Regional sensitivities of seasonal snowpack to elevation, aspect, and vegetation cover in western North America

NASA Astrophysics Data System (ADS)

Tennant, Christopher J.; Harpold, Adrian A.; Lohse, Kathleen Ann; Godsey, Sarah E.; Crosby, Benjamin T.; Larsen, Laurel G.; Brooks, Paul D.; Van Kirk, Robert W.; Glenn, Nancy F.

2017-08-01

In mountains with seasonal snow cover, the effects of climate change on snowpack will be constrained by landscape-vegetation interactions with the atmosphere. Airborne lidar surveys used to estimate snow depth, topography, and vegetation were coupled with reanalysis climate products to quantify these interactions and to highlight potential snowpack sensitivities to climate and vegetation change across the western U.S. at Rocky Mountain (RM), Northern Basin and Range (NBR), and Sierra Nevada (SNV) sites. In forest and shrub areas, elevation captured the greatest amount of variability in snow depth (16-79%) but aspect explained more variability (11-40%) in alpine areas. Aspect was most important at RM sites where incoming shortwave to incoming net radiation (SW:NetR↓) was highest (˜0.5), capturing 17-37% of snow depth variability in forests and 32-37% in shrub areas. Forest vegetation height exhibited negative relationships with snow depth and explained 3-6% of its variability at sites with greater longwave inputs (NBR and SNV). Variability in the importance of physiography suggests differential sensitivities of snowpack to climate and vegetation change. The high SW:NetR↓ and importance of aspect suggests RM sites may be more responsive to decreases in SW:NetR↓ driven by warming or increases in humidity or cloud cover. Reduced canopy-cover could increase snow depths at SNV sites, and NBR and SNV sites are currently more sensitive to shifts from snow to rain. The consistent importance of aspect and elevation indicates that changes in SW:NetR↓ and the elevation of the rain/snow transition zone could have widespread and varied effects on western U.S. snowpacks.

Climate change effects on above- and below-ground interactions in a dryland ecosystem.

PubMed

González-Megías, Adela; Menéndez, Rosa

2012-11-19

Individual species respond to climate change by altering their abundance, distribution and phenology. Less is known, however, about how climate change affects multitrophic interactions, and its consequences for food-web dynamics. Here, we investigate the effect of future changes in rainfall patterns on detritivore-plant-herbivore interactions in a semiarid region in southern Spain by experimentally manipulating rainfall intensity and frequency during late spring-early summer. Our results show that rain intensity changes the effect of below-ground detritivores on both plant traits and above-ground herbivore abundance. Enhanced rain altered the interaction between detritivores and plants affecting flower and fruit production, and also had a direct effect on fruit and seed set. Despite this finding, there was no net effect on plant reproductive output. This finding supports the idea that plants will be less affected by climatic changes than by other trophic levels. Enhanced rain also affected the interaction between detritivores and free-living herbivores. The effect, however, was apparent only for generalist and not for specialist herbivores, demonstrating a differential response to climate change within the same trophic level. The complex responses found in this study suggest that future climate change will affect trophic levels and their interactions differentially, making extrapolation from individual species' responses and from one ecosystem to another very difficult.

SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803.

PubMed

Kim, Woo-Yeon; Kang, Sungsoo; Kim, Byoung-Chul; Oh, Jeehyun; Cho, Seongwoong; Bhak, Jong; Choi, Jong-Soon

2008-01-01

Cyanobacteria are model organisms for studying photosynthesis, carbon and nitrogen assimilation, evolution of plant plastids, and adaptability to environmental stresses. Despite many studies on cyanobacteria, there is no web-based database of their regulatory and signaling protein-protein interaction networks to date. We report a database and website SynechoNET that provides predicted protein-protein interactions. SynechoNET shows cyanobacterial domain-domain interactions as well as their protein-level interactions using the model cyanobacterium, Synechocystis sp. PCC 6803. It predicts the protein-protein interactions using public interaction databases that contain mutually complementary and redundant data. Furthermore, SynechoNET provides information on transmembrane topology, signal peptide, and domain structure in order to support the analysis of regulatory membrane proteins. Such biological information can be queried and visualized in user-friendly web interfaces that include the interactive network viewer and search pages by keyword and functional category. SynechoNET is an integrated protein-protein interaction database designed to analyze regulatory membrane proteins in cyanobacteria. It provides a platform for biologists to extend the genomic data of cyanobacteria by predicting interaction partners, membrane association, and membrane topology of Synechocystis proteins. SynechoNET is freely available at http://synechocystis.org/ or directly at http://bioportal.kobic.kr/SynechoNET/.

Factors affecting the viscosity in high concentration solutions of different monoclonal antibodies.

PubMed

Yadav, Sandeep; Shire, Steven J; Kalonia, Devendra S

2010-12-01

The viscosity profiles of four different IgG(1) molecules were studied as a function of concentration at pH 6.0. At high concentrations, MAb-H and -A showed significantly higher viscosities as compared to MAb-G and -E. Zeta Potential (ξ) measurements showed that all the IgG(1) molecules carried a net positive charge at this pH. MAb-G showed the highest positive zeta potential followed by MAb-E, -H, and -A. A consistent interpretation of the impact of net charge on viscosity for these MAbs is not possible, suggesting that electroviscous effects cannot explain the differences in viscosity. Values of k(D) (dynamic light scattering) indicated that the intermolecular interactions were repulsive for MAb-E and -G; and attractive for MAb-H and -A. Solution storage modulus (G') in high concentration solutions was consistent with attractive intermolecular interactions for MAb-H and -A, and repulsive interactions for MAb-G and -E. Effect of salt addition on solution G' and k(D) indicated that the interactions were primarily electrostatic in nature. The concentration dependent viscosity data were analyzed using a modified Ross and Minton equation. The analysis explicitly differentiates between the effect of molecular shape, size, self-crowding, and electrostatic intermolecular interactions in governing high concentration viscosity behavior. © 2010 Wiley-Liss, Inc. and the American Pharmacists Association

Interactions among resource partitioning, sampling effect, and facilitation on the biodiversity effect: a modeling approach.

PubMed

Flombaum, Pedro; Sala, Osvaldo E; Rastetter, Edward B

2014-02-01

Resource partitioning, facilitation, and sampling effect are the three mechanisms behind the biodiversity effect, which is depicted usually as the effect of plant-species richness on aboveground net primary production. These mechanisms operate simultaneously but their relative importance and interactions are difficult to unravel experimentally. Thus, niche differentiation and facilitation have been lumped together and separated from the sampling effect. Here, we propose three hypotheses about interactions among the three mechanisms and test them using a simulation model. The model simulated water movement through soil and vegetation, and net primary production mimicking the Patagonian steppe. Using the model, we created grass and shrub monocultures and mixtures, controlled root overlap and grass water-use efficiency (WUE) to simulate gradients of biodiversity, resource partitioning and facilitation. The presence of shrubs facilitated grass growth by increasing its WUE and in turn increased the sampling effect, whereas root overlap (resource partitioning) had, on average, no effect on sampling effect. Interestingly, resource partitioning and facilitation interacted so the effect of facilitation on sampling effect decreased as resource partitioning increased. Sampling effect was enhanced by the difference between the two functional groups in their efficiency in using resources. Morphological and physiological differences make one group outperform the other; once these differences were established further differences did not enhance the sampling effect. In addition, grass WUE and root overlap positively influence the biodiversity effect but showed no interactions.

Differential Internalization Rates and Postendocytic Sorting of the Norepinephrine and Dopamine Transporters Are Controlled by Structural Elements in the N Termini*

PubMed Central

Vuorenpää, Anne; Jørgensen, Trine N.; Newman, Amy H.; Madsen, Kenneth L.; Scheinin, Mika

2016-01-01

The norepinephrine transporter (NET) mediates reuptake of synaptically released norepinephrine in central and peripheral noradrenergic neurons. The molecular processes governing availability of NET in the plasma membrane are poorly understood. Here we use the fluorescent cocaine analogue JHC 1-64, as well as several other approaches, to investigate the trafficking itinerary of NET in live noradrenergic neurons. Confocal imaging revealed extensive constitutive internalization of JHC 1-64-labeled NET in the neuronal somata, proximal extensions and presynaptic boutons. Phorbol 12-myristate 13-acetate increased intracellular accumulation of JHC 1-64-labeled NET and caused a parallel reduction in uptake capacity. Internalized NET strongly colocalized with the “long loop” recycling marker Rab11, whereas less overlap was seen with the “short loop” recycling marker Rab4 and the late endosomal marker Rab7. Moreover, mitigating Rab11 function by overexpression of dominant negative Rab11 impaired NET function. Sorting of NET to the Rab11 recycling compartment was further supported by confocal imaging and reversible biotinylation experiments in transfected differentiated CATH.a cells. In contrast to NET, the dopamine transporter displayed markedly less constitutive internalization and limited sorting to the Rab11 recycling compartment in the differentiated CATH.a cells. Exchange of domains between the two homologous transporters revealed that this difference was determined by non-conserved structural elements in the intracellular N terminus. We conclude that NET displays a distinct trafficking itinerary characterized by continuous shuffling between the plasma membrane and the Rab11 recycling compartment and that the functional integrity of the Rab11 compartment is critical for maintaining proper presynaptic NET function. PMID:26786096

Management of gastric and duodenal neuroendocrine tumors

PubMed Central

Sato, Yuichi; Hashimoto, Satoru; Mizuno, Ken-ichi; Takeuchi, Manabu; Terai, Shuji

2016-01-01

Gastrointestinal neuroendocrine tumors (GI-NETs) are rare neoplasms, like all NETs. However, the incidence of GI-NETS has been increasing in recent years. Gastric NETs (G-NETs) and duodenal NETs (D-NETs) are the common types of upper GI-NETs based on tumor location. G-NETs are classified into three distinct subgroups: type I, II, and III. Type I G-NETs, which are the most common subtype (70%-80% of all G-NETs), are associated with chronic atrophic gastritis, including autoimmune gastritis and Helicobacter pylori associated atrophic gastritis. Type II G-NETs (5%-6%) are associated with multiple endocrine neoplasia type 1 and Zollinger-Ellison syndrome (MEN1-ZES). Both type I and II G-NETs are related to hypergastrinemia, are small in size, occur in multiple numbers, and are generally benign. In contrast, type III G-NETs (10%-15%) are not associated with hypergastrinemia, are large-sized single tumors, and are usually malignant. Therefore, surgical resection and chemotherapy are generally necessary for type III G-NETs, while endoscopic resection and follow-up, which are acceptable for the treatment of most type I and II G-NETs, are only acceptable for small and well differentiated type III G-NETs. D-NETs include gastrinomas (50%-60%), somatostatin-producing tumors (15%), nonfunctional serotonin-containing tumors (20%), poorly differentiated neuroendocrine carcinomas (< 3%), and gangliocytic paragangliomas (< 2%). Most D-NETs are located in the first or second part of the duodenum, with 20% occurring in the periampullary region. Therapy for D-NETs is based on tumor size, location, histological grade, stage, and tumor type. While endoscopic resection may be considered for small nonfunctional D-NETs (G1) located in the higher papilla region, surgical resection is necessary for most other D-NETs. However, there is no consensus regarding the ideal treatment of D-NETs. PMID:27570419

The gender wealth gap:structural and material constraints and implications for later life.

PubMed

Denton, Margaret; Boos, Linda

2007-01-01

Wealth is an important measure of economic well-being, because while income captures the current state of inequality, wealth has the potential for examining accumulated and historically structured inequality. This presentation documents the extent of gender inequality in wealth for Canadian women and men aged 45 and older. The analysis uses data from the 1999 Canadian Survey of Financial Security, a large nationally representative survey of household wealth in Canada. Wealth is measured by total net worth as measured by total assets minus debt. We test two general hypotheses to account for gender differences in wealth. The differential exposure hypothesis suggests that women report less wealth accumulation because of their reduced access to the material and social conditions of life that foster economic security. The differential vulnerability hypothesis suggests that women report lower levels of wealth because they receive differential returns to material and social conditions of their lives. Support is found for both hypotheses. Much of the gender differences in wealth can be explained by the gendering of work and family roles that restricts women's ability to build up assets over the life course. But beyond this, there are significant gender interaction effects that indicate that women are further penalized by their returns to participation in family life, their health and where they live. When women do work, net of other factors, they are better able to accumulate wealth than their male counterparts.

Correlation between Standardized Uptake Value of 68Ga-DOTA-NOC Positron Emission Tomography/Computed Tomography and Pathological Classification of Neuroendocrine Tumors.

PubMed

Kaewput, Chalermrat; Suppiah, Subapriya; Vinjamuri, Sobhan

2018-01-01

The aim of our study was to correlate tumor uptake of 68 Ga-DOTA-NOC positron emission tomography/computed tomography (PET/CT) with the pathological grade of neuroendocrine tumors (NETs). 68 Ga-DOTA-NOC PET/CT examinations in 41 patients with histopathologically proven NETs were included in the study. Maximum standardized uptake value (SUV max ) and averaged SUV SUV mean of "main tumor lesions" were calculated for quantitative analyses after background subtraction. Uptake on main tumor lesions was compared and correlated with the tumor histological grade based on Ki-67 index and pathological differentiation. Classification was performed into three grades according to Ki-67 levels; low grade: Ki-67 <2, intermediate grade: Ki-67 3-20, and high grade: Ki-67 >20. Pathological differentiation was graded into well- and poorly differentiated groups. The values were compared and evaluated for correlation and agreement between the two parameters was performed. Our study revealed negatively fair agreement between SUV max of tumor and Ki-67 index ( r = -0.241) and negatively poor agreement between SUV mean of tumor and Ki-67 index ( r = -0.094). SUV max of low-grade, intermediate-grade, and high-grade Ki-67 index is 26.18 ± 14.56, 30.71 ± 24.44, and 6.60 ± 4.59, respectively. Meanwhile, SUV mean of low-grade, intermediate-grade, and high-grade Ki-67 is 8.92 ± 7.15, 9.09 ± 5.18, and 3.00 ± 1.38, respectively. As expected, there was statistically significant decreased SUV max and SUV mean in high-grade tumors (poorly differentiated NETs) as compared with low- and intermediate-grade tumors (well-differentiated NETs). SUV of 68 Ga-DOTA-NOC PET/CT is not correlated with histological grade of NETs. However, there was statistically significant decreased tumor uptake of 68 Ga-DOTA-NOC in poorly differentiated NETs as compared with the well-differentiated group. As a result of this pilot study, we confirm that the lower tumor uptake of 68 Ga-DOTA-NOC may be associated with aggressive behavior and may, therefore, result in poor prognosis.

Measuring health-relevant businesses over 21 years: refining the National Establishment Time-Series (NETS), a dynamic longitudinal data set.

PubMed

Kaufman, Tanya K; Sheehan, Daniel M; Rundle, Andrew; Neckerman, Kathryn M; Bader, Michael D M; Jack, Darby; Lovasi, Gina S

2015-09-29

The densities of food retailers, alcohol outlets, physical activity facilities, and medical facilities have been associated with diet, physical activity, and management of medical conditions. Most of the research, however, has relied on cross-sectional studies. In this paper, we assess methodological issues raised by a data source that is increasingly used to characterize change in the local business environment: the National Establishment Time Series (NETS) dataset. Longitudinal data, such as NETS, offer opportunities to assess how differential access to resources impacts population health, to consider correlations among multiple environmental influences across the life course, and to gain a better understanding of their interactions and cumulative health effects. Longitudinal data also introduce new data management, geoprocessing, and business categorization challenges. Examining geocoding accuracy and categorization over 21 years of data in 23 counties surrounding New York City (NY, USA), we find that health-related business environments change considerably over time. We note that re-geocoding data may improve spatial precision, particularly in early years. Our intent with this paper is to make future public health applications of NETS data more efficient, since the size and complexity of the data can be difficult to exploit fully within its 2-year data-licensing period. Further, standardized approaches to NETS and other "big data" will facilitate the veracity and comparability of results across studies.

EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.

PubMed

Jeggari, Ashwini; Alekseenko, Zhanna; Petrov, Iurii; Dias, José M; Ericson, Johan; Alexeyenko, Andrey

2018-06-09

The new web resource EviNet provides an easily run interface to network enrichment analysis for exploration of novel, experimentally defined gene sets. The major advantages of this analysis are (i) applicability to any genes found in the global network rather than only to those with pathway/ontology term annotations, (ii) ability to connect genes via different molecular mechanisms rather than within one high-throughput platform, and (iii) statistical power sufficient to detect enrichment of very small sets, down to individual genes. The users' gene sets are either defined prior to upload or derived interactively from an uploaded file by differential expression criteria. The pathways and networks used in the analysis can be chosen from the collection menu. The calculation is typically done within seconds or minutes and the stable URL is provided immediately. The results are presented in both visual (network graphs) and tabular formats using jQuery libraries. Uploaded data and analysis results are kept in separated project directories not accessible by other users. EviNet is available at https://www.evinet.org/.

Hybrid modeling in biochemical systems theory by means of functional petri nets.

PubMed

Wu, Jialiang; Voit, Eberhard

2009-02-01

Many biological systems are genuinely hybrids consisting of interacting discrete and continuous components and processes that often operate at different time scales. It is therefore desirable to create modeling frameworks capable of combining differently structured processes and permitting their analysis over multiple time horizons. During the past 40 years, Biochemical Systems Theory (BST) has been a very successful approach to elucidating metabolic, gene regulatory, and signaling systems. However, its foundation in ordinary differential equations has precluded BST from directly addressing problems containing switches, delays, and stochastic effects. In this study, we extend BST to hybrid modeling within the framework of Hybrid Functional Petri Nets (HFPN). First, we show how the canonical GMA and S-system models in BST can be directly implemented in a standard Petri Net framework. In a second step we demonstrate how to account for different types of time delays as well as for discrete, stochastic, and switching effects. Using representative test cases, we validate the hybrid modeling approach through comparative analyses and simulations with other approaches and highlight the feasibility, quality, and efficiency of the hybrid method.

Inclusive fitness and differential productivity across the life course determine intergenerational transfers in a small-scale human society.

PubMed

Hooper, Paul L; Gurven, Michael; Winking, Jeffrey; Kaplan, Hillard S

2015-03-22

Transfers of resources between generations are an essential element in current models of human life-history evolution accounting for prolonged development, extended lifespan and menopause. Integrating these models with Hamilton's theory of inclusive fitness, we predict that the interaction of biological kinship with the age-schedule of resource production should be a key driver of intergenerational transfers. In the empirical case of Tsimane' forager-horticulturalists in Bolivian Amazonia, we provide a detailed characterization of net transfers of food according to age, sex, kinship and the net need of donors and recipients. We show that parents, grandparents and siblings provide significant net downward transfers of food across generations. We demonstrate that the extent of provisioning responds facultatively to variation in the productivity and demographic composition of families, as predicted by the theory. We hypothesize that the motivation to provide these critical transfers is a fundamental force that binds together human nuclear and extended families. The ubiquity of three-generational families in human societies may thus be a direct reflection of fundamental evolutionary constraints on an organism's life-history and social organization.

Thermodynamic and hydration effects for the incorporation of a cationic 3-aminopropyl chain into DNA

PubMed Central

Soto, Ana Maria; Kankia, Besik I.; Dande, Prasad; Gold, Barry; Marky, Luis A.

2002-01-01

The introduction of cationic 5-(ω-aminoalkyl)-2′-deoxypyrimidines into duplex DNA has been shown to induce DNA bending. In order to understand the energetic and hydration contributions for the incorporation of a cationic side chain in DNA a combination of spectroscopy, calorimetry and density techniques were used. Specifically, the temperature unfolding and isothermal formation was studied for a pair of duplexes with sequence d(CGTAGUCG TGC)/d(GCACGACTACG), where U represents 2′-deoxyuridine (‘control’) or 5-(3-aminopropyl)-2′-deoxyuridine (‘modified’). Continuous variation experiments confirmed 1:1 stoichiometries for each duplex and the circular dichroism spectra show that both duplexes adopted the B conformation. UV and differential scanning calorimetry melting experiments reveal that each duplex unfolds in two-state transitions. In low salt buffer, the ‘modified’ duplex is more stable and unfolds with a lower endothermic heat and lower release of counterion and water. This electrostatic stabilization is entropy driven and disappears at higher salt concentrations. Complete thermodynamic profiles at 15°C show that the favorable formation of each duplex results from the compensation of a favorable exothermic heat with an unfavorable entropy contribution. However, the isothermal profiles yielded a differential enthalpy of 8.8 kcal/mol, which is 4.3 kcal/mol higher than the differential enthalpy observed in the unfolding profiles. This indicates that the presence of the aminopropyl chain induces an increase in base stacking interactions in the modified single strand and a decrease in base stacking interactions in the modified duplex. Furthermore, the formation of the ‘control’ duplex releases water while the ‘modified’ duplex takes up water. Relative to the control duplex, formation of the modified duplex at 15°C yielded a marginal differential ΔG° term, positive ΔΔHITC–Δ(TΔS) compensation, negative ΔΔV and a net release of counterions. The opposite signs of the differential enthalpy–entropy compensation and differential volume change terms show a net uptake of structural water around polar and non-polar groups. This indicates that incorporation of the aminopropyl chain induces a higher exposure of aromatic bases to the solvent, which may be consistent with a small and local bend in the ‘modified’ duplex. PMID:12136099

Application of Petri Nets in Bone Remodeling

PubMed Central

Li, Lingxi; Yokota, Hiroki

2009-01-01

Understanding a mechanism of bone remodeling is a challenging task for both life scientists and model builders, since this highly interactive and nonlinear process can seldom be grasped by simple intuition. A set of ordinary differential equations (ODEs) have been built for simulating bone formation as well as bone resorption. Although solving ODEs numerically can provide useful predictions for dynamical behaviors in a continuous time frame, an actual bone remodeling process in living tissues is driven by discrete events of molecular and cellular interactions. Thus, an event-driven tool such as Petri nets (PNs), which may dynamically and graphically mimic individual molecular collisions or cellular interactions, seems to augment the existing ODE-based systems analysis. Here, we applied PNs to expand the ODE-based approach and examined discrete, dynamical behaviors of key regulatory molecules and bone cells. PNs have been used in many engineering areas, but their application to biological systems needs to be explored. Our PN model was based on 8 ODEs that described an osteoprotegerin linked molecular pathway consisting of 4 types of bone cells. The models allowed us to conduct both qualitative and quantitative evaluations and evaluate homeostatic equilibrium states. The results support that application of PN models assists understanding of an event-driven bone remodeling mechanism using PN-specific procedures such as places, transitions, and firings. PMID:19838338

The role of nurse functional types in seedling recruitment dynamics of alternative states in rangelands

NASA Astrophysics Data System (ADS)

López, Dardo R.; Cavallero, Laura

2017-02-01

In arid ecosystems, recruitment dynamics are limited by harsh environmental conditions and greatly depend on the net outcome of the balance between facilitation and competition. This outcome can change as a consequence of degradation caused by livestock overgrazing. Also, distinct plant species may show a differential response to a common neighbour under the same environmental conditions. Therefore, ecosystem degradation could affect the net balance of plant-plant interactions, which can also depend on the functional traits of potential nurse species. The aim of this study is to assess the influence of alternative degradation states on (i) the density of seedlings of perennial species emerging in four microsite types, and on (ii) the relative interaction intensity (RII) between seedlings and potential nurses belonging to three functional types (deep- and shallow-rooted shrubs, and tussock grasses). During three years, we recorded seedling density of perennial species in four alternative degradation states in grass-shrubby steppes from northwestern Patagonia. The density of emerged seedlings of perennial species decreased sharply as degradation increased, showing non-linear responses in most microsites. Seedling density underneath deep-rooted shrubs was higher than underneath shallow-rooted shrubs and tussock grasses. Also, deep-rooted shrubs were the only functional type that recorded seedling emergence in highly degraded states. Deep-rooted shrubs had facilitative effects on the seedlings emerging and surviving underneath them, independently of ecosystem degradation. In contrast, RII between shallow-rooted shrubs and recently emerged seedlings, switched from positive effects in the less degraded states, to negative effects in the most degraded state. Tussock grasses recorded the weakest intensity of facilitative interactions with recently emerged seedlings, switching to competitive interactions as degradation increased. Our results suggest that species with key functional traits should be considered in management and restoration plans for rangelands with different degradation levels, since they have a strong influence in the net outcome of plant-plant interactions and in the recruitment dynamics of arid ecosystems.

Actin-membrane interactions mediated by NETWORKED2 in Arabidopsis pollen tubes through associations with Pollen Receptor-Like Kinase 4 and 5.

PubMed

Duckney, Patrick; Deeks, Michael J; Dixon, Martin R; Kroon, Johan; Hawkins, Timothy J; Hussey, Patrick J

2017-12-01

During fertilization, Pollen Receptor-Like Kinases (PRKs) control pollen tube growth through the pistil in response to extracellular signals, and regulate the actin cytoskeleton at the tube apex to drive tip growth. We investigated a novel link between membrane-integral PRKs and the actin cytoskeleton, mediated through interactions between PRKs and NET2A; a pollen-specific member of the NETWORKED superfamily of actin-binding proteins. We characterize NET2A as a novel actin-associated protein that localizes to punctae at the plasma membrane of the pollen tube shank, which are stably associated with cortical longitudinal actin cables. NET2A was demonstrated to interact specifically with PRK4 and PRK5 in Nicotiana benthamiana transient expression assays, and associated at discreet foci at the shank membrane of Arabidopsis pollen tubes. Our data indicate that NET2A is recruited to the plasma membrane by PRK4 and PRK5, and that PRK kinase activity is important in facilitating its interaction with NET2A. We conclude that NET2A-PRK interactions mediate discreet sites of stable interactions between the cortical longitudinal actin cables and plasma membrane in the shank region of growing pollen tubes, which we have termed Actin-Membrane Contact Sites (AMCSs). Interactions between PRKs and NET2A implicate a role for NET2A in signal transduction to the actin cytoskeleton during fertilization. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Astronomical bounds on a cosmological model allowing a general interaction in the dark sector

NASA Astrophysics Data System (ADS)

Pan, Supriya; Mukherjee, Ankan; Banerjee, Narayan

2018-06-01

Non-gravitational interaction between two barotropic dark fluids, namely the pressureless dust and the dark energy in a spatially flat Friedmann-Lemaître-Robertson-Walker model, has been discussed. It is shown that for the interactions that are linear in terms the energy densities of the dark components and their first order derivatives, the net energy density is governed by a second-order differential equation with constant coefficients. Taking a generalized interaction, which includes a number of already known interactions as special cases, the dynamics of the universe is described for three types of the dark energy equation of state, namely that of interacting quintessence, interacting vacuum energy density, and interacting phantom. The models have been constrained using the standard cosmological probes, Supernovae Type Ia data from joint light curve analysis and the observational Hubble parameter data. Two geometric tests, the cosmographic studies, and the Om diagnostic have been invoked so as to ascertain the behaviour of the present model vis-a-vis the Λ-cold dark matter model. We further discussed the interacting scenarios taking into account the thermodynamic considerations.

NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis.

PubMed

Sun, Duanchen; Liu, Yinliang; Zhang, Xiang-Sun; Wu, Ling-Yun

2017-09-21

High-throughput experimental techniques have been dramatically improved and widely applied in the past decades. However, biological interpretation of the high-throughput experimental results, such as differential expression gene sets derived from microarray or RNA-seq experiments, is still a challenging task. Gene Ontology (GO) is commonly used in the functional enrichment studies. The GO terms identified via current functional enrichment analysis tools often contain direct parent or descendant terms in the GO hierarchical structure. Highly redundant terms make users difficult to analyze the underlying biological processes. In this paper, a novel network-based probabilistic generative model, NetGen, was proposed to perform the functional enrichment analysis. An additional protein-protein interaction (PPI) network was explicitly used to assist the identification of significantly enriched GO terms. NetGen achieved a superior performance than the existing methods in the simulation studies. The effectiveness of NetGen was explored further on four real datasets. Notably, several GO terms which were not directly linked with the active gene list for each disease were identified. These terms were closely related to the corresponding diseases when accessed to the curated literatures. NetGen has been implemented in the R package CopTea publicly available at GitHub ( http://github.com/wulingyun/CopTea/ ). Our procedure leads to a more reasonable and interpretable result of the functional enrichment analysis. As a novel term combination-based functional enrichment analysis method, NetGen is complementary to current individual term-based methods, and can help to explore the underlying pathogenesis of complex diseases.

Detection of colorectal masses in CT colonography: application of deep residual networks for differentiating masses from normal colon anatomy

NASA Astrophysics Data System (ADS)

Näppi, Janne J.; Hironaka, Toru; Yoshida, Hiroyuki

2018-02-01

Even though the clinical consequences of a missed colorectal cancer far outweigh those of a missed polyp, there has been little work on computer-aided detection (CADe) for colorectal masses in CT colonography (CTC). One of the problems is that it is not clear how to manually design mathematical image-based features that could be used to differentiate effectively between masses and certain types of normal colon anatomy such as ileocecal valves (ICVs). Deep learning has demonstrated ability to automatically determine effective discriminating features in many image-based problems. Recently, residual networks (ResNets) were developed to address the practical problems of constructing deep network architectures for optimizing the performance of deep learning. In this pilot study, we compared the classification performance of a conventional 2D-convolutional ResNet (2D-ResNet) with that of a volumetric 3D-convolutional ResNet (3D-ResNet) in differentiating masses from normal colon anatomy in CTC. For the development and evaluation of the ResNets, 695 volumetric images of biopsy-proven colorectal masses, ICVs, haustral folds, and rectal tubes were sampled from 196 clinical CTC cases and divided randomly into independent training, validation, and test datasets. The training set was expanded by use of volumetric data augmentation. Our preliminary results on the 140 test samples indicate that it is feasible to train a deep volumetric 3D-ResNet for performing effective image-based discriminations in CTC. The 3D-ResNet slightly outperformed the 2D-ResNet in the discrimination of masses and normal colon anatomy, but the statistical difference between their very high classification accuracies was not significant. The highest classification accuracy was obtained by combining the mass-likelihood estimates of the 2D- and 3D-ResNets, which enabled correct classification of all of the masses.

Neuroendocrine Tumors of the Lung: Current Challenges and Advances in the Diagnosis and Management of Well-Differentiated Disease.

PubMed

Hendifar, Andrew E; Marchevsky, Alberto M; Tuli, Richard

2017-03-01

Neuroendocrine tumors (NETs) comprise a heterogeneous group of malignancies that arise from neuroendocrine cells throughout the body, most commonly originating from the lungs and gastrointestinal tract. Lung NETs can be classified as well differentiated (low-grade typical carcinoids [TCs] and intermediate-grade atypical carcinoids [ACs]) and poorly differentiated (high-grade large cell neuroendocrine carcinoma or SCLC). The incidence of these tumors is increasing, but disease awareness remains low among thoracic specialists, who are often involved in the diagnosis and early treatment for these patients. An accurate and timely diagnosis can ensure the implementation of appropriate treatment and have a substantial impact on prognosis. However, lung NET classification and diagnosis, particularly for TCs/ACs, are complicated by several factors, including a variable natural history and nonspecific symptoms. Surgery remains the only curative option for TCs/ACs, but there is a lack of consensus between lung NET management guidelines regarding optimal treatment approaches in the unresectable/metastatic setting on account of the limited availability of high-level clinical evidence. As a result, a multidisciplinary approach to management of lung NETs is required to ensure a consistent and optimal level of care. RADIANT-4 is the first phase III trial involving a large subpopulation of patients with advanced well-differentiated lung NETs to report reductions in the risk for disease progression and death with everolimus over placebo. This led to the recent U.S. approval of everolimus-the first agent approved for advanced lung TCs/ACs. To further improve evidence-based care, additional randomized controlled trials in patients with lung carcinoids are needed. Copyright © 2016 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Compartmental and Spatial Rule-Based Modeling with Virtual Cell.

PubMed

Blinov, Michael L; Schaff, James C; Vasilescu, Dan; Moraru, Ion I; Bloom, Judy E; Loew, Leslie M

2017-10-03

In rule-based modeling, molecular interactions are systematically specified in the form of reaction rules that serve as generators of reactions. This provides a way to account for all the potential molecular complexes and interactions among multivalent or multistate molecules. Recently, we introduced rule-based modeling into the Virtual Cell (VCell) modeling framework, permitting graphical specification of rules and merger of networks generated automatically (using the BioNetGen modeling engine) with hand-specified reaction networks. VCell provides a number of ordinary differential equation and stochastic numerical solvers for single-compartment simulations of the kinetic systems derived from these networks, and agent-based network-free simulation of the rules. In this work, compartmental and spatial modeling of rule-based models has been implemented within VCell. To enable rule-based deterministic and stochastic spatial simulations and network-free agent-based compartmental simulations, the BioNetGen and NFSim engines were each modified to support compartments. In the new rule-based formalism, every reactant and product pattern and every reaction rule are assigned locations. We also introduce the rule-based concept of molecular anchors. This assures that any species that has a molecule anchored to a predefined compartment will remain in this compartment. Importantly, in addition to formulation of compartmental models, this now permits VCell users to seamlessly connect reaction networks derived from rules to explicit geometries to automatically generate a system of reaction-diffusion equations. These may then be simulated using either the VCell partial differential equations deterministic solvers or the Smoldyn stochastic simulator. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Detection of Significant Pneumococcal Meningitis Biomarkers by Ego Network.

PubMed

Wang, Qian; Lou, Zhifeng; Zhai, Liansuo; Zhao, Haibin

2017-06-01

To identify significant biomarkers for detection of pneumococcal meningitis based on ego network. Based on the gene expression data of pneumococcal meningitis and global protein-protein interactions (PPIs) data recruited from open access databases, the authors constructed a differential co-expression network (DCN) to identify pneumococcal meningitis biomarkers in a network view. Here EgoNet algorithm was employed to screen the significant ego networks that could accurately distinguish pneumococcal meningitis from healthy controls, by sequentially seeking ego genes, searching candidate ego networks, refinement of candidate ego networks and significance analysis to identify ego networks. Finally, the functional inference of the ego networks was performed to identify significant pathways for pneumococcal meningitis. By differential co-expression analysis, the authors constructed the DCN that covered 1809 genes and 3689 interactions. From the DCN, a total of 90 ego genes were identified. Starting from these ego genes, three significant ego networks (Module 19, Module 70 and Module 71) that could predict clinical outcomes for pneumococcal meningitis were identified by EgoNet algorithm, and the corresponding ego genes were GMNN, MAD2L1 and TPX2, respectively. Pathway analysis showed that these three ego networks were related to CDT1 association with the CDC6:ORC:origin complex, inactivation of APC/C via direct inhibition of the APC/C complex pathway, and DNA strand elongation, respectively. The authors successfully screened three significant ego modules which could accurately predict the clinical outcomes for pneumococcal meningitis and might play important roles in host response to pathogen infection in pneumococcal meningitis.

U(SMes*)n, (n = 3, 4) and Ln(SMes*)3 (Ln = La, Ce, Pr, Nd): lanthanide(III)/actinide(III) differentiation in agostic interactions and an unprecedented eta3 ligation mode of the arylthiolate ligand, from X-ray diffraction and DFT analysis.

PubMed

Roger, Mathieu; Barros, Noémi; Arliguie, Thérèse; Thuéry, Pierre; Maron, Laurent; Ephritikhine, Michel

2006-07-12

Reaction of U(NEt(2))(4) with HS-2,4,6-(t)Bu(3)C(6)H(2) (HSMes) gave U(SMes)(3)(NEt(2))(py) (1), whereas similar treatment of U[N(SiMe(3))SiMe(2)CH(2)][N(SiMe(3))(2)](2) afforded U(SMes)[N(SiMe(3))(2)](3) (2) and U(SMes)(3)[N(SiMe(3))(2)]. The first neutral homoleptic uranium(IV) thiolate to have been crystallographically characterized, U(SMes)(4) (4), was isolated from the reaction of U(BH(4))(4) and KSMes. The first homoleptic thiolate complex of uranium(III), U(SMes)(3) (5), was synthesized by protonolysis of U[N(SiMe(3))(2)](3) with HSMes in cyclohexane. The crystal structure of 5 exhibits the novel eta(3) ligation mode for the arylthiolate ligand. Comparison of the crystal structure of 5 with those of the isomorphous lanthanide congeners Ln(SMes)(3) (Ln = La, Ce, Pr, and Nd) indicates that the U-S, U-C(ipso)(), and U-C(ortho)() bond lengths are shorter than the corresponding ones in the 4f-element analogues, when taking into account the variation in the ionic radii of the metals. The distance between the uranium and the carbon atoms involved in the U...H-C epsilon agostic interaction of each thiolate ligand is shorter, by approximately 0.05 A, than that expected from a purely ionic bonding model. The lanthanide(III)/actinide(III) differentiation was analyzed by density functional theory (DFT). The nature of the M-S bond is shown to be ionic strongly polarized at the sulfur for M = U and iono-covalent (i.e. strongly ionic with low orbital interaction), for M = Ln. The strength of the U...H-C epsilon agostic interaction is proposed to be controlled by the maximization of the interaction between U(+) and S(-) under steric constraints. The eta(3) ligation mode of the arylthiolate ligand is also obtained from DFT.

Observational study of patients with gastroenteropancreatic and bronchial neuroendocrine tumors in Argentina: Results from the large database of a multidisciplinary group clinical multicenter study

PubMed Central

O’CONNOR, JUAN MANUEL; MARMISSOLLE, FABIANA; BESTANI, CLAUDIA; PESCE, VERONICA; BELLI, SUSANA; DOMINICHINI, ENZO; MENDEZ, GUILLERMO; PRICE, PAOLA; GIACOMI, NORA; PAIROLA, ALEJANDRO; LORIA, FERNANDO SÁNCHEZ; HUERTAS, EDUARDO; MARTIN, CLAUDIO; PATANE, KARINA; POLERI, CLAUDIA; ROSENBERG, MOISES; CABANNE, ANA; KUJARUK, MIRTA; CAINO, ANALIA; ZAMORA, VICTOR; MARIANI, JAVIER; DIOCA, MARIANO; PARMA, PATRICIA; PODESTA, GUSTAVO; ANDRIANI, OSCAR; GONDOLESI, GABRIEL; ROCA, ENRIQUE

2014-01-01

Neuroendocrine tumors (NET) include a spectrum of malignancies arising from neuroendocrine cells throughout the body. The objective of this clinical investigation of retrospectively and prospectively collected data was to describe the prevalence, demographic data, clinical symptoms and methods of diagnosis of NET and the treatment and long-term follow-up of patients with NET. Data were provided by the participating centers and assessed for consistency by internal reviewers. All the cases were centrally evaluated (when necessary) by the pathologists in our group. The tissue samples were reviewed by hematoxylin and eosin and immunohistochemical staining techniques to confirm the diagnosis of NET. In total, 532 cases were documented: 461 gastroenteropancreatic-NET (GEP-NET) and 71 bronchial NET (BNET). All the tumors were immunohistochemically defined according to the World Health Organization (WHO) and European Neuroendocrine Tumor Society criteria. The most common initial symptoms in GEP-NET were abdominal pain, diarrhea, bowel obstruction, flushing, gastrointestinal bleeding and weight loss. The most common tumor types were carcinoid (58.0%), non-functional pancreatic tumor (23.0%), metastatic NET of unknown primary (16.0%) and functional pancreatic tumor (3.0%). Of the BNET, 89.0% were typical and 11.0% atypical carcinoids. Of the patients with GEP-NET, 59.2% had distant metastasis at diagnosis. The locations of the primary tumors in GEP-NET were the small bowel (26.9%), pancreas (25.2%), colon-rectum (12.4%), appendix (7.6%), stomach (6.9%), esophagus (2.8%), duodenum (2.0%) and unknown primary (16.3%). The histological subtypes based on the WHO classification were well-differentiated NET (20.1%), well-differentiated neuroendocrine carcinomas (66.5%) and poorly differentiated neuroendocrine carcinomas (10.3%). Overall, 67.3% of the patients underwent surgery, 41.2% with curative intent and 26.1% for palliative purposes. The 5-year survival rates were 65.1% (95% confidence interval, 58.0–71.4%) in GEP-NET and 100.0% in typical carcinoid of the lung. This observational, non-interventional, longitudinal study aimed to accumulate relevant information regarding the epidemiology, clinical presentation and current practices in the treatment of NET patients in Argentina, providing insight into regional differences and patterns of care in this heterogeneous disease. PMID:25054030

Informatics in radiology: radiology gamuts ontology: differential diagnosis for the Semantic Web.

PubMed

Budovec, Joseph J; Lam, Cesar A; Kahn, Charles E

2014-01-01

The Semantic Web is an effort to add semantics, or "meaning," to empower automated searching and processing of Web-based information. The overarching goal of the Semantic Web is to enable users to more easily find, share, and combine information. Critical to this vision are knowledge models called ontologies, which define a set of concepts and formalize the relations between them. Ontologies have been developed to manage and exploit the large and rapidly growing volume of information in biomedical domains. In diagnostic radiology, lists of differential diagnoses of imaging observations, called gamuts, provide an important source of knowledge. The Radiology Gamuts Ontology (RGO) is a formal knowledge model of differential diagnoses in radiology that includes 1674 differential diagnoses, 19,017 terms, and 52,976 links between terms. Its knowledge is used to provide an interactive, freely available online reference of radiology gamuts ( www.gamuts.net ). A Web service allows its content to be discovered and consumed by other information systems. The RGO integrates radiologic knowledge with other biomedical ontologies as part of the Semantic Web. © RSNA, 2014.

Budget impact of everolimus for the treatment of progressive, well-differentiated, non-functional neuroendocrine tumors of gastrointestinal or lung origin that are advanced or metastatic.

PubMed

Rose, Darya B; Nellesen, Dave; Neary, Maureen P; Cai, Beilei

2017-04-01

Advanced neuroendocrine tumors (NETs) are a rare malignancy with considerable need for effective therapies. Everolimus is a mammalian target of rapamycin (mTOR) inhibitor approved by the US Food and Drug Administration (FDA) and European Medicines Agency (EMA) in 2016 for treatment of adults with progressive, well-differentiated, non-functional NETs of gastrointestinal (GI) or lung origin that are unresectable, locally advanced, or metastatic. To assess the 3-year budget impact for a typical US health plan following availability of everolimus for treatment of GI and lung NETs. Methods An economic model was developed that considered two perspectives: an entire health plan and a pharmacy budget. The total budget impact included costs of drug therapies, administration, hospitalizations, physician visits, monitoring, and adverse events (AEs). The pharmacy model only considered drug costs. In a US health plan with 1 million members, the model estimated 66 patients with well-differentiated, non-functional, and advanced or metastatic GI NETs and 20 with lung NETs undergoing treatment each year. Total budget impact in the first through third year after FDA approval ranged from $0.0568-$0.1443 per member per month (PMPM) for GI NETs and from $0.0181-$0.0355 PMPM for lung NETs. The total budget impact was lower than the pharmacy budget impact because it included cost offsets from administration and AE management for everolimus compared with alternative therapies (e.g. chemotherapies). Because GI and lung NETs are rare diseases with limited published data, several assumptions were made that may influence interpretation of results. The budget impact for everolimus was minimal in this rare disease area with a high unmet need, largely due to low disease prevalence. These results should be considered in the context of significant clinical benefits potentially provided by everolimus, including significantly longer progression-free survival (PFS) for advanced GI and lung NET patients.

Ethnicity and fertility in Nigeria.

PubMed

Kollehlon, Konia T

2003-01-01

Using a sample of Hausa-Fulani, Yoruba, Ibo, and all other women from the 1990 Nigerian Demographic and Health Survey, this study examines ethnic fertility differentials in Nigeria within the context of the social characteristics and cultural hypotheses. Among all women, we find the net fertility of Hausa-Fulani women to be lower than that of Other women; with no statistically significant difference in the net fertility of Ibo, Yourba, and Other women. But, among currently married women, we find the net fertility of Hausa-Fulani and Yoruba women to be lower than that of Other women, while the net fertility of Ibo women is higher than that of Other women. Overall, the findings of this study are more consistent with the cultural hypothesis, because statistically significant fertility differentials by ethnicity remain, even after controlling for selected socioeconomic and demographic variables.

CellNet: Network Biology Applied to Stem Cell Engineering

PubMed Central

Cahan, Patrick; Li, Hu; Morris, Samantha A.; da Rocha, Edroaldo Lummertz; Daley, George Q.; Collins, James J.

2014-01-01

SUMMARY Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. Analyzing expression data from 56 published reports, we found that cells derived via directed differentiation more closely resemble their in vivo counterparts than products of direct conversion, as reflected by the establishment of target cell-type gene regulatory networks (GRNs). Furthermore, we discovered that directly converted cells fail to adequately silence expression programs of the starting population, and that the establishment of unintended GRNs is common to virtually every cellular engineering paradigm. CellNet provides a platform for quantifying how closely engineered cell populations resemble their target cell type and a rational strategy to guide enhanced cellular engineering. PMID:25126793

Logical Differential Prediction Bayes Net, improving breast cancer diagnosis for older women.

PubMed

Nassif, Houssam; Wu, Yirong; Page, David; Burnside, Elizabeth

2012-01-01

Overdiagnosis is a phenomenon in which screening identities cancer which may not go on to cause symptoms or death. Women over 65 who develop breast cancer bear the heaviest burden of overdiagnosis. This work introduces novel machine learning algorithms to improve diagnostic accuracy of breast cancer in aging populations. At the same time, we aim at minimizing unnecessary invasive procedures (thus decreasing false positives) and concomitantly addressing overdiagnosis. We develop a novel algorithm. Logical Differential Prediction Bayes Net (LDP-BN), that calculates the risk of breast disease based on mammography findings. LDP-BN uses Inductive Logic Programming (ILP) to learn relational rules, selects older-specific differentially predictive rules, and incorporates them into a Bayes Net, significantly improving its performance. In addition, LDP-BN offers valuable insight into the classification process, revealing novel older-specific rules that link mass presence to invasive, and calcification presence and lack of detectable mass to DCIS.

A Bayesian approach to estimating hidden variables as well as missing and wrong molecular interactions in ordinary differential equation-based mathematical models.

PubMed

Engelhardt, Benjamin; Kschischo, Maik; Fröhlich, Holger

2017-06-01

Ordinary differential equations (ODEs) are a popular approach to quantitatively model molecular networks based on biological knowledge. However, such knowledge is typically restricted. Wrongly modelled biological mechanisms as well as relevant external influence factors that are not included into the model are likely to manifest in major discrepancies between model predictions and experimental data. Finding the exact reasons for such observed discrepancies can be quite challenging in practice. In order to address this issue, we suggest a Bayesian approach to estimate hidden influences in ODE-based models. The method can distinguish between exogenous and endogenous hidden influences. Thus, we can detect wrongly specified as well as missed molecular interactions in the model. We demonstrate the performance of our Bayesian dynamic elastic-net with several ordinary differential equation models from the literature, such as human JAK-STAT signalling, information processing at the erythropoietin receptor, isomerization of liquid α -Pinene, G protein cycling in yeast and UV-B triggered signalling in plants. Moreover, we investigate a set of commonly known network motifs and a gene-regulatory network. Altogether our method supports the modeller in an algorithmic manner to identify possible sources of errors in ODE-based models on the basis of experimental data. © 2017 The Author(s).

An advanced environment for hybrid modeling of biological systems based on modelica.

PubMed

Pross, Sabrina; Bachmann, Bernhard

2011-01-20

Biological systems are often very complex so that an appropriate formalism is needed for modeling their behavior. Hybrid Petri Nets, consisting of time-discrete Petri Net elements as well as continuous ones, have proven to be ideal for this task. Therefore, a new Petri Net library was implemented based on the object-oriented modeling language Modelica which allows the modeling of discrete, stochastic and continuous Petri Net elements by differential, algebraic and discrete equations. An appropriate Modelica-tool performs the hybrid simulation with discrete events and the solution of continuous differential equations. A special sub-library contains so-called wrappers for specific reactions to simplify the modeling process. The Modelica-models can be connected to Simulink-models for parameter optimization, sensitivity analysis and stochastic simulation in Matlab. The present paper illustrates the implementation of the Petri Net component models, their usage within the modeling process and the coupling between the Modelica-tool Dymola and Matlab/Simulink. The application is demonstrated by modeling the metabolism of Chinese Hamster Ovary Cells.

Non-destructive imaging of spinor Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Samson, E.; Vinit, Anshuman; Raman, Chandra

2013-05-01

We present a non-destructive differential imaging technique that enables the observation of the spatial distribution of the magnetization in a spinor Bose-Einstein condensate (BEC) through a Faraday rotation protocol. In our procedure, we utilize a linearly polarized, far-detuned laser beam as our imaging probe, and upon interaction with the condensate, the beam's polarization direction undergoes Faraday rotation. A differential measurement of the orthogonal polarization components of the rotated beam provides a spatial map of the net magnetization density within the BEC. The non-destructive aspect of this method allows for continuous imaging of the condensate. This imaging technique will prove useful in experimental BEC studies, such as spatially resolved magnetometry using ultracold atoms, and non-destructive imaging of non-equilibrium behavior of antiferromagnetic spinor condensates. This work was supported by the DARPA QuASAR program through a grant from ARO.

[Analysis of syndrome discipline of generalized anxiety disorder using data mining techniques].

PubMed

Tang, Qi-sheng; Sun, Wen-jun; Qu, Miao; Guo, Dong-fang

2012-09-01

To study the use of data mining techniques in analyzing the syndrome discipline of generalized anxiety disorder (GAD). From August 1, 2009 to July 31, 2010, 705 patients with GAD in 10 hospitals of Beijing were investigated over one year. Data mining techniques, such as Bayes net and cluster analysis, were used to analyze the syndrome discipline of GAD. A total of 61 symptoms of GAD were screened out. By using Bayes net, nine syndromes of GAD were abstracted based on the symptoms. Eight syndromes were abstracted by cluster analysis. After screening for duplicate syndromes and combining the experts' experience and traditional Chinese medicine theory, six syndromes of GAD were defined. These included depressed liver qi transforming into fire, phlegm-heat harassing the heart, liver depression and spleen deficiency, heart-kidney non-interaction, dual deficiency of the heart and spleen, and kidney deficiency and liver yang hyperactivity. Based on the results, the draft of Syndrome Diagnostic Criteria for Generalized Anxiety Disorder was developed. Data mining techniques such as Bayes net and cluster analysis have certain future potential for establishing syndrome models and analyzing syndrome discipline, thus they are suitable for the research of syndrome differentiation.

Prognostic Evaluations Tailored to Specific Gastric Neuroendocrine Neoplasms: Analysis Of 200 Cases with Extended Follow-Up.

PubMed

Vanoli, Alessandro; La Rosa, Stefano; Miceli, Emanuela; Klersy, Catherine; Maragliano, Roberta; Capuano, Francesca; Persichella, Andrea; Martino, Michele; Inzani, Frediano; Luinetti, Ombretta; Di Sabatino, Antonio; Sessa, Fausto; Paulli, Marco; Corazza, Gino Roberto; Rindi, Guido; Bordi, Cesare; Capella, Carlo; Solcia, Enrico

2018-06-12

Gastric neuroendocrine neoplasms (NENs) are very heterogeneous, ranging from mostly indolent, atrophic gastritis-associated, type I neuroendocrine tumors (NETs), through highly malignant, poorly differentiated neuroendocrine carcinomas (pdNECs), to sporadic type III NETs with intermediate prognosis, and various rare tumor types. Histologic differentiation, proliferative grade, size, level of gastric wall invasion, and local or distant metastases are used as prognostic markers. However, their value remains to be tailored to specific gastric NENs. Series of type I NETs (n = 123 cases), type III NETs (n = 34 cases), and pdNECs (n = 43 cases) were retrospectively collected from four pathology centers specializing in endocrine pathology. All cases were characterized clinically and histopathologically. During follow-up (median 93 months) data were recorded to assess disease-specific patient survival. Type I NETs, type III NETs, and pdNECs differed markedly in terms of tumor size, grade, invasive and metastatic power, as well as patient outcome. Size was used to stratify type I NETs into subgroups with significantly different invasive and metastatic behavior. All 70 type I NETs < 0.5 cm (micro-NETs) were uneventful. Ki67-based grading proved efficient for the prognostic stratification of type III NETs; however, grade 2 (G2) was not associated with tumor behavior in type I NETs. Although G3 NETs (2 type I and 9 type III) had a very poor prognosis, it was found that patient survival was longer with type III G3 NETs compared to pdNECs. Given the marked, tumor type-related behavior differences, evaluation of gastric NEN prognostic parameters should be tailored to the type of neoplastic disease. © 2018 S. Karger AG, Basel.

Co-evolution in a landrace meta-population: two closely related pathogens interacting with the same host can lead to different adaptive outcomes.

PubMed

Rau, Domenico; Rodriguez, Monica; Leonarda Murgia, Maria; Balmas, Virgilio; Bitocchi, Elena; Bellucci, Elisa; Nanni, Laura; Attene, Giovanna; Papa, Roberto

2015-08-07

We examined the local adaptation patterns in a system comprising several interconnected heterogeneous plant populations from which populations of two phylogenetically closely related pathogens were also sampled. The host is Hordeum vulgare (cultivated barley); the pathogens are Pyrenophora teres f. teres (net form) and Pyrenophora teres f. maculata (spot form), the causal agents of barley net blotch. We integrated two approaches, the comparison between the population structures of the host and the pathogens, and a cross-inoculation test. We demonstrated that two closely related pathogens with very similar niche specialisation and life-styles can give rise to different co-evolutionary outcomes on the same host. Indeed, we detected local adaptation for the net form of the pathogen but not for the spot form. We also provided evidence that an a-priori well-known resistance quantitative-trait-locus on barley chromosome 6H is involved in the co-evolutionary 'arms race' between the plant and the net-form pathogen. Moreover, data suggested latitudinal clines of host resistance and that different ecological conditions can result in differential selective pressures at different sites. Our data are of interest for on-farm conservation of plant genetic resources, as also in establishing efficient breeding programs and strategies for deployment of resistance genes of P. teres.

