: [Universidad Nacional de La Plata, IFLP (Argentina); Ceolin, M. [Instituto de Investigaciones Fisicoquimicas Teoricas y Aplicadas, Dto de Quimica, Fac. Cs. Exactas, UNLP (Argentina); Pasquevich, A. F. [Universidad Nacional de La Plata, IFLP (Argentina)


    In this paper possible applications of the Perturbed Angular Correlations (PAC) technique in Biology are considered. Previous PAC experiments in biology are globally analyzed. All the work that appears in the literature has been grouped in a few research lines, just to make the analysis and discussion easy. The commonly used radioactive probes are listed and the experimental difficulties are analyzed. We also report applications of {sup 181}Hf and {sup 111}In isotopes in life sciences other than their use in PAC. The possibility of extending these studies using the PAC technique is discussed.

  20. Biological and Pharmaceutical Nanomaterials (United States)

    Kumar, Challa S. S. R.


    This first comprehensive yet concise overview of all important classes of biological and pharmaceutical nanomaterials presents in one volume the different kinds of natural biological compounds that form nanomaterials or that may be used to purposefully create them. This unique single source of information brings together the many articles published in specialized journals, which often remain unseen by members of other, related disciplines. Covering pharmaceutical, nucleic acid, peptide and DNA-Chitosan nanoparticles, the book focuses on those innovative materials and technologies needed for the continued growth of medicine, healthcare, pharmaceuticals and human wellness. For chemists, biochemists, cell biologists, materials scientists, biologists, and those working in the pharmaceutical and chemical industries.

  1. Gait Variability and Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    Michael J. Socie


    Full Text Available Gait variability, that is, fluctuations in movement during walking, is an indicator of walking function and has been associated with various adverse outcomes such as falls. In this paper, current research concerning gait variability in persons with multiple sclerosis (MS is discussed. It is well established that persons with MS have greater gait variability compared to age and gender matched controls without MS. The reasons for the increase in gait variability are not completely understood. Evidence indicates that disability level, assistive device use, attentional requirement, and fatigue are related to gait variability in persons with MS. Future research should address the time-evolving structure (i.e., temporal characteristics of gait variability, the clinical importance of gait variability, and underlying mechanisms that drive gait variability in individuals with MS.

  2. Systems biology in animal sciences

    NARCIS (Netherlands)

    Woelders, H.; Pas, te M.F.W.; Bannink, A.; Veerkamp, R.F.; Smits, M.A.


    Systems biology is a rapidly expanding field of research and is applied in a number of biological disciplines. In animal sciences, omics approaches are increasingly used, yielding vast amounts of data, but systems biology approaches to extract understanding from these data of biological processes an

  3. Strong Decomposition of Random Variables

    DEFF Research Database (Denmark)

    Hoffmann-Jørgensen, Jørgen; Kagan, Abram M.; Pitt, Loren D.;


    A random variable X is stongly decomposable if X=Y+Z where Y=Φ(X) and Z=X-Φ(X) are independent non-degenerated random variables (called the components). It is shown that at least one of the components is singular, and we derive a necessary and sufficient condition for strong decomposability...... of a discrete random variable....

  4. Plant Systems Biology (editorial) (United States)

    In June 2003, Plant Physiology published an Arabidopsis special issue devoted to plant systems biology. The intention of Natasha Raikhel and Gloria Coruzzi, the two editors of this first-of-its-kind issue, was ‘‘to help nucleate this new effort within the plant community’’ as they considered that ‘‘...

  5. Evolution, Entropy, & Biological Information (United States)

    Peterson, Jacob


    A logical question to be expected from students: "How could life develop, that is, change, evolve from simple, primitive organisms into the complex forms existing today, while at the same time there is a generally observed decline and disorganization--the second law of thermodynamics?" The explanations in biology textbooks relied upon by…

  6. Doublethink in Biological Education (United States)

    Cox, Donald D.


    Presents the material given in a talk at the 1974 convention of the National Science Teachers Association in which the author compares practices in biology education to George Orwell's concept of "doublethink," i.e., the ability to hold two contradictory beliefs in one's mind simultaneously and to accept both of them. Developments in curriculum…

  7. Next-generation biology

    DEFF Research Database (Denmark)

    Rodrigues da Fonseca, Rute Andreia; Albrechtsen, Anders; Themudo, Goncalo Espregueira Cruz;


    As sequencing technologies become more affordable, it is now realistic to propose studying the evolutionary history of virtually any organism on a genomic scale. However, when dealing with non-model organisms it is not always easy to choose the best approach given a specific biological question, ...

  8. Openers for Biology Classes. (United States)

    Gridley, C. Robert R.

    This teaching guide contains 200 activities that are suitable for openers and demonstrations in biology classes. Details are provided regarding the use of these activities. Some of the broad topics under which the activities are organized include algae, amphibians, bacteria, biologists, crustaceans, dinosaurs, ecology, evolution, flowering plants,…

  9. Biological Warfare Agents

    Directory of Open Access Journals (Sweden)

    Dev Vrat Kamboj


    Full Text Available There is a long historic record of use of biological warfare (BW agents by warring countriesagainst their enemies. However, the frequency of their use has increased since the beginningof the twentieth century. World war I witnessed the use of anthrax agent against human beingsand animals by Germans, followed by large-scale field trials by Japanese against war prisonersand Chinese population during world war II. Ironically, research and development in biologicalwarfare agents increased tremendously after the Geneva Protocol, signed in 1925, because ofits drawbacks which were overcome by Biological and Toxin Weapons Convention (BTWC in1972. Biological warfare programme took back seat after the 1972 convention but biologicalagents regained their importance after the bioterrorist attacks of anthrax powder in 2001. In thelight of these attacks, many of which turned out to be hoax, general awareness is required aboutbiological warfare agents that can be used against them. This review has been written highlightingimportant biological warfare agents, diseases caused by them, possible therapies and otherprotection measures.

  10. Diversity in Biological Molecules (United States)

    Newbury, H. John


    One of the striking characteristics of fundamental biological processes, such as genetic inheritance, development and primary metabolism, is the limited amount of variation in the molecules involved. Natural selective pressures act strongly on these core processes and individuals carrying mutations and producing slightly sub-optimal versions of…

  11. Next-generation biology

    DEFF Research Database (Denmark)

    Rodrigues da Fonseca, Rute Andreia; Albrechtsen, Anders; Themudo, Goncalo Espregueira Cruz


    we present an overview of the current sequencing technologies and the methods used in typical high-throughput data analysis pipelines. Subsequently, we contextualize high-throughput DNA sequencing technologies within their applications in non-model organism biology. We include tips regarding managing...

  12. Bayes in biological anthropology. (United States)

    Konigsberg, Lyle W; Frankenberg, Susan R


    In this article, we both contend and illustrate that biological anthropologists, particularly in the Americas, often think like Bayesians but act like frequentists when it comes to analyzing a wide variety of data. In other words, while our research goals and perspectives are rooted in probabilistic thinking and rest on prior knowledge, we often proceed to use statistical hypothesis tests and confidence interval methods unrelated (or tenuously related) to the research questions of interest. We advocate for applying Bayesian analyses to a number of different bioanthropological questions, especially since many of the programming and computational challenges to doing so have been overcome in the past two decades. To facilitate such applications, this article explains Bayesian principles and concepts, and provides concrete examples of Bayesian computer simulations and statistics that address questions relevant to biological anthropology, focusing particularly on bioarchaeology and forensic anthropology. It also simultaneously reviews the use of Bayesian methods and inference within the discipline to date. This article is intended to act as primer to Bayesian methods and inference in biological anthropology, explaining the relationships of various methods to likelihoods or probabilities and to classical statistical models. Our contention is not that traditional frequentist statistics should be rejected outright, but that there are many situations where biological anthropology is better served by taking a Bayesian approach. To this end it is hoped that the examples provided in this article will assist researchers in choosing from among the broad array of statistical methods currently available.

  13. Antiprotons get biological

    CERN Multimedia


    After its final run in September, the first results of the Antiproton Cell Experiment (ACE) look very promising. It was the first experiment to take data on the biological effects of antiproton beams to evaluate the potential of antiprotons in radiation therapy.

  14. Biology Curriculum Support Document. (United States)

    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. Biological Isolation Garment (United States)


    A spinoff of astronaut's biological garment will allow hospital patients who are highly vulnerable to infection to leave their sterile habitats for several hours, carrying their germ free environment with them. Garments can be used in any of some 200 hospitals where isolation rooms are installed to treat leukemia.

  16. Commercializing Biological Control (United States)

    LeLeu, K. L.; Young, M. A.


    Describes the only commercial establishment involved in biological control in Australia. The wasp Aphitis melinus, which parasitizes the insect Red Scale, is bred in large numbers and released in the citrus groves where Red Scale is causing damage to the fruit. (JR)

  17. Biological trade and markets. (United States)

    Hammerstein, Peter; Noë, Ronald


    Cooperation between organisms can often be understood, like trade between merchants, as a mutually beneficial exchange of services, resources or other 'commodities'. Mutual benefits alone, however, are not sufficient to explain the evolution of trade-based cooperation. First, organisms may reject a particular trade if another partner offers a better deal. Second, while human trade often entails binding contracts, non-human trade requires unwritten 'terms of contract' that 'self-stabilize' trade and prevent cheating even if all traders strive to maximize fitness. Whenever trading partners can be chosen, market-like situations arise in nature that biologists studying cooperation need to account for. The mere possibility of exerting partner choice stabilizes many forms of otherwise cheatable trade, induces competition, facilitates the evolution of specialization and often leads to intricate forms of cooperation. We discuss selected examples to illustrate these general points and review basic conceptual approaches that are important in the theory of biological trade and markets. Comparing these approaches with theory in economics, it turns out that conventional models-often called 'Walrasian' markets-are of limited relevance to biology. In contrast, early approaches to trade and markets, as found in the works of Ricardo and Cournot, contain elements of thought that have inspired useful models in biology. For example, the concept of comparative advantage has biological applications in trade, signalling and ecological competition. We also see convergence between post-Walrasian economics and biological markets. For example, both economists and biologists are studying 'principal-agent' problems with principals offering jobs to agents without being sure that the agents will do a proper job. Finally, we show that mating markets have many peculiarities not shared with conventional economic markets. Ideas from economics are useful for biologists studying cooperation but need

  18. Systems biology, emergence and antireductionism. (United States)

    Kesić, Srdjan


    This study explores the conceptual history of systems biology and its impact on philosophical and scientific conceptions of reductionism, antireductionism and emergence. Development of systems biology at the beginning of 21st century transformed biological science. Systems biology is a new holistic approach or strategy how to research biological organisms, developed through three phases. The first phase was completed when molecular biology transformed into systems molecular biology. Prior to the second phase, convergence between applied general systems theory and nonlinear dynamics took place, hence allowing the formation of systems mathematical biology. The second phase happened when systems molecular biology and systems mathematical biology, together, were applied for analysis of biological data. Finally, after successful application in science, medicine and biotechnology, the process of the formation of modern systems biology was completed. Systems and molecular reductionist views on organisms were completely opposed to each other. Implications of systems and molecular biology on reductionist-antireductionist debate were quite different. The analysis of reductionism, antireductionism and emergence issues, in the era of systems biology, revealed the hierarchy between methodological, epistemological and ontological antireductionism. Primarily, methodological antireductionism followed from the systems biology. Only after, epistemological and ontological antireductionism could be supported.

  19. Inferring Biologically Relevant Models: Nested Canalyzing Functions

    CERN Document Server

    Hinkelmann, Franziska


    Inferring dynamic biochemical networks is one of the main challenges in systems biology. Given experimental data, the objective is to identify the rules of interaction among the different entities of the network. However, the number of possible models fitting the available data is huge and identifying a biologically relevant model is of great interest. Nested canalyzing functions, where variables in a given order dominate the function, have recently been proposed as a framework for modeling gene regulatory networks. Previously we described this class of functions as an algebraic toric variety. In this paper, we present an algorithm that identifies all nested canalyzing models that fit the given data. We demonstrate our methods using a well-known Boolean model of the cell cycle in budding yeast.

  20. [Disseminated intravascular coagulation: clinical and biological diagnosis]. (United States)

    Touaoussa, Aziz; El Youssi, Hind; El Hassani, Imane; Hanouf, Daham; El Bergui, Imane; Zoulati, Ghizlane; Amrani Hassani, Moncef


    Disseminated intravascular coagulation (DIC) is a syndrome characterized by the systemic activation of blood coagulation. Its pathophysiological mechanisms are complex and dependent on the underlying pathology, making the clinical and biological expression of quite variable DIC. Among the various biological parameters disrupted, most are not specific, and none of them allows in itself to make the diagnosis. All this does not facilitate the task of the practitioner for diagnosis of overt DIC, much less that of the non-overt DIC, early stage whose treatment would improve the prognosis. These considerations have led to develop scores, combining several parameters depending on their availability in daily practice, as well as their diagnostic relevance. Of all the scores, the ISTH (International society of thrombosis and hemostasis) remains the most used.

  1. Biologically active substances of stone crop fruits

    Directory of Open Access Journals (Sweden)

    Margarita Makarkina


    Full Text Available Stone fruit crops are successfully cultivated in many regions of Russia. Their fruits contain a great diversity of biologically active and mineral substances. The stone fruit varietal collection of the All Russia Research Institute of Fruit Crop Breeding has been estimated on the content of biologically active substances (ascorbic acid and phenolic compounds in fruits: 80 sour cherry varieties, 28 sweet cherry varieties, 29 plum varieties and 24 apricot varieties. High cultivar variability of the content of ascorbic acid and P-active sub-stances in fruits has been determined in each crop. The best genotypes have been singled out according to each biochemical component and a complex of characters.

  2. Biology and hemodynamics of aneurismal vasculopathies

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Vitor Mendes, E-mail: [Interventional Neuroradiology Unit, Service of Neuroradiology, University Hospital of Geneva (Switzerland); Brina, Olivier, E-mail: [Interventional Neuroradiology Unit, Service of Neuroradiology, University Hospital of Geneva (Switzerland); Gonzalez, Ana Marcos, E-mail: [Interventional Neuroradiology Unit, Service of Neuroradiology, University Hospital of Geneva (Switzerland); Narata, Ana Paula, E-mail: [Interventional Neuroradiology Unit, Service of Neuroradiology, University Hospital of Geneva (Switzerland); Ouared, Rafik, E-mail: [Interventional Neuroradiology Unit, Service of Neuroradiology, University Hospital of Geneva (Switzerland); Karl-Olof, Lovblad, E-mail: [Interventional Neuroradiology Unit, Service of Neuroradiology, University Hospital of Geneva (Switzerland)


    Aneurysm vasculopathies represents a group of vascular disorders that share a common morphological diagnosis: a vascular dilation, the aneurysm. They can have a same etiology and a different clinical presentation or morphology, or have different etiology and very similar anatomical geometry. The biology of the aneurysm formation is a complex process that will be a result of an endogenous predisposition and epigenetic factors later on including the intracranial hemodynamics. We describe the biology of saccular aneurysms, its growth and rupture, as well as, current concepts of hemodynamics derived from application of computational flow dynamics on patient specific vascular models. Furthermore, we describe different aneurysm phenotypes and its extremely variability on morphological and etiological presentation.

  3. Wastewater evaluation by analytical and biological procedures

    Directory of Open Access Journals (Sweden)

    M. Carballo


    Full Text Available Some procedures, based on analytical and biological methods, are useful tools for risk assessment of treatment plant wastewater. In fact, urban effluents, called “complex mixtures” due to their nature, origin and toxicologic and environmental variability, need a more realistic evaluation. In this study, 11 municipal wastewater effluents were studied. Chemical analysis (GC/MS and biological methods (acute and chronic toxicity bioassays and estrogenicity, mutagenity and teratogeny tests were carried out to identify the most frequent organic compounds and toxic effluents. Results showed 7 effluents with acute toxicity, 3 with chronic toxicity and 4, with estrogenic effects. When toxicity and analytical results were compared, it was observed that in effluents with estrogenic effects, at least 3 estrogenic substances were identified. Attending all these results, the inclusion of combined methodologies must be considered to get more realistic information about these situations.

  4. Biological risk factors for deep vein trombosis. (United States)

    Vayá, Amparo; Mira, Yolanda; Martínez, Marcial; Villa, Piedad; Ferrando, Fernando; Estellés, Amparo; Corella, Dolores; Aznar, Justo


    Hypercoagulable states due either to inherited or acquired thrombotic risk factors are only present in approximately half of cases of DVT, but the causes in the other half, remain unknown. The importance of biological risk factors such as hyperlipidemia, hypofibrinolysis and hemorheological alterations in the pathogenesis of DVT has not been well established. In order to ascertain whether the above mentioned biological factors are associated with DVT and could constitute independent risk factors, we carried out a case-control study in 109 first DVT patients in whom inherited or acquired thrombophilic risk factors had been ruled out and 121 healthy controls age (42+/-15 years) and sex matched. From all the biological variables analyzed (cholesterol, triglycerides, glucose, fibrinogen, erythrocyte aggregation, hematocrit, plasma viscosity and PAI-1) only fibrinogen concentration reached a statistically significant difference on the comparison of means (290+/-73 mg/dl in cases vs 268+/-58 mg/dl in controls, p220 mg/dl, hematocrit >45% and fibrinogen >300 mg/dl was higher in cases than in controls: 38% vs 22%; p30 ng/ml, 37% vs 25% was borderline significant; p=0.055. Multivariate logistic regression analysis showed that cholesterolemia >220 mg/dl and fibrinogen >300 mg/dl constitute independent predictors of venous thrombotic risk. The adjusted OR's were 2.03 (95% CI; 1.12-3.70) for cholesterolemia and 1.94 (95% CI; 1.07-3.55) for fibrinogen. When these two variables combined DVT risk rose about fourfold (3.96; p<0.05). Our results suggest that hypercholesterolemia and hyperfibrinogenemia should be added to the list of known DVT risk factors and we recommend adopting measures to decrease these variables in the population with a high risk of DVT.

  5. Biological components of Greek lagoonal ecosystems: an overview

    Directory of Open Access Journals (Sweden)



    Full Text Available The paper summarises the available information on the main biological components – phytoplankton, zooplankton, phytobenthos, zoobenthos and fish – of Greek lagoonal ecosystems. Meiobenthos was also studied in one of the lagoons. All components show great variability both in space and time, which is attributed to the variability of environmental conditions. The most important variable influencing species distribution and diversity is the degree of communication with the sea and the nutrient load introduced through fresh water inputs. Certain new methods, which have been applied for evaluation of the ecological quality state of the lagoons, are also presented.

  6. Variable subsistence indemnity

    CERN Document Server


    At its meeting on 8 November 2000, the Finance Committee approved, with effect from 1st January 2001, adjustments to the Variable Subsistence Indemnity according to the rates published by the United Nations Organization given in document CERN/FC/4339. This decision maintained the reference method in force since 1983. The Management now proposes to adjust the CERN rates of indemnities, with effect from 1st January 2002, on the basis of the United Nations 2001 rates. Simply to give some examples extracted from the complete United Nations lists, the attached Annex shows the rates for a number of typical CERN duty travel destinations. For those countries concerned, the rates will be expressed in Euros from 2002. It is to be noted that the cost level for most destinations will not change significantly if calculated in Swiss Francs and, in any case, the Management will ensure that the total volume of costs for duty travel is contained within the limits of the 2002 budget. It is also to be noted that, since 1st Janu...

  7. Variable subsistence indemnity

    CERN Document Server


    At its meeting on 15 December 1999, the Finance Committee approved, with effect from 1st January 2000, adjustments to the Variable Subsistence Indemnity according to the rates published by the United Nations Organization given in document CERN/FC/4219. This decision maintained the reference method in force since 1983. The Management now proposes to adjust the CERN rates of indemnities, with effect from 1st January 2001, on the basis of the United Nations 2000 rates. The table contained in this document shows the rates for typical destinations, but they are only extracts from the complete UN table. Although a precise estimate of the cost effect for duty travel is difficult to achieve due to currency exchange values, it is probable that this will remain unchanged if calculated in Swiss francs. It may also be noted that, since 1 January this year, Article R IV 1.41 of the Staff Rules and Regulations has been changed in order to formalize the practice of the payment of a lower subsistence indemnity than the appro...

  8. Variable subsistence indemnity

    CERN Document Server


    At its meeting on 9 December 1998, the Finance Committee approved, with effect from 1st January 1999, adjustments to the Variable Subsistence Indemnity according to the rates published by the United Nations Organization given in document CERN/FC/4113. This decision maintained the reference method in force since 1983. The Management now proposes to adjust the CERN rates of indemnities, with effect from 1st January 2000, on the basis of the United Nations 1999 rates, as shown for typical destinations in the table contained in this document. Although a precise estimate of the cost effect for duty travel is difficult to achieve due to currency exchange values, it is probable that this will remain unchanged if calculated in Swiss francs. The Management also proposes to formalise the practice of paying a lower subsistence indemnity than the approved basic amount, wherever feasible for events such as group duty travel to conferences or similar events, as discussed at the Finance Committee in December 1998. An amendm...

  9. Variable angle correlation spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Y K [Univ. of California, Berkeley, CA (United States)


    In this dissertation, a novel nuclear magnetic resonance (NMR) technique, variable angle correlation spectroscopy (VACSY) is described and demonstrated with {sup 13}C nuclei in rapidly rotating samples. These experiments focus on one of the basic problems in solid state NMR: how to extract the wealth of information contained in the anisotropic component of the NMR signal while still maintaining spectral resolution. Analysis of the anisotropic spectral patterns from poly-crystalline systems reveal information concerning molecular structure and dynamics, yet in all but the simplest of systems, the overlap of spectral patterns from chemically distinct sites renders the spectral analysis difficult if not impossible. One solution to this problem is to perform multi-dimensional experiments where the high-resolution, isotropic spectrum in one dimension is correlated with the anisotropic spectral patterns in the other dimensions. The VACSY technique incorporates the angle between the spinner axis and the static magnetic field as an experimental parameter that may be incremented during the course of the experiment to help correlate the isotropic and anisotropic components of the spectrum. The two-dimensional version of the VACSY experiments is used to extract the chemical shift anisotropy tensor values from multi-site organic molecules, study molecular dynamics in the intermediate time regime, and to examine the ordering properties of partially oriented samples. The VACSY technique is then extended to three-dimensional experiments to study slow molecular reorientations in a multi-site polymer system.

  10. Variables moderadoras del estres

    Directory of Open Access Journals (Sweden)

    María Cristina Richaud de Minzi


    Full Text Available El objetivo del presente trabajo es analizar la influenciadel estilo atribucional, la confianza interpersonal y el soporte social sobre la percepción de la amenaza. Se administraron la Escala de Estilo Atribucional; la Manheim Interview 01 Social Support, la Escala de Confianza Interpersonal; y el Inventario de Situaciones y Respuestas de Ansiedad, a 260 sujetos de ambos sexos, de 30 años de edad promedio, de nivel socioeconómico medio, residentes en la ciudad de Buenos Aires. El soporte social no demostró influencia significativa sobre la percepción de la amenaza. Con respecto a la influencia del estilo atribucional se puede decir que las personas indefensas perciben más amenaza, especialmente expresada como ansiedad cognitiva y, en menor grado, como ansiedad motora o conductual. La confianza interpersonal demostró ser una variable importante en la percepción de la amenaza. Los sujetos que presentaron alta desconfianza hacia las personas de su entorno perciben un mundo amenazante, que se manifiesta como ansiedad cognitiva, fisiológica y motora o conductual.

  11. Stochasticity in cell biology: Modeling across levels (United States)

    Pedraza, Juan Manuel


    Effective modeling of biological processes requires focusing on a particular level of description, and this requires summarizing de details of lower levels into effective variables and properly accounting for the constrains that other levels impose. In the context of stochasticity in gene expression, I will show how the details of the stochastic process can be characterized by a few effective parameters, which facilitates modeling but complicates interpretation of current experiments. I will show how the resulting noise can provide advantageous or deleterious phenotypic fluctuation and how noise control in the copy number control system of plasmids can change the selective pressures. This system illustrates the direct connection between molecular dynamics and evolutionary dynamics.

  12. The telomere lengthening conundrum - artifact or biology?

    DEFF Research Database (Denmark)

    Steenstrup, Troels; Hjelmborg, Jacob V B; Kark, Jeremy D;


    Recent longitudinal studies of age-dependent leukocyte telomere length (LTL) attrition have reported that variable proportions of individuals experience LTL lengthening. Often, LTL lengthening has been taken at face value, and authors have speculated about the biological causation of this finding....... Based on empirical data and theoretical considerations, we show that regardless of the method used to measure telomere length (Southern blot or quantitative polymerase chain reaction-based methods), measurement error of telomere length and duration of follow-up explain almost entirely the absence of age...

  13. The biology of the Arabian Sea and Bay of Bengal

    Digital Repository Service at National Institute of Oceanography (India)

    Gauns, M.

    This article focusses on the variability in physics and chemistry of the region and investigate its influence on the biology. This article is largely based on the recent observations made during the India JGOFS and BOBPS (Bay of Bengal Process Study...

  14. Explaining Choice and Share of Category Requirements of Biologic Meat

    NARCIS (Netherlands)

    P.C. Verhoef (Peter); K. Vlagsma-Brangule (Kristine)


    textabstractIn this paper we examine factors determining choice and consumption of biologic or organic meat. In our model explaining choice and share of category requirements, we consider economic/marketing variables (quality, price, and distribution), emotions (fear, empathy, andguilt), social norm

  15. Designing neural networks that process mean values of random variables

    Energy Technology Data Exchange (ETDEWEB)

    Barber, Michael J. [AIT Austrian Institute of Technology, Innovation Systems Department, 1220 Vienna (Austria); Clark, John W. [Department of Physics and McDonnell Center for the Space Sciences, Washington University, St. Louis, MO 63130 (United States); Centro de Ciências Matemáticas, Universidade de Madeira, 9000-390 Funchal (Portugal)


    We develop a class of neural networks derived from probabilistic models posed in the form of Bayesian networks. Making biologically and technically plausible assumptions about the nature of the probabilistic models to be represented in the networks, we derive neural networks exhibiting standard dynamics that require no training to determine the synaptic weights, that perform accurate calculation of the mean values of the relevant random variables, that can pool multiple sources of evidence, and that deal appropriately with ambivalent, inconsistent, or contradictory evidence. - Highlights: • High-level neural computations are specified by Bayesian belief networks of random variables. • Probability densities of random variables are encoded in activities of populations of neurons. • Top-down algorithm generates specific neural network implementation of given computation. • Resulting “neural belief networks” process mean values of random variables. • Such networks pool multiple sources of evidence and deal properly with inconsistent evidence.

  16. Boosted Regression Tree Models to Explain Watershed Nutrient Concentrations and Biological Condition (United States)

    Boosted regression tree (BRT) models were developed to quantify the nonlinear relationships between landscape variables and nutrient concentrations in a mesoscale mixed land cover watershed during base-flow conditions. Factors that affect instream biological components, based on ...

  17. Quantum physics meets biology

    CERN Document Server

    Arndt, Markus; Vedral, Vlatko


    Quantum physics and biology have long been regarded as unrelated disciplines, describing nature at the inanimate microlevel on the one hand and living species on the other hand. Over the last decades the life sciences have succeeded in providing ever more and refined explanations of macroscopic phenomena that were based on an improved understanding of molecular structures and mechanisms. Simultaneously, quantum physics, originally rooted in a world view of quantum coherences, entanglement and other non-classical effects, has been heading towards systems of increasing complexity. The present perspective article shall serve as a pedestrian guide to the growing interconnections between the two fields. We recapitulate the generic and sometimes unintuitive characteristics of quantum physics and point to a number of applications in the life sciences. We discuss our criteria for a future quantum biology, its current status, recent experimental progress and also the restrictions that nature imposes on bold extrapolat...

  18. [Cell biology and cosmetology]. (United States)

    Traniello, S; Cavalletti, T


    Cellular biology can become the natural support of research in the field of cosmetics because it is able to provide alternative experimental models which can partially replace the massive use of laboratory animals. Cultures of human skin cells could be used in tests investigating irritation of the skin. We have developed an "in vitro" experimental model that allows to evaluate the damage caused by the free radicals to the fibroblasts in culture and to test the protective action of the lipoaminoacids. Experimenting on human cell cultures presents the advantage of eliminating the extrapolation between the different species, of allowing a determination of the biological action of a substance and of evaluating its dose/response effect. This does not mean that "in vitro" experimenting could completely replace experimenting on living animals, but the "in vitro" model can be introduced in the realisation of preliminary screenings.

  19. Biological scaling and physics

    Indian Academy of Sciences (India)

    A R P Rau


    Kleiber’s law in biology states that the specific metabolic rate (metabolic rate per unit mass) scales as -1/4 in terms of the mass of the organism. A long-standing puzzle is the (- 1/4) power in place of the usual expectation of (- 1/3) based on the surface to volume ratio in three-dimensions. While recent papers by physicists have focused exclusively on geometry in attempting to explain the puzzle, we consider here a specific law of physics that governs fluid flow to show how the (- 1/4) power arises under certain conditions. More generally, such a line of approach that identifies a specific physical law as involved and then examines the implications of a power law may illuminate better the role of physics in biology.

  20. Next-generation biology

    DEFF Research Database (Denmark)

    Rodrigues da Fonseca, Rute Andreia; Albrechtsen, Anders; Themudo, Gonçalo Espregueira;


    we present an overview of the current sequencing technologies and the methods used in typical high-throughput data analysis pipelines. Subsequently, we contextualize high-throughput DNA sequencing technologies within their applications in non-model organism biology. We include tips regarding managing......As sequencing technologies become more affordable, it is now realistic to propose studying the evolutionary history of virtually any organism on a genomic scale. However, when dealing with non-model organisms it is not always easy to choose the best approach given a specific biological question......, a limited budget, and challenging sample material. Furthermore, although recent advances in technology offer unprecedented opportunities for research in non-model organisms, they also demand unprecedented awareness from the researcher regarding the assumptions and limitations of each method. In this review...

  1. Quantum physics meets biology. (United States)

    Arndt, Markus; Juffmann, Thomas; Vedral, Vlatko


    Quantum physics and biology have long been regarded as unrelated disciplines, describing nature at the inanimate microlevel on the one hand and living species on the other hand. Over the past decades the life sciences have succeeded in providing ever more and refined explanations of macroscopic phenomena that were based on an improved understanding of molecular structures and mechanisms. Simultaneously, quantum physics, originally rooted in a world-view of quantum coherences, entanglement, and other nonclassical effects, has been heading toward systems of increasing complexity. The present perspective article shall serve as a "pedestrian guide" to the growing interconnections between the two fields. We recapitulate the generic and sometimes unintuitive characteristics of quantum physics and point to a number of applications in the life sciences. We discuss our criteria for a future "quantum biology," its current status, recent experimental progress, and also the restrictions that nature imposes on bold extrapolations of quantum theory to macroscopic phenomena.

  2. Biological scaling and physics. (United States)

    Rau, A R P


    Kleiber's law in biology states that the specific metabolic rate (metabolic rate per unit mass) scales as M- 1/4 in terms of the mass M of the organism. A long-standing puzzle is the (- 1/4) power in place of the usual expectation of (- 1/3) based on the surface to volume ratio in three-dimensions. While recent papers by physicists have focused exclusively on geometry in attempting to explain the puzzle, we consider here a specific law of physics that governs fluid flow to show how the (- 1/4) power arises under certain conditions. More generally, such a line of approach that identifies a specific physical law as involved and then examines the implications of a power law may illuminate better the role of physics in biology.

  3. Topology in Molecular Biology

    CERN Document Server

    Monastyrsky, Michail Ilych


    The book presents a class of new results in molecular biology for which topological methods and ideas are important. These include: the large-scale conformation properties of DNA; computational methods (Monte Carlo) allowing the simulation of large-scale properties of DNA; the tangle model of DNA recombination and other applications of Knot theory; dynamics of supercoiled DNA and biocatalitic properties of DNA; the structure of proteins; and other very recent problems in molecular biology. The text also provides a short course of modern topology intended for the broad audience of biologists and physicists. The authors are renowned specialists in their fields and some of the new results presented here are documented for the first time in monographic form.

  4. Traceability of biologicals

    DEFF Research Database (Denmark)

    Vermeer, Niels S; Spierings, Irina; Mantel-Teeuwisse, Aukje K


    not support the routine recording of batch information. Expected changes in supply chain standards provide opportunities to systematically record detailed exposure information. Spontaneous reporting systems are the most vulnerable link in ensuring traceability, due to the manual nature of data transfer...... individual products within pharmacovigilance databases. AREAS COVERED: The authors discuss the present challenges in the traceability of biologicals in relation to pharmacovigilance, by exploring the processes involved in ensuring traceability. They explore both the existing systems that are in place...

  5. Milli-Biology (United States)


    inefficient at low RPM because power is wasted as heat in the coils, requiring gearing at low RPM, and power is required to maintain static position...soldering to join metal parts, epoxy to join the heat -sensitive permanent magnets, and screws to reversibly fasten subassemblies that might require...aerospace, and heliostat pointing for solar power. These are now transitioning to commercial development. The milli-biology workflow for coded

  6. Menstrual Cycle: Basic Biology



    The basic biology of the menstrual cycle is a complex, coordinated sequence of events involving the hypothalamus, anterior pituitary, ovary, and endometrium. The menstrual cycle with all its complexities can be easily perturbed by environmental factors such as stress, extreme exercise, eating disorders, and obesity. Furthermore, genetic influences such as fragile X premutations (Chapter X), X chromosome abnormalities (Chapter X), and galactose-1-phosphate uridyltransferase (GALT) point mutati...

  7. Biological Correlates of Empathy

    Directory of Open Access Journals (Sweden)

    E. Timucin Oral


    Full Text Available Empathy can be defined as the capacity to know emotionally what another is experiencing from within the frame of reference of that other person and the capacity to sample the feelings of another or it can be metaphorized as to put oneself in another’s shoes. Although the concept of empathy was firstly described in psychological theories, researches studying the biological correlates of psychological theories have been increasing recently. Not suprisingly, dinamically oriented psychotherapists Freud, Kohut, Basch and Fenichel had suggested theories about the biological correlates of empathy concept and established the basis of this modality decades ago. Some other theorists emphasized the importance of empathy in the early years of lifetime regarding mother-child attachment in terms of developmental psychology and investigated its role in explanation of psychopathology. The data coming from some of the recent brain imaging and animal model studies also seem to support these theories. Although increased activity in different brain regions was shown in many of the brain imaging studies, the role of cingulate cortex for understanding mother-child relationship was constantly emphasized in nearly all of the studies. In addition to these studies, a group of Italian scientists has defined a group of neurons as “mirror neurons” in their studies observing rhesus macaque monkeys. Later, they also defined mirror neurons in human studies, and suggested them as “empathy neurons”. After the discovery of mirror neurons, the hopes of finding the missing part of the puzzle for understanding the biological correlates of empathy raised again. Although the roles of different biological parameters such as skin conductance and pupil diameter for defining empathy have not been certain yet, they are going to give us the opportunity to revise the inconsistent basis of structural validity in psychiatry and to stabilize descriptive validity. In this review, the

  8. Biological therapies for spondyloarthritis


    Bruner, Vincenzo; Atteno, Mariangela; Spanò, Angelo; Scarpa, Raffaele; Peluso, Rosario


    Biological therapies and new imaging techniques have changed the therapeutic and diagnostic approach to spondyloarthritis. In patients with axial spondyloarthritis, tumor necrosis factor α (TNFα) inhibitor treatment is currently the only effective therapy in patients for whom conventional therapy with nonsteroidal anti-inflammatory drugs (NSAIDs) has failed. TNFα inhibitor treatment is more effective in preventing articular damage in peripheral joints than in axial ones. It is important to tr...

  9. Dominating biological networks.

    Directory of Open Access Journals (Sweden)

    Tijana Milenković

    Full Text Available Proteins are essential macromolecules of life that carry out most cellular processes. Since proteins aggregate to perform function, and since protein-protein interaction (PPI networks model these aggregations, one would expect to uncover new biology from PPI network topology. Hence, using PPI networks to predict protein function and role of protein pathways in disease has received attention. A debate remains open about whether network properties of "biologically central (BC" genes (i.e., their protein products, such as those involved in aging, cancer, infectious diseases, or signaling and drug-targeted pathways, exhibit some topological centrality compared to the rest of the proteins in the human PPI network.To help resolve this debate, we design new network-based approaches and apply them to get new insight into biological function and disease. We hypothesize that BC genes have a topologically central (TC role in the human PPI network. We propose two different concepts of topological centrality. We design a new centrality measure to capture complex wirings of proteins in the network that identifies as TC those proteins that reside in dense extended network neighborhoods. Also, we use the notion of domination and find dominating sets (DSs in the PPI network, i.e., sets of proteins such that every protein is either in the DS or is a neighbor of the DS. Clearly, a DS has a TC role, as it enables efficient communication between different network parts. We find statistically significant enrichment in BC genes of TC nodes and outperform the existing methods indicating that genes involved in key biological processes occupy topologically complex and dense regions of the network and correspond to its "spine" that connects all other network parts and can thus pass cellular signals efficiently throughout the network. To our knowledge, this is the first study that explores domination in the context of PPI networks.

  10. Quantum Effects in Biology (United States)

    Mohseni, Masoud; Omar, Yasser; Engel, Gregory S.; Plenio, Martin B.


    List of contributors; Preface; Part I. Introduction: 1. Quantum biology: introduction Graham R. Fleming and Gregory D. Scholes; 2. Open quantum system approaches to biological systems Alireza Shabani, Masoud Mohseni, Seogjoo Jang, Akihito Ishizaki, Martin Plenio, Patrick Rebentrost, Alàn Aspuru-Guzik, Jianshu Cao, Seth Lloyd and Robert Silbey; 3. Generalized Förster resonance energy transfer Seogjoo Jang, Hoda Hossein-Nejad and Gregory D. Scholes; 4. Multidimensional electronic spectroscopy Tomáš Mančal; Part II. Quantum Effects in Bacterial Photosynthetic Energy Transfer: 5. Structure, function, and quantum dynamics of pigment protein complexes Ioan Kosztin and Klaus Schulten; 6. Direct observation of quantum coherence Gregory S. Engel; 7. Environment-assisted quantum transport Masoud Mohseni, Alàn Aspuru-Guzik, Patrick Rebentrost, Alireza Shabani, Seth Lloyd, Susana F. Huelga and Martin B. Plenio; Part III. Quantum Effects in Higher Organisms and Applications: 8. Excitation energy transfer in higher plants Elisabet Romero, Vladimir I. Novoderezhkin and Rienk van Grondelle; 9. Electron transfer in proteins Spiros S. Skourtis; 10. A chemical compass for bird navigation Ilia A. Solov'yov, Thorsten Ritz, Klaus Schulten and Peter J. Hore; 11. Quantum biology of retinal Klaus Schulten and Shigehiko Hayashi; 12. Quantum vibrational effects on sense of smell A. M. Stoneham, L. Turin, J. C. Brookes and A. P. Horsfield; 13. A perspective on possible manifestations of entanglement in biological systems Hans J. Briegel and Sandu Popescu; 14. Design and applications of bio-inspired quantum materials Mohan Sarovar, Dörthe M. Eisele and K. Birgitta Whaley; 15. Coherent excitons in carbon nanotubes Leonas Valkunas and Darius Abramavicius; Glossary; References; Index.

  11. Calculi of meta-variables

    Institute of Scientific and Technical Information of China (English)

    Masahiko SATO; Takafumi SAKURAI; Yukiyoshi KAMEYAMA; Atsushi IGARASH


    The notion of meta-variable plays a fun-damental role when we define formal systems such as logical and computational calculi. Yet it has been usually understood only informally as is seen in most textbooks of logic. Based on our observations of the usages of meta-variables in textbooks, we propose two formal systems that have the notion of meta-variable. In both calculi, each variable is given a level (non-negative integer), which classifies variables into object variables (level 0), meta-variables (level 1), metameta-variables (level 2) and so on. Then, simple arity systems are. used to exclude meaningless terms like a meta-level function operating on the metameta-level. A main difference of the two calculi lies in the definitions of substitution. The first calculus uses textual substitution, which can often be found in definitions of quantified formulae: when a term is substituted for a meta-variable, free object-level variables in the term may be captured. The second cal-culus is based on the observation that predicates can be regarded as meta-level functions on object-level terms, hence uses capture-avoiding substitution. We show that both calculi enjoy a number of properties including Church-Rosser and Strong Normalization, which are indispensable when we use them as frameworks to define logical systems.

  12. Synthetic biology: advancing biological frontiers by building synthetic systems


    Chen, Yvonne Yu-Hsuan; Galloway, Kate E; Smolke, Christina D.


    Advances in synthetic biology are contributing to diverse research areas, from basic biology to biomanufacturing and disease therapy. We discuss the theoretical foundation, applications, and potential of this emerging field.

  13. Biological heart valves. (United States)

    Ciubotaru, Anatol; Cebotari, Serghei; Tudorache, Igor; Beckmann, Erik; Hilfiker, Andres; Haverich, Axel


    Cardiac valvular pathologies are often caused by rheumatic fever in young adults, atherosclerosis in elderly patients, or by congenital malformation of the heart in children, in effect affecting almost all population ages. Almost 300,000 heart valve operations are performed worldwide annually. Tissue valve prostheses have certain advantages over mechanical valves such as biocompatibility, more physiological hemodynamics, and no need for life-long systemic anticoagulation. However, the major disadvantage of biological valves is related to their durability. Nevertheless, during the last decade, the number of patients undergoing biological, rather than mechanical, valve replacement has increased from half to more than three-quarters for biological implants. Continuous improvement in valve fabrication includes development of new models and shapes, novel methods of tissue treatment, and preservation and implantation techniques. These efforts are focused not only on the improvement of morbidity and mortality of the patients but also on the improvement of their quality of life. Heart valve tissue engineering aims to provide durable, "autologous" valve prostheses. These valves demonstrate adaptive growth, which may avoid the need of repeated operations in growing patients.

  14. Absolute biological needs. (United States)

    McLeod, Stephen


    Absolute needs (as against instrumental needs) are independent of the ends, goals and purposes of personal agents. Against the view that the only needs are instrumental needs, David Wiggins and Garrett Thomson have defended absolute needs on the grounds that the verb 'need' has instrumental and absolute senses. While remaining neutral about it, this article does not adopt that approach. Instead, it suggests that there are absolute biological needs. The absolute nature of these needs is defended by appeal to: their objectivity (as against mind-dependence); the universality of the phenomenon of needing across the plant and animal kingdoms; the impossibility that biological needs depend wholly upon the exercise of the abilities characteristic of personal agency; the contention that the possession of biological needs is prior to the possession of the abilities characteristic of personal agency. Finally, three philosophical usages of 'normative' are distinguished. On two of these, to describe a phenomenon or claim as 'normative' is to describe it as value-dependent. A description of a phenomenon or claim as 'normative' in the third sense does not entail such value-dependency, though it leaves open the possibility that value depends upon the phenomenon or upon the truth of the claim. It is argued that while survival needs (or claims about them) may well be normative in this third sense, they are normative in neither of the first two. Thus, the idea of absolute need is not inherently normative in either of the first two senses.

  15. Biologics for tendon repair. (United States)

    Docheva, Denitsa; Müller, Sebastian A; Majewski, Martin; Evans, Christopher H


    Tendon injuries are common and present a clinical challenge to orthopedic surgery mainly because these injuries often respond poorly to treatment and require prolonged rehabilitation. Therapeutic options used to repair ruptured tendons have consisted of suture, autografts, allografts, and synthetic prostheses. To date, none of these alternatives has provided a successful long-term solution, and often the restored tendons do not recover their complete strength and functionality. Unfortunately, our understanding of tendon biology lags far behind that of other musculoskeletal tissues, thus impeding the development of new treatment options for tendon conditions. Hence, in this review, after introducing the clinical significance of tendon diseases and the present understanding of tendon biology, we describe and critically assess the current strategies for enhancing tendon repair by biological means. These consist mainly of applying growth factors, stem cells, natural biomaterials and genes, alone or in combination, to the site of tendon damage. A deeper understanding of how tendon tissue and cells operate, combined with practical applications of modern molecular and cellular tools could provide the long awaited breakthrough in designing effective tendon-specific therapeutics and overall improvement of tendon disease management.

  16. Biological surface science (United States)

    Kasemo, Bengt


    Biological surface science (BioSS), as defined here is the broad interdisciplinary area where properties and processes at interfaces between synthetic materials and biological environments are investigated and biofunctional surfaces are fabricated. Six examples are used to introduce and discuss the subject: Medical implants in the human body, biosensors and biochips for diagnostics, tissue engineering, bioelectronics, artificial photosynthesis, and biomimetic materials. They are areas of varying maturity, together constituting a strong driving force for the current rapid development of BioSS. The second driving force is the purely scientific challenges and opportunities to explore the mutual interaction between biological components and surfaces. Model systems range from the unique water structures at solid surfaces and water shells around proteins and biomembranes, via amino and nucleic acids, proteins, DNA, phospholipid membranes, to cells and living tissue at surfaces. At one end of the spectrum the scientific challenge is to map out the structures, bonding, dynamics and kinetics of biomolecules at surfaces in a similar way as has been done for simple molecules during the past three decades in surface science. At the other end of the complexity spectrum one addresses how biofunctional surfaces participate in and can be designed to constructively participate in the total communication system of cells and tissue. Biofunctional surfaces call for advanced design and preparation in order to match the sophisticated (bio) recognition ability of biological systems. Specifically this requires combined topographic, chemical and visco-elastic patterns on surfaces to match proteins at the nm scale and cells at the micrometer scale. Essentially all methods of surface science are useful. High-resolution (e.g. scanning probe) microscopies, spatially resolved and high sensitivity, non-invasive optical spectroscopies, self-organizing monolayers, and nano- and microfabrication


    Directory of Open Access Journals (Sweden)

    Ashish Agarwal


    Full Text Available In order to understand the dynamic behavior of the variables that can play a major role in the performance improvement in a supply chain, a System Dynamics-based model is proposed. The model provides an effective framework for analyzing different variables affecting supply chain performance. Among different variables, a causal relationship among different variables has been identified. Variables emanating from performance measures such as gaps in customer satisfaction, cost minimization, lead-time reduction, service level improvement and quality improvement have been identified as goal-seeking loops. The proposed System Dynamics-based model analyzes the affect of dynamic behavior of variables for a period of 10 years on performance of case supply chain in auto business.

  18. Benchmarking Variable Selection in QSAR. (United States)

    Eklund, Martin; Norinder, Ulf; Boyer, Scott; Carlsson, Lars


    Variable selection is important in QSAR modeling since it can improve model performance and transparency, as well as reduce the computational cost of model fitting and predictions. Which variable selection methods that perform well in QSAR settings is largely unknown. To address this question we, in a total of 1728 benchmarking experiments, rigorously investigated how eight variable selection methods affect the predictive performance and transparency of random forest models fitted to seven QSAR datasets covering different endpoints, descriptors sets, types of response variables, and number of chemical compounds. The results show that univariate variable selection methods are suboptimal and that the number of variables in the benchmarked datasets can be reduced with about 60 % without significant loss in model performance when using multivariate adaptive regression splines MARS and forward selection.

  19. Behavioral variability in an evolutionary theory of behavior dynamics. (United States)

    Popa, Andrei; McDowell, J J


    McDowell's evolutionary theory of behavior dynamics (McDowell, 2004) instantiates populations of behaviors (abstractly represented by integers) that evolve under the selection pressure of the environment in the form of positive reinforcement. Each generation gives rise to the next via low-level Darwinian processes of selection, recombination, and mutation. The emergent patterns can be analyzed and compared to those produced by biological organisms. The purpose of this project was to explore the effects of high mutation rates on behavioral variability in environments that arranged different reinforcer rates and magnitudes. Behavioral variability increased with the rate of mutation. High reinforcer rates and magnitudes reduced these effects; low reinforcer rates and magnitudes augmented them. These results are in agreement with live-organism research on behavioral variability. Various combinations of mutation rates, reinforcer rates, and reinforcer magnitudes produced similar high-level outcomes (equifinality). These findings suggest that the independent variables that describe an experimental condition interact; that is, they do not influence behavior independently. These conclusions have implications for the interpretation of high levels of variability, mathematical undermatching, and the matching theory. The last part of the discussion centers on a potential biological counterpart for the rate of mutation, namely spontaneous fluctuations in the brain's default mode network.

  20. Population Synthesis for Mira Variables

    Institute of Scientific and Technical Information of China (English)

    Chun-Hua Zhu; Chao-Zheng Zha


    By means of a population synthesis code, we investigate the Mira variables. Their birth rate (over 0.65yr-1) and their number (~ 130000) in the Galaxy are estimated. For all possible Mira variables, ranges of their initial masses,pulsating periods, mass losses and lifetimes are given. We check our model with the observed Mira variables near the Sun and our results prove to be valid.

  1. Variable Sampling Mapping (United States)

    Smith, Jeffrey, S.; Aronstein, David L.; Dean, Bruce H.; Lyon, Richard G.