Co-evolution in a landrace meta-population: two closely related pathogens interacting with the same host can lead to different adaptive outcomes

PubMed Central

Rau, Domenico; Rodriguez, Monica; Leonarda Murgia, Maria; Balmas, Virgilio; Bitocchi, Elena; Bellucci, Elisa; Nanni, Laura; Attene, Giovanna; Papa, Roberto

2015-01-01

We examined the local adaptation patterns in a system comprising several interconnected heterogeneous plant populations from which populations of two phylogenetically closely related pathogens were also sampled. The host is Hordeum vulgare (cultivated barley); the pathogens are Pyrenophora teres f. teres (net form) and Pyrenophora teres f. maculata (spot form), the causal agents of barley net blotch. We integrated two approaches, the comparison between the population structures of the host and the pathogens, and a cross-inoculation test. We demonstrated that two closely related pathogens with very similar niche specialisation and life-styles can give rise to different co-evolutionary outcomes on the same host. Indeed, we detected local adaptation for the net form of the pathogen but not for the spot form. We also provided evidence that an a-priori well-known resistance quantitative-trait-locus on barley chromosome 6H is involved in the co-evolutionary ‘arms race’ between the plant and the net-form pathogen. Moreover, data suggested latitudinal clines of host resistance and that different ecological conditions can result in differential selective pressures at different sites. Our data are of interest for on-farm conservation of plant genetic resources, as also in establishing efficient breeding programs and strategies for deployment of resistance genes of P. teres. PMID:26248796

Serotonin, ATRX, and DAXX Expression in Pituitary Adenomas: Markers in the Differential Diagnosis of Neuroendocrine Tumors of the Sellar Region.

PubMed

Casar-Borota, Olivera; Botling, Johan; Granberg, Dan; Stigare, Jerker; Wikström, Johan; Boldt, Henning Bünsow; Kristensen, Bjarne Winther; Pontén, Fredrik; Trouillas, Jacqueline

2017-09-01

Differential diagnosis based on morphology and immunohistochemistry between a clinically nonfunctioning pituitary neuroendocrine tumor (NET)/pituitary adenoma and a primary or secondary NET of nonpituitary origin in the sellar region may be difficult. Serotonin, a frequently expressed marker in the NETs, has not been systematically evaluated in pituitary NETs. Although mutations in ATRX or DAXX have been reported in a significant proportion of pancreatic NETs, the mutational status of ATRX and DAXX and their possible pathogenetic role in pituitary NETs are unknown. Facing a difficult diagnostic case of an invasive serotonin and adrenocorticotroph hormone immunoreactive NET in the sellar region, we explored the immunohistochemical expression of serotonin, ATRX, and DAXX in a large series of pituitary endocrine tumors of different types from 246 patients and in 2 corticotroph carcinomas. None of the pituitary tumors expressed serotonin, suggesting that serotonin immunoreactive sellar tumors represent primary or secondary NETs of nonpituitary origin. Normal expression of ATRX and DAXX in pituitary tumors suggests that ATRX and DAXX do not play a role in the pathogenesis of pituitary endocrine tumors that remain localized to the sellar and perisellar region. A lack of ATRX or DAXX in a sellar NET suggests a nonpituitary NET, probably of pancreatic origin. One of the 2 examined corticotroph carcinomas, however, demonstrated negative ATRX immunolabeling due to an ATRX gene mutation. Further studies on a larger cohort of pituitary carcinomas are needed to clarify whether ATRX mutations may contribute to the metastatic potential in a subset of pituitary NETs.

BMRF-Net: a software tool for identification of protein interaction subnetworks by a bagging Markov random field-based method.

PubMed

Shi, Xu; Barnes, Robert O; Chen, Li; Shajahan-Haq, Ayesha N; Hilakivi-Clarke, Leena; Clarke, Robert; Wang, Yue; Xuan, Jianhua

2015-07-15

Identification of protein interaction subnetworks is an important step to help us understand complex molecular mechanisms in cancer. In this paper, we develop a BMRF-Net package, implemented in Java and C++, to identify protein interaction subnetworks based on a bagging Markov random field (BMRF) framework. By integrating gene expression data and protein-protein interaction data, this software tool can be used to identify biologically meaningful subnetworks. A user friendly graphic user interface is developed as a Cytoscape plugin for the BMRF-Net software to deal with the input/output interface. The detailed structure of the identified networks can be visualized in Cytoscape conveniently. The BMRF-Net package has been applied to breast cancer data to identify significant subnetworks related to breast cancer recurrence. The BMRF-Net package is available at http://sourceforge.net/projects/bmrfcjava/. The package is tested under Ubuntu 12.04 (64-bit), Java 7, glibc 2.15 and Cytoscape 3.1.0. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A Cross-Species Analysis in Pancreatic Neuroendocrine Tumors Reveals Molecular Subtypes with Distinctive Clinical, Metastatic, Developmental, and Metabolic Characteristics

PubMed Central

Sadanandam, Anguraj; Wullschleger, Stephan; Lyssiotis, Costas A.; Grötzinger, Carsten; Barbi, Stefano; Bersani, Samantha; Körner, Jan; Wafy, Ismael; Mafficini, Andrea; Lawlor, Rita T.; Simbolo, Michele; Asara, John M.; Bläker, Hendrik; Cantley, Lewis C.; Wiedenmann, Bertram; Scarpa, Aldo; Hanahan, Douglas

2016-01-01

Seeking to assess the representative and instructive value of an engineered mouse model of pancreatic neuroendocrine tumors (PanNET) for its cognate human cancer, we profiled and compared mRNA and miRNA transcriptomes of tumors from both. Mouse PanNET tumors could be classified into two distinctive subtypes, well-differentiated islet/insulinoma tumors (IT) and poorly differentiated tumors associated with liver metastases, dubbed metastasis-like primary (MLP). Human PanNETs were independently classified into these same two subtypes, along with a third, specific gene mutation–enriched subtype. The MLP subtypes in human and mouse were similar to liver metastases in terms of miRNA and mRNA transcriptome profiles and signature genes. The human/mouse MLP subtypes also similarly expressed genes known to regulate early pancreas development, whereas the IT subtypes expressed genes characteristic of mature islet cells, suggesting different tumorigenesis pathways. In addition, these subtypes exhibit distinct metabolic profiles marked by differential pyruvate metabolism, substantiating the significance of their separate identities. SIGNIFICANCE This study involves a comprehensive cross-species integrated analysis of multi-omics profiles and histology to stratify PanNETs into subtypes with distinctive characteristics. We provide support for the RIP1-TAG2 mouse model as representative of its cognate human cancer with prospects to better understand PanNET heterogeneity and consider future applications of personalized cancer therapy. PMID:26446169

A Cross-Species Analysis in Pancreatic Neuroendocrine Tumors Reveals Molecular Subtypes with Distinctive Clinical, Metastatic, Developmental, and Metabolic Characteristics.

PubMed

Sadanandam, Anguraj; Wullschleger, Stephan; Lyssiotis, Costas A; Grötzinger, Carsten; Barbi, Stefano; Bersani, Samantha; Körner, Jan; Wafy, Ismael; Mafficini, Andrea; Lawlor, Rita T; Simbolo, Michele; Asara, John M; Bläker, Hendrik; Cantley, Lewis C; Wiedenmann, Bertram; Scarpa, Aldo; Hanahan, Douglas

2015-12-01

Seeking to assess the representative and instructive value of an engineered mouse model of pancreatic neuroendocrine tumors (PanNET) for its cognate human cancer, we profiled and compared mRNA and miRNA transcriptomes of tumors from both. Mouse PanNET tumors could be classified into two distinctive subtypes, well-differentiated islet/insulinoma tumors (IT) and poorly differentiated tumors associated with liver metastases, dubbed metastasis-like primary (MLP). Human PanNETs were independently classified into these same two subtypes, along with a third, specific gene mutation-enriched subtype. The MLP subtypes in human and mouse were similar to liver metastases in terms of miRNA and mRNA transcriptome profiles and signature genes. The human/mouse MLP subtypes also similarly expressed genes known to regulate early pancreas development, whereas the IT subtypes expressed genes characteristic of mature islet cells, suggesting different tumorigenesis pathways. In addition, these subtypes exhibit distinct metabolic profiles marked by differential pyruvate metabolism, substantiating the significance of their separate identities. This study involves a comprehensive cross-species integrated analysis of multi-omics profiles and histology to stratify PanNETs into subtypes with distinctive characteristics. We provide support for the RIP1-TAG2 mouse model as representative of its cognate human cancer with prospects to better understand PanNET heterogeneity and consider future applications of personalized cancer therapy. ©2015 American Association for Cancer Research.

Surface salt bridges modulate DNA wrapping by the type II DNA-binding protein TF1.

PubMed

Grove, Anne

2003-07-29

The histone-like protein HU is involved in compaction of the bacterial genome. Up to 37 bp of DNA may be wrapped about some HU homologues in a process that has been proposed to depend on a linked disruption of surface salt bridges that liberates cationic side chains for interaction with the DNA. Despite significant sequence conservation between HU homologues, binding sites from 9 to 37 bp have been reported. TF1, an HU homologue that is encoded by Bacillus subtilis bacteriophage SPO1, has nM affinity for 37 bp preferred sites in DNA with 5-hydroxymethyluracil (hmU) in place of thymine. On the basis of electrophoretic mobility shift assays, we show that TF1-DNA complex formation is associated with a net release of only approximately 0.5 cations. The structure of TF1 suggests that Asp13 can form a dehydrated surface salt bridge with Lys23; substitution of Asp13 with Ala increases the net release of cations to approximately 1. These data are consistent with complex formation linked to disruption of surface salt bridges. Substitution of Glu90 with Ala, which would expose Lys87 predicted to contact DNA immediately distal to a proline-mediated DNA kink, causes an increase in affinity and an abrogation of the preference for hmU-containing DNA. We propose that hmU preference is due to finely tuned interactions at the sites of kinking that expose a differential flexibility of hmU- and T-containing DNA. Our data further suggest that the difference in binding site size for HU homologues is based on a differential ability to stabilize the DNA kinks.

Differences in gene expression profiles and signaling pathways in rhabdomyolysis-induced acute kidney injury.

PubMed

Geng, Xiaodong; Wang, Yuanda; Hong, Quan; Yang, Jurong; Zheng, Wei; Zhang, Gang; Cai, Guangyan; Chen, Xiangmei; Wu, Di

2015-01-01

Rhabdomyolysis is a threatening syndrome because it causes the breakdown of skeletal muscle. Muscle destruction leads to the release of myoglobin, intracellular proteins, and electrolytes into the circulation. The aim of this study was to investigate the differences in gene expression profiles and signaling pathways upon rhabdomyolysis-induced acute kidney injury (AKI). In this study, we used glycerol-induced renal injury as a model of rhabdomyolysis-induced AKI. We analyzed data and relevant information from the Gene Expression Omnibus database (No: GSE44925). The gene expression data for three untreated mice were compared to data for five mice with rhabdomyolysis-induced AKI. The expression profiling of the three untreated mice and the five rhabdomyolysis-induced AKI mice was performed using microarray analysis. We examined the levels of Cyp3a13, Rela, Aldh7a1, Jun, CD14. And Cdkn1a using RT-PCR to determine the accuracy of the microarray results. The microarray analysis showed that there were 1050 downregulated and 659 upregulated genes in the rhabdomyolysis-induced AKI mice compared to the control group. The interactions of all differentially expressed genes in the Signal-Net were analyzed. Cyp3a13 and Rela had the most interactions with other genes. The data showed that Rela and Aldh7a1 were the key nodes and had important positions in the Signal-Net. The genes Jun, CD14, and Cdkn1a were also significantly upregulated. The pathway analysis classified the differentially expressed genes into 71 downregulated and 48 upregulated pathways including the PI3K/Akt, MAPK, and NF-κB signaling pathways. The results of this study indicate that the NF-κB, MAPK, PI3K/Akt, and apoptotic pathways are regulated in rhabdomyolysis-induced AKI.

Combining Costs and Benefits of Animal Activities to Assess Net Yield Outcomes in Apple Orchards

PubMed Central

Luck, Gary W.

2016-01-01

Diverse animal communities influence ecosystem function in agroecosystems through positive and negative plant-animal interactions. Yet, past research has largely failed to examine multiple interactions that can have opposing impacts on agricultural production in a given context. We collected data on arthropod communities and yield quality and quantity parameters (fruit set, yield loss and net outcomes) in three major apple-growing regions in south-eastern Australia. We quantified the net yield outcome (accounting for positive and negative interactions) of multiple animal activities (pollination, fruit damage, biological control) across the entire growing season on netted branches, which excluded vertebrate predators of arthropods, and open branches. Net outcome was calculated as the number of undamaged fruit at harvest as a proportion of the number of blossoms (i.e., potential fruit yield). Vertebrate exclusion resulted in lower levels of fruit set and higher levels of arthropod damage to apples, but did not affect net outcomes. Yield quality and quantity parameters (fruit set, yield loss, net outcomes) were not directly associated with arthropod functional groups. Model variance and significant differences between the ratio of pest to beneficial arthropods between regions indicated that complex relationships between environmental factors and multiple animal interactions have a combined effect on yield. Our results show that focusing on a single crop stage, species group or ecosystem function/service can overlook important complexity in ecological processes within the system. Accounting for this complexity and quantifying the net outcome of ecological interactions within the system, is more informative for research and management of biodiversity and ecosystem services in agricultural landscapes. PMID:27391022

Combining Costs and Benefits of Animal Activities to Assess Net Yield Outcomes in Apple Orchards.

PubMed

Saunders, Manu E; Luck, Gary W

2016-01-01

Diverse animal communities influence ecosystem function in agroecosystems through positive and negative plant-animal interactions. Yet, past research has largely failed to examine multiple interactions that can have opposing impacts on agricultural production in a given context. We collected data on arthropod communities and yield quality and quantity parameters (fruit set, yield loss and net outcomes) in three major apple-growing regions in south-eastern Australia. We quantified the net yield outcome (accounting for positive and negative interactions) of multiple animal activities (pollination, fruit damage, biological control) across the entire growing season on netted branches, which excluded vertebrate predators of arthropods, and open branches. Net outcome was calculated as the number of undamaged fruit at harvest as a proportion of the number of blossoms (i.e., potential fruit yield). Vertebrate exclusion resulted in lower levels of fruit set and higher levels of arthropod damage to apples, but did not affect net outcomes. Yield quality and quantity parameters (fruit set, yield loss, net outcomes) were not directly associated with arthropod functional groups. Model variance and significant differences between the ratio of pest to beneficial arthropods between regions indicated that complex relationships between environmental factors and multiple animal interactions have a combined effect on yield. Our results show that focusing on a single crop stage, species group or ecosystem function/service can overlook important complexity in ecological processes within the system. Accounting for this complexity and quantifying the net outcome of ecological interactions within the system, is more informative for research and management of biodiversity and ecosystem services in agricultural landscapes.

A structural study of the complex between neuroepithelial cell transforming gene 1 (Net1) and RhoA reveals a potential anticancer drug hot spot.

PubMed

Petit, Alain-Pierre; Garcia-Petit, Christel; Bueren-Calabuig, Juan A; Vuillard, Laurent M; Ferry, Gilles; Boutin, Jean A

2018-06-08

The GTPase RhoA is a major player in many different regulatory pathways. RhoA catalyzes GTP hydrolysis, and its catalysis is accelerated when RhoA forms heterodimers with proteins of the guanine nucleotide exchange factor (GEF) family. Neuroepithelial cell transforming gene 1 (Net1) is a RhoA-interacting GEF implicated in cancer, but the structural features supporting the RhoA/Net1 interaction are unknown. Taking advantage of a simple production and purification process, here we solved the structure of a RhoA/Net1 heterodimer with X-ray crystallography at 2-Å resolution. Using a panel of several techniques, including molecular dynamics simulations, we characterized the RhoA/Net1 interface. Moreover, deploying an extremely simple peptide-based scanning approach, we found that short peptides (penta- to nonapeptides) derived from the protein/protein interaction region of RhoA could disrupt the RhoA/Net1 interaction and thereby diminish the rate of nucleotide exchange. The most inhibitory peptide, EVKHF, spanning residues 102-106 in the RhoA sequence, displayed an IC 50 of ∼100 μm without further modifications. The peptides identified here could be useful in further investigations of the RhoA/Net1 interaction region. We propose that our structural and functional insights might inform chemical approaches for transforming the pentapeptide into an optimized pseudopeptide that antagonizes Net1-mediated RhoA activation with therapeutic anticancer potential. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Concordance between results of somatostatin receptor scintigraphy with 111In-DOTA-DPhe 1-Tyr 3-octreotide and chromogranin A assay in patients with neuroendocrine tumours.

PubMed

Rodrigues, Margarida; Gabriel, Michael; Heute, Dirk; Putzer, Daniel; Griesmacher, Andrea; Virgolini, Irene

2008-10-01

Somatostatin receptor scintigraphy (SRS) and chromogranin A (CgA) assay have successfully been implemented in the clinical work-up and management of neuroendocrine tumour (NET) patients. However, there is still a lack of studies comparing results in these patients. Our aim was to compare directly in NET patients SRS and CgA assay results with special regard to tumour features such as grade of malignancy, primary origin, disease extent and function. One hundred twenty consecutive patients with histological confirmed NETs were investigated with (111)In-DOTA-DPhe(1)-Tyr(3)-octreotide ((111)In-DOTA-TOC) SRS and CgA immunoradiometric assay. Tumours were classified by cell characteristics [well-differentiated NETs, well-differentiated neuroendocrine carcinomas, poorly differentiated neuroendocrine carcinomas (PDNECs)], primary origin (foregut, midgut, hindgut, undetermined), disease extent (limited disease, metastases, primary tumour and metastases) and functionality (secretory, nonsecretory). SRS was positive in 107 (89%) patients; CgA levels were increased in 95 (79%) patients. Overall, concordance between SRS and CgA results was found in 84 patients. Positive SRS but normal CgA level were found in 24 patients, with higher prevalence (p<0.05) in patients with nonsecretory tumours. Conversely, negative SRS but CgA level increased were seen in 12 patients, with higher proportion (p<0.05) in patients with PDNECs and tumours of hindgut origin. Overall, (111)In-DOTA-TOC SRS proved to be more sensitive than CgA in NETs patients. Tumour differentiation, disease extent and presence of liver metastases impact both SRS and CgA results, whereas nonsecretory activity is a negative predictor of only CgA increase. PDNECs and hindgut origin of tumours predispose to discrepancies with negative SRS but increased CgA levels.

BiomeNet: A Bayesian Model for Inference of Metabolic Divergence among Microbial Communities

PubMed Central

Chipman, Hugh; Gu, Hong; Bielawski, Joseph P.

2014-01-01

Metagenomics yields enormous numbers of microbial sequences that can be assigned a metabolic function. Using such data to infer community-level metabolic divergence is hindered by the lack of a suitable statistical framework. Here, we describe a novel hierarchical Bayesian model, called BiomeNet (Bayesian inference of metabolic networks), for inferring differential prevalence of metabolic subnetworks among microbial communities. To infer the structure of community-level metabolic interactions, BiomeNet applies a mixed-membership modelling framework to enzyme abundance information. The basic idea is that the mixture components of the model (metabolic reactions, subnetworks, and networks) are shared across all groups (microbiome samples), but the mixture proportions vary from group to group. Through this framework, the model can capture nested structures within the data. BiomeNet is unique in modeling each metagenome sample as a mixture of complex metabolic systems (metabosystems). The metabosystems are composed of mixtures of tightly connected metabolic subnetworks. BiomeNet differs from other unsupervised methods by allowing researchers to discriminate groups of samples through the metabolic patterns it discovers in the data, and by providing a framework for interpreting them. We describe a collapsed Gibbs sampler for inference of the mixture weights under BiomeNet, and we use simulation to validate the inference algorithm. Application of BiomeNet to human gut metagenomes revealed a metabosystem with greater prevalence among inflammatory bowel disease (IBD) patients. Based on the discriminatory subnetworks for this metabosystem, we inferred that the community is likely to be closely associated with the human gut epithelium, resistant to dietary interventions, and interfere with human uptake of an antioxidant connected to IBD. Because this metabosystem has a greater capacity to exploit host-associated glycans, we speculate that IBD-associated communities might arise from opportunist growth of bacteria that can circumvent the host's nutrient-based mechanism for bacterial partner selection. PMID:25412107

CellNet: network biology applied to stem cell engineering.

PubMed

Cahan, Patrick; Li, Hu; Morris, Samantha A; Lummertz da Rocha, Edroaldo; Daley, George Q; Collins, James J

2014-08-14

Somatic cell reprogramming, directed differentiation of pluripotent stem cells, and direct conversions between differentiated cell lineages represent powerful approaches to engineer cells for research and regenerative medicine. We have developed CellNet, a network biology platform that more accurately assesses the fidelity of cellular engineering than existing methodologies and generates hypotheses for improving cell derivations. Analyzing expression data from 56 published reports, we found that cells derived via directed differentiation more closely resemble their in vivo counterparts than products of direct conversion, as reflected by the establishment of target cell-type gene regulatory networks (GRNs). Furthermore, we discovered that directly converted cells fail to adequately silence expression programs of the starting population and that the establishment of unintended GRNs is common to virtually every cellular engineering paradigm. CellNet provides a platform for quantifying how closely engineered cell populations resemble their target cell type and a rational strategy to guide enhanced cellular engineering. Copyright © 2014 Elsevier Inc. All rights reserved.

Neoplasms of the Neuroendocrine Pancreas: An Update in the Classification, Definition, and Molecular Genetic Advances.

PubMed

Guilmette, Julie M; Nosé, Vania

2018-06-14

This review focuses on discussing the main modifications of the recently published 2017 WHO Classification of Neoplasms of the Neuroendocrine Pancreas (panNEN). Recent updates separate pancreatic neuroendocrine tumors into 2 broad categories: well-differentiated pancreatic neuroendocrine tumors (panNET) and poorly differentiated pancreatic neuroendocrine carcinoma (panNEC), and incorporates a new subcategory of "well-differentiated high-grade NET (G3)" to the well-differentiated NET category. This new classification algorithm aims to improve the prediction of clinical outcomes and survival and help clinicians select better therapeutic strategies for patient care and management. In addition, these neuroendocrine neoplasms are capable of producing large quantity of hormones leading to clinical hormone hypersecretion syndromes. These functioning tumors include, insulinomas, glucagonomas, somatostatinomas, gastrinomas, VIPomas, serotonin-producing tumors, and ACTH-producing tumors. Although most panNENs arise as sporadic diseases, a subset of these heterogeneous tumors present as parts on inherited genetic syndromes, such as multiple endocrine neoplasia type 1, von Hippel-Lindau, neurofibromatosis type 1, tuberous sclerosis, and glucagon cell hyperplasia and neoplasia syndromes. Characteristic clinical and morphologic findings for certain functioning and syndromic panNENs should alert both pathologists and clinicians as appropriate patient management and possible genetic counseling may be necessary.

75 FR 11115 - Proposed Information Collection; Comment Request; Reporting Requirements for Sea Otter...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-10

... Collection; Comment Request; Reporting Requirements for Sea Otter Interactions with the Pacific Sardine... conservation measures under the CPS FMP. This included the requirement to report any interactions that may... interactions (defined as otters within encircled nets or coming into contact with nets or vessels, including...

Shannon entropic temperature and its lower and upper bounds for non-Markovian stochastic dynamics

NASA Astrophysics Data System (ADS)

Ray, Somrita; Bag, Bidhan Chandra

2014-09-01

In this article we have studied Shannon entropic nonequilibrium temperature (NET) extensively for a system which is coupled to a thermal bath that may be Markovian or non-Markovian in nature. Using the phase-space distribution function, i.e., the solution of the generalized Fokker Planck equation, we have calculated the entropy production, NET, and their bounds. Other thermodynamic properties like internal energy of the system, heat, and work, etc. are also measured to study their relations with NET. The present study reveals that the heat flux is proportional to the difference between the temperature of the thermal bath and the nonequilibrium temperature of the system. It also reveals that heat capacity at nonequilibrium state is independent of both NET and time. Furthermore, we have demonstrated the time variations of the above-mentioned and related quantities to differentiate between the equilibration processes for the coupling of the system with the Markovian and the non-Markovian thermal baths, respectively. It implies that in contrast to the Markovian case, a certain time is required to develop maximum interaction between the system and the non-Markovian thermal bath (NMTB). It also implies that longer relaxation time is needed for a NMTB compared to a Markovian one. Quasidynamical behavior of the NMTB introduces an oscillation in the variation of properties with time. Finally, we have demonstrated how the nonequilibrium state is affected by the memory time of the thermal bath.

GLP1 and glucagon co-secreting pancreatic neuroendocrine tumor presenting as hypoglycemia after gastric bypass

PubMed Central

Guimarães, Marta; Rodrigues, Pedro; Pereira, Sofia S; Nora, Mário; Gonçalves, Gil; Albrechtsen, Nicolai Wewer; Hartmann, Bolette; Holst, Jens Juul

2015-01-01

Summary Post-prandial hypoglycemia is frequently found after bariatric surgery. Although rare, pancreatic neuroendocrine tumors (pNET), which occasionally are mixed hormone secreting, can lead to atypical clinical manifestations, including reactive hypoglycemia. Two years after gastric bypass surgery for the treatment of severe obesity, a 54-year-old female with previous type 2 diabetes, developed post-prandial sweating, fainting and hypoglycemic episodes, which eventually led to the finding by ultrasound of a 1.8-cm solid mass in the pancreatic head. The 72-h fast test and the plasma chromogranin A levels were normal but octreotide scintigraphy showed a single focus of abnormal radiotracer uptake at the site of the nodule. There were no other clinical signs of hormone secreting pNET and gastrointestinal hormone measurements were not performed. The patient underwent surgical enucleation with complete remission of the hypoglycemic episodes. Histopathology revealed a well-differentiated neuroendocrine carcinoma with low-grade malignancy with positive chromogranin A and glucagon immunostaining. An extract of the resected tumor contained a high concentration of glucagon (26.707 pmol/g tissue), in addition to traces of GLP1 (471 pmol/g), insulin (139 pmol/g) and somatostatin (23 pmol/g). This is the first report of a GLP1 and glucagon co-secreting pNET presenting as hypoglycemia after gastric bypass surgery. Although pNET are rare, they should be considered in the differential diagnosis of the clinical approach to the post-bariatric surgery hypoglycemia patient. Learning points pNETs can be multihormonal-secreting, leading to atypical clinical manifestations.Reactive hypoglycemic episodes are frequent after gastric bypass.pNETs should be considered in the differential diagnosis of hypoglycemia after bariatric surgery. PMID:26266036

EgoNet: identification of human disease ego-network modules

PubMed Central

2014-01-01

Background Mining novel biomarkers from gene expression profiles for accurate disease classification is challenging due to small sample size and high noise in gene expression measurements. Several studies have proposed integrated analyses of microarray data and protein-protein interaction (PPI) networks to find diagnostic subnetwork markers. However, the neighborhood relationship among network member genes has not been fully considered by those methods, leaving many potential gene markers unidentified. The main idea of this study is to take full advantage of the biological observation that genes associated with the same or similar diseases commonly reside in the same neighborhood of molecular networks. Results We present EgoNet, a novel method based on egocentric network-analysis techniques, to exhaustively search and prioritize disease subnetworks and gene markers from a large-scale biological network. When applied to a triple-negative breast cancer (TNBC) microarray dataset, the top selected modules contain both known gene markers in TNBC and novel candidates, such as RAD51 and DOK1, which play a central role in their respective ego-networks by connecting many differentially expressed genes. Conclusions Our results suggest that EgoNet, which is based on the ego network concept, allows the identification of novel biomarkers and provides a deeper understanding of their roles in complex diseases. PMID:24773628

68Ga-DOTA-TOC uptake in neuroendocrine tumour and healthy tissue: differentiation of physiological uptake and pathological processes in PET/CT.

PubMed

Kroiss, A; Putzer, D; Decristoforo, C; Uprimny, C; Warwitz, B; Nilica, B; Gabriel, M; Kendler, D; Waitz, D; Widmann, G; Virgolini, I J

2013-04-01

We wanted to establish the range of (68)Ga-DOTA-TOC uptake in liver and bone metastases of patients with neuroendocrine tumours (NET) and to establish the range of its uptake in pancreatic NET. This would allow differentiation between physiological uptake and tumour-related somatostatin receptor expression in the pancreas (including the uncinate process), liver and bone. Finally, we wanted to test for differences in patients with NET, either treated or not treated with peptide receptor radionuclide therapy (PRRT). In 249 patients, 390 (68)Ga-DOTA-TOC PET/CT studies were performed. The clinical indications for PET/CT were gastroenteropancreatic NET (194 studies), nongastroenteropancreatic NET (origin in the lung and rectum; 46 studies), NET of unknown primary (111 studies), phaeochromocytoma/glomus tumours (18 studies), and radioiodine-negative metastatic thyroid carcinoma (21 studies). SUVmax (mean ± standard deviation) values of (68)Ga-DOTA-TOC were 29.8 ± 16.5 in 162 liver metastases, 19.8 ± 18.8 in 89 bone metastases and 34.6 ± 17.1 in 43 pancreatic NET (33.6 ± 14.3 in 30 tumours of the uncinate process and 36.3 ± 21.5 in 13 tumours of the pancreatic tail). A significant difference in SUVmax (p < 0.02) was found in liver metastases of NET patients treated with PRRT. There were significant differences in SUVmax between nonmalignant and malignant tissue for both bone and liver metastases and for pancreatic NET including the uncinate process (p < 0.0001). At a cut-off value of 17.1 the specificity and sensitivity of SUVmax for differentiating tumours in the uncinate process were 93.6 % and 90.0 %, respectively (p < 0.0001). (68)Ga-DOTA-TOC is an excellent tracer for the imaging of tumours expressing somatostatin receptors on the tumour cell surface, facilitating the detection of even small tumour lesions. The noninvasive PET/CT approach by measurement of regional SUVmax can offer important clinical information to distinguish between physiological and pathological somatostatin receptor expression, especially in the uncinate process. PRRT does not significantly influence SUVmax, except in liver metastases of patients with NET.

The Influence of Herbivory on the net rate of Increase of Gypsy Moth Abundance: A Modeling Analysis

Treesearch

 Harry T.  Valentine

1983-01-01

A differential equation model of gypsy moth abundance, average larval dry weight, and food abundance was used to analyze the effects of changes in foliar chemistry on the net per capita rate of increase in a gypsy moth population. If relative consumption rate per larva is unaffected by herbivory, a reduction in the nutritional value of foliage reduces the net rate of...

Fusing literature and full network data improves disease similarity computation.

PubMed

Li, Ping; Nie, Yaling; Yu, Jingkai

2016-08-30

Identifying relatedness among diseases could help deepen understanding for the underlying pathogenic mechanisms of diseases, and facilitate drug repositioning projects. A number of methods for computing disease similarity had been developed; however, none of them were designed to utilize information of the entire protein interaction network, using instead only those interactions involving disease causing genes. Most of previously published methods required gene-disease association data, unfortunately, many diseases still have very few or no associated genes, which impeded broad adoption of those methods. In this study, we propose a new method (MedNetSim) for computing disease similarity by integrating medical literature and protein interaction network. MedNetSim consists of a network-based method (NetSim), which employs the entire protein interaction network, and a MEDLINE-based method (MedSim), which computes disease similarity by mining the biomedical literature. Among function-based methods, NetSim achieved the best performance. Its average AUC (area under the receiver operating characteristic curve) reached 95.2 %. MedSim, whose performance was even comparable to some function-based methods, acquired the highest average AUC in all semantic-based methods. Integration of MedSim and NetSim (MedNetSim) further improved the average AUC to 96.4 %. We further studied the effectiveness of different data sources. It was found that quality of protein interaction data was more important than its volume. On the contrary, higher volume of gene-disease association data was more beneficial, even with a lower reliability. Utilizing higher volume of disease-related gene data further improved the average AUC of MedNetSim and NetSim to 97.5 % and 96.7 %, respectively. Integrating biomedical literature and protein interaction network can be an effective way to compute disease similarity. Lacking sufficient disease-related gene data, literature-based methods such as MedSim can be a great addition to function-based algorithms. It may be beneficial to steer more resources torward studying gene-disease associations and improving the quality of protein interaction data. Disease similarities can be computed using the proposed methods at http:// www.digintelli.com:8000/ .

Challenges in QCD matter physics -The scientific programme of the Compressed Baryonic Matter experiment at FAIR

NASA Astrophysics Data System (ADS)

Ablyazimov, T.; Abuhoza, A.; Adak, R. P.; Adamczyk, M.; Agarwal, K.; Aggarwal, M. M.; Ahammed, Z.; Ahmad, F.; Ahmad, N.; Ahmad, S.; Akindinov, A.; Akishin, P.; Akishina, E.; Akishina, T.; Akishina, V.; Akram, A.; Al-Turany, M.; Alekseev, I.; Alexandrov, E.; Alexandrov, I.; Amar-Youcef, S.; Anđelić, M.; Andreeva, O.; Andrei, C.; Andronic, A.; Anisimov, Yu.; Appelshäuser, H.; Argintaru, D.; Atkin, E.; Avdeev, S.; Averbeck, R.; Azmi, M. D.; Baban, V.; Bach, M.; Badura, E.; Bähr, S.; Balog, T.; Balzer, M.; Bao, E.; Baranova, N.; Barczyk, T.; Bartoş, D.; Bashir, S.; Baszczyk, M.; Batenkov, O.; Baublis, V.; Baznat, M.; Becker, J.; Becker, K.-H.; Belogurov, S.; Belyakov, D.; Bendarouach, J.; Berceanu, I.; Bercuci, A.; Berdnikov, A.; Berdnikov, Y.; Berendes, R.; Berezin, G.; Bergmann, C.; Bertini, D.; Bertini, O.; Beşliu, C.; Bezshyyko, O.; Bhaduri, P. P.; Bhasin, A.; Bhati, A. K.; Bhattacharjee, B.; Bhattacharyya, A.; Bhattacharyya, T. K.; Biswas, S.; Blank, T.; Blau, D.; Blinov, V.; Blume, C.; Bocharov, Yu.; Book, J.; Breitner, T.; Brüning, U.; Brzychczyk, J.; Bubak, A.; Büsching, H.; Bus, T.; Butuzov, V.; Bychkov, A.; Byszuk, A.; Cai, Xu; Cãlin, M.; Cao, Ping; Caragheorgheopol, G.; Carević, I.; Cătănescu, V.; Chakrabarti, A.; Chattopadhyay, S.; Chaus, A.; Chen, Hongfang; Chen, LuYao; Cheng, Jianping; Chepurnov, V.; Cherif, H.; Chernogorov, A.; Ciobanu, M. I.; Claus, G.; Constantin, F.; Csanád, M.; D'Ascenzo, N.; Das, Supriya; Das, Susovan; de Cuveland, J.; Debnath, B.; Dementiev, D.; Deng, Wendi; Deng, Zhi; Deppe, H.; Deppner, I.; Derenovskaya, O.; Deveaux, C. A.; Deveaux, M.; Dey, K.; Dey, M.; Dillenseger, P.; Dobyrn, V.; Doering, D.; Dong, Sheng; Dorokhov, A.; Dreschmann, M.; Drozd, A.; Dubey, A. K.; Dubnichka, S.; Dubnichkova, Z.; Dürr, M.; Dutka, L.; Dželalija, M.; Elsha, V. V.; Emschermann, D.; Engel, H.; Eremin, V.; Eşanu, T.; Eschke, J.; Eschweiler, D.; Fan, Huanhuan; Fan, Xingming; Farooq, M.; Fateev, O.; Feng, Shengqin; Figuli, S. P. D.; Filozova, I.; Finogeev, D.; Fischer, P.; Flemming, H.; Förtsch, J.; Frankenfeld, U.; Friese, V.; Friske, E.; Fröhlich, I.; Frühauf, J.; Gajda, J.; Galatyuk, T.; Gangopadhyay, G.; García Chávez, C.; Gebelein, J.; Ghosh, P.; Ghosh, S. K.; Gläßel, S.; Goffe, M.; Golinka-Bezshyyko, L.; Golovatyuk, V.; Golovnya, S.; Golovtsov, V.; Golubeva, M.; Golubkov, D.; Gómez Ramírez, A.; Gorbunov, S.; Gorokhov, S.; Gottschalk, D.; Gryboś, P.; Grzeszczuk, A.; Guber, F.; Gudima, K.; Gumiński, M.; Gupta, A.; Gusakov, Yu.; Han, Dong; Hartmann, H.; He, Shue; Hehner, J.; Heine, N.; Herghelegiu, A.; Herrmann, N.; Heß, B.; Heuser, J. M.; Himmi, A.; Höhne, C.; Holzmann, R.; Hu, Dongdong; Huang, Guangming; Huang, Xinjie; Hutter, D.; Ierusalimov, A.; Ilgenfritz, E.-M.; Irfan, M.; Ivanischev, D.; Ivanov, M.; Ivanov, P.; Ivanov, Valery; Ivanov, Victor; Ivanov, Vladimir; Ivashkin, A.; Jaaskelainen, K.; Jahan, H.; Jain, V.; Jakovlev, V.; Janson, T.; Jiang, Di; Jipa, A.; Kadenko, I.; Kähler, P.; Kämpfer, B.; Kalinin, V.; Kallunkathariyil, J.; Kampert, K.-H.; Kaptur, E.; Karabowicz, R.; Karavichev, O.; Karavicheva, T.; Karmanov, D.; Karnaukhov, V.; Karpechev, E.; Kasiński, K.; Kasprowicz, G.; Kaur, M.; Kazantsev, A.; Kebschull, U.; Kekelidze, G.; Khan, M. M.; Khan, S. A.; Khanzadeev, A.; Khasanov, F.; Khvorostukhin, A.; Kirakosyan, V.; Kirejczyk, M.; Kiryakov, A.; Kiš, M.; Kisel, I.; Kisel, P.; Kiselev, S.; Kiss, T.; Klaus, P.; Kłeczek, R.; Klein-Bösing, Ch.; Kleipa, V.; Klochkov, V.; Kmon, P.; Koch, K.; Kochenda, L.; Koczoń, P.; Koenig, W.; Kohn, M.; Kolb, B. W.; Kolosova, A.; Komkov, B.; Korolev, M.; Korolko, I.; Kotte, R.; Kovalchuk, A.; Kowalski, S.; Koziel, M.; Kozlov, G.; Kozlov, V.; Kramarenko, V.; Kravtsov, P.; Krebs, E.; Kreidl, C.; Kres, I.; Kresan, D.; Kretschmar, G.; Krieger, M.; Kryanev, A. V.; Kryshen, E.; Kuc, M.; Kucewicz, W.; Kucher, V.; Kudin, L.; Kugler, A.; Kumar, Ajit; Kumar, Ashwini; Kumar, L.; Kunkel, J.; Kurepin, A.; Kurepin, N.; Kurilkin, A.; Kurilkin, P.; Kushpil, V.; Kuznetsov, S.; Kyva, V.; Ladygin, V.; Lara, C.; Larionov, P.; Laso García, A.; Lavrik, E.; Lazanu, I.; Lebedev, A.; Lebedev, S.; Lebedeva, E.; Lehnert, J.; Lehrbach, J.; Leifels, Y.; Lemke, F.; Li, Cheng; Li, Qiyan; Li, Xin; Li, Yuanjing; Lindenstruth, V.; Linnik, B.; Liu, Feng; Lobanov, I.; Lobanova, E.; Löchner, S.; Loizeau, P.-A.; Lone, S. A.; Lucio Martínez, J. A.; Luo, Xiaofeng; Lymanets, A.; Lyu, Pengfei; Maevskaya, A.; Mahajan, S.; Mahapatra, D. P.; Mahmoud, T.; Maj, P.; Majka, Z.; Malakhov, A.; Malankin, E.; Malkevich, D.; Malyatina, O.; Malygina, H.; Mandal, M. M.; Mandal, S.; Manko, V.; Manz, S.; Marin Garcia, A. M.; Markert, J.; Masciocchi, S.; Matulewicz, T.; Meder, L.; Merkin, M.; Mialkovski, V.; Michel, J.; Miftakhov, N.; Mik, L.; Mikhailov, K.; Mikhaylov, V.; Milanović, B.; Militsija, V.; Miskowiec, D.; Momot, I.; Morhardt, T.; Morozov, S.; Müller, W. F. J.; Müntz, C.; Mukherjee, S.; Muñoz Castillo, C. E.; Murin, Yu.; Najman, R.; Nandi, C.; Nandy, E.; Naumann, L.; Nayak, T.; Nedosekin, A.; Negi, V. S.; Niebur, W.; Nikulin, V.; Normanov, D.; Oancea, A.; Oh, Kunsu; Onishchuk, Yu.; Ososkov, G.; Otfinowski, P.; Ovcharenko, E.; Pal, S.; Panasenko, I.; Panda, N. R.; Parzhitskiy, S.; Patel, V.; Pauly, C.; Penschuck, M.; Peshekhonov, D.; Peshekhonov, V.; Petráček, V.; Petri, M.; Petriş, M.; Petrovici, A.; Petrovici, M.; Petrovskiy, A.; Petukhov, O.; Pfeifer, D.; Piasecki, K.; Pieper, J.; Pietraszko, J.; Płaneta, R.; Plotnikov, V.; Plujko, V.; Pluta, J.; Pop, A.; Pospisil, V.; Poźniak, K.; Prakash, A.; Prasad, S. K.; Prokudin, M.; Pshenichnov, I.; Pugach, M.; Pugatch, V.; Querchfeld, S.; Rabtsun, S.; Radulescu, L.; Raha, S.; Rami, F.; Raniwala, R.; Raniwala, S.; Raportirenko, A.; Rautenberg, J.; Rauza, J.; Ray, R.; Razin, S.; Reichelt, P.; Reinecke, S.; Reinefeld, A.; Reshetin, A.; Ristea, C.; Ristea, O.; Rodriguez Rodriguez, A.; Roether, F.; Romaniuk, R.; Rost, A.; Rostchin, E.; Rostovtseva, I.; Roy, Amitava; Roy, Ankhi; Rożynek, J.; Ryabov, Yu.; Sadovsky, A.; Sahoo, R.; Sahu, P. K.; Sahu, S. K.; Saini, J.; Samanta, S.; Sambyal, S. S.; Samsonov, V.; Sánchez Rosado, J.; Sander, O.; Sarangi, S.; Satława, T.; Sau, S.; Saveliev, V.; Schatral, S.; Schiaua, C.; Schintke, F.; Schmidt, C. J.; Schmidt, H. R.; Schmidt, K.; Scholten, J.; Schweda, K.; Seck, F.; Seddiki, S.; Selyuzhenkov, I.; Semennikov, A.; Senger, A.; Senger, P.; Shabanov, A.; Shabunov, A.; Shao, Ming; Sheremetiev, A. D.; Shi, Shusu; Shumeiko, N.; Shumikhin, V.; Sibiryak, I.; Sikora, B.; Simakov, A.; Simon, C.; Simons, C.; Singaraju, R. N.; Singh, A. K.; Singh, B. K.; Singh, C. P.; Singhal, V.; Singla, M.; Sitzmann, P.; Siwek-Wilczyńska, K.; Škoda, L.; Skwira-Chalot, I.; Som, I.; Song, Guofeng; Song, Jihye; Sosin, Z.; Soyk, D.; Staszel, P.; Strikhanov, M.; Strohauer, S.; Stroth, J.; Sturm, C.; Sultanov, R.; Sun, Yongjie; Svirida, D.; Svoboda, O.; Szabó, A.; Szczygieł, R.; Talukdar, R.; Tang, Zebo; Tanha, M.; Tarasiuk, J.; Tarassenkova, O.; Târzilă, M.-G.; Teklishyn, M.; Tischler, T.; Tlustý, P.; Tölyhi, T.; Toia, A.; Topil'skaya, N.; Träger, M.; Tripathy, S.; Tsakov, I.; Tsyupa, Yu.; Turowiecki, A.; Tuturas, N. G.; Uhlig, F.; Usenko, E.; Valin, I.; Varga, D.; Vassiliev, I.; Vasylyev, O.; Verbitskaya, E.; Verhoeven, W.; Veshikov, A.; Visinka, R.; Viyogi, Y. P.; Volkov, S.; Volochniuk, A.; Vorobiev, A.; Voronin, Aleksey; Voronin, Alexander; Vovchenko, V.; Vznuzdaev, M.; Wang, Dong; Wang, Xi-Wei; Wang, Yaping; Wang, Yi; Weber, M.; Wendisch, C.; Wessels, J. P.; Wiebusch, M.; Wiechula, J.; Wielanek, D.; Wieloch, A.; Wilms, A.; Winckler, N.; Winter, M.; Wiśniewski, K.; Wolf, Gy.; Won, Sanguk; Wu, Ke-Jun; Wüstenfeld, J.; Xiang, Changzhou; Xu, Nu; Yang, Junfeng; Yang, Rongxing; Yin, Zhongbao; Yoo, In-Kwon; Yuldashev, B.; Yushmanov, I.; Zabołotny, W.; Zaitsev, Yu.; Zamiatin, N. I.; Zanevsky, Yu.; Zhalov, M.; Zhang, Yifei; Zhang, Yu; Zhao, Lei; Zheng, Jiajun; Zheng, Sheng; Zhou, Daicui; Zhou, Jing; Zhu, Xianglei; Zinchenko, A.; Zipper, W.; Żoładź, M.; Zrelov, P.; Zryuev, V.; Zumbruch, P.; Zyzak, M.

2017-03-01

Substantial experimental and theoretical efforts worldwide are devoted to explore the phase diagram of strongly interacting matter. At LHC and top RHIC energies, QCD matter is studied at very high temperatures and nearly vanishing net-baryon densities. There is evidence that a Quark-Gluon-Plasma (QGP) was created at experiments at RHIC and LHC. The transition from the QGP back to the hadron gas is found to be a smooth cross over. For larger net-baryon densities and lower temperatures, it is expected that the QCD phase diagram exhibits a rich structure, such as a first-order phase transition between hadronic and partonic matter which terminates in a critical point, or exotic phases like quarkyonic matter. The discovery of these landmarks would be a breakthrough in our understanding of the strong interaction and is therefore in the focus of various high-energy heavy-ion research programs. The Compressed Baryonic Matter (CBM) experiment at FAIR will play a unique role in the exploration of the QCD phase diagram in the region of high net-baryon densities, because it is designed to run at unprecedented interaction rates. High-rate operation is the key prerequisite for high-precision measurements of multi-differential observables and of rare diagnostic probes which are sensitive to the dense phase of the nuclear fireball. The goal of the CBM experiment at SIS100 (√{s_{NN}}= 2.7-4.9 GeV) is to discover fundamental properties of QCD matter: the phase structure at large baryon-chemical potentials ( μ_B > 500 MeV), effects of chiral symmetry, and the equation of state at high density as it is expected to occur in the core of neutron stars. In this article, we review the motivation for and the physics programme of CBM, including activities before the start of data taking in 2024, in the context of the worldwide efforts to explore high-density QCD matter.

NetProt: Complex-based Feature Selection.

PubMed

Goh, Wilson Wen Bin; Wong, Limsoon

2017-08-04

Protein complex-based feature selection (PCBFS) provides unparalleled reproducibility with high phenotypic relevance on proteomics data. Currently, there are five PCBFS paradigms, but not all representative methods have been implemented or made readily available. To allow general users to take advantage of these methods, we developed the R-package NetProt, which provides implementations of representative feature-selection methods. NetProt also provides methods for generating simulated differential data and generating pseudocomplexes for complex-based performance benchmarking. The NetProt open source R package is available for download from https://github.com/gohwils/NetProt/releases/ , and online documentation is available at http://rpubs.com/gohwils/204259 .

Characterizing the Pyrenophora teres f. maculata–Barley Interaction Using Pathogen Genetics

PubMed Central

Carlsen, Steven A.; Neupane, Anjan; Wyatt, Nathan A.; Richards, Jonathan K.; Faris, Justin D.; Xu, Steven S.; Brueggeman, Robert S.; Friesen, Timothy L.

2017-01-01

Pyrenophora teres f. maculata is the cause of the foliar disease spot form net blotch (SFNB) on barley. To evaluate pathogen genetics underlying the P. teres f. maculata–barley interaction, we developed a 105-progeny population by crossing two globally diverse isolates, one from North Dakota and the other from Western Australia. Progeny were phenotyped on a set of four barley genotypes showing a differential reaction to the parental isolates, then genotyped using a restriction site-associated-genotype-by-sequencing (RAD-GBS) approach. Genetic maps were developed for use in quantitative trait locus (QTL) analysis to identify virulence-associated QTL. Six QTL were identified on five different linkage groups and individually accounted for 20–37% of the disease variation, with the number of significant QTL ranging from two to four for the barley genotypes evaluated. The data presented demonstrate the complexity of virulence involved in the P. teres f. maculata–barley pathosystem and begins to lay the foundation for understanding this important interaction. PMID:28659291

Regulated Norepinephrine Transporter Interaction with the Neurokinin-1 Receptor Establishes Transporter Subcellular Localization*

PubMed Central

Arapulisamy, Obulakshmi; Mannangatti, Padmanabhan; Jayanthi, Lankupalle D.

2013-01-01

Neurokinin-1 receptor (NK1R) mediates down-regulation of human norepinephrine (NE) transporter (hNET) via protein kinase C (PKC). However, native NET regulation by NK1R and the mechanism by which NK1R targets NET among other potential effectors are unknown. Effect of NK1R activation on native NET regulation and NET/NK1R interaction were studied using rat brain synaptosomes expressing native NET and NK1R as well as human placental trophoblast (HTR) cells coexpressing WT-hNET or NK1R/PKC-resistant hNET-T258A,S259A double mutant (NET-DM) and hNK1R. The selective NK1R agonist, GR73632, and Substance-P (SP) inhibited NE transport and reduced plasma membrane expression of NET and NK1R. Pretreatment with the NK1R antagonist, EMEND (aprepitant) prevented these NK1R-mediated effects. Immunoprecipitation experiments showed that NET forms stable complexes with NK1R. In HTR cells, combined biotinylation and immunoprecipitation studies revealed plasma membrane localization of NET·NK1R complexes. Receptor activation resulted in the internalization of NET·NK1R complexes. Lipid raft and immunoprecipitation analyses revealed the presence of NET·NK1R complexes exclusively in non-raft membrane fractions under basal/unstimulated conditions. However, NK1R activation led to translocation of NET·NK1R complexes to raft-rich membrane fractions. Importantly, PKCα was found in association with raft-localized NET following SP treatment. Similar to WT-NET, PKC-resistant NET-DM was found in association with NK1R exclusively in non-raft fractions. However, SP treatment failed to translocate NET-DM·NK1R complexes from non-raft fractions to raft fractions. Collectively, these results suggest that NK1R forms physical complexes with NET and that the receptor-mediated Thr258 + Ser259 motif-dependent translocation of NET·NK1R complexes into raft-rich microdomains facilitates NET/NK1R interaction with PKCα to coordinate spatially restricted NET regulation. PMID:23979140

Regulated norepinephrine transporter interaction with the neurokinin-1 receptor establishes transporter subcellular localization.

PubMed

Arapulisamy, Obulakshmi; Mannangatti, Padmanabhan; Jayanthi, Lankupalle D

2013-10-04

Neurokinin-1 receptor (NK1R) mediates down-regulation of human norepinephrine (NE) transporter (hNET) via protein kinase C (PKC). However, native NET regulation by NK1R and the mechanism by which NK1R targets NET among other potential effectors are unknown. Effect of NK1R activation on native NET regulation and NET/NK1R interaction were studied using rat brain synaptosomes expressing native NET and NK1R as well as human placental trophoblast (HTR) cells coexpressing WT-hNET or NK1R/PKC-resistant hNET-T258A,S259A double mutant (NET-DM) and hNK1R. The selective NK1R agonist, GR73632, and Substance-P (SP) inhibited NE transport and reduced plasma membrane expression of NET and NK1R. Pretreatment with the NK1R antagonist, EMEND (aprepitant) prevented these NK1R-mediated effects. Immunoprecipitation experiments showed that NET forms stable complexes with NK1R. In HTR cells, combined biotinylation and immunoprecipitation studies revealed plasma membrane localization of NET·NK1R complexes. Receptor activation resulted in the internalization of NET·NK1R complexes. Lipid raft and immunoprecipitation analyses revealed the presence of NET·NK1R complexes exclusively in non-raft membrane fractions under basal/unstimulated conditions. However, NK1R activation led to translocation of NET·NK1R complexes to raft-rich membrane fractions. Importantly, PKCα was found in association with raft-localized NET following SP treatment. Similar to WT-NET, PKC-resistant NET-DM was found in association with NK1R exclusively in non-raft fractions. However, SP treatment failed to translocate NET-DM·NK1R complexes from non-raft fractions to raft fractions. Collectively, these results suggest that NK1R forms physical complexes with NET and that the receptor-mediated Thr(258) + Ser(259) motif-dependent translocation of NET·NK1R complexes into raft-rich microdomains facilitates NET/NK1R interaction with PKCα to coordinate spatially restricted NET regulation.

Norepinephrine transporter: a candidate gene for initial ethanol sensitivity in inbred long-sleep and short-sleep mice.

PubMed

Haughey, Heather M; Kaiser, Alan L; Johnson, Thomas E; Bennett, Beth; Sikela, James M; Zahniser, Nancy R

2005-10-01

Altered noradrenergic neurotransmission is associated with depression and may contribute to drug abuse and alcoholism. Differential initial sensitivity to ethanol is an important predictor of risk for future alcoholism, making the inbred long-sleep (ILS) and inbred short-sleep (ISS) mice a useful model for identifying genes that may contribute to alcoholism. In this study, molecular biological, neurochemical, and behavioral approaches were used to test the hypothesis that the norepinephrine transporter (NET) contributes to the differences in ethanol-induced loss of righting reflex (LORR) in ILS and ISS mice. We used these mice to investigate the NET as a candidate gene contributing to this phenotype. The ILS and ISS mice carry different DNA haplotypes for NET, showing eight silent differences between allelic coding regions. Only the ILS haplotype is found in other mouse strains thus far sequenced. Brain regional analyses revealed that ILS mice have 30 to 50% lower [3H]NE uptake, NET binding, and NET mRNA levels than ISS mice. Maximal [3H]NE uptake and NET number were reduced, with no change in affinity, in the ILS mice. These neurobiological changes were associated with significant influences on the behavioral phenotype of these mice, as demonstrated by (1) a differential response in the duration of ethanol-induced LORR in ILS and ISS mice pretreated with a NET inhibitor and (2) increased ethanol-induced LORR in LXS recombinant inbred (RI) strains, homozygous for ILS in the NET chromosomal region (44-47 cM), compared with ISS homozygous strains. This is the first report to suggest that the NET gene is one of many possible genetic factors influencing ethanol sensitivity in ILS, ISS, and LXS RI mouse strains.

Learning Petri net models of non-linear gene interactions.

PubMed

Mayo, Michael

2005-10-01

Understanding how an individual's genetic make-up influences their risk of disease is a problem of paramount importance. Although machine-learning techniques are able to uncover the relationships between genotype and disease, the problem of automatically building the best biochemical model or "explanation" of the relationship has received less attention. In this paper, I describe a method based on random hill climbing that automatically builds Petri net models of non-linear (or multi-factorial) disease-causing gene-gene interactions. Petri nets are a suitable formalism for this problem, because they are used to model concurrent, dynamic processes analogous to biochemical reaction networks. I show that this method is routinely able to identify perfect Petri net models for three disease-causing gene-gene interactions recently reported in the literature.