    The performance of an optical system (for example, a telescope) is limited by the misalignments and manufacturing imperfections of the optical elements in the system. The impact of these misalignments and imperfections can be quantified by the phase variations imparted on light traveling through the system. Phase retrieval is a methodology for determining these variations. Phase retrieval uses images taken with the optical system and using a light source of known shape and characteristics. Unlike interferometric methods, which require an optical reference for comparison, and unlike Shack-Hartmann wavefront sensors that require special optical hardware at the optical system's exit pupil, phase retrieval is an in situ, image-based method for determining the phase variations of light at the system s exit pupil. Phase retrieval can be used both as an optical metrology tool (during fabrication of optical surfaces and assembly of optical systems) and as a sensor used in active, closed-loop control of an optical system, to optimize performance. One class of phase-retrieval algorithms is the iterative transform algorithm (ITA). ITAs estimate the phase variations by iteratively enforcing known constraints in the exit pupil and at the detector, determined from modeled or measured data. The Variable Sampling Mapping (VSM) technique is a new method for enforcing these constraints in ITAs. VSM is an open framework for addressing a wide range of issues that have previously been considered detrimental to high-accuracy phase retrieval, including undersampled images, broadband illumination, images taken at or near best focus, chromatic aberrations, jitter or vibration of the optical system or detector, and dead or noisy detector pixels. The VSM is a model-to-data mapping procedure. In VSM, fully sampled electric fields at multiple wavelengths are modeled inside the phase-retrieval algorithm, and then these fields are mapped to intensities on the light detector, using the properties

  2. Variable Speed Rotor System Project (United States)

    National Aeronautics and Space Administration — Variable speed rotors will give helicopters several advantages: higher top speed, greater fuel efficiency, momentary emergency over-power, resonance detuning...

  3. Conditional acceptability of random variables

    Directory of Open Access Journals (Sweden)

    Tasos C Christofides


    Full Text Available Abstract Acceptable random variables introduced by Giuliano Antonini et al. (J. Math. Anal. Appl. 338:1188-1203, 2008 form a class of dependent random variables that contains negatively dependent random variables as a particular case. The concept of acceptability has been studied by authors under various versions of the definition, such as extended acceptability or wide acceptability. In this paper, we combine the concept of acceptability with the concept of conditioning, which has been the subject of current research activity. For conditionally acceptable random variables, we provide a number of probability inequalities that can be used to obtain asymptotic results.

  4. Molecular Biology of Nitrogen Fixation (United States)

    Shanmugam, K. T.; Valentine, Raymond C.


    Reports that as a result of our increasing knowledge of the molecular biology of nitrogen fixation it might eventually be possible to increase the biological production of nitrogenous fertilizer from atmospheric nitrogen. (GS)

  5. Is Our Biology to Blame? (United States)

    Schneider, Scott


    Brief analyses of three recent examples of biological determinism: sex roles, overpopulation, and sociobiology, are presented in this article. Also a brief discussion of biological determinism and education is presented. (MR)

  6. Logical analysis of biological systems

    DEFF Research Database (Denmark)

    Mardare, Radu Iulian


    R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005.......R. Mardare, Logical analysis of biological systems. Fundamenta Informaticae, N 64:271-285, 2005....

  7. Biological treatment of Crohn's disease

    DEFF Research Database (Denmark)

    Nielsen, Ole Haagen; Bjerrum, Jacob Tveiten; Seidelin, Jakob Benedict


    Introduction of biological agents for the treatment of Crohn's disease (CD) has led to a transformation of the treatment paradigm. Several biological compounds have been approved for patients with CD refractory to conventional treatment: infliximab, adalimumab and certolizumab pegol (and...

  8. Logical impossibilities in biological networks

    Directory of Open Access Journals (Sweden)

    Monendra Grover


    Full Text Available Biological networks are complex and involve several kinds of molecules. For proper biological function it is important for these biomolecules to act at an individual level and act at the level of interaction of these molecules. In this paper some of the logical impossibilities that may arise in the biological networks and their possible solutions are discussed. It may be important to understand these paradoxes and their possible solutions in order to develop a holistic view of biological function.

  9. Efficient, sparse biological network determination

    Directory of Open Access Journals (Sweden)

    Papachristodoulou Antonis


    Full Text Available Abstract Background Determining the interaction topology of biological systems is a topic that currently attracts significant research interest. Typical models for such systems take the form of differential equations that involve polynomial and rational functions. Such nonlinear models make the problem of determining the connectivity of biochemical networks from time-series experimental data much harder. The use of linear dynamics and linearization techniques that have been proposed in the past can circumvent this, but the general problem of developing efficient algorithms for models that provide more accurate system descriptions remains open. Results We present a network determination algorithm that can treat model descriptions with polynomial and rational functions and which does not make use of linearization. For this purpose, we make use of the observation that biochemical networks are in general 'sparse' and minimize the 1-norm of the decision variables (sum of weighted network connections while constraints keep the error between data and the network dynamics small. The emphasis of our methodology is on determining the interconnection topology rather than the specific reaction constants and it takes into account the necessary properties that a chemical reaction network should have – something that techniques based on linearization can not. The problem can be formulated as a Linear Program, a convex optimization problem, for which efficient algorithms are available that can treat large data sets efficiently and uncertainties in data or model parameters. Conclusion The presented methodology is able to predict with accuracy and efficiency the connectivity structure of a chemical reaction network with mass action kinetics and of a gene regulatory network from simulation data even if the dynamics of these systems are non-polynomial (rational and uncertainties in the data are taken into account. It also produces a network structure that can

  10. Biological Computing Fundamentals and Futures


    Akula, Balaji; Cusick, James


    The fields of computing and biology have begun to cross paths in new ways. In this paper a review of the current research in biological computing is presented. Fundamental concepts are introduced and these foundational elements are explored to discuss the possibilities of a new computing paradigm. We assume the reader to possess a basic knowledge of Biology and Computer Science

  11. Functions in Biological Kind Classification (United States)

    Lombrozo, Tania; Rehder, Bob


    Biological traits that serve functions, such as a zebra's coloration (for camouflage) or a kangaroo's tail (for balance), seem to have a special role in conceptual representations for biological kinds. In five experiments, we investigate whether and why functional features are privileged in biological kind classification. Experiment 1…

  12. Semiconductor nanostructures in biological applications

    Energy Technology Data Exchange (ETDEWEB)

    Alexson, Dimitri [Department of Electrical and Computer Engineering, University of Illinois at Chicago, Chicago, IL 60607 (United States); Chen Hongfeng [Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607 (United States); Cho, Michael [Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607 (United States); Department of Physics, University of Illinois at Chicago, Chicago, IL 60607 (United States); Dutta, Mitra [Department of Electrical and Computer Engineering, University of Illinois at Chicago, Chicago, IL 60607 (United States); Department of Physics, University of Illinois at Chicago, Chicago, IL 60607 (United States); Li Yang [Department of Electrical and Computer Engineering, University of Illinois at Chicago, Chicago, IL 60607 (United States); Shi, Peng [Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607 (United States); Raichura, Amit [Department of Electrical and Computer Engineering, University of Illinois at Chicago, Chicago, IL 60607 (United States); Ramadurai, Dinakar [Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607 (United States); Parikh, Shaunak [Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607 (United States); Stroscio, Michael A [Department of Electrical and Computer Engineering, University of Illinois at Chicago, Chicago, IL 60607 (United States); Department of Physics, University of Illinois at Chicago, Chicago, IL 60607 (United States); Vasudev, Milana [Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607 (United States)


    Semiconductor nanostructures in biological applications are discussed. Results are presented on the use of colloidal semiconductor quantum dots both as biological tags and as structures that interact with and influence biomolecules. Results are presented on the use of semiconducting carbon nanotubes in biological applications. (topical review)


    Directory of Open Access Journals (Sweden)

    T. I. Burak


    Full Text Available The methodology for computer modeling of complex eco-biological models is presented in this paper. It is based on system approach of J. Forrester. Developed methodology is universal for complex ecological and biological systems. Modeling algorithm considers specialties of eco-biological systems and shows adequate and accurate results in practice. 

  14. Marine molecular biology: an emerging field of biological sciences. (United States)

    Thakur, Narsinh L; Jain, Roopesh; Natalio, Filipe; Hamer, Bojan; Thakur, Archana N; Müller, Werner E G


    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. NASA Biological Specimen Repository (United States)

    McMonigal, K. A.; Pietrzyk, R. A.; Sams, C. F.; Johnson, M. A.


    The NASA Biological Specimen Repository (NBSR) was established in 2006 to collect, process, preserve and distribute spaceflight-related biological specimens from long duration ISS astronauts. This repository provides unique opportunities to study longitudinal changes in human physiology spanning may missions. The NBSR collects blood and urine samples from all participating ISS crewmembers who have provided informed consent. These biological samples are collected once before flight, during flight scheduled on flight days 15, 30, 60, 120 and within 2 weeks of landing. Postflight sessions are conducted 3 and 30 days after landing. The number of in-flight sessions is dependent on the duration of the mission. Specimens are maintained under optimal storage conditions in a manner that will maximize their integrity and viability for future research The repository operates under the authority of the NASA/JSC Committee for the Protection of Human Subjects to support scientific discovery that contributes to our fundamental knowledge in the area of human physiological changes and adaptation to a microgravity environment. The NBSR will institute guidelines for the solicitation, review and sample distribution process through establishment of the NBSR Advisory Board. The Advisory Board will be composed of representatives of all participating space agencies to evaluate each request from investigators for use of the samples. This process will be consistent with ethical principles, protection of crewmember confidentiality, prevailing laws and regulations, intellectual property policies, and consent form language. Operations supporting the NBSR are scheduled to continue until the end of U.S. presence on the ISS. Sample distribution is proposed to begin with selections on investigations beginning in 2017. The availability of the NBSR will contribute to the body of knowledge about the diverse factors of spaceflight on human physiology.

  16. Biology Reflective Assessment Curriculum (United States)

    Bayley, Cheryl Ann

    Often students and educators view assessments as an obligation and finality for a unit. In the current climate of high-stakes testing and accountability, the balance of time, resources and emphasis on students' scores related to assessment have been slanted considerably toward the summative side. This tension between assessment for accountability and assessment to inform teaching strains instruction and educators' ability to use that information to design learning opportunities that help students develop deeper conceptual understanding. A substantive body of research indicates that formative and reflective assessment can significantly improve student learning. Biology Reflective Assessment Curriculum (BRAC) examines support provided for high school science students through assessment practices. This investigation incorporates the usage of reflective assessments as a guiding practice for differentiated instruction and student choice. Reflective assessment is a metacognitive strategy that promotes self-monitoring and evaluation. The goals of the curriculum are to promote self-efficacy and conceptual understanding in students learning biology through developing their metacognitive awareness. BRAC was implemented in a high school biology classroom. Data from assessments, metacognitive surveys, self-efficacy surveys, reflective journals, student work, a culminating task and field notes were used to evaluate the effectiveness of the curriculum. The results suggest that students who develop their metacognitive skills developed a deeper conceptual understanding and improved feelings of self-efficacy when they were engaged in a reflective assessment unit embedded with student choice. BRAC is a tool for teachers to use assessments to assist students in becoming metacognitive and to guide student choice in learning opportunities.

  17. Linear and Nonlinear Heart Rate Variability Indexes in Clinical Practice

    Directory of Open Access Journals (Sweden)

    Buccelletti Francesco


    Full Text Available Biological organisms have intrinsic control systems that act in response to internal and external stimuli maintaining homeostasis. Human heart rate is not regular and varies in time and such variability, also known as heart rate variability (HRV, is not random. HRV depends upon organism's physiologic and/or pathologic state. Physicians are always interested in predicting patient's risk of developing major and life-threatening complications. Understanding biological signals behavior helps to characterize patient's state and might represent a step toward a better care. The main advantage of signals such as HRV indexes is that it can be calculated in real time in noninvasive manner, while all current biomarkers used in clinical practice are discrete and imply blood sample analysis. In this paper HRV linear and nonlinear indexes are reviewed and data from real patients are provided to show how these indexes might be used in clinical practice.

  18. Biology-environment interaction and evocative biology-environment correlation: contributions of harsh discipline and parental psychopathology to problem adolescent behaviors. (United States)

    Riggins-Caspers, Kristin M; Cadoret, Remi J; Knutson, John F; Langbehn, Douglas


    Using an adoption paradigm, the Bioecological Model of development proposed by Bronfenbrenner and Ceci in 1994 was tested by concurrently modeling for biology-environment interaction and evocative biology-environment correlation. A sample of 150 adult adoptees (ages, 18-45 years) provided retrospective reports of harsh adoptive parent discipline, which served as the environmental independent variables. Birth parent psychopathology served as the biological predictor. The dependent variables were retrospective adoptee and adoptive parent reports on adolescent aggressive and conduct-disordered behaviors. Finally, adoptees were classified as experiencing contextual environmental risk using the presence of two or more adverse factors in the adoptive home (e.g., adoptive parent psychopathology) as the cutoff. The contextual environment was found to moderate the biological process of evocative biology-environment correlation, providing empirical support for the Bronfenbrenner and Ceci (1994) Bioecological Model.

  19. The Promises of Biology and the Biology of Promises

    DEFF Research Database (Denmark)

    Lee, Jieun


    commitments with differently imagined futures. I argue that promises are constitutive of the stem cell biology, rather than being derivative of it. Since the biological concept of stem cells is predicated on the future that they promise, the biological life of stem cells is inextricably intertwined...... patients’ bodies in anticipation of materializing the promises of stem cell biology, they are produced as a new form of biovaluable. The promises of biology move beyond the closed circuit of scientific knowledge production, and proliferate in the speculative marketplaces of promises. Part II looks at how...... of technologized biology and biological time can appear promising with the backdrop of the imagined intransigence of social, political, and economic order in the Korean society....

  20. Illuminating Cell Biology (United States)


    NASA's Ames Research Center awarded Ciencia, Inc., a Small Business Innovation Research contract to develop the Cell Fluorescence Analysis System (CFAS) to address the size, mass, and power constraints of using fluorescence spectroscopy in the International Space Station's Life Science Research Facility. The system will play an important role in studying biological specimen's long-term adaptation to microgravity. Commercial applications for the technology include diverse markets such as food safety, in situ environmental monitoring, online process analysis, genomics and DNA chips, and non-invasive diagnostics. Ciencia has already sold the system to the private sector for biosensor applications.

  1. Biological hydrogen production

    Energy Technology Data Exchange (ETDEWEB)

    Benemann, J.R. [Univ. of California, Berkeley, CA (United States)


    Biological hydrogen production can be accomplished by either thermochemical (gasification) conversion of woody biomass and agricultural residues or by microbiological processes that yield hydrogen gas from organic wastes or water. Biomass gasification is a well established technology; however, the synthesis gas produced, a mixture of CO and H{sub 2}, requires a shift reaction to convert the CO to H{sub 2}. Microbiological processes can carry out this reaction more efficiently than conventional catalysts, and may be more appropriate for the relatively small-scale of biomass gasification processes. Development of a microbial shift reaction may be a near-term practical application of microbial hydrogen production.

  2. Biological Petri Nets

    CERN Document Server

    Wingender, E


    It was suggested some years ago that Petri nets might be well suited to modeling metabolic networks, overcoming some of the limitations encountered by the use of systems employing ODEs (ordinary differential equations). Much work has been done since then which confirms this and demonstrates the usefulness of this concept for systems biology. Petri net technology is not only intuitively understood by scientists trained in the life sciences, it also has a robust mathematical foundation and provides the required degree of flexibility. As a result it appears to be a very promising approach to mode

  3. Systems biology: experimental design. (United States)

    Kreutz, Clemens; Timmer, Jens


    Experimental design has a long tradition in statistics, engineering and life sciences, dating back to the beginning of the last century when optimal designs for industrial and agricultural trials were considered. In cell biology, the use of mathematical modeling approaches raises new demands on experimental planning. A maximum informative investigation of the dynamic behavior of cellular systems is achieved by an optimal combination of stimulations and observations over time. In this minireview, the existing approaches concerning this optimization for parameter estimation and model discrimination are summarized. Furthermore, the relevant classical aspects of experimental design, such as randomization, replication and confounding, are reviewed.

  4. Biology of Nanobots (United States)

    Duan, Wentao; Pavlick, Ryan; Sen, Ayusman


    One of the more interesting recent discoveries has been the ability to design nano/microbots which catalytically harness the chemical energy in their environment to move autonomously. Their potential applications include delivery of materials, self-assembly of superstructures, and roving sensors. One emergent area of research is the study of their collective behavior and how they emulate living systems. The aim of this chapter is to describe the "biology" of nanobots, summarizing the fundamentals physics behind their motion and how the bots interact with each other to initiate complex emergent behavior.

  5. Menstrual Cycle: Basic Biology (United States)

    Hawkins, Shannon M.; Matzuk, Martin M.


    The basic biology of the menstrual cycle is a complex, coordinated sequence of events involving the hypothalamus, anterior pituitary, ovary, and endometrium. The menstrual cycle with all its complexities can be easily perturbed by environmental factors such as stress, extreme exercise, eating disorders, and obesity. Furthermore, genetic influences such as fragile X premutations (Chapter X), X chromosome abnormalities (Chapter X), and galactose-1-phosphate uridyltransferase (GALT) point mutations (galactosemia) also contribute to perturbations of the menstrual cycle. Although not perfect, mouse model have helped to identify and confirm additional components and pathways in menstrual cycle function and dysfunction in humans. PMID:18574203

  6. [Tuberculosis and molecular biology]. (United States)

    Andersen, Ase Bengård; Lillebaek, Troels; Søborg, Christian; Johansen, Isik Somuncu; Thomsen, Vibeke Østergaard


    Mycobacterium tuberculosis, the causative agent of tuberculosis (TB) hunting millions worldwide, is a challenge to work with in the laboratory. Modern molecular biology has provided extremely useful tools which have changed conventional diagnostic procedures in the TB laboratories. Research in molecular epidemiology is currently expanding our knowledge of the natural history of TB. Access to the genome sequence has opened new avenues for research in drug development and new vaccines. However, we are still awaiting the impact of these efforts in the resource-poor TB endemic countries.

  7. Biology of Bilirubin Photoisomers. (United States)

    Hansen, Thor Willy Ruud


    Phototherapy is the main treatment for neonatal hyperbilirubinemia. In acute treatment of extreme hyperbilirubinemia, intensive phototherapy may have a role in 'detoxifying' the bilirubin molecule to more polar photoisomers, which should be less prone to crossing the blood-brain barrier, providing a 'brain-sparing' effect. This article reviews the biology of bilirubin isomers. Although there is evidence supporting the lower toxicity of bilirubin photoisomers, there are studies showing the opposite. There are methodologic weaknesses in most studies and better-designed experiments are needed. In an infant acutely threatened by bilirubin-induced brain damage, intensified phototherapy should be used expediently and aggressively.

  8. Nanoindentation of biological composites (United States)

    Dickinson, M.


    This investigation studied the effect of storage conditions on the mechanical properties as measured by nanoindentation of mineralised tissue samples. The three storage solutions were Hanks balanced salt solution, phosphate buffered saline and deionised water and all had a significant effect on the surface properties, namely hardness and modulus of enamel, dentin and bone tested. The effect was significant with a greater than 70% reduction in surface mechanical properties after 8 days immersion in the solutions. This study highlights the importance of testing biological tissues immediately after extraction, and the possible structural and chemistry changes that may occur by artificially storing the tissues.

  9. Biological fathers and stepfathers who molest their daughters: psychological, phallometric, and criminal features. (United States)

    Greenberg, David M; Firestone, Philip; Nunes, Kevin L; Bradford, John M; Curry, Susan


    A sample (N=143) of men who sexually abused their biological daughters or their step/adopted daughters were examined on a comprehensive array of demographic and historical information, offense characteristics, psychological and phallometric measures, and recidivism. Biological fathers were significantly less sexually aroused by children than were the stepfathers. On all the remaining variables, however, no statistically significant differences were found. Overall, biological and stepfathers in the present study appear to be much more similar than different from one another.

  10. "Raza" : Variables Históricas

    Directory of Open Access Journals (Sweden)

    Max S. Hering Torres


    Full Text Available This article addresses "race" as a social practice, a construction, and as an idea that has been developed through the power of discourse. This category, rather than a biological reality, is an intellectual and social construction which has had a variety of meanings attributed to it through history. The concept of "race," however, has preserved its functionality: to differentiate, segregate, and distort otherness. In this way, it has racialized social relations through biological determinism. To substantiate this hypothesis, the article undertakes a historical analysis to demonstrate the dynamics and variability of the racial imaginary. It sketches the outline of a history of race that includes the Spanish idea of the "Purityof Blood" (16-17th centuries, the legitimizing discoursesofthe French nobility (17-18th centuries, the ambivalence of the Enlightenment, aswell as 19th century scientific racism as a preludeofthe Holocaustor Shoah. The article concludeswithsome reflections derived from genetics as additional proof of the fictional nature of the concept of "race."

  11. Variability in human body size (United States)

    Annis, J. F.


    The range of variability found among homogeneous groups is described and illustrated. Those trends that show significantly marked differences between sexes and among a number of racial/ethnic groups are also presented. Causes of human-body size variability discussed include genetic endowment, aging, nutrition, protective garments, and occupation. The information is presented to aid design engineers of space flight hardware and equipment.

  12. Predictor variables of clergy pedophiles. (United States)

    Ruzicka, M F


    File data on familial traits, past sexual experience as a victim, and other traits identified in the literature as leading toward pedophilia, were summarized for 10 convicted clergy pedophiles to construct a set of variables possibly useful for screening. Further research is underway to identify trauma in early life and those personality-related variables current studies indicate as relevant.

  13. Complex Variables in Secondary Schools (United States)

    Dwyer, Jerry; Moskal, Barbara; Duke, Billy; Wilhelm, Jennifer


    This article describes the work of outreach mathematicians introducing the topic of complex variables to eighth and ninth grade students (13- to 15-year-olds) in the US. Complex variables is an area of mathematics that is not typically studied at secondary level. The authors developed seven lessons designed to stimulate students' interest in…

  14. Variable Selection in Discriminant Analysis. (United States)

    Huberty, Carl J.; Mourad, Salah A.

    Methods for ordering and selecting variables for discriminant analysis in multiple group comparison or group prediction studies include: univariate Fs, stepwise analysis, learning discriminant function (LDF) variable correlations, communalities, LDF standardized coefficients, and weighted standardized coefficients. Five indices based on distance,…


    Institute of Scientific and Technical Information of China (English)

    Sofiya Ostrovska


    New measures of independence for n random variables, based on their moments, are studied. A scale of degrees of independence for random variables which starts with uncorrelatedness (for n = 2) and finishes at independence is constructed. The scale provides a countable linearly ordered set of measures of independence.

  16. From biologically-inspired physics to physics-inspired biology From biologically-inspired physics to physics-inspired biology (United States)

    Kornyshev, Alexei A.


    couple of billion years of evolutionary history; 'you cannot expect to explain so wise an old bird in a few simple words'. It is indisputably so, but it is followed by two other competing sub-dogmas: Dogma N6a: Physics wants to simplify and unify things, as much as possible, biology resists the reductionist approach and is happy about diversification and complexity. In my opinion all these dogmas have been beaten by this icon, the understanding of which gave rise to the idea of DNA replication and all the following principles of molecular biology. Not only 'this will happen again' but on a smaller scale this happens all the time. Generally, through centuries, physics and mathematics have changed our lives completely. In a short article one cannot give a full list of such achievements from Aristotle's time, but I name just a few of the summits of the last two centuries. A great physicist Rutherford (who was, by the way, a Nobel Laureate in Chemistry for 'his investigations into the disintegration of the elements, and the chemistry of radioactive substances') was also famous for an extreme (and definitely outdated) statement: 'All science is either stamp collecting or physics'. Let us paraphrase him and collect some stamps. I have no space to stop on the Faraday-Ampere laws of stationary electricity (who cares, electric current comes from a plug would be the answer of most of people unfamiliar with physics, and forget about electricity that is supplied to biological laboratories). So, let us go straight away to James Clerk Maxwell. He derived four equations that related electricity and magnetism and, as the legend tells us, it took him seven years to write the fourth equation to complete the set with four unknown variables. The story of the fourth Maxwell equation is one of the most dramatic stories in the history of science [4]. As a solution of that set he obtained relativistically-invariant electromagnetic waves, which no one saw and the consequences of which no one had

  17. Opportunities in plant synthetic biology. (United States)

    Cook, Charis; Martin, Lisa; Bastow, Ruth


    Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the 2013 GARNet workshop on plant synthetic biology.

  18. Index for Wind Power Variability

    Energy Technology Data Exchange (ETDEWEB)

    Kiviluoma, Juha; Holttinen, Hannele; Cutululis, Nicolaos Antonio; Litong-Palima, Marisciel; Scharff, Richard; Milligan, Michael; Weir, David Edward


    Variability of large scale wind power generation is dependent on several factors: characteristics of installed wind power plants, size of the area where the plants are installed, geographic dispersion within that area and its weather regime(s). Variability can be described by ramps in power generation, i.e. changes from time period to time period. Given enough data points, it can be described with a probability density function. This approach focuses on two dimensions of variability: duration of the ramp and probability distribution. This paper proposes an index based on these two dimensions to enable comparisons and characterizations of variability under different conditions. The index is tested with real, large scale wind power generation data from several countries. Considerations while forming an index are discussed, as well as the main results regarding what the drivers of variability experienced for different data.

  19. [Biological activity of Spirulina]. (United States)

    Blinkova, L P; Gorobets, O B; Baturo, A P


    In this review information of Spirulina platensis (SP), a blue-green alga (photosynthesizing cyanobacterium) having diverse biological activity is presented. Due to high content of highly valuable proteins, indispensable amino acids, vitamins, beta-carotene and other pigments, mineral substances, indispensable fatty acids and polysaccharides, PS has been found suitable for use as bioactive additive. SP produces an immunostimulating effect by enhancing the resistance of humans, mammals, chickens and fish to infections, the capacity of influencing hemopoiesis, stimulating the production of antibodies and cytokines. Under the influence of SP macrophages, T and B cells are activated. SP sulfolipids have proved to be effective against HIV. Preparations obtained from SP biomass have also been found active against herpesvirus, cytomegalovirus, influenza virus, etc. SP extracts are capable in inhibiting cancerogenesis. SP preparations are regarded as functional products contributing to the preservation of the resident intestinal microflora, especially lactic acid bacilli and bifidobacteria, and to a decrease in the level of Candida albicans. The biological activity of SP with respect to microorganisms holds good promise for using these microalgae as components of culture media.

  20. Biological hydrogen photoproduction

    Energy Technology Data Exchange (ETDEWEB)

    Nemoto, Y. [Univ. of Miami, FL (United States)


    Following are the major accomplishments of the 6th year`s study of biological hydrogen photoproduction which were supported by DOE/NREL. (1) We have been characterizing a biological hydrogen production system using synchronously growing aerobically nitrogen-fixing unicellular cyanobacterium, Synechococcus sp. Miami BG 043511. So far it was necessary to irradiate the cells to produce hydrogen. Under darkness they did not produce hydrogen. However, we found that, if the cells are incubated with oxygen, they produce hydrogen under the dark. Under 80% argon + 20% oxygen condition, the hydrogen production activity under the dark was about one third of that under the light + argon condition. (2) Also it was necessary so far to incubate the cells under argon atmosphere to produce hydrogen in this system. Argon treatment is very expensive and should be avoided in an actual hydrogen production system. We found that, if the cells are incubated at a high cell density and in a container with minimum headspace, it is not necessary to use argon for the hydrogen production. (3) Calcium ion was found to play an important role in the mechanisms of protection of nitrogenase from external oxygen. This will be a clue to understand the reason why the hydrogen production is so resistant to oxygen in this strain. (4) In this strain, sulfide can be used as electron donor for the hydrogen production. This result shows that waste water can be used for the hydrogen production system using this strain.

  1. Synthetic biology in plastids. (United States)

    Scharff, Lars B; Bock, Ralph


    Plastids (chloroplasts) harbor a small gene-dense genome that is amenable to genetic manipulation by transformation. During 1 billion years of evolution from the cyanobacterial endosymbiont to present-day chloroplasts, the plastid genome has undergone a dramatic size reduction, mainly as a result of gene losses and the large-scale transfer of genes to the nuclear genome. Thus the plastid genome can be regarded as a naturally evolved miniature genome, the gradual size reduction and compaction of which has provided a blueprint for the design of minimum genomes. Furthermore, because of the largely prokaryotic genome structure and gene expression machinery, the high transgene expression levels attainable in transgenic chloroplasts and the very low production costs in plant systems, the chloroplast lends itself to synthetic biology applications that are directed towards the efficient synthesis of green chemicals, biopharmaceuticals and other metabolites of commercial interest. This review describes recent progress with the engineering of plastid genomes with large constructs of foreign or synthetic DNA, and highlights the potential of the chloroplast as a model system in bottom-up and top-down synthetic biology approaches.

  2. Oscillations in Mathematical Biology

    CERN Document Server


    The papers in this volume are based on talks given at a one day conference held on the campus of Adelphi University in April 1982. The conference was organized with the title "Oscillations in Mathematical Biology;" however the speakers were allowed considerable latitutde in their choice of topics. In the event, the talks all concerned the dynamics of non-linear systems arising in biology so that the conference achieved a good measure of cohesion. Some of the speakers cho~e not to submit a manuscript for these proceedings, feeling that their material was too conjectural to be committed to print. Also the paper of Rinzel and Troy is a distillation of the two separate talks that the authors gave. Otherwise the material reproduces the conference proceedings. The conference was made possible by the generous support of the Office of the Dean of the College of Arts and Sciences at Adelphi. The bulk of the organization of the conference was carried out by Dr. Ronald Grisell whose energy was in large measure responsib...

  3. Neutron instrumentation for biology

    Energy Technology Data Exchange (ETDEWEB)

    Mason, S.A. [Institut Laue-Langevin, Grenoble (France)


    In the October 1994 round of proposals at the ILL, the external biology review sub- committee was asked to allocate neutron beam time to a wide range of experiments, on almost half the total number of scheduled neutron instruments: on 3 diffractometers, on 3 small angle scattering instruments, and on some 6 inelastic scattering spectrometers. In the 3.5 years since the temporary reactor shutdown, the ILL`s management structure has been optimized, budgets and staff have been trimmed, the ILL reactor has been re-built, and many of the instruments up-graded, many powerful (mainly Unix) workstations have been introduced, and the neighboring European Synchrotron Radiation Facility has established itself as the leading synchrotron radiation source and has started its official user program. The ILL reactor remains the world`s most intense dedicated neutron source. In this challenging context, it is of interest to review briefly the park of ILL instruments used to study the structure and energetics of small and large biological systems. A brief summary will be made of each class of experiments actually proposed in the latest ILL proposal round.

  4. Industrial systems biology. (United States)

    Otero, José Manuel; Nielsen, Jens


    The chemical industry is currently undergoing a dramatic change driven by demand for developing more sustainable processes for the production of fuels, chemicals, and materials. In biotechnological processes different microorganisms can be exploited, and the large diversity of metabolic reactions represents a rich repository for the design of chemical conversion processes that lead to efficient production of desirable products. However, often microorganisms that produce a desirable product, either naturally or because they have been engineered through insertion of heterologous pathways, have low yields and productivities, and in order to establish an economically viable process it is necessary to improve the performance of the microorganism. Here metabolic engineering is the enabling technology. Through metabolic engineering the metabolic landscape of the microorganism is engineered such that there is an efficient conversion of the raw material, typically glucose, to the product of interest. This process may involve both insertion of new enzymes activities, deletion of existing enzyme activities, but often also deregulation of existing regulatory structures operating in the cell. In order to rapidly identify the optimal metabolic engineering strategy the industry is to an increasing extent looking into the use of tools from systems biology. This involves both x-ome technologies such as transcriptome, proteome, metabolome, and fluxome analysis, and advanced mathematical modeling tools such as genome-scale metabolic modeling. Here we look into the history of these different techniques and review how they find application in industrial biotechnology, which will lead to what we here define as industrial systems biology.


    Directory of Open Access Journals (Sweden)

    Christoph Randler


    Full Text Available Recent psychological studies highlight emotional aspects, and they show an important role within individual learning processes. Hereby, positive emotions were supposed to positively influence learning and achievement processes and negative ones do the contrary. In this study, an educational unit “ecosystem lake” was used during which achievement (three tests and emotional variables (interest, well-being, anxiety and boredom; measured at the end of three pre-selected lessons were monitored. The research question was to explore correlations between emotional variables and the learning outcome of the teaching unit. Prior knowledge was regressed against the subsequent tests to account for its confounding effect. Regressions showed a highly significant influence of prior knowledge on the subsequent measurements of achievement. However, after accounting for prior knowledge, a positive correlation between interest/well-being and achievement and a negative correlation between anxiety/boredom and achievement was found. Further research and interventions should try to enhance positive emotions in biology lessons to positively influence achievement.

  6. Mathematical modeling of biological processes

    CERN Document Server

    Friedman, Avner


    This book on mathematical modeling of biological processes includes a wide selection of biological topics that demonstrate the power of mathematics and computational codes in setting up biological processes with a rigorous and predictive framework. Topics include: enzyme dynamics, spread of disease, harvesting bacteria, competition among live species, neuronal oscillations, transport of neurofilaments in axon, cancer and cancer therapy, and granulomas. Complete with a description of the biological background and biological question that requires the use of mathematics, this book is developed for graduate students and advanced undergraduate students with only basic knowledge of ordinary differential equations and partial differential equations; background in biology is not required. Students will gain knowledge on how to program with MATLAB without previous programming experience and how to use codes in order to test biological hypothesis.

  7. Protein microarrays for systems biology

    Institute of Scientific and Technical Information of China (English)

    Lina Yang; Shujuan Guo; Yang Li; Shumin Zhou; Shengce Tao


    Systems biology holds the key for understanding biological systems on a system level. It eventually holds the key for the treatment and cure of complex diseases such as cancer,diabetes, obesity, mental disorders, and many others. The '-omics' technologies, such as genomics, transcriptomics,proteomics, and metabonomics, are among the major driving forces of systems biology. Featured as highthroughput, miniaturized, and capable of parallel analysis,protein microarrays have already become an important technology platform for systems biology, In this review, we will focus on the system level or global analysis of biological systems using protein microarrays. Four major types of protein microarrays will be discussed: proteome microarrays, antibody microarrays, reverse-phase protein arrays,and lectin microarrays. We will also discuss the challenges and future directions of protein microarray technologies and their applications for systems biology. We strongly believe that protein microarrays will soon become an indispensable and invaluable tool for systems biology.

  8. Microgravity Fluids for Biology, Workshop (United States)

    Griffin, DeVon; Kohl, Fred; Massa, Gioia D.; Motil, Brian; Parsons-Wingerter, Patricia; Quincy, Charles; Sato, Kevin; Singh, Bhim; Smith, Jeffrey D.; Wheeler, Raymond M.


    Microgravity Fluids for Biology represents an intersection of biology and fluid physics that present exciting research challenges to the Space Life and Physical Sciences Division. Solving and managing the transport processes and fluid mechanics in physiological and biological systems and processes are essential for future space exploration and colonization of space by humans. Adequate understanding of the underlying fluid physics and transport mechanisms will provide new, necessary insights and technologies for analyzing and designing biological systems critical to NASAs mission. To enable this mission, the fluid physics discipline needs to work to enhance the understanding of the influence of gravity on the scales and types of fluids (i.e., non-Newtonian) important to biology and life sciences. In turn, biomimetic, bio-inspired and synthetic biology applications based on physiology and biology can enrich the fluid mechanics and transport phenomena capabilities of the microgravity fluid physics community.

  9. Synthetic biology: ethical ramifications 2009. (United States)

    Rabinow, Paul; Bennett, Gaymon


    During 2007 and 2008 synthetic biology moved from the manifesto stage to research programs. As of 2009, synthetic biology is ramifying; to ramify means to produce differentiated trajectories from previous determinations. From its inception, most of the players in synthetic biology agreed on the need for (a) rationalized design and construction of new biological parts, devices, and systems as well as (b) the re-design of natural biological systems for specified purposes, and that (c) the versatility of designed biological systems makes them suitable to address such challenges as renewable energy, the production of inexpensive drugs, and environmental remediation, as well as providing a catalyst for further growth of biotechnology. What is understood by these goals, however, is diverse. Those assorted understandings are currently contributing to different ramifications of synthetic biology. The Berkeley Human Practices Lab, led by Paul Rabinow, is currently devoting its efforts to documenting and analyzing these ramifications as they emerge.

  10. Bridging the gap between systems biology and synthetic biology. (United States)

    Liu, Di; Hoynes-O'Connor, Allison; Zhang, Fuzhong


    Systems biology is an inter-disciplinary science that studies the complex interactions and the collective behavior of a cell or an organism. Synthetic biology, as a technological subject, combines biological science and engineering, allowing the design and manipulation of a system for certain applications. Both systems and synthetic biology have played important roles in the recent development of microbial platforms for energy, materials, and environmental applications. More importantly, systems biology provides the knowledge necessary for the development of synthetic biology tools, which in turn facilitates the manipulation and understanding of complex biological systems. Thus, the combination of systems and synthetic biology has huge potential for studying and engineering microbes, especially to perform advanced tasks, such as producing biofuels. Although there have been very few studies in integrating systems and synthetic biology, existing examples have demonstrated great power in extending microbiological capabilities. This review focuses on recent efforts in microbiological genomics, transcriptomics, proteomics, and metabolomics, aiming to fill the gap between systems and synthetic biology.

  11. Mechanics of biological polymer composites (United States)

    Lomakin, Joseph


    Cartilage and cuticle are two natural materials capable of remarkable mechanical performance, especially considering the limitations on composition and processing conditions under which they are constructed. Their impressive properties are postulated to be a consequence of their complex multi-scale organization which has commonly been characterized by biochemical and microscopic methods. The objective of this dissertation is to overcome the limitations of such methods with mechanical analysis techniques generally reserved for the study of synthetic polymers. Methods for transient and dynamic mechanical analysis (DMA) of porcine TMJ disc sections and Tribolium castaneum and Tenebrio molitor elytral (modified forewing) cuticle were developed to characterize the mechanical performance of these biomaterials. The TMJ disc dynamic elastic modulus (E') was determined to be a strong function of disc orientation and pretension ranging from 700+/-240 kPa at (1g pretension) in the mediolateral direction to 73+/-8.5 MPa (150g preload) in the anteroposterior direction. Analogous mechanical testing was used to understand the relationship between composition and mechanical properties of beetle elytral cuticle at variable stages of maturation (tanning). Untanned elytra of both beetle species were ductile with a Young's modulus (E) of 44+/-8 MPa, but became brittle with an E of 2400+/-1100 MPa when fully tanned. Significantly, the E' of the TMJ disc and elytral cuticle exhibited a weak power law increase as a function of oscillation frequency. The exponent of the power law fit ( n) was determined to be a sensitive measure of molecular structure within these biomaterials. With increasing cuticular tanning, more so than with drying, the frequency dependence of cuticle E' diminished, suggesting cuticular cross-linking was an important component of tanning, as postulated by the quinone tanning hypothesis. The natural Black phenotype as well as TcADC iRNA suppressed Tribolium cuticle

  12. Human movement variability, nonlinear dynamics, and pathology: is there a connection? (United States)

    Stergiou, Nicholas; Decker, Leslie M


    Fields studying movement generation, including robotics, psychology, cognitive science, and neuroscience utilize concepts and tools related to the pervasiveness of variability in biological systems. The concept of variability and the measures for nonlinear dynamics used to evaluate this concept open new vistas for research in movement dysfunction of many types. This review describes innovations in the exploration of variability and their potential importance in understanding human movement. Far from being a source of error, evidence supports the presence of an optimal state of variability for healthy and functional movement. This variability has a particular organization and is characterized by a chaotic structure. Deviations from this state can lead to biological systems that are either overly rigid and robotic or noisy and unstable. Both situations result in systems that are less adaptable to perturbations, such as those associated with unhealthy pathological states or absence of skillfulness.

  13. Association between oral variables and heart rate variability. (United States)

    Santana, Milana Drumond Ramos; de Souza, Ana Cecilia Amorim; de Abreu, Luiz Carlos; Valenti, Vitor E


    The heart rate variability is a useful method to assess cardiac autonomic modulation in patients undergoing dental procedures, because knowledge of physiological conditions provides greater security to the professional as well as the possibility of a better plan treatment to patient benefit. The aim of our study was to describe the association between cardiac autonomic control and dental variables. We consulted the databases Medline, SciELO, Lilacs and Cochrane, using the terms "autonomic", "dentistry", "heart rate variability", "cardiovascular physiology." The selected studies indicated a strong relationship between dental variables and HRV. There was an association between malocclusion, TMD, dental procedures cirugia and low HRV. Thus, they become more studies that relate to HRV in dental science, especially in clinical practice.

  14. Molecular biology of potyviruses. (United States)

    Revers, Frédéric; García, Juan Antonio


    Potyvirus is the largest genus of plant viruses causing significant losses in a wide range of crops. Potyviruses are aphid transmitted in a nonpersistent manner and some of them are also seed transmitted. As important pathogens, potyviruses are much more studied than other plant viruses belonging to other genera and their study covers many aspects of plant virology, such as functional characterization of viral proteins, molecular interaction with hosts and vectors, structure, taxonomy, evolution, epidemiology, and diagnosis. Biotechnological applications of potyviruses are also being explored. During this last decade, substantial advances have been made in the understanding of the molecular biology of these viruses and the functions of their various proteins. After a general presentation on the family Potyviridae and the potyviral proteins, we present an update of the knowledge on potyvirus multiplication, movement, and transmission and on potyvirus/plant compatible interactions including pathogenicity and symptom determinants. We end the review providing information on biotechnological applications of potyviruses.

  15. Networks in Cell Biology (United States)

    Buchanan, Mark; Caldarelli, Guido; De Los Rios, Paolo; Rao, Francesco; Vendruscolo, Michele


    Introduction; 1. Network views of the cell Paolo De Los Rios and Michele Vendruscolo; 2. Transcriptional regulatory networks Sarath Chandra Janga and M. Madan Babu; 3. Transcription factors and gene regulatory networks Matteo Brilli, Elissa Calistri and Pietro Lió; 4. Experimental methods for protein interaction identification Peter Uetz, Björn Titz, Seesandra V. Rajagopala and Gerard Cagney; 5. Modeling protein interaction networks Francesco Rao; 6. Dynamics and evolution of metabolic networks Daniel Segré; 7. Hierarchical modularity in biological networks: the case of metabolic networks Erzsébet Ravasz Regan; 8. Signalling networks Gian Paolo Rossini; Appendix 1. Complex networks: from local to global properties D. Garlaschelli and G. Caldarelli; Appendix 2. Modelling the local structure of networks D. Garlaschelli and G. Caldarelli; Appendix 3. Higher-order topological properties S. Ahnert, T. Fink and G. Caldarelli; Appendix 4. Elementary mathematical concepts A. Gabrielli and G. Caldarelli; References.

  16. The biology of strigolactones

    KAUST Repository

    Ruyter-Spira, Carolien P.


    The strigolactones are rhizosphere signaling molecules as well as a new class of plant hormones with a still increasing number of biological functions being uncovered. Here, we review a recent major breakthrough in our understanding of strigolactone biosynthesis, which has revealed the unexpected simplicity of the originally postulated complex pathway. Moreover, the discovery and localization of a strigolactone exporter sheds new light on putative strigolactone fluxes to the rhizosphere as well as within the plant. The combination of these data with information on the expression and regulation of strigolactone biosynthetic and downstream signaling genes provides new insights into how strigolactones control the many different aspects of plant development and how their rhizosphere signaling role may have evolved. © 2012 Elsevier Ltd.

  17. Plant Vascular Biology 2010

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Biao


    This grant supported the Second International Conference on Plant Vascular Biology (PVB 2010) held July 24-28, 2010 on the campus of Ohio State University, Columbus, Ohio. Biao Ding (Ohio State University; OSU) and David Hannapel (Iowa State University; ISU) served as co-chairs of this conference. Biao Ding served as the local organizer. PVB is defined broadly here to include studies on the biogenesis, structure and function of transport systems in plants, under conditions of normal plant growth and development as well as of plant interactions with pathogens. The transport systems cover broadly the xylem, phloem, plasmodesmata and vascular cell membranes. The PVB concept has emerged in recent years to emphasize the integrative nature of the transport systems and approaches to investigate them.

  18. A Biologically Inspired Classifier

    CERN Document Server

    Bagnoli, Franco


    We present a method for measuring the distance among records based on the correlations of data stored in the corresponding database entries. The original method (F. Bagnoli, A. Berrones and F. Franci. Physica A 332 (2004) 509-518) was formulated in the context of opinion formation. The opinions expressed over a set of topic originate a ``knowledge network'' among individuals, where two individuals are nearer the more similar their expressed opinions are. Assuming that individuals' opinions are stored in a database, the authors show that it is possible to anticipate an opinion using the correlations in the database. This corresponds to approximating the overlap between the tastes of two individuals with the correlations of their expressed opinions. In this paper we extend this model to nonlinear matching functions, inspired by biological problems such as microarray (probe-sample pairing). We investigate numerically the error between the correlation and the overlap matrix for eight sequences of reference with r...

  19. Biology of Sexual Dysfunction

    Directory of Open Access Journals (Sweden)

    Anil Kumar Mysore Nagaraj


    Full Text Available Sexual activity is a multifaceted activity, involving complex interactions between the nervous system, the endocrine system, the vascular system and a variety of structures that are instrumental in sexual excitement, intercourse and satisfaction. Sexual function has three components i.e., desire, arousal and orgasm. Many sexual dysfunctions can be categorized according to the phase of sexual response that is affected. In actual clinical practice however, sexual desire, arousal and orgasmic difficulties more often than not coexist, suggesting an integration of phases. Sexual dysfunction can result from a wide variety of psychological and physiological causes including derangements in the levels of sex hormones and neurotrensmitters. This review deals with the biology of different phases of sexual function as well as implications of hormones and neurotransmitters in sexual dysfunction

  20. Evolutionary biology of cancer. (United States)

    Crespi, Bernard; Summers, Kyle


    Cancer is driven by the somatic evolution of cell lineages that have escaped controls on replication and by the population-level evolution of genes that influence cancer risk. We describe here how recent evolutionary ecological studies have elucidated the roles of predation by the immune system and competition among normal and cancerous cells in the somatic evolution of cancer. Recent analyses of the evolution of cancer at the population level show how rapid changes in human environments have augmented cancer risk, how strong selection has frequently led to increased cancer risk as a byproduct, and how anticancer selection has led to tumor-suppression systems, tissue designs that slow somatic evolution, constraints on morphological evolution and even senescence itself. We discuss how applications of the tools of ecology and evolutionary biology are poised to revolutionize our understanding and treatment of this disease.

  1. Variability In Sloan's Equatorial Stripe (United States)

    Rashkov, Valery; Spergel, D.; Strauss, M.; Ivezic, Z.; Sesar, B.


    The Sloan Digital Sky Survey (SDSS) equatorial Stripe 82 is located between 22h 24min Branimir Sesar (Sesar et al., 2007) have put together a list of 13051 variable sources, each of which was observed an average of 20 times. I have calculated fits for two variability parameters (amplitude and characteristic timescale) for these objects using maximum likelihood statistics. The list is being probed for violent variability, as from BL Lac Objects and OVVs. Knowledge of these objects' parameters will help separate their contribution in the microwave from that of the CMB when the equatorial Stripe 82 is eventually observed with the Atacama Cosmology Telescope.

  2. Biology of Schwann cells. (United States)

    Kidd, Grahame J; Ohno, Nobuhiko; Trapp, Bruce D


    The fundamental roles of Schwann cells during peripheral nerve formation and regeneration have been recognized for more than 100 years, but the cellular and molecular mechanisms that integrate Schwann cell and axonal functions continue to be elucidated. Derived from the embryonic neural crest, Schwann cells differentiate into myelinating cells or bundle multiple unmyelinated axons into Remak fibers. Axons dictate which differentiation path Schwann cells follow, and recent studies have established that axonal neuregulin1 signaling via ErbB2/B3 receptors on Schwann cells is essential for Schwann cell myelination. Extracellular matrix production and interactions mediated by specific integrin and dystroglycan complexes are also critical requisites for Schwann cell-axon interactions. Myelination entails expansion and specialization of the Schwann cell plasma membrane over millimeter distances. Many of the myelin-specific proteins have been identified, and transgenic manipulation of myelin genes have provided novel insights into myelin protein function, including maintenance of axonal integrity and survival. Cellular events that facilitate myelination, including microtubule-based protein and mRNA targeting, and actin based locomotion, have also begun to be understood. Arguably, the most remarkable facet of Schwann cell biology, however, is their vigorous response to axonal damage. Degradation of myelin, dedifferentiation, division, production of axonotrophic factors, and remyelination all underpin the substantial regenerative capacity of the Schwann cells and peripheral nerves. Many of these properties are not shared by CNS fibers, which are myelinated by oligodendrocytes. Dissecting the molecular mechanisms responsible for the complex biology of Schwann cells continues to have practical benefits in identifying novel therapeutic targets not only for Schwann cell-specific diseases but other disorders in which axons degenerate.