VirHostNet 2.0: surfing on the web of virus/host molecular interactions data.

PubMed

Guirimand, Thibaut; Delmotte, Stéphane; Navratil, Vincent

2015-01-01

VirHostNet release 2.0 (http://virhostnet.prabi.fr) is a knowledgebase dedicated to the network-based exploration of virus-host protein-protein interactions. Since the previous VirhostNet release (2009), a second run of manual curation was performed to annotate the new torrent of high-throughput protein-protein interactions data from the literature. This resource is shared publicly, in PSI-MI TAB 2.5 format, using a PSICQUIC web service. The new interface of VirHostNet 2.0 is based on Cytoscape web library and provides a user-friendly access to the most complete and accurate resource of virus-virus and virus-host protein-protein interactions as well as their projection onto their corresponding host cell protein interaction networks. We hope that the VirHostNet 2.0 system will facilitate systems biology and gene-centered analysis of infectious diseases and will help to identify new molecular targets for antiviral drugs design. This resource will also continue to help worldwide scientists to improve our knowledge on molecular mechanisms involved in the antiviral response mediated by the cell and in the viral strategies selected by viruses to hijack the host immune system. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.

PubMed

Levy, Roie; Carr, Rogan; Kreimer, Anat; Freilich, Shiri; Borenstein, Elhanan

2015-05-17

Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, several studies have demonstrated how such interactions are reflected in the organization of the metabolic networks of the interacting species, and introduced various graph theory-based methods to predict host-microbe and microbe-microbe interactions directly from network topology. Using these methods, such studies have revealed evolutionary and ecological processes that shape species interactions and community assembly, highlighting the potential of this reverse-ecology research paradigm. NetCooperate is a web-based tool and a software package for determining host-microbe and microbe-microbe cooperative potential. It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms' niches. NetCooperate takes as input a pair of metabolic networks, and returns the pairwise metrics as well as a list of potential syntrophic metabolic compounds. The Biosynthetic Support Score and Metabolic Complementarity Index provide insight into host-microbe and microbe-microbe metabolic interactions. NetCooperate determines these interaction indices from metabolic network topology, and can be used for small- or large-scale analyses. NetCooperate is provided as both a web-based tool and an open-source Python module; both are freely available online at http://elbo.gs.washington.edu/software_netcooperate.html.

Pasireotide in the treatment of neuroendocrine tumors: a review of the literature.

PubMed

Vitale, Giovanni; Dicitore, Alessandra; Sciammarella, Concetta; Di Molfetta, Sergio; Rubino, Manila; Faggiano, Antongiulio; Colao, Annamaria

2018-06-01

Somatostatin analogs have an important role in the medical therapy of neuroendocrine tumors (NETs). Octreotide and lanreotide, both somatostatin analogs binding with high affinity for the somatostatin receptor (SSTR)2, can control symptoms in functional NETs. In addition, these compounds, because of their antiproliferative effects, can stabilize growth of well-differentiated NETs. Pasireotide is a novel multireceptor-targeted somatostatin analog with high affinity for SSTR1, 2, 3, and 5. This review provides an overview of the state of the art of pasireotide in the treatment of NETs, with the aim of addressing clinical relevance and future perspectives for this molecule in the management of NETs. © 2018 Society for Endocrinology.

Proto-experiences and subjective experiences: classical and quantum concepts.

PubMed

Vimal, Ram Lakhan Pandey

2008-03-01

Deterministic reductive monism and non-reductive substance dualism are two opposite views for consciousness, and both have serious problems. An alternative view is needed. For this, we hypothesize that strings or elementary particles (fermions and bosons) have two aspects: (i) elemental proto-experiences (PEs) as phenomenal aspect, and (ii) mass, charge, and spin as material aspect. Elemental PEs are hypothesized to be the properties of elementary particles and their interactions, which are composed of irreducible fundamental subjective experiences (SEs)/PEs that are in superimposed form in elementary particles and in their interactions. Since SEs/PEs are superimposed, elementary particles are not specific to any SE/PE; they (and all inert matter) are carriers of SEs/PEs, and hence, appear as non-experiential material entities. Furthermore, our hypothesis is that matter and associated elemental PEs co-evolved and co-developed into neural-nets and associated neural-net PEs (neural Darminism), respectively. The signals related to neural PEs interact in a neural-net and neural-net PEs emerges from random process of self-organization. The neural-net PEs are a set of SEs embedded in the neural-net by a non-computational or non-algorithmic process. The non-specificity of elementary particles is transformed into the specificity of neural-nets by neural Darwinism. The specificity of SEs emerges when feedforward and feedback signal interacts in the neuropil and are dependent on wakefulness (i.e., activation) attention, re-entry between neural populations, working memory, stimulus at above threshold, and neural net PE signals. This PE-SE framework integrates reductive and non-reductive views, complements the existing models, bridges the explanatory gaps, and minimizes the problem of causation.

The degree of mutual anisotropy of biological liquids polycrystalline nets as a parameter in diagnostics and differentiations of hominal inflammatory processes

NASA Astrophysics Data System (ADS)

Angelsky, O. V.; Ushenko, Yu. A.; Balanetska, V. O.

2011-09-01

To characterize the degree of consistency of parameters of the optically uniaxial birefringent protein nets of blood plasma a new parameter - complex degree of mutual anisotropy is suggested. The technique of polarization measuring the coordinate distributions of the complex degree of mutual anisotropy of blood plasma is developed. It is shown that statistic approach to the analysis of the complex degree of mutual anisotropy distributions of blood plasma is effective during the diagnostics and differentiation of an acute inflammatory processes as well as acute and gangrenous appendicitis.

NETWORKED 3B: a novel protein in the actin cytoskeleton-endoplasmic reticulum interaction.

PubMed

Wang, Pengwei; Hussey, Patrick J

2017-03-01

In plants movement of the endoplasmic reticulum (ER) is dependent on the actin cytoskeleton. However little is known about proteins that link the ER membrane and the actin cytoskeleton. Here we identified a novel protein, NETWORKED 3B (NET3B), which is associated with the ER and actin cytoskeleton in vivo. NET3B belongs to a superfamily of plant specific actin binding proteins, the NETWORKED family. NET3B associates with the actin cytoskeleton in vivo through an N-terminal NET actin binding (NAB) domain, which has been well-characterized in other members of the NET family. A three amino acid insertion, Val-Glu-Asp, in the NAB domain of NET3B appears to lower its ability to localize to the actin cytoskeleton compared with NET1A, the founding member of the NET family. The C-terminal domain of NET3B links the protein to the ER. Overexpression of NET3B enhanced the association between the ER and the actin cytoskeleton, and the extent of this association was dependent on the amount of NET3B available. Another effect of NET3B overexpression was a reduction in ER membrane diffusion. In conclusion, our results revealed that NET3B modulates ER and actin cytoskeleton interactions in higher plants. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Prediction and functional analysis of the sweet orange protein-protein interaction network.

PubMed

Ding, Yu-Duan; Chang, Ji-Wei; Guo, Jing; Chen, Dijun; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Cheng, Yun-Jiang; Chen, Ling-Ling

2014-08-05

Sweet orange (Citrus sinensis) is one of the most important fruits world-wide. Because it is a woody plant with a long growth cycle, genetic studies of sweet orange are lagging behind those of other species. In this analysis, we employed ortholog identification and domain combination methods to predict the protein-protein interaction (PPI) network for sweet orange. The K-nearest neighbors (KNN) classification method was used to verify and filter the network. The final predicted PPI network, CitrusNet, contained 8,195 proteins with 124,491 interactions. The quality of CitrusNet was evaluated using gene ontology (GO) and Mapman annotations, which confirmed the reliability of the network. In addition, we calculated the expression difference of interacting genes (EDI) in CitrusNet using RNA-seq data from four sweet orange tissues, and also analyzed the EDI distribution and variation in different sub-networks. Gene expression in CitrusNet has significant modular features. Target of rapamycin (TOR) protein served as the central node of the hormone-signaling sub-network. All evidence supported the idea that TOR can integrate various hormone signals and affect plant growth. CitrusNet provides valuable resources for the study of biological functions in sweet orange.

Rewiring of the inferred protein interactome during blood development studied with the tool PPICompare.

PubMed

Will, Thorsten; Helms, Volkhard

2017-04-04

Differential analysis of cellular conditions is a key approach towards understanding the consequences and driving causes behind biological processes such as developmental transitions or diseases. The progress of whole-genome expression profiling enabled to conveniently capture the state of a cell's transcriptome and to detect the characteristic features that distinguish cells in specific conditions. In contrast, mapping the physical protein interactome for many samples is experimentally infeasible at the moment. For the understanding of the whole system, however, it is equally important how the interactions of proteins are rewired between cellular states. To overcome this deficiency, we recently showed how condition-specific protein interaction networks that even consider alternative splicing can be inferred from transcript expression data. Here, we present the differential network analysis tool PPICompare that was specifically designed for isoform-sensitive protein interaction networks. Besides detecting significant rewiring events between the interactomes of grouped samples, PPICompare infers which alterations to the transcriptome caused each rewiring event and what is the minimal set of alterations necessary to explain all between-group changes. When applied to the development of blood cells, we verified that a reasonable amount of rewiring events were reported by the tool and found that differential gene expression was the major determinant of cellular adjustments to the interactome. Alternative splicing events were consistently necessary in each developmental step to explain all significant alterations and were especially important for rewiring in the context of transcriptional control. Applying PPICompare enabled us to investigate the dynamics of the human protein interactome during developmental transitions. A platform-independent implementation of the tool PPICompare is available at https://sourceforge.net/projects/ppicompare/ .

Differential influences of local subpopulations on regional diversity and differentiation for greater sage-grouse (Centrocercus urophasianus)

USGS Publications Warehouse

Row, Jeffery R.; Oyler-McCance, Sara J.; Fedy, Brad C.

2016-01-01

The distribution of spatial genetic variation across a region can shape evolutionary dynamics and impact population persistence. Local population dynamics and among-population dispersal rates are strong drivers of this spatial genetic variation, yet for many species we lack a clear understanding of how these population processes interact in space to shape within-species genetic variation. Here, we used extensive genetic and demographic data from 10 subpopulations of greater sage-grouse to parameterize a simulated approximate Bayesian computation (ABC) model and (i) test for regional differences in population density and dispersal rates for greater sage-grouse subpopulations in Wyoming, and (ii) quantify how these differences impact subpopulation regional influence on genetic variation. We found a close match between observed and simulated data under our parameterized model and strong variation in density and dispersal rates across Wyoming. Sensitivity analyses suggested that changes in dispersal (via landscape resistance) had a greater influence on regional differentiation, whereas changes in density had a greater influence on mean diversity across all subpopulations. Local subpopulations, however, varied in their regional influence on genetic variation. Decreases in the size and dispersal rates of central populations with low overall and net immigration (i.e. population sources) had the greatest negative impact on genetic variation. Overall, our results provide insight into the interactions among demography, dispersal and genetic variation and highlight the potential of ABC to disentangle the complexity of regional population dynamics and project the genetic impact of changing conditions.

Small cell and large cell neuroendocrine carcinomas of the pancreas are genetically similar and distinct from well-differentiated pancreatic neuroendocrine tumors.

PubMed

Yachida, Shinichi; Vakiani, Efsevia; White, Catherine M; Zhong, Yi; Saunders, Tyler; Morgan, Richard; de Wilde, Roeland F; Maitra, Anirban; Hicks, Jessica; Demarzo, Angelo M; Shi, Chanjuan; Sharma, Rajni; Laheru, Daniel; Edil, Barish H; Wolfgang, Christopher L; Schulick, Richard D; Hruban, Ralph H; Tang, Laura H; Klimstra, David S; Iacobuzio-Donahue, Christine A

2012-02-01

Poorly differentiated neuroendocrine carcinomas (NECs) of the pancreas are rare malignant neoplasms with a poor prognosis. The aim of this study was to determine the clinicopathologic and genetic features of poorly differentiated NECs and compare them with other types of pancreatic neoplasms. We investigated alterations of KRAS, CDKN2A/p16, TP53, SMAD4/DPC4, DAXX, ATRX, PTEN, Bcl2, and RB1 by immunohistochemistry and/or targeted exomic sequencing in surgically resected specimens of 9 small cell NECs, 10 large cell NECs, and 11 well-differentiated neuroendocrine tumors (PanNETs) of the pancreas. Abnormal immunolabeling patterns of p53 and Rb were frequent (p53, 18 of 19, 95%; Rb, 14 of 19, 74%) in both small cell and large cell NECs, whereas Smad4/Dpc4, DAXX, and ATRX labeling was intact in virtually all of these same carcinomas. Abnormal immunolabeling of p53 and Rb proteins correlated with intragenic mutations in the TP53 and RB1 genes. In contrast, DAXX and ATRX labeling was lost in 45% of PanNETs, whereas p53 and Rb immunolabeling was intact in these same cases. Overexpression of Bcl-2 protein was observed in all 9 small cell NECs (100%) and in 5 of 10 (50%) large cell NECs compared with only 2 of 11 (18%) PanNETs. Bcl-2 overexpression was significantly correlated with higher mitotic rate and Ki67 labeling index in neoplasms in which it was present. Small cell NECs are genetically similar to large cell NECs, and these genetic changes are distinct from those reported in PanNETs. The finding of Bcl-2 overexpression in poorly differentiated NECs, particularly small cell NEC, suggests that Bcl-2 antagonists/inhibitors may be a viable treatment option for these patients.

A Population-Based Analysis of Application of WHO Nomenclature in Pathology Reports of Pulmonary Neuroendocrine Tumors.

PubMed

Derks, Jules L; van Suylen, Robert Jan; Thunnissen, Erik; den Bakker, Michael A; Smit, Egbert F; Groen, Harry J M; Speel, Ernst J M; Dingemans, Anne-Marie C

2016-04-01

Pulmonary neuroendocrine tumors (pNETs) are difficult to classify. We performed a population-based analysis to investigate the application of pNET nomenclature in daily pathology practice. Conclusions from pathology reports (2003-2012) describing carcinoids, (large cell) neuroendocrine carcinomas (NECs), and carcinomas with neuroendocrine features/differentiation were retrieved from the Dutch Pathology Registry by queries on location and diagnosis and screened for terminology. Cases with a nonpulmonary or unknown origin and small cell lung cancer were excluded. Diagnoses were clustered into subgroups and the retrieved terminology was compared with the 2015 World Health Organization (WHO) diagnoses. By means of an online questionnaire, interpretation of the non-WHO nomenclature retrieved from pathology reports was evaluated (by 35 physicians and 19 pathologists). A total of 3216 unique pathology report conclusions with 55 different pNET diagnoses (n = 3052) and 20 uncertain diagnoses (n = 164) were analyzed. Non-WHO nomenclature was used in 15% of diagnoses (n = 488). Diagnoses could be clustered into carcinoids (n = 1086), NEC (n = 1316), carcinomas with neuroendocrine features/differentiation (n = 624), and unspecified pNETs (n = 26). Non-WHO nomenclature within these clusters was found for 7% of carcinoids, 20% of NECs, 13% of carcinomas with neuroendocrine features/differentiation, and 100% of unspecified pNETs and was observed more often in conclusions regarding biopsy or cytological specimens (62% and 12%) compared with resection specimens (26%). Analysis of the questionnaire results revealed that 4 of 19 diagnoses based on non-WHO nomenclature were uniformly interpreted (>50% agreement) by physicians, as were 10 of 19 diagnoses by pathologists. In 15% of pNETs other than small cell lung cancer, a non-WHO nomenclature diagnosis was provided, more frequently on the basis of smaller specimens. The interpretation was different between physicians and pathologists. Application of uniform nomenclature among all clinicians is advocated. Copyright © 2016 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Identification of Phosphohistone H3 Cutoff Values Corresponding to Original WHO Grades but Distinguishable in Well-Differentiated Gastrointestinal Neuroendocrine Tumors.

PubMed

Kim, Min Jeong; Kwon, Mi Jung; Kang, Ho Suk; Choi, Kyung Chan; Nam, Eun Sook; Cho, Seong Jin; Park, Hye-Rim; Min, Soo Kee; Seo, Jinwon; Choe, Ji-Young; Park, Hyoung-Chul

2018-01-01

Mitotic counts in the World Health Organization (WHO) grading system have narrow cutoff values. True mitotic figures, however, are not always distinguishable from apoptotic bodies and darkly stained nuclei, complicating the ability of the WHO grading system to diagnose well-differentiated neuroendocrine tumors (NETs). The mitosis-specific marker phosphohistone H3 (PHH3) can identify true mitoses and grade tumors reliably. The aim of this study was to investigate the correspondence of tumor grades, as determined by PHH3 mitotic index (MI) and mitotic counts according to WHO criteria, and to determine the clinically relevant cutoffs of PHH3 MI in rectal and nonrectal gastrointestinal NETs. Mitotic counts correlated with both the Ki-67 labeling index and PHH3 MI, but the correlation with PHH3 MI was slightly higher. The PHH3 MI cutoff ≥4 correlated most closely with original WHO grades for both rectal NETs. A PHH3 MI cutoff ≥4, which could distinguish between G1 and G2 tumors, was associated with disease-free survival in patients with rectal NETs, whereas that cutoff value showed marginal significance for overall survival in patient with rectal NETs. In conclusion, the use of PHH3 ≥4 correlated most closely with original WHO grades.

Identification of Phosphohistone H3 Cutoff Values Corresponding to Original WHO Grades but Distinguishable in Well-Differentiated Gastrointestinal Neuroendocrine Tumors

PubMed Central

Kim, Min Jeong; Kang, Ho Suk; Choi, Kyung Chan; Nam, Eun Sook; Cho, Seong Jin; Park, Hye-Rim; Seo, Jinwon; Choe, Ji-Young

2018-01-01

Mitotic counts in the World Health Organization (WHO) grading system have narrow cutoff values. True mitotic figures, however, are not always distinguishable from apoptotic bodies and darkly stained nuclei, complicating the ability of the WHO grading system to diagnose well-differentiated neuroendocrine tumors (NETs). The mitosis-specific marker phosphohistone H3 (PHH3) can identify true mitoses and grade tumors reliably. The aim of this study was to investigate the correspondence of tumor grades, as determined by PHH3 mitotic index (MI) and mitotic counts according to WHO criteria, and to determine the clinically relevant cutoffs of PHH3 MI in rectal and nonrectal gastrointestinal NETs. Mitotic counts correlated with both the Ki-67 labeling index and PHH3 MI, but the correlation with PHH3 MI was slightly higher. The PHH3 MI cutoff ≥4 correlated most closely with original WHO grades for both rectal NETs. A PHH3 MI cutoff ≥4, which could distinguish between G1 and G2 tumors, was associated with disease-free survival in patients with rectal NETs, whereas that cutoff value showed marginal significance for overall survival in patient with rectal NETs. In conclusion, the use of PHH3 ≥4 correlated most closely with original WHO grades. PMID:29780816

Whole-Body 68Ga-DOTANOC PET/MRI Versus 68Ga-DOTANOC PET/CT in Patients With Neuroendocrine Tumors

PubMed Central

Berzaczy, Dominik; Giraudo, Chiara; Haug, Alexander R.; Raderer, Markus; Senn, Daniela; Karanikas, Georgios; Weber, Michael; Mayerhoefer, Marius E.

2017-01-01

Purpose The aim of this study was to assess the diagnostic performance of simultaneous whole-body 68Ga-DOTANOC PET/MRI compared with 68Ga-DOTANOC PET/CT for detection of distant metastatic disease in patients with well-differentiated neuroendocrine tumors (NETs). Methods Patients with histologically proven, well-differentiated NET (G1 or G2) were included in this prospective, institutional review board–approved study. Patients underwent 68Ga-DOTANOC PET/CT and subsequent 68Ga-DOTANOC PET/MRI after a single tracer injection on the same day for staging or restaging purposes. Images were evaluated for the presence of NET lesions by 2 rater teams, each consisting of a nuclear medicine physician and a radiologist, in an observer-blinded fashion. Overall agreement, accuracy, sensitivity, and specificity, relative to a composite reference standard (consensus review including follow-up data), were calculated. Results Between July 2014 and June 2016, 28 patients were enrolled. Overall agreement and accuracy between the 2 rater teams were 91.7% (95% confidence interval [CI], 87.5%–95.9%) and 97% (95% CI, 94.4%–99.6%) for PET/MRI and 92.3% (95% CI, 88.3%–96.3%) and 94.6% (95% CI, 91.2%–98.1%) for PET/CT, respectively (P = 1.00). Overall, PET/MRI reached 89.8% sensitivity (95% CI, 77.8%–96.6%) and 100% specificity (95% CI, 97%–100%); PET/CT showed 81.6% sensitivity (95% CI, 68%–91.2%) and 100% specificity (95% CI, 97%–100%) for the detection of metastatic disease in NETs. Conclusions Whole-body 68Ga-DOTANOC PET/MRI appears to be comparable to 68Ga-DOTANOC PET/CT for lesion detection in patients with well-differentiated NETs. PMID:28682844

Differentiating Obstructive from Central and Complex Sleep Apnea Using an Automated Electrocardiogram-Based Method

PubMed Central

Thomas, Robert Joseph; Mietus, Joseph E.; Peng, Chung-Kang; Gilmartin, Geoffrey; Daly, Robert W.; Goldberger, Ary L.; Gottlieb, Daniel J.

2007-01-01

Study Objectives: Complex sleep apnea is defined as sleep disordered breathing secondary to simultaneous upper airway obstruction and respiratory control dysfunction. The objective of this study was to assess the utility of an electrocardiogram (ECG)-based cardiopulmonary coupling technique to distinguish obstructive from central or complex sleep apnea. Design: Analysis of archived polysomnographic datasets. Setting: A laboratory for computational signal analysis. Interventions: None. Measurements and Results: The PhysioNet Sleep Apnea Database, consisting of 70 polysomnograms including single-lead ECG signals of approximately 8 hours duration, was used to train an ECG-based measure of autonomic and respiratory interactions (cardiopulmonary coupling) to detect periods of apnea and hypopnea, based on the presence of elevated low-frequency coupling (e-LFC). In the PhysioNet BIDMC Congestive Heart Failure Database (ECGs of 15 subjects), a pattern of “narrow spectral band” e-LFC was especially common. The algorithm was then applied to the Sleep Heart Health Study–I dataset, to select the 15 records with the highest amounts of broad and narrow spectral band e-LFC. The latter spectral characteristic seemed to detect not only periods of central apnea, but also obstructive hypopneas with a periodic breathing pattern. Applying the algorithm to 77 sleep laboratory split-night studies showed that the presence of narrow band e-LFC predicted an increased sensitivity to induction of central apneas by positive airway pressure. Conclusions: ECG-based spectral analysis allows automated, operator-independent characterization of probable interactions between respiratory dyscontrol and upper airway anatomical obstruction. The clinical utility of spectrographic phenotyping, especially in predicting failure of positive airway pressure therapy, remains to be more thoroughly tested. Citation: Thomas RJ; Mietus JE; Peng CK; Gilmartin G; Daly RW; Goldberger AL; Gottlieb DJ. Differentiating obstructive from central and complex sleep apnea using an automated electrocardiogram-based method. SLEEP 2007;30(12):1756-1769. PMID:18246985

Differences in gene expression profiles and signaling pathways in rhabdomyolysis-induced acute kidney injury

PubMed Central

Geng, Xiaodong; Wang, Yuanda; Hong, Quan; Yang, Jurong; Zheng, Wei; Zhang, Gang; Cai, Guangyan; Chen, Xiangmei; Wu, Di

2015-01-01

Purpose: Rhabdomyolysis is a threatening syndrome because it causes the breakdown of skeletal muscle. Muscle destruction leads to the release of myoglobin, intracellular proteins, and electrolytes into the circulation. The aim of this study was to investigate the differences in gene expression profiles and signaling pathways upon rhabdomyolysis-induced acute kidney injury (AKI). Methods: In this study, we used glycerol-induced renal injury as a model of rhabdomyolysis-induced AKI. We analyzed data and relevant information from the Gene Expression Omnibus database (No: GSE44925). The gene expression data for three untreated mice were compared to data for five mice with rhabdomyolysis-induced AKI. The expression profiling of the three untreated mice and the five rhabdomyolysis-induced AKI mice was performed using microarray analysis. We examined the levels of Cyp3a13, Rela, Aldh7a1, Jun, CD14. And Cdkn1a using RT-PCR to determine the accuracy of the microarray results. Results: The microarray analysis showed that there were 1050 downregulated and 659 upregulated genes in the rhabdomyolysis-induced AKI mice compared to the control group. The interactions of all differentially expressed genes in the Signal-Net were analyzed. Cyp3a13 and Rela had the most interactions with other genes. The data showed that Rela and Aldh7a1 were the key nodes and had important positions in the Signal-Net. The genes Jun, CD14, and Cdkn1a were also significantly upregulated. The pathway analysis classified the differentially expressed genes into 71 downregulated and 48 upregulated pathways including the PI3K/Akt, MAPK, and NF-κB signaling pathways. Conclusion: The results of this study indicate that the NF-κB, MAPK, PI3K/Akt, and apoptotic pathways are regulated in rhabdomyolysis-induced AKI. PMID:26823722

The Best of LM_Net Select, 2001.

ERIC Educational Resources Information Center

Milbury, Peter; Eisenberg, Michael B.; Walker, Michelle

LM_NET, the most successful educational listserv in the world has approximately 15,000 subscribed members from every state in the United States and from over 65 countries. LM_NET covers a wide range of interests, all related to library and information work in education, and interactions on LM_NET result in in-depth treatments of the major…

Dynamic modelling of microRNA regulation during mesenchymal stem cell differentiation.

PubMed

Weber, Michael; Sotoca, Ana M; Kupfer, Peter; Guthke, Reinhard; van Zoelen, Everardus J

2013-11-12

Network inference from gene expression data is a typical approach to reconstruct gene regulatory networks. During chondrogenic differentiation of human mesenchymal stem cells (hMSCs), a complex transcriptional network is active and regulates the temporal differentiation progress. As modulators of transcriptional regulation, microRNAs (miRNAs) play a critical role in stem cell differentiation. Integrated network inference aimes at determining interrelations between miRNAs and mRNAs on the basis of expression data as well as miRNA target predictions. We applied the NetGenerator tool in order to infer an integrated gene regulatory network. Time series experiments were performed to measure mRNA and miRNA abundances of TGF-beta1+BMP2 stimulated hMSCs. Network nodes were identified by analysing temporal expression changes, miRNA target gene predictions, time series correlation and literature knowledge. Network inference was performed using NetGenerator to reconstruct a dynamical regulatory model based on the measured data and prior knowledge. The resulting model is robust against noise and shows an optimal trade-off between fitting precision and inclusion of prior knowledge. It predicts the influence of miRNAs on the expression of chondrogenic marker genes and therefore proposes novel regulatory relations in differentiation control. By analysing the inferred network, we identified a previously unknown regulatory effect of miR-524-5p on the expression of the transcription factor SOX9 and the chondrogenic marker genes COL2A1, ACAN and COL10A1. Genome-wide exploration of miRNA-mRNA regulatory relationships is a reasonable approach to identify miRNAs which have so far not been associated with the investigated differentiation process. The NetGenerator tool is able to identify valid gene regulatory networks on the basis of miRNA and mRNA time series data.

Infrared video tracking of Anopheles gambiae at insecticide-treated bed nets reveals rapid decisive impact after brief localised net contact

PubMed Central

Parker, Josephine E.A.; Angarita-Jaimes, Natalia; Abe, Mayumi; Towers, Catherine E.; Towers, David; McCall, Philip J.

2015-01-01

Long-lasting insecticidal bed nets (LLINs) protect humans from malaria transmission and are fundamental to malaria control worldwide, but little is known of how mosquitoes interact with nets. Elucidating LLIN mode of action is essential to maintain or improve efficacy, an urgent need as emerging insecticide resistance threatens their future. Tracking multiple free-flying Anopheles gambiae responding to human-occupied bed nets in a novel large-scale system, we characterised key behaviours and events. Four behavioural modes with different levels of net contact were defined: swooping, visiting, bouncing and resting. Approximately 75% of all activity occurred at the bed net roof where multiple brief contacts were focussed above the occupant’s torso. Total flight and net contact times were lower at LLINs than untreated nets but the essential character of the response was unaltered. LLINs did not repel mosquitoes but impacted rapidly: LLIN contact of less than 1 minute per mosquito during the first ten minutes reduced subsequent activity; after thirty minutes, activity at LLINs was negligible. Velocity measurements showed that mosquitoes detected nets, including unbaited untreated nets, prior to contact. This is the most complete characterisation of mosquito-LLIN interactions to date, and reveals many aspects of LLIN mode of action, important for developing the next generation of LLINs. PMID:26323965

Identification of non-classical C-H···M interactions in early and late transition metal complexes containing the CH(ArO)3 ligand.

PubMed

Lein, Matthias; Harrison, John A; Nielson, Alastair J

2013-08-14

The fully optimised DFT structure of the d(0) complex [{CH(ArO)3}Ti(NEt2)] (2) at the B3LYP level compares well with the distorted tetrahedral geometry shown by the X-ray crystal structure. QTAIM analysis of the electron density associated with the C-H···Ti interaction shows a well defined bond critical point, a bond path between the hydrogen and titanium centres and a negative value for the energy density indicative of covalency. A natural bond orbital (NBO) picture of the interaction shows that the C-H σ bond electron density donates to a d hybrid orbital on the metal in a linear fashion. Calculated IR and NMR data for the components of the interaction are consistent with experiment. The computed structures for [{CH(ArO)3}Ti(OPh)] (3), [{CH(ArO)3}Zr(NEt2)] (4), [{CH(ArO)3}Hf(NEt2)] (5), show tetrahedral geometries and QTAIM and NBO properties similar to (2). [{CH(ArO)3}Mo(NEt2)] (6) shows distortion of the tripodal ligand and a reduced C-H···M bond angle with properties more consistent with a C-H···M side-on donor interaction. In [{CH(ArO)3}Fe(NEt2)] (7) the C-H···M bond angle is linear and involves a donor interaction. An energy minimised structure maintaining the three fold coordination to the tripodal ligand was not obtained for [{CH(ArO)3}Ni(NEt2)](2-) but changing from a diethyl amide ligand to phenolato gave energy minimised [{CH(ArO)3}Ni(OPh)](2-) (8). This structure shows a distorted square planar geometry with a substantially bent phenoxo ligand and a near linear C-H···M covalent interaction with donor and back bonding properties. The work shows that linear C-H···M interactions can have both agostic and weak hydrogen bond-like covalency.

77 FR 14347 - Proposed Information Collection; Comment Request; Reporting of Sea Turtle Incidental Take in...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-09

... interactions with endangered and threatened sea turtles, found both live and dead, in their pound net operations. When a live or dead sea turtle is discovered during a pound net trip, the Virginia pound net...

Ohio SchoolNet. Schools on the Move.

ERIC Educational Resources Information Center

Ohio State Dept. of Education, Columbus.

SchoolNet is a state-funded partnership that will facilitate the installation of computer and communications networking technology in public schools and classrooms across Ohio and coordinate its use. SchoolNet seeks to provide Ohio students with expanded course offerings; more individualized educational opportunities; interactive learning…

Differential Signalling and Kinetics of Neutrophil Extracellular Trap Release Revealed by Quantitative Live Imaging.

PubMed

van der Linden, Maarten; Westerlaken, Geertje H A; van der Vlist, Michiel; van Montfrans, Joris; Meyaard, Linde

2017-07-26

A wide variety of microbial and inflammatory factors induce DNA release from neutrophils as neutrophil extracellular traps (NETs). Consensus on the kinetics and mechanism of NET release has been hindered by the lack of distinctive methods to specifically quantify NET release in time. Here, we validate and refine a semi-automatic live imaging approach for quantification of NET release. Importantly, our approach is able to correct for neutrophil input and distinguishes NET release from neutrophil death by other means, aspects that are lacking in many NET quantification methods. Real time visualization shows that opsonized S. aureus rapidly induces cell death by toxins, while actual NET formation occurs after 90 minutes, similar to the kinetics of NET release by immune complexes and PMA. Inhibition of SYK, PI3K and mTORC2 attenuates NET release upon challenge with physiological stimuli but not with PMA. In contrast, neutrophils from chronic granulomatous disease patients show decreased NET release only in response to PMA. With this refined method, we conclude that NET release in primary human neutrophils is dependent on the SYK-PI3K-mTORC2 pathway and that PMA stimulation should be regarded as mechanistically distinct from NET formation induced by natural triggers.

O6-Methylguanine DNA Methyltransferase Status Does Not Predict Response or Resistance to Alkylating Agents in Well-Differentiated Pancreatic Neuroendocrine Tumors.

PubMed

Raj, Nitya; Klimstra, David S; Horvat, Natally; Zhang, Liying; Chou, Joanne F; Capanu, Marinela; Basturk, Olca; Do, Richard Kinh Gian; Allen, Peter J; Reidy-Lagunes, Diane

2017-07-01

Alkylating agents have activity in well-differentiated pancreatic neuroendocrine tumors (WD panNETs). In glioblastoma multiforme, decreased activity of O-methylguanine DNA methyltransferase (MGMT) predicts response; in panNETs, MGMT relevance is unknown. We identified patients with WD panNETs treated with alkylating agents, determined best overall response by Response Evaluation Criteria In Solid Tumors (RECIST) 1.1, and performed MGMT activity testing. Fifty-six patients were identified; 26 (46%) of the 56 patients experienced partial response, 24 (43%) of 56 experienced stable disease, and 6 (11%) of 56 experienced progression of disease. O-methylguanine DNA methyltransferase status was available for 36 tumors. For tumors with partial response, 10 (67%) of 15 were MGMT deficient, and 5 (33%) of 15 were MGMT intact. For tumors with stable disease, 7 (47%) of 15 were MGMT deficient, and 8 (53%) of 15 were MGMT intact. For tumors with progression of disease, 3 (50%) of 6 were MGMT deficient, and 3 (50%) of 6 were MGMT intact. We observed response and resistance to alkylating agents in MGMT-deficient and MGMT-intact tumors. O-methylguanine DNA methyltransferase status should not guide alkylating agent therapy in WD panNETs.

Development and use of the Cytoscape app GFD-Net for measuring semantic dissimilarity of gene networks

PubMed Central

Diaz-Montana, Juan J.; Diaz-Diaz, Norberto

2014-01-01

Gene networks are one of the main computational models used to study the interaction between different elements during biological processes being widely used to represent gene–gene, or protein–protein interaction complexes. We present GFD-Net, a Cytoscape app for visualizing and analyzing the functional dissimilarity of gene networks. PMID:25400907

The Female-Male Differential in Unemployment Rates

ERIC Educational Resources Information Center

Niemi, Beth

1974-01-01

The male-female differential in unemployment is attributed to three major factors. They are frictional unemployment, cyclical layoff often connected with lack of specific training, and occupational and geographic immobility. Women receive less specific training then men; however, the net effect of this lack on female unemployment is quite small.…

Blood circulation in the lower limbs

NASA Astrophysics Data System (ADS)

Pen'kovskiy, V. I.; Korsakova, N. K.

2018-03-01

Blood circulation process in inferior limbs is considered in the terms of the previously proposed mathematical model of sanguimotion in living organism tissues. The model includes the equations of homogeneous fluid flower in heterogeneous medium that consists of two or more interpenetrating continua. The continua (distributing net of arteries and collecting net of veins) interact through ramified capillary net. A volume of blood flowering from arterial net to venous one is proportional to pressure (head) difference in the nets. Some analytical solutions and numerical results are given.

Open issues on G3 neuroendocrine neoplasms: back to the future.

PubMed

Zatelli, Maria Chiara; Guadagno, Elia; Messina, Erika; Lo Calzo, Fabio; Faggiano, Antongiulio; Colao, Annamaria

2018-06-01

The recent recognition that grade 3 (G3) neuroendocrine neoplasms (NENs) can be divided into two different categories according to the histopathological differentiation, that is G3 neuroendocrine tumors (NETs) and G3 neuroendocrine carcinomas (NECs) has generated a lot of interest concerning not only the diagnosis, but also the differential management of such new group of NENs. However, several issues need to be fully clarified in order to put G3 NETs and G3 NECs in the right place. The aim of this review is to focus on those issues that are still undetermined starting from the current knowledge, evaluating the available evidence and the possible clinical implications. © 2018 Society for Endocrinology.

Multi-tasking arbitration and behaviour design for human-interactive robots

NASA Astrophysics Data System (ADS)

Kobayashi, Yuichi; Onishi, Masaki; Hosoe, Shigeyuki; Luo, Zhiwei

2013-05-01

Robots that interact with humans in household environments are required to handle multiple real-time tasks simultaneously, such as carrying objects, collision avoidance and conversation with human. This article presents a design framework for the control and recognition processes to meet these requirements taking into account stochastic human behaviour. The proposed design method first introduces a Petri net for synchronisation of multiple tasks. The Petri net formulation is converted to Markov decision processes and processed in an optimal control framework. Three tasks (safety confirmation, object conveyance and conversation) interact and are expressed by the Petri net. Using the proposed framework, tasks that normally tend to be designed by integrating many if-then rules can be designed in a systematic manner in a state estimation and optimisation framework from the viewpoint of the shortest time optimal control. The proposed arbitration method was verified by simulations and experiments using RI-MAN, which was developed for interactive tasks with humans.

Thermal, conformational and rheological properties of κ-carrageenan-sodium stearoyl lactylate gels and solutions.

PubMed

Ortiz-Tafoya, M C; Rolland-Sabaté, Agnès; Garnier, Catherine; Valadez-García, Josefina; Tecante, Alberto

2018-08-01

Polysaccharide-surfactant blends are widely used in foods. However, their possible mutual interactions have not been extensively studied. The purpose of this work was to examine how the anionic surfactant sodium stearoyl lactylate (SSL) affects different properties of κ-carrageenan solutions and gels. Rheometry, differential scanning calorimetry, asymmetrical flow field-flow fractionation coupled with multiangle laser light scattering, among others, were used to determine the flow and viscoelastic behavior, thermal transitions, and conformation changes, respectively. Interference caused by SSL is postulated as the primary factor to explain the variations in the conformation of κ-carrageenan in gels and solutions. However, electrostatic repulsions between κ-carrageenan and SSL can also be involved. These latter interactions are more important for high SSL concentrations (13 mmol dm -3 ) without addition of KCl, because of the higher net negative charge density of the system. SSL significantly modifies the properties of κ-carrageenan in aqueous media. Copyright © 2018 Elsevier Ltd. All rights reserved.

Impacts of tropospheric ozone and climate change on net primary productivity and net carbon exchange of China’s forest ecosystems

Treesearch

Wei Ren; Hanqin Tian; Bo Tao; Art Chappelka; Ge Sun; et al

2011-01-01

Aim We investigated how ozone pollution and climate change/variability have interactively affected net primary productivity (NPP) and net carbon exchange (NCE) across China’s forest ecosystem in the past half century. Location Continental China. Methods Using the dynamic land ecosystem model (DLEM) in conjunction with 10-km-resolution gridded historical data sets (...

Combination of cross-sectional and molecular imaging studies in the localization of gastroenteropancreatic neuroendocrine tumors.

PubMed

Toumpanakis, Christos; Kim, Michelle K; Rinke, Anja; Bergestuen, Deidi S; Thirlwell, Christina; Khan, Mohid S; Salazar, Ramon; Oberg, Kjell

2014-01-01

Molecular imaging modalities exploit aspects of neuroendocrine tumors (NET) pathophysiology for both diagnostic imaging and therapeutic purposes. The characteristic metabolic pathways of NET determine which tracers are useful for their visualization. In this review, we summarize the diagnostic value of all available molecular imaging studies, present data about their use in daily practice in NET centers globally, and finally make recommendations about the appropriate use of those modalities in specific clinical scenarios. Somatostatin receptor scintigraphy (SRS) continues to have a central role in the diagnostic workup of patients with NET, as it is also widely available. However, and despite the lack of prospective randomized studies, many NET experts predict that Gallium-68 ((68)Ga)-DOTA positron emission tomography (PET) techniques may replace SRS in the future, not only because of their technical advantages, but also because they are superior in patients with small-volume disease, in patients with skeletal metastases, and in those with occult primary tumors. Carbon-11 ((11)C)-5-hydroxy-L-tryptophan (5-HTP) PET and (18)F-dihydroxyphenylalanine ((18)F-DOPA) PET are new molecular imaging techniques of limited availability, and based on retrospective data, their sensitivities seem to be inferior to that of (68)Ga-DOTA PET. Glucagon-like-peptide-1 (GLP-1) receptor imaging seems promising for localization of the primary in benign insulinomas, but is currently available only in a few centers. Fluorine-18 ((18)F)-fluorodeoxyglucose ((18)F-FDG) PET was initially thought to be of limited value in NET, due to their usually slow-growing nature. However, according to subsequent data, (18)F-FDG PET is particularly helpful for visualizing the more aggressive NET, such as poorly differentiated neuroendocrine carcinomas, and well-differentiated tumors with Ki67 values >10%. According to limited data, (18)F-FDG-avid tumor lesions, even in slow-growing NET, may indicate a more aggressive disease course. When a secondary malignancy has already been established or is strongly suspected, combining molecular imaging techniques (e.g. (18)F-FDG PET and (68)Ga-DOTA PET) takes advantage of the diverse avidities of different tumor types to differentiate lesions of different origins. All the above-mentioned molecular imaging studies should always be reviewed and interpreted in a multidisciplinary (tumor board) meeting in combination with the conventional cross-sectional imaging, as the latter remains the imaging of choice for the evaluation of treatment response and disease follow-up. © 2014 S. Karger AG, Basel

Balancing charge in the complementarity-determining regions of humanized mAbs without affecting pI reduces non-specific binding and improves the pharmacokinetics.

PubMed

Datta-Mannan, Amita; Thangaraju, Arunkumar; Leung, Donmienne; Tang, Ying; Witcher, Derrick R; Lu, Jirong; Wroblewski, Victor J

2015-01-01

Lowering the isoelectric point (pI) through engineering the variable region or framework of an IgG can improve its exposure and half-life via a reduction in clearance mediated through non-specific interactions. As such, net charge is a potentially important property to consider in developing therapeutic IgG molecules having favorable pharmaceutical characteristics. Frequently, it may not be possible to shift the pI of monoclonal antibodies (mAbs) dramatically without the introduction of other liabilities such as increased off-target interactions or reduced on-target binding properties. In this report, we explored the influence of more subtle modifications of molecular charge on the in vivo properties of an IgG1 and IgG4 monoclonal antibody. Molecular surface modeling was used to direct residue substitutions in the complementarity-determining regions (CDRs) to disrupt positive charge patch regions, resulting in a reduction in net positive charge without affecting the overall pI of the mAbs. The effect of balancing the net positive charge on non-specific binding was more significant for the IgG4 versus the IgG1 molecule that we examined. This differential effect was connected to the degree of influence on cellular degradation in vitro and in vivo clearance, distribution and metabolism in mice. In the more extreme case of the IgG4, balancing the charge yielded an ∼7-fold improvement in peripheral exposure, as well as significantly reduced tissue catabolism and subsequent excretion of proteolyzed products in urine. Balancing charge on the IgG1 molecule had a more subtle influence on non-specific binding and yielded only a modest alteration in clearance, distribution and elimination. These results suggest that balancing CDR charge without affecting the pI can lead to improved mAb pharmacokinetics, the magnitude of which is likely dependent on the relative influence of charge imbalance and other factors affecting the molecule's disposition.

Balancing charge in the complementarity-determining regions of humanized mAbs without affecting pI reduces non-specific binding and improves the pharmacokinetics

PubMed Central

Datta-Mannan, Amita; Thangaraju, Arunkumar; Leung, Donmienne; Tang, Ying; Witcher, Derrick R; Lu, Jirong; Wroblewski, Victor J

2015-01-01

Lowering the isoelectric point (pI) through engineering the variable region or framework of an IgG can improve its exposure and half-life via a reduction in clearance mediated through non-specific interactions. As such, net charge is a potentially important property to consider in developing therapeutic IgG molecules having favorable pharmaceutical characteristics. Frequently, it may not be possible to shift the pI of monoclonal antibodies (mAbs) dramatically without the introduction of other liabilities such as increased off-target interactions or reduced on-target binding properties. In this report, we explored the influence of more subtle modifications of molecular charge on the in vivo properties of an IgG1 and IgG4 monoclonal antibody. Molecular surface modeling was used to direct residue substitutions in the complementarity-determining regions (CDRs) to disrupt positive charge patch regions, resulting in a reduction in net positive charge without affecting the overall pI of the mAbs. The effect of balancing the net positive charge on non-specific binding was more significant for the IgG4 versus the IgG1 molecule that we examined. This differential effect was connected to the degree of influence on cellular degradation in vitro and in vivo clearance, distribution and metabolism in mice. In the more extreme case of the IgG4, balancing the charge yielded an ∼7-fold improvement in peripheral exposure, as well as significantly reduced tissue catabolism and subsequent excretion of proteolyzed products in urine. Balancing charge on the IgG1 molecule had a more subtle influence on non-specific binding and yielded only a modest alteration in clearance, distribution and elimination. These results suggest that balancing CDR charge without affecting the pI can lead to improved mAb pharmacokinetics, the magnitude of which is likely dependent on the relative influence of charge imbalance and other factors affecting the molecule's disposition. PMID:25695748

The altered expression of perineuronal net elements during neural differentiation.

PubMed

Eskici, Nazli F; Erdem-Ozdamar, Sevim; Dayangac-Erden, Didem

2018-01-01

Perineuronal nets (PNNs), which are localized around neurons during development, are specialized forms of neural extracellular matrix with neuroprotective and plasticity-regulating roles. Hyaluronan and proteoglycan link protein 1 (HAPLN1), tenascin-R (TNR) and aggrecan (ACAN) are key elements of PNNs. In diseases characterized by neuritogenesis defects, the expression of these proteins is known to be downregulated, suggesting that PNNs may have a role in neural differentiation. In this study, the mRNA and protein levels of HAPLN1, TNR and ACAN were determined and compared at specific time points of neural differentiation. We used PC12 cells as the in vitro model because they reflect this developmental process. On day 7, the HAPLN1 mRNA level showed a 2.9-fold increase compared to the non-differentiated state. However, the cellular HAPLN1 protein level showed a decrease, indicating that the protein may have roles in neural differentiation, and may be secreted during the early period of differentiation. By contrast, TNR mRNA and protein levels remained unchanged, and the amount of cellular ACAN protein showed a 3.7-fold increase at day 7. These results suggest that ACAN may be secreted after day 7, possibly due to its large amount of post-translational modifications. Our results provide preliminary data on the expression of PNN elements during neural differentiation. Further investigations will be performed on the role of these elements in neurological disease models.

IntNetDB v1.0: an integrated protein-protein interaction network database generated by a probabilistic model

PubMed Central

Xia, Kai; Dong, Dong; Han, Jing-Dong J

2006-01-01

Background Although protein-protein interaction (PPI) networks have been explored by various experimental methods, the maps so built are still limited in coverage and accuracy. To further expand the PPI network and to extract more accurate information from existing maps, studies have been carried out to integrate various types of functional relationship data. A frequently updated database of computationally analyzed potential PPIs to provide biological researchers with rapid and easy access to analyze original data as a biological network is still lacking. Results By applying a probabilistic model, we integrated 27 heterogeneous genomic, proteomic and functional annotation datasets to predict PPI networks in human. In addition to previously studied data types, we show that phenotypic distances and genetic interactions can also be integrated to predict PPIs. We further built an easy-to-use, updatable integrated PPI database, the Integrated Network Database (IntNetDB) online, to provide automatic prediction and visualization of PPI network among genes of interest. The networks can be visualized in SVG (Scalable Vector Graphics) format for zooming in or out. IntNetDB also provides a tool to extract topologically highly connected network neighborhoods from a specific network for further exploration and research. Using the MCODE (Molecular Complex Detections) algorithm, 190 such neighborhoods were detected among all the predicted interactions. The predicted PPIs can also be mapped to worm, fly and mouse interologs. Conclusion IntNetDB includes 180,010 predicted protein-protein interactions among 9,901 human proteins and represents a useful resource for the research community. Our study has increased prediction coverage by five-fold. IntNetDB also provides easy-to-use network visualization and analysis tools that allow biological researchers unfamiliar with computational biology to access and analyze data over the internet. The web interface of IntNetDB is freely accessible at . Visualization requires Mozilla version 1.8 (or higher) or Internet Explorer with installation of SVGviewer. PMID:17112386

The RhoGEF Net1 Is Required for Normal Mammary Gland Development

PubMed Central

Zuo, Yan; Berdeaux, Rebecca

2014-01-01

Neuroepithelial transforming gene 1 (Net1) is a RhoA subfamily-specific guanine nucleotide exchange factor that is overexpressed in human breast cancer and is required for breast cancer cell migration and invasion. However, the role of Net1 in normal mammary gland development or function has never been assessed. To understand the role of Net1 in the mammary gland, we have created a conditional Net1 knockout mouse model. Whole-body deletion of Net1 results in delayed mammary gland development during puberty characterized by slowed of ductal extension and reduced ductal branching. Epithelial cells within the developing ducts show reduced proliferation that is accompanied by diminished estrogen receptor-α expression and activity. Net1-deficient mammary glands also exhibit reduced phosphorylation of regulatory subunits of myosin light chain and myosin light-chain phosphatase, indicating that RhoA-dependent actomyosin contraction is compromised. Net1 deficiency also leads to disorganization of myoepithelial and ductal epithelial cells and increased periductal collagen deposition. Mammary epithelial cell transplantation experiments indicate that reduced ductal branching and disorganization are cell autonomous. These data identify for the first time a role for NET1 in vivo and indicate that NET1 expression is essential for the proliferation and differentiation of mammary epithelial cells in the developing mammary gland. PMID:25321414

GeneNetFinder2: Improved Inference of Dynamic Gene Regulatory Relations with Multiple Regulators.

PubMed

Han, Kyungsook; Lee, Jeonghoon

2016-01-01

A gene involved in complex regulatory interactions may have multiple regulators since gene expression in such interactions is often controlled by more than one gene. Another thing that makes gene regulatory interactions complicated is that regulatory interactions are not static, but change over time during the cell cycle. Most research so far has focused on identifying gene regulatory relations between individual genes in a particular stage of the cell cycle. In this study we developed a method for identifying dynamic gene regulations of several types from the time-series gene expression data. The method can find gene regulations with multiple regulators that work in combination or individually as well as those with single regulators. The method has been implemented as the second version of GeneNetFinder (hereafter called GeneNetFinder2) and tested on several gene expression datasets. Experimental results with gene expression data revealed the existence of genes that are not regulated by individual genes but rather by a combination of several genes. Such gene regulatory relations cannot be found by conventional methods. Our method finds such regulatory relations as well as those with multiple, independent regulators or single regulators, and represents gene regulatory relations as a dynamic network in which different gene regulatory relations are shown in different stages of the cell cycle. GeneNetFinder2 is available at http://bclab.inha.ac.kr/GeneNetFinder and will be useful for modeling dynamic gene regulations with multiple regulators.

Angiogenesis in neuroendocrine tumors: therapeutic applications.

PubMed

Scoazec, Jean-Yves

2013-01-01

The considerable research efforts devoted to the understanding of the mechanisms of tumor angiogenesis have resulted in the development of targeted anti-angiogenic therapies and finally in their introduction in clinical practice. Neuroendocrine tumors (NETs), which are characterized by a high vascular supply and a strong expression of VEGF-A, one of the most potent pro-angiogenic factors, are an attractive indication for these new treatments. However, several lines of evidence show that the dense vascular networks associated with low-grade NETs are more likely to be a marker of differentiation than a marker of aggressiveness, as in other epithelial tumors. These observations form the basis for the so-called 'neuroendocrine paradox', according to which the most vascularized are the most differentiated and the less angiogenic NETs. This must be kept in mind when discussing the role of anti-angiogenic strategies in the treatment of NETs. Nevertheless, several targeted therapies, with direct or indirect anti-angiogenic properties, including anti-VEGF antibodies, tyrosine kinase inhibitors (sunitinib) and mTOR inhibitors (everolimus), have recently proven to be of clinical benefit. In addition, some drugs already used in NET treatment, such as somatostatin analogues and interferon-α, may also have anti-angiogenic properties. The main challenges for the next future are to validate biomarkers for the selection of patients and the prediction of their response to refine the indications of anti-angiogenic targeted therapies and to overcome the mechanisms of resistance, which explain the limited duration of action of most of these treatments. Copyright © 2012 S. Karger AG, Basel.

Global energy transports and the influence of clouds on transport requirements - A satellite analysis

NASA Technical Reports Server (NTRS)

Sohn, Byung-Ju; Smith, Eric A.

1992-01-01

This report investigates the impact of differential net radiative heating on 2D energy transports within the atmosphere ocean system and the role of clouds on this process. The 2D mean energy transports, in answer to zonal and meridional gradients in the net radiation field, show an east-west coupled dipole structure in which the Pacific acts as the major energy source and North Africa as the major energy sink. It is demonstrated that the dipole is embedded in the secondary energy transports arising mainly from the differential heating between land and oceans in the tropics in which the tropical east-west (zonal) transports are up to 30 percent of the tropical north-south (meridional) transports.

Modeling formalisms in Systems Biology

PubMed Central

2011-01-01

Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future. PMID:22141422

Current in nanojunctions: Effects of reservoir coupling

NASA Astrophysics Data System (ADS)

Yadalam, Hari Kumar; Harbola, Upendra

2018-07-01

We study the effect of system reservoir coupling on currents flowing through quantum junctions. We consider two simple double-quantum dot configurations coupled to two external fermionic reservoirs and study the net current flowing between the two reservoirs. The net current is partitioned into currents carried by the eigenstates of the system and by the coherences between the eigenstates induced due to coupling with the reservoirs. We find that current carried by populations is always positive whereas current carried by coherences are negative for large couplings. This results in a non-monotonic dependence of the net current on the coupling strength. We find that in certain cases, the net current can vanish at large couplings due to cancellation between currents carried by the eigenstates and by the coherences. These results provide new insights into the non-trivial role of system-reservoir couplings on electron transport through quantum dot junctions. In the presence of weak coulomb interactions, net current as a function of system reservoir coupling strength shows similar trends as for the non-interacting case.

Fluctuations of cell population in a colonic crypt

NASA Astrophysics Data System (ADS)

Pei, Qi-ming; Zhan, Xuan; Yang, Li-jian; Bao, Chun; Cao, Wei; Li, An-bang; Rozi, Anvar; Jia, Ya

2014-03-01

The number of stem cells in a colonic crypt is often very small, which leads to large intrinsic fluctuations in the cell population. Based on the model of cell population dynamics with linear feedback in a colonic crypt, we present a stochastic dynamics of the cell population [including stem cells (SCs), transit amplifying cells (TACs), and fully differentiated cells (FDCs)]. The Fano factor, covariance, and susceptibility formulas of the cell population around the steady state are derived by using the Langevin theory. In the range of physiologically reasonable parameter values, it is found that the stationary populations of TACs and FDCs exhibit an approximately threshold behavior as a function of the net growth rate of TACs, and the reproductions of TACs and FDCs can be classified into three regimens: controlled, crossover, and uncontrolled. With the increasing of the net growth rate of TACs, there is a maximum of the relative intrinsic fluctuations (i.e., the Fano factors) of TACs and FDCs in the crossover region. For a fixed differentiation rate and the net growth rate of SCs, the covariance of fluctuations between SCs and TACs has a maximum in the crossover region. However, the susceptibilities of both TACs and FDCs to the net growth rate of TACs have a minimum in the crossover region.

Telotristat ethyl: proof of principle and the first oral agent in the management of well-differentiated metastatic neuroendocrine tumor and carcinoid syndrome diarrhea.

PubMed

Masab, Muhammad; Saif, Muhammad Wasif

2017-12-01

Metastatic neuroendocrine tumors (NETs) are associated with carcinoid syndrome that is typically characterized by diarrhea, cutaneous flushing and bronchospasm. Treatment with somatostatin analogues (SSA) improves the symptom burden but a significant proportion of patients stop responding to SSA therapy eventually. Novel agents with the potential to effectively control the symptoms are urgently needed. This article reviews an in-depth analysis of the phase I-III clinical trials determining the clinical rationale for the use of tryptophan hydroxylase inhibitor, telotristat ethyl in patients with well-differentiated metastatic NETs and uncontrolled carcinoid syndrome. Telotristat ethyl has already been approved for the treatment of inadequately controlled carcinoid syndrome symptoms in metastatic NET patients on SSA therapy. Results from multiple phase I-III clinical studies of telotristat ethyl therapy have reported a significant decrease in the daily bowel movement frequency, increase in quality of life and the subsequent decrease in annual health costs related to carcinoid syndrome symptoms in NET patients. The associated decrease in urinary 5-hydroxyindoleacetic acid (u5-HIAA) provides evidence that telotristat ethyl effectively decreases serotonin production, and therefore, offers a rationale to investigate this agent to mitigate serotonin-mediated complications in this patient population, especially cardiac valvular disease or mesenteric fibrosis.

Evaluation of common methods for sampling invertebrate pollinator assemblages: net sampling out-perform pan traps.

PubMed

Popic, Tony J; Davila, Yvonne C; Wardle, Glenda M

2013-01-01

Methods for sampling ecological assemblages strive to be efficient, repeatable, and representative. Unknowingly, common methods may be limited in terms of revealing species function and so of less value for comparative studies. The global decline in pollination services has stimulated surveys of flower-visiting invertebrates, using pan traps and net sampling. We explore the relative merits of these two methods in terms of species discovery, quantifying abundance, function, and composition, and responses of species to changing floral resources. Using a spatially-nested design we sampled across a 5000 km(2) area of arid grasslands, including 432 hours of net sampling and 1296 pan trap-days, between June 2010 and July 2011. Net sampling yielded 22% more species and 30% higher abundance than pan traps, and better reflected the spatio-temporal variation of floral resources. Species composition differed significantly between methods; from 436 total species, 25% were sampled by both methods, 50% only by nets, and the remaining 25% only by pans. Apart from being less comprehensive, if pan traps do not sample flower-visitors, the link to pollination is questionable. By contrast, net sampling functionally linked species to pollination through behavioural observations of flower-visitation interaction frequency. Netted specimens are also necessary for evidence of pollen transport. Benefits of net-based sampling outweighed minor differences in overall sampling effort. As pan traps and net sampling methods are not equivalent for sampling invertebrate-flower interactions, we recommend net sampling of invertebrate pollinator assemblages, especially if datasets are intended to document declines in pollination and guide measures to retain this important ecosystem service.

Evaluation of Common Methods for Sampling Invertebrate Pollinator Assemblages: Net Sampling Out-Perform Pan Traps

PubMed Central

Popic, Tony J.; Davila, Yvonne C.; Wardle, Glenda M.

2013-01-01

Methods for sampling ecological assemblages strive to be efficient, repeatable, and representative. Unknowingly, common methods may be limited in terms of revealing species function and so of less value for comparative studies. The global decline in pollination services has stimulated surveys of flower-visiting invertebrates, using pan traps and net sampling. We explore the relative merits of these two methods in terms of species discovery, quantifying abundance, function, and composition, and responses of species to changing floral resources. Using a spatially-nested design we sampled across a 5000 km2 area of arid grasslands, including 432 hours of net sampling and 1296 pan trap-days, between June 2010 and July 2011. Net sampling yielded 22% more species and 30% higher abundance than pan traps, and better reflected the spatio-temporal variation of floral resources. Species composition differed significantly between methods; from 436 total species, 25% were sampled by both methods, 50% only by nets, and the remaining 25% only by pans. Apart from being less comprehensive, if pan traps do not sample flower-visitors, the link to pollination is questionable. By contrast, net sampling functionally linked species to pollination through behavioural observations of flower-visitation interaction frequency. Netted specimens are also necessary for evidence of pollen transport. Benefits of net-based sampling outweighed minor differences in overall sampling effort. As pan traps and net sampling methods are not equivalent for sampling invertebrate-flower interactions, we recommend net sampling of invertebrate pollinator assemblages, especially if datasets are intended to document declines in pollination and guide measures to retain this important ecosystem service. PMID:23799127

A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.

PubMed

Vo, Tommy V; Das, Jishnu; Meyer, Michael J; Cordero, Nicolas A; Akturk, Nurten; Wei, Xiaomu; Fair, Benjamin J; Degatano, Andrew G; Fragoza, Robert; Liu, Lisa G; Matsuyama, Akihisa; Trickey, Michelle; Horibata, Sachi; Grimson, Andrew; Yamano, Hiroyuki; Yoshida, Minoru; Roth, Frederick P; Pleiss, Jeffrey A; Xia, Yu; Yu, Haiyuan

2016-01-14

Here, we present FissionNet, a proteome-wide binary protein interactome for S. pombe, comprising 2,278 high-quality interactions, of which ∼ 50% were previously not reported in any species. FissionNet unravels previously unreported interactions implicated in processes such as gene silencing and pre-mRNA splicing. We developed a rigorous network comparison framework that accounts for assay sensitivity and specificity, revealing extensive species-specific network rewiring between fission yeast, budding yeast, and human. Surprisingly, although genes are better conserved between the yeasts, S. pombe interactions are significantly better conserved in human than in S. cerevisiae. Our framework also reveals that different modes of gene duplication influence the extent to which paralogous proteins are functionally repurposed. Finally, cross-species interactome mapping demonstrates that coevolution of interacting proteins is remarkably prevalent, a result with important implications for studying human disease in model organisms. Overall, FissionNet is a valuable resource for understanding protein functions and their evolution. Copyright © 2016 Elsevier Inc. All rights reserved.

Governance in Open Source Software Development Projects: Towards a Model for Network-Centric Edge Organizations

DTIC Science & Technology

2008-06-01

project is not an isolated OSSD project. Instead, the NetBeans IDE which is the focus of development activities in the NetBeans.org project community...facilitate or constrain the intended usage of the NetBeans IDE. Figure 1 provides a rendering of some of the more visible OSSD projects that...as BioBeans and RefactorIT communities build tools on top of or extending the NetBeans platform or IDE. How do these organizations interact with

Lymphoma as a second malignancy in a patient with neuroendocrine tumor: mimicking dedifferentiation on dual-tracer PET/CT with 68Ga-DOTANOC and 18F-FDG.

PubMed

Jain, Sachin; Sharma, Punit; Dhull, Varun Singh; Bal, Chandrasekhar; Kumar, Rakesh

2014-04-01

Neuroendocrine tumors (NETs) are rare tumors which express somatostatin receptors (SSTRs). We here present a case of a 50-year-old female patient with metastatic bronchial carcinoid. She underwent 68Ga-DOTANOC PET/CT and 18F-FDG PET/CT which suggested a diagnosis of poorly differentiated NET. Biopsy of the lesion, however, revealed a second malignancy in the form of diffuse large B-cell lymphoma. Thus, very rarely, other primary tumors can mimic NETs on dual-tracer PET/CT, and biopsy is advised in doubtful cases.

MONALISA for stochastic simulations of Petri net models of biochemical systems.

PubMed

Balazki, Pavel; Lindauer, Klaus; Einloft, Jens; Ackermann, Jörg; Koch, Ina

2015-07-10

The concept of Petri nets (PN) is widely used in systems biology and allows modeling of complex biochemical systems like metabolic systems, signal transduction pathways, and gene expression networks. In particular, PN allows the topological analysis based on structural properties, which is important and useful when quantitative (kinetic) data are incomplete or unknown. Knowing the kinetic parameters, the simulation of time evolution of such models can help to study the dynamic behavior of the underlying system. If the number of involved entities (molecules) is low, a stochastic simulation should be preferred against the classical deterministic approach of solving ordinary differential equations. The Stochastic Simulation Algorithm (SSA) is a common method for such simulations. The combination of the qualitative and semi-quantitative PN modeling and stochastic analysis techniques provides a valuable approach in the field of systems biology. Here, we describe the implementation of stochastic analysis in a PN environment. We extended MONALISA - an open-source software for creation, visualization and analysis of PN - by several stochastic simulation methods. The simulation module offers four simulation modes, among them the stochastic mode with constant firing rates and Gillespie's algorithm as exact and approximate versions. The simulator is operated by a user-friendly graphical interface and accepts input data such as concentrations and reaction rate constants that are common parameters in the biological context. The key features of the simulation module are visualization of simulation, interactive plotting, export of results into a text file, mathematical expressions for describing simulation parameters, and up to 500 parallel simulations of the same parameter sets. To illustrate the method we discuss a model for insulin receptor recycling as case study. We present a software that combines the modeling power of Petri nets with stochastic simulation of dynamic processes in a user-friendly environment supported by an intuitive graphical interface. The program offers a valuable alternative to modeling, using ordinary differential equations, especially when simulating single-cell experiments with low molecule counts. The ability to use mathematical expressions provides an additional flexibility in describing the simulation parameters. The open-source distribution allows further extensions by third-party developers. The software is cross-platform and is licensed under the Artistic License 2.0.

Foliar bacteria and soil fertility mediate seedling performance: a new and cryptic dimension of niche differentiation.

PubMed

Griffin, Eric A; Traw, M Brian; Morin, Peter J; Pruitt, Jonathan N; Wright, S Joseph; Carson, Walter P

2016-11-01

The phyllosphere (comprising the leaf surface and interior) is one of the world's largest microbial habitats and is host to an abundant and diverse array of bacteria. Nonetheless, the degree to which bacterial communities are benign, harmful, or beneficial to plants in situ is unknown. We tested the hypothesis that the net effect of reducing bacterial abundance and diversity would vary substantially among host species (from harmful to beneficial) and this would be strongly mediated by soil resource availability. To test this, we monitored tree seedling growth responses to commercial antibiotics among replicated resource supply treatments (N, P, K) in a tropical forest in Panama for 29 months. We applied either antibiotics or control water to replicated seedlings of five common tree species (Alseis blackiana, Desmopsis panamensis, Heisteria concinna, Sorocea affinis, and Tetragastris panamensis). These antibiotic treatments significantly reduced both the abundance and diversity of bacteria epiphytically as well as endophytically. Overall, the effect of antibiotics on performance was highly host specific. Applying antibiotics increased growth for three species by as much as 49% (Alseis, Heisteria, and Tetragastris), decreased growth for a fourth species by nearly 20% (Sorocea), and had no impact on a fifth species (Desmopsis). Perhaps more importantly, the degree to which foliar bacteria were harmful or not varied with soil resource supply. Specifically, applying antibiotics had no effect when potassium was added but increased growth rate by almost 40% in the absence of potassium. Alternatively, phosphorus enrichment caused the effect of bacteria to switch from being primarily beneficial to harmful or vice versa, but this depended entirely on the presence or absence of nitrogen enrichment (i.e., important and significant interactions). Our results are the first to demonstrate that the net effect of reducing the abundance and diversity of bacteria can have very strong positive and negative effects on seedling performance. Moreover, these effects were clearly mediated by soil resource availability. Though speculative, we suggest that foliar bacteria may interact with soil fertility to comprise an important, yet cryptic dimension of niche differentiation, which can have important implications for species coexistence. © 2016 by the Ecological Society of America.

Spectrum of Gastroenteropancreatic NENs in Routine Histological Examinations of Bioptic and Surgical Specimen: A Study of 161 Cases Collected from 17 Departments of Pathology in the Czech Republic

PubMed Central

Mandys, Václav

2014-01-01

Objective. To characterize GEP-NENs in routine biopsies and surgical specimen in the Czech Republic and to evaluate how WHO Classification (2010) is acceptable in diagnostic practice. Methods. Paraffin-embedded blocks and bioptic reports were collected from 17 departments of pathology. Histologic slides were stained with H&E and immunohistologically for CgA, synaptophysin, and Ki-67. Results. Out of 28 gastric NENs, there were 22 NETs, G1, 5 NETs, G2, and 1 NEC. Ten duodenal NENs were NETs, G1. Among 27 NENs of jejunum and ileum, 23 were NETs, G1, 2 NETs, G2, and 1 NEC and 1 mixed adenoneuroendocrine carcinoma (MANEC). Among 42 appendiceal “incidentalomas”, 39 were NETs G1, 2 goblet cell carcinoids, and 1 MANEC. Out of 34 large intestinal NENs, 30 were NETs, G1, 3 NETs, G2, and 1 NEC. One small intestinal and 6 large bowel neoplasms were reclassified as poorly differentiated adenocarcinomas. In 12 pancreatic NENs, there were 7 NETs, G1, 3 NETs, G2, and 2 NECs. Conclusions. Our study demonstrates differences in GEP-NENs frequency in sites of origin in our region, comparing to other countries. Regarding routine bioptic diagnostics, we gave evidence that the WHO 2010 classification of NENs is fully acceptable for exact categorisation of tumours. PMID:24695372

Interactions between soy protein from water-soluble soy extract and polysaccharides in solutions with polydextrose.

PubMed

Spada, Jordana C; Marczak, Ligia D F; Tessaro, Isabel C; Cardozo, Nilo S M

2015-12-10

This study focuses on the investigation of the interactions between polysaccharides (carrageenan and carboxymethylcellulose--CMC) and soy proteins from the water-soluble soy extract. The influence of pH (2-7) and protein-polysaccharide ratio (5:1-40:1) on the interaction between these polyelectrolytes was investigated in aqueous solutions with 10% of polydextrose and without polydextrose. The studied systems were analyzed in terms of pH-solubility profile of protein, ζ-potential, methylene blue-polysaccharide interactions, differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FTIR), and confocal laser scanning microscopy. Although the mixtures of soy extract with both carrageenan and CMC showed dependency on the pH and protein-polysaccharide ratio, they did not present the same behavior. Both polysaccharides modified the pH-solubility profile of the soy protein, shifting the pH range in which the coacervate is formed to a lower pH region with the decrease of the soy extract-polysaccharide ratio. The samples also presented detectable differences regarding to ζ-potential, DSC, FTIR and microscopy analyses. The complex formation was also detected even in a pH range where both biopolymers were net-negatively charged. The changes promoted by the presence of polydextrose were mainly detected by blue-polysaccharide interactions measures and confocal microscopy. Copyright © 2015 Elsevier Ltd. All rights reserved.

50 CFR 660.520 - Reporting requirements.

Code of Federal Regulations, 2013 CFR

2013-10-01

... net, regardless of whether the animal is injured or killed, the vessel operator must report this... interaction; the otter's behavior during interaction; measures taken to avoid interaction. (b) [Reserved] [72...

50 CFR 660.520 - Reporting requirements.

Code of Federal Regulations, 2014 CFR

2014-10-01

... net, regardless of whether the animal is injured or killed, the vessel operator must report this... interaction; the otter's behavior during interaction; measures taken to avoid interaction. (b) [Reserved] [72...

50 CFR 660.520 - Reporting requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... net, regardless of whether the animal is injured or killed, the vessel operator must report this... interaction; the otter's behavior during interaction; measures taken to avoid interaction. (b) [Reserved] [72...

50 CFR 660.520 - Reporting requirements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... net, regardless of whether the animal is injured or killed, the vessel operator must report this... interaction; the otter's behavior during interaction; measures taken to avoid interaction. (b) [Reserved] [72...

50 CFR 660.520 - Reporting requirements.

Code of Federal Regulations, 2012 CFR

2012-10-01

... net, regardless of whether the animal is injured or killed, the vessel operator must report this... interaction; the otter's behavior during interaction; measures taken to avoid interaction. (b) [Reserved] [72...

Prospects for detecting a net photon circular polarization produced by decaying dark matter

NASA Astrophysics Data System (ADS)

Elagin, Andrey; Kumar, Jason; Sandick, Pearl; Teng, Fei

2017-11-01

If dark matter interactions with Standard Model particles are C P violating, then dark matter annihilation/decay can produce photons with a net circular polarization. We consider the prospects for experimentally detecting evidence for such a circular polarization. We identify optimal models for dark matter interactions with the Standard Model, from the point of view of detectability of the net polarization, for the case of either symmetric or asymmetric dark matter. We find that, for symmetric dark matter, evidence for net polarization could be found by a search of the Galactic center by an instrument sensitive to circular polarization with an efficiency-weighted exposure of at least 50 ,000 cm2 yr , provided the systematic detector uncertainties are constrained at the 1% level. Better sensitivity can be obtained in the case of asymmetric dark matter. We discuss the prospects for achieving the needed level of performance using possible detector technologies.

EnviroNET: An online environmental interactions resource

NASA Technical Reports Server (NTRS)

Lauriente, Michael

1991-01-01

EnviroNET is a centralized depository for technical information on environmentally induced interactions likely to be encountered by spacecraft in both low-altitude and high-altitude orbits. It provides a user-friendly, menu-driven format on networks that are connected globally and is available 24 hours a day - every day. The service pools space data collected over the years by NASA, USAF, other government research facilities, industry, universities, and the European Space Agency. This information contains text, tables and over one hundred high resolution figures and graphs based on empirical data. These graphics can be accessed while still in the chapters, making it easy to flip from text to graphics and back. Interactive graphics programs are also available on space debris, the neutral atmosphere, magnetic field, and ionosphere. EnviroNET can help designers meet tough environmental flight criteria before committing to flight hardware built for experiments, instrumentation, or payloads.

Investigating ego modules and pathways in osteosarcoma by integrating the EgoNet algorithm and pathway analysis.

PubMed

Chen, X Y; Chen, Y H; Zhang, L J; Wang, Y; Tong, Z C

2017-02-16

Osteosarcoma (OS) is the most common primary bone malignancy, but current therapies are far from effective for all patients. A better understanding of the pathological mechanism of OS may help to achieve new treatments for this tumor. Hence, the objective of this study was to investigate ego modules and pathways in OS utilizing EgoNet algorithm and pathway-related analysis, and reveal pathological mechanisms underlying OS. The EgoNet algorithm comprises four steps: constructing background protein-protein interaction (PPI) network (PPIN) based on gene expression data and PPI data; extracting differential expression network (DEN) from the background PPIN; identifying ego genes according to topological features of genes in reweighted DEN; and collecting ego modules using module search by ego gene expansion. Consequently, we obtained 5 ego modules (Modules 2, 3, 4, 5, and 6) in total. After applying the permutation test, all presented statistical significance between OS and normal controls. Finally, pathway enrichment analysis combined with Reactome pathway database was performed to investigate pathways, and Fisher's exact test was conducted to capture ego pathways for OS. The ego pathway for Module 2 was CLEC7A/inflammasome pathway, while for Module 3 a tetrasaccharide linker sequence was required for glycosaminoglycan (GAG) synthesis, and for Module 6 was the Rho GTPase cycle. Interestingly, genes in Modules 4 and 5 were enriched in the same pathway, the 2-LTR circle formation. In conclusion, the ego modules and pathways might be potential biomarkers for OS therapeutic index, and give great insight of the molecular mechanism underlying this tumor.

Investigating ego modules and pathways in osteosarcoma by integrating the EgoNet algorithm and pathway analysis

PubMed Central

Chen, X.Y.; Chen, Y.H.; Zhang, L.J.; Wang, Y.; Tong, Z.C.

2017-01-01

Osteosarcoma (OS) is the most common primary bone malignancy, but current therapies are far from effective for all patients. A better understanding of the pathological mechanism of OS may help to achieve new treatments for this tumor. Hence, the objective of this study was to investigate ego modules and pathways in OS utilizing EgoNet algorithm and pathway-related analysis, and reveal pathological mechanisms underlying OS. The EgoNet algorithm comprises four steps: constructing background protein-protein interaction (PPI) network (PPIN) based on gene expression data and PPI data; extracting differential expression network (DEN) from the background PPIN; identifying ego genes according to topological features of genes in reweighted DEN; and collecting ego modules using module search by ego gene expansion. Consequently, we obtained 5 ego modules (Modules 2, 3, 4, 5, and 6) in total. After applying the permutation test, all presented statistical significance between OS and normal controls. Finally, pathway enrichment analysis combined with Reactome pathway database was performed to investigate pathways, and Fisher's exact test was conducted to capture ego pathways for OS. The ego pathway for Module 2 was CLEC7A/inflammasome pathway, while for Module 3 a tetrasaccharide linker sequence was required for glycosaminoglycan (GAG) synthesis, and for Module 6 was the Rho GTPase cycle. Interestingly, genes in Modules 4 and 5 were enriched in the same pathway, the 2-LTR circle formation. In conclusion, the ego modules and pathways might be potential biomarkers for OS therapeutic index, and give great insight of the molecular mechanism underlying this tumor. PMID:28225867

Net (ERP/SAP2) one of the Ras-inducible TCFs, has a novel inhibitory domain with resemblance to the helix-loop-helix motif.

PubMed Central

Maira, S M; Wurtz, J M; Wasylyk, B

1996-01-01

The three ternary complex factors (TCFs), Net (ERP/ SAP-2), ELK-1 and SAP-1, are highly related ets oncogene family members that participate in the response of the cell to Ras and growth signals. Understanding the different roles of these factors will provide insights into how the signals result in coordinate regulation of the cell. We show that Net inhibits transcription under basal conditions, in which SAP-1a is inactive and ELK-1 stimulates. Repression is mediated by the NID, the Net Inhibitory Domain of about 50 amino acids, which autoregulates the Net protein and also inhibits when it is isolated in a heterologous fusion protein. Net is particularly sensitive to Ras activation. Ras activates Net through the C-domain, which is conserved between the three TCFs, and the NID is an efficient inhibitor of Ras activation. The NID, as well as more C-terminal sequences, inhibit DNA binding. Net is more refractory to DNA binding than the other TCFs, possibly due to the presence of multiple inhibitory elements. The NID may adopt a helix-loop-helix (HLH) structure, as evidenced by homology to other HLH motifs, structure predictions, model building and mutagenesis of critical residues. The sequence resemblance with myogenic factors suggested that Net may form complexes with the same partners. Indeed, we found that Net can interact in vivo with the basic HLH factor, E47. We propose that Net is regulated at the level of its latent DNA-binding activity by protein interactions and/or phosphorylation. Net may form complexes with HLH proteins as well as SRF on specific promotor sequences. The identification of the novel inhibitory domain provides a new inroad into exploring the different roles of the ternary complex factors in growth control and transformation. Images PMID:8918463

Net (ERP/SAP2) one of the Ras-inducible TCFs, has a novel inhibitory domain with resemblance to the helix-loop-helix motif.

PubMed

Maira, S M; Wurtz, J M; Wasylyk, B

1996-11-01

The three ternary complex factors (TCFs), Net (ERP/ SAP-2), ELK-1 and SAP-1, are highly related ets oncogene family members that participate in the response of the cell to Ras and growth signals. Understanding the different roles of these factors will provide insights into how the signals result in coordinate regulation of the cell. We show that Net inhibits transcription under basal conditions, in which SAP-1a is inactive and ELK-1 stimulates. Repression is mediated by the NID, the Net Inhibitory Domain of about 50 amino acids, which autoregulates the Net protein and also inhibits when it is isolated in a heterologous fusion protein. Net is particularly sensitive to Ras activation. Ras activates Net through the C-domain, which is conserved between the three TCFs, and the NID is an efficient inhibitor of Ras activation. The NID, as well as more C-terminal sequences, inhibit DNA binding. Net is more refractory to DNA binding than the other TCFs, possibly due to the presence of multiple inhibitory elements. The NID may adopt a helix-loop-helix (HLH) structure, as evidenced by homology to other HLH motifs, structure predictions, model building and mutagenesis of critical residues. The sequence resemblance with myogenic factors suggested that Net may form complexes with the same partners. Indeed, we found that Net can interact in vivo with the basic HLH factor, E47. We propose that Net is regulated at the level of its latent DNA-binding activity by protein interactions and/or phosphorylation. Net may form complexes with HLH proteins as well as SRF on specific promotor sequences. The identification of the novel inhibitory domain provides a new inroad into exploring the different roles of the ternary complex factors in growth control and transformation.

Effects of elevated turbidity and nutrients on the net production of a tropical seagrass community

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

Caldwell, J.W.

1985-01-01

Dredging effects on seagrass communities in the Florida Keys were examined by (1) comparing impacts on net production resulting from dredging and natural weather events, (2) determining changes in community photosynthetic efficiency, (3) evaluating shading and nutrient effects on net production, and (4) developing a systems dynamics model. Net community production was estimated during numerous meteorological and dredging events using the Odum-Hoskins oxygen technique in flow-through field microcosms. In other experiments, shading and nutrients (phosphorus, nitrate, and ammonia) were manipulated to simulate dredge plume conditions. The greatest depression in net community production resulted from severe thunderstorms and dredging events, respectively.more » In field microcosm experiments, significant interaction occurred between shading and nutrient concentration. The model of seagrass production was most sensitive to changes in nutrient-seagrass relationships, seagrass production estimates, and seagrass-light interactions. Recovery of seagrass biomass following numerous dredging events (3.5 years) was longer than that from the estimated total annual thunderstorms encountered (1 year) but shorter than recovery from hurricane events (4.1 years).« less

Petri net modeling of high-order genetic systems using grammatical evolution.

PubMed

Moore, Jason H; Hahn, Lance W

2003-11-01

Understanding how DNA sequence variations impact human health through a hierarchy of biochemical and physiological systems is expected to improve the diagnosis, prevention, and treatment of common, complex human diseases. We have previously developed a hierarchical dynamic systems approach based on Petri nets for generating biochemical network models that are consistent with genetic models of disease susceptibility. This modeling approach uses an evolutionary computation approach called grammatical evolution as a search strategy for optimal Petri net models. We have previously demonstrated that this approach routinely identifies biochemical network models that are consistent with a variety of genetic models in which disease susceptibility is determined by nonlinear interactions between two DNA sequence variations. In the present study, we evaluate whether the Petri net approach is capable of identifying biochemical networks that are consistent with disease susceptibility due to higher order nonlinear interactions between three DNA sequence variations. The results indicate that our model-building approach is capable of routinely identifying good, but not perfect, Petri net models. Ideas for improving the algorithm for this high-dimensional problem are presented.

Peptidylarginine deiminase inhibition is immunomodulatory and vasculoprotective in murine lupus

PubMed Central

Knight, Jason S.; Zhao, Wenpu; Luo, Wei; Subramanian, Venkataraman; O’Dell, Alexander A.; Yalavarthi, Srilakshmi; Hodgin, Jeffrey B.; Eitzman, Daniel T.; Thompson, Paul R.; Kaplan, Mariana J.

2013-01-01

Recent evidence suggests that enhanced neutrophil extracellular trap (NET) formation activates plasmacytoid dendritic cells and serves as a source of autoantigens in SLE. We propose that aberrant NET formation is also linked to organ damage and to the premature vascular disease characteristic of human SLE. Here, we demonstrate enhanced NET formation in the New Zealand mixed 2328 (NZM) model of murine lupus. NZM mice also developed autoantibodies to NETs as well as the ortholog of human cathelicidin/LL37 (CRAMP), a molecule externalized in the NETs. NZM mice were treated with Cl-amidine, an inhibitor of peptidylarginine deiminases (PAD), to block NET formation and were evaluated for lupus-like disease activity, endothelial function, and prothrombotic phenotype. Cl-amidine treatment inhibited NZM NET formation in vivo and significantly altered circulating autoantibody profiles and complement levels while reducing glomerular IgG deposition. Further, Cl-amidine increased the differentiation capacity of bone marrow endothelial progenitor cells, improved endothelium-dependent vasorelaxation, and markedly delayed time to arterial thrombosis induced by photochemical injury. Overall, these findings suggest that PAD inhibition can modulate phenotypes crucial for lupus pathogenesis and disease activity and may represent an important strategy for mitigating cardiovascular risk in lupus patients. PMID:23722903

Differential ubiquitination in NETs regulates macrophage responses in systemic lupus erythematosus.

PubMed

Barrera-Vargas, Ana; Gómez-Martín, Diana; Carmona-Rivera, Carmelo; Merayo-Chalico, Javier; Torres-Ruiz, Jiram; Manna, Zerai; Hasni, Sarfaraz; Alcocer-Varela, Jorge; Kaplan, Mariana J

2018-06-01

To assess if ubiquitinated proteins potentially present in neutrophil extracellular traps (NETs) can modify cellular responses and induce inflammatory mechanisms in patients with systemic lupus erythematosus (SLE) and healthy subjects. We studied 74 subjects with SLE and 77 healthy controls. Neutrophils and low-density granulocytes were isolated, and NETs were induced. Ubiquitin content was quantified in NETs by western blot analysis, ELISA and immunofluorescence microscopy, while ubiquitination of NET proteins was assessed by immunoprecipitation. Monocyte-derived macrophages from SLE and controls were isolated and stimulated with NETs or ubiquitin. Calcium flux and cytokine synthesis were measured following these stimuli. NETs contain ubiquitinated proteins, with a lower expression of polyubiquitinated proteins in subjects with SLE than in controls. Myeloperoxidase (MPO) is present in ubiquitinated form in NETs. Patients with SLE develop antiubiquitinated MPO antibodies, and titres positively correlate with Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) score (P<0.01), and negatively correlate with complement components (P<0.01). Stimulation of monocyte-derived macrophages with NETs or with ubiquitin led to enhanced calcium flux. In addition, stimulation with NETs led to enhanced cytokine (tumour necrosis factor-α and interleukin-10) production in macrophages from patients with SLE when compared with controls, which was hampered by inhibition of NET internalisation by macrophages. This is the first study to find ubiquitinated proteins in NETs, and evidence for adaptive immune responses directed towards ubiquitinated NET proteins in SLE. The distinct differences in ubiquitin species profile in NETs compared with healthy controls may contribute to dampened anti-inflammatory responses observed in SLE. These results also support a role for extracellular ubiquitin in inflammation in SLE. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Struct2Net: a web service to predict protein–protein interactions using a structure-based approach

PubMed Central

Singh, Rohit; Park, Daniel; Xu, Jinbo; Hosur, Raghavendra; Berger, Bonnie

2010-01-01

Struct2Net is a web server for predicting interactions between arbitrary protein pairs using a structure-based approach. Prediction of protein–protein interactions (PPIs) is a central area of interest and successful prediction would provide leads for experiments and drug design; however, the experimental coverage of the PPI interactome remains inadequate. We believe that Struct2Net is the first community-wide resource to provide structure-based PPI predictions that go beyond homology modeling. Also, most web-resources for predicting PPIs currently rely on functional genomic data (e.g. GO annotation, gene expression, cellular localization, etc.). Our structure-based approach is independent of such methods and only requires the sequence information of the proteins being queried. The web service allows multiple querying options, aimed at maximizing flexibility. For the most commonly studied organisms (fly, human and yeast), predictions have been pre-computed and can be retrieved almost instantaneously. For proteins from other species, users have the option of getting a quick-but-approximate result (using orthology over pre-computed results) or having a full-blown computation performed. The web service is freely available at http://struct2net.csail.mit.edu. PMID:20513650

Development of a 5,000 m(3) super-pressure balloon with a diamond-shaped net

NASA Astrophysics Data System (ADS)

Saito, Yoshitaka; Tanaka, Shigeki; Nakashino, Kyoichi; Matsushima, Kiyoho; Goto, Ken; Furuta, Ryosuke; Domoto, Kodai; Akita, Daisuke; Hashimoto, Hiroyuki

A light super-pressure balloon of which weight will be comparable to the weight of the zero-pressure balloon has been developed using a method to cover a balloon with a diamond-shaped net of high-tensile fibers. The goal is to fly a payload of 900 kg to the altitude of 37 km with a 300,000 m(3) balloon. A flight test of a 3,000 m(3) balloon in the tandem balloon configuration with a 15,000 m(3) zero-pressure balloon was performed in 2012. Although a small gas leak occurred in the super-pressure balloon at the differential pressure of 400 to 500 Pa, the differential pressure reached the highest value of 814 Pa and kept positive through the level flight lasting for 25 minutes due to its slow leakage. To avoid a possible stress concentration to films at the polar area, a new design setting the meridian length of the balloon gore film equal to the length of the net was adopted. A 3-m balloon with the design was developed and its capacity to resist pressure at room temperature and at -30 (°) C was checked through the ground inflation tests. In 2013, a balloon of the same model was launched in the tandem balloon configuration with 2 kg rubber balloons. It was confirmed that the balloon could withstand the maximum differential pressure of 6,280 Pa, could withstand the differential pressure of 5,600 Pa for 2 hours, and there was a small gas leak through a hole with an area of 0.4 mm(2) which was also found in the ground leakage test. These results indicated that the improvement was adequate and there was no problem for the super-pressure balloon to fly in the environment of the stratosphere except for the problem of the small gas leak. In 2014, a flight test of a 5,000 m(3) balloon will be performed. In this paper, after reviewing the method to cover a balloon with a diamond-shaped net, the current status of the development will be reported.

Fluorescence Competition Assay Measurements of Free Energy Changes for RNA Pseudoknots†

PubMed Central

2009-01-01

RNA pseudoknots have important functions, and thermodynamic stability is a key to predicting pseudoknots in RNA sequences and to understanding their functions. Traditional methods, such as UV melting and differential scanning calorimetry, for measuring RNA thermodynamics are restricted to temperature ranges around the melting temperature for a pseudoknot. Here, we report RNA pseudoknot free energy changes at 37 °C measured by fluorescence competition assays. Sequence-dependent studies for the loop 1−stem 2 region reveal (1) the individual nearest-neighbor hydrogen bonding (INN-HB) model provides a reasonable estimate for the free energy change when a Watson−Crick base pair in stem 2 is changed, (2) the loop entropy can be estimated by a statistical polymer model, although some penalty for certain loop sequences is necessary, and (3) tertiary interactions can significantly stabilize pseudoknots and extending the length of stem 2 may alter tertiary interactions such that the INN-HB model does not predict the net effect of adding a base pair. The results can inform writing of algorithms for predicting and/or designing RNA secondary structures. PMID:19921809

Interactive effects of oxygen, carbon dioxide and flow on photosynthesis and respiration in the scleractinian coral Galaxea fascicularis.

PubMed

Osinga, Ronald; Derksen-Hooijberg, Marlous; Wijgerde, Tim; Verreth, Johan A J

2017-06-15

Rates of dark respiration and net photosynthesis were measured for six replicate clonal fragments of the stony coral Galaxea fascicularis (Linnaeus 1767), which were incubated under 12 different combinations of dissolved oxygen (20%, 100% and 150% saturation), dissolved carbon dioxide (9.5 and 19.1 µmol l -1 ) and water flow (1-1.6 versus 4-13 cm s -1 ) in a repeated measures design. Dark respiration was enhanced by increased flow and increased oxygen saturation in an interactive way, which relates to improved oxygen influx into the coral tissue. Oxygen saturation did not influence net photosynthesis: neither hypoxia nor hyperoxia affected net photosynthesis, irrespective of flow and pH, which suggests that hyperoxia does not induce high rates of photorespiration in this coral. Flow and pH had a synergistic effect on net photosynthesis: at high flow, a decrease in pH stimulated net photosynthesis by 14%. These results indicate that for this individual of G. fascicularis , increased uptake of carbon dioxide rather than increased efflux of oxygen explains the beneficial effect of water flow on photosynthesis. Rates of net photosynthesis measured in this study are among the highest ever recorded for scleractinian corals and confirm a strong scope for growth. © 2017. Published by The Company of Biologists Ltd.

Disentangling Facilitation Along the Life Cycle: Impacts of Plant-Plant Interactions at Vegetative and Reproductive Stages in a Mediterranean Forb.

PubMed

García-Cervigón, Ana I; Iriondo, José M; Linares, Juan C; Olano, José M

2016-01-01

Facilitation enables plants to improve their fitness in stressful environments. The overall impact of plant-plant interactions on the population dynamics of protégées is the net result of both positive and negative effects that may act simultaneously along the plant life cycle, and depends on the environmental context. This study evaluates the impact of the nurse plant Juniperus sabina on different stages of the life cycle of the forb Helleborus foetidus. Growth, number of leaves, flowers, carpels, and seeds per flower were compared for 240 individuals collected under nurse canopies and in open areas at two sites with contrasting stress levels. Spatial associations with nurse plants and age structures were also checked. A structural equation model was built to test the effect of facilitation on fecundity, accounting for sequential steps from flowering to seed production. The net impact of nurse plants depended on a combination of positive and negative effects on vegetative and reproductive variables. Although nurse plants caused a decrease in flower production at the low-stress site, their net impact there was neutral. In contrast, at the high-stress site the net outcome of plant-plant interactions was positive due to an increase in effective recruitment, plant density, number of viable carpels per flower, and fruit set under nurse canopies. The naturally lower rates of secondary growth and flower production at the high-stress site were compensated by the net positive impact of nurse plants here. Our results emphasize the need to evaluate entire processes and not only final outcomes when studying plant-plant interactions.

The net effect of abiotic conditions and biotic interactions in a semi-arid ecosystem NE Spain: implications for the management and restoration.

NASA Astrophysics Data System (ADS)

Pueyo, Yolanda; Arroyo, Antonio I.; Saiz, Hugo; Alados, Concepción L.

2014-05-01

Degradation in arid and semiarid lands can be irreversible without human intervention, due to a positive plant-soil feedback where the loss of vegetation cover leads to soil degradation, which in turn hampers plant establishment. Human intervention in restoration actions usually involves the amendment of the degraded abiotic conditions, revegetation of bare areas, or both. However, abiotic amelioration is often expensive and too intrusive, and revegetation is not successful in many cases. Biotic interactions between plants, and more specifically facilitation by a "nurse" plant, have been proposed as a new via to take profit of improved abiotic conditions without intervention, and to increase the success rate of revegetation actions. But "nurse" plants can also interfere with others (i.e. by competition for resources or the release of allelopathic compounds), and the net balance between facilitation and interference could depend on plant types involved. We present recent observational and experimental studies performed in the semiarid ecosystems of the Middle Ebro Valley (NE Spain) about the role of abiotic conditions and biotic interactions in the productivity, dynamics and diversity of plant communities under different stress conditions (aridity and grazing). We found that all plant types studied (shrubs and perennial grasses) improved abiotic conditions (soil temperature and water availability for plants) with respect to open areas. However, only some shrubs (mainly Salsola vermiculata) had a positive net balance in the biotic interactions between plants, while other shrubs (Artemisia herba-alba) and perennial grasses (Lygeum spartum) showed interference with other plants. Moreover, the net balance between facilitation and interference among plants in the community shifted from competitive to neutral or from neutral to facilitative with increasing aridity. Grazing status did not strongly change the net biotic interactions between plants. Our results suggest that the success of the restoration actions with "nurse" plants will be highly dependent on the plant type involved and the abiotic site conditions, fact that needs to be considered in restoration plans.

Clustering of host-seeking activity of Anopheles gambiae mosquitoes at the top surface of a human-baited bed net

PubMed Central

2013-01-01

Background Knowledge of the interactions between mosquitoes and humans, and how vector control interventions affect them, is sparse. A study exploring host-seeking behaviour at a human-occupied bed net, a key event in such interactions, is reported here. Methods Host-seeking female Anopheles gambiae activity was studied using a human-baited ‘sticky-net’ (a bed net without insecticide, coated with non-setting adhesive) to trap mosquitoes. The numbers and distribution of mosquitoes captured on each surface of the bed net were recorded and analysed using non-parametric statistical methods and random effects regression analysis. To confirm sticky-net reliability, the experiment was repeated using a pitched sticky-net (tilted sides converging at apex, i.e., neither horizontal nor vertical). The capture efficiency of horizontal and vertical sticky surfaces were compared, and the potential repellency of the adhesive was investigated. Results In a semi-field experiment, more mosquitoes were caught on the top (74-87%) than on the sides of the net (p < 0.001). In laboratory experiments, more mosquitoes were caught on the top than on the sides in human-baited tests (p < 0.001), significantly different to unbaited controls (p < 0.001) where most mosquitoes were on the sides (p = 0.047). In both experiments, approximately 70% of mosquitoes captured on the top surface were clustered within a 90 × 90 cm (or lesser) area directly above the head and chest (p < 0.001). In pitched net tests, similar clustering occurred over the sleeper’s head and chest in baited tests only (p < 0.001). Capture rates at horizontal and vertical surfaces were not significantly different and the sticky-net was not repellent. Conclusion This study demonstrated that An. gambiae activity occurs predominantly within a limited area of the top surface of bed nets. The results provide support for the two-in-one bed net design for managing pyrethroid-resistant vector populations. Further exploration of vector behaviour at the bed net interface could contribute to additional improvements in insecticide-treated bed net design or the development of novel vector control tools. PMID:23902661

Optimal Control of Malaria Transmission using Insecticide Treated Nets and Spraying

NASA Astrophysics Data System (ADS)

Athina, D.; Bakhtiar, T.; Jaharuddin

2017-03-01

In this paper, we consider a model of the transmission of malaria which was developed by Silva and Torres equipped with two control variables, namely the use of insecticide treated nets (ITN) to reduce the number of human beings infected and spraying to reduce the number of mosquitoes. Pontryagin maximum principle was applied to derive the differential equation system as optimality conditions which must be satisfied by optimal control variables. The Mangasarian sufficiency theorem shows that Pontryagin maximum principle is necessary as well as sufficient conditions for optimization problem. The 4th-order Runge Kutta method was then performed to solve the differential equations system. The numerical results show that both controls given at once can reduce the number of infected individuals as well as the number of mosquitoes which reduce the impact of malaria transmission.

Bevacizumab plus capecitabine in patients with progressive advanced well-differentiated neuroendocrine tumors of the gastro-intestinal (GI-NETs) tract (BETTER trial)--a phase II non-randomised trial.

PubMed

Mitry, Emmanuel; Walter, Thomas; Baudin, Eric; Kurtz, Jean-Emmanuel; Ruszniewski, Philippe; Dominguez-Tinajero, Sophie; Bengrine-Lefevre, Leïla; Cadiot, Guillaume; Dromain, Clarisse; Farace, Françoise; Rougier, Philippe; Ducreux, Michel

2014-12-01

Gastro-intestinal neuroendocrine tumours (GI-NETs) are chemotherapy-resistant tumours. Bevacizumab, an inhibitor of vascular endothelial growth factor (VEGF), has shown promising results in several phase II trials of gastro-entero-pancreatic-NETs. We assessed bevacizumab combined with capecitabine, specifically in GI-NET patients. BEvacizumab in The Treament of neuroEndocrine tumoRs (BETTER) was a multicentre, open-label, non-randomised, two-group phase II trial. Here we present the group of patients with progressive, metastatic, well-differentiated GI-NETs. Patients Eastern Cooperative Oncology Group-performance status (ECOG-PS)⩽2, Ki-67 proliferation rate <15% and no prior systemic chemotherapy were treated with bevacizumab (7.5 mg/kg/q3w) and capecitabine (1000 mg/m2 twice daily, orally d1-14, resumed on d22) for 6-24 months. The primary end-point was progression-free survival (PFS); secondary end-points included overall survival (OS), response rate, safety and quality of life. Of the 49 patients included, 53% were men, median age was 60 years (41-82), primary tumour site was ileal in 82% patients and Ki-67 was <15% in 48 patients and not available for one patient. After a maximum of 24 month follow-up per patient, the median PFS by investigator assessment was 23.4 months [95% confidence interval (CI): 13.2; not reached] and the overall disease control rate was 88% (18% partial response, 70% stable disease). The 2-year survival rate was 85%. Median OS was not reached. The most frequent grade 3-4 adverse events were hypertension (31%), diarrhoea (14%) and hand-foot syndrome (10%). The combination of bevacizumab and capecitabine showed clinical activity and a manageable safety profile in the treatment of GI-NETs that warrant confirmation in a randomised phase III trial. Copyright © 2014 Elsevier Ltd. All rights reserved.

White blood cells identification system based on convolutional deep neural learning networks.

PubMed

Shahin, A I; Guo, Yanhui; Amin, K M; Sharawi, Amr A

2017-11-16

White blood cells (WBCs) differential counting yields valued information about human health and disease. The current developed automated cell morphology equipments perform differential count which is based on blood smear image analysis. Previous identification systems for WBCs consist of successive dependent stages; pre-processing, segmentation, feature extraction, feature selection, and classification. There is a real need to employ deep learning methodologies so that the performance of previous WBCs identification systems can be increased. Classifying small limited datasets through deep learning systems is a major challenge and should be investigated. In this paper, we propose a novel identification system for WBCs based on deep convolutional neural networks. Two methodologies based on transfer learning are followed: transfer learning based on deep activation features and fine-tuning of existed deep networks. Deep acrivation featues are extracted from several pre-trained networks and employed in a traditional identification system. Moreover, a novel end-to-end convolutional deep architecture called "WBCsNet" is proposed and built from scratch. Finally, a limited balanced WBCs dataset classification is performed through the WBCsNet as a pre-trained network. During our experiments, three different public WBCs datasets (2551 images) have been used which contain 5 healthy WBCs types. The overall system accuracy achieved by the proposed WBCsNet is (96.1%) which is more than different transfer learning approaches or even the previous traditional identification system. We also present features visualization for the WBCsNet activation which reflects higher response than the pre-trained activated one. a novel WBCs identification system based on deep learning theory is proposed and a high performance WBCsNet can be employed as a pre-trained network. Copyright © 2017. Published by Elsevier B.V.

Low dose DTIC is effective and safe in pretreated patients with well differentiated neuroendocrine tumors.

PubMed

Mueller, Daniela; Krug, Sebastian; Majumder, Moushumee; Rinke, Anja; Gress, Thomas Matthias

2016-08-18

Streptozocin (STZ) based chemotherapy is recommended for patients with metastatic pancreatic neuroendocrine tumors (pNET). Temozolomide as mono- or combination therapy has been suggested to be a promising alternative. However, the treatment is costly and not approved for the treatment of pNETs. Dacarbazine (DTIC) shares the active metabolite with temozolomide and is broadly available at a low cost. The aim of this study was a retrospective evaluation of the efficacy and tolerability of a lower dose DTIC-regimen in patients with progressive advanced NETs. We retrospectively analyzed 75 patients with NETs predominantly of pancreatic origin treated at our center between 1998 and 2013. 650 mg/m(2) of DTIC were administered intravenously over 60 min every 4 weeks. Morphological response was assessed according to RECIST1.1 criteria. The median progression free survival (PFS) was calculated using Kaplan-Meier and Cox regression methods, respectively. Univariate analyses of possible prognostic markers were performed. The objective response rate (ORR) was 27 % for the entire cohort and 32 % in 50 pNET patients, respectively. Stable disease (SD) was documented in 29 patients (39 %). Median PFS (mPFS) in patients receiving DTIC was 7 months (3.9-10; 95 % confidence interval). Radiological and biochemical response were the only significant prognostic markers for longer PFS in univariate analysis. Treatment was well tolerated. Nausea was the most common side effect (31 %), only one case (1.3 %) of grade 3 toxicity (vomiting) occurred. Low dose DTIC chemotherapy is an effective and well-tolerated treatment option in patients with progressive well differentiated neuroendocrine neoplasms, especially of pancreatic origin.

Which is the best strategy for diagnosing bronchial carcinoid tumours? The role of dual tracer PET/CT scan.

PubMed

Lococo, Filippo; Treglia, Giorgio

2014-01-01

Bronchial carcinoids (BC) are rare well-differentiated neuroendocrine tumours (NET) sub-classified into typical (TC) and atypical carcinoids (AC). A correct pathological identification in the pre-operative setting is a key element for planning the best strategy of care, considering the different biological behavior of TC and AC. Controversial results have been reported on the diagnostic accuracy of fluorine-18-fluorodeoxyglucose positron emission tomography/computed tomography ((18)F-FDG PET/CT) in BC. On the other hand, there is increasing evidence supporting the use of PET with somatostatin analogues (dotanoc, dotatoc or dotatate) labeled with gallium-68 ((68)Ga) in pulmonary NET. Based on information obtained by using different radiopharmaceuticals and different (68)Ga labeled somatostatin analogues in PET and PET/CT studies, we are able to diagnose BC. In conclusion, by using somatostatin receptor imaging and (18)F-FDG PET/CT scan, we can differentiate BC from benign pulmonary lesions and TC from AC by specific diagnostic patterns. Clinical trials on larger groups of patient would allow for a better and "tailored" therapeutic strategy in NET patients using dual-tracer PET/CT to identify BC and distinguish between TC and AC.

Bone age detection via carpogram analysis using convolutional neural networks

NASA Astrophysics Data System (ADS)

Torres, Felipe; Bravo, María. Alejandra; Salinas, Emmanuel; Triana, Gustavo; Arbeláez, Pablo

2017-11-01

Bone age assessment is a critical factor for determining delayed development in children, which can be a sign of pathologies such as endocrine diseases, growth abnormalities, chromosomal, neurological and congenital disorders among others. In this paper we present BoneNet, a methodology to assess automatically the skeletal maturity state in pediatric patients based on Convolutional Neural Networks. We train and evaluate our algorithm on a database of X-Ray images provided by the hospital Fundacion Santa Fe de Bogot ´ a with around 1500 images of patients between the ages 1 to 18. ´ We compare two different architectures to classify the given data in order to explore the generality of our method. To accomplish this, we define multiple binary age assessment problems, dividing the data by bone age and differentiating the patients by their gender. Thus, exploring several parameters, we develop BoneNet. Our approach is holistic, efficient, and modular, since it is possible for the specialists to use all the networks combined to determine how is the skeletal maturity of a patient. BoneNet achieves over 90% accuracy for most of the critical age thresholds, when differentiating the images between over or under a given age.

Thermal adaptation of net ecosystem exchange

USDA-ARS?s Scientific Manuscript database

Thermal adaptation of gross primary production and ecosystem respiration has been well documented over broad thermal gradients. However, no study has examined their interaction as a function of temperature, i.e. the thermal responses of net ecosystem exchange of carbon (NEE). In this study, we const...

Formation of a new archetypal Metal-Organic Framework from a simple monatomic liquid

NASA Astrophysics Data System (ADS)

Metere, Alfredo; Oleynikov, Peter; Dzugutov, Mikhail; O'Keeffe, Michael

2014-12-01

We report a molecular-dynamics simulation of a single-component system of particles interacting via a spherically symmetric potential that is found to form, upon cooling from a liquid state, a low-density porous crystalline phase. Its structure analysis demonstrates that the crystal can be described by a net with a topology that belongs to the class of topologies characteristic of the Metal-Organic Frameworks (MOFs). The observed net is new, and it is now included in the Reticular Chemistry Structure Resource database. The observation that a net topology characteristic of MOF crystals, which are known to be formed by a coordination-driven self-assembly process, can be reproduced by a thermodynamically stable configuration of a simple single-component system of particles opens a possibility of using these models in studies of MOF nets. It also indicates that structures with MOF topology, as well as other low-density porous crystalline structures can possibly be produced in colloidal systems of spherical particles, with an appropriate tuning of interparticle interaction.

78 FR 34652 - Proposed Information Collection; Comment Request; Reporting Requirements for Sea Otter...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-10

.... If a southern sea otter is entangled in a net, regardless of whether the animal is injured or killed... of interaction; otter's behavior during interaction; and, measures taken to avoid interaction. II...

Predicting catalyst-support interactions between metal nanoparticles and amorphous silica supports

NASA Astrophysics Data System (ADS)

Ewing, Christopher S.; Veser, Götz; McCarthy, Joseph J.; Lambrecht, Daniel S.; Johnson, J. Karl

2016-10-01

Metal-support interactions significantly affect the stability and activity of supported catalytic nanoparticles (NPs), yet there is no simple and reliable method for estimating NP-support interactions, especially for amorphous supports. We present an approach for rapid prediction of catalyst-support interactions between Pt NPs and amorphous silica supports for NPs of various sizes and shapes. We use density functional theory calculations of 13 atom Pt clusters on model amorphous silica supports to determine linear correlations relating catalyst properties to NP-support interactions. We show that these correlations can be combined with fast discrete element method simulations to predict adhesion energy and NP net charge for NPs of larger sizes and different shapes. Furthermore, we demonstrate that this approach can be successfully transferred to Pd, Au, Ni, and Fe NPs. This approach can be used to quickly screen stability and net charge transfer and leads to a better fundamental understanding of catalyst-support interactions.