  3. The Promises of Biology and the Biology of Promises

    DEFF Research Database (Denmark)

    Lee, Jieun


    This dissertation considers the ontology of stem cells as a future-oriented life form characterized by its potentiality in relation to the anticipatory mode of living in contemporary Korea. The biological notion that stem cells have the potential for differentiation and the capacity for self-rene...... of technologized biology and biological time can appear promising with the backdrop of the imagined intransigence of social, political, and economic order in the Korean society....

  4. Systems biology: a biologist's viewpoint. (United States)

    Bose, Biplab


    The debate over reductionism and antireductionism in biology is very old. Even the systems approach in biology is more than five decades old. However, mainstream biology, particularly experimental biology, has broadly sidestepped those debates and ideas. Post-genome data explosion and development of high-throughput techniques led to resurfacing of those ideas and debates as a new incarnation called Systems Biology. Though experimental biologists have co-opted systems biology and hailed it as a paradigm shift, it is practiced in different shades and understood with divergent meanings. Biology has certain questions linked with organization of multiple components and processes. Often such questions involve multilevel systems. Here in this essay we argue that systems theory provides required framework and abstractions to explore those questions. We argue that systems biology should follow the logical and mathematical approach of systems theory and transmogrification of systems biology to mere collection of higher dimensional data must be avoided. Therefore, the questions that we ask and the priority of those questions should also change. Systems biology should focus on system-level properties and investigate complexity without shying away from it.

  5. Adaptive neural-based fuzzy modeling for biological systems. (United States)

    Wu, Shinq-Jen; Wu, Cheng-Tao; Chang, Jyh-Yeong


    The inverse problem of identifying dynamic biological networks from their time-course response data set is a cornerstone of systems biology. Hill and Michaelis-Menten model, which is a forward approach, provides local kinetic information. However, repeated modifications and a large amount of experimental data are necessary for the parameter identification. S-system model, which is composed of highly nonlinear differential equations, provides the direct identification of an interactive network. However, the identification of skeletal-network structure is challenging. Moreover, biological systems are always subject to uncertainty and noise. Are there suitable candidates with the potential to deal with noise-contaminated data sets? Fuzzy set theory is developed for handing uncertainty, imprecision and complexity in the real world; for example, we say "driving speed is high" wherein speed is a fuzzy variable and high is a fuzzy set, which uses the membership function to indicate the degree of a element belonging to the set (words in Italics to denote fuzzy variables or fuzzy sets). Neural network possesses good robustness and learning capability. In this study we hybrid these two together into a neural-fuzzy modeling technique. A biological system is formulated to a multi-input-multi-output (MIMO) Takagi-Sugeno (T-S) fuzzy system, which is composed of rule-based linear subsystems. Two kinds of smooth membership functions (MFs), Gaussian and Bell-shaped MFs, are used. The performance of the proposed method is tested with three biological systems.

  6. Biology of biological meshes used in hernia repair. (United States)

    Novitsky, Yuri W


    Successful repair of most hernias requires the use of a prosthetic implant for reinforcement of the defect. Because of the need for prosthetic implants to resist infections as well to support repairs in contaminated or potentially contaminated fields, biological meshes have been developed to take the place of nondegradable synthetic meshes in cases where mesh infection is of high concern. The ideal is a biological matrix that resists infection while providing durable reinforcement of a hernia repair. This article reviews the validity of assumptions that support the purported notion of the biological behavior of biological meshes.

  7. Elbow joint variability for different hand positions of the round off in gymnastics. (United States)

    Farana, Roman; Irwin, Gareth; Jandacka, Daniel; Uchytil, Jaroslav; Mullineaux, David R


    The aim of the present study was to conduct within-gymnast analyses of biological movement variability in impact forces, elbow joint kinematics and kinetics of expert gymnasts in the execution of the round-off with different hand positions. Six international level female gymnasts performed 10 trials of the round-off from a hurdle step to a back-handspring using two hand potions: parallel and T-shape. Two force plates were used to determine ground reaction forces. Eight infrared cameras were employed to collect the kinematic data automatically. Within gymnast variability was calculated using biological coefficient of variation (BCV) discretely for ground reaction force, kinematic and kinetic measures. Variability of the continuous data was quantified using coefficient of multiple correlations (CMC). Group BCV and CMC were calculated and T-test with effect size statistics determined differences between the variability of the two techniques examined in this study. The major observation was a higher level of biological variability in the elbow joint abduction angle and adduction moment of force in the T-shaped hand position. This finding may lead to a reduced repetitive abduction stress and thus protect the elbow joint from overload. Knowledge of the differences in biological variability can inform clinicians and practitioners with effective skill selection.

  8. Mirador - Climate Variability and Change (United States)

    National Aeronautics and Space Administration — Earth Science data access made simple. NASA's role in climate variability study is centered around providing the global scale observational data sets on oceans and...

  9. Solar Variability and Planetary Climates

    CERN Document Server

    Calisesi, Y; Gray, L; Langen, J; Lockwood, M


    Variations in solar activity, as revealed by variations in the number of sunspots, have been observed since ancient times. To what extent changes in the solar output may affect planetary climates, though, remains today more than ever a subject of controversy. In 2000, the SSSI volume on Solar Variability and Climate reviewed the to-date understanding of the physics of solar variability and of the associated climate response. The present volume on Solar Variability and Planetary Climates provides an overview of recent advances in this field, with particular focus at the Earth's middle and lower atmosphere. The book structure mirrors that of the ISSI workshop held in Bern in June 2005, the collection of invited workshop contributions and of complementary introductory papers synthesizing the current understanding in key research areas such as middle atmospheric processes, stratosphere-troposphere dynamical coupling, tropospheric aerosols chemistry, solar storm influences, solar variability physics, and terrestri...

  10. Electrochromic Variable-Emissivity Surfaces (United States)

    Rauh, R. David; Cogan, Stuart F.


    Temperature controlled by altering infrared radiative properties. Infrared emissivity of electrochromically active layer changed by applying voltage to insert or remove Li atoms electrochemically. Change reversible and continuously variable between specified limits of layered structure.

  11. Automated Searches for Variable Stars

    CERN Document Server

    Van Noord, Daniel M; Steenwyk, Steven D


    With recent developments in imaging and computer technology the amount of available astronomical data has increased dramatically. Although most of these data sets are not dedicated to the study of variable stars much of it can, with the application of proper software tools, be recycled for the discovery of new variable stars. Fits Viewer and Data Retrieval System is a new software package that takes advantage of modern computer advances to search astronomical data for new variable stars. More than 200 new variable stars have been found in a data set taken with the Calvin College Rehoboth Robotic telescope using FVDRS. One particularly interesting example is a very fast subdwarf B with a 95 minute orbital period, the fastest currently known of the HW Vir type.

  12. Variable Heat Rejection (VHR) Project (United States)

    National Aeronautics and Space Administration — Develop advanced technologies to enable a variable heat rejection Thermal Control System (TCS) capable of operating through a wide range of thermal environments...

  13. Investigation of load reduction for a variable speed, variable pitch, and variable coning wind turbine

    Energy Technology Data Exchange (ETDEWEB)

    Pierce, K. [Univ. of Utah, Salt Lake City, UT (United States)


    A two bladed, variable speed and variable pitch wind turbine was modeled using ADAMS{reg_sign} to evaluate load reduction abilities of a variable coning configuration as compared to a teetered rotor, and also to evaluate control methods. The basic dynamic behavior of the variable coning turbine was investigated and compared to the teetered rotor under constant wind conditions as well as turbulent wind conditions. Results indicate the variable coning rotor has larger flap oscillation amplitudes and much lower root flap bending moments than the teetered rotor. Three methods of control were evaluated for turbulent wind simulations. These were a standard IPD control method, a generalized predictive control method, and a bias estimate control method. Each control method was evaluated for both the variable coning configuration and the teetered configuration. The ability of the different control methods to maintain the rotor speed near the desired set point is evaluated from the RMS error of rotor speed. The activity of the control system is evaluated from cycles per second of the blade pitch angle. All three of the methods were found to produce similar results for the variable coning rotor and the teetered rotor, as well as similar results to each other.

  14. Variable stars in the classroom

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-Bajo, F [Departamento de Electronica e IngenierIa Electromecanica, Escuela de IngenierIas Industriales, Universidad de Extremadura, Avda de Elvas s/n, 06071 Badajoz (Spain); Vaquero, J M [Departamento de Fisica, Escuela Politecnica, Universidad de Extremadura, Avda de la Universidad s/n, 10071 Caceres (Spain)


    Variable stars offer interesting possibilities from the point of view of educational applications, from the experimental collection of data to analysis to obtain physical information. In this paper, brightness measurements of two periodic variable stars easily accessible with small telescopes are presented and analysed. This practical experiment is highly appropriate for educational use in undergraduate physics and astrophysics laboratories and allows students to approximate scientific research.

  15. Granger causality for circular variables

    Energy Technology Data Exchange (ETDEWEB)

    Angelini, Leonardo; Pellicoro, Mario [Istituto Nazionale di Fisica Nucleare, Sezione di Bari (Italy); Dipartimento di Fisica, University of Bari (Italy); Stramaglia, Sebastiano, E-mail: sebastiano.stramaglia@ba.infn.i [Istituto Nazionale di Fisica Nucleare, Sezione di Bari (Italy); Dipartimento di Fisica, University of Bari (Italy)


    In this Letter we discuss the use of Granger causality to the analyze systems of coupled circular variables, by modifying a recently proposed method for multivariate analysis of causality. We show the application of the proposed approach on several Kuramoto systems, in particular one living on networks built by preferential attachment and a model for the transition from deeply to lightly anaesthetized states. Granger causalities describe the flow of information among variables.

  16. The winds of cataclysmic variables

    Energy Technology Data Exchange (ETDEWEB)

    Mauche, C.W. [Lawrence Livermore National Lab., CA (United States). Lab. for Experimental Astrophysics; Raymond, J.C. [Harvard-Smithsonian Center for Astrophysics, Cambridge, MA (United States)


    The authors present an observational and theoretical review of the winds of cataclysmic variables (CVs). Specifically, they consider the related problems of the geometry and mass-loss rate of the winds of CVs, their ionization state and variability, and the results from studies of eclipsing CVs. Finally, they consider the properties of accretion disk wind models. Some of these models predict substantial angular momentum loss, which could affect both disk structure and binary evolution.

  17. Microfluidic Technologies for Synthetic Biology

    Directory of Open Access Journals (Sweden)

    Sung Kuk Lee


    Full Text Available Microfluidic technologies have shown powerful abilities for reducing cost, time, and labor, and at the same time, for increasing accuracy, throughput, and performance in the analysis of biological and biochemical samples compared with the conventional, macroscale instruments. Synthetic biology is an emerging field of biology and has drawn much attraction due to its potential to create novel, functional biological parts and systems for special purposes. Since it is believed that the development of synthetic biology can be accelerated through the use of microfluidic technology, in this review work we focus our discussion on the latest microfluidic technologies that can provide unprecedented means in synthetic biology for dynamic profiling of gene expression/regulation with high resolution, highly sensitive on-chip and off-chip detection of metabolites, and whole-cell analysis.

  18. Quantum Effects in Biological Systems

    CERN Document Server


    Since the last decade the study of quantum mechanical phenomena in biological systems has become a vibrant field of research. Initially sparked by evidence of quantum effects in energy transport that is instrumental for photosynthesis, quantum biology asks the question of how methods and models from quantum theory can help us to understand fundamental mechanisms in living organisms. This approach entails a paradigm change challenging the related disciplines: The successful framework of quantum theory is taken out of its low-temperature, microscopic regimes and applied to hot and dense macroscopic environments, thereby extending the toolbox of biology and biochemistry at the same time. The Quantum Effects in Biological Systems conference is a platform for researchers from biology, chemistry and physics to present and discuss the latest developments in the field of quantum biology. After meetings in Lisbon (2009), Harvard (2010), Ulm (2011), Berkeley (2012), Vienna (2013), Singapore (2014) and Florence (2015),...

  19. Estuary–ocean connectivity: fast physics, slow biology (United States)

    Raimonet, Mélanie; Cloern, James E.


    Estuaries are connected to both land and ocean so their physical, chemical, and biological dynamics are influenced by climate patterns over watersheds and ocean basins. We explored climate-driven oceanic variability as a source of estuarine variability by comparing monthly time series of temperature and chlorophyll-a inside San Francisco Bay with those in adjacent shelf waters of the California Current System (CCS) that are strongly responsive to wind-driven upwelling. Monthly temperature fluctuations inside and outside the Bay were synchronous, but their correlations weakened with distance from the ocean. These results illustrate how variability of coastal water temperature (and associated properties such as nitrate and oxygen) propagates into estuaries through fast water exchanges that dissipate along the estuary. Unexpectedly, there was no correlation between monthly chlorophyll-a variability inside and outside the Bay. However, at the annual scale Bay chlorophyll-a was significantly correlated with the Spring Transition Index (STI) that sets biological production supporting fish recruitment in the CCS. Wind forcing of the CCS shifted in the late 1990s when the STI advanced 40 days. This shift was followed, with lags of 1–3 years, by 3- to 19-fold increased abundances of five ocean-produced demersal fish and crustaceans and 2.5-fold increase of summer chlorophyll-a in the Bay. These changes reflect a slow biological process of estuary–ocean connectivity operating through the immigration of fish and crustaceans that prey on bivalves, reduce their grazing pressure, and allow phytoplankton biomass to build. We identified clear signals of climate-mediated oceanic variability in this estuary and discovered that the response patterns vary with the process of connectivity and the timescale of ocean variability. This result has important implications for managing nutrient inputs to estuaries connected to upwelling systems, and for assessing their responses to

  20. Values, Advocay and Conservation Biology



    In this essay, I examine the controversy concerning the advocacy of ethical values in conservation biology. First, I argue, as others have, that conservation biology is a science laden with values both ethical and non-ethical. Second, after clarifying the notion of advocacy at work, I contend that conservation biologists should advocate the preservation of biological diversity. Third, I explore what ethical grounds should be used for advocating the preservation of ecological systems by conser...

  1. Relations between intuitive biological thinking and biological misconceptions in biology majors and nonmajors. (United States)

    Coley, John D; Tanner, Kimberly


    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.

  2. NASA space biology accomplishments, 1982 (United States)

    Halstead, T. W.; Pleasant, L. G.


    Summaries of NASA's Space Biology Program projects are provided. The goals, objectives, accomplishments, and future plans of each project are described in this publication as individual technical summaries.

  3. Engineering Nanoscale Biological Molecular Motors


    Korosec, Chapin; Forde, Nancy R.


    Understanding the operation of biological molecular motors, nanoscale machines that transduce electrochemical energy into mechanical work, is enhanced by bottom-up strategies to synthesize novel motors.

  4. Telemetry System of Biological Parameters

    Directory of Open Access Journals (Sweden)

    Jan Spisak


    Full Text Available The mobile telemetry system of biological parameters serves for reading and wireless data transfer of measured values of selected biological parameters to an outlying computer. It concerns basically long time monitoring of vital function of car pilot.The goal of this projects is to propose mobile telemetry system for reading, wireless transfer and processing of biological parameters of car pilot during physical and psychical stress. It has to be made with respect to minimal consumption, weight and maximal device mobility. This system has to eliminate signal noise, which is created by biological artifacts and disturbances during the data transfer.

  5. Biological and medical sensor technologies

    CERN Document Server

    Iniewski, Krzysztof


    Biological and Medical Sensor Technologies presents contributions from top experts who explore the development and implementation of sensors for various applications used in medicine and biology. Edited by a pioneer in the area of advanced semiconductor materials, the book is divided into two sections. The first part covers sensors for biological applications. Topics include: Advanced sensing and communication in the biological world DNA-derivative architectures for long-wavelength bio-sensing Label-free silicon photonics Quartz crystal microbalance-based biosensors Lab-on-chip technologies fo

  6. American Institute of Biological Sciences (United States)

    ... organizations advancing biology through membership in AIBS News Trump's FY 2018 Budget Request Would Slash Most Science Programs President Trump's first budget request seeks historically deep budget cuts ...

  7. Synthetic biology for therapeutic applications. (United States)

    Abil, Zhanar; Xiong, Xiong; Zhao, Huimin


    Synthetic biology is a relatively new field with the key aim of designing and constructing biological systems with novel functionalities. Today, synthetic biology devices are making their first steps in contributing new solutions to a number of biomedical challenges, such as emerging bacterial antibiotic resistance and cancer therapy. This review discusses some synthetic biology approaches and applications that were recently used in disease mechanism investigation and disease modeling, drug discovery and production, as well as vaccine development and treatment of infectious diseases, cancer, and metabolic disorders.

  8. Computer algebra in systems biology

    CERN Document Server

    Laubenbacher, Reinhard


    Systems biology focuses on the study of entire biological systems rather than on their individual components. With the emergence of high-throughput data generation technologies for molecular biology and the development of advanced mathematical modeling techniques, this field promises to provide important new insights. At the same time, with the availability of increasingly powerful computers, computer algebra has developed into a useful tool for many applications. This article illustrates the use of computer algebra in systems biology by way of a well-known gene regulatory network, the Lac Operon in the bacterium E. coli.

  9. Bioinspired materials: Boosting plant biology (United States)

    Scholes, Gregory D.; Sargent, Edward H.


    Chloroplasts with extended photosynthetic activity beyond the visible absorption spectrum, and living leaves that perform non-biological functions, are made possible by localizing nanoparticles within plant organelles.

  10. Relationships between attitude and achievement among college biology students (United States)

    Mitchell, Harold E.; Simpson, Ronald D.

    The purposes of this study were to (1) study changes in attitude toward science, school, and academic self among college biology students, and (2) to examine relationships between attitudes and achievement in an introductory college course in biology. The three attitude variables were assessed at the beginning and end of the study. Each of the three constructs was measured by the semantic differential and one additional instrument. One cognitive measure, biology achievement, was taken at the beginning and end of the study. This was accomplished by using the Nelson Biology Test. Another cognitive measure, grade in the course, as given by the instructor, was recorded at the end of the course. Normative data and correlation coefficients among pre- and postadministrations were calculated for each institution and the composite sample as well. An analysis of variance showed that while gains in scores on the Nelson Biology Test were significant beyond the 0.01 level of probability, changes in attitude scores were not. Correlations were calculated between the attitude and cognitive variables in this study. Relationships between academic self-concept and achievement in biology were the strongest. Data from this study show that while student cognitive behavior was changed during an introductory college biology course, selected attitudes either stayed the same or became slightly more negative. Affective as well as cognitive gains would appear to be desirable goals in college courses. As we learn more about relationships that exist between cognition and affect, science educators at all levels will become better equipped to improve learning in science.

  11. Rotating Biological Contractors (RBC's). Instructor's Guide. Biological Treatment Process Control. (United States)

    Zickefoose, Charles S.

    This two-lesson unit on rotating biological contactors (RBC's) is designed to be used with students who have had some experience in wastewater treatment and a basic understanding of biological treatment. The first lesson provides information on the concepts and components of RBC treatment systems. The second lesson focuses on design operation and…

  12. Exploring Visuomotor Priming Following Biological and Non-Biological Stimuli (United States)

    Gowen, E.; Bradshaw, C.; Galpin, A.; Lawrence, A.; Poliakoff, E.


    Observation of human actions influences the observer's own motor system, termed visuomotor priming, and is believed to be caused by automatic activation of mirror neurons. Evidence suggests that priming effects are larger for biological (human) as opposed to non-biological (object) stimuli and enhanced when viewing stimuli in mirror compared to…

  13. Quantitative biology: where modern biology meets physical sciences. (United States)

    Shekhar, Shashank; Zhu, Lian; Mazutis, Linas; Sgro, Allyson E; Fai, Thomas G; Podolski, Marija


    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.

  14. "Protected biological control"- Biological pest management in the greenhouse industry

    NARCIS (Netherlands)

    Pilkington, L.J.; Messelink, G.J.; Lenteren, van J.C.; Mottee, Le K.


    This paper briefly describes the foundations and characteristics of biological control in protected cropping and what drivers are behind adoption of this management system within this industry. Examining a brief history of biological control in greenhouses and what makes it a successful management s

  15. Crystallogenesis of biological macromolecules. Biological, microgravity and other physicochemical aspects

    NARCIS (Netherlands)

    Giege, R; Drenth, J; Ducruix, A; McPherson, A; Saenger, W


    After an historical introduction and justification of the importance of proteins (as well as other macromolecules or macromolecular assemblies of biological origin) in modern biology but also in physics, this review presents the state of the field of macromolecular crystallogenesis. The basic questi

  16. [Hemodialysis with biological object]. (United States)

    Eventov, V L; Maksimenko, V A; Zhidkov, I L; Andrianova, M Iu


    The essence of the method of biodialysis (hemodialysis with biological object) developed and suggested by the authors for clinical use consists in that the healthy organism exerts, through a system of mass transfer, a therapeutic action on the sick organism. Blood from the affected and healthy organisms is perfused through individual mass exchangers (dialyzers, hemodiafilters and hemofilters), which are hydraulically connected by a circulating transport medium. Metabolites that accumulate in blood of the affected organism diffuse into the transport medium and, from there, into blood of the healthy organism, which metabolizes them. The reverse process occurs simultaneously: substances, whose concentration in blood of the sick organism is less versus the healthy organism, diffuse from blood of the healthy organism to blood of patient. The method suggested by us can be used in clinical practice for normalizing a variety of parameters in patients with hepatic and renal insufficiency. Besides, a number of substances can be transferred from the healthy donor to patient in the process of biodialysis, which opens promising potentialities for the treatment of many diseases.

  17. Consciousness and biological evolution. (United States)

    Lindahl, B I


    It has been suggested that if the preservation and development of consciousness in the biological evolution is a result of natural selection, it is plausible that consciousness not only has been influenced by neural processes, but has had a survival value itself; and it could only have had this, if it had also been efficacious. This argument for mind-brain interaction is examined, both as the argument has been developed by William James and Karl Popper and as it has been discussed by C.D. Broad. The problem of identifying mental phenomena with certain neural phenomena is also addressed. The main conclusion of the analysis is that an explanation of the evolution of consciousness in Darwinian terms of natural selection does not rule out that consciousness may have evolved as a mere causally inert effect of the evolution of the nervous system, or that mental phenomena are identical with certain neural phenomena. However, the interactionistic theory still seems, more plausible and more fruitful for other reasons brought up in the discussion.

  18. Flotation of Biological Materials

    Directory of Open Access Journals (Sweden)

    George Z. Kyzas


    Full Text Available Flotation constitutes a gravity separation process, which originated from the minerals processing field. However, it has, nowadays, found several other applications, as for example in the wastewater treatment field. Concerning the necessary bubble generation method, typically dispersed-air or dissolved-air flotation was mainly used. Various types of biological materials were tested and floated efficiently, such as bacteria, fungi, yeasts, activated sludge, grape stalks, etc. Innovative processes have been studied in our Laboratory, particularly for metal ions removal, involving the initial abstraction of heavy metal ions onto a sorbent (including a biosorbent: in the first, the application of a flotation stage followed for the efficient downstream separation of metal-laden particles. The ability of microorganisms to remove metal ions from dilute aqueous solutions (as most wastewaters are is a well-known property. The second separation process, also applied effectively, was a new hybrid cell of microfiltration combined with flotation. Sustainability in this field and its significance for the chemical and process industry is commented.

  19. [Biology molecular of glioblastomas]. (United States)

    Franco-Hernández, C; Martínez-Glez, V; Rey, J A


    Glioblastomas, the most frequent and malignant human brain tumors, may develop de novo (primary glioblastoma) or by progression from low-grade or anapalsic astrocytoma (secondary glioblastoma). The molecular alteration most frequent in these tumor-like types is the loss of heterozygosity on chromosome 10, in which several genes have been identified as tumors suppressor. The TP53/MDM2/P14arf and CDK4/RB1/ P16ink4 genetic pathways involved in cycle control are deregulated in the majority of gliomas as well as genes that promote the cellular division, EGFR. Finally the increase of growth and angiogenics factors is also involved in the development of glioblastomas. One of the objectives of molecular biology in tumors of glial ancestry is to try to find the genetic alterations that allow to approach better the classification of glioblastomas, its evolution prediction and treatment. The new pathmolecular classification of gliomas should improve the old one, especially being concerned about the oncogenesis and heterogeneity of these tumors. It is desirable that this classification had clinical applicability and integrates new molecular findings with some known histological features with pronostic value. In this paper we review the most frequent molecular mechanisms involved in the patogenesis of glioblastomas.