Validated simulator for space debris removal with nets and other flexible tethers applications

NASA Astrophysics Data System (ADS)

Gołębiowski, Wojciech; Michalczyk, Rafał; Dyrek, Michał; Battista, Umberto; Wormnes, Kjetil

2016-12-01

In the context of active debris removal technologies and preparation activities for the e.Deorbit mission, a simulator for net-shaped elastic bodies dynamics and their interactions with rigid bodies, has been developed. Its main application is to aid net design and test scenarios for space debris deorbitation. The simulator can model all the phases of the debris capturing process: net launch, flight and wrapping around the target. It handles coupled simulation of rigid and flexible bodies dynamics. Flexible bodies were implemented using Cosserat rods model. It allows to simulate flexible threads or wires with elasticity and damping for stretching, bending and torsion. Threads may be combined into structures of any topology, so the software is able to simulate nets, pure tethers, tether bundles, cages, trusses, etc. Full contact dynamics was implemented. Programmatic interaction with simulation is possible - i.e. for control implementation. The underlying model has been experimentally validated and due to significant gravity influence, experiment had to be performed in microgravity conditions. Validation experiment for parabolic flight was a downscaled process of Envisat capturing. The prepacked net was launched towards the satellite model, it expanded, hit the model and wrapped around it. The whole process was recorded with 2 fast stereographic camera sets for full 3D trajectory reconstruction. The trajectories were used to compare net dynamics to respective simulations and then to validate the simulation tool. The experiments were performed on board of a Falcon-20 aircraft, operated by National Research Council in Ottawa, Canada. Validation results show that model reflects phenomenon physics accurately enough, so it may be used for scenario evaluation and mission design purposes. The functionalities of the simulator are described in detail in the paper, as well as its underlying model, sample cases and methodology behind validation. Results are presented and typical use cases are discussed showing that the software may be used to design throw nets for space debris capturing, but also to simulate deorbitation process, chaser control system or general interactions between rigid and elastic bodies - all in convenient and efficient way. The presented work was led by SKA Polska under the ESA contract, within the CleanSpace initiative.

Positive interactions between irrawaddy dolphins and artisanal fishers in the Chilika Lagoon of eastern India are driven by ecology, socioeconomics, and culture.

PubMed

D'Lima, Coralie; Marsh, Helene; Hamann, Mark; Sinha, Anindya; Arthur, Rohan

2014-09-01

In human-dominated landscapes, interactions and perceptions towards wildlife are influenced by multidimensional drivers. Understanding these drivers could prove useful for wildlife conservation. We surveyed the attitudes and perceptions of fishers towards threatened Irrawaddy dolphins (Orcaella brevirostris) at Chilika Lagoon India. To validate the drivers of fisher perceptions, we : (1) observed dolphin foraging behavior at stake nets, and (2) compared catch per unit effort (CPUE) and catch income of fishers from stake nets in the presence and absence of foraging dolphins. We found that fishers were mostly positive towards dolphins, believing that dolphins augmented their fish catch and using culture to express their perceptions. Foraging dolphins were observed spending half their time at stake nets and were associated with significantly higher catch income and CPUE of mullet (Liza sp.), a locally preferred food fish species. Wildlife conservation efforts should use the multidimensional drivers of human-wildlife interactions to involve local stakeholders in management.

Facilitative and competitive interaction components among New England salt marsh plants

USDA-ARS?s Scientific Manuscript database

Intra- and interspecific interactions can be broken down into facilitative and competitive components. The net interaction between two organisms is simply the sum of these counteracting elements. Disentangling the positive and negative components of species interactions is a critical step in advanc...

CoryneRegNet 3.0--an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli.

PubMed

Baumbach, Jan; Wittkop, Tobias; Rademacher, Katrin; Rahmann, Sven; Brinkrolf, Karina; Tauch, Andreas

2007-04-30

CoryneRegNet is an ontology-based data warehouse for the reconstruction and visualization of transcriptional regulatory interactions in prokaryotes. To extend the biological content of CoryneRegNet, we added comprehensive data on transcriptional regulations in the model organism Escherichia coli K-12, originally deposited in the international reference database RegulonDB. The enhanced web interface of CoryneRegNet offers several types of search options. The results of a search are displayed in a table-based style and include a visualization of the genetic organization of the respective gene region. Information on DNA binding sites of transcriptional regulators is depicted by sequence logos. The results can also be displayed by several layouters implemented in the graphical user interface GraphVis, allowing, for instance, the visualization of genome-wide network reconstructions and the homology-based inter-species comparison of reconstructed gene regulatory networks. In an application example, we compare the composition of the gene regulatory networks involved in the SOS response of E. coli and Corynebacterium glutamicum. CoryneRegNet is available at the following URL: http://www.cebitec.uni-bielefeld.de/groups/gi/software/coryneregnet/.

NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks.

PubMed

Hu, Jialu; Kehr, Birte; Reinert, Knut

2014-02-15

Owing to recent advancements in high-throughput technologies, protein-protein interaction networks of more and more species become available in public databases. The question of how to identify functionally conserved proteins across species attracts a lot of attention in computational biology. Network alignments provide a systematic way to solve this problem. However, most existing alignment tools encounter limitations in tackling this problem. Therefore, the demand for faster and more efficient alignment tools is growing. We present a fast and accurate algorithm, NetCoffee, which allows to find a global alignment of multiple protein-protein interaction networks. NetCoffee searches for a global alignment by maximizing a target function using simulated annealing on a set of weighted bipartite graphs that are constructed using a triplet approach similar to T-Coffee. To assess its performance, NetCoffee was applied to four real datasets. Our results suggest that NetCoffee remedies several limitations of previous algorithms, outperforms all existing alignment tools in terms of speed and nevertheless identifies biologically meaningful alignments. The source code and data are freely available for download under the GNU GPL v3 license at https://code.google.com/p/netcoffee/.

Molecular Architecture and Functional Analysis of NetB, a Pore-forming Toxin from Clostridium perfringens*

PubMed Central

Savva, Christos G.; Fernandes da Costa, Sérgio P.; Bokori-Brown, Monika; Naylor, Claire E.; Cole, Ambrose R.; Moss, David S.; Titball, Richard W.; Basak, Ajit K.

2013-01-01

NetB is a pore-forming toxin produced by Clostridium perfringens and has been reported to play a major role in the pathogenesis of avian necrotic enteritis, a disease that has emerged due to the removal of antibiotics in animal feedstuffs. Here we present the crystal structure of the pore form of NetB solved to 3.9 Å. The heptameric assembly shares structural homology to the staphylococcal α-hemolysin. However, the rim domain, a region that is thought to interact with the target cell membrane, shows sequence and structural divergence leading to the alteration of a phosphocholine binding pocket found in the staphylococcal toxins. Consistent with the structure we show that NetB does not bind phosphocholine efficiently but instead interacts directly with cholesterol leading to enhanced oligomerization and pore formation. Finally we have identified conserved and non-conserved amino acid positions within the rim loops that significantly affect binding and toxicity of NetB. These findings present new insights into the mode of action of these pore-forming toxins, enabling the design of more effective control measures against necrotic enteritis and providing potential new tools to the field of bionanotechnology. PMID:23239883

Protein destabilisation in ionic liquids: the role of preferential interactions in denaturation.

PubMed

Figueiredo, Angelo Miguel; Sardinha, Joao; Moore, Geoffrey R; Cabrita, Eurico J

2013-12-07

The preferential binding of anions and cations in aqueous solutions of the ionic liquids (ILs) 1-butyl-3-methylimidazolium ([C4mim](+)) and 1-ethyl-3-methylimidazolium ([C2mim](+)) chloride and dicyanamide (dca(-)) with the small alpha-helical protein Im7 was investigated using a combination of differential scanning calorimetry, NMR spectroscopy and molecular dynamics (MD) simulations. Our results show that direct ion interactions are crucial to understand the effects of ILs on the stability of proteins and that an anion effect is dominant. We show that the binding of weakly hydrated anions to positively charged or polar residues leads to the partial dehydration of the backbone groups, and is critical to control stability, explaining why dca(-) is more denaturing than Cl(-). Direct cation-protein interactions also mediate stability; cation size and hydrophobicity are relevant to account for destabilisation as shown by the effect of [C4mim](+) compared to [C2mim](+). The specificity in the interaction of IL ions with protein residues established by weak favourable interactions is confirmed by NMR chemical shift perturbation, amide hydrogen exchange data and MD simulations. Differences in specificity are due to the balance of interaction established between ion pairs and ion-solvent that determine the type of residues affected. When the interaction of both cation and anion with the protein is strong the net result is similar to a non-specific interaction, leading ultimately to unfolding. Since the nature of the ions is a determinant of the level of interaction with the protein towards denaturation or stabilisation, ILs offer a unique possibility to modulate protein stabilisation or even folding events.

Glyoxalase 1 copy number variation in patients with well differentiated gastro-entero-pancreatic neuroendocrine tumours (GEP-NET)

PubMed Central

Xue, Mingzhan; Shafie, Alaa; Qaiser, Talha; Rajpoot, Nasir M.; Kaltsas, Gregory; James, Sean; Gopalakrishnan, Kishore; Fisk, Adrian; Dimitriadis, Georgios K.; Grammatopoulos, Dimitris K.; Rabbani, Naila; Thornalley, Paul J.; Weickert, Martin O.

2017-01-01

Background The glyoxalase-1 gene (GLO1) is a hotspot for copy-number variation (CNV) in human genomes. Increased GLO1 copy-number is associated with multidrug resistance in tumour chemotherapy, but prevalence of GLO1 CNV in gastro-entero-pancreatic neuroendocrine tumours (GEP-NET) is unknown. Methods GLO1 copy-number variation was measured in 39 patients with GEP-NET (midgut NET, n = 25; pancreatic NET, n = 14) after curative or debulking surgical treatment. Primary tumour tissue, surrounding healthy tissue and, where applicable, additional metastatic tumour tissue were analysed, using real time qPCR. Progression and survival following surgical treatment were monitored over 4.2 ± 0.5 years. Results In the pooled GEP-NET cohort, GLO1 copy-number in healthy tissue was 2.0 in all samples but significantly increased in primary tumour tissue in 43% of patients with pancreatic NET and in 72% of patients with midgut NET, mainly driven by significantly higher GLO1 copy-number in midgut NET. In tissue from additional metastases resection (18 midgut NET and one pancreatic NET), GLO1 copy number was also increased, compared with healthy tissue; but was not significantly different compared with primary tumour tissue. During mean 3 - 5 years follow-up, 8 patients died and 16 patients showed radiological progression. In midgut NET, a high GLO1 copy-number was associated with earlier progression. In NETs with increased GLO1 copy number, there was increased Glo1 protein expression compared to non-malignant tissue. Conclusions GLO1 copy-number was increased in a large percentage of patients with GEP-NET and correlated positively with increased Glo1 protein in tumour tissue. Analysis of GLO1 copy-number variation particularly in patients with midgut NET could be a novel prognostic marker for tumour progression. PMID:29100361

BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks

PubMed Central

Rialle, Stéphanie; Felicori, Liza; Dias-Lopes, Camila; Pérès, Sabine; El Atia, Sanaâ; Thierry, Alain R.; Amar, Patrick; Molina, Franck

2010-01-01

Motivation: Synthetic biology studies how to design and construct biological systems with functions that do not exist in nature. Biochemical networks, although easier to control, have been used less frequently than genetic networks as a base to build a synthetic system. To date, no clear engineering principles exist to design such cell-free biochemical networks. Results: We describe a methodology for the construction of synthetic biochemical networks based on three main steps: design, simulation and experimental validation. We developed BioNetCAD to help users to go through these steps. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB, a database of parts for synthetic biology. BioNetCAD enables also simulations with the HSim software and the classical Ordinary Differential Equations (ODE). We demonstrate with a case study that BioNetCAD can rationalize and reduce further experimental validation during the construction of a biochemical network. Availability and implementation: BioNetCAD is freely available at http://www.sysdiag.cnrs.fr/BioNetCAD. It is implemented in Java and supported on MS Windows. CompuBioTicDB is freely accessible at http://compubiotic.sysdiag.cnrs.fr/ Contact: stephanie.rialle@sysdiag.cnrs.fr; franck.molina@sysdiag.cnrs.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20628073

A transmission-line model of back-cavity dynamics for in-plane pressure-differential microphones.

PubMed

Kim, Donghwan; Kuntzman, Michael L; Hall, Neal A

2014-11-01

Pressure-differential microphones inspired by the hearing mechanism of a special parasitoid fly have been described previously. The designs employ a beam structure that rotates about two pivots over an enclosed back volume. The back volume is only partially enclosed due to open slits around the perimeter of the beam. The open slits enable incoming sound waves to affect the pressure profile in the microphone's back volume. The goal of this work is to study the net moment applied to pressure-differential microphones by an incoming sound wave, which in-turn requires modeling the acoustic pressure distribution within the back volume. A lumped-element distributed transmission-line model of the back volume is introduced for this purpose. It is discovered that the net applied moment follows a low-pass filter behavior such that, at frequencies below a corner frequency depending on geometrical parameters of the design, the applied moment is unaffected by the open slits. This is in contrast to the high-pass filter behavior introduced by barometric pressure vents in conventional omnidirectional microphones. The model accurately predicts observed curvature in the frequency response of a prototype pressure-differential microphone 2 mm × 1 mm × 0.5 mm in size and employing piezoelectric readout.

Differences in emergency colorectal surgery in Medicaid and uninsured patients by hospital safety net status.

PubMed

Bradley, Cathy J; Dahman, Bassam; Sabik, Lindsay M

2015-02-01

We examined whether safety net hospitals reduce the likelihood of emergency colorectal cancer (CRC) surgery in uninsured and Medicaid-insured patients. If these patients have better access to care through safety net providers, they should be less likely to undergo emergency resection relative to similar patients at non- safety net hospitals. Using population-based data, we estimated the relationship between safety net hospitals, patient insurance status, and emergency CRC surgery. We extracted inpatient admission data from the Virginia Health Information discharge database and matched them to the Virginia Cancer Registry for patients aged 21 to 64 years who underwent a CRC resection between January 1, 1999, and December 31, 2005 (n = 5488). We differentiated between medically defined emergencies and those that originated in the emergency department (ED). For each definition of emergency surgery, we estimated the linear probability models of the effects of being treated at a safety net hospital on the probability of having an emergency resection. Safety net hospitals reduce emergency surgeries among uninsured and Medicaid CRC patients. When defining an emergency resection as those that involved an ED visit, these patients were 15 to 20 percentage points less likely to have an emergency resection when treated in a safety net hospital. Our results suggest that these hospitals provide a benefit, most likely through the access they afford to timely and appropriate care, to uninsured and Medicaid-insured patients relative to hospitals without a safety net mission.

SWMPrats.net: A Web-Based Resource for Exploring SWMP Data

EPA Science Inventory

SWMPrats.net is a web-based resource that provides accessible approaches to using SWMP data. The website includes a user forum with instructional ‘Plots of the Month’; links to workshop content; and a description of the SWMPr data analysis package for R. Interactive...

Game Theory .net.

ERIC Educational Resources Information Center

Shor, Mikhael

2003-01-01

States making game theory relevant and accessible to students is challenging. Describes the primary goal of GameTheory.net is to provide interactive teaching tools. Indicates the site strives to unite educators from economics, political and computer science, and ecology by providing a repository of lecture notes and tests for courses using…

Neutrophil extracellular traps possess anti-human respiratory syncytial virus activity: Possible interaction with the viral F protein.

PubMed

Souza, Priscila Silva Sampaio; Barbosa, Lia Vezenfard; Diniz, Larissa Figueiredo Alves; da Silva, Gabriel Soares; Lopes, Bruno Rafael Pereira; Souza, Pedro Miyadaira Ribeiro; de Araujo, Gabriela Campos; Pessoa, Diogo; de Oliveira, Juliana; Souza, Fátima Pereira; Toledo, Karina Alves

2018-06-02

Human respiratory syncytial virus (hRSV) is one of the main etiological agents of diseases of the lower respiratory tract, and is often responsible for the hospitalization of children and the elderly. To date, treatments are only palliative and there is no vaccine available. The airways of patients infected with hRSV exhibit intense neutrophil infiltration, which is responsible for the release of neutrophil extracellular traps (NETs). These are extracellular structures consisting of DNA associated with intracellular proteins, and are efficient in capturing and eliminating various microorganisms, including some viruses. hRSV induces the release of NETs into the lung tissue of infected individuals; however, the pathophysiological consequences of this event have not been elucidated. The objective of this study was to utilize in vitro and in silico assays to investigate the impact of NETs on hRSV infection. NETs, generated by neutrophils stimulated with phorbol myristate acetate (PMA), displayed long fragments of DNA and an electrophoretic profile suggestive of the presence of proteins that are classically associated with these structures (elastase, cathepsin G, myeloperoxidase, and histones). The presence of NETs (>2 μg/ml) in HEp-2 cell culture medium resulted in cellular cytotoxicity of less than 50%. Pre-incubation (1 h) of viral particles (multiplicity of infection (MOI) values of 0.1, 0.5, and 1.0) with NETs (2-32 μg/ml) resulted in cellular protection from virus-induced death of HEp-2 cells. Concurrently, there was a reduction in the formation of syncytia, which is related to decreased viral spread in infected tissue. Results from western blotting and molecular docking, suggest interactions between F protein of the hRSV viral envelope and BPI (bactericidal permeability-increasing protein), a microbicidal member of NETs. Interactions occurred at sites important for the neutralization and coordination of the hRSV infection/replication process. Our results showed that the presence of NETs decreases hRSV-induced cellular damage, possibly by directly affecting viral particle capture and/or interfering with the fusion activity of the F protein. These findings broaden the understanding of the role of NETs during hRSV infection. Copyright © 2018 Elsevier B.V. All rights reserved.

Deep Convolutional Neural Networks for Endotracheal Tube Position and X-ray Image Classification: Challenges and Opportunities.

PubMed

Lakhani, Paras

2017-08-01

The goal of this study is to evaluate the efficacy of deep convolutional neural networks (DCNNs) in differentiating subtle, intermediate, and more obvious image differences in radiography. Three different datasets were created, which included presence/absence of the endotracheal (ET) tube (n = 300), low/normal position of the ET tube (n = 300), and chest/abdominal radiographs (n = 120). The datasets were split into training, validation, and test. Both untrained and pre-trained deep neural networks were employed, including AlexNet and GoogLeNet classifiers, using the Caffe framework. Data augmentation was performed for the presence/absence and low/normal ET tube datasets. Receiver operating characteristic (ROC), area under the curves (AUC), and 95% confidence intervals were calculated. Statistical differences of the AUCs were determined using a non-parametric approach. The pre-trained AlexNet and GoogLeNet classifiers had perfect accuracy (AUC 1.00) in differentiating chest vs. abdominal radiographs, using only 45 training cases. For more difficult datasets, including the presence/absence and low/normal position endotracheal tubes, more training cases, pre-trained networks, and data-augmentation approaches were helpful to increase accuracy. The best-performing network for classifying presence vs. absence of an ET tube was still very accurate with an AUC of 0.99. However, for the most difficult dataset, such as low vs. normal position of the endotracheal tube, DCNNs did not perform as well, but achieved a reasonable AUC of 0.81.

Gene network biological validity based on gene-gene interaction relevance.

PubMed

Gómez-Vela, Francisco; Díaz-Díaz, Norberto

2014-01-01

In recent years, gene networks have become one of the most useful tools for modeling biological processes. Many inference gene network algorithms have been developed as techniques for extracting knowledge from gene expression data. Ensuring the reliability of the inferred gene relationships is a crucial task in any study in order to prove that the algorithms used are precise. Usually, this validation process can be carried out using prior biological knowledge. The metabolic pathways stored in KEGG are one of the most widely used knowledgeable sources for analyzing relationships between genes. This paper introduces a new methodology, GeneNetVal, to assess the biological validity of gene networks based on the relevance of the gene-gene interactions stored in KEGG metabolic pathways. Hence, a complete KEGG pathway conversion into a gene association network and a new matching distance based on gene-gene interaction relevance are proposed. The performance of GeneNetVal was established with three different experiments. Firstly, our proposal is tested in a comparative ROC analysis. Secondly, a randomness study is presented to show the behavior of GeneNetVal when the noise is increased in the input network. Finally, the ability of GeneNetVal to detect biological functionality of the network is shown.

A net-shaped multicellular formation facilitates the maturation of hPSC-derived cardiomyocytes through mechanical and electrophysiological stimuli

PubMed Central

Liu, Taoyan; Huang, Chengwu; Li, Hongxia; Wu, Fujian; Luo, Jianwen; Lu, Wenjing

2018-01-01

The use of human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) is limited in drug discovery and cardiac disease mechanism studies due to cell immaturity. Although many approaches have been reported to improve the maturation of hiPSC-CMs, the elucidation of the process of maturation is crucial. We applied a small-molecule-based differentiation method to generate cardiomyocytes (CMs) with multiple aggregation forms. The motion analysis revealed significant physical differences in the differently shaped CMs, and the net-shaped CMs had larger motion amplitudes and faster velocities than the sheet-shaped CMs. The net-shaped CMs displayed accelerated maturation at the transcriptional level and were more similar to CMs with a prolonged culture time (30 days) than to sheet-d15. Ion channel genes and gap junction proteins were up-regulated in net-shaped CMs, indicating that robust contraction was coupled with enhanced ion channel and connexin expression. The net-shaped CMs also displayed improved myofibril ultrastructure under transmission electron microscopy. In conclusion, different multicellular hPSC-CM structures, such as the net-shaped pattern, are formed using the conditioned induction method, providing a useful tool to improve cardiac maturation. PMID:29661985

A Novel Petri Nets-Based Modeling Method for the Interaction between the Sensor and the Geographic Environment in Emerging Sensor Networks

PubMed Central

Zhang, Feng; Xu, Yuetong; Chou, Jarong

2016-01-01

The service of sensor device in Emerging Sensor Networks (ESNs) is the extension of traditional Web services. Through the sensor network, the service of sensor device can communicate directly with the entity in the geographic environment, and even impact the geographic entity directly. The interaction between the sensor device in ESNs and geographic environment is very complex, and the interaction modeling is a challenging problem. This paper proposed a novel Petri Nets-based modeling method for the interaction between the sensor device and the geographic environment. The feature of the sensor device service in ESNs is more easily affected by the geographic environment than the traditional Web service. Therefore, the response time, the fault-tolerant ability and the resource consumption become important factors in the performance of the whole sensor application system. Thus, this paper classified IoT services as Sensing services and Controlling services according to the interaction between IoT service and geographic entity, and classified GIS services as data services and processing services. Then, this paper designed and analyzed service algebra and Colored Petri Nets model to modeling the geo-feature, IoT service, GIS service and the interaction process between the sensor and the geographic enviroment. At last, the modeling process is discussed by examples. PMID:27681730

Impact of Nurse Staffing Mandates on Safety-Net Hospitals: Lessons from California

PubMed Central

McHugh, Matthew D; Brooks Carthon, Margo; Sloane, Douglas M; Wu, Evan; Kelly, Lesly; Aiken, Linda H

2012-01-01

Context California is the first and only state to implement a patient-to-nurse ratio mandate for hospitals. Increasing nurse staffing is an important organizational intervention for improving patient outcomes. Evidence suggests that staffing improved in California hospitals after the mandate was enacted, but the outcome for hospitals bearing a disproportionate share of uncompensated care—safety-net hospitals—remains unclear. One concern was that California's mandate would burden safety-net hospitals without improving staffing or that hospitals would reduce their skill mix, that is, the proportion of registered nurses of all nursing staff. We examined the differential effect of California's staffing mandate on safety-net and non-safety-net hospitals. Methods We used a time-series design with Annual Hospital Disclosure data files from the California Office of Statewide Health Planning and Development (OSHPD) for the years 1998 to 2007 to assess differences in the effect of California's mandate on staffing outcomes in safety-net and non-safety-net hospitals. Findings The mandate resulted in significant staffing improvements, on average nearly a full patient per nurse fewer (−0.98) for all California hospitals. The greatest effect was in those hospitals with the lowest staffing levels at the outset, both safety-net and non-safety-net hospitals, as the legislation intended. The mandate led to significantly improved staffing levels for safety-net hospitals, although there was a small but significant difference in the effect on staffing levels of safety-net and non-safety-net hospitals. Regarding skill mix, a marginally higher proportion of registered nurses was seen in non-safety-net hospitals following the mandate, while the skill mix remained essentially unchanged for safety-net hospitals. The difference between the two groups of hospitals was not significant. Conclusions California's mandate improved staffing for all hospitals, including safety-net hospitals. Furthermore, improvement did not come at the cost of a reduced skill mix, as was feared. Alternative and more targeted designs, however, might yield further improvement for safety-net hospitals and reduce potential disparities in the staffing and skill mix of safety-net and non-safety-net hospitals. PMID:22428696

[Internet addiction disorder and social networks: statistical analysis of correlation and study of the association with social interaction anxiousness].

PubMed

Rusconi, Anna Carlotta; Valeriani, Giuseppe; Carlone, Cristiano; Raimondo, Pasquale; Quartini, Adele; Coccanari de' Fornari, Maria Antonietta; Biondi, Massimo

2012-01-01

Internet Addiction Disorder (IAD) is an emerging psychiatric disorder, assimilable to impulse control problems and related to maladaptive use of new networks and social and virtual technologies. Our study aims to analyze the presence of IAD among adolescents and to study the correlation with social interaction anxiousness. We investigated also the possibility that the Social Network (SN) represent a source of risk for the development of IAD. The test group was composed of 250 subjects, aged between 14 and 18 years. They were administered: Young's IAT; IAS (Interaction Anxiousness Scale), AAS (Audience Anxiousness Scale) and SISST (Social Interaction Self-Statement Test) to analyze the dimension of social interaction anxiousness. We found a rate of 2% of the IAD. The SN are the most common use of the Net in our sample, but not the most clicked sites by subjects with IAD. It should be noted, finally, a correlation between social interaction anxiety and IAD, but not a significant difference in scores of social anxiousness scales based on the SN use/non-use. The use of SN intended as single variable doesn't correlate with increased risk for IAD, or for increased social interaction anxiousness. However, if associated with prolonged use of the net for 5-6 hours or more, or concomitant use of chat rooms and/or net gambling, we find a more significant risk of psychopathology. The data presented require further investigations, in order to guide new pathogenetic models and appropriate intervention strategies.

BioNetSim: a Petri net-based modeling tool for simulations of biochemical processes.

PubMed

Gao, Junhui; Li, Li; Wu, Xiaolin; Wei, Dong-Qing

2012-03-01

BioNetSim, a Petri net-based software for modeling and simulating biochemistry processes, is developed, whose design and implement are presented in this paper, including logic construction, real-time access to KEGG (Kyoto Encyclopedia of Genes and Genomes), and BioModel database. Furthermore, glycolysis is simulated as an example of its application. BioNetSim is a helpful tool for researchers to download data, model biological network, and simulate complicated biochemistry processes. Gene regulatory networks, metabolic pathways, signaling pathways, and kinetics of cell interaction are all available in BioNetSim, which makes modeling more efficient and effective. Similar to other Petri net-based softwares, BioNetSim does well in graphic application and mathematic construction. Moreover, it shows several powerful predominances. (1) It creates models in database. (2) It realizes the real-time access to KEGG and BioModel and transfers data to Petri net. (3) It provides qualitative analysis, such as computation of constants. (4) It generates graphs for tracing the concentration of every molecule during the simulation processes.

Somatostatin Analogues according to Ki67 index in neuroendocrine tumours: an observational retrospective-prospective analysis from real life

PubMed Central

Faggiano, Antongiulio; Carratù, Anna Chiara; Guadagno, Elia; Tafuto, Salvatore; Tatangelo, Fabiana; Riccardi, Ferdinando; Mocerino, Carmela; Palmieri, Giovannella; Damiano, Vincenzo; Siciliano, Roberta; Leo, Silvana; Mauro, Annamaria; Tozzi, Lucia Franca; Battista, Claudia; De Rosa, Gaetano; Colao, Annamaria

2016-01-01

Somatostatin analogues (SSAs) have shown limited and variable antiproliferative effects in neuroendocrine tumours (NETs). Whether tumour control by SSAs depends on grading based on the 2010 WHO NET classification is still unclear. The aim of this study is to evaluate the efficacy of long-acting SSAs in NETs according to Ki67 index. An observational Italian multicentre study was designed to collect data in patients with gastro-entero-pancreatic or thoracic NETs under SSA treatment. Both retrospective and prospective data were included and they were analysed in line with Ki67 index, immunohistochemically evaluated in tumour samples and graded according to WHO classification (G1 = Ki67 index 0-2%, G2 = Ki67 index 3-20%, G3 = Ki67 index > 20%). Among 601 patients with NET, 140 with a histologically confirmed gastro-entero-pancreatic or thoracic NET or NET with unknown primary were treated with lanreotide autogel or octreotide LAR. An objective tumour response was observed in 11%, stability in 58% and progression in 31%. Objective response and tumour stability were not significantly different between G1 and G2 NETs. Progression free survival was longer but not significantly different in G1 than G2 NETs (median: 89 vs 43 months, p = 0.15). The median PFS was significantly longer in NETs showing Ki67 < 5% than in those showing Ki67 ≥5% (89 vs 35 months, p = 0.005). SSA therapy shows significant antiproliferative effects in well differentiated low/intermediate-proliferating NETs, not only G1 but also in G2 type. A Ki67 index of 5% seems to work better than 3% to select the best candidates for SSA therapy. PMID:26701729

Somatostatin analogues according to Ki67 index in neuroendocrine tumours: an observational retrospective-prospective analysis from real life.

PubMed

Faggiano, Antongiulio; Carratù, Anna Chiara; Guadagno, Elia; Tafuto, Salvatore; Tatangelo, Fabiana; Riccardi, Ferdinando; Mocerino, Carmela; Palmieri, Giovannella; Damiano, Vincenzo; Siciliano, Roberta; Leo, Silvana; Mauro, Annamaria; Tozzi, Lucia Franca; Battista, Claudia; De Rosa, Gaetano; Colao, Annamaria

2016-02-02

Somatostatin analogues (SSAs) have shown limited and variable antiproliferative effects in neuroendocrine tumours (NETs). Whether tumour control by SSAs depends on grading based on the 2010 WHO NET classification is still unclear. The aim of this study is to evaluate the efficacy of long-acting SSAs in NETs according to Ki67 index. An observational Italian multicentre study was designed to collect data in patients with gastro-entero-pancreatic or thoracic NETs under SSA treatment. Both retrospective and prospective data were included and they were analysed in line with Ki67 index, immunohistochemically evaluated in tumour samples and graded according to WHO classification (G1 = Ki67 index 0-2%, G2 = Ki67 index 3-20%, G3 = Ki67 index > 20%). Among 601 patients with NET, 140 with a histologically confirmed gastro-entero-pancreatic or thoracic NET or NET with unknown primary were treated with lanreotide autogel or octreotide LAR. An objective tumour response was observed in 11%, stability in 58% and progression in 31%. Objective response and tumour stability were not significantly different between G1 and G2 NETs. Progression free survival was longer but not significantly different in G1 than G2 NETs (median: 89 vs 43 months, p = 0.15). The median PFS was significantly longer in NETs showing Ki67 < 5% than in those showing Ki67 ≥ 5% (89 vs 35 months, p = 0.005). SSA therapy shows significant antiproliferative effects in well differentiated low/intermediate-proliferating NETs, not only G1 but also in G2 type. A Ki67 index of 5% seems to work better than 3% to select the best candidates for SSA therapy.

Place-Based Learning: Interactive Learning and Net-Zero Design

ERIC Educational Resources Information Center

Holser, Alec; Becker, Michael

2011-01-01

Food and conservation science curriculum, net-zero design and student-based building performance monitoring have come together in the unique and innovative new Music and Science Building for Oregon's Hood River Middle School. The school's Permaculture-based curriculum both informed the building design and was also transformed through the…

Teaching Petri Nets Using P3

ERIC Educational Resources Information Center

Gasevic, Dragan; Devedzic, Vladan

2004-01-01

This paper presents Petri net software tool P3 that is developed for training purposes of the Architecture and organization of computers (AOC) course. The P3 has the following features: graphical modeling interface, interactive simulation by single and parallel (with previous conflict resolution) transition firing, two well-known Petri net…

Army Net Zero Prove Out. Net Zero Waste Best Practices

DTIC Science & Technology

2014-11-20

targeted efforts may be needed in barracks and other areas with significant occupant turn-over. Conventional media (e.g., posters and signage ) can be...significant occupant turn-over. Conventional media (e.g., posters and signage ) can be used, along with innovative ideas and interactive events (e.g

Tunable interactions between paramagnetic colloidal particles driven in a modulated ratchet potential.

PubMed

Straube, Arthur V; Tierno, Pietro

2014-06-14

We study experimentally and theoretically the interactions between paramagnetic particles dispersed in water and driven above the surface of a stripe patterned magnetic garnet film. An external rotating magnetic field modulates the stray field of the garnet film and generates a translating potential landscape which induces directed particle motion. By varying the ellipticity of the rotating field, we tune the inter-particle interactions from net repulsive to net attractive. For attractive interactions, we show that pairs of particles can approach each other and form stable doublets which afterwards travel along the modulated landscape at a constant mean speed. We measure the strength of the attractive force between the moving particles and propose an analytically tractable model that explains the observations and is in quantitative agreement with experiment.

Evaluation of the Utility of Static and Adaptive Mesh Refinement for Idealized Tropical Cyclone Problems in a Spectral Element Shallow Water Model

DTIC Science & Technology

2015-04-09

where u is the zonal momentum per unit mass, v is the meridional momentum per unit mass, h is the fluid depth, and f is the Coriolis parameter. An...from each cyclone advects the other116 creating a net cyclonic motion (the Fujiwhara effect ; Fujiwhara 1921) (case 2 idealization).117 In Fig. 2c, the...the interaction of the two136 vortices cause a net cyclonic motion (the Fujiwhara effect ).137 The initial condition for the binary vortex interaction

The Anterior Cingulate Gyrus Signals the Net Value of Others' Rewards

PubMed Central

Ramnani, Narender

2014-01-01

Evaluating the costs and benefits of our own choices is central to most forms of decision-making and its mechanisms in the brain are becoming increasingly well understood. To interact successfully in social environments, it is also essential to monitor the rewards that others receive. Previous studies in nonhuman primates have found neurons in the anterior cingulate cortex (ACC) that signal the net value (benefit minus cost) of rewards that will be received oneself and also neurons that signal when a reward will be received by someone else. However, little is understood about the way in which the human brain engages in cost–benefit analyses during social interactions. Does the ACC signal the net value (the benefits minus the costs) of rewards that others will receive? Here, using fMRI, we examined activity time locked to cues that signaled the anticipated reward magnitude (benefit) to be gained and the level of effort (cost) to be incurred either by a subject themselves or by a social confederate. We investigated whether activity in the ACC covaries with the net value of rewards that someone else will receive when that person is required to exert effort for the reward. We show that, although activation in the sulcus of the ACC signaled the costs on all trials, gyral ACC (ACCg) activity varied parametrically only with the net value of rewards gained by others. These results suggest that the ACCg plays an important role in signaling cost–benefit information by signaling the value of others' rewards during social interactions. PMID:24790190

Blood Based Biomarkers of Early Onset Breast Cancer

DTIC Science & Technology

2016-12-01

discretizes the data, and also using logistic elastic net – a form of linear regression - we were unable to build a classifier that could accurately...classifier for differentiating cases from controls off discretized data. The first pass analysis demonstrated a 35 gene signature that differentiated...to the discretized data for mRNA gene signature, the samples used to “train” were also included in the final samples used to “test” the algorithm

Long-term economic benefits attributed to IVF-conceived children: a lifetime tax calculation.

PubMed

Connolly, Mark P; Pollard, Michael S; Hoorens, Stijn; Kaplan, Brian R; Oskowitz, Selwyn P; Silber, Sherman J

2008-09-01

To evaluate whether lifetime future net tax revenues from an in vitro fertilization (IVF)-conceived child are substantial enough to warrant public subsidy relative to the mean IVF treatment costs required to obtain 1 live birth. Mathematical generational accounting model. The model estimates direct financial interactions between the IVF-conceived child and the government during the child's projected lifetime. In the model, we accrue IVF costs required to conceive the child to the government, and then we estimate future net tax revenue to the federal and state governments from this individual, offset by direct financial transfers from the government (eg, child allowances, education, Medicare, and Social Security). We discount lifetime costs and gross tax payments at Treasury Department rates to establish the present value of investing in IVF. We applied US Congressional Budget Office projected changes in tax rates over the course of the model. An IVF-conceived child, average in every respect (eg, future earnings, healthcare consumption, and life expectancy), represents a net positive return to the government. Based on an average employed individual born in 2005, the projected net lifetime tax contribution is US $606,200. Taking into consideration IVF costs and all direct financial interactions, the net present value is US $155,870. Lifetime net taxes paid from a child relative to the child's initial IVF investment represent a 700% net return to the government in discounted US dollars from fully employed individuals. This suggests that removing barriers to IVF would have positive tax benefits for the government, notwithstanding its beneficial effect on overall economic growth.

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

The technology necessary to build net zero energy buildings (NZEBs) is ready and available today, however, building to net zero energy performance levels can be challenging. Energy efficiency measures, onsite energy generation resources, load matching and grid interaction, climatic factors, and local policies vary from location to location and require unique methods of constructing NZEBs. It is recommended that Components start looking into how to construct and operate NZEBs now as there is a learning curve to net zero construction and FY 2020 is just around the corner.

Origin of the net magnetic moment in LaCoO3

NASA Astrophysics Data System (ADS)

Kaminsky, G. M.; Belanger, D. P.; Ye, F.; Fernandez-Baca, J. A.; Wang, J.; Matsuda, M.; Yan, J.-Q.

2018-01-01

We use polarized neutron scattering to characterize the Bragg scattering intensity below TC=89.5 K at the (1,0,0) pseudocubic nuclear Bragg point of LaCoO3. Upon cooling in a field (FC), a net magnetic moment is apparent in Bragg scattering intensity, just as it was in previous magnetization measurements. Critical behavior associated with the net moment near TC upon cooling in small applied fields rapidly rounds with increasing field strength. We show, using a mean-field calculation, that this net moment can develop in a metastable state that forms upon FC, even when all the interactions in the system are antiferromagnetic.

Patient-Reported Burden of a Neuroendocrine Tumor (NET) Diagnosis: Results From the First Global Survey of Patients With NETs

PubMed Central

Granberg, Dan; Wolin, Edward; Warner, Richard; Sissons, Maia; Kolarova, Teodora; Goldstein, Grace; Pavel, Marianne; Öberg, Kjell; Leyden, John

2017-01-01

Purpose Despite the considerable impact of neuroendocrine tumors (NETs) on patients’ daily lives, the journey of the patient with a NET has rarely been documented, with published data to date being limited to small qualitative studies. NETs are heterogeneous malignancies with nonspecific symptomology, leading to extensive health care use and diagnostic delays that affect survival. A large, international patient survey was conducted to increase understanding of the experience of the patient with a NET and identify unmet needs, with the aim of improving disease awareness and care worldwide. Methods An anonymous, self-reported survey was conducted (online or on paper) from February to May 2014, recruiting patients with NETs from > 12 countries as a collaboration between the International Neuroendocrine Cancer Alliance and Novartis Pharmaceuticals. Survey questions captured information on sociodemographics, clinical characteristics, NET diagnostic experience, disease impact/management, interaction with medical teams, NET knowledge/awareness, and sources of information. This article reports the most relevant findings on patient experience with NETs and the impact of NETs on health care system resources. Results A total of 1,928 patients with NETs participated. A NET diagnosis had a substantially negative impact on patients’ personal and work lives. Patients reported delayed diagnosis and extensive NET-related health care resource use. Patients desired improvement in many aspects of NET care, including availability of a wider range of NET-specific treatment options, better access to NET experts or specialist centers, and a more knowledgeable, better-coordinated/-aligned NET medical team. Conclusion This global patient-reported survey demonstrates the considerable burden of NETs with regard to symptoms, work and daily life, and health care resource use, and highlights considerable unmet needs. Further intervention is required to improve the patient experience among those with NETs. PMID:28717741

Patient-Reported Burden of a Neuroendocrine Tumor (NET) Diagnosis: Results From the First Global Survey of Patients With NETs.

PubMed

Singh, Simron; Granberg, Dan; Wolin, Edward; Warner, Richard; Sissons, Maia; Kolarova, Teodora; Goldstein, Grace; Pavel, Marianne; Öberg, Kjell; Leyden, John

2017-02-01

Despite the considerable impact of neuroendocrine tumors (NETs) on patients' daily lives, the journey of the patient with a NET has rarely been documented, with published data to date being limited to small qualitative studies. NETs are heterogeneous malignancies with nonspecific symptomology, leading to extensive health care use and diagnostic delays that affect survival. A large, international patient survey was conducted to increase understanding of the experience of the patient with a NET and identify unmet needs, with the aim of improving disease awareness and care worldwide. An anonymous, self-reported survey was conducted (online or on paper) from February to May 2014, recruiting patients with NETs from > 12 countries as a collaboration between the International Neuroendocrine Cancer Alliance and Novartis Pharmaceuticals. Survey questions captured information on sociodemographics, clinical characteristics, NET diagnostic experience, disease impact/management, interaction with medical teams, NET knowledge/awareness, and sources of information. This article reports the most relevant findings on patient experience with NETs and the impact of NETs on health care system resources. A total of 1,928 patients with NETs participated. A NET diagnosis had a substantially negative impact on patients' personal and work lives. Patients reported delayed diagnosis and extensive NET-related health care resource use. Patients desired improvement in many aspects of NET care, including availability of a wider range of NET-specific treatment options, better access to NET experts or specialist centers, and a more knowledgeable, better-coordinated/-aligned NET medical team. This global patient-reported survey demonstrates the considerable burden of NETs with regard to symptoms, work and daily life, and health care resource use, and highlights considerable unmet needs. Further intervention is required to improve the patient experience among those with NETs.

Predicting the impact of insecticide-treated bed nets on malaria transmission: the devil is in the detail.

PubMed

Gu, Weidong; Novak, Robert J

2009-11-16

Insecticide-treated bed nets (ITNs), including long-lasting insecticidal nets (LLINs), play a primary role in global campaigns to roll back malaria in tropical Africa. Effectiveness of treated nets depends on direct impacts on individual mosquitoes including killing and excite-repellency, which vary considerably among vector species due to variations in host-seeking behaviours. While monitoring and evaluation programmes of ITNs have focuses on morbidity and all-cause mortality in humans, local entomological context receives little attention. Without knowing the dynamics of local vector species and their responses to treated nets, it is difficult to predict clinical outcomes when ITN applications are scaled up across African continent. Sound model frameworks incorporating intricate interactions between mosquitoes and treated nets are needed to develop the predictive capacity for scale-up applications of ITNs. An established agent-based model was extended to incorporate the direct outcomes, e.g. killing and avoidance, of individual mosquitoes exposing to ITNs in a hypothetical village setting with 50 houses and 90 aquatic habitats. Individual mosquitoes were tracked throughout the life cycle across the landscape. Four levels of coverage, i.e. 40, 60, 80 and 100%, were applied at the household level with treated houses having only one bed net. By using Latin hypercube sampling scheme, parameters governing killing, diverting and personal protection of net users were evaluated for their relative roles in containing mosquito populations, entomological inoculation rates (EIRs) and malaria incidence. There were substantial gaps in coverage between households and individual persons, and 100% household coverage resulted in circa 50% coverage of the population. The results show that applications of ITNs could give rise to varying impacts on population-level metrics depending on values of parameters governing interactions of mosquitoes and treated nets at the individual level. The most significant factor in determining effectiveness was killing capability of treated nets. Strong excito-repellent effect of impregnated nets might lead to higher risk exposure to non-bed net users. With variabilities of vector mosquitoes in host-seeking behaviours and the responses to treated nets, it is anticipated that scale-up applications of INTs might produce varying degrees of success dependent on local entomological and epidemiological contexts. This study highlights that increased ITN coverage led to significant reduction in risk exposure and malaria incidence only when treated nets yielded high killing effects. It is necessary to test efficacy of treated nets on local dominant vector mosquitoes, at least in laboratory, for monitoring and evaluation of ITN programmes.

Microarray and network-based identification of functional modules and pathways of active tuberculosis.

PubMed

Bian, Zhong-Rui; Yin, Juan; Sun, Wen; Lin, Dian-Jie

2017-04-01

Diagnose of active tuberculosis (TB) is challenging and treatment response is also difficult to efficiently monitor. The aim of this study was to use an integrated analysis of microarray and network-based method to the samples from publically available datasets to obtain a diagnostic module set and pathways in active TB. Towards this goal, background protein-protein interactions (PPI) network was generated based on global PPI information and gene expression data, following by identification of differential expression network (DEN) from the background PPI network. Then, ego genes were extracted according to the degree features in DEN. Next, module collection was conducted by ego gene expansion based on EgoNet algorithm. After that, differential expression of modules between active TB and controls was evaluated using random permutation test. Finally, biological significance of differential modules was detected by pathways enrichment analysis based on Reactome database, and Fisher's exact test was implemented to extract differential pathways for active TB. Totally, 47 ego genes and 47 candidate modules were identified from the DEN. By setting the cutoff-criteria of gene size >5 and classification accuracy ≥0.9, 7 ego modules (Module 4, Module 7, Module 9, Module 19, Module 25, Module 38 and Module 43) were extracted, and all of them had the statistical significance between active TB and controls. Then, Fisher's exact test was conducted to capture differential pathways for active TB. Interestingly, genes in Module 4, Module 25, Module 38, and Module 43 were enriched in the same pathway, formation of a pool of free 40S subunits. Significant pathway for Module 7 and Module 9 was eukaryotic translation termination, and for Module 19 was nonsense mediated decay enhanced by the exon junction complex (EJC). Accordingly, differential modules and pathways might be potential biomarkers for treating active TB, and provide valuable clues for better understanding of molecular mechanism of active TB. Copyright © 2017 Elsevier Ltd. All rights reserved.

Conserved charge fluctuations at vanishing and non-vanishing chemical potential

NASA Astrophysics Data System (ADS)

Karsch, Frithjof

2017-11-01

Up to 6th order cumulants of fluctuations of net baryon-number, net electric charge and net strangeness as well as correlations among these conserved charge fluctuations are now being calculated in lattice QCD. These cumulants provide a wealth of information on the properties of strong-interaction matter in the transition region from the low temperature hadronic phase to the quark-gluon plasma phase. They can be used to quantify deviations from hadron resonance gas (HRG) model calculations which frequently are used to determine thermal conditions realized in heavy ion collision experiments. Already some second order cumulants like the correlations between net baryon-number and net strangeness or net electric charge differ significantly at temperatures above 155 MeV in QCD and HRG model calculations. We show that these differences increase at non-zero baryon chemical potential constraining the applicability range of HRG model calculations to even smaller values of the temperature.

A Petri net synthesis theory for modeling flexible manufacturing systems.

PubMed

Jeng, M D

1997-01-01

A theory that synthesizes Petri nets for modeling flexible manufacturing systems is presented. The theory adopts a bottom-up or modular-composition approach to construct net models. Each module is modeled as a resource control net (RCN), which represents a subsystem that controls a resource type in a flexible manufacturing system. Interactions among the modules are described as the common transition and transition subnets. The net obtained by merging the modules with two minimal restrictions is shown to be conservative and thus bounded. An algorithm is developed to detect two sufficient conditions for structural liveness of the net. The algorithm examines only the net's structure and the initial marking, and appears to be more efficient than state enumeration techniques such as the reachability tree method. In this paper, the sufficient conditions for liveness are shown to be related to some structural objects called siphons. To demonstrate the applicability of the theory, a flexible manufacturing system of a moderate size is modeled and analyzed using the proposed theory.

Human dental stem cells suppress PMN activity after infection with the periodontopathogens Prevotella intermedia and Tannerella forsythia

PubMed Central

Hieke, Cathleen; Kriebel, Katja; Engelmann, Robby; Müller-Hilke, Brigitte; Lang, Hermann; Kreikemeyer, Bernd

2016-01-01

Periodontitis is characterized by inflammation associated with the colonization of different oral pathogens. We here aimed to investigate how bacteria and host cells shape their environment in order to limit inflammation and tissue damage in the presence of the pathogen. Human dental follicle stem cells (hDFSCs) were co-cultured with gram-negative P. intermedia and T. forsythia and were quantified for adherence and internalization as well as migration and interleukin secretion. To delineate hDFSC-specific effects, gingival epithelial cells (Ca9-22) were used as controls. Direct effects of hDFSCs on neutrophils (PMN) after interaction with bacteria were analyzed via chemotactic attraction, phagocytic activity and NET formation. We show that P. intermedia and T. forsythia adhere to and internalize into hDFSCs. This infection decreased the migratory capacity of the hDFSCs by 50%, did not disturb hDFSC differentiation potential and provoked an increase in IL-6 and IL-8 secretion while leaving IL-10 levels unaltered. These environmental modulations correlated with reduced PMN chemotaxis, phagocytic activity and NET formation. Our results suggest that P. intermedia and T. forsythia infected hDFSCs maintain their stem cell functionality, reduce PMN-induced tissue and bone degradation via suppression of PMN-activity, and at the same time allow for the survival of the oral pathogens. PMID:27974831

Complex Social Structure of an Endangered Population of Bottlenose Dolphins (Tursiops truncatus) in the Aeolian Archipelago (Italy)

PubMed Central

Blasi, Monica F.; Boitani, Luigi

2014-01-01

We investigated social structure and association patterns for a small population of Mediterranean bottlenose dolphins, Tursiops truncatus, inhabiting the Aeolian Archipelago (southern Italy). Specifically we evaluate the role of sex and age composition, residency patterns and interaction with trammel nets on this social organization. Association data for 23 regularly sighted individuals were obtained from summer photoidentification surveys collected from 2005–2012. Using a combined cluster and social network analysis approach, we found associations between dolphins were hierarchically structured, where two mixed-sex social units were subdivided into smaller temporarily dynamic groups. We found non-random and long-term preferred associations in the population; however, the degree of social cohesion, residence pattern and interaction with trammel nets differed considerably between the two social units. Six of eight females occurred in the more resident social unit-1; in addition, social unit-1 individuals had significantly stronger associations, higher preferred associates, lived in larger groups and occurred less frequently with trammel nets. Nine of eleven males were clustered in social unit-2 and five of these males, interacting with trammel nets, formed small groups and preferred associations. We propose that female and male groups associate in the study area during the breeding season and that some males choose to interact with reproductive females forming a distinct but interrelated social unit. Other males may be associating in a larger fission-fusion network, which consists of dolphins that appear to temporarily join the network from the coastal population. We cannot exclude that some males specialized in trammel net foraging, suggesting that this foraging technique may favor a solitary lifestyle. Large group sizes and high degree of social cohesion for females could be an indication of greater protection and more efficiency in detecting, deterring or repelling anthropogenic pressures. Most likely dolphins' social organization depends on a combination of socio-ecological, demographic and anthropogenic factors. PMID:25494331

Googling Allusions: Teaching Eliot to the Net Generation

ERIC Educational Resources Information Center

Hoff, Ann K.

2009-01-01

For years, 20th century American poetry professor Ann Hoff resisted digital pedagogy. However, for students of the Net Generation electronic communication is their main mode of interaction with peers and often with their professors. Further, their instinct when seeking information, is to seek it online. They are not merely computer proficient and…

Formation of a new archetypal Metal-Organic Framework from a simple monatomic liquid

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

Metere, Alfredo, E-mail: alfredo.metere@mmk.su.se; Oleynikov, Peter; Dzugutov, Mikhail

2014-12-21

We report a molecular-dynamics simulation of a single-component system of particles interacting via a spherically symmetric potential that is found to form, upon cooling from a liquid state, a low-density porous crystalline phase. Its structure analysis demonstrates that the crystal can be described by a net with a topology that belongs to the class of topologies characteristic of the Metal-Organic Frameworks (MOFs). The observed net is new, and it is now included in the Reticular Chemistry Structure Resource database. The observation that a net topology characteristic of MOF crystals, which are known to be formed by a coordination-driven self-assembly process,more » can be reproduced by a thermodynamically stable configuration of a simple single-component system of particles opens a possibility of using these models in studies of MOF nets. It also indicates that structures with MOF topology, as well as other low-density porous crystalline structures can possibly be produced in colloidal systems of spherical particles, with an appropriate tuning of interparticle interaction.« less

Using hierarchical Bayesian multi-species mixture models to estimate tandem hoop-net based habitat associations and detection probabilities of fishes in reservoirs

USGS Publications Warehouse

Stewart, David R.; Long, James M.

2015-01-01

Species distribution models are useful tools to evaluate habitat relationships of fishes. We used hierarchical Bayesian multispecies mixture models to evaluate the relationships of both detection and abundance with habitat of reservoir fishes caught using tandem hoop nets. A total of 7,212 fish from 12 species were captured, and the majority of the catch was composed of Channel Catfish Ictalurus punctatus (46%), Bluegill Lepomis macrochirus(25%), and White Crappie Pomoxis annularis (14%). Detection estimates ranged from 8% to 69%, and modeling results suggested that fishes were primarily influenced by reservoir size and context, water clarity and temperature, and land-use types. Species were differentially abundant within and among habitat types, and some fishes were found to be more abundant in turbid, less impacted (e.g., by urbanization and agriculture) reservoirs with longer shoreline lengths; whereas, other species were found more often in clear, nutrient-rich impoundments that had generally shorter shoreline length and were surrounded by a higher percentage of agricultural land. Our results demonstrated that habitat and reservoir characteristics may differentially benefit species and assemblage structure. This study provides a useful framework for evaluating capture efficiency for not only hoop nets but other gear types used to sample fishes in reservoirs.

A 3D Active Learning Application for NeMO-Net, the NASA Neural Multi-Modal Observation and Training Network for Global Coral Reef Assessment

NASA Technical Reports Server (NTRS)

van den Bergh, Jarrett; Schutz, Joey; Li, Alan; Chirayath, Ved

2017-01-01

NeMO-Net, the NASA neural multi-modal observation and training network for global coral reef assessment, is an open-source deep convolutional neural network and interactive active learning training software aiming to accurately assess the present and past dynamics of coral reef ecosystems through determination of percent living cover and morphology as well as mapping of spatial distribution. We present an interactive video game prototype for tablet and mobile devices where users interactively label morphology classifications over mm-scale 3D coral reef imagery captured using fluid lensing to create a dataset that will be used to train NeMO-Nets convolutional neural network. The application currently allows for users to classify preselected regions of coral in the Pacific and will be expanded to include additional regions captured using our NASA FluidCam instrument, presently the highest-resolution remote sensing benthic imaging technology capable of removing ocean wave distortion, as well as lower-resolution airborne remote sensing data from the ongoing NASA CORAL campaign. Active learning applications present a novel methodology for efficiently training large-scale Neural Networks wherein variances in identification can be rapidly mitigated against control data. NeMO-Net periodically checks users input against pre-classified coral imagery to gauge their accuracy and utilize in-game mechanics to provide classification training. Users actively communicate with a server and are requested to classify areas of coral for which other users had conflicting classifications and contribute their input to a larger database for ranking. In partnering with Mission Blue and IUCN, NeMO-Net leverages an international consortium of subject matter experts to classify areas of confusion identified by NeMO-Net and generate additional labels crucial for identifying decision boundary locations in coral reef assessment.

Population dynamics and the ecological stability of obligate pollination mutualisms

USGS Publications Warehouse

Holland, J. Nathaniel; DeAngelis, Donald L.

2001-01-01

Mutualistic interactions almost always produce both costs and benefits for each of the interacting species. It is the difference between gross benefits and costs that determines the net benefit and the per-capita effect on each of the interacting populations. For example, the net benefit of obligate pollinators, such as yucca and senita moths, to plants is determined by the difference between the number of ovules fertilized from moth pollination and the number of ovules eaten by the pollinator's larvae. It is clear that if pollinator populations are large, then, because many eggs are laid, costs to plants are large, whereas, if pollinator populations are small, gross benefits are low due to lack of pollination. Even though the size and dynamics of the pollinator population are likely to be crucial, their importance has been neglected in the investigation of mechanisms, such as selective fruit abortion, that can limit costs and increase net benefits. Here, we suggest that both the population size and dynamics of pollinators are important in determining the net benefits to plants, and that fruit abortion can significantly affect these. We develop a model of mutualism between populations of plants and their pollinating seed-predators to explore the ecological consequences of fruit abortion on pollinator population dynamics and the net effect on plants. We demonstrate that the benefit to a plant population is unimodal as a function of pollinator abundance, relative to the abundance of flowers. Both selective abortion of fruit with eggs and random abortion of fruit, without reference to whether they have eggs or not, can limit pollinator population size. This can increase the net benefits to the plant population by limiting the number of eggs laid, if the pollination rate remains high. However, fruit abortion can possibly destabilize the pollinator population, with negative consequences for the plant population.

A 3D Active Learning Application for NeMO-Net, the NASA Neural Multi-Modal Observation and Training Network for Global Coral Reef Assessment

NASA Astrophysics Data System (ADS)

van den Bergh, J.; Schutz, J.; Chirayath, V.; Li, A.

2017-12-01

NeMO-Net, the NASA neural multi-modal observation and training network for global coral reef assessment, is an open-source deep convolutional neural network and interactive active learning training software aiming to accurately assess the present and past dynamics of coral reef ecosystems through determination of percent living cover and morphology as well as mapping of spatial distribution. We present an interactive video game prototype for tablet and mobile devices where users interactively label morphology classifications over mm-scale 3D coral reef imagery captured using fluid lensing to create a dataset that will be used to train NeMO-Net's convolutional neural network. The application currently allows for users to classify preselected regions of coral in the Pacific and will be expanded to include additional regions captured using our NASA FluidCam instrument, presently the highest-resolution remote sensing benthic imaging technology capable of removing ocean wave distortion, as well as lower-resolution airborne remote sensing data from the ongoing NASA CORAL campaign.Active learning applications present a novel methodology for efficiently training large-scale Neural Networks wherein variances in identification can be rapidly mitigated against control data. NeMO-Net periodically checks users' input against pre-classified coral imagery to gauge their accuracy and utilizes in-game mechanics to provide classification training. Users actively communicate with a server and are requested to classify areas of coral for which other users had conflicting classifications and contribute their input to a larger database for ranking. In partnering with Mission Blue and IUCN, NeMO-Net leverages an international consortium of subject matter experts to classify areas of confusion identified by NeMO-Net and generate additional labels crucial for identifying decision boundary locations in coral reef assessment.

Antiproliferative effects of lanreotide autogel in patients with progressive, well-differentiated neuroendocrine tumours: a Spanish, multicentre, open-label, single arm phase II study.

PubMed

Martín-Richard, Marta; Massutí, Bartomeu; Pineda, Eva; Alonso, Vicente; Marmol, Maribel; Castellano, Daniel; Fonseca, Emilio; Galán, Antonio; Llanos, Marta; Sala, Maria Angeles; Pericay, Carlos; Rivera, Fernando; Sastre, Javier; Segura, Angel; Quindós, Maria; Maisonobe, Pascal

2013-09-20

Somatostatin analogues (SSAs) are indicated to relieve carcinoid syndrome but seem to have antiproliferative effects on neuroendocrine tumours (NETs). This is the first prospective study investigating tumour stabilisation with the long-acting SSA lanreotide Autogel in patients with progressive NETs. This was a multicentre, open-label, phase II trial conducted in 17 Spanish specialist centres. Patients with well-differentiated NETs and radiologically confirmed progression within the previous 6 months received lanreotide Autogel, 120 mg every 28 days over ≤92 weeks. The primary endpoint was progression-free survival (PFS). Secondary endpoints were response rate, tumour biomarkers, symptom control, quality of life (QoL), and safety. Radiographic imaging was assessed by a blinded central radiologist. Of 30 patients included in the efficacy and safety analyses, 40% had midgut tumours and 27% pancreatic tumours; 63% of tumours were functioning. Median PFS time was 12.9 (95% CI: 7.9, 16.5) months, and most patients achieved disease stabilisation (89%) or partial response (4%). No deterioration in QoL was observed. Nineteen patients (63%) experienced treatment-related adverse events, most frequently diarrhoea and asthenia; only one treatment-related adverse event (aerophagia) was severe. Lanreotide Autogel provided effective tumour stabilisation and PFS >12 months in patients with progressive NETs ineligible for surgery or chemotherapy, with a safety profile consistent with the pharmacology of the class. ClinicalTrials.gov Identifier NCT00326469; EU Clinical Trial Register EudraCT no 2004-002871-18.

Antiproliferative effects of lanreotide autogel in patients with progressive, well-differentiated neuroendocrine tumours: a Spanish, multicentre, open-label, single arm phase II study

PubMed Central

2013-01-01

Background Somatostatin analogues (SSAs) are indicated to relieve carcinoid syndrome but seem to have antiproliferative effects on neuroendocrine tumours (NETs). This is the first prospective study investigating tumour stabilisation with the long-acting SSA lanreotide Autogel in patients with progressive NETs. Methods This was a multicentre, open-label, phase II trial conducted in 17 Spanish specialist centres. Patients with well-differentiated NETs and radiologically confirmed progression within the previous 6 months received lanreotide Autogel, 120 mg every 28 days over ≤92 weeks. The primary endpoint was progression-free survival (PFS). Secondary endpoints were response rate, tumour biomarkers, symptom control, quality of life (QoL), and safety. Radiographic imaging was assessed by a blinded central radiologist. Results Of 30 patients included in the efficacy and safety analyses, 40% had midgut tumours and 27% pancreatic tumours; 63% of tumours were functioning. Median PFS time was 12.9 (95% CI: 7.9, 16.5) months, and most patients achieved disease stabilisation (89%) or partial response (4%). No deterioration in QoL was observed. Nineteen patients (63%) experienced treatment-related adverse events, most frequently diarrhoea and asthenia; only one treatment-related adverse event (aerophagia) was severe. Conclusion Lanreotide Autogel provided effective tumour stabilisation and PFS >12 months in patients with progressive NETs ineligible for surgery or chemotherapy, with a safety profile consistent with the pharmacology of the class. Trial registration ClinicalTrials.gov Identifier NCT00326469; EU Clinical Trial Register EudraCT no 2004-002871-18. PMID:24053191

Case of a tumor comprising gastric cancer and duodenal neuroendocrine tumor

PubMed Central

Kaneko, Hiroaki; Miyake, Akio; Ishii, Yasuaki; Sue, Soichiro; Miwa, Haruo; Sasaki, Tomohiko; Tamura, Toshihide; Kondo, Masaaki; Maeda, Shin

2016-01-01

The present report describes a rare case of a tumor composed of early gastric cancer and a duodenal neuroendocrine tumor (NET). A 78-year-old woman underwent esophagogastroduodenoscopy at a local institution for screening of the upper gastrointestinal tract which revealed a protruded tumor through the pyloric ring from the pyloric antrum. The tumor was too large to treat at the facility; consequently, she was referred to our hospital for further management. Esophagogastroduodenoscopy with tumor biopsy of the lesion revealed the diagnosis of early gastric cancer. Endoscopic submucosal dissection was performed with sufficient free margins in both vertical and horizontal directions. Histopathological findings showed NET confined to the submucosal layer and covered by well-differentiated adenocarcinoma. Immunohistochemical stainings showed that the two lesions existed continuously. While the possibility of a collision cancer was considered, it was suggested that the two lesions existed continuously. Finally, the tumor was diagnosed as gastric cancer composed of duodenal NET G1, with a lymphatic invasion of NET component. PMID:27688667

Determinants of general practitioners' wages in England.

PubMed

Morris, Stephen; Goudie, Rosalind; Sutton, Matt; Gravelle, Hugh; Elliott, Robert; Hole, Arne Risa; Ma, Ada; Sibbald, Bonnie; Skåtun, Diane

2011-02-01

We analyse the determinants of annual net income and wages (net income/hours) of general practitioners (GPs) using data for 2271 GPs in England recorded during Autumn 2008. The average GP had an annual net income of £97,500 and worked 43 h per week. The mean wage was £51 per h. Net income and wages depended on gender, experience, list size, partnership size, whether or not the GP worked in a dispensing practice, whether they were salaried of self-employed, whether they worked in a practice with a nationally or locally negotiated contract, and the characteristics of the local population (proportion from ethnic minorities, rurality, and income deprivation). The findings have implications for pay discrimination by GP gender and ethnicity, GP preferences for partnership size, incentives for competition for patients, and compensating differentials for local population characteristics. They also shed light on the attractiveness to GPs in England of locally negotiated (personal medical services) versus nationally negotiated (general medical services) contracts.

Measures of net oxidant concentration in seawater

NASA Astrophysics Data System (ADS)

Jackson, George A.; Williams, Peter M.

1988-02-01

Dissolved oxygen deficits in the ocean have been used as a measure of the organic matter oxidized in a volume of water. Such organic matter is usually assumed to be predominantly settled particles. Using dissolved oxygen concentration in this way has two problems: first, it does not differentiate between oxidant consumed by the pool of dissolved organic matter present near the ocean surface and oxidant consumed by organic matter contained by falling particles; second, it does not account for other oxidant sources, such as nitrate, which can be as important to organic matter decay as oxygen in low-oxygen water, such as off Peru or in the Southern California submarine basins. New parameters provide better measures of the net oxidant concentration in a water parcel. One such, NetOx, is changed only by gaseous exchange with the atmosphere, exchange with the benthos, or the production or consumption of sinking particles. A simplified version of NetOx, NetOx = [O2] + 1.25[NO3-] - [TOC], where TOC (total organic carbon), the dissolved organic carbon (DOC) plus the suspended particulate organic carbon (POC), provides an index based on the usually dominant variables. Calculation of NetOx and a second property, NetOC ([O2] - [TOC]), for data from GEOSECS and ourselves in the Atlantic and Pacific oceans using property-property graphs show differences from those from oxygen deficits alone. Comparison of NetOx and NetOC concentrations at high and low latitudes of the Pacific Ocean shows the difference in surface water oxidant concentrations is even larger than the difference in oxygen concentration. Vertical particle fluxes off Peru calculated from NetOx gradients are much greater than those calculated from oxygen gradients. The potential value of NetOx and NetOC as parameters to understand particle fluxes implies that determination of TOC should be a routine part of hydrographic measurements.

Altered MENIN expression disrupts the MAFA differentiation pathway in insulinoma.

PubMed

Hamze, Z; Vercherat, C; Bernigaud-Lacheretz, A; Bazzi, W; Bonnavion, R; Lu, J; Calender, A; Pouponnot, C; Bertolino, P; Roche, C; Stein, R; Scoazec, J Y; Zhang, C X; Cordier-Bussat, M

2013-12-01

The protein MENIN is the product of the multiple endocrine neoplasia type I (MEN1) gene. Altered MENIN expression is one of the few events that are clearly associated with foregut neuroendocrine tumours (NETs), classical oncogenes or tumour suppressors being not involved. One of the current challenges is to understand how alteration of MENIN expression contributes to the development of these tumours. We hypothesised that MENIN might regulate factors maintaining endocrine-differentiated functions. We chose the insulinoma model, a paradigmatic example of well-differentiated pancreatic NETs, to study whether MENIN interferes with the expression of v-MAF musculoaponeurotic fibrosarcoma oncogene homologue A (MAFA), a master glucose-dependent transcription factor in differentiated β-cells. Immunohistochemical analysis of a series of human insulinomas revealed a correlated decrease in both MENIN and MAFA. Decreased MAFA expression resulting from targeted Men1 ablation was also consistently observed in mouse insulinomas. In vitro analyses using insulinoma cell lines showed that MENIN regulated MAFA protein and mRNA levels, and bound to Mafa promoter sequences. MENIN knockdown concomitantly decreased mRNA expression of both Mafa and β-cell differentiation markers (Ins1/2, Gck, Slc2a2 and Pdx1) and, in parallel, increased the proliferation rate of tumours as measured by bromodeoxyuridine incorporation. Interestingly, MAFA knockdown alone also increased proliferation rate but did not affect the expression of candidate proliferation genes regulated by MENIN. Finally, MENIN variants with missense mutations detected in patients with MEN1 lost the WT MENIN properties to regulate MAFA. Together, our findings unveil a previously unsuspected MENIN/MAFA connection regarding control of the β-cell differentiation/proliferation balance, which could contribute to tumorigenesis.

Patient-Reported Experience of Diagnosis, Management, and Burden of Neuroendocrine Tumors

PubMed Central

Wolin, Edward M.; Leyden, John; Goldstein, Grace; Kolarova, Teodora; Hollander, Ron; Warner, Richard R.P.

2017-01-01

Objectives The aim of this survey was to examine the experience of patients with neuroendocrine tumors (NETs) to raise awareness of the NET-related burden and identify unmet needs. Here, we report data from patients in the United States. Methods Patients with NETs participated in a 25-minute anonymous survey, conducted primarily online from February to May 2014. Survey questions captured information on sociodemographics, clinical characteristics, NET diagnostic experience, disease impact/management, interaction with medical teams, and NETs knowledge/awareness. Results Of 1928 patients who participated globally, the largest percentage was from the United States (39%). Approximately 50% of US patients reported being diagnosed with other conditions before receiving their NET diagnosis, which for 34% took 5 years or more. Patients experienced many symptoms on a daily basis as a result of NETs, which had a substantial negative impact on their work and daily lives. Numerous improvements were suggested by patients, including better access to NET-specific treatments and medical teams/centers and better education for the management of disease-related and treatment-related symptoms. Conclusions This survey demonstrated the significant burden of NETs on patients' lives and identified key areas for improvement in diagnosis and long-term management, including better access to NET-specific treatments and specialist medical teams/centers. PMID:28328615

Timing is everything

PubMed Central

Carr, Heather S; Frost, Jeffrey A

2013-01-01

Cell adhesion to the extracellular matrix elicits a temporal reorganization of the actin cytoskeleton that is regulated first by Rac1 and later by RhoA. The signaling mechanisms controlling late stage RhoA activation are incompletely understood. Net1A is a RhoA/RhoB-specific guanine nucleotide exchange factor that is required for cancer cell motility. The ability of Net1A to stimulate RhoA activation is negatively regulated by nuclear sequestration. However, mechanisms controlling the plasma membrane localization of Net1A had not previously been reported. Recently we have shown that Rac1 activation stimulates plasma membrane relocalization and activation of Net1A. Net1A relocalization is independent of its catalytic activity and does not require its C-terminal pleckstrin homology or PDZ interacting domains. Rac1 activation during cell adhesion stimulates a transient relocalization of Net1A that is terminated by proteasomal degradation of Net1A. Importantly, plasma membrane localization of Net1A is required for efficient myosin light chain phosphorylation, focal adhesion maturation, and cell spreading. These data show for the first time a physiological mechanism controlling Net1A relocalization from the nucleus. They also demonstrate a previously unrecognized role for Net1A in controlling actomyosin contractility and focal adhesion dynamics during cell adhesion. PMID:23792411

Origin of the net magnetic moment in LaCoO 3

DOE PAGES

Kaminsky, G.; Belanger, David P.; Ye, Feng; ...

2018-01-19

We use polarized neutron scattering to characterize the Bragg scattering intensity below T C=89.5 K at the (1,0,0) pseudocubic nuclear Bragg point of LaCoO 3. Upon cooling in a field (FC), a net magnetic moment is apparent in Bragg scattering intensity, just as it was in previous magnetization measurements. Critical behavior associated with the net moment near T C upon cooling in small applied fields rapidly rounds with increasing field strength. We show, using a mean-field calculation, that this net moment can develop in a metastable state that forms upon FC, even when all the interactions in the system aremore » antiferromagnetic.« less

Effects of Insect-Proof Net Cultivation, Rice-Duck Farming, and Organic Matter Return on Rice Dry Matter Accumulation and Nitrogen Utilization

PubMed Central

Liu, Xin; Xu, Guochun; Wang, Qiangsheng; Hang, Yuhao

2017-01-01

Insect-proof net cultivation (IPN), rice-duck farming (RD), and organic matter return (OM) are important methods to realize sustainable development of rice production. A split-plot field experiment was performed to study the effects of IPN, RD, and OM on the rice yield, dry matter accumulation and N utilization. Results showed that compared to inorganic N fertilizer (IN), wheat straw return, and biogas residue return increased the rice yield by 2.11–4.28 and 4.78–7.67%, respectively, and also improved dry matter and N accumulation after the elongation stage (EG), dry matter and N translocation, and N recovery efficiency (NRE). These results attributed to an increase in leaf SPAD values and net photosynthetic rate (Pn) after the EG. Compared to conventional rice farming (CR), RD promoted the rice yield by 1.52–3.74%, and contributed to higher the leaf photosynthesis, dry matter and N accumulation, dry matter and N translocation, and NRE. IPN decreased the intensity of sun radiation in the nets due to the coverage of the insect-proof nets, which declined the leaf Pn, dry matter accumulation and translocation, N absorption and translocation, and NRE compared to open field cultivation (OFC). The rice yield of IPN were 2.48–4.98% lower than that of OFC. Compared to the interaction between CR and IN, the interaction between RD and OM improved the rice yield by 5.26–9.33%, and increased dry matter and N accumulation after the EG, dry matter and N translocation, and NRE. These results indicated that OM, RD and the interaction between RD and OM could promote dry matter accumulation and N utilization, which was beneficial to improve the rice yield. PMID:28174589

ClueNet: Clustering a temporal network based on topological similarity rather than denseness.

PubMed

Crawford, Joseph; Milenković, Tijana

2018-01-01

Network clustering is a very popular topic in the network science field. Its goal is to divide (partition) the network into groups (clusters or communities) of "topologically related" nodes, where the resulting topology-based clusters are expected to "correlate" well with node label information, i.e., metadata, such as cellular functions of genes/proteins in biological networks, or age or gender of people in social networks. Even for static data, the problem of network clustering is complex. For dynamic data, the problem is even more complex, due to an additional dimension of the data-their temporal (evolving) nature. Since the problem is computationally intractable, heuristic approaches need to be sought. Existing approaches for dynamic network clustering (DNC) have drawbacks. First, they assume that nodes should be in the same cluster if they are densely interconnected within the network. We hypothesize that in some applications, it might be of interest to cluster nodes that are topologically similar to each other instead of or in addition to requiring the nodes to be densely interconnected. Second, they ignore temporal information in their early steps, and when they do consider this information later on, they do so implicitly. We hypothesize that capturing temporal information earlier in the clustering process and doing so explicitly will improve results. We test these two hypotheses via our new approach called ClueNet. We evaluate ClueNet against six existing DNC methods on both social networks capturing evolving interactions between individuals (such as interactions between students in a high school) and biological networks capturing interactions between biomolecules in the cell at different ages. We find that ClueNet is superior in over 83% of all evaluation tests. As more real-world dynamic data are becoming available, DNC and thus ClueNet will only continue to gain importance.

MetNet: Software to Build and Model the Biogenetic Lattice of Arabidopsis

DOE PAGES

Wurtele, Eve Syrkin; Li, Jie; Diao, Lixia; ...

2003-01-01

MetNet (http://www.botany.iastate.edu/∼mash/metnetex/metabolicnetex.html) is publicly available software in development for analysis of genome-wide RNA, protein and metabolite profiling data. The software is designed to enable the biologist to visualize, statistically analyse and model a metabolic and regulatory network map of Arabidopsis , combined with gene expression profiling data. It contains a JAVA interface to an interactions database (MetNetDB) containing information on regulatory and metabolic interactions derived from a combination of web databases (TAIR, KEGG, BRENDA) and input from biologists in their area of expertise. FCModeler captures input from MetNetDB in a graphical form. Sub-networks can be identified and interpreted using simplemore » fuzzy cognitive maps. FCModeler is intended to develop and evaluate hypotheses, and provide a modelling framework for assessing the large amounts of data captured by high-throughput gene expression experiments. FCModeler and MetNetDB are currently being extended to three-dimensional virtual reality display. The MetNet map, together with gene expression data, can be viewed using multivariate graphics tools in GGobi linked with the data analytic tools in R. Users can highlight different parts of the metabolic network and see the relevant expression data highlighted in other data plots. Multi-dimensional expression data can be rotated through different dimensions. Statistical analysis can be computed alongside the visual. MetNet is designed to provide a framework for the formulation of testable hypotheses regarding the function of specific genes, and in the long term provide the basis for identification of metabolic and regulatory networks that control plant composition and development.« less

Talkin' 'bout My Generation

ERIC Educational Resources Information Center

Rickes, Persis C.

2010-01-01

The monikers are many: (1) "Generation Y"; (2) "Echo Boomers"; (3) "GenMe"; (4) the "Net Generation"; (5) "RenGen"; and (6) "Generation Next". One name that appears to be gaining currency is "Millennials," perhaps as a way to better differentiate the current generation from its…

Trends in readmission rates for safety net hospitals and non-safety net hospitals in the era of the US Hospital Readmission Reduction Program: a retrospective time series analysis using Medicare administrative claims data from 2008 to 2015.

PubMed

Salerno, Amy M; Horwitz, Leora I; Kwon, Ji Young; Herrin, Jeph; Grady, Jacqueline N; Lin, Zhenqiu; Ross, Joseph S; Bernheim, Susannah M

2017-07-13

To compare trends in readmission rates among safety net and non-safety net hospitals under the US Hospital Readmission Reduction Program (HRRP). A retrospective time series analysis using Medicare administrative claims data from January 2008 to June 2015. We examined 3254 US hospitals eligible for penalties under the HRRP, categorised as safety net or non-safety net hospitals based on the hospital's proportion of patients with low socioeconomic status. Admissions for Medicare fee-for-service patients, age ≥65 years, discharged alive, who had a valid five-digit zip code and did not have a principal discharge diagnosis of cancer or psychiatric illness were included, for a total of 52 516 213 index admissions. Mean hospital-level, all-condition, 30-day risk-adjusted standardised unplanned readmission rate, measured quarterly, along with quarterly rate of change, and an interrupted time series examining: April-June 2010, after HRRP was passed, and October-December 2012, after HRRP penalties were implemented. 58.0% (SD 15.3) of safety net hospitals and 17.1% (SD 10.4) of non-safety net hospitals' patients were in the lowest quartile of socioeconomic status. The mean safety net hospital standardised readmission rate declined from 17.0% (SD 3.7) to 13.6% (SD 3.6), whereas the mean non-safety net hospital declined from 15.4% (SD 3.0) to 12.7% (SD 2.5). The absolute difference in rates between safety net and non-safety net hospitals declined from 1.6% (95% CI 1.3 to 1.9) to 0.9% (0.7 to 1.2). The quarterly decline in standardised readmission rates was 0.03 percentage points (95% CI 0.03 to 0.02, p<0.001) greater among safety net hospitals over the entire study period, and no differential change among safety net and non-safety net hospitals was found after either HRRP was passed or penalties enacted. Since HRRP was passed and penalties implemented, readmission rates for safety net hospitals have decreased more rapidly than those for non-safety net hospitals. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Small-unit Training for Adaptability and Resilience in Decision Making (STAR-DM)

DTIC Science & Technology

2017-01-23

based training compared with theoretically less stressful (e.g. classroom lecture) and more Design Interactive, Inc... Design Interactive, Inc. Contract #: N00014-12-G-0427 1... Design Interactive, Inc. 3504 Lake Lynda Drive Suite 400 Orlando, FL 32825 407-706-0977, www.designinteractive.net Corporate Official: John

Reconciling catch differences from multiple fishery independent gill net surveys

USGS Publications Warehouse

Kraus, Richard T.; Vandergoot, Christopher; Kocovsky, Patrick M.; Rogers, Mark W.; Cook, H. Andrew; Brenden, Travis O.

2017-01-01

Fishery independent gill net surveys provide valuable demographic information for population assessment and resource management, but relative to net construction, the effects of ancillary species, and environmental variables on focal species catch rates are poorly understood. In response, we conducted comparative deployments with three unique, inter-agency, survey gill nets used to assess walleye Sander vitreus in Lake Erie. We used an information-theoretic approach with Akaike’s second-order information criterion (AICc) to evaluate linear mixed models of walleye catch as a function of net type (multifilament and two types of monofilament netting), mesh size (categorical), Secchi depth, temperature, water depth, catch of ancillary species, and interactions among selected variables. The model with the greatest weight of evidence showed that walleye catches were positively associated with potential prey and intra-guild predators and negatively associated with water depth and temperature. In addition, the multifilament net had higher average walleye catches than either of the two monofilament nets. Results from this study both help inform decisions about proposed gear changes to stock assessment surveys in Lake Erie, and advance our understanding of how multispecies associations explain variation in gill net catches. Of broader interest to fishery-independent gill net studies, effects of abiotic variables and ancillary species on focal specie’s catch rates were small in comparison with net characteristics of mesh size or twine type.

Timing is everything: Rac1 controls Net1A localization to regulate cell adhesion.

PubMed

Carr, Heather S; Frost, Jeffrey A

2013-01-01

Cell adhesion to the extracellular matrix elicits a temporal reorganization of the actin cytoskeleton that is regulated first by Rac1 and later by RhoA. The signaling mechanisms controlling late stage RhoA activation are incompletely understood. Net1A is a RhoA/RhoB-specific guanine nucleotide exchange factor that is required for cancer cell motility. The ability of Net1A to stimulate RhoA activation is negatively regulated by nuclear sequestration. However, mechanisms controlling the plasma membrane localization of Net1A had not previously been reported. Recently we have shown that Rac1 activation stimulates plasma membrane relocalization and activation of Net1A. Net1A relocalization is independent of its catalytic activity and does not require its C-terminal pleckstrin homology or PDZ interacting domains. Rac1 activation during cell adhesion stimulates a transient relocalization of Net1A that is terminated by proteasomal degradation of Net1A. Importantly, plasma membrane localization of Net1A is required for efficient myosin light chain phosphorylation, focal adhesion maturation, and cell spreading. These data show for the first time a physiological mechanism controlling Net1A relocalization from the nucleus. They also demonstrate a previously unrecognized role for Net1A in controlling actomyosin contractility and focal adhesion dynamics during cell adhesion.

Net-generation attributes and seductive properties of the internet as predictors of online activities and internet addiction.

PubMed

Leung, Louis

2004-06-01

Born between 1977 and 1997, Net-generation is the first generation to grow up surrounded by home computers, video games, and the Internet. As children of the Baby Boomers, the Internet is the medium of choice for the Net-geners. Based on the assumption that Net-generation has unique characteristics, this study examined (1) how Net-geners addicted to the Internet differ from the non-addicted and (2) how these attributes, together with the seductive properties of the Internet, are related to Internet addiction. Data were gathered from a probability sample of 699 Net-geners between the ages of 16 and 24. Results show that Net-geners addicted to the Internet tend to be young female students. Being emotionally open on the Net and a heavy user of ICQ were most influential in predicting Net-geners' problematic use of the Internet. Addicted Net-geners are also strongly linked to the pleasure of being able to control the simulated world in online games. The finding reinforces previous research that "dependents" of the Internet spend most of their time in the synchronous communication environment engaging in interactive online games, chat rooms, and ICQ for pleasure-seeking or escape, while "non-dependents" use information-gathering functions available on the Internet. Furthermore, Internet addicts tend to watch television significantly less, indicating a displacement effect on traditional media use for the Net-generation.

A classification prognostic score to predict OS in stage IV well-differentiated neuroendocrine tumors

PubMed Central

Pusceddu, Sara; Barretta, Francesco; Trama, Annalisa; Botta, Laura; Milione, Massimo; Buzzoni, Roberto; De Braud, Filippo; Mazzaferro, Vincenzo; Pastorino, Ugo; Seregni, Ettore; Mariani, Luigi; Gatta, Gemma; Di Bartolomeo, Maria; Femia, Daniela; Prinzi, Natalie; Coppa, Jorgelina; Panzuto, Francesco; Antonuzzo, Lorenzo; Bajetta, Emilio; Brizzi, Maria Pia; Campana, Davide; Catena, Laura; Comber, Harry; Dwane, Fiona; Fazio, Nicola; Faggiano, Antongiulio; Giuffrida, Dario; Henau, Kris; Ibrahim, Toni; Marconcini, Riccardo; Massironi, Sara; Žakelj, Maja Primic; Spada, Francesca; Tafuto, Salvatore; Van Eycken, Elizabeth; Van der Zwan, Jan Maaten; Žagar, Tina; Giacomelli, Luca; Miceli, Rosalba; Aroldi, Francesca; Bongiovanni, Alberto; Berardi, Rossana; Brighi, Nicole; Cingarlini, Sara; Cauchi, Carolina; Cavalcoli, Federica; Carnaghi, Carlo; Corti, Francesca; Duro, Marilina; Davì, Maria Vittoria; De Divitiis, Chiara; Ermacora, Paola; La Salvia, Anna; Luppi, Gabriele; Lo Russo, Giuseppe; Nichetti, Federico; Raimondi, Alessandra; Perfetti, Vittorio; Razzore, Paola; Rinzivillo, Maria; Siesling, Sabine; Torchio, Martina; Van Dijk, Boukje; Visser, Otto; Vernieri, Claudio

2018-01-01

No validated prognostic tool is available for predicting overall survival (OS) of patients with well-differentiated neuroendocrine tumors (WDNETs). This study, conducted in three independent cohorts of patients from five different European countries, aimed to develop and validate a classification prognostic score for OS in patients with stage IV WDNETs. We retrospectively collected data on 1387 patients: (i) patients treated at the Istituto Nazionale Tumori (Milan, Italy; n = 515); (ii) European cohort of rare NET patients included in the European RARECAREnet database (n = 457); (iii) Italian multicentric cohort of pancreatic NET (pNETs) patients treated at 24 Italian institutions (n = 415). The score was developed using data from patients included in cohort (i) (training set); external validation was performed by applying the score to the data of the two independent cohorts (ii) and (iii) evaluating both calibration and discriminative ability (Harrell C statistic). We used data on age, primary tumor site, metastasis (synchronous vs metachronous), Ki-67, functional status and primary surgery to build the score, which was developed for classifying patients into three groups with differential 10-year OS: (I) favorable risk group: 10-year OS ≥70%; (II) intermediate risk group: 30% ≤ 10-year OS < 70%; (III) poor risk group: 10-year OS <30%. The Harrell C statistic was 0.661 in the training set, and 0.626 and 0.601 in the RARECAREnet and Italian multicentric validation sets, respectively. In conclusion, based on the analysis of three ‘field-practice’ cohorts collected in different settings, we defined and validated a prognostic score to classify patients into three groups with different long-term prognoses. PMID:29559553

Structure, Antimicrobial Activities and Mode of Interaction with Membranes of Bovel Phylloseptins from the Painted-Belly Leaf Frog, Phyllomedusa sauvagii

PubMed Central

Raja, Zahid; André, Sonia; Piesse, Christophe; Sereno, Denis; Nicolas, Pierre; Foulon, Thierry

2013-01-01

Transcriptomic and peptidomic analysis of skin secretions from the Painted-belly leaf frog Phyllomedusa sauvagii led to the identification of 5 novel phylloseptins (PLS-S2 to -S6) and also of phylloseptin-1 (PSN-1, here renamed PLS-S1), the only member of this family previously isolated in this frog. Synthesis and characterization of these phylloseptins revealed differences in their antimicrobial activities. PLS-S1, -S2, and -S4 (79–95% amino acid sequence identity; net charge  = +2) were highly potent and cidal against Gram-positive bacteria, including multidrug resistant S. aureus strains, and killed the promastigote stage of Leishmania infantum, L. braziliensis and L. major. By contrast, PLS-S3 (95% amino acid identity with PLS-S2; net charge  = +1) and -S5 (net charge  = +2) were found to be almost inactive against bacteria and protozoa. PLS-S6 was not studied as this peptide was closely related to PLS-S1. Differential scanning calorimetry on anionic and zwitterionic multilamellar vesicles combined with circular dichroism spectroscopy and membrane permeabilization assays on bacterial cells indicated that PLS-S1, -S2, and -S4 are structured in an amphipathic α-helix that disrupts the acyl chain packing of anionic lipid bilayers. As a result, regions of two coexisting phases could be formed, one phase rich in peptide and the other lipid-rich. After reaching a threshold peptide concentration, the disruption of lipid packing within the bilayer may lead to local cracks and disintegration of the microbial membrane. Differences in the net charge, α-helical folding propensity, and/or degree of amphipathicity between PLS-S1, -S2 and -S4, and between PLS-S3 and -S5 appear to be responsible for their marked differences in their antimicrobial activities. In addition to the detailed characterization of novel phylloseptins from P. sauvagii, our study provides additional data on the previously isolated PLS-S1 and on the mechanism of action of phylloseptins. PMID:23967105

Analysis of 320 gastroenteropancreatic neuroendocrine tumors identifies TS expression as independent biomarker for survival.

PubMed

Lee, Hye Seung; Chen, Min; Kim, Ji Hun; Kim, Woo Ho; Ahn, Soyeon; Maeng, Kyungah; Allegra, Carmen J; Kaye, Frederic J; Hochwald, Steven N; Zajac-Kaye, Maria

2014-07-01

Thymidylate synthase (TS), a critical enzyme for DNA synthesis and repair, is both a potential tumor prognostic biomarker as well as a tumorigenic oncogene in animal models. We have now studied the clinical implications of TS expression in gastroenteropancreatic (GEP) neuroendocrine tumors (NETs) and compared these results to other cell cycle biomarker genes. Protein tissue arrays were used to study TS, Ki-67, Rb, pRb, E2F1, p18, p21, p27 and menin expression in 320 human GEP-NETs samples. Immunohistochemical expression was correlated with univariate and multivariate predictors of survival utilizing Kaplan Meier and Cox proportional hazards models. Real time RT-PCR was used to validate these findings. We found that 78 of 320 GEP-NETs (24.4%) expressed TS. NETs arising in the colon, stomach and pancreas showed the highest expression of TS (47.4%, 42.6% and 37.3%, respectively), whereas NETs of the appendix, rectum and duodenum displayed low TS expression (3.3%, 12.9% and 15.4%, respectively). TS expression in GEP-NETs was associated with poorly differentiated endocrine carcinoma, angiolymphatic invasion, lymph node metastasis and distant metastasis (p < 0.05). Patients with TS-positive NETs had markedly worse outcomes than TS-negative NETs as shown by univariate (p < 0.001) and multivariate (p = 0.01) survival analyses. Expression of p18 predicted survival in TS-positive patients that received chemotherapy (p = 0.015). In conclusion, TS protein expression was an independent prognostic biomarker for GEP-NETs. The strong association of increased TS expression with aggressive disease and early death supports the role of TS as a cancer promoting agent in these tumors. © 2013 UICC.

High expression of dopamine receptor subtype 2 in a large series of neuroendocrine tumors.

PubMed

Grossrubatscher, Erika; Veronese, Silvio; Ciaramella, Paolo Dalino; Pugliese, Raffaele; Boniardi, Marco; De Carlis, Luciano; Torre, Massimo; Ravini, Mario; Gambacorta, Marcello; Loli, Paola

2008-12-01

To evaluate by immumohistochemistry the presence of DR subtype 2 (D2R) in well differentiated NETs of different sites and in normal islet cells. Recent data in vitro and in vivo support that dopaminergic drugs might exert an inhibitory effect on hormone secretion and, possibly, on tumor growth in neuroendocrine tumors (NET)s. Their potential therapeutic role needs the demonstration of dopamine receptors (DR) in tumor cells. Little is known on the expression of DR in NETs. 85% of samples (100% of bronchial carcinoids and 93% of islet cell tumors) showed positivity for D2R; intensity of immunoreaction in NETs was similar or higher than in pituitary (54% and respectively 31% of cases). D2R positivity in more than 70% of tumor cells was observed in 46% of samples. Same intensity of D2R-immunoreactivity was found in pituitary and normal islet cells. No differences in D2R expression were recorded on considering tumor grading, size, proliferative activity, presence of metastases, endocrine activity and gender. A significant difference (62.5% vs 96.4%, p = 0.039) was observed in the prevalence of D2R expression between patients with more aggressive tumors and patients without recurrence/progression of disease during follow-up. 46 NET samples from 44 patients and normal endocrine pancreatic tissue were studied. D2R-staining was performed on NETs and compared with six non-secreting pituitary adenomas and related to clinical-pathological data. The present data demonstrate a high expression of D2R in NETs; this finding is of clinical relevance in view of the potential role of dopaminergic drugs in inhibiting secretion and/or cell proliferation in NETs.

Management of neuroendocrine tumors.

PubMed

Chung, Clement

2016-11-01

Current strategies for managing neuroendocrine tumors (NETs) in adult patients are reviewed, with a focus on medication safety concerns. NETs usually originate in the gastrointestinal or bronchopulmonary tract. Symptoms due to hormonal hypersecretion often occur in patients with foregut or midgut NETs or liver metastases. Surgical resection is recommended for most localized NETs, while systemic cytotoxic chemotherapy is typically used for high-grade and pancreatic tumors. The standard of care for metastatic NETs is somatostatin analog therapy with octreotide (available in both short- and long-acting formulations) or a depot formulation of lanreotide. Everolimus and sunitinib are targeted therapies with approved indications for use in treating advanced pancreatic NETs. Some patients with liver-predominant disease or liver metastases may undergo regional chemoembolization procedures. Pharmacists should be cognizant of differences between newer and older chemoembolization agents and procedures, as well as differences between somatostatin analog products used as medications and the radiolabelled forms used in diagnostic scintigraphy. Other medication safety issues in NET management arise during perioperative supportive care, patient education, compliance counseling, and management of adverse effects of targeted therapies and chemotherapy, including stomatitis, hyperthyroidism, and hand-foot skin reaction. Somatostatin analog therapy is the mainstay for management of locally advanced or metastatic NETs. Liver-directed therapy is an option for localized unresectable disease; platinum-based chemotherapy is the first-line treatment for poorly differentiated tumors. Optimal sequencing of these treatments and targeted therapies such as everolimus and tyrosine kinase inhibitors remains to be elucidated. Copyright © 2016 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

Clinical application of SPECT-CT with 99mTc-Tektrotyd in bronchial and thymic neuroendocrine tumors (NETs).

PubMed

Sergieva, Sonya; Robev, Bozhil; Dimcheva, Milena; Fakirova, Albena; Hristoskova, Radka

2016-01-01

Neuroendocrine tumors (NETs) of the thorax including bronchial and thymic tumors belong to foregut NETs. Limited loco-regional thoracic NETs can be resected with surgery, but in extensive metastatic disease the treatment is mainly palliative. A high incidence and density of somatostatin receptors (SSTR2, SSTR3, and SSTR5) are found in thoracic NETs. The purpose of this study was to evaluate the role of SPECT-CT somatostatin receptor scintigraphy (SRS) with 99mTc-Tektrotyd for imaging, staging and follow up of patients with bronchial and thymic neuroendocrine tumors. Forty-one patients with thoracic tumors with neuroendocrine differentiation were studied. Sixty-eight examinations including SPECT-CT studies of the neck and chest and/or abdomen and pelvis were carried out 2-4 hrs. post i.v. administration of aver-age 740 MBq activity dose of 99mTc-EDDA/HYNIC-TOC (Tektrotyd, Polatom). In all 41 investigated patients we obtained 81.25% (13/16), 88% (22/25) and 85.36% (35/41) of sensitivity, specificity and accuracy of this diagnostic approach, respectively. Somatostatin-receptor scintigraphy correctly identified all primary NETs located in the lungs and thymus. SPECT-CT studies with 99mTc-EDDA/HYNIC-TOC resulted in exact pre-surgical and pre-treatment N/M staging of bronchial and thymic NETs, except 2 cases with multiple hepatic metastases and 1 with massive suprarenal metastasis. It can be concluded that SPECT-CT with 99mTc-EDDA/HYNIC-TOC is a valuable tool for staging and follow-up of patients with thoracic NETs.

Metallurgical failure analysis of MH-1A reactor core hold-down bolts. Final report

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

Hawthorne, J.R.; Watson, H.E.

1976-11-01

The Naval Research Laboratory has performed a failure analysis on two MH-1A reactor core hold-down bolts that broke in service. Adherence to fabrication specifications, post-service properties and possible causes of bolt failure were investigated. The bolt material was verified as 17-4PH precipitation hardening stainless steel. Measured bolt dimensions also were in accordance with fabrication drawing specifications. Bolt failure occurred in the region of a locking pin hole which reduced the bolt net section by 47 percent. The failure analysis indicates that the probable cause of failure was net section overloading resulting from a lateral bending force on the bolt. Themore » analysis indicates that net section overloading could also have resulted from combined tensile stresses (bolt preloading plus differential thermal expansion). Recommendations are made for improved bolting.« less

atBioNet--an integrated network analysis tool for genomics and biomarker discovery.

PubMed

Ding, Yijun; Chen, Minjun; Liu, Zhichao; Ding, Don; Ye, Yanbin; Zhang, Min; Kelly, Reagan; Guo, Li; Su, Zhenqiang; Harris, Stephen C; Qian, Feng; Ge, Weigong; Fang, Hong; Xu, Xiaowei; Tong, Weida

2012-07-20

Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. An effective network analysis tool should integrate different content-specific PPI databases into a comprehensive network format with a user-friendly platform to identify key functional modules/pathways and the underlying mechanisms of disease and toxicity. atBioNet integrates seven publicly available PPI databases into a network-specific knowledge base. Knowledge expansion is achieved by expanding a user supplied proteins/genes list with interactions from its integrated PPI network. The statistically significant functional modules are determined by applying a fast network-clustering algorithm (SCAN: a Structural Clustering Algorithm for Networks). The functional modules can be visualized either separately or together in the context of the whole network. Integration of pathway information enables enrichment analysis and assessment of the biological function of modules. Three case studies are presented using publicly available disease gene signatures as a basis to discover new biomarkers for acute leukemia, systemic lupus erythematosus, and breast cancer. The results demonstrated that atBioNet can not only identify functional modules and pathways related to the studied diseases, but this information can also be used to hypothesize novel biomarkers for future analysis. atBioNet is a free web-based network analysis tool that provides a systematic insight into proteins/genes interactions through examining significant functional modules. The identified functional modules are useful for determining underlying mechanisms of disease and biomarker discovery. It can be accessed at: http://www.fda.gov/ScienceResearch/BioinformaticsTools/ucm285284.htm.

Streptococcus suis DNase SsnA contributes to degradation of neutrophil extracellular traps (NETs) and evasion of NET-mediated antimicrobial activity.

PubMed

de Buhr, Nicole; Neumann, Ariane; Jerjomiceva, Natalja; von Köckritz-Blickwede, Maren; Baums, Christoph G

2014-02-01

Streptococcus suis is an important cause of different pathologies in pigs and humans, most importantly fibrinosuppurative meningitis. Tissue infected with this pathogen is substantially infiltrated with neutrophils, but the function of neutrophil extracellular traps (NETs) - a more recently discovered antimicrobial strategy of neutrophils - in host defence against Strep. suis has not been investigated. The objective of this work was to investigate the interaction of Strep. suis with NETs in vitro. Strep. suis induced NET formation in porcine neutrophils and was entrapped but not killed by those NETs. As the amount of NETs decreased over time, we hypothesized that a known extracellular DNase of Strep. suis degrades NETs. Though this nuclease was originally designated Strep. suis-secreted nuclease A (SsnA), this work demonstrated surface association in accordance with an LPXTG cell wall anchor motif and partial release into the supernatant. Confirming our hypothesis, an isogenic ssnA mutant was significantly attenuated in NET degradation and in protection against the antimicrobial activity of NETs as determined in assays with phorbol myristate acetate (PMA)-stimulated human neutrophils. Though assays with PMA-stimulated porcine neutrophils suggested that SsnA also degrades porcine NETs, phenotypic differences between wt and the isogenic ssnA mutant were less distinct. As SsnA expression was crucial for neither growth in vitro nor for survival in porcine or human blood, the results indicated that SsnA is the first specific NET evasion factor to be identified in Strep. suis.

Neutrophil Extracellular Traps Directly Induce Epithelial and Endothelial Cell Death: A Predominant Role of Histones

PubMed Central

Saffarzadeh, Mona; Juenemann, Christiane; Queisser, Markus A.; Lochnit, Guenter; Barreto, Guillermo; Galuska, Sebastian P.; Lohmeyer, Juergen; Preissner, Klaus T.

2012-01-01

Neutrophils play an important role in innate immunity by defending the host organism against invading microorganisms. Antimicrobial activity of neutrophils is mediated by release of antimicrobial peptides, phagocytosis as well as formation of neutrophil extracellular traps (NET). These structures are composed of DNA, histones and granular proteins such as neutrophil elastase and myeloperoxidase. This study focused on the influence of NET on the host cell functions, particularly on human alveolar epithelial cells as the major cells responsible for gas exchange in the lung. Upon direct interaction with epithelial and endothelial cells, NET induced cytotoxic effects in a dose-dependent manner, and digestion of DNA in NET did not change NET-mediated cytotoxicity. Pre-incubation of NET with antibodies against histones, with polysialic acid or with myeloperoxidase inhibitor but not with elastase inhibitor reduced NET-mediated cytotoxicity, suggesting that histones and myeloperoxidase are responsible for NET-mediated cytotoxicity. Although activated protein C (APC) did decrease the histone-induced cytotoxicity in a purified system, it did not change NET-induced cytotoxicity, indicating that histone-dependent cytotoxicity of NET is protected against APC degradation. Moreover, in LPS-induced acute lung injury mouse model, NET formation was documented in the lung tissue as well as in the bronchoalveolar lavage fluid. These data reveal the important role of protein components in NET, particularly histones, which may lead to host cell cytotoxicity and may be involved in lung tissue destruction. PMID:22389696

Contribution of Electrostatics in the Fibril Stability of a Model Ionic-Complementary Peptide.

PubMed

Owczarz, Marta; Casalini, Tommaso; Motta, Anna C; Morbidelli, Massimo; Arosio, Paolo

2015-12-14

In this work we quantified the role of electrostatic interactions in the self-assembly of a model amphiphilic peptide (RADA 16-I) into fibrillar structures by a combination of size exclusion chromatography and molecular simulations. For the peptide under investigation, it is found that a net charge of +0.75 represents the ideal condition to promote the formation of regular amyloid fibrils. Lower net charges favor the formation of amorphous precipitates, while larger net charges destabilize the fibrillar aggregates and promote a reversible dissociation of monomers from the ends of the fibrils. By quantifying the dependence of the equilibrium constant of this reversible reaction on the pH value and the peptide net charge, we show that electrostatic interactions contribute largely to the free energy of fibril formation. The addition of both salt and a charged destabilizer (guanidinium hydrochloride) at moderate concentration (0.3-1 M) shifts the monomer-fibril equilibrium toward the fibrillar state. Whereas the first effect can be explained by charge screening of electrostatic repulsion only, the promotion of fibril formation in the presence of guanidinium hydrochloride is also attributed to modifications of the peptide conformation. The results of this work indicate that the global peptide net charge is a key property that correlates well with the fibril stability, although the peptide conformation and the surface charge distribution also contribute to the aggregation propensity.

NetDecoder: a network biology platform that decodes context-specific biological networks and gene activities.

PubMed

da Rocha, Edroaldo Lummertz; Ung, Choong Yong; McGehee, Cordelia D; Correia, Cristina; Li, Hu

2016-06-02

The sequential chain of interactions altering the binary state of a biomolecule represents the 'information flow' within a cellular network that determines phenotypic properties. Given the lack of computational tools to dissect context-dependent networks and gene activities, we developed NetDecoder, a network biology platform that models context-dependent information flows using pairwise phenotypic comparative analyses of protein-protein interactions. Using breast cancer, dyslipidemia and Alzheimer's disease as case studies, we demonstrate NetDecoder dissects subnetworks to identify key players significantly impacting cell behaviour specific to a given disease context. We further show genes residing in disease-specific subnetworks are enriched in disease-related signalling pathways and information flow profiles, which drive the resulting disease phenotypes. We also devise a novel scoring scheme to quantify key genes-network routers, which influence many genes, key targets, which are influenced by many genes, and high impact genes, which experience a significant change in regulation. We show the robustness of our results against parameter changes. Our network biology platform includes freely available source code (http://www.NetDecoder.org) for researchers to explore genome-wide context-dependent information flow profiles and key genes, given a set of genes of particular interest and transcriptome data. More importantly, NetDecoder will enable researchers to uncover context-dependent drug targets. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Interactions of signaling proteins, growth factors and other proteins with heparan sulfate: mechanisms and mysteries.

PubMed

Billings, Paul C; Pacifici, Maurizio

2015-01-01

Heparan sulfate (HS) is a component of cell surface and matrix-associated proteoglycans (HSPGs) that, collectively, play crucial roles in many physiologic processes including cell differentiation, organ morphogenesis and cancer. A key function of HS is to bind and interact with signaling proteins, growth factors, plasma proteins, immune-modulators and other factors. In doing so, the HS chains and HSPGs are able to regulate protein distribution, bio-availability and action on target cells and can also serve as cell surface co-receptors, facilitating ligand-receptor interactions. These proteins contain an HS/heparin-binding domain (HBD) that mediates their association and contacts with HS. HBDs are highly diverse in sequence and predicted structure, contain clusters of basic amino acids (Lys and Arg) and possess an overall net positive charge, most often within a consensus Cardin-Weintraub (CW) motif. Interestingly, other domains and residues are now known to influence protein-HS interactions, as well as interactions with other glycosaminoglycans, such as chondroitin sulfate. In this review, we provide a description and analysis of HBDs in proteins including amphiregulin, fibroblast growth factor family members, heparanase, sclerostin and hedgehog protein family members. We discuss HBD structural and functional features and important roles carried out by other protein domains, and also provide novel conformational insights into the diversity of CW motifs present in Sonic, Indian and Desert hedgehogs. Finally, we review progress in understanding the pathogenesis of a rare pediatric skeletal disorder, Hereditary Multiple Exostoses (HME), characterized by HS deficiency and cartilage tumor formation. Advances in understanding protein-HS interactions will have broad implications for basic biology and translational medicine as well as for the development of HS-based therapeutics.

Ontology-based Vaccine and Drug Adverse Event Representation and Theory-guided Systematic Causal Network Analysis toward Integrative Pharmacovigilance Research.

PubMed

He, Yongqun

2016-06-01

Compared with controlled terminologies ( e.g. , MedDRA, CTCAE, and WHO-ART), the community-based Ontology of AEs (OAE) has many advantages in adverse event (AE) classifications. The OAE-derived Ontology of Vaccine AEs (OVAE) and Ontology of Drug Neuropathy AEs (ODNAE) serve as AE knowledge bases and support data integration and analysis. The Immune Response Gene Network Theory explains molecular mechanisms of vaccine-related AEs. The OneNet Theory of Life treats the whole process of a life of an organism as a single complex and dynamic network ( i.e. , OneNet). A new "OneNet effectiveness" tenet is proposed here to expand the OneNet theory. Derived from the OneNet theory, the author hypothesizes that one human uses one single genotype-rooted mechanism to respond to different vaccinations and drug treatments, and experimentally identified mechanisms are manifestations of the OneNet blueprint mechanism under specific conditions. The theories and ontologies interact together as semantic frameworks to support integrative pharmacovigilance research.

β2 integrin mediates hantavirus-induced release of neutrophil extracellular traps

PubMed Central

Raftery, Martin J.; Lalwani, Pritesh; Krautkrӓmer, Ellen; Peters, Thorsten; Scharffetter-Kochanek, Karin; Krüger, Renate; Hofmann, Jörg; Seeger, Karl; Krüger, Detlev H.

2014-01-01

Rodent-borne hantaviruses are emerging human pathogens that cause severe human disease. The underlying mechanisms are not well understood, as hantaviruses replicate in endothelial and epithelial cells without causing any cytopathic effect. We demonstrate that hantaviruses strongly stimulated neutrophils to release neutrophil extracellular traps (NETs). Hantavirus infection induced high systemic levels of circulating NETs in patients and this systemic NET overflow was accompanied by production of autoantibodies to nuclear antigens. Analysis of the responsible mechanism using neutrophils from β2 null mice identified β2 integrin receptors as a master switch for NET induction. Further experiments suggested that β2 integrin receptors such as complement receptor 3 (CR3) and 4 (CR4) may act as novel hantavirus entry receptors. Using adenoviruses, we confirmed that viral interaction with β2 integrin induced strong NET formation. Collectively, β2 integrin–mediated systemic NET overflow is a novel viral mechanism of immunopathology that may be responsible for characteristic aspects of hantavirus-associated disease such as kidney and lung damage. PMID:24889201

WhaleNet/environet

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

Williamson, J.M.

1994-12-31

WhaleNet has established a network where students, educators, and scientists can interact and share data for use in interdisciplinary curricular and student research activities in classrooms around the world by utilizing telecommunication. This program enables students to participate in marine/whale research programs in real-time with WhaleNet data and supplementary curriculum materials regardless of their geographic location. Systems have been established with research organizations and whale watch companies whereby research data is posted by scientists and students participating in whale watches on the WhaleNet bulletin board and shared with participating classrooms. WhaleNet presently has contacts with classrooms across the nation, andmore » with research groups, whale watch organizations, science museums, and universities from Alaska to North Carolina, Hawaii to Maine, and Belize to Norway. WhaleNet has plans to make existing whale and fisheries research databases available for classroom use and to have research data from satellite tagging programs on various species of whales available for classroom access in real-time.« less

Mentornet - E-Mentoring for Women Students in Engineering and Science

NASA Astrophysics Data System (ADS)

Single, Peg Boyle; Muller, Carol B.; Cunningham, Christine M.; Single, Richard M.; Carlsen, William S.

MentorNet www.MentorNet.net;, the E-Mentoring Network for Diversity in Engineering and Science, addresses the underrepresentation of women in science, technology, engineering, and mathematics "STEM". MentorNet offers a multiinstitutional, structured, electronic mentoring "e-mentoring" program that pairs undergraduate and graduate students, primarily women, with professionals and supports them through e-mentoring relationships of specified lengths. The program evaluations established that over 90% of the participants would recommend MentorNet to a friend or colleague. The e-mentoring program allowed participants to establish satisfactory and beneficial e-mentoring relationships based on investments of approximately 20 minutes per week - in between more serious exchanges, email exchanges that included light-hearted social interactions and jokes were an important aspect of sustaining e-mentoring relationships. Participation in MentorNet increased the students' self-confidence in their f elds - desire to obtain work in industry, national laboratories, or national agencies; and intent to pursue careers in their fields. Three years of evaluation results support the need for and efficacy of the program.