  20. Mesangial cell biology

    Energy Technology Data Exchange (ETDEWEB)

    Abboud, Hanna E., E-mail:


    Mesangial cells originate from the metanephric mesenchyme and maintain structural integrity of the glomerular microvascular bed and mesangial matrix homeostasis. In response to metabolic, immunologic or hemodynamic injury, these cells undergo apoptosis or acquire an activated phenotype and undergo hypertrophy, proliferation with excessive production of matrix proteins, growth factors, chemokines and cytokines. These soluble factors exert autocrine and paracrine effects on the cells or on other glomerular cells, respectively. MCs are primary targets of immune-mediated glomerular diseases such as IGA nephropathy or metabolic diseases such as diabetes. MCs may also respond to injury that primarily involves podocytes and endothelial cells or to structural and genetic abnormalities of the glomerular basement membrane. Signal transduction and oxidant stress pathways are activated in MCs and likely represent integrated input from multiple mediators. Such responses are convenient targets for therapeutic intervention. Studies in cultured MCs should be supplemented with in vivo studies as well as examination of freshly isolated cells from normal and diseases glomeruli. In addition to ex vivo morphologic studies in kidney cortex, cells should be studied in their natural environment, isolated glomeruli or even tissue slices. Identification of a specific marker of MCs should help genetic manipulation as well as selective therapeutic targeting of these cells. Identification of biological responses of MCs that are not mediated by the renin–angiotensin system should help development of novel and effective therapeutic strategies to treat diseases characterized by MC pathology.

  1. Biological rhythms and preeclampsia

    Directory of Open Access Journals (Sweden)

    Agnès eDitisheim


    Full Text Available The impact of impaired circadian rhythm on health has been widely studied in shift workers and trans-meridian travelers. A part from its correlation with sleep and mood disorders, biological rhythm impairment is a recognized risk factor for cardiovascular diseases and breast cancer.Preeclampsia is a major public health issue, associated with a significant maternal and fetal morbidity and mortality worldwide. While the risks factors for this condition such as obesity, diabetes, pre-existing hypertension have been identified, the underlying mechanism of this multi-factorial disease is yet not fully understood.The disruption of the light/dark cycle in pregnancy has been associated with adverse outcomes. Slightly increased risk for small for gestational age babies, low birth weight babies and preterm deliveries has been reported in shift working women. Whether altered circadian cycle represents a risk factor for preeclampsia or preeclampsia is itself linked with an abnormal circadian cycle is less clear. There are only few reports available, showing conflicting results. In this review, we will discuss recent observations concerning circadian pattern of blood pressure in normotensive and hypertensive pregnancies. We explore the hypothesis that circadian misalignments may represent a risk factor for preeclampsia. Unraveling potential link between circadian clock gene and preeclampsia could offer a novel approach to our understanding of this multi-system disease specific to pregnancy.

  2. Biological control of ticks (United States)

    Samish, M.; Ginsberg, H.; Glazer, I.; Bowman, A.S.; Nuttall, P.


    Ticks have numerous natural enemies, but only a few species have been evaluated as tick biocontrol agents (BCAs). Some laboratory results suggest that several bacteria are pathogenic to ticks, but their mode of action and their potential value as biocontrol agents remain to be determined. The most promising entomopathogenic fungi appear to be Metarhizium anisopliae and Beauveria bassiana, strains of which are already commercially available for the control of some pests. Development of effective formulations is critical for tick management. Entomopathogenic nematodes that are pathogenic to ticks can potentially control ticks, but improved formulations and selection of novel nematode strains are needed. Parasitoid wasps of the genus Ixodiphagus do not typically control ticks under natural conditions, but inundative releases show potential value. Most predators of ticks are generalists, with a limited potential for tick management (one possible exception is oxpeckers in Africa). Biological control is likely to play a substantial role in future IPM programmes for ticks because of the diversity of taxa that show high potential as tick BCAs. Considerable research is required to select appropriate strains, develop them as BCAs, establish their effectiveness, and devise production strategies to bring them to practical use.

  3. Aristotle's biopolitics: a defense of biological teleology against biological nihilism. (United States)

    Arnhart, L


    Modern Darwinian biology seems to promote nihilism, for it seems to teach that there is no rationally discoverable standard in nature for giving meaning to life. The purpose of this article is to argue for a revival of Aristotle's biological teleology as a reasonable alternative to biological nihilism. The article begins with Edward Wilson's vain struggle against nihilism. Then it is argued that a teleological understanding of nature is assumed in the practice of medicine, as illustrated by one case from Oliver Sacks' neurological practice. The article then considers the importance of biological teleology for Aristotle's moral and political philosophy, and attention is given to some points of agreement and disagreement with contemporary sociobiologists. The main part of the article is then devoted to a defense of Aristotle's biology against the five objections that might be made by a Darwinian biologist. Finally, the article illustrates the practical implications of this issue for bioethics by considering the recent work of Engelhardt.

  4. Cardinality-dependent Variability in Orthogonal Variability Models

    DEFF Research Database (Denmark)

    Mærsk-Møller, Hans Martin; Jørgensen, Bo Nørregaard


    During our work on developing and running a software product line for eco-sustainable greenhouse-production software tools, which currently have three products members we have identified a need for extending the notation of the Orthogonal Variability Model (OVM) to support what we refer to as car......During our work on developing and running a software product line for eco-sustainable greenhouse-production software tools, which currently have three products members we have identified a need for extending the notation of the Orthogonal Variability Model (OVM) to support what we refer...

  5. Biological effects of resveratrol. (United States)

    Frémont, L


    Resveratrol (3, 4', 5 trihydroxystilbene) is a naturally occuring phytoalexin produced by some spermatophytes, such as grapevines, in response to injury. Given that it is present in grape berry skins but not in flesh, white wine contains very small amounts of resveratrol, compared to red wine. The concentrations in the form of trans- and cis- isomers of aglycone and glucosides are subjected to numerous variables. In red wine, the concentrations of the trans-isomer, which is the major form, generally ranges between 0.1 and 15 mg/L. As phenolic compound, resveratrol contributes to the antioxidant potential of red wine and thereby may play a role in the prevention of human cardiovascular diseases. Resveratrol has been shown to modulate the metabolism of lipids, and to inhibit the oxidation of low-density lipoproteins and the aggregation of platelets. Moreover, as phytoestrogen, resveratrol may provide cardiovascular protection. This compound also possesses anti-inflammatory and anticancer properties. However, the bioavailability and metabolic pathways must be known before drawing any conclusions on the benefits of dietary resveratrol to health.

  6. Biological risk factors in informal recyclers of Medellin city, 2005

    Directory of Open Access Journals (Sweden)

    Viviana L. Ballesteros


    Full Text Available The informal recyclers constitute a vulnerable population to problems of health by their constant exhibition to biological, chemical, physical and social risks, without protection. Objective: this work identify the biological risk facts to which the informal recyclers of the Bazaar of the Bridges of Medellin city. Methods: it was performed a Cross-sectional study. The sample was no probabilistic with 88 recyclers and the analysis unit was the informal recycler. It was applied a survey, a guide of observation of the activity of the recycler and were studied variables of person, place, time, type of biological risk facts, frequency of exhibition, felt morbidity and measures of protection. The analysis was statistical descriptive. Results: it was identified biological risk facts related to the contact with material in decomposition (96.6%, contaminated material (96.6%, animals (62.5% and arthropoda (79.5%. The se The se--curity measures to protect them from biological risk facts are used in less than 52% of recyclers; in addition, only 13.6% of the population were vaccinated, which increases the probability of becoming ill in this population. Conclusions: that the informal recyclers are exposed to different biological risk facts with little prevention, causing that population be vulnerable for the acquisition of infectious diseases.

  7. Biologic relativity: Who is the observer and what is observed? (United States)

    Torday, John S; Miller, William B


    When quantum physics and biological phenomena are analogously explored, it emerges that biologic causation must also be understood independently of its overt appearance. This is similar to the manner in which Bohm characterized the explicate versus the implicate order as overlapping frames of ambiguity. Placed in this context, the variables affecting epigenetic inheritance can be properly assessed as a key mechanistic principle of evolution that significantly alters our understanding of homeostasis, pleiotropy, and heterochrony, and the purposes of sexual reproduction. Each of these become differing manifestations of a new biological relativity in which biologic space-time becomes its own frame. In such relativistic cellular contexts, it is proper to question exactly who has observer status, and who and what are being observed. Consideration within this frame reduces biology to cellular information sharing through cell-cell communication to resolve ambiguities at every scope and scale. In consequence, it becomes implicit that eukaryotic evolution derives from the unicellular state, remaining consistently adherent to it in a continuous evolutionary arc based upon elemental, non-stochastic physiologic first principles. Furthermore, the entire cell including its cytoskeletal apparatus and membranes that participate in the resolution of biological uncertainties must be considered as having equivalent primacy with genomes in evolutionary terms.

  8. Introduction to Biology, Tropical Edition. (United States)

    Mackean, D. G.

    This pupil's reference book is intended to provide biological information, using plants and animals which are suitable for study over a wide range of tropical countries. Its topics are taken mostly from the biology syllabi for the British General Certification of Education at the Ordinary Level and are written principally for pupils in the last…

  9. Biology and Water Pollution Control. (United States)

    Warren, Charles E.

    Within this text, the reader is attuned to the role biology can and should play in combating the alarming increase in water pollution. Both the urgency of the problem and the biological techniques that are being developed to cope with the water pollution crisis are scrutinized; what is and is not known about the problem is explained; past,…

  10. Space Biology: Patterns of Life (United States)

    Salisbury, Frank B.


    Present knowledge about Mars is compared with past beliefs about the planet. Biological experiments that indicate life may exist on Mars are interpreted. Life patterns or biological features that might be postulated for extraterrestrial life are presented at the molecular, cellular, organism, and ecosystem levels. (DS)

  11. Marine Biology and Human Affairs (United States)

    Russell, F. S.


    Marine biology has become an important area for study throughout the world. The author of this article discusses some of the important discoveries and fields of research in marine biology that are useful for mankind. Topics include food from the sea, fish farming, pesticides, pollution, and conservation. (MA)

  12. Querying Large Biological Network Datasets (United States)

    Gulsoy, Gunhan


    New experimental methods has resulted in increasing amount of genetic interaction data to be generated every day. Biological networks are used to store genetic interaction data gathered. Increasing amount of data available requires fast large scale analysis methods. Therefore, we address the problem of querying large biological network datasets.…

  13. Validation of systems biology models

    NARCIS (Netherlands)

    Hasdemir, D.


    The paradigm shift from qualitative to quantitative analysis of biological systems brought a substantial number of modeling approaches to the stage of molecular biology research. These include but certainly are not limited to nonlinear kinetic models, static network models and models obtained by the

  14. Structural Biology Guides Antibiotic Discovery (United States)

    Polyak, Steven


    Modern drug discovery programs require the contribution of researchers in a number of specialist areas. One of these areas is structural biology. Using X-ray crystallography, the molecular basis of how a drug binds to its biological target and exerts its mode of action can be defined. For example, a drug that binds into the active site of an…

  15. Biological Effectiveness of Antiproton Annihilation

    DEFF Research Database (Denmark)

    Maggiore, C.; Agazaryan, N.; Bassler, N.;


    from the annihilation of antiprotons produce an increase in ‘‘biological dose’’ in the vicinity of the narrow Bragg peak for antiprotons compared to protons. This experiment is the first direct measurement of the biological effects of antiproton annihilation. The background, description, and status...

  16. Static Analysis for Systems Biology

    DEFF Research Database (Denmark)

    Nielson, Flemming; Nielson, Hanne Riis; Rosa, D. Schuch da


    This paper shows how static analysis techniques can help understanding biological systems. Based on a simple example we illustrate the outcome of performing three different analyses extracting information of increasing precision. We conclude by reporting on the potential impact and exploitation o...... of these techniques in systems biology....

  17. Interfacing DNA nanodevices with biology

    DEFF Research Database (Denmark)

    Vinther, Mathias; Kjems, Jørgen


    in biology and biomedicine acting as a molecular ‘nanorobot’ or smart drug interacting with the cellular machinery. In this review, we will explore and examine the perspective of DNA nanotechnology for such use. We summarize which requirements DNA nanostructures must fulfil to function in cellular...... environments and inside living organisms. In addition, we highlight recent advances in interfacing DNA nanostructures with biology....

  18. From Biology to Quality (BQ)

    DEFF Research Database (Denmark)

    Nielsen, Michael Engelbrecht; Ingerslev, Hans-Christian


    “Quality is never an accident; it is always the result of high intention, sincere effort, intelligent direction and skilful execution; it represents the wise choice of many alternatives.” (William A. Foster) The quality of fish meat is dependent upon a wide range of biological and non-biological ...

  19. The Ethics of Synthetic Biology

    DEFF Research Database (Denmark)

    Christiansen, Andreas

    The dissertation analyses and discusses a number of ethical issues that have been raised in connection with the development of synthetic biology. Synthetic biology is a set of new techniques for DNA-level design and construction of living beings with useful properties. The dissertation especially...

  20. Biological clocks: riding the tides. (United States)

    de la Iglesia, Horacio O; Johnson, Carl Hirschie


    Animals with habitats in the intertidal zone often display biological rhythms that coordinate with both the tidal and the daily environmental cycles. Two recent studies show that the molecular components of the biological clocks mediating tidal rhythms are likely different from the phylogenetically conserved components that mediate circadian (daily) rhythms.

  1. BIological Psychology, Exercise, and Stress. (United States)

    Dishman, Rod K.


    Reviews theory and methods used by the field of biological psychology to study stress that have potential for understanding how behavioral and biological adaptations to the stress of exercise are integrated. The overview focuses on anxiety, depression, and physiological responsiveness to nonexercise stressors from the perspective of biological…

  2. Virtual Environments in Biology Teaching (United States)

    Mikropoulos, Tassos A.; Katsikis, Apostolos; Nikolou, Eugenia; Tsakalis, Panayiotis


    This article reports on the design, development and evaluation of an educational virtual environment for biology teaching. In particular it proposes a highly interactive three-dimensional synthetic environment involving certain learning tasks for the support of teaching plant cell biology and the process of photosynthesis. The environment has been…

  3. An Exercise in Biological Control. (United States)

    Lennox, John; Duke, Michael


    Discusses the history of the use of pesticides and biological control. Introduces the concept of biological control as illustrated in the use of the entomopathogenic bacterium Bacillus thuringiensis and highlights laboratory demonstrations of Koch's postulates. Includes an exercise that offers the student and teacher several integrated learning…

  4. Vitalism in Naive Biological Thinking. (United States)

    Morris, Suzanne C.; Taplin, John E.; Gelman, Susan A.


    Three experiments investigated use of vitalistic explanations for biological phenomena by 5- and 10-year-olds and by adults. Results replicated the original Japanese finding of vitalistic thinking among English-speaking 5-year-olds, identified the more active component of vitalism as a belief in the transfer of energy during biological processes,…

  5. Segmentation and classification of biological objects

    DEFF Research Database (Denmark)

    Schultz, Nette


    The present thesis is on segmentation and classification of biological objects using statistical methods. It is based on case studies dealing with different kinds of pork meat images, and we introduce appropriate statistical methods to solve the tasks in the case studies. The case studies concern...... classification of back bacon slices from images of back bacon, prediction of ham weight from images of the carcass, and estimation of meat percent from cross-sectional images of the carcass. The first case study investigates three different classifiers ability to classify the quality of back bacon slices....... The back bacon slices are classified into four ordered classes representing the quality, and we use the sizes of different meat and fat areas of the slices as variables. The classifiers are Bayesian discriminant functions, Classification and Regression Trees, and feed-forward neural networks with back...

  6. The structural biology of patellamide biosynthesis. (United States)

    Koehnke, Jesko; Bent, Andrew F; Houssen, Wael E; Mann, Greg; Jaspars, Marcel; Naismith, James H


    The biosynthetic pathways for patellamide and related natural products have recently been studied by structural biology. These pathways produce molecules that have a complex framework and exhibit a diverse array of activity due to the variability of the amino acids that are found in them. As these molecules are difficult to synthesize chemically, exploitation of their properties has been modest. The patellamide pathway involves amino acid heterocyclization, peptide cleavage, peptide macrocyclization, heterocycle oxidation and epimerization; closely related products are also prenylated. Enzyme activities have been identified for all these transformations except epimerization, which may be spontaneous. This review highlights the recent structural and mechanistic work on amino acid heterocyclization, peptide cleavage and peptide macrocyclization. This work should help in using the enzymes to produce novel analogs of the natural products enabling an exploitation of their properties.

  7. Synthetic biology and genetic causation. (United States)

    Oftedal, Gry; Parkkinen, Veli-Pekka


    Synthetic biology research is often described in terms of programming cells through the introduction of synthetic genes. Genetic material is seemingly attributed with a high level of causal responsibility. We discuss genetic causation in synthetic biology and distinguish three gene concepts differing in their assumptions of genetic control. We argue that synthetic biology generally employs a difference-making approach to establishing genetic causes, and that this approach does not commit to a specific notion of genetic program or genetic control. Still, we suggest that a strong program concept of genetic material can be used as a successful heuristic in certain areas of synthetic biology. Its application requires control of causal context, and may stand in need of a modular decomposition of the target system. We relate different modularity concepts to the discussion of genetic causation and point to possible advantages of and important limitations to seeking modularity in synthetic biology systems.

  8. Combining supramolecular chemistry with biology. (United States)

    Uhlenheuer, Dana A; Petkau, Katja; Brunsveld, Luc


    Supramolecular chemistry has primarily found its inspiration in biological molecules, such as proteins and lipids, and their interactions. Currently the supramolecular assembly of designed compounds can be controlled to great extent. This provides the opportunity to combine these synthetic supramolecular elements with biomolecules for the study of biological phenomena. This tutorial review focuses on the possibilities of the marriage of synthetic supramolecular architectures and biological systems. It highlights that synthetic supramolecular elements are for example ideal platforms for the recognition and modulation of proteins and cells. The unique features of synthetic supramolecular systems with control over size, shape, valency, and interaction strength allow the generation of structures fitting the demands to approach the biological problems at hand. Supramolecular chemistry has come full circle, studying the biology and its molecules which initially inspired its conception.

  9. Engineering life through Synthetic Biology. (United States)

    Chopra, Paras; Kamma, Akhil


    Synthetic Biology is a field involving synthesis of novel biological systems which are not generally found in nature. It has brought a new paradigm in science as it has enabled scientists to create life from the scratch, hence helping better understand the principles of biology. The viability of living organisms that use unnatural molecules is also being explored. Unconventional projects such as DNA playing tic-tac-toe, bacterial photographic film, etc. are taking biology to its extremes. The field holds a promise for mass production of cheap drugs and programming bacteria to seek-and-destroy tumors in the body. However, the complexity of biological systems make the field a challenging one. In addition to this, there are other major technical and ethical challenges which need to be addressed before the field realizes its true potential.

  10. Grand challenges for biological engineering. (United States)

    Yoon, Jeong-Yeol; Riley, Mark R


    Biological engineering will play a significant role in solving many of the world's problems in medicine, agriculture, and the environment. Recently the U.S. National Academy of Engineering (NAE) released a document "Grand Challenges in Engineering," covering broad realms of human concern from sustainability, health, vulnerability and the joy of living. Biological engineers, having tools and techniques at the interface between living and non-living entities, will play a prominent role in forging a better future. The 2010 Institute of Biological Engineering (IBE) conference in Cambridge, MA, USA will address, in part, the roles of biological engineering in solving the challenges presented by the NAE. This letter presents a brief outline of how biological engineers are working to solve these large scale and integrated problems of our society.

  11. Grand challenges for biological engineering

    Directory of Open Access Journals (Sweden)

    Riley Mark R


    Full Text Available Abstract Biological engineering will play a significant role in solving many of the world's problems in medicine, agriculture, and the environment. Recently the U.S. National Academy of Engineering (NAE released a document "Grand Challenges in Engineering," covering broad realms of human concern from sustainability, health, vulnerability and the joy of living. Biological engineers, having tools and techniques at the interface between living and non-living entities, will play a prominent role in forging a better future. The 2010 Institute of Biological Engineering (IBE conference in Cambridge, MA, USA will address, in part, the roles of biological engineering in solving the challenges presented by the NAE. This letter presents a brief outline of how biological engineers are working to solve these large scale and integrated problems of our society.

  12. Hierarchical structure of biological systems (United States)

    Alcocer-Cuarón, Carlos; Rivera, Ana L; Castaño, Victor M


    A general theory of biological systems, based on few fundamental propositions, allows a generalization of both Wierner and Berthalanffy approaches to theoretical biology. Here, a biological system is defined as a set of self-organized, differentiated elements that interact pair-wise through various networks and media, isolated from other sets by boundaries. Their relation to other systems can be described as a closed loop in a steady-state, which leads to a hierarchical structure and functioning of the biological system. Our thermodynamical approach of hierarchical character can be applied to biological systems of varying sizes through some general principles, based on the exchange of energy information and/or mass from and within the systems. PMID:24145961

  13. Fourier Analysis of Blazar Variability

    CERN Document Server

    Finke, Justin D


    Blazars display strong variability on multiple timescales and in multiple radiation bands. Their variability is often characterized by power spectral densities (PSDs) and time lags plotted as functions of the Fourier frequency. We develop a new theoretical model based on the analysis of the electron transport (continuity) equation, carried out in the Fourier domain. The continuity equation includes electron cooling and escape, and a derivation of the emission properties includes light travel time effects associated with a radiating blob in a relativistic jet. The model successfully reproduces the general shapes of the observed PSDs and predicts specific PSD and time lag behaviors associated with variability in the synchrotron, synchrotron self-Compton (SSC), and external Compton (EC) emission components, from sub-mm to gamma-rays. We discuss applications to BL Lacertae objects and to flat-spectrum radio quasars (FSRQs), where there are hints that some of the predicted features have already been observed. We a...

  14. Hidden Variables or Positive Probabilities?

    CERN Document Server

    Rothman, T; Rothman, Tony


    Despite claims that Bell's inequalities are based on the Einstein locality condition, or equivalent, all derivations make an identical mathematical assumption: that local hidden-variable theories produce a set of positive-definite probabilities for detecting a particle with a given spin orientation. The standard argument is that because quantum mechanics assumes that particles are emitted in a superposition of states the theory cannot produce such a set of probabilities. We examine a paper by Eberhard who claims to show that a generalized Bell inequality, the CHSH inequality, can be derived solely on the basis of the locality condition, without recourse to hidden variables. We point out that he nonetheless assumes a set of positive-definite probabilities, which supports the claim that hidden variables or "locality" is not at issue here, positive-definite probabilities are. We demonstrate that quantum mechanics does predict a set of probabilities that violate the CHSH inequality; however these probabilities ar...


    Institute of Scientific and Technical Information of China (English)

    吕恩琳; 钟佑明


    Mathematic description about the second kind fuzzy random variable namely the random variable with crisp event-fuzzy probability was studied. Based on the interval probability and using the fuzzy resolution theorem, the feasible condition about a probability fuzzy number set was given, go a step further the definition arid characters of random variable with fuzzy probability ( RVFP ) and the fuzzy distribution function and fuzzy probability distribution sequence of the RVFP were put forward. The fuzzy probability resolution theorem with the closing operation of fuzzy probability was given and proved. The definition and characters of mathematical expectation and variance of the RVFP were studied also. All mathematic description about the RVFP has the closing operation for fuzzy probability, as a result, the foundation of perfecting fuzzy probability operation method is laid.

  16. Time as a dynamical variable (United States)

    Thron, Christopher


    Since the time of Galileo, the equations of physics have expressed dynamical variables such as particle position or electromagnetic field strength as functions of time. In this paper, we argue that this assumption reflects observational bias, and that there are many good reasons for viewing time also as a dynamical variable. We hypothesize that the spacetime universe is an outcome of a process, rather than a process unfolding in time. This new viewpoint gives rise to a physical interpretation of the wavefunction as a complex vibrational amplitude in a non-spacetime independent variable. It resolves quantum mechanical paradoxes involving wavefunction entanglement, and gives a much simpler solution to the problem of wavefunction collapse than the many-worlds interpretation. The Born rule is also shown to be a natural consequence. We also show that small deviations from conventional quantum probabilities are predicted.

  17. Monitoring Variability of the Sky

    CERN Document Server

    Paczynski, B


    Variability in the sky has been known for centuries, even millennia, but our knowledge of it is very incomplete even at the bright end. Current technology makes it possible to built small, robotic optical instruments, to record images and to process data in real time, and to archive them on-line, all at a low cost. In addition to obtaining complete catalogs of all kinds of variable objects, spectacular discoveries can be made, like the optical flash associated with GRB 990123 and a planetary transit in front of HD 209458. While prototypes of such robotic instruments have been in operation for several years, it is not possible to purchase a complete system at this time. I expect (hope) that complete systems will become available `off the shelf' in the near future, as monitoring bright sky for variability has a great scientific, educational and public outreach potential.