Interactive Model Visualization for NET-VISA

NASA Astrophysics Data System (ADS)

Kuzma, H. A.; Arora, N. S.

2013-12-01

NET-VISA is a probabilistic system developed for seismic network processing of data measured on the International Monitoring System (IMS) of the Comprehensive nuclear Test Ban Treaty Organization (CTBTO). NET-VISA is composed of a Generative Model (GM) and an Inference Algorithm (IA). The GM is an explicit mathematical description of the relationships between various factors in seismic network analysis. Some of the relationships inside the GM are deterministic and some are statistical. Statistical relationships are described by probability distributions, the exact parameters of which (such as mean and standard deviation) are found by training NET-VISA using recent data. The IA uses the GM to evaluate the probability of various events and associations, searching for the seismic bulletin which has the highest overall probability and is consistent with a given set of measured arrivals. An Interactive Model Visualization tool (IMV) has been developed which makes 'peeking into' the GM simple and intuitive through a web-based interfaced. For example, it is now possible to access the probability distributions for attributes of events and arrivals such as the detection rate for each station for each of 14 phases. It also clarifies the assumptions and prior knowledge that are incorporated into NET-VISA's event determination. When NET-VISA is retrained, the IMV will be a visual tool for quality control both as a means of testing that the training has been accomplished correctly and that the IMS network has not changed unexpectedly. A preview of the IMV will be shown at this poster presentation. Homepage for the IMV IMV shows current model file and reference image.

Predicting multicellular function through multi-layer tissue networks

PubMed Central

Zitnik, Marinka; Leskovec, Jure

2017-01-01

Abstract Motivation: Understanding functions of proteins in specific human tissues is essential for insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular function remains a critical challenge for biomedicine. Results: Here, we present OhmNet, a hierarchy-aware unsupervised node feature learning approach for multi-layer networks. We build a multi-layer network, where each layer represents molecular interactions in a different human tissue. OhmNet then automatically learns a mapping of proteins, represented as nodes, to a neural embedding-based low-dimensional space of features. OhmNet encourages sharing of similar features among proteins with similar network neighborhoods and among proteins activated in similar tissues. The algorithm generalizes prior work, which generally ignores relationships between tissues, by modeling tissue organization with a rich multiscale tissue hierarchy. We use OhmNet to study multicellular function in a multi-layer protein interaction network of 107 human tissues. In 48 tissues with known tissue-specific cellular functions, OhmNet provides more accurate predictions of cellular function than alternative approaches, and also generates more accurate hypotheses about tissue-specific protein actions. We show that taking into account the tissue hierarchy leads to improved predictive power. Remarkably, we also demonstrate that it is possible to leverage the tissue hierarchy in order to effectively transfer cellular functions to a functionally uncharacterized tissue. Overall, OhmNet moves from flat networks to multiscale models able to predict a range of phenotypes spanning cellular subsystems. Availability and implementation: Source code and datasets are available at http://snap.stanford.edu/ohmnet. Contact: jure@cs.stanford.edu PMID:28881986

Benefit and cost curves for typical pollination mutualisms.

PubMed

Morris, William F; Vázquez, Diego P; Chacoff, Natacha P

2010-05-01

Mutualisms provide benefits to interacting species, but they also involve costs. If costs come to exceed benefits as population density or the frequency of encounters between species increases, the interaction will no longer be mutualistic. Thus curves that represent benefits and costs as functions of interaction frequency are important tools for predicting when a mutualism will tip over into antagonism. Currently, most of what we know about benefit and cost curves in pollination mutualisms comes from highly specialized pollinating seed-consumer mutualisms, such as the yucca moth-yucca interaction. There, benefits to female reproduction saturate as the number of visits to a flower increases (because the amount of pollen needed to fertilize all the flower's ovules is finite), but costs continue to increase (because pollinator offspring consume developing seeds), leading to a peak in seed production at an intermediate number of visits. But for most plant-pollinator mutualisms, costs to the plant are more subtle than consumption of seeds, and how such costs scale with interaction frequency remains largely unknown. Here, we present reasonable benefit and cost curves that are appropriate for typical pollinator-plant interactions, and we show how they can result in a wide diversity of relationships between net benefit (benefit minus cost) and interaction frequency. We then use maximum-likelihood methods to fit net-benefit curves to measures of female reproductive success for three typical pollination mutualisms from two continents, and for each system we chose the most parsimonious model using information-criterion statistics. We discuss the implications of the shape of the net-benefit curve for the ecology and evolution of plant-pollinator mutualisms, as well as the challenges that lie ahead for disentangling the underlying benefit and cost curves for typical pollination mutualisms.

Modeling and performance analysis using extended fuzzy-timing Petri nets for networked virtual environments.

PubMed

Zhou, Y; Murata, T; Defanti, T A

2000-01-01

Despite their attractive properties, networked virtual environments (net-VEs) are notoriously difficult to design, implement, and test due to the concurrency, real-time and networking features in these systems. Net-VEs demand high quality-of-service (QoS) requirements on the network to maintain natural and real-time interactions among users. The current practice for net-VE design is basically trial and error, empirical, and totally lacks formal methods. This paper proposes to apply a Petri net formal modeling technique to a net-VE-NICE (narrative immersive constructionist/collaborative environment), predict the net-VE performance based on simulation, and improve the net-VE performance. NICE is essentially a network of collaborative virtual reality systems called the CAVE-(CAVE automatic virtual environment). First, we introduce extended fuzzy-timing Petri net (EFTN) modeling and analysis techniques. Then, we present EFTN models of the CAVE, NICE, and transport layer protocol used in NICE: transmission control protocol (TCP). We show the possibility analysis based on the EFTN model for the CAVE. Then, by using these models and design/CPN as the simulation tool, we conducted various simulations to study real-time behavior, network effects and performance (latencies and jitters) of NICE. Our simulation results are consistent with experimental data.

TreeNetViz: revealing patterns of networks over tree structures.

PubMed

Gou, Liang; Zhang, Xiaolong Luke

2011-12-01

Network data often contain important attributes from various dimensions such as social affiliations and areas of expertise in a social network. If such attributes exhibit a tree structure, visualizing a compound graph consisting of tree and network structures becomes complicated. How to visually reveal patterns of a network over a tree has not been fully studied. In this paper, we propose a compound graph model, TreeNet, to support visualization and analysis of a network at multiple levels of aggregation over a tree. We also present a visualization design, TreeNetViz, to offer the multiscale and cross-scale exploration and interaction of a TreeNet graph. TreeNetViz uses a Radial, Space-Filling (RSF) visualization to represent the tree structure, a circle layout with novel optimization to show aggregated networks derived from TreeNet, and an edge bundling technique to reduce visual complexity. Our circular layout algorithm reduces both total edge-crossings and edge length and also considers hierarchical structure constraints and edge weight in a TreeNet graph. These experiments illustrate that the algorithm can reduce visual cluttering in TreeNet graphs. Our case study also shows that TreeNetViz has the potential to support the analysis of a compound graph by revealing multiscale and cross-scale network patterns. © 2011 IEEE

Flexible body control using neural networks

NASA Technical Reports Server (NTRS)

Mccullough, Claire L.

1992-01-01

Progress is reported on the control of Control Structures Interaction suitcase demonstrator (a flexible structure) using neural networks and fuzzy logic. It is concluded that while control by neural nets alone (i.e., allowing the net to design a controller with no human intervention) has yielded less than optimal results, the neural net trained to emulate the existing fuzzy logic controller does produce acceptible system responses for the initial conditions examined. Also, a neural net was found to be very successful in performing the emulation step necessary for the anticipatory fuzzy controller for the CSI suitcase demonstrator. The fuzzy neural hybrid, which exhibits good robustness and noise rejection properties, shows promise as a controller for practical flexible systems, and should be further evaluated.

A distributed Petri Net controller for a dual arm testbed

NASA Technical Reports Server (NTRS)

Bjanes, Atle

1991-01-01

This thesis describes the design and functionality of a Distributed Petri Net Controller (DPNC). The controller runs under X Windows to provide a graphical interface. The DPNC allows users to distribute a Petri Net across several host computers linked together via a TCP/IP interface. A sub-net executes on each host, interacting with the other sub-nets by passing a token vector from host to host. One host has a command window which monitors and controls the distributed controller. The input to the DPNC is a net definition file generated by Great SPN. Thus, a net may be designed, analyzed and verified using this package before implementation. The net is distributed to the hosts by tagging transitions that are host-critical with the appropriate host number. The controller will then distribute the remaining places and transitions to the hosts by generating the local nets, the local marking vectors and the global marking vector. Each transition can have one or more preconditions which must be fulfilled before the transition can fire, as well as one or more post-processes to be executed after the transition fires. These implement the actual input/output to the environment (machines, signals, etc.). The DPNC may also be used to simulate a Great SPN net since stochastic and deterministic firing rates are implemented in the controller for timed transitions.

CONDUCTION ELECTRON-MAGNETIC ION INTERACTION IN RARE EARTHS

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

Anderson, G.S.; Legvold, S.

1958-11-01

The proposal is maade that there is an additional effective electron- electron interaction in the rare earths which results from the conduction electron-magnetic ion exchange. The strength of the net electron-electron interaction should tnen be expected to be a function of spin as well as solute concentrations. (W.D.M.)

Fishery gear interactions from stranded bottlenose dolphins, Florida manatees and sea turtles in Florida, U.S.A.

PubMed

Adimey, Nicole M; Hudak, Christine A; Powell, Jessica R; Bassos-Hull, Kim; Foley, Allen; Farmer, Nicholas A; White, Linda; Minch, Karrie

2014-04-15

Documenting the extent of fishery gear interactions is critical to wildlife conservation efforts, especially for reducing entanglements and ingestion. This study summarizes fishery gear interactions involving common bottlenose dolphins (Tursiops truncatus truncatus), Florida manatees (Trichechus manatus latirostris) and sea turtles: loggerhead (Caretta caretta), green turtle (Chelonia mydas), leatherback (Dermochelys coriacea), hawksbill (Eretmochelys imbricata), Kemp's ridley (Lepidochelys kempii), and olive ridley (Lepidochelys olivacea) stranding in Florida waters during 1997-2009. Fishery gear interactions for all species combined were 75.3% hook and line, 18.2% trap pot gear, 4.8% fishing nets, and 1.7% in multiple gears. Total reported fishery gear cases increased over time for dolphins (p<0.05), manatees (p<0.01), loggerheads (p<0.05) and green sea turtles (p<0.05). The proportion of net interaction strandings relative to total strandings for loggerhead sea turtles increased (p<0.05). Additionally, life stage and sex patterns were examined, fishery gear interaction hotspots were identified and generalized linear regression modeling was conducted. Published by Elsevier Ltd.

Differential effects of protoporphyrin and uroporphyrin on murine mast cells

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

Lim, H.W.; Gigli, I.; Wasserman, S.I.

1987-03-01

To investigate the mechanisms responsible for the distinct cutaneous manifestations of erythropoietic protoporphyria and porphyria cutanea tarda, the effects of protoporphyrin (PP) and uroporphyrin (URO), the predominant porphyrins in the respective disease, on mast cells were examined. Release of preformed and generated mediators was assessed by the release of radioactivity from cells labeled with (/sup 3/H)serotonin and (/sup 14/C)arachidonic acid, respectively. Clinically relevant doses of PP (25-500 ng/ml) and 396-407 nm irradiation (3-16 X 10(2)J/m2) induced maximal net release of preformed mediators ,f 44.52 +/- 6.6 to 58.01 +/- 4.0% (mean +/- SE). In contrast, irradiation in the presence ofmore » URO (50-5000 ng/ml) resulted in less than 5% net release. (3H)Serotonin release induced by PP and irradiation was calcium-independent, and was not enhanced by phorbol 12-myristate 13-acetate, a known activator of protein kinase C. This release was suppressed by catalase, a scavenger of hydrogen peroxide. Furthermore, irradiation in the presence of PP, but not in the presence of URO, resulted in perturbation of cell membrane. Irradiation in the presence of PP also resulted in a maximal net release of generated mediators of 9.98 +/- 3.5% (mean +/- SE), whereas similar treatment in the presence of URO induced less than 0.5% net release. These results suggested that the burning, stinging, erythema, and edema experienced by patients with erythropoietic protoporphyria following sun exposure, and the lack of such findings in patients with porphyria cutanea tarda, may be explained, at least in part, by the differential effects of PP and URO on mast cells.« less

Dissolution-induced preferential flow in a limestone fracture.

PubMed

Liu, Jishan; Polak, Amir; Elsworth, Derek; Grader, Avrami

2005-06-01

Flow in a rock fracture is surprisingly sensitive to the evolution of flow paths that develop as a result of dissolution. Net dissolution may either increase or decrease permeability uniformly within the fracture, or may form a preferential flow path through which most of the injected fluid flows, depending on the prevailing ambient mechanical and chemical conditions. A flow-through test was completed on an artificial fracture in limestone at room temperature under ambient confining stress of 3.5 MPa. The sample was sequentially circulated by water of two different compositions through the 1500 h duration of the experiment; the first 935 h by tap groundwater, followed by 555 h of distilled water. Measurements of differential pressures between the inlet and the outlet, fluid and dissolved mass fluxes, and concurrent X-ray CT imaging and sectioning were used to characterize the evolution of flow paths within the limestone fracture. During the initial circulation of groundwater, the differential pressure increased almost threefold, and was interpreted as a net reduction in permeability as the contacting asperities across the fracture are removed, and the fracture closes. With the circulation of distilled water, permeability initially reduces threefold, and ultimately increases by two orders of magnitude. This spontaneous switch from net decrease in permeability, to net increase occurred with no change in flow rate or applied effective stress, and is attributed to the evolving localization of flow path as evidenced by CT images. Based on the X-ray CT characterizations, a flow path-dependent flow model was developed to simulate the evolution of flow paths within the fracture and its influence on the overall flow behaviors of the injected fluid in the fracture.

Fine-scale behaviour of bottlenose dolphins around gillnets.

PubMed

Read, Andrew J; Waples, Danielle M; Urian, Kim W; Swanner, Dave

2003-08-07

We studied the fine-scale behaviour of bottlenose dolphins Tursiops truncatus around gillnets in North Carolina, USA, during May and June 2002. We made observations from an overhead digital video camera, suspended from a helium-filled aerostat, tethered 70 m above a fishing vessel. We positioned the camera above a gillnet set for Spanish mackerel Scomberomorus maculatus. We observed frequent encounters (n = 36) and interactions (n = 27) between dolphins and the net, but no dolphins became entangled. Most dolphins diverted their course around the net, but on nine occasions we observed dolphins engaging in depredation. We conclude that interactions between dolphins and these gillnets are common, but that entanglement is rare.

Comparison of a Conceptual Groundwater Model and Physically Based Groundwater Mode

NASA Astrophysics Data System (ADS)

Yang, J.; Zammit, C.; Griffiths, J.; Moore, C.; Woods, R. A.

2017-12-01

Groundwater is a vital resource for human activities including agricultural practice and urban water demand. Hydrologic modelling is an important way to study groundwater recharge, movement and discharge, and its response to both human activity and climate change. To understand the groundwater hydrologic processes nationally in New Zealand, we have developed a conceptually based groundwater flow model, which is fully integrated into a national surface-water model (TopNet), and able to simulate groundwater recharge, movement, and interaction with surface water. To demonstrate the capability of this groundwater model (TopNet-GW), we applied the model to an irrigated area with water shortage and pollution problems in the upper Ruamahanga catchment in Great Wellington Region, New Zealand, and compared its performance with a physically-based groundwater model (MODFLOW). The comparison includes river flow at flow gauging sites, and interaction between groundwater and river. Results showed that the TopNet-GW produced similar flow and groundwater interaction patterns as the MODFLOW model, but took less computation time. This shows the conceptually-based groundwater model has the potential to simulate national groundwater process, and could be used as a surrogate for the more physically based model.

Cloud Radiation Forcings and Feedbacks: General Circulation Model Tests and Observational Validation

NASA Technical Reports Server (NTRS)

Lee,Wan-Ho; Iacobellis, Sam F.; Somerville, Richard C. J.

1997-01-01

Using an atmospheric general circulation model (the National Center for Atmospheric Research Community Climate Model: CCM2), the effects on climate sensitivity of several different cloud radiation parameterizations have been investigated. In addition to the original cloud radiation scheme of CCM2, four parameterizations incorporating prognostic cloud water were tested: one version with prescribed cloud radiative properties and three other versions with interactive cloud radiative properties. The authors' numerical experiments employ perpetual July integrations driven by globally constant sea surface temperature forcings of two degrees, both positive and negative. A diagnostic radiation calculation has been applied to investigate the partial contributions of high, middle, and low cloud to the total cloud radiative forcing, as well as the contributions of water vapor, temperature, and cloud to the net climate feedback. The high cloud net radiative forcing is positive, and the middle and low cloud net radiative forcings are negative. The total net cloud forcing is negative in all of the model versions. The effect of interactive cloud radiative properties on global climate sensitivity is significant. The net cloud radiative feedbacks consist of quite different shortwave and longwave components between the schemes with interactive cloud radiative properties and the schemes with specified properties. The increase in cloud water content in the warmer climate leads to optically thicker middle- and low-level clouds and in turn to negative shortwave feedbacks for the interactive radiative schemes, while the decrease in cloud amount simply produces a positive shortwave feedback for the schemes with a specified cloud water path. For the longwave feedbacks, the decrease in high effective cloudiness for the schemes without interactive radiative properties leads to a negative feedback, while for the other cases, the longwave feedback is positive. These cloud radiation parameterizations are empirically validated by using a single-column diagnostic model. together with measurements from the Atmospheric Radiation Measurement program and from the Tropical Ocean Global Atmosphere Combined Ocean-Atmosphere Response Experiment. The inclusion of prognostic cloud water produces a notable improvement in the realism of the parameterizations, as judged by these observations. Furthermore, the observational evidence suggests that deriving cloud radiative properties from cloud water content and microphysical characteristics is a promising route to further improvement.

CTCF-Mediated and Pax6-Associated Gene Expression in Corneal Epithelial Cell-Specific Differentiation

PubMed Central

Tsui, Shanli; Wang, Jie; Wang, Ling; Dai, Wei; Lu, Luo

2016-01-01

Background The purpose of the study is to elicit the epigenetic mechanism involving CCCTC binding factor (CTCF)-mediated chromatin remodeling that regulates PAX6 gene interaction with differentiation-associated genes to control corneal epithelial differentiation. Methods Cell cycle progression and specific keratin expressions were measured to monitor changes of differentiation-induced primary human limbal stem/progenitor (HLS/P), human corneal epithelial (HCE) and human telomerase-immortalized corneal epithelial (HTCE) cells. PAX6-interactive and differentiation-associated genes in chromatin remodeling mediated by the epigenetic factor CTCF were detected by circular chromosome conformation capture (4C) and ChIP (Chromatin immunoprecipitation)-on-chip approaches, and verified by FISH (Fluorescent in situ hybridization). Furthermore, CTCF activities were altered by CTCF-shRNA to study the effect of CTCF on mediating interaction of Pax6 and differentiation-associated genes in corneal epithelial cell fate. Results Our results demonstrated that differentiation-induced human corneal epithelial cells expressed typical corneal epithelial characteristics including morphological changes, increased keratin12 expression and G0/G1 accumulations. Expressions of CTCF and PAX6 were suppressed and elevated following the process of differentiation, respectively. During corneal epithelial cell differentiation, differentiation-induced RCN1 and ADAM17 were found interacting with PAX6 in the process of CTCF-mediated chromatin remodeling detected by 4C and verified by ChIP-on-chip and FISH. Diminished CTCF mRNA with CTCF-shRNA in HTCE cells weakened the interaction of PAX6 gene in controlling RCN1/ADAM17 and enhanced early onset of the genes in cell differentiation. Conclusion Our results explain how epigenetic factor CTCF-mediated chromatin remodeling regulates interactions between eye-specific PAX6 and those genes that are induced/associated with cell differentiation to modulate corneal epithelial cell-specific differentiation. PMID:27583466

Functionally charged nanosize particles differentially activate BV2 microglia.

EPA Science Inventory

The effect of particle surface charge on the biological activation of immortalized mouse microglia (BV2) was examined. Nanosize (860-950 nm) spherical polystyrene microparticles (SPM) were coated with carboxyl (COOH-) or dimethyl amino (CH3)2-N- groups to give a net negative or p...

Isolation of Mesophyll Cells and Bundle Sheath Cells from Digitaria sanguinalis (L.) Scop. Leaves and a Scanning Microscopy Study of the Internal Leaf Cell Morphology 1

PubMed Central

Edwards, Gerald E.; Black, Clanton C.

1971-01-01

A technique is described for the separation of mesophyll and bundle sheath cells from Digitaria sanguinalis leaves and evidence for separation is given with light and scanning electron micrographs. Gentle grinding of fully differentiated leaves in a mortar releases mesophyll cells which are isolated on nylon nets by filtration. More extensive grinding of the remaining tissue yields bundle sheath strands which are isolated by filtration with stainless steel sieves and nylon nets. Further grinding of bundle sheath strands in a tissue homogenizer releases bundle sheath cells which are collected on nylon nets. Percentage of purity derived from cell counts and yield data on a chlorophyll basis are given. The internal leaf cell morphology is presented in scanning electron micrographs and compared with light micrographs of fully-differentiated D. sanguinalis leaves. In leaves of plants which possess the C4-dicarboxylic acid cycle of photosynthesis, the relationship of leaf morphology to photosynthesis in mesophyll and bundle sheath cells is considered, and the hypothesis is presented that as atmospheric CO2 enters a leaf about 85% is fixed by the C4-dicarboxylic acid cycle in the mesophyll cells and 10 to 15% is fixed by the reductive pentose phosphate cycle in the bundle sheath cells. A technique also is given for the isolation of mesophyll cells from spinach leaves. Images PMID:16657571

Isolation of Mesophyll Cells and Bundle Sheath Cells from Digitaria sanguinalis (L.) Scop. Leaves and a Scanning Microscopy Study of the Internal Leaf Cell Morphology.

PubMed

Edwards, G E; Black, C C

1971-01-01

A technique is described for the separation of mesophyll and bundle sheath cells from Digitaria sanguinalis leaves and evidence for separation is given with light and scanning electron micrographs. Gentle grinding of fully differentiated leaves in a mortar releases mesophyll cells which are isolated on nylon nets by filtration. More extensive grinding of the remaining tissue yields bundle sheath strands which are isolated by filtration with stainless steel sieves and nylon nets. Further grinding of bundle sheath strands in a tissue homogenizer releases bundle sheath cells which are collected on nylon nets. Percentage of purity derived from cell counts and yield data on a chlorophyll basis are given.The internal leaf cell morphology is presented in scanning electron micrographs and compared with light micrographs of fully-differentiated D. sanguinalis leaves. In leaves of plants which possess the C(4)-dicarboxylic acid cycle of photosynthesis, the relationship of leaf morphology to photosynthesis in mesophyll and bundle sheath cells is considered, and the hypothesis is presented that as atmospheric CO(2) enters a leaf about 85% is fixed by the C(4)-dicarboxylic acid cycle in the mesophyll cells and 10 to 15% is fixed by the reductive pentose phosphate cycle in the bundle sheath cells.A technique also is given for the isolation of mesophyll cells from spinach leaves.

Comparing ownership and use of bed nets at two sites with differential malaria transmission in western Kenya.

PubMed

Ernst, Kacey C; Hayden, Mary H; Olsen, Heather; Cavanaugh, Jamie L; Ruberto, Irene; Agawo, Maurice; Munga, Stephen

2016-04-14

Challenges persist in ensuring access to and optimal use of long-lasting, insecticidal bed nets (LLINs). Factors associated with ownership and use may differ depending on the history of malaria and prevention control efforts in a specific region. Understanding how the cultural and social-environmental context of bed net use may differ between high- and low-risk regions is important when identifying solutions to improve uptake and appropriate use. Community forums and a household, cross-sectional survey were used to collect information on factors related to bed net ownership and use in western Kenya. Sites with disparate levels of transmission were selected, including an endemic lowland area, Miwani, and a highland epidemic-prone area, Kapkangani. Analysis of ownership was stratified by site. A combined site analysis was conducted to examine factors associated with use of all available bed nets. Logistic regression modelling was used to determine factors associated with ownership and use of owned bed nets. Access to bed nets as the leading barrier to their use was identified in community forums and cross-sectional surveys. While disuse of available bed nets was discussed in the forums, it was a relatively rare occurrence in both sites. Factors associated with ownership varied by site. Education, perceived risk of malaria and knowledge of individuals who had died of malaria were associated with higher bed net ownership in the highlands, while in the lowlands individuals reporting it was easy to get a bed net were more likely to own one. A combined site analysis indicated that not using an available bed net was associated with the attitudes that taking malaria drugs is easier than using a bed net and that use of a bed net will not prevent malaria. In addition, individuals with an unused bed net in the household were more likely to indicate that bed nets are difficult to use, that purchased bed nets are better than freely distributed ones, and that bed nets should only be used during the rainy season. Variations in factors associated with ownership should be acknowledged when constructing messaging and distribution campaigns. Despite reports of bed nets being used for other purposes, those in the home were rarely unused in these communities. Disuse seemed to be related to beliefs that can be addressed through education programmes. As mass distributions continue to take place, additional research is needed to determine if factors associated with LLIN ownership and use change with increasing availability of LLIN.

Real-time science and outreach from the UNOLS fleet via HiSeasNet

NASA Astrophysics Data System (ADS)

Foley, S.; Berger, J.; Orcutt, J. A.; Brice, D.; Coleman, D. F.; Grabowski, E. M.

2010-12-01

The HiSeasNet satellite communications network has ben providing cost-effective, reliable, continuous Internet connectivity to the UNOLS oceanographic research fleet for nearly nine years. During that time, HiSeasNet has supported science and outreach programs with a variety of real-time interactions back to shore including videoconferencing, webcasting, shared whiteboards, and streaming high-definition video feeds. Solutions have varied in scale, cost, and capability. As real-time science and outreach becomes more common, experience with a variety of technologies continues to build, and more opportunities yet to explore.

NetCTLpan: pan-specific MHC class I pathway epitope predictions

PubMed Central

Larsen, Mette Voldby; Lundegaard, Claus; Nielsen, Morten

2010-01-01

Reliable predictions of immunogenic peptides are essential in rational vaccine design and can minimize the experimental effort needed to identify epitopes. In this work, we describe a pan-specific major histocompatibility complex (MHC) class I epitope predictor, NetCTLpan. The method integrates predictions of proteasomal cleavage, transporter associated with antigen processing (TAP) transport efficiency, and MHC class I binding affinity into a MHC class I pathway likelihood score and is an improved and extended version of NetCTL. The NetCTLpan method performs predictions for all MHC class I molecules with known protein sequence and allows predictions for 8-, 9-, 10-, and 11-mer peptides. In order to meet the need for a low false positive rate, the method is optimized to achieve high specificity. The method was trained and validated on large datasets of experimentally identified MHC class I ligands and cytotoxic T lymphocyte (CTL) epitopes. It has been reported that MHC molecules are differentially dependent on TAP transport and proteasomal cleavage. Here, we did not find any consistent signs of such MHC dependencies, and the NetCTLpan method is implemented with fixed weights for proteasomal cleavage and TAP transport for all MHC molecules. The predictive performance of the NetCTLpan method was shown to outperform other state-of-the-art CTL epitope prediction methods. Our results further confirm the importance of using full-type human leukocyte antigen restriction information when identifying MHC class I epitopes. Using the NetCTLpan method, the experimental effort to identify 90% of new epitopes can be reduced by 15% and 40%, respectively, when compared to the NetMHCpan and NetCTL methods. The method and benchmark datasets are available at http://www.cbs.dtu.dk/services/NetCTLpan/. Electronic supplementary material The online version of this article (doi:10.1007/s00251-010-0441-4) contains supplementary material, which is available to authorized users. PMID:20379710

Protein charge ladders reveal that the net charge of ALS-linked superoxide dismutase can be different in sign and magnitude from predicted values

PubMed Central

Shi, Yunhua; Abdolvahabi, Alireza; Shaw, Bryan F

2014-01-01

This article utilized “protein charge ladders”—chemical derivatives of proteins with similar structure, but systematically altered net charge—to quantify how missense mutations that cause amyotrophic lateral sclerosis (ALS) affect the net negative charge (Z) of superoxide dismutase-1 (SOD1) as a function of subcellular pH and Zn2+ stoichiometry. Capillary electrophoresis revealed that the net charge of ALS-variant SOD1 can be different in sign and in magnitude—by up to 7.4 units per dimer at lysosomal pH—than values predicted from standard pKa values of amino acids and formal oxidation states of metal ions. At pH 7.4, the G85R, D90A, and G93R substitutions diminished the net negative charge of dimeric SOD1 by up to +2.29 units more than predicted; E100K lowered net charge by less than predicted. The binding of a single Zn2+ to mutant SOD1 lowered its net charge by an additional +2.33 ± 0.01 to +3.18 ± 0.02 units, however, each protein regulated net charge when binding a second, third, or fourth Zn2+ (ΔZ < 0.44 ± 0.07 per additional Zn2+). Both metalated and apo-SOD1 regulated net charge across subcellular pH, without inverting from negative to positive at the theoretical pI. Differential scanning calorimetry, hydrogen-deuterium exchange, and inductively coupled plasma mass spectrometry confirmed that the structure, stability, and metal content of mutant proteins were not significantly affected by lysine acetylation. Measured values of net charge should be used when correlating the biophysical properties of a specific ALS-variant SOD1 protein with its observed aggregation propensity or clinical phenotype. PMID:25052939

Phenomenological and molecular-level Petri net modeling and simulation of long-term potentiation.

PubMed

Hardy, S; Robillard, P N

2005-10-01

Petri net-based modeling methods have been used in many research projects to represent biological systems. Among these, the hybrid functional Petri net (HFPN) was developed especially for biological modeling in order to provide biologists with a more intuitive Petri net-based method. In the literature, HFPNs are used to represent kinetic models at the molecular level. We present two models of long-term potentiation previously represented by differential equations which we have transformed into HFPN models: a phenomenological synapse model and a molecular-level model of the CaMKII regulation pathway. Through simulation, we obtained results similar to those of previous studies using these models. Our results open the way to a new type of modeling for systems biology where HFPNs are used to combine different levels of abstraction within one model. This approach can be useful in fully modeling a system at the molecular level when kinetic data is missing or when a full study of a system at the molecular level it is not within the scope of the research.

Seasonal seepage investigation on an urbanized reach of the lower Boise River, southwestern Idaho, water year 2010

USGS Publications Warehouse

Williams, Marshall L.

2011-01-01

The U.S. Geological Survey in cooperation with the Idaho Department of Water Resources Treasure Valley Comprehensive Aquifer Management Planning effort investigated seasonal groundwater gains and losses on the Boise River, Idaho, starting in November 2009 through August 2010. The investigation was conducted using seepage runs in 11 subreaches over a 14-mile reach from downstream of the inactive streamgage, Boise River below Diversion Dam (U.S. Geological Survey station No. 13203510) to the active Boise River at Glenwood Bridge streamgage (U.S. Geological Survey station No. 13206000). The seepage runs measured mainstem discharge, and significant tributary contributions and diversions along the reach. In addition, an evaluation of the groundwater hydraulic gradient was simultaneously conducted through shallow groundwater mini-piezometers adjacent to the river during February (low stream discharge) and May (high stream discharge) measurement timeframes. November discharge estimates, representative of autumn, had gains and losses that varied by subreach with an overall net gain of 42 ± 8 cubic feet per second (ft3/s). This finding compares favorably to a previous U.S. Geological Survey seepage investigation in November 1996 that found a gaining reach with an estimated gain of 52 ft3/s. This finding also is supported by a U.S. Geological Survey investigation in the study reach in November 1971 that estimated a gain of 74 ft3/s, which largely came from groundwater. The February discharge estimates, representative of winter conditions, showed variability in the reach with a net gain of 52 ft3/s with an uncertainty estimate of ± 7 ft3/s, which is consistent with the low stream discharge findings from November 2009. This finding is further supported by the differential hydraulic head measured at transect sites that qualitatively indicated groundwater to surface-water movement with few exceptions. The May discharge estimates, representative of the spring-time conditions, were gaining or potentially gaining in all but one of the upper subreaches between Boise River below Diversion Dam and Boise River near MK Nature Center sites, with seepage run results supported by hydraulic head differentials indicating a groundwater to surface-water movement. The lower end of the study reach between Boise River near MK Nature Center and Boise River at Glenwood Bridge sites showed more variability with observed hydraulic head differentials that partially supported the potential gains or losses in the reach. Overall, the reach had a calculated net gain of 24 ± 51 ft3/s and, therefore, this estimate may or may not reflect the actual conditions in the reach. The groundwater gains and losses in August, representative of summer conditions, varied in both the upper and lower parts of the reach, with a net loss of -88 ± 69 ft3/s. Overall, the reach experienced a net gain from groundwater at low stream discharges (November and February), a net loss to groundwater at moderately high stream discharge (August), and an ambiguous finding at a higher stream discharge (May). The hydraulic head differentials measured between the groundwater and surface water largely supported the calculated gain and loss estimates in the subreaches, with a potential for groundwater to surface-water movement at low stream discharge in February, and variability during high stream discharge conditions in May.

ELASTIC NET FOR COX'S PROPORTIONAL HAZARDS MODEL WITH A SOLUTION PATH ALGORITHM.

PubMed

Wu, Yichao

2012-01-01

For least squares regression, Efron et al. (2004) proposed an efficient solution path algorithm, the least angle regression (LAR). They showed that a slight modification of the LAR leads to the whole LASSO solution path. Both the LAR and LASSO solution paths are piecewise linear. Recently Wu (2011) extended the LAR to generalized linear models and the quasi-likelihood method. In this work we extend the LAR further to handle Cox's proportional hazards model. The goal is to develop a solution path algorithm for the elastic net penalty (Zou and Hastie (2005)) in Cox's proportional hazards model. This goal is achieved in two steps. First we extend the LAR to optimizing the log partial likelihood plus a fixed small ridge term. Then we define a path modification, which leads to the solution path of the elastic net regularized log partial likelihood. Our solution path is exact and piecewise determined by ordinary differential equation systems.

PROFIT-PC: a program for estimating maximum net revenue from multiproduct harvests in Appalachian hardwoods

Treesearch

Chris B. LeDoux; John E. Baumgras; R. Bryan Selbe

1989-01-01

PROFIT-PC is a menu driven, interactive PC (personal computer) program that estimates optimum product mix and maximum net harvesting revenue based on projected product yields and stump-to-mill timber harvesting costs. Required inputs include the number of trees/acre by species and 2 inches diameter at breast-height class, delivered product prices by species and product...

Transport interactions of different organic cations during their excretion by the intact rat kidney.

PubMed

Pietruck, F; Ullrich, K J

1995-06-01

Organic cations, in addition to being filtrated, are secreted or reabsorbed in the proximal renal tubule whereby they have to pass the contraluminal and the luminal cell membrane. Interactions with the transport of other organic cations can occur at either cell side, leading to inhibition or stimulation of net secretion or net reabsorption. A qualitative evaluation of such processes is possible by using the in vivo bolus injection of an organic cation as test substance. Measuring its urinary excretion profile in relation to that of inulin, under control conditions and after application of interfering organic cations, in combination with simultaneous registration of its tissue concentration, allows the demonstration of interaction and also the tentative identification of the cell side at which interference has taken place. As test substance the fluorescent organic cation 4-(4-dimethylaminostyryl)-N-methylpyridinium (4-Di-1-ASP+; denotes permanent positively-charged organic cations was used, having a protein binding of 47% under the given experimental conditions. As interfering organic cations amiloride, benzylamiloride, choline+, cimetidine, and 2-methyl-4-(heptafluorobutoxy)-N-methylpyridinium+ were injected. It was found that: (1) 4-Di-1-ASP+ is filtered and net reabsorbed under control conditions (fractional excretion 0.54 +/- 0.1). All net secreted interfering substances, except bidirectional transported choline+, injected simultaneously with 4-Di-1-ASP+, showed an interference with renal excretion of net reabsorbed 4-Di-1-ASP+, by (2) instantaneously increasing its reabsorption, resulting in a 28 to 33% decrease in urinary excretion, and (3) augmenting its tissue concentration by 19 to 58%. (4) A prolonged effect of the interfering substrates could be observed after a third injection of 4-Di-1-ASP+ (without inhibitor) showing an increased tissue concentration of 4-Di-1-ASP+ of 36 to 46%. The complex interfering pattern of the applied organic cations can be explained by a trans-stimulation of 4-Di-1-ASP+ net reabsorption at the luminal cell side, leading to an increased intracellular content of 4-Di-1-ASP+.

A gel as an array of channels.

PubMed

Zimm, B H

1996-06-01

We consider the theory of charged point molecules ('probes') being pulled by an electric field through a two-dimensional net of channels that represents a piece of gel. Associated with the position in the net is a free energy of interaction between the probe and the net; this free energy fluctuates randomly with the position of the probe in the net. The free energy is intended to represent weak interactions between the probe and the gel, such as entropy associated with the restriction of the freedom of motion of the probe by the gel, or electrostatic interactions between the probe and charges fixed to the gel. The free energy can be thought of as a surface with the appearance of a rough, hilly landscape spread over the net; the roughness is measured by the standard deviation of the free-energy distribution. Two variations of the model are examined: (1) the net is assumed to have all channels open, or (2) only channels parallel to the electric field are open and all the cross-connecting channels are closed. Model (1) is more realistic but presents a two-dimensional mathematical problem which can only be solved by slow iteration methods, while model (2) is less realistic but presents a one-dimensional problem that can be reduced to simple quadratures and is easy to solve by numerical integration. In both models the mobility of the probe decreases as the roughness parameter is increased, but the effect is larger in the less realistic model (2) if the same free-energy surface is used in both. The mobility in model (2) is reduced both by high points in the rough surface ('bumps') and by low points ('traps'), while in model (1) only the traps are effective, since the probes can flow around the bumps through the cross channels. The mobility in model (2) can be made to agree with model (1) simply by cutting off the bumps of the surface. Thus the simple model (2) can be used in place of the more realistic model (1) that is more difficult to compute.

Identification of protein-interacting nucleotides in a RNA sequence using composition profile of tri-nucleotides.

PubMed

Panwar, Bharat; Raghava, Gajendra P S

2015-04-01

The RNA-protein interactions play a diverse role in the cells, thus identification of RNA-protein interface is essential for the biologist to understand their function. In the past, several methods have been developed for predicting RNA interacting residues in proteins, but limited efforts have been made for the identification of protein-interacting nucleotides in RNAs. In order to discriminate protein-interacting and non-interacting nucleotides, we used various classifiers (NaiveBayes, NaiveBayesMultinomial, BayesNet, ComplementNaiveBayes, MultilayerPerceptron, J48, SMO, RandomForest, SMO and SVM(light)) for prediction model development using various features and achieved highest 83.92% sensitivity, 84.82 specificity, 84.62% accuracy and 0.62 Matthew's correlation coefficient by SVM(light) based models. We observed that certain tri-nucleotides like ACA, ACC, AGA, CAC, CCA, GAG, UGA, and UUU preferred in protein-interaction. All the models have been developed using a non-redundant dataset and are evaluated using five-fold cross validation technique. A web-server called RNApin has been developed for the scientific community (http://crdd.osdd.net/raghava/rnapin/). Copyright © 2015 Elsevier Inc. All rights reserved.

Additive Interaction between Heterogeneous Environmental Quality Domains (Air, Water, Land, Sociodemographic, and Built Environment) on Preterm Birth.

PubMed

Grabich, Shannon C; Rappazzo, Kristen M; Gray, Christine L; Jagai, Jyotsna S; Jian, Yun; Messer, Lynne C; Lobdell, Danelle T

2016-01-01

Environmental exposures often occur in tandem; however, epidemiological research often focuses on singular exposures. Statistical interactions among broad, well-characterized environmental domains have not yet been evaluated in association with health. We address this gap by conducting a county-level cross-sectional analysis of interactions between Environmental Quality Index (EQI) domain indices on preterm birth in the Unites States from 2000 to 2005. The EQI, a county-level index constructed for the 2000-2005 time period, was constructed from five domain-specific indices (air, water, land, built, and sociodemographic) using principal component analyses. County-level preterm birth rates ( n  = 3141) were estimated using live births from the National Center for Health Statistics. Linear regression was used to estimate prevalence differences (PDs) and 95% confidence intervals (CIs) comparing worse environmental quality to the better quality for each model for (a) each individual domain main effect, (b) the interaction contrast, and (c) the two main effects plus interaction effect (i.e., the "net effect") to show departure from additivity for the all U.S. counties. Analyses were also performed for subgroupings by four urban/rural strata. We found the suggestion of antagonistic interactions but no synergism, along with several purely additive (i.e., no interaction) associations. In the non-stratified model, we observed antagonistic interactions, between the sociodemographic/air domains [net effect (i.e., the association, including main effects and interaction effects) PD: -0.004 (95% CI: -0.007, 0.000), interaction contrast: -0.013 (95% CI: -0.020, -0.007)] and built/air domains [net effect PD: 0.008 (95% CI 0.004, 0.011), interaction contrast: -0.008 (95% CI: -0.015, -0.002)]. Most interactions were between the air domain and other respective domains. Interactions differed by urbanicity, with more interactions observed in non-metropolitan regions. Observed antagonistic associations may indicate that those living in areas with multiple detrimental domains may have other interfering factors reducing the burden of environmental exposure. This study is the first to explore interactions across different environmental domains and demonstrates the utility of the EQI to examine the relationship between environmental domain interactions and human health. While we did observe some departures from additivity, many observed effects were additive. This study demonstrated that interactions between environmental domains should be considered in future analyses.

Analysis and prediction of leucine-rich nuclear export signals.

PubMed

la Cour, Tanja; Kiemer, Lars; Mølgaard, Anne; Gupta, Ramneek; Skriver, Karen; Brunak, Søren

2004-06-01

We present a thorough analysis of nuclear export signals and a prediction server, which we have made publicly available. The machine learning prediction method is a significant improvement over the generally used consensus patterns. Nuclear export signals (NESs) are extremely important regulators of the subcellular location of proteins. This regulation has an impact on transcription and other nuclear processes, which are fundamental to the viability of the cell. NESs are studied in relation to cancer, the cell cycle, cell differentiation and other important aspects of molecular biology. Our conclusion from this analysis is that the most important properties of NESs are accessibility and flexibility allowing relevant proteins to interact with the signal. Furthermore, we show that not only the known hydrophobic residues are important in defining a nuclear export signals. We employ both neural networks and hidden Markov models in the prediction algorithm and verify the method on the most recently discovered NESs. The NES predictor (NetNES) is made available for general use at http://www.cbs.dtu.dk/.

Binding of the water of primary hydration to the sodium and cesium salts of deoxyribonucleic acid and potassium hyaluronate

NASA Astrophysics Data System (ADS)

Whitson, K. B.; Lukan, A. M.; Marlowe, R. L.; Lee, S. A.; Anthony, L.; Rupprecht, A.

1998-08-01

Differential scanning calorimetry (DSC) has been used to evaluate the average enthalpy of desorption of the water of primary hydration bound to wet-spun films of potassium hyaluronate (KHA) and CsDNA. The enthalpies were measured to be 0.24+/-0.08 eV/H2O molecule for KHA and 0.32+/-0.10 eV/H2O molecule for CsDNA. A Kissinger analysis was used to extract the net activation energy (0.61+/-0.04 eV) for the desorption of this water from KHA by analyzing DSC data acquired at different heating rates. The average effective force constants at 295 K of this water bound to KHA (63+/-3 μdyn/Å) and NaDNA (17+/-4 μdyn/Å) are determined from Rayleigh scattering of Mossbauer radiation data [G. Albanese, A. Deriu, F. Cavatorta, and A. Rupprecht, Hyperfine Interact. 95, 97 (1995)] via a harmonic approximation.

Behavioral resilience in the post-genomic era: emerging models linking genes with environment

PubMed Central

Rende, Richard

2012-01-01

One of the most important deliverables of the post-genomic era has been a new and nuanced appreciation of how the environment shapes—and holds potential to alter—the expression of susceptibility genes for behavioral dimensions and disorders. This paper will consider three themes that have emerged from cutting-edge research studies that utilize newer molecular genetic approaches as well as tried-and-true genetic epidemiological methodologies, with particular reference to evolving perspectives on resilience and plasticity. These themes are: (1) evidence for replicable and robust shared environmental effects on a number of clinically relevant behaviors in childhood and adolescence; (2) evolving research on gene-environment interaction; and (3) a newer focus on differential susceptibility and plasticity. The net sum of these themes is that consideration of genetic effects on behavioral dimensions and disorders needs to be connected to thinking about the role of environment as a potent source for promoting resilience and change. PMID:22461772

Geometric pumping in autophoretic channels.

PubMed

Michelin, Sébastien; Montenegro-Johnson, Thomas D; De Canio, Gabriele; Lobato-Dauzier, Nicolas; Lauga, Eric

2015-08-07

Many microfluidic devices use macroscopic pressure differentials to overcome viscous friction and generate flows in microchannels. In this work, we investigate how the chemical and geometric properties of the channel walls can drive a net flow by exploiting the autophoretic slip flows induced along active walls by local concentration gradients of a solute species. We show that chemical patterning of the wall is not required to generate and control a net flux within the channel, rather channel geometry alone is sufficient. Using numerical simulations, we determine how geometric characteristics of the wall influence channel flow rate, and confirm our results analytically in the asymptotic limit of lubrication theory.

PHASE DIFFERENTIAL INDICATING CIRCUIT

DOEpatents

Kirsten, F.A.

1962-01-01

An electronic circuit for totalizing the net phase difference between two alternating current signals is designed which responds to both increasing and decreasing phase changes. A phase comparator provldes an output pulse for each 360 deg of phase difference occurring, there being a negative pulse for phase shtft in one direction and a positive pulse for a phase shift in the opposite direction. A counting circuit utilizing glow discharge tubes receives the negative and positive pulses at a single input terminal and provides a running net total, pulses of one polarity dded and pulses of the opposite polarity being subtracted. The glow discharge tubes may be decaded to increase the total count capacity. (AEC)

A Petri net approach to the study of persistence in chemical reaction networks.

PubMed

Angeli, David; De Leenheer, Patrick; Sontag, Eduardo D

2007-12-01

Persistence is the property, for differential equations in R(n), that solutions starting in the positive orthant do not approach the boundary of the orthant. For chemical reactions and population models, this translates into the non-extinction property: provided that every species is present at the start of the reaction, no species will tend to be eliminated in the course of the reaction. This paper provides checkable conditions for persistence of chemical species in reaction networks, using concepts and tools from Petri net theory, and verifies these conditions on various systems which arise in the modeling of cell signaling pathways.

Patterns of Interactive Media Use among Contemporary Youth

ERIC Educational Resources Information Center

van den Beemt, A.; Akkerman, S.; Simons, P. R. J.

2011-01-01

The intensive use of interactive media has led to assertions about the effect of these media on youth. Rather than following the assumption of a distinct Net generation, this study investigates diversity in interactive media use among youth. Results from a pilot study show that contemporary youth can be divided into clusters based on the use of…

Competitive Al3+ Inhibition of Net Mg2+ Uptake by Intact Lolium multiflorum Roots 1

PubMed Central

Rengel, Zdenko; Robinson, Donald L.

1989-01-01

Aluminum impairs uptake of Mg2+, but the mechanisms of this inhibition are not understood. The depletion technique was used to monitor net Mg2+ uptake from nutrient solution by intact, 23-day-old plants of ryegrass (Lolium multiflorum Lam., cv Gulf and Wilo). Activities of Mg2+ and monomeric Al species in nutrient solution were calculated and used as the basis for expressing the results. The kinetics of net Mg2+ absorption was resolved into (a) a transpiration-dependent uptake component, (b) a metabolically mediated, discontinuous saturable component that is Al3+ sensitive and p-chloromercuribenzene sulfonic acid (PCMBS) resistant, and (c) a linear, carbonyl cyanide m-chlorophenylhydrazone resistant, Al3+ sensitive component that might be a type of facilitated diffusion. Lowering the pH from 6.0 to 4.2 exerted a noncompetitive inhibition of net Mg2+ uptake, while aluminum at 6.6 micromolar Al3+ activity exerted competitive inhibition of net Mg2+ uptake at pH 4.2. The Al3+-induced effect was obvious after 30 minutes. Cultivar-specific ability to retain a higher affinity for Mg2+ by postulated transport proteins in the presence of Al3+ might be one of the mechanisms of differential Al tolerance among ryegrass cultivars. PMID:16667193

Interactions in Undersaturated and Supersaturated Lysozyme Solutions: Static and Dynamic Light Scattering Results

NASA Technical Reports Server (NTRS)

Muschol, Martin; Rosenberger, Franz

1995-01-01

We have performed multiangle static and dynamic light scattering studies of lysozyme solutions at pH=4.7. The Rayleigh ratio R(sub g) and the collective diffusion coefficient D(sub c) were determined as function of both protein concentration c(sub p) and salt concentration c(sub s) with two different salts. At low salt concentrations, the scattering ratio K(sub c)(sub p)/R(sub theta) and diffusivity increased with protein concentration above the values for a monomeric, ideal solution. With increasing salt concentration this trend was eventually reversed. The hydrodynamic interactions of lysozyme in solution, extracted from the combination of static and dynamic scattering data, decreased significantly with increasing salt concentration. These observations reflect changes in protein interactions, in response to increased salt screening, from net repulsion to net attraction. Both salts had the same qualitative effect, but the quantitative behavior did not scale with the ionic strength of the solution. This indicates the presence of salt specific effects. At low protein concentrations, the slopes of K(sub c)(sub p)/R(sub theta) and D(sub c) vs c(sub p) were obtained. The dependence of the slopes on ionic strength was modeled using a DLVO potential for colloidal interactions of two spheres, with the net protein charge Z(sub e) and Hamaker constant A(sub H) as fitting parameters. The model reproduces the observed variations with ionic strength quite well. Independent fits to the static and dynamic data, however, led to different values of the fitting parameters. These and other shortcomings suggest that colloidal interaction models alone are insufficient to explain protein interactions in solutions.

Genetic, environmental and interaction effects on lifetime production efficiency of crossbred ewes.

PubMed

Saoud, N B; Hohenboken, W D

1984-09-01

A total of 399 crossbred ewes born in 2 yr were maintained either on irrigated or dryland hill pastures. The ewes were sired by North Country Cheviot, Dorset, Finnsheep or Romney rams mated to Suffolk or Columbia-type ewes. The crossbred ewes were mated to Hampshire rams throughout the study and had the opportunity for either 4 or 5 yr of production. Annual feed cost was calculated based upon estimated annual metabolizable energy (ME) requirements for maintenance, ewe growth, pregnancy and lactation. Income from weaned feeder lambs and from orphan lambs sold shortly after birth, feed cost and net revenue were analyzed during each ewe's first production year, as well as for the entire period of the experiment. Crossbred group significantly affected income from lambs produced, feed cost and net revenue for the ewes' first production year. Crossbred group and crossbred group X management system interactions generally influenced lifetime income from lambs produced and from orphans sold, gross income, total cost and net revenue per ewe. Finnsheep X Suffolk ewes performed best on irrigated pastures but were below average for lifetime net revenue on hill pastures. Finnsheep X Columbia ewes performed best on hill pastures and, with Dorset X Suffolk and Dorset X Columbia ewes, were well above average for lifetime net revenue on irrigated pastures as well. Suffolk crossbreds consistently performed better on irrigated than on hill pastures. While most ewes with Columbia-type inheritance were more efficient on hill than on irrigated pastures, this result was not always consistent.

Educational Technology Network: a computer conferencing system dedicated to applications of computers in radiology practice, research, and education.

PubMed

D'Alessandro, M P; Ackerman, M J; Sparks, S M

1993-11-01

Educational Technology Network (ET Net) is a free, easy to use, on-line computer conferencing system organized and funded by the National Library of Medicine that is accessible via the SprintNet (SprintNet, Reston, VA) and Internet (Merit, Ann Arbor, MI) computer networks. It is dedicated to helping bring together, in a single continuously running electronic forum, developers and users of computer applications in the health sciences, including radiology. ET Net uses the Caucus computer conferencing software (Camber-Roth, Troy, NY) running on a microcomputer. This microcomputer is located in the National Library of Medicine's Lister Hill National Center for Biomedical Communications and is directly connected to the SprintNet and the Internet networks. The advanced computer conferencing software of ET Net allows individuals who are separated in space and time to unite electronically to participate, at any time, in interactive discussions on applications of computers in radiology. A computer conferencing system such as ET Net allows radiologists to maintain contact with colleagues on a regular basis when they are not physically together. Topics of discussion on ET Net encompass all applications of computers in radiological practice, research, and education. ET Net has been in successful operation for 3 years and has a promising future aiding radiologists in the exchange of information pertaining to applications of computers in radiology.

Streptococcus suis Serotype 2 Biofilms Inhibit the Formation of Neutrophil Extracellular Traps.

PubMed

Ma, Fang; Yi, Li; Yu, Ningwei; Wang, Guangyu; Ma, Zhe; Lin, Huixing; Fan, Hongjie

2017-01-01

Invasive infections caused by Streptococcus suis serotype 2 (SS2) has emerged as a clinical problem in recent years. Neutrophil extracellular traps (NETs) are an important mechanism for the trapping and killing of pathogens that are resistant to phagocytosis. Biofilm formation can protect bacteria from being killed by phagocytes. Until now, there have only been a few studies that focused on the interactions between bacterial biofilms and NETs. SS2 in both a biofilm state and a planktonic cell state were incubated with phagocytes and NETs, and bacterial survival was assessed. DNase I and cytochalasin B were used to degrade NET DNA or suppress phagocytosis, respectively. Extracellular DNA was stained with impermeable fluorescent dye to quantify NET formation. Biofilm formation increased up to 6-fold in the presence of neutrophils, and biofilms were identified in murine tissue. Both planktonic and biofilm cells induced neutrophils chemotaxis to the infection site, with neutrophils increasing by 85.1 and 73.8%, respectively. The bacteria in biofilms were not phagocytized. The bactericidal efficacy of NETs on the biofilms and planktonic cells were equal; however, the biofilm extracellular matrix can inhibit NET release. Although biofilms inhibit NETs release, NETs appear to be an important mechanism to eliminate SS2 biofilms. This knowledge advances the understanding of biofilms and may aid in the development of treatments for persistent infections with a biofilm component.