  18. Optical Spectral Variability of Blazars

    Indian Academy of Sciences (India)

    Haritma Gaur


    It is well established that blazars show flux variations in the complete electromagnetic (EM) spectrum on all possible time scales ranging from a few tens of minutes to several years. Here, we report the review of optical flux and spectral variability properties of different classes of blazars on IDV and STV time-scales. Our analysis show HSPs are less variable in optical bands as compared to LSPs. Also, we investigated the spectral slope variability and found that the average spectral slopes of LSPs showed a good agreement with the synchrotron self-Compton loss-dominated model. However, spectra of the HSPs and FSRQs have significant additional emission components. In general, spectra of BL Lacs get flatter when they become brighter, while for FSRQs the opposite trend appears to hold.

  19. Biological Extreme Events - Past, Present, and Future (United States)

    Gutschick, V. P.


    Biological extreme events span wide ranges temporally and spatially and in type - population dieoffs, extinctions, ecological reorganizations, changes in biogeochemical fluxes, and more. Driving variables consist in meteorology, tectonics, orbital changes, anthropogenic changes (land-use change, species introductions, reactive N injection into the biosphere), and evolution (esp. of diseases). However, the mapping of extremes in the drivers onto biological extremes as organismal responses is complex, as laid out originally in the theoretical framework of Gutschick and BassiriRad (New Phytologist [2003] 100:21-42). Responses are nonlinear and dependent on (mostly unknown and) complex temporal sequences - often of multiple environmental variables. The responses are species- and genotype specific. I review extreme events over from past to present over wide temporal scales, while noting that they are not wholly informative of responses to the current and near-future drivers for at least two reasons: 1) the current combination of numerous environmental extremes - changes in CO2, temperature, precipitation, reactive N, land fragmentation, O3, etc. -is unprecedented in scope, and 2) adaptive genetic variation for organismal responses is constrained by poorly-characterized genetic structures (in organisms and populations) and by loss of genetic variation by genetic drift over long periods. We may expect radical reorganizations of ecosystem and biogeochemical functions. These changes include many ecosystem services in flood control, crop pollination and insect/disease control, C-water-mineral cycling, and more, as well as direct effects on human health. Predictions of such changes will necessarily be very weak in the critical next few decades, given the great deal of observation, experimentation, and theory construction that will be necessary, on both organisms and drivers. To make the research efforts most effective will require extensive, insightful planning, beginning

  20. Variables Bounding Based Retiming Algorithm

    Institute of Scientific and Technical Information of China (English)

    宫宗伟; 林争辉; 陈后鹏


    Retiming is a technique for optimizing sequential circuits. In this paper, wediscuss this problem and propose an improved retiming algorithm based on variables bounding.Through the computation of the lower and upper bounds on variables, the algorithm can signi-ficantly reduce the number of constraints and speed up the execution of retiming. Furthermore,the elements of matrixes D and W are computed in a demand-driven way, which can reducethe capacity of memory. It is shown through the experimental results on ISCAS89 benchmarksthat our algorithm is very effective for large-scale sequential circuits.

  1. Complex variable methods in elasticity

    CERN Document Server

    England, A H


    The plane strain and generalized plane stress boundary value problems of linear elasticity are the focus of this graduate-level text, which formulates and solves these problems by employing complex variable theory. The text presents detailed descriptions of the three basic methods that rely on series representation, Cauchy integral representation, and the solution via continuation. Its five-part treatment covers functions of a complex variable, the basic equations of two-dimensional elasticity, plane and half-plane problems, regions with circular boundaries, and regions with curvilinear bounda

  2. Variable rules meet Impoverishment theory

    DEFF Research Database (Denmark)

    Parrott, Jeffrey K.; Nevins, Andrew


    This paper revives the sociolinguistic notion of ‘variable rules’ (Labov 1969, Cedergren and Sankoff 1974, Guy 1991) as a specific and restricted mechanism within the theoretical framework of Distributed Morphology (Halle and Marantz 1993, Embick and Noyer 2007). We propose that intra-individual ......This paper revives the sociolinguistic notion of ‘variable rules’ (Labov 1969, Cedergren and Sankoff 1974, Guy 1991) as a specific and restricted mechanism within the theoretical framework of Distributed Morphology (Halle and Marantz 1993, Embick and Noyer 2007). We propose that intra...

  3. Calculus with a quaternionic variable (United States)

    Schwartz, Charles


    Most of theoretical physics is based on the mathematics of functions of a real or a complex variable; yet we frequently are drawn in trying to extend our reach to include quaternions. The noncommutativity of the quaternion algebra poses obstacles for the usual manipulations of calculus, but we show in this paper how many of those obstacles can be overcome. The surprising result is that the first order term in the expansion of F(x +δ) is a compact formula involving both F'(x) and [F(x )-F(x∗)]/(x -x∗). This advance in the differential calculus for quaternionic variables also leads us to some progress in studying integration.

  4. Advanced calculus of several variables

    CERN Document Server

    Kumar, Devendra


    ADVANCED CALCULUS OF SEVERAL VARIABLES covers important topics of Transformations and topology on Euclidean in n-space Rn Functions of several variables, Differentiation in Rn, Multiple integrals and Integration in Rn. The topics have been presented in a simple clear and coherent style with a number of examples and exercises. Proofs have been made direct and simple. Unsolved problems just after relevant articles in the form of exercises and typical problems followed by suggestions have been given. This book will help the reader work on the problems of Numerical Analysis, Operations Research, Differential Equations and Engineering applications.

  5. Loop Quantum Theory Applied to Biology and Nonlinear Whole Biology

    CERN Document Server

    Chang, Yi-Fang


    The loop quantum theory, which constitutes a very small discontinuous space, as new method is applied to biology. The model of protein folding and lungs is proposed. In the model, some known results are used, and four approximate conclusions are obtained: their structures are quantized, their space regions are finite, various singularities correspond to folding and crossed points, and different types of catastrophe exist. Further, based on the inseparability and correlativity of the biological systems, the nonlinear whole biology is proposed, and four basic hypotheses are formed. It may unify reductionism and holism, structuralism and functionalism. Finally, the medical meaning of the theory is discussed briefly.

  6. Biology and Economics: Metaphors that Economists usually take from Biology

    Directory of Open Access Journals (Sweden)

    Danny García Callejas


    Full Text Available Adam Smith, Alfred Marshall, Stanley Jevons, Karl Marx, Francois Quesnay and Joseph Schumpeter all have at least one thing in common: they used biological metaphors when speaking about economics. Nonetheless, today, this relation subsists and biology and economics are viewed as complementary sciences that have a lot to gain from joint research in fields like: evolutionary economics, economic growth, cognitive economics and environmental and ecological economics, among others. This paper, divided in four sections, will show this conclusion and explain that biology and economics are more sisters than strangers

  7. What is the perception of biological risk by undergraduate nursing students? (United States)

    Moreno-Arroyo, Mª Carmen; Puig-Llobet, Montserrat; Falco-Pegueroles, Anna; Lluch-Canut, Maria Teresa; García, Irma Casas; Roldán-Merino, Juan


    Abstract Objective: to analyze undergraduate nursing students' perception of biological risk and its relationship with their prior practical training. Method: a descriptive cross-sectional study was conducted among undergraduate nursing students enrolled in clinical practice courses in the academic year 2013-2014 at the School of Nursing at the University of Barcelona. Variables: sociodemographic variables, employment, training, clinical experience and other variables related to the assessment of perceived biological risk were collected. Both a newly developed tool and the Dimensional Assessment of Risk Perception at the worker level scale (Escala de Evaluación Dimensional del Riesgo Percibido por el Trabajador, EDRP-T) were used. Statistical analysis: descriptive and univariate analysis were used to identify differences between the perception of biological risk of the EDRP-T scale items and sociodemographic variables. Results: students without prior practical training had weaker perceptions of biological risk compared to students with prior practical training (p=0.05 and p=0.04, respectively). Weaker perceptions of biological risk were found among students with prior work experience. Conclusion: practical training and work experience influence the perception of biological risk among nursing students. PMID:27384468

  8. What is the perception of biological risk by undergraduate nursing students?

    Directory of Open Access Journals (Sweden)

    Mª Carmen Moreno-Arroyo


    Full Text Available Abstract Objective: to analyze undergraduate nursing students' perception of biological risk and its relationship with their prior practical training. Method: a descriptive cross-sectional study was conducted among undergraduate nursing students enrolled in clinical practice courses in the academic year 2013-2014 at the School of Nursing at the University of Barcelona. Variables: sociodemographic variables, employment, training, clinical experience and other variables related to the assessment of perceived biological risk were collected. Both a newly developed tool and the Dimensional Assessment of Risk Perception at the worker level scale (Escala de Evaluación Dimensional del Riesgo Percibido por el Trabajador, EDRP-T were used. Statistical analysis: descriptive and univariate analysis were used to identify differences between the perception of biological risk of the EDRP-T scale items and sociodemographic variables. Results: students without prior practical training had weaker perceptions of biological risk compared to students with prior practical training (p=0.05 and p=0.04, respectively. Weaker perceptions of biological risk were found among students with prior work experience. Conclusion: practical training and work experience influence the perception of biological risk among nursing students.

  9. The molecular biology of vertebrate olfaction. (United States)

    Hayden, Sara; Teeling, Emma C


    The importance of chemosensation for vertebrates is reflected in the vast and variable nature of their chemosensory tissues, neurons, and genes, which we explore in this review. Immense progress has been made in elucidating the molecular biology of olfaction since the discovery of the olfactory receptor genes by Buck and Axel, which eventually won the authors the Nobel Prize. In particular, research linking odor ligands to olfactory receptors (ORs) is truly revolutionizing our understanding of how a large but limited number of chemosensory receptors can allow us to perceive the massive diversity of odors in our habitat. This research is providing insight into the evolution of genomes and providing the raw data needed to explore links between genotype and phenotype, still a grand challenge in biology. Research into olfaction is still developing and will no doubt continue until we have a clear understanding of how all odors are detected and the evolutionary forces that have molded the chemosensory subgenome in vertebrates. This knowledge will not only be a huge step in elucidating olfactory function, advancing scientific knowledge and techniques, but there are also commercial applications for this research. This review focuses on the molecular basis of chemosensation, particularly olfaction, its evolution across vertebrates and the recent molecular advances linking odors to their cognate receptors.

  10. Biological Systems, Energy Sources, and Biology Teaching. Biology and Human Welfare. (United States)

    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…

  11. Biological modulation of tectonics (United States)

    Sleep, N. H.; Bird, D. K.


    Photosynthesis has had geologic consequences over the Earth's history. In addition to modifying Earth's atmosphere and ocean chemistry, it has also modulated tectonic processes through enhanced weathering and modification of the nature and composition of sedimentary rocks within fold mountain belts and convergent margins. Molecular biological studies indicate that bacterial photosynthesis evolved just once and that most bacterial clades descend from this photosynthetic common ancestor. Iron-based photosynthesis (ideally 4FeO + CO2 + H2O = 2Fe2O3 + CH2O) was the most bountiful anoxygenic niche on land. The back reaction provided energy to heterotrophic microbes and returned FeO to the photosynthetic microbes. Bacterial land colonists evolved into ecosystems that effectively weathered FeO-bearing minerals and volcanic glass. Clays, sands, and dissolved cations from the weathering process entered the ocean and formed our familiar classes sedimentary rocks: shales, sandstones, and carbonates. Marine photosynthesis caused organic carbon to accumulate in black shales. In contrast, non-photosynthetic ecosystems do not cause organic carbon to accumulate in shale. These evolutionary events occurred before 3.8 Ga as black shales are among the oldest rock types (Rosing and Frei, Earth Planet. Sci. Lett. 217, 237-244, 2004). Thick sedimentary sequences deformed into fold mountain belts. They remelted at depth to form granitic rocks (Rosing et al., Palaeoclimatol. Palaeoecol. 232, 99-11, 2006). Regions of outcropping low-FeO rocks including granites, quartzites, and some shales were a direct result. This dearth of FeO favored the evolution of oxic photosynthesis of cyanobacteria from photosynthetic soil bacteria. Black shales have an additional modulation effect on tectonics as they concentrate radioactive elements, particularly uranium (e.g. so that the surface heat flow varies by a factor of ca. 2). Thick sequences of black shales at continental rises of passive margins are

  12. The Relationships between Epistemic Beliefs in Biology and Approaches to Learning Biology among Biology-Major University Students in Taiwan (United States)

    Lin, Yi-Chun; Liang, Jyh-Chong; Tsai, Chin-Chung


    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…

  13. The meaning of biological information. (United States)

    Koonin, Eugene V


    Biological information encoded in genomes is fundamentally different from and effectively orthogonal to Shannon entropy. The biologically relevant concept of information has to do with 'meaning', i.e. encoding various biological functions with various degree of evolutionary conservation. Apart from direct experimentation, the meaning, or biological information content, can be extracted and quantified from alignments of homologous nucleotide or amino acid sequences but generally not from a single sequence, using appropriately modified information theoretical formulae. For short, information encoded in genomes is defined vertically but not horizontally. Informally but substantially, biological information density seems to be equivalent to 'meaning' of genomic sequences that spans the entire range from sharply defined, universal meaning to effective meaninglessness. Large fractions of genomes, up to 90% in some plants, belong within the domain of fuzzy meaning. The sequences with fuzzy meaning can be recruited for various functions, with the meaning subsequently fixed, and also could perform generic functional roles that do not require sequence conservation. Biological meaning is continuously transferred between the genomes of selfish elements and hosts in the process of their coevolution. Thus, in order to adequately describe genome function and evolution, the concepts of information theory have to be adapted to incorporate the notion of meaning that is central to biology.

  14. Digital 'faces' of synthetic biology. (United States)

    Friedrich, Kathrin


    In silicio design plays a fundamental role in the endeavour to synthesise biological systems. In particular, computer-aided design software enables users to manage the complexity of biological entities that is connected to their construction and reconfiguration. The software's graphical user interface bridges the gap between the machine-readable data on the algorithmic subface of the computer and its human-amenable surface represented by standardised diagrammatic elements. Notations like the Systems Biology Graphical Notation (SBGN), together with interactive operations such as drag & drop, allow the user to visually design and simulate synthetic systems as 'bio-algorithmic signs'. Finally, the digital programming process should be extended to the wet lab to manufacture the designed synthetic biological systems. By exploring the different 'faces' of synthetic biology, I argue that in particular computer-aided design (CAD) is pushing the idea to automatically produce de novo objects. Multifaceted software processes serve mutually aesthetic, epistemic and performative purposes by simultaneously black-boxing and bridging different data sources, experimental operations and community-wide standards. So far, synthetic biology is mainly a product of digital media technologies that structurally mimic the epistemological challenge to take both qualitative as well as quantitative aspects of biological systems into account in order to understand and produce new and functional entities.

  15. Synthetic biology and metabolic engineering. (United States)

    Stephanopoulos, Gregory


    Metabolic engineering emerged 20 years ago as the discipline occupied with the directed modification of metabolic pathways for the microbial synthesis of various products. As such, it deals with the engineering (design, construction, and optimization) of native as well as non-natural routes of product synthesis, aided in this task by the availability of synthetic DNA, the core enabling technology of synthetic biology. The two fields, however, only partially overlap in their interest in pathway engineering. While fabrication of biobricks, synthetic cells, genetic circuits, and nonlinear cell dynamics, along with pathway engineering, have occupied researchers in the field of synthetic biology, the sum total of these areas does not constitute a coherent definition of synthetic biology with a distinct intellectual foundation and well-defined areas of application. This paper reviews the origins of the two fields and advances two distinct paradigms for each of them: that of unit operations for metabolic engineering and electronic circuits for synthetic biology. In this context, metabolic engineering is about engineering cell factories for the biological manufacturing of chemical and pharmaceutical products, whereas the main focus of synthetic biology is fundamental biological research facilitated by the use of synthetic DNA and genetic circuits.

  16. Synthetic biology as red herring. (United States)

    Preston, Beth


    It has become commonplace to say that with the advent of technologies like synthetic biology the line between artifacts and living organisms, policed by metaphysicians since antiquity, is beginning to blur. But that line began to blur 10,000 years ago when plants and animals were first domesticated; and has been thoroughly blurred at least since agriculture became the dominant human subsistence pattern many millennia ago. Synthetic biology is ultimately only a late and unexceptional offshoot of this prehistoric development. From this perspective, then, synthetic biology is a red herring, distracting us from more thorough philosophical consideration of the most truly revolutionary human practice-agriculture. In the first section of this paper I will make this case with regard to ontology, arguing that synthetic biology crosses no ontological lines that were not crossed already in the Neolithic. In the second section I will construct a parallel case with regard to cognition, arguing that synthetic biology as biological engineering represents no cognitive advance over what was required for domestication and the new agricultural subsistence pattern it grounds. In the final section I will make the case with regard to human existence, arguing that synthetic biology, even if wildly successful, is not in a position to cause significant existential change in what it is to be human over and above the massive existential change caused by the transition to agriculture. I conclude that a longer historical perspective casts new light on some important issues in philosophy of technology and environmental philosophy.

  17. Fostering synergy between cell biology and systems biology. (United States)

    Eddy, James A; Funk, Cory C; Price, Nathan D


    In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship.

  18. Agroterrorism, Biological Crimes, and Biological Warfare Targeting Animal Agriculture

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, Terry M.; Logan-Henfrey, Linda; Weller, Richard E.; Kellman, Brian


    There is a rising level of concern that agriculture might be targeted for economic sabotage by terrorists. Knowledge gathered about the Soviet Union biological weapons program and Iraq following the Gulf War, confirmed that animals and agricultural crops were targets of bioweapon development. These revelations are particularly disturbing in light of the fact that both countries are States Parties to the Biological and Toxin Weapons Convention that entered into force in 1975. The potential for misusing biotechnology to create more virulent pathogens and the lack of international means to detect unethical uses of new technologies to create destructive bioweapons is of increasing concern. Disease outbreaks, whether naturally occurring or intentionally, involving agricultural pathogens that destroy livestock and crops would have a profound impact on a country's infrastructure, economy and export markets. This chapter deals with the history of agroterrorism, biological crimes and biological warfare directed toward animal agriculture, specifically, horses, cattle, swine, sheep, goats, and poultry.

  19. Hybrid Unifying Variable Supernetwork Model

    Institute of Scientific and Technical Information of China (English)

    LIU; Qiang; FANG; Jin-qing; LI; Yong


    In order to compare new phenomenon of topology change,evolution,hybrid ratio and network characteristics of unified hybrid network theoretical model with unified hybrid supernetwork model,this paper constructed unified hybrid variable supernetwork model(HUVSM).The first layer introduces a hybrid ratio dr,the

  20. Operating Reserves and Variable Generation

    Energy Technology Data Exchange (ETDEWEB)

    Ela, E.; Milligan, M.; Kirby, B.


    This report tries to first generalize the requirements of the power system as it relates to the needs of operating reserves. It also includes a survey of operating reserves and how they are managed internationally in system operations today and then how new studies and research are proposing they may be managed in the future with higher penetrations of variable generation.

  1. Several topics in complex variables

    NARCIS (Netherlands)

    Smit, I.M.


    This thesis is based on three articles in the field of Several Complex Variables. The first article, which is joint work with M. El Kadiri, defines and studies the concept of maximality for plurifinely plurisubharmonic functions. Its main result is that a finite plurifinely plurisubharmonic function

  2. Tropical deforestation and climate variability

    Energy Technology Data Exchange (ETDEWEB)

    Voldoire, A.; Royer, J.F. [CNRM/GMGEC/UDC, Meteo-France, 42 Avenue G. Coriolis, 31057, Toulouse Cedex 1 (France)


    A new tropical deforestation experiment has been performed, with the ARPEGE-Climat atmospheric global circulation model associated with the ISBA land surface scheme. Simulations are forced with observed monthly mean sea surface temperatures and thus inter-annual variability of the ocean system is taken into account. The local mean response to deforestation over Amazonia and Africa is relatively weak compared with most published studies and compensation effects are particularly important. However, a large increase in daily maximum temperatures is obtained during the dry season when soil water stress dominates. The analysis of daily variability shows that the distributions of daily minimum and maximum temperatures are noticeably modified with an increase in extreme temperatures. Daily precipitation amounts also indicate a weakening of the convective activity. Conditions for the onset of convection are less frequently gathered, particularly over southern Amazonia and western equatorial Africa. At the same time, the intensity of convective events is reduced, especially over equatorial deforested regions. The inter-annual variability is also enhanced. For instance, El Nino events generally induce a large drying over northern Amazonia, which is well reproduced in the control simulation. In the deforested experiment, a positive feedback effect leads to a strong intensification of this drying and a subsequent increase in surface temperature. The change in variability as a response to deforestation can be more crucial than the change of the mean climate since more intense extremes could be more detrimental for agriculture than an increase in mean temperatures. (orig.)

  3. Unconditional Continuous Variable Dense Coding

    CERN Document Server

    Ralph, T C


    We investigate the conditions under which unconditional dense coding can be achieved using continuous variable entanglement. We consider the effect of entanglement impurity and detector efficiency and discuss experimental verification. We conclude that the requirements for a strong demonstration are not as stringent as previously thought and are within the reach of present technology.

  4. Three-Dimensional Complex Variables (United States)

    Martin, E. Dale


    Report presents new theory of analytic functions of three-dimensional complex variables. While three-dimensional system subject to more limitations and more difficult to use than the two-dimensional system, useful in analysis of three-dimensional fluid flows, electrostatic potentials, and other phenomena involving harmonic functions.

  5. UXOR Hunting among Algol Variables (United States)

    Poxon, M.


    The class of variable typified by UX Orionis (UXORs or UXors) are young stars characterised by aperiodic or semiperiodic fades from maximum. This has led to several of the class being formerly catalogued as Algol-type eclipsing binaries (EAs), which can show superficially similar light variations. With this in view, I propose a campaign to search for more UX Ori type stars.

  6. Extracting Information from AGN Variability

    CERN Document Server

    Kasliwal, Vishal P; Richards, Gordon T


    AGN exhibit rapid, high amplitude stochastic flux variability across the entire electromagnetic spectrum on timescales ranging from hours to years. The cause of this variability is poorly understood. We present a new method for using variability to (1) measure the time-scales on which flux perturbations evolve and (2) characterize the driving flux perturbations. We model the observed light curve of an AGN as a linear differential equation driven by stochastic impulses. Physically, the impulses could be local `hot-spots' in the accretion disk---the linear differential equation then governs how the hot spots evolve and dissipate. The impulse-response function of the accretion disk material is given by the Green's function of the linear differential equation. The timescales on which the hot-spots radiate energy is characterized by the powerspectrum of the driving stochastic impulses. We analyze the light curve of the \\Kepler AGN Zw 229-15 and find that the observed variability behavior can be modeled as a damped...

  7. Monitoring All Sky for Variability

    CERN Document Server

    Paczynski, B


    A few percent of all stars are variable, yet over 90% of variables brighter than 12 magnitude have not been discovered yet. There is a need for an all sky search and for the early detection of any unexpected events: optical flashes from gamma-ray bursts, novae, dwarf novae, supernovae, `killer asteroids'. The ongoing projects like ROTSE, ASAS, TASS, and others, using instruments with just 4 inch aperture, have already discovered thousands of new variable stars, a flash from an explosion at a cosmological distance, and the first partial eclipse of a nearby star by its Jupiter like planet. About one million variables may be discovered with such small instruments, and many more with larger telescopes. The critical elements are software and full automation of the hardware. A complete census of the brightest eclipsing binaries is needed to select objects for a robust empirical calibration of the the accurate distance determination to the Magellanic Clouds, the first step towards the Hubble constant. An archive to ...

  8. Compact plasmonic variable optical attenuator

    DEFF Research Database (Denmark)

    Leosson, Kristjan; Rosenzveig, Tiberiu; Hermannsson, Pétur Gordon


    We demonstrate plasmonic nanowire-based thermo-optic variable optical attenuators operating in the 1525-1625 nm wavelength range. The devices have a footprint as low as 1 mm, extinction ratio exceeding 40 dB, driving voltage below 3 V, and full modulation bandwidth of 1 kHz. The polarization...

  9. City scale pollen concentration variability (United States)

    van der Molen, Michiel; van Vliet, Arnold; Krol, Maarten


    Pollen are emitted in the atmosphere both in the country-side and in cities. Yet the majority of the population is exposed to pollen in cities. Allergic reactions may be induced by short-term exposure to pollen. This raises the question how variable pollen concentration in cities are in temporally and spatially, and how much of the pollen in cities are actually produced in the urban region itself. We built a high resolution (1 × 1 km) pollen dispersion model based on WRF-Chem to study a city's pollen budget and the spatial and temporal variability in concentration. It shows that the concentrations are highly variable, as a result of source distribution, wind direction and boundary layer mixing, as well as the release rate as a function of temperature, turbulence intensity and humidity. Hay Fever Forecasts based on such high resolution emission and physical dispersion modelling surpass traditional hay fever warning methods based on temperature sum methods. The model gives new insights in concentration variability, personal and community level exposure and prevention. The model will be developped into a new forecast tool to serve allergic people to minimize their exposure and reduce nuisance, coast of medication and sick leave. This is an innovative approach in hay fever warning systems.