Interactions between CO2 enhancement and N addition on net primary productivity and water-use efficiency in a mesocosm with multiple subtropical tree species.

PubMed

Yan, Junhua; Zhang, Deqiang; Liu, Juxiu; Zhou, Guoyi

2014-07-01

Carbon dioxide (CO2 ) enhancement (eCO2 ) and N addition (aN) have been shown to increase net primary production (NPP) and to affect water-use efficiency (WUE) for many temperate ecosystems, but few studies have been made on subtropical tree species. This study compared the responses of NPP and WUE from a mesocosm composing five subtropical tree species to eCO2 (700 ppm), aN (10 g N m(-2) yr(-1) ) and eCO2 × aN using open-top chambers. Our results showed that mean annual ecosystem NPP did not changed significantly under eCO2 , increased by 56% under aN and 64% under eCO2 × aN. Ecosystem WUE increased by 14%, 55%, and 61% under eCO2 , aN and eCO2 × aN, respectively. We found that the observed responses of ecosystem WUE were largely driven by the responses of ecosystem NPP. Statistical analysis showed that there was no significant interactions between eCO2 and aN on ecosystem NPP (P = 0.731) or WUE (P = 0.442). Our results showed that increasing N deposition was likely to have much stronger effects on ecosystem NPP and WUE than increasing CO2 concentration for the subtropical forests. However, different tree species responded quite differently. aN significantly increased annual NPP of the fast-growing species (Schima superba). Nitrogen-fixing species (Ormosia pinnata) grew significantly faster only under eCO2 × aN. eCO2 had no effects on annual NPP of those two species but significantly increased annual NPP of other two species (Castanopsis hystrix and Acmena acuminatissima). Differential responses of the NPP among different tree species to eCO2 and aN will likely have significant implications on the species composition of subtropical forests under future global change. © 2013 John Wiley & Sons Ltd.

Neural network error correction for solving coupled ordinary differential equations

NASA Technical Reports Server (NTRS)

Shelton, R. O.; Darsey, J. A.; Sumpter, B. G.; Noid, D. W.

1992-01-01

A neural network is presented to learn errors generated by a numerical algorithm for solving coupled nonlinear differential equations. The method is based on using a neural network to correctly learn the error generated by, for example, Runge-Kutta on a model molecular dynamics (MD) problem. The neural network programs used in this study were developed by NASA. Comparisons are made for training the neural network using backpropagation and a new method which was found to converge with fewer iterations. The neural net programs, the MD model and the calculations are discussed.

Induction of CD4 T cell memory by local cellular collectivity.

PubMed

Polonsky, Michal; Rimer, Jacob; Kern-Perets, Amos; Zaretsky, Irina; Miller, Stav; Bornstein, Chamutal; David, Eyal; Kopelman, Naama Meira; Stelzer, Gil; Porat, Ziv; Chain, Benjamin; Friedman, Nir

2018-06-15

Cell differentiation is directed by signals driving progenitors into specialized cell types. This process can involve collective decision-making, when differentiating cells determine their lineage choice by interacting with each other. We used live-cell imaging in microwell arrays to study collective processes affecting differentiation of naïve CD4 + T cells into memory precursors. We found that differentiation of precursor memory T cells sharply increases above a threshold number of locally interacting cells. These homotypic interactions involve the cytokines interleukin-2 (IL-2) and IL-6, which affect memory differentiation orthogonal to their effect on proliferation and survival. Mathematical modeling suggests that the differentiation rate is continuously modulated by the instantaneous number of locally interacting cells. This cellular collectivity can prioritize allocation of immune memory to stronger responses. Copyright © 2018, American Association for the Advancement of Science.

On Complex Networks Representation and Computation of Hydrologycal Quantities

NASA Astrophysics Data System (ADS)

Serafin, F.; Bancheri, M.; David, O.; Rigon, R.

2017-12-01

Water is our blue gold. Despite results of discovery-based science keep warning public opinion about the looming worldwide water crisis, water is still treated as a not worth taking resource. Could a different multi-scale perspective affect environmental decision-making more deeply? Can also a further pairing to a new graphical representation of processes interaction sway decision-making more effectively and public opinion consequently?This abstract introduces a complex networks driven way to represent catchments eco-hydrology and related flexible informatics to manage it. The representation is built upon mathematical category. A category is an algebraic structure that comprises "objects" linked by "arrows". It is an evolution of Petri Nets said Time Continuous Petri Nets (TCPN). It aims to display (water) budgets processes and catchment interactions using explicative and self-contained symbolism. The result improves readability of physical processes compared to current descriptions. The IT perspective hinges on the Object Modeling System (OMS) v3. The latter is a non-invasive flexible environmental modeling framework designed to support component-based model development. The implementation of a Directed Acyclic Graph (DAG) data structure, named Net3, has recently enhanced its flexibility. Net3 represents interacting systems as complex networks: vertices match up with any sort of time evolving quantity; edges correspond to their data (fluxes) interchange. It currently hosts JGrass-NewAge components, and those implementing travel time analysis of fluxes. Further bio-physical or management oriented components can be easily added.This talk introduces both graphical representation and related informatics exercising actual applications and examples.

Development of a super-pressure balloon with a diamond-shaped net --- result of a ground inflation test of a 2,000 cubic-meter balloon ---

NASA Astrophysics Data System (ADS)

Saito, Yoshitaka; Nakashino, Kyoichi; Akita, Daisuke; Matsushima, Kiyoho; Shimadu, Shigeyuki; Goto, Ken; Hashimoto, Hiroyuki; Matsuo, Takuma

2016-07-01

A light super-pressure balloon has been developed using a method to cover a balloon with a diamond-shaped net of high-tensile fibers. The goal is to fly a payload of 900 kg to the altitude of 37 km with a 300,000 m^{3} balloon. Beginning from a demonstration test of the net-balloon with a 10 m^{3} balloon in 2010, we have been polished the net-balloon through ground inflation tests and flight tests, including a flight test of a 3,000 m ^{3} balloon in the tandem balloon configuration with a 15,000 m^{3} zero-pressure balloon in 2012, and a flight test of a 10 m^{3} balloon in the tandem balloon configuration with a 2 kg rubber balloon in 2013, as reported in the last COSPAR. In 2014, we developed a 5,000 m^{3} balloon and performed a ground inflation test to find that the balloon burst from a lip panel for termination with a differential pressure of 425 Pa. It was due to a stress concentration at the edge of a thick tape attached along the termination mechanism. In 2015, we modified the balloon by adding tapes on the lip panel to avoid the stress concentration, and also shorten the net length to leave some margin of the film and performed a ground inflation test again to find the balloon showed asymmetrical deployment and burst from the edge of the net with a differential pressure of 348 Pa. We consider it is due to the margin of the film along the circumferential direction, and proposed a gore shape which circumference length is kept as determined by the pumpkin shape of the balloon but setting meridian length longer than that. We developed a 10 m^{3} balloon with the gore design to find that the balloon deployed symmetrically and showed the burst pressure of 10,000 Pa. In 2016, we are going to develop a 2,000 m^{3} balloon with the gore design and perform its ground inflation test. In this paper, we are going to report its result with the sequence of the development.

Ontology-based Vaccine and Drug Adverse Event Representation and Theory-guided Systematic Causal Network Analysis toward Integrative Pharmacovigilance Research

PubMed Central

He, Yongqun

2016-01-01

Compared with controlled terminologies (e.g., MedDRA, CTCAE, and WHO-ART), the community-based Ontology of AEs (OAE) has many advantages in adverse event (AE) classifications. The OAE-derived Ontology of Vaccine AEs (OVAE) and Ontology of Drug Neuropathy AEs (ODNAE) serve as AE knowledge bases and support data integration and analysis. The Immune Response Gene Network Theory explains molecular mechanisms of vaccine-related AEs. The OneNet Theory of Life treats the whole process of a life of an organism as a single complex and dynamic network (i.e., OneNet). A new “OneNet effectiveness” tenet is proposed here to expand the OneNet theory. Derived from the OneNet theory, the author hypothesizes that one human uses one single genotype-rooted mechanism to respond to different vaccinations and drug treatments, and experimentally identified mechanisms are manifestations of the OneNet blueprint mechanism under specific conditions. The theories and ontologies interact together as semantic frameworks to support integrative pharmacovigilance research. PMID:27458549

ScaleNet: a literature-based model of scale insect biology and systematics

PubMed Central

García Morales, Mayrolin; Denno, Barbara D.; Miller, Douglass R.; Miller, Gary L.; Ben-Dov, Yair; Hardy, Nate B.

2016-01-01

Scale insects (Hemiptera: Coccoidea) are small herbivorous insects found on all continents except Antarctica. They are extremely invasive, and many species are serious agricultural pests. They are also emerging models for studies of the evolution of genetic systems, endosymbiosis and plant-insect interactions. ScaleNet was launched in 1995 to provide insect identifiers, pest managers, insect systematists, evolutionary biologists and ecologists efficient access to information about scale insect biological diversity. It provides comprehensive information on scale insects taken directly from the primary literature. Currently, it draws from 23 477 articles and describes the systematics and biology of 8194 valid species. For 20 years, ScaleNet ran on the same software platform. That platform is no longer viable. Here, we present a new, open-source implementation of ScaleNet. We have normalized the data model, begun the process of correcting invalid data, upgraded the user interface, and added online administrative tools. These improvements make ScaleNet easier to use and maintain and make the ScaleNet data more accurate and extendable. Database URL: http://scalenet.info PMID:26861659

Ratchet Effects in Active Matter Systems

NASA Astrophysics Data System (ADS)

Reichhardt, C. J. Olson; Reichhardt, C.

2017-03-01

Ratchet effects can arise for single or collectively interacting Brownian particles on an asymmetric substrate when a net dc transport is produced by an externally applied ac driving force or by periodically flashing the substrate. Recently, a new class of active ratchet systems that do not require the application of external driving has been realized through the use of active matter; they are self-propelled units that can be biological or nonbiological in nature. When active materials such as swimming bacteria interact with an asymmetric substrate, a net dc directed motion can arise even without external driving, opening a wealth of possibilities such as sorting, cargo transport, or micromachine construction. We review the current status of active matter ratchets for swimming bacteria, cells, active colloids, and swarming models, focusing on the role of particle-substrate interactions. We describe ratchet reversals produced by collective effects and the use of active ratchets to transport passive particles. We discuss future directions including deformable substrates or particles, the role of different swimming modes, varied particle-particle interactions, and nondissipative effects.

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

Reichhardt, Cynthia Jane; Reichhardt, Charles

Ratchet effects can arise for single or collectively interacting Brownian particles on an asymmetric substrate when a net dc transport is produced by an externally applied ac driving force or by periodically flashing the substrate. Recently, a new class of active ratchet systems that do not require the application of external driving has been realized through the use of active matter; they are self-propelled units that can be biological or nonbiological in nature. When active materials such as swimming bacteria interact with an asymmetric substrate, a net dc directed motion can arise even without external driving, opening a wealth ofmore » possibilities such as sorting, cargo transport, or micromachine construction. We review the current status of active matter ratchets for swimming bacteria, cells, active colloids, and swarming models, focusing on the role of particle-substrate interactions. Here, we describe ratchet reversals produced by collective effects and the use of active ratchets to transport passive particles. We discuss future directions including deformable substrates or particles, the role of different swimming modes, varied particle–particle interactions, and nondissipative effects.« less

ClueNet: Clustering a temporal network based on topological similarity rather than denseness

PubMed Central

Milenković, Tijana

2018-01-01

Network clustering is a very popular topic in the network science field. Its goal is to divide (partition) the network into groups (clusters or communities) of “topologically related” nodes, where the resulting topology-based clusters are expected to “correlate” well with node label information, i.e., metadata, such as cellular functions of genes/proteins in biological networks, or age or gender of people in social networks. Even for static data, the problem of network clustering is complex. For dynamic data, the problem is even more complex, due to an additional dimension of the data—their temporal (evolving) nature. Since the problem is computationally intractable, heuristic approaches need to be sought. Existing approaches for dynamic network clustering (DNC) have drawbacks. First, they assume that nodes should be in the same cluster if they are densely interconnected within the network. We hypothesize that in some applications, it might be of interest to cluster nodes that are topologically similar to each other instead of or in addition to requiring the nodes to be densely interconnected. Second, they ignore temporal information in their early steps, and when they do consider this information later on, they do so implicitly. We hypothesize that capturing temporal information earlier in the clustering process and doing so explicitly will improve results. We test these two hypotheses via our new approach called ClueNet. We evaluate ClueNet against six existing DNC methods on both social networks capturing evolving interactions between individuals (such as interactions between students in a high school) and biological networks capturing interactions between biomolecules in the cell at different ages. We find that ClueNet is superior in over 83% of all evaluation tests. As more real-world dynamic data are becoming available, DNC and thus ClueNet will only continue to gain importance. PMID:29738568

The impact of a hybrid social marketing intervention on inequities in access, ownership and use of insecticide-treated nets.

PubMed

Agha, Sohail; Van Rossem, Ronan; Stallworthy, Guy; Kusanthan, Thankian

2007-01-29

An ITN intervention was initiated in three predominantly rural districts of Eastern Province, Zambia, that lacked commercial distribution and communication infrastructures. Social marketing techniques were used for product and message development. Public sector clinics and village-based volunteers promoted and distributed subsidized ITNs priced at 2.5 dollars per net. A study was conducted to assess the effects of the intervention on inequities in knowledge, access, ownership and use of ITNs. A post-test only quasi-experimental study design was used to compare intervention and comparison districts. A total of 2,986 respondents were interviewed. Survey respondents were grouped into four socio-economic (SES) categories: low, medium-low, medium and high. Knowledge, access, ownership and use indicators are compared. Concentration index scores are calculated. Interactions between intervention status and SES help determine how different SES groups benefited from the intervention. Although overall use of nets remained relatively low, post-test data show that knowledge, access, ownership and use of mosquito nets was higher in intervention districts. A decline in SES inequity in access to nets occurred in intervention districts, resulting from a disproportionately greater increase in access among the low SES group. Declines in SES inequities in net ownership and use of nets were associated with the intervention. The largest increases in net ownership and use occurred among medium and high SES categories. Increasing access to nets among the poorest respondents in rural areas may not lead to increases in net use unless the price of nets is no longer a barrier to their purchase.

NET23/STING Promotes Chromatin Compaction from the Nuclear Envelope

PubMed Central

de las Heras, Jose I.; Saiz-Ros, Natalia; Makarov, Alexandr A.; Lazou, Vassiliki; Meinke, Peter; Waterfall, Martin; Kelly, David A.; Schirmer, Eric C.

2014-01-01

Changes in the peripheral distribution and amount of condensed chromatin are observed in a number of diseases linked to mutations in the lamin A protein of the nuclear envelope. We postulated that lamin A interactions with nuclear envelope transmembrane proteins (NETs) that affect chromatin structure might be altered in these diseases and so screened thirty-one NETs for those that promote chromatin compaction as determined by an increase in the number of chromatin clusters of high pixel intensity. One of these, NET23 (also called STING, MITA, MPYS, ERIS, Tmem173), strongly promoted chromatin compaction. A correlation between chromatin compaction and endogenous levels of NET23/STING was observed for a number of human cell lines, suggesting that NET23/STING may contribute generally to chromatin condensation. NET23/STING has separately been found to be involved in innate immune response signaling. Upon infection cells make a choice to either apoptose or to alter chromatin architecture to support focused expression of interferon genes and other response factors. We postulate that the chromatin compaction induced by NET23/STING may contribute to this choice because the cells expressing NET23/STING eventually apoptose, but the chromatin compaction effect is separate from this as the condensation was still observed when cells were treated with Z-VAD to block apoptosis. NET23/STING-induced compacted chromatin revealed changes in epigenetic marks including changes in histone methylation and acetylation. This indicates a previously uncharacterized nuclear role for NET23/STING potentially in both innate immune signaling and general chromatin architecture. PMID:25386906

Fine-scale behaviour of bottlenose dolphins around gillnets.

PubMed Central

Read, Andrew J; Waples, Danielle M; Urian, Kim W; Swanner, Dave

2003-01-01

We studied the fine-scale behaviour of bottlenose dolphins Tursiops truncatus around gillnets in North Carolina, USA, during May and June 2002. We made observations from an overhead digital video camera, suspended from a helium-filled aerostat, tethered 70 m above a fishing vessel. We positioned the camera above a gillnet set for Spanish mackerel Scomberomorus maculatus. We observed frequent encounters (n = 36) and interactions (n = 27) between dolphins and the net, but no dolphins became entangled. Most dolphins diverted their course around the net, but on nine occasions we observed dolphins engaging in depredation. We conclude that interactions between dolphins and these gillnets are common, but that entanglement is rare. PMID:12952646

Trend-outflow method for understanding interactions of surface water with groundwater and atmospheric water for eight reaches of the Upper Rio Grande

NASA Astrophysics Data System (ADS)

Liu, Yi; Sheng, Zhuping

2011-11-01

SummaryAtmospheric water, surface water, and groundwater interact very actively through hydrologic processes such as precipitation, infiltration, seepage, irrigation, drainage, evaporation, and evapotranspiration in the Upper Rio Grande Basin. A trend-outflow method has been developed in this paper to gain a better understanding of the interactions based on cumulated inflow and outflow data for any river reaches of interest. A general trend-outflow equation was derived by associating the net interaction of surface water with atmospheric water as a polynomial of inflow and the net interaction of surface water with groundwater as a constant based on surface water budget. Linear and quadratic relations are probably two common trend-outflow types in the real world. It was found that trend-outflows of the Upper Rio Grande reaches, Española, Albuquerque, Socorro-Engle, Palomas, and Rincon are linear with inflow, while those of reaches, Belen, Mesilla and Hueco are quadratic. Reaches Belen, Mesilla and Hueco are found as water deficit reaches mainly for irrigated agriculture in extreme drought years.

Electronic distributions within protein phenylalanine aromatic rings are reflected by the three-dimensional oxygen atom environments.

PubMed Central

Thomas, K A; Smith, G M; Thomas, T B; Feldmann, R J

1982-01-01

The atomic environments of 170 phenylalanine-residue aromatic rings from 28 protein crystal structures are transformed into a common orientation and combined to calculate an average three-dimensional environment. The spatial distribution of atom types in this environment reveals a preferred interaction between oxygen atoms and the edge of the planar aromatic rings. From the difference in frequency of interaction of oxygen atoms with the edge and the top of the ring, an apparent net free energy difference of interaction favoring the edge of the ring is estimated to be about -1 kcal/mol (1 cal = 4.184 J). Ab initio quantum mechanical calculations, performed on a model consisting of benzene and formamide, indicate that the observed geometry is stabilized by a favorable enthalpic interaction. Although benzene rings are considered to be nonpolar, the electron distribution is a complex multipole with no net dipole moment. The observed interaction orientation frequencies demonstrate that these multipolar electron distributions, when occurring at the short distances encountered in densely packed protein molecules, are significant determinants of internal packing geometries. PMID:6956896

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures.

PubMed

Duan, Qiaonan; Flynn, Corey; Niepel, Mario; Hafner, Marc; Muhlich, Jeremy L; Fernandez, Nicolas F; Rouillard, Andrew D; Tan, Christopher M; Chen, Edward Y; Golub, Todd R; Sorger, Peter K; Subramanian, Aravind; Ma'ayan, Avi

2014-07-01

For the Library of Integrated Network-based Cellular Signatures (LINCS) project many gene expression signatures using the L1000 technology have been produced. The L1000 technology is a cost-effective method to profile gene expression in large scale. LINCS Canvas Browser (LCB) is an interactive HTML5 web-based software application that facilitates querying, browsing and interrogating many of the currently available LINCS L1000 data. LCB implements two compacted layered canvases, one to visualize clustered L1000 expression data, and the other to display enrichment analysis results using 30 different gene set libraries. Clicking on an experimental condition highlights gene-sets enriched for the differentially expressed genes from the selected experiment. A search interface allows users to input gene lists and query them against over 100 000 conditions to find the top matching experiments. The tool integrates many resources for an unprecedented potential for new discoveries in systems biology and systems pharmacology. The LCB application is available at http://www.maayanlab.net/LINCS/LCB. Customized versions will be made part of the http://lincscloud.org and http://lincs.hms.harvard.edu websites. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Use of wastewater : challenge against scarcity,enhancement of crop disease and environment damage.

NASA Astrophysics Data System (ADS)

Dahchour, Abdelmalek; El Hajjaji, Souad; El Makhoukhi, Fadoua

2015-04-01

Reuse of treated wastewater in agriculture is a potential alternative to face shortage in water resources mainly in arid regions. Morocco is among countries that have experienced long and severe period of drought associated with shortage in water resources. Though the large efforts deployed in providing water supplies to different regions, this resource remains sufficiently available in northern part of the country only. This situation has pushed growers to use non treated wastewater for irrigation without any environmental or health cautions. Trials with waste water for irrigation have demonstrated net increase in production of irrigated crops, good improvement of soil texture and availability of nutrients. However interactions with pesticides remain neglected. Actually this interaction could be associated with an improvement or reduction of the efficacy of a given pesticide. On environmental point of view, it could improve or reduce adsorption, mobility of soil applied pesticides toward groundwater. Laboratory test with a selected fungicide showed net reduction of the efficacy of the pesticide against the target fungus. Comparison between growing species in medium spiked with pesticide/ wastewater and pesticide only shoed net increase of the growth in presence of wastewater. In the column of soil, low mobility herbicide showed net increase in mobility after percolation with water spiked with wastewater under laboratory conditions. .

OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space.

PubMed

Zhou, Guangyan; Xia, Jianguo

2018-06-07

Biological networks play increasingly important roles in omics data integration and systems biology. Over the past decade, many excellent tools have been developed to support creation, analysis and visualization of biological networks. However, important limitations remain: most tools are standalone programs, the majority of them focus on protein-protein interaction (PPI) or metabolic networks, and visualizations often suffer from 'hairball' effects when networks become large. To help address these limitations, we developed OmicsNet - a novel web-based tool that allows users to easily create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space. Users can upload one or multiple lists of molecules of interest (genes/proteins, microRNAs, transcription factors or metabolites) to create and merge different types of biological networks. The 3D network visualization system was implemented using the powerful Web Graphics Library (WebGL) technology that works natively in most major browsers. OmicsNet supports force-directed layout, multi-layered perspective layout, as well as spherical layout to help visualize and navigate complex networks. A rich set of functions have been implemented to allow users to perform coloring, shading, topology analysis, and enrichment analysis. OmicsNet is freely available at http://www.omicsnet.ca.

SpectralNET – an application for spectral graph analysis and visualization

PubMed Central

Forman, Joshua J; Clemons, Paul A; Schreiber, Stuart L; Haggarty, Stephen J

2005-01-01

Background Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices) and interactions (edges) that can carry different weights. SpectralNET is a flexible application for analyzing and visualizing these biological and chemical networks. Results Available both as a standalone .NET executable and as an ASP.NET web application, SpectralNET was designed specifically with the analysis of graph-theoretic metrics in mind, a computational task not easily accessible using currently available applications. Users can choose either to upload a network for analysis using a variety of input formats, or to have SpectralNET generate an idealized random network for comparison to a real-world dataset. Whichever graph-generation method is used, SpectralNET displays detailed information about each connected component of the graph, including graphs of degree distribution, clustering coefficient by degree, and average distance by degree. In addition, extensive information about the selected vertex is shown, including degree, clustering coefficient, various distance metrics, and the corresponding components of the adjacency, Laplacian, and normalized Laplacian eigenvectors. SpectralNET also displays several graph visualizations, including a linear dimensionality reduction for uploaded datasets (Principal Components Analysis) and a non-linear dimensionality reduction that provides an elegant view of global graph structure (Laplacian eigenvectors). Conclusion SpectralNET provides an easily accessible means of analyzing graph-theoretic metrics for data modeling and dimensionality reduction. SpectralNET is publicly available as both a .NET application and an ASP.NET web application from . Source code is available upon request. PMID:16236170

SpectralNET--an application for spectral graph analysis and visualization.

PubMed

Forman, Joshua J; Clemons, Paul A; Schreiber, Stuart L; Haggarty, Stephen J

2005-10-19

Graph theory provides a computational framework for modeling a variety of datasets including those emerging from genomics, proteomics, and chemical genetics. Networks of genes, proteins, small molecules, or other objects of study can be represented as graphs of nodes (vertices) and interactions (edges) that can carry different weights. SpectralNET is a flexible application for analyzing and visualizing these biological and chemical networks. Available both as a standalone .NET executable and as an ASP.NET web application, SpectralNET was designed specifically with the analysis of graph-theoretic metrics in mind, a computational task not easily accessible using currently available applications. Users can choose either to upload a network for analysis using a variety of input formats, or to have SpectralNET generate an idealized random network for comparison to a real-world dataset. Whichever graph-generation method is used, SpectralNET displays detailed information about each connected component of the graph, including graphs of degree distribution, clustering coefficient by degree, and average distance by degree. In addition, extensive information about the selected vertex is shown, including degree, clustering coefficient, various distance metrics, and the corresponding components of the adjacency, Laplacian, and normalized Laplacian eigenvectors. SpectralNET also displays several graph visualizations, including a linear dimensionality reduction for uploaded datasets (Principal Components Analysis) and a non-linear dimensionality reduction that provides an elegant view of global graph structure (Laplacian eigenvectors). SpectralNET provides an easily accessible means of analyzing graph-theoretic metrics for data modeling and dimensionality reduction. SpectralNET is publicly available as both a .NET application and an ASP.NET web application from http://chembank.broad.harvard.edu/resources/. Source code is available upon request.

Neutrophil Extracellular Traps Identification in Tegumentary Lesions of Patients with Paracoccidioidomycosis and Different Patterns of NETs Generation In Vitro

PubMed Central

Della Coletta, Amanda Manoel; Bachiega, Tatiana Fernanda; de Quaglia e Silva, Juliana Carvalho; Soares, Ângela Maria Victoriano de Campos; De Faveri, Julio; Marques, Silvio Alencar; Marques, Mariângela Esther Alencar; Ximenes, Valdecir Farias; Dias-Melicio, Luciane Alarcão

2015-01-01

Paracoccidioidomycosis (PCM) is a systemic mycosis, endemic in most Latin American countries, especially in Brazil. It is caused by the thermo-dimorphic fungus of the genus Paracoccidioides (Paracoccidioides brasiliensis and Paracoccidioides lutzii). Innate immune response plays a crucial role in host defense against fungal infections, and neutrophils (PMNs) are able to combat microorganisms with three different mechanisms: phagocytosis, secretion of granular proteins, which have antimicrobial properties, and the most recent described mechanism called NETosis. This new process is characterized by the release of net-like structures called Neutrophil Extracellular Traps (NETs), which is composed of nuclear (decondensed DNA and histones) and granular material such as elastase. Several microorganisms have the ability of inducing NETs formation, including gram-positive and gram-negative bacteria, viruses and some fungi. We proposed to identify NETs in tegumentary lesions of patients with PCM and to analyze the interaction between two strains of P. brasiliensis and human PMNs by NETs formation in vitro. In this context, the presence of NETs in vivo was evidenced in tegumentary lesions of patients with PCM by confocal spectrum analyzer. Furthermore, we showed that the high virulent P. brasiliensis strain 18 (Pb18) and the lower virulent strain Pb265 are able to induce different patterns of NETs formation in vitro. The quantification of extracellular DNA corroborates the idea of the ability of P. brasiliensis in inducing NETs release. In conclusion, our data show for the first time the identification of NETs in lesions of patients with PCM and demonstrate distinct patterns of NETs in cultures challenged with fungi in vitro. The presence of NETs components both in vivo and in vitro open new possibilities for the detailed investigation of immunity in PCM. PMID:26327485

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

Kaminsky, G.; Belanger, David P.; Ye, Feng

We use polarized neutron scattering to characterize the Bragg scattering intensity below T C=89.5 K at the (1,0,0) pseudocubic nuclear Bragg point of LaCoO 3. Upon cooling in a field (FC), a net magnetic moment is apparent in Bragg scattering intensity, just as it was in previous magnetization measurements. Critical behavior associated with the net moment near T C upon cooling in small applied fields rapidly rounds with increasing field strength. We show, using a mean-field calculation, that this net moment can develop in a metastable state that forms upon FC, even when all the interactions in the system aremore » antiferromagnetic.« less

Neural net applied to anthropological material: a methodical study on the human nasal skeleton.

PubMed

Prescher, Andreas; Meyers, Anne; Gerf von Keyserlingk, Diedrich

2005-07-01

A new information processing method, an artificial neural net, was applied to characterise the variability of anthropological features of the human nasal skeleton. The aim was to find different types of nasal skeletons. A neural net with 15*15 nodes was trained by 17 standard anthropological parameters taken from 184 skulls of the Aachen collection. The trained neural net delivers its classification in a two-dimensional map. Different types of noses were locally separated within the map. Rare and frequent types may be distinguished after one passage of the complete collection through the net. Statistical descriptive analysis, hierarchical cluster analysis, and discriminant analysis were applied to the same data set. These parallel applications allowed comparison of the new approach to the more traditional ones. In general the classification by the neural net is in correspondence with cluster analysis and discriminant analysis. However, it goes beyond these classifications because of the possibility of differentiating the types in multi-dimensional dependencies. Furthermore, places in the map are kept blank for intermediate forms, which may be theoretically expected, but were not included in the training set. In conclusion, the application of a neural network is a suitable method for investigating large collections of biological material. The gained classification may be helpful in anatomy and anthropology as well as in forensic medicine. It may be used to characterise the peculiarity of a whole set as well as to find particular cases within the set.

A Role for p38 Mitogen-activated Protein Kinase-mediated Threonine 30-dependent Norepinephrine Transporter Regulation in Cocaine Sensitization and Conditioned Place Preference*

PubMed Central

Mannangatti, Padmanabhan; NarasimhaNaidu, Kamalakkannan; Damaj, Mohamad Imad; Ramamoorthy, Sammanda; Jayanthi, Lankupalle Damodara

2015-01-01

The noradrenergic and p38 mitogen-activated protein kinase (p38 MAPK) systems are implicated in cocaine-elicited behaviors. Previously, we demonstrated a role for p38 MAPK-mediated norepinephrine transporter (NET) Thr30 phosphorylation in cocaine-induced NET up-regulation (Mannangatti, P., Arapulisamy, O., Shippenberg, T. S., Ramamoorthy, S., and Jayanthi, L. D. (2011) J. Biol. Chem. 286, 20239–20250). The present study explored the functional interaction between p38 MAPK-mediated NET regulation and cocaine-induced behaviors. In vitro cocaine treatment of mouse prefrontal cortex synaptosomes resulted in enhanced NET function, surface expression, and phosphorylation. Pretreatment with PD169316, a p38 MAPK inhibitor, completely blocked cocaine-mediated NET up-regulation and phosphorylation. In mice, in vivo administration of p38 MAPK inhibitor SB203580 completely blocked cocaine-induced NET up-regulation and p38 MAPK activation in the prefrontal cortex and nucleus accumbens. When tested for cocaine-induced locomotor sensitization and conditioned place preference (CPP), mice receiving SB203580 on cocaine challenge day or on postconditioning test day exhibited significantly reduced cocaine sensitization and CPP. A transactivator of transcription (TAT) peptide strategy was utilized to test the involvement of the NET-Thr30 motif. In vitro treatment of synaptosomes with TAT-NET-Thr30 (wild-type peptide) completely blocked cocaine-mediated NET up-regulation and phosphorylation. In vivo administration of TAT-NET-Thr30 peptide but not TAT-NET-T30A (mutant peptide) completely blocked cocaine-mediated NET up-regulation and phosphorylation. In the cocaine CPP paradigm, mice receiving TAT-NET-Thr30 but not TAT-NET-T30A on postconditioning test day exhibited significantly reduced cocaine CPP. Following extinction, TAT-NET-Thr30 when given prior to cocaine challenge significantly reduced reinstatement of cocaine CPP. These results demonstrate that the direct inhibition of p38 MAPK or the manipulation of NET-Thr30 motif/phosphorylation via a TAT peptide strategy prevents cocaine-induced NET up-regulation, locomotor sensitization, and CPP, suggesting a role for Thr30-linked NET regulation in cocaine-elicited behaviors. PMID:25724654

Cost and cost effectiveness of long-lasting insecticide-treated bed nets - a model-based analysis

PubMed Central

2012-01-01

Background The World Health Organization recommends that national malaria programmes universally distribute long-lasting insecticide-treated bed nets (LLINs). LLINs provide effective insecticide protection for at least three years while conventional nets must be retreated every 6-12 months. LLINs may also promise longer physical durability (lifespan), but at a higher unit price. No prospective data currently available is sufficient to calculate the comparative cost effectiveness of different net types. We thus constructed a model to explore the cost effectiveness of LLINs, asking how a longer lifespan affects the relative cost effectiveness of nets, and if, when and why LLINs might be preferred to conventional insecticide-treated nets. An innovation of our model is that we also considered the replenishment need i.e. loss of nets over time. Methods We modelled the choice of net over a 10-year period to facilitate the comparison of nets with different lifespan (and/or price) and replenishment need over time. Our base case represents a large-scale programme which achieves high coverage and usage throughout the population by distributing either LLINs or conventional nets through existing health services, and retreats a large proportion of conventional nets regularly at low cost. We identified the determinants of bed net programme cost effectiveness and parameter values for usage rate, delivery and retreatment cost from the literature. One-way sensitivity analysis was conducted to explicitly compare the differential effect of changing parameters such as price, lifespan, usage and replenishment need. Results If conventional and long-lasting bed nets have the same physical lifespan (3 years), LLINs are more cost effective unless they are priced at more than USD 1.5 above the price of conventional nets. Because a longer lifespan brings delivery cost savings, each one year increase in lifespan can be accompanied by a USD 1 or more increase in price without the cheaper net (of the same type) becoming more cost effective. Distributing replenishment nets each year in addition to the replacement of all nets every 3-4 years increases the number of under-5 deaths averted by 5-14% at a cost of USD 17-25 per additional person protected per annum or USD 1080-1610 per additional under-5 death averted. Conclusions Our results support the World Health Organization recommendation to distribute only LLINs, while giving guidance on the price thresholds above which this recommendation will no longer hold. Programme planners should be willing to pay a premium for nets which have a longer physical lifespan, and if planners are willing to pay USD 1600 per under-5 death averted, investing in replenishment is cost effective. PMID:22475679

Watershed Land Use and Seasonal Variation Constrain the ...

EPA Pesticide Factsheets

While watershed and local scale controls on stream metabolism have been independently investigated, little is known about how controls exerted at these different scales interact to determine stream metabolic rates, or how these interactions vary across seasons. To address this knowledge gap, we measured ecosystem metabolism in four urban and four reference streams in northern Kentucky, USA, with paired closed and open riparian canopies, during each of the four seasons of the year. Gross primary production (GPP), ecosystem respiration (ER), and net ecosystem production (NEP) were all best predicted by models with season as a main effect, but interactions between season, canopy and watershed varied for each response. Urban streams exhibited higher GPP during most seasons, likely due to elevated nutrient loads. Open canopy reaches in both urban and forested streams supported higher rates of GPP than the closed canopy reaches during the summer and fall when the overhead vegetation shaded the closed reaches. Surprisingly, the effect of canopy cover on GPP was similar among urban and forested streams. The combination of watershed and local-scale controls resulted in urban streams that alternated between net heterotrophy (NEP 0) between seasons with and without dense canopy cover. This finding has management relevance because net production can lead to accumulation of algal biomass and associated issues like dissolved oxygen sags at night. Our study reinforces

AdaNET prototype library administration manual

NASA Technical Reports Server (NTRS)

Hanley, Lionel

1989-01-01

The functions of the AdaNET Prototype Library of Reusable Software Parts is described. Adopted from the Navy Research Laboratory's Reusability Guidebook (V.5.0), this is a working document, customized for use the the AdaNET Project. Within this document, the term part is used to denote the smallest unit controlled by a library and retrievable from it. A part may have several constituents, which may not be individually tracked. Presented are the types of parts which may be stored in the library and the relationships among those parts; a concept of trust indicators which provide measures of confidence that a user of a previously developed part may reasonably apply to a part for a new application; search and retrieval, configuration management, and communications among those who interact with the AdaNET Prototype Library; and the AdaNET Prototype, described from the perspective of its three major users: the part reuser and retriever, the part submitter, and the librarian and/or administrator.

Metabolism: Part II. The Tricarboxylic Acid (TCA), Citric Acid, or Krebs Cycle.

ERIC Educational Resources Information Center

Bodner, George M.

1986-01-01

Differentiates the tricarboxylic acid (TCA) cycle (or Krebs cycle) from glycolysis, and describes the bridge between the two as being the conversion of pyruvate into acetyl coenzyme A. Discusses the eight steps in the TCA cycle, the results of isotopic labeling experiments, and the net effects of the TCA cycle. (TW)

Characterization of differentially expressed genes in calf rumen epithelium in response to weaning

USDA-ARS?s Scientific Manuscript database

During weaning, rumen epithelial cell function must transition from a pre-ruminant to a true ruminant state for efficient nutrient absorption and metabolism. During this time, the rumen grows to represent from 30 to 70% of the capacity of the gut, directly impacting net efficiency of feed conversion...

Differential Uptake Mechanisms of Fluorescent Substrates into Stem-Cell-Derived Serotonergic Neurons.

PubMed

Matthaeus, Friederike; Schloss, Patrick; Lau, Thorsten

2015-12-16

The actions of the neurotransmitters serotonin, dopamine, and norepinephrine are partly terminated by diffusion and in part by their uptake into neurons via the selective, high-affinity transporters for serotonin (SERT), dopamine (DAT), and norepinephrine (NET), respectively. There is also growing evidence that all three monoamines are taken up into neurons by low-affinity, high-capacity organic cation transporters (OCT) and the plasma membrane monoamine transporter (PMAT). Pharmacological characterization of these low-affinity recombinant transporter proteins in heterologous expression systems has revealed that they are not antagonized by classical inhibitors of SERT, DAT, or NET but that decynium-22 (D22) antagonizes OCT3 and PMAT, whereas corticosterone and progesterone selectively inhibit OCT3. Here, we show that SERT, PMAT, and OCT3, but not OCT1 and OCT2, are coexpressed in murine stem cell-derived serotonergic neurons. Using selective antagonists, we provide evidence that uptake of the fluorescent substrates FFN511, ASP+, and 5-HT into stem cell-derived serotonergic neurons is mediated differentially by these transporters and also involves an as yet unknown transport mechanism.

TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models.

PubMed

Yao, Zhi-Jiang; Dong, Jie; Che, Yu-Jing; Zhu, Min-Feng; Wen, Ming; Wang, Ning-Ning; Wang, Shan; Lu, Ai-Ping; Cao, Dong-Sheng

2016-05-01

Drug-target interactions (DTIs) are central to current drug discovery processes and public health fields. Analyzing the DTI profiling of the drugs helps to infer drug indications, adverse drug reactions, drug-drug interactions, and drug mode of actions. Therefore, it is of high importance to reliably and fast predict DTI profiling of the drugs on a genome-scale level. Here, we develop the TargetNet server, which can make real-time DTI predictions based only on molecular structures, following the spirit of multi-target SAR methodology. Naïve Bayes models together with various molecular fingerprints were employed to construct prediction models. Ensemble learning from these fingerprints was also provided to improve the prediction ability. When the user submits a molecule, the server will predict the activity of the user's molecule across 623 human proteins by the established high quality SAR model, thus generating a DTI profiling that can be used as a feature vector of chemicals for wide applications. The 623 SAR models related to 623 human proteins were strictly evaluated and validated by several model validation strategies, resulting in the AUC scores of 75-100 %. We applied the generated DTI profiling to successfully predict potential targets, toxicity classification, drug-drug interactions, and drug mode of action, which sufficiently demonstrated the wide application value of the potential DTI profiling. The TargetNet webserver is designed based on the Django framework in Python, and is freely accessible at http://targetnet.scbdd.com .

TargetNet: a web service for predicting potential drug-target interaction profiling via multi-target SAR models

NASA Astrophysics Data System (ADS)

Yao, Zhi-Jiang; Dong, Jie; Che, Yu-Jing; Zhu, Min-Feng; Wen, Ming; Wang, Ning-Ning; Wang, Shan; Lu, Ai-Ping; Cao, Dong-Sheng

2016-05-01

Drug-target interactions (DTIs) are central to current drug discovery processes and public health fields. Analyzing the DTI profiling of the drugs helps to infer drug indications, adverse drug reactions, drug-drug interactions, and drug mode of actions. Therefore, it is of high importance to reliably and fast predict DTI profiling of the drugs on a genome-scale level. Here, we develop the TargetNet server, which can make real-time DTI predictions based only on molecular structures, following the spirit of multi-target SAR methodology. Naïve Bayes models together with various molecular fingerprints were employed to construct prediction models. Ensemble learning from these fingerprints was also provided to improve the prediction ability. When the user submits a molecule, the server will predict the activity of the user's molecule across 623 human proteins by the established high quality SAR model, thus generating a DTI profiling that can be used as a feature vector of chemicals for wide applications. The 623 SAR models related to 623 human proteins were strictly evaluated and validated by several model validation strategies, resulting in the AUC scores of 75-100 %. We applied the generated DTI profiling to successfully predict potential targets, toxicity classification, drug-drug interactions, and drug mode of action, which sufficiently demonstrated the wide application value of the potential DTI profiling. The TargetNet webserver is designed based on the Django framework in Python, and is freely accessible at http://targetnet.scbdd.com.

Genetic Dissection of Photoreceptor Subtype Specification by the Drosophila melanogaster Zinc Finger Proteins Elbow and No ocelli

PubMed Central

Wernet, Mathias F.; Meier, Kerstin M.; Baumann-Klausener, Franziska; Dorfman, Ruslan; Weihe, Ulrich; Labhart, Thomas; Desplan, Claude

2014-01-01

The elbow/no ocelli (elb/noc) complex of Drosophila melanogaster encodes two paralogs of the evolutionarily conserved NET family of zinc finger proteins. These transcriptional repressors share a conserved domain structure, including a single atypical C2H2 zinc finger. In flies, Elb and Noc are important for the development of legs, eyes and tracheae. Vertebrate NET proteins play an important role in the developing nervous system, and mutations in the homolog ZNF703 human promote luminal breast cancer. However, their interaction with transcriptional regulators is incompletely understood. Here we show that loss of both Elb and Noc causes mis-specification of polarization-sensitive photoreceptors in the ‘dorsal rim area’ (DRA) of the fly retina. This phenotype is identical to the loss of the homeodomain transcription factor Homothorax (Hth)/dMeis. Development of DRA ommatidia and expression of Hth are induced by the Wingless/Wnt pathway. Our data suggest that Elb/Noc genetically interact with Hth, and we identify two conserved domains crucial for this function. Furthermore, we show that Elb/Noc specifically interact with the transcription factor Orthodenticle (Otd)/Otx, a crucial regulator of rhodopsin gene transcription. Interestingly, different Elb/Noc domains are required to antagonize Otd functions in transcriptional activation, versus transcriptional repression. We propose that similar interactions between vertebrate NET proteins and Meis and Otx factors might play a role in development and disease. PMID:24625735

Heavy section fracture toughness screening specimen

NASA Technical Reports Server (NTRS)

Shannon, J. L., Jr.; Donald, J. K.; Brown, W. F., Jr.

1976-01-01

Size requirements for a pin loaded double edge notch + crack tension specimen proposed for fracture toughness screening heavy section alloys were studied. Ranking of eight selected alloys based on the specimen's net strength was compared with that based on the valid plane strain fracture toughness separately determined. Performance of the specimen was judged on the basis of that comparison. The specimen's net strength was influenced by three critical specimen dimensions: distance between the crack plane and the loading hole, specimen width, and specimen thickness. Interaction between the stress fields of the crack and the loading holes reduced the net strength, but this effect disappeared as the separation reached a dimension equal to the specimen width. The effects of specimen width and thickness are interrelated and affect the net strength through their influence on the development of the crack tip plastic zone.

Lanreotide autogel every 6 weeks compared with Lanreotide microparticles every 3 weeks in patients with well differentiated neuroendocrine tumors: a Phase III Study.

PubMed

Bajetta, Emilio; Procopio, Giuseppe; Catena, Laura; Martinetti, Antonia; De Dosso, Sara; Ricci, Sergio; Lecchi, Alberto S; Boscani, Paolo F; Iacobelli, Stefano; Carteni, Giacomo; De Braud, Filippo; Loli, Paola; Tartaglia, Andreas; Bajetta, Roberto; Ferrari, Leonardo

2006-11-15

The noninferiority of a 6-week dosing schedule of lanreotide Autogel (Lan ATG) at a dose of 120 mg compared with a 3-week dosing schedule of lanreotide microparticles (Lan MP) at a dose of 60 mg was investigated in patients with neuroendocrine tumors (NET). Patients who had sporadic, well differentiated NET with a low grade of malignancy were recruited for this open-label, Phase III, multicenter trial. Patients were randomized to receive either 3 deep subcutaneous injections of Lan ATG (120 mg, every 6 weeks) or 6 intramuscular injections of Lan MP (60 mg, every 3 weeks). Tumor markers, tumor size, and symptoms were assessed between baseline and Week 18. Success was classified as a response that ranged from disappearance to an increase <25% in tumor marker, tumor size, or symptom frequency. Sixty patients were randomized, and 46 patients completed the study. Both for tumor markers and for tumor size, Lan ATG was not inferior to Lan MP (55% and 59% of patients responded on tumor markers, respectively; 68% and 66% of patients responded on tumor size, respectively). There were too few symptomatic patients to compare carcinoid symptoms. Both treatments were tolerated well, and no safety concerns were identified. Lan ATG at a dose of 120 mg every 6 weeks was as effective for controlling NET as Lan MP at a dose of 60 mg every 3 weeks.

Comparing the catch composition, profitability and discard survival from different trammel net designs targeting common spiny lobster (Palinurus elephas) in a Mediterranean fishery.

PubMed

Catanese, Gaetano; Hinz, Hilmar; Gil, Maria Del Mar; Palmer, Miquel; Breen, Michael; Mira, Antoni; Pastor, Elena; Grau, Amalia; Campos-Candela, Andrea; Koleva, Elka; Grau, Antoni Maria; Morales-Nin, Beatriz

2018-01-01

In the Balearic Islands, different trammel net designs have been adopted to promote fisheries sustainability and reduce discards. Here, we compare the catch performance of three trammel net designs targeting the spiny lobster Palinurus elephas in terms of biomass, species composition and revenue from commercial catches and discards. Designs differ in the netting fiber type (standard polyfilament, PMF, or a new polyethylene multi-monofilament, MMF) and the use of a guarding net or greca , a mesh piece intended to reduce discards. Catches were surveyed by an on-board observer from 1,550 netting walls corresponding to 70 nets. The number of marketable species captured indicated that the lobster trammel net fishery has multiple targets, which contribute significantly to the total revenue. The discarded species ranged from habitat-forming species to elasmobranches, but the magnitude of gear-habitat interactions on the long term dynamics of benthos remains unclear. No relevant differences in revenue and weight of discards were detected after Bayesian analyses. However, the species composition of discards was different when using greca . Interestingly, high immediate survival was found for discarded undersized lobsters, while a seven day survival assessment, using captive observation, gave an asymptotic estimate of survival probability as 0.64 (95% CI [0.54-0.76]). Therefore, it is recommended that it would be beneficial for this stock if an exemption from the EU landing obligation regulation was sought for undersized lobsters in the Balearic trammel net fishery.

Genetic moderation of child maltreatment effects on depression and internalizing symptoms by 5-HTTLPR, BDNF, NET, and CRHR1 genes in African-American children

PubMed Central

Cicchetti, Dante; Rogosch, Fred A.

2014-01-01

Genetic moderation of the effects of child maltreatment on depression and internalizing symptoms was investigated in a sample of low-income maltreated and nonmaltreated African-American children (N = 1,096). Lifetime child maltreatment experiences were independently coded from Child Protective Services records and maternal report. Child depression and internalizing problems were assessed in the context of a summer research camp by self-report (Children’s Depression Inventory, CDI) and adult counselor-report (Teacher Report Form, TRF). DNA was obtained from buccal cell or saliva samples and genotyped for polymorphisms of the following genes: 5-HTTLPR, BDNF, NET, and CRHR1. ANCOVAs with age and gender as covariates were conducted, with maltreatment status and respective polymorphism as main effects and their GxE interactions. Maltreatment consistently was associated with higher CDI and TRF symptoms. Results for child self-report symptoms indicated a GxE interaction for BDNF and maltreatment. Additionally, BDNF and tri-allelic 5-HTTLPR interacted with child maltreatment in a GxGxE interaction. Analyses for counselor-report of child anxiety/depression symptoms on the TRF indicated moderation of child maltreatment effects by tri-allelic 5-HTTLPR. These effects were elaborated based on variation in developmental timing of maltreatment experiences. NET was found to further moderate the GxE interaction of 5-HTTLPR and maltreatment status revealing a GxGxE interaction. This GxGxE was extended by consideration of variation in maltreatment subtype experiences. Finally, GxGxE effects were observed for the co-action of BDNF and the CRHR1 haplotype. The findings illustrate the variable influence of specific genotypes in GxE interactions based on variation in maltreatment experiences and the importance of a multi-genic approach for understanding influences on depression and internalizing symptoms among African-American children. PMID:25422957

Mineralization and nitrification patterns at eight northeastern USA forested research sites

USGS Publications Warehouse

Ross, D.S.; Lawrence, G.B.; Fredriksen, G.

2004-01-01

Nitrogen transformation rates in eight northeastern US research sites were measured in soil samples taken in the early season of 2000 and the late season of 2001. Net mineralization and nitrification rates were determined on Oa or A horizon samples by two different sampling methods - intact cores and repeated measurements on composite samples taken from around the cores. Net rates in the composite samples (n=30) showed three different temporal patterns: high net nitrification with minimal NH4+ accumulation, high net nitrification and high NH4+ accumulation, and minimal net nitrification and moderate NH4+ accumulation. The 4-week net rates in intact cores were about half that of the rates from the composite samples but were well related (R2 > 0.70). Composite samples from sites that exhibited high net nitrification were incubated with acetylene and net nitrification was completely stopped, suggesting an autotrophic pathway. Gross mineralization and nitrification (2000 only) rates were estimated using the isotope dilution technique. Gross rates of nitrification and consumption in intact cores were relatively low. Gross rates of mineralization and net rates of nitrification were both related to the soil C/N ratio, with higher rates generally occurring in sites containing Acer saccharum as a dominant or co-dominant species. The comparison of methods suggests that all provide a similar hierarchy of potential rates but that the degree of net nitrification is strongly influenced by the degree of sample disturbance. Differences between sites appear to be related to an interaction of soil (C/N) and vegetation (A. saccharum contribution) characteristics. ?? 2003 Elsevier B.V. All rights reserved.

Cloud types and the tropical Earth radiation budget, revised

NASA Technical Reports Server (NTRS)

Dhuria, Harbans L.; Kyle, H. Lee

1989-01-01

Nimbus-7 cloud and Earth radiation budget data are compared in a study of the effects of clouds on the tropical radiation budget. The data consist of daily averages over fixed 500 sq km target areas, and the months of July 1979 and January 1980 were chosen to show the effect of seasonal changes. Six climate regions, consisting of 14 to 24 target areas each, were picked for intensive analysis because they exemplified the range in the tropical cloud/net radiation interactions. The normal analysis was to consider net radiation as the independent variable and examine how cloud cover, cloud type, albedo and emitted radiation varied with the net radiation. Two recurring themes keep repeating on a local, regional, and zonal basis: the net radiation is strongly influenced by the average cloud type and amount present, but most net radiation values could be produced by several combinations of cloud types and amount. The regions of highest net radiation (greater than 125 W/sq m) tend to have medium to heavy cloud cover. In these cases, thin medium altitude clouds predominate. Their cloud tops are normally too warm to be classified as cirrus by the Nimbus cloud algorithm. A common feature in the tropical oceans are large regions where the total regional cloud cover varies from 20 to 90 percent, but with little regional difference in the net radiation. The monsoon and rain areas are high net radiation regions.

Immune Checkpoint Inhibitors in the Treatment of Patients with Neuroendocrine Neoplasia.

PubMed

Weber, Matthias M; Fottner, Christian

2018-01-01

Well-differentiated neuroendocrine neoplasms (NENs) are usually controlled by antiproliferative, local ablative and/or radionuclide therapies, whereas poorly differentiated NENs generally require cytotoxic chemotherapy. However, treatment options for patients with advanced/metastatic high-grade NENs remain limited. Review of the literature and international congress abstracts on the efficacy and safety of immunotherapy by checkpoint inhibition in advanced/metastatic NENs. Evidence points to an important role of immune phenomena in the pathogenesis and treatment of neuroendocrine tumors (NETs). Programmed cell death 1 (PD-1) protein and its ligand are mainly expressed in poorly differentiated NENs. Microsatellite instability and high mutational load are more pronounced in high-grade NENs and may predict response to immunotherapy. Clinical experience of immune checkpoint blockade mainly exists for Merkel cell carcinoma, a high-grade cutaneous neuroendocrine carcinoma (NEC), which has led to approval of the anti-PD-1 antibody avelumab. In addition, there is anecdotal evidence for the efficacy of checkpoint inhibitors in large-cell lung NECs, ovarian NECs and others, including gastroenteropancreatic NENs. Currently, phase II studies investigate PDR001, pembrolizumab, combined durvalumab and tremelimumab, and avelumab treatment in patients with advanced/metastatic NENs. Immune checkpoint inhibitors are a promising therapeutic option, especially in progressive NECs or high-grade NETs with high tumor burden, microsatellite instability, and/or mutational load. © 2018 S. Karger GmbH, Freiburg.

The impact of kin availability, parental religiosity, and nativity on fertility differentials in the late 19th-century United States

PubMed Central

Hacker, J. David; Roberts, Evan

2017-01-01

METHODS Most quantitative research on fertility decline in the United States ignores the potential impact of cultural and familial factors. We rely on new complete-count data from the 1880 U.S. census to construct couple-level measures of nativity/ethnicity, religiosity, and kin availability. We include these measures with a comprehensive set of demographic, economic, and contextual variables in Poisson regression models of net marital fertility to assess their relative importance. We construct models with and without area fixed effects to control for unobserved heterogeneity. CONTRIBUTION All else being equal, we find a strong impact of nativity on recent net marital fertility. Fertility differentials among second generation couples relative to the native-born white population of native parentage were in most cases less than half of the differential observed among first generation immigrants, suggesting greater assimilation to native-born American childbearing norms. Our measures