  10. Extraction Methods, Variability Encountered in

    NARCIS (Netherlands)

    Bodelier, P.L.E.; Nelson, K.E.


    Synonyms Bias in DNA extractions methods; Variation in DNA extraction methods Definition The variability in extraction methods is defined as differences in quality and quantity of DNA observed using various extraction protocols, leading to differences in outcome of microbial community composition as

  11. A variable frequency semiconductor laser

    Energy Technology Data Exchange (ETDEWEB)

    Tosikhiro, F.; Khiromoto, S.


    A variable frequency, power stabilized semiconductor laser is patented. This laser includes, in addition to an active layer, a photoconducting channel layer and a layer made from a material manifesting a Pockels effect. A voltage is injected between these two layers to vary the emission frequency. The laser pumping voltage is stabilized.

  12. Sequence variability of Campylobacter temperate bacteriophages

    Directory of Open Access Journals (Sweden)

    Ng Lai-King


    Full Text Available Abstract Background Prophages integrated within the chromosomes of Campylobacter jejuni isolates have been demonstrated very recently. Prior work with Campylobacter temperate bacteriophages, as well as evidence from prophages in other enteric bacteria, suggests these prophages might have a role in the biology and virulence of the organism. However, very little is known about the genetic variability of Campylobacter prophages which, if present, could lead to differential phenotypes in isolates carrying the phages versus those that do not. As a first step in the characterization of C. jejuni prophages, we investigated the distribution of prophage DNA within a C. jejuni population assessed the DNA and protein sequence variability within a subset of the putative prophages found. Results Southern blotting of C. jejuni DNA using probes from genes within the three putative prophages of the C. jejuni sequenced strain RM 1221 demonstrated the presence of at least one prophage gene in a large proportion (27/35 of isolates tested. Of these, 15 were positive for 5 or more of the 7 Campylobacter Mu-like phage 1 (CMLP 1, also designated Campylobacter jejuni integrated element 1, or CJIE 1 genes tested. Twelve of these putative prophages were chosen for further analysis. DNA sequencing of a 9,000 to 11,000 nucleotide region of each prophage demonstrated a close homology with CMLP 1 in both gene order and nucleotide sequence. Structural and sequence variability, including short insertions, deletions, and allele replacements, were found within the prophage genomes, some of which would alter the protein products of the ORFs involved. No insertions of novel genes were detected within the sequenced regions. The 12 prophages and RM 1221 had a % G+C very similar to C. jejuni sequenced strains, as well as promoter regions characteristic of C. jejuni. None of the putative prophages were successfully induced and propagated, so it is not known if they were functional or

  13. Statistical Analysis of Tsunami Variability (United States)

    Zolezzi, Francesca; Del Giudice, Tania; Traverso, Chiara; Valfrè, Giulio; Poggi, Pamela; Parker, Eric J.


    The purpose of this paper was to investigate statistical variability of seismically generated tsunami impact. The specific goal of the work was to evaluate the variability in tsunami wave run-up due to uncertainty in fault rupture parameters (source effects) and to the effects of local bathymetry at an individual location (site effects). This knowledge is critical to development of methodologies for probabilistic tsunami hazard assessment. Two types of variability were considered: • Inter-event; • Intra-event. Generally, inter-event variability refers to the differences of tsunami run-up at a given location for a number of different earthquake events. The focus of the current study was to evaluate the variability of tsunami run-up at a given point for a given magnitude earthquake. In this case, the variability is expected to arise from lack of knowledge regarding the specific details of the fault rupture "source" parameters. As sufficient field observations are not available to resolve this question, numerical modelling was used to generate run-up data. A scenario magnitude 8 earthquake in the Hellenic Arc was modelled. This is similar to the event thought to have caused the infamous 1303 tsunami. The tsunami wave run-up was computed at 4020 locations along the Egyptian coast between longitudes 28.7° E and 33.8° E. Specific source parameters (e.g. fault rupture length and displacement) were varied, and the effects on wave height were determined. A Monte Carlo approach considering the statistical distribution of the underlying parameters was used to evaluate the variability in wave height at locations along the coast. The results were evaluated in terms of the coefficient of variation of the simulated wave run-up (standard deviation divided by mean value) for each location. The coefficient of variation along the coast was between 0.14 and 3.11, with an average value of 0.67. The variation was higher in areas of irregular coast. This level of variability is

  14. Marine molecular biology: An emerging field of biological sciences

    Digital Repository Service at National Institute of Oceanography (India)

    Thakur, N.L.; Jain, R.; Natalio, F.; Hamer, B.; Thakur, A.N.; Muller, W.E.G.

    to tackle problems associated with global climate changes, bio- diversity, environmental quality and use of marine living re- sources (Molecular biology in marine science, 1994). Marine biologists study oceanic life in relation to marine environment... that often range from small to global scale, whereas, molecular biologist study biological events in terms of the physiochemical properties of molecules. The immediate benefits of the collab- orative research between these two disciplines could include...

  15. Biological Databases for Human Research

    Institute of Scientific and Technical Information of China (English)

    Dong Zou; Lina Ma; Jun Yu; Zhang Zhang


    The completion of the Human Genome Project lays a foundation for systematically studying the human genome from evolutionary history to precision medicine against diseases. With the explosive growth of biological data, there is an increasing number of biological databases that have been developed in aid of human-related research. Here we present a collection of human-related biological databases and provide a mini-review by classifying them into different categories according to their data types. As human-related databases continue to grow not only in count but also in volume, challenges are ahead in big data storage, processing, exchange and curation.

  16. The Ethics of Synthetic Biology

    DEFF Research Database (Denmark)

    Christiansen, Andreas

    The dissertation analyses and discusses a number of ethical issues that have been raised in connection with the development of synthetic biology. Synthetic biology is a set of new techniques for DNA-level design and construction of living beings with useful properties. The dissertation especially......) popular responsesto them succeed, and whether the objections are ultimately persuasive.2. Given that synthetic biology is a new technology, there is a certain degree of uncertainty about its ultimate effects, and many perceive the technology as risky. I discuss two common approaches in risk regulation...

  17. Bilingual teaching of molecular biology

    Institute of Scientific and Technical Information of China (English)


    Recently bilingual teaching in China's universities has been widely carried out and become a popular subject for study. In this paper, the reasons for bilingual teaching of molecular biology are pointed out, the textbook of molecular biology and teaching method in bilingual teaching classes are determined after investigation and the practice of bilingually teaching molecular biology use both English and Chinese in a class. The effect has proved good. The bilingual teaching methods, the problem of bilingual teaching, the importance of understanding its significance and the possibilities of improving such teaching of the subject are also discussed.

  18. The renaissance of developmental biology. (United States)

    St Johnston, Daniel


    Since its heyday in the 1980s and 90s, the field of developmental biology has gone into decline; in part because it has been eclipsed by the rise of genomics and stem cell biology, and in part because it has seemed less pertinent in an era with so much focus on translational impact. In this essay, I argue that recent progress in genome-wide analyses and stem cell research, coupled with technological advances in imaging and genome editing, have created the conditions for the renaissance of a new wave of developmental biology with greater translational relevance.

  19. Ten questions about systems biology

    DEFF Research Database (Denmark)

    Joyner, Michael J; Pedersen, Bente K


    to understand how whole animals adapt to the real world. We argue that a lack of fluency in these concepts is a major stumbling block for what has been narrowly defined as 'systems biology' by some of its leading advocates. We also point out that it is a failure of regulation at multiple levels that causes many......In this paper we raise 'ten questions' broadly related to 'omics', the term systems biology, and why the new biology has failed to deliver major therapeutic advances for many common diseases, especially diabetes and cardiovascular disease. We argue that a fundamentally narrow and reductionist...

  20. Basic radiotherapy physics and biology

    CERN Document Server

    Chang, David S; Das, Indra J; Mendonca, Marc S; Dynlacht, Joseph R


    This book is a concise and well-illustrated review of the physics and biology of radiation therapy intended for radiation oncology residents, radiation therapists, dosimetrists, and physicists. It presents topics that are included on the Radiation Therapy Physics and Biology examinations and is designed with the intent of presenting information in an easily digestible format with maximum retention in mind. The inclusion of mnemonics, rules of thumb, and reader-friendly illustrations throughout the book help to make difficult concepts easier to grasp. Basic Radiotherapy Physics and Biology is a

  1. Biological Optimisation for Nurse Scheduling

    CERN Document Server

    Twycross, Jamie


    Artificial immune systems (AISs) to date have generally been inspired by naive biological metaphors. This has limited the effectiveness of these systems. In this position paper two ways in which AISs could be made more biologically realistic are discussed. We propose that AISs should draw their inspiration from organisms which possess only innate immune systems, and that AISs should employ systemic models of the immune system to structure their overall design. An outline of plant and invertebrate immune systems is presented, and a number of contemporary research that more biologically-realistic AISs could have is also discussed.

  2. Robust design of biological circuits: evolutionary systems biology approach. (United States)

    Chen, Bor-Sen; Hsu, Chih-Yuan; Liou, Jing-Jia


    Artificial gene circuits have been proposed to be embedded into microbial cells that function as switches, timers, oscillators, and the Boolean logic gates. Building more complex systems from these basic gene circuit components is one key advance for biologic circuit design and synthetic biology. However, the behavior of bioengineered gene circuits remains unstable and uncertain. In this study, a nonlinear stochastic system is proposed to model the biological systems with intrinsic parameter fluctuations and environmental molecular noise from the cellular context in the host cell. Based on evolutionary systems biology algorithm, the design parameters of target gene circuits can evolve to specific values in order to robustly track a desired biologic function in spite of intrinsic and environmental noise. The fitness function is selected to be inversely proportional to the tracking error so that the evolutionary biological circuit can achieve the optimal tracking mimicking the evolutionary process of a gene circuit. Finally, several design examples are given in silico with the Monte Carlo simulation to illustrate the design procedure and to confirm the robust performance of the proposed design method. The result shows that the designed gene circuits can robustly track desired behaviors with minimal errors even with nontrivial intrinsic and external noise.

  3. Heart rate variability and suicidal behavior. (United States)

    Wilson, Scott T; Chesin, Megan; Fertuck, Eric; Keilp, John; Brodsky, Beth; Mann, J John; Sönmez, Cemile Ceren; Benjamin-Phillips, Christopher; Stanley, Barbara


    Identification of biological indicators of suicide risk is important given advantages of biomarker-based models. Decreased high frequency heart rate variability (HF HRV) may be a biomarker of suicide risk. The aim of this research was to determine whether HF HRV differs between suicide attempters and non-attempters. Using the Trier Social Stress Test (TSST), we compared HF HRV between females with and without a history of suicide attempt, all with a lifetime diagnosis of a mood disorder. To investigate a potential mechanism explaining association between HF HRV and suicide, we examined the association between self-reported anger and HF HRV. Results of an Area under the Curve (AUC) analysis showed attempters had a lower cumulative HF HRV during the TSST than non-attempters. In addition, while there was no difference in self-reported anger at baseline, the increase in anger was greater in attempters, and negatively associated with HF HRV. Results suggest that suicide attempters have a reduced capacity to regulate their response to stress, and that reduced capacity to regulate anger may be a mechanism through which decreased HF HRV can lead to an increase in suicide risk. Our results have implications for the prevention of suicidal behavior in at-risk populations.

  4. Drowsiness detection using heart rate variability. (United States)

    Vicente, José; Laguna, Pablo; Bartra, Ariadna; Bailón, Raquel


    It is estimated that 10-30 % of road fatalities are related to drowsy driving. Driver's drowsiness detection based on biological and vehicle signals is being studied in preventive car safety. Autonomous nervous system activity, which can be measured noninvasively from the heart rate variability (HRV) signal obtained from surface electrocardiogram, presents alterations during stress, extreme fatigue and drowsiness episodes. We hypothesized that these alterations manifest on HRV and thus could be used to detect driver's drowsiness. We analyzed three driving databases in which drivers presented different sleep-deprivation levels, and in which each driving minute was annotated as drowsy or awake. We developed two different drowsiness detectors based on HRV. While the drowsiness episodes detector assessed each minute of driving as "awake" or "drowsy" with seven HRV derived features (positive predictive value 0.96, sensitivity 0.59, specificity 0.98 on 3475 min of driving), the sleep-deprivation detector discerned if a driver was suitable for driving or not, at driving onset, as function of his sleep-deprivation state. Sleep-deprivation state was estimated from the first three minutes of driving using only one HRV feature (positive predictive value 0.80, sensitivity 0.62, specificity 0.88 on 30 drivers). Incorporating drowsiness assessment based on HRV signal may add significant improvements to existing car safety systems.

  5. Beat to beat variability in cardiovascular variables: noise or music? (United States)

    Appel, M. L.; Berger, R. D.; Saul, J. P.; Smith, J. M.; Cohen, R. J.


    Cardiovascular variables such as heart rate, arterial blood pressure, stroke volume and the shape of electrocardiographic complexes all fluctuate on a beat to beat basis. These fluctuations have traditionally been ignored or, at best, treated as noise to be averaged out. The variability in cardiovascular signals reflects the homeodynamic interplay between perturbations to cardiovascular function and the dynamic response of the cardiovascular regulatory systems. Modern signal processing techniques provide a means of analyzing beat to beat fluctuations in cardiovascular signals, so as to permit a quantitative, noninvasive or minimally invasive method of assessing closed loop hemodynamic regulation and cardiac electrical stability. This method promises to provide a new approach to the clinical diagnosis and management of alterations in cardiovascular regulation and stability.

  6. Spatial and temporal variability in nutrients and carbon uptake during 2004 and 2005 in the eastern equatorial Pacific Ocean

    DEFF Research Database (Denmark)

    Palacz, A. P.; Chai, F.


    The eastern equatorial Pacific plays a great role in the global carbon budget due to its enhanced biological productivity linked to the equatorial upwelling. However, as confirmed by the Equatorial Biocomplexity cruises in 2004 and 2005, nutrient upwelling supply varies strongly, partly due...... and biological rate estimates, and patterns of spatio-temporal variability in primary productivity. We confirmed that TIWs have the potential to enhance phytoplankton biomass through an increased supply of nutrients and elevated local and instantaneous phytoplankton nutrient uptake as opposed to only advecting...... to the tropical instability waves (TIWs). The aim of this study was to examine patterns of spatial and temporal variability in the biological uptake of NO3, Si(OH)(4) and carbon in this region, and to evaluate the role of biological and physical interactions controlling this variability over seasonal...

  7. Systems biology of human atherosclerosis. (United States)

    Shalhoub, Joseph; Sikkel, Markus B; Davies, Kerry J; Vorkas, Panagiotis A; Want, Elizabeth J; Davies, Alun H


    Systems biology describes a holistic and integrative approach to understand physiology and pathology. The "omic" disciplines include genomics, transcriptomics, proteomics, and metabolic profiling (metabonomics and metabolomics). By adopting a stance, which is opposing (yet complimentary) to conventional research techniques, systems biology offers an overview by assessing the "net" biological effect imposed by a disease or nondisease state. There are a number of different organizational levels to be understood, from DNA to protein, metabolites, cells, organs and organisms, even beyond this to an organism's context. Systems biology relies on the existence of "nodes" and "edges." Nodes are the constituent part of the system being studied (eg, proteins in the proteome), while the edges are the way these constituents interact. In future, it will be increasingly important to collaborate, collating data from multiple studies to improve data sets, making them freely available and undertaking integrative analyses.

  8. VT Biodiversity Project - Biological Hotspots (United States)

    Vermont Center for Geographic Information — (Link to Metadata) This dataset is the result of an effort to map biological "hotspots" in Vermont based on the "element occurrences" in the Nongame and Natural...

  9. Quivira NWR biological baseline data (United States)

    US Fish and Wildlife Service, Department of the Interior — This dataset is biological baseline data for Quivira National Wildlife Refuge as of January 2016. It contains data on species found on the refuge, when and where...

  10. Sex and the Biology Teacher (United States)

    Keller, Dolores Elaine


    Summarizes evidence that mammals are basically female, with masculine characteristics being imposed by hormonal changes in embryos or post-natally. Advocates the removal of male-dominant terminology in biological research and teaching. (AL)

  11. Synthetic Biology for Specialty Chemicals. (United States)

    Markham, Kelly A; Alper, Hal S


    In this review, we address recent advances in the field of synthetic biology and describe how those tools have been applied to produce a wide variety of chemicals in microorganisms. Here we classify the expansion of the synthetic biology toolbox into three different categories based on their primary function in strain engineering-for design, for construction, and for optimization. Next, focusing on recent years, we look at how chemicals have been produced using these new synthetic biology tools. Advances in producing fuels are briefly described, followed by a more thorough treatment of commodity chemicals, specialty chemicals, pharmaceuticals, and nutraceuticals. Throughout this review, an emphasis is placed on how synthetic biology tools are applied to strain engineering. Finally, we discuss organism and host strain diversity and provide a future outlook in the field.

  12. Systems biology and cardiac arrhythmias. (United States)

    Grace, Andrew A; Roden, Dan M


    During the past few years, the development of effective, empirical technologies for treatment of cardiac arrhythmias has exceeded the pace at which detailed knowledge of the underlying biology has accumulated. As a result, although some clinical arrhythmias can be cured with techniques such as catheter ablation, drug treatment and prediction of the risk of sudden death remain fairly primitive. The identification of key candidate genes for monogenic arrhythmia syndromes shows that to bring basic biology to the clinic is a powerful approach. Increasingly sophisticated experimental models and methods of measurement, including stem cell-based models of human cardiac arrhythmias, are being deployed to study how perturbations in several biologic pathways can result in an arrhythmia-prone heart. The biology of arrhythmia is largely quantifiable, which allows for systematic analysis that could transform treatment strategies that are often still empirical into management based on molecular evidence.

  13. Aging and computational systems biology. (United States)

    Mooney, Kathleen M; Morgan, Amy E; Mc Auley, Mark T


    Aging research is undergoing a paradigm shift, which has led to new and innovative methods of exploring this complex phenomenon. The systems biology approach endeavors to understand biological systems in a holistic manner, by taking account of intrinsic interactions, while also attempting to account for the impact of external inputs, such as diet. A key technique employed in systems biology is computational modeling, which involves mathematically describing and simulating the dynamics of biological systems. Although a large number of computational models have been developed in recent years, these models have focused on various discrete components of the aging process, and to date no model has succeeded in completely representing the full scope of aging. Combining existing models or developing new models may help to address this need and in so doing could help achieve an improved understanding of the intrinsic mechanisms which underpin aging.

  14. Inference problems in structural biology

    DEFF Research Database (Denmark)

    Olsson, Simon

    The structure and dynamics of biological molecules are essential for their function. Consequently, a wealth of experimental techniques have been developed to study these features. However, while experiments yield detailed information about geometrical features of molecules, this information is of...

  15. The relativity of biological function. (United States)

    Laubichler, Manfred D; Stadler, Peter F; Prohaska, Sonja J; Nowick, Katja


    Function is a central concept in biological theories and explanations. Yet discussions about function are often based on a narrow understanding of biological systems and processes, such as idealized molecular systems or simple evolutionary, i.e., selective, dynamics. Conflicting conceptions of function continue to be used in the scientific literature to support certain claims, for instance about the fraction of "functional DNA" in the human genome. Here we argue that all biologically meaningful interpretations of function are necessarily context dependent. This implies that they derive their meaning as well as their range of applicability only within a specific theoretical and measurement context. We use this framework to shed light on the current debate about functional DNA and argue that without considering explicitly the theoretical and measurement contexts all attempts to integrate biological theories are prone to fail.

  16. Text mining for systems biology. (United States)

    Fluck, Juliane; Hofmann-Apitius, Martin


    Scientific communication in biomedicine is, by and large, still text based. Text mining technologies for the automated extraction of useful biomedical information from unstructured text that can be directly used for systems biology modelling have been substantially improved over the past few years. In this review, we underline the importance of named entity recognition and relationship extraction as fundamental approaches that are relevant to systems biology. Furthermore, we emphasize the role of publicly organized scientific benchmarking challenges that reflect the current status of text-mining technology and are important in moving the entire field forward. Given further interdisciplinary development of systems biology-orientated ontologies and training corpora, we expect a steadily increasing impact of text-mining technology on systems biology in the future.

  17. Risk assessment of groundwater level variability using variable Kriging methods (United States)

    Spanoudaki, Katerina; Kampanis, Nikolaos A.


    Assessment of the water table level spatial variability in aquifers provides useful information regarding optimal groundwater management. This information becomes more important in basins where the water table level has fallen significantly. The spatial variability of the water table level in this work is estimated based on hydraulic head measured during the wet period of the hydrological year 2007-2008, in a sparsely monitored basin in Crete, Greece, which is of high socioeconomic and agricultural interest. Three Kriging-based methodologies are elaborated in Matlab environment to estimate the spatial variability of the water table level in the basin. The first methodology is based on the Ordinary Kriging approach, the second involves auxiliary information from a Digital Elevation Model in terms of Residual Kriging and the third methodology calculates the probability of the groundwater level to fall below a predefined minimum value that could cause significant problems in groundwater resources availability, by means of Indicator Kriging. The Box-Cox methodology is applied to normalize both the data and the residuals for improved prediction results. In addition, various classical variogram models are applied to determine the spatial dependence of the measurements. The Matérn model proves to be the optimal, which in combination with Kriging methodologies provides the most accurate cross validation estimations. Groundwater level and probability maps are constructed to examine the spatial variability of the groundwater level in the basin and the associated risk that certain locations exhibit regarding a predefined minimum value that has been set for the sustainability of the basin's groundwater resources. Acknowledgement The work presented in this paper has been funded by the Greek State Scholarships Foundation (IKY), Fellowships of Excellence for Postdoctoral Studies (Siemens Program), 'A simulation-optimization model for assessing the best practices for the

  18. Topographic mapping of biological specimens: flexure and curvature characterization (United States)

    Baron, William S.; Baron, Sandra F.


    Shape quantification of tissue and biomaterials can be central to many studies and applications in bioengineering and biomechanics. Often, shape is mapped with photogrammetry or projected light techniques that provide XYZ point cloud data, and shape is quantified using derived flexure and curvature calculations based on the point cloud data. Accordingly, the accuracy of the calculated curvature depends on the properties of the point cloud data set. In this study, we present a curvature variability prediction (CVP) software model that predicts the distribution, i.e., the standard deviation, of curvature measurements associated with surface topography point cloud data properties. The CVP model point cloud data input variables include XYZ noise, sampling density, and map extent. The CVP model outputs the curvature variability statistic in order to assess performance in the curvature domain. Representative point cloud data properties are obtained from an automated biological specimen video topographer, the BioSpecVT (ver. 1.02) (Vision Metrics, Inc.,). The BioSpecVT uses a calibrated, structured light pattern to support automated computer vision feature extraction software for precisely converting video images of biological specimens, within seconds, into three dimensional point cloud data. In representative sample point cloud data obtained with the BioSpecVT, sampling density is about 11 pts/mm2 for an XYZ mapping volume encompassing about 16 mm x 13.5 mm x 18.5 mm, average XY per point variability is about +/-2 μm, and Z axis variability is about +/-40 μm (50% level) with a Gaussian distribution. A theoretical study with the CVP model shows that for derived point cloud data properties, curvature mapping accuracy increases, i.e. measurement variability decreases, when curvature increases from about 30 m-1 to 137 m-1. This computed result is consistent with the Z axis noise becoming less significant as the measured depth increases across an approximately fixed XY

  19. Language from a biological perspective

    Indian Academy of Sciences (India)

    Mohinish Shukla


    The faculty of language is unique to the human species. This implies that there are human-specific biological changes that lie at the basis of human language. However, it is not clear what the nature of such changes are, and how they could be shaped by evolution. In this paper, emphasis is laid on describing language in a Chomskyan manner, as a mental object. This serves as a standpoint to speculate about the biological basis of the emergence and evolution of language.

  20. Feller's Contributions to Mathematical Biology


    Baake, Ellen; Wakolbinger, Anton


    This is a review of William Feller's important contributions to mathematical biology. The seminal paper [Feller1951] "Diffusion processes in genetics" was particularly influential on the development of stochastic processes at the interface to evolutionary biology, and interesting ideas in this direction (including a first characterization of what is nowadays known as "Feller's branching diffusion") already shaped up in the paper [Feller 1939] (written in German) "The foundations of a probabis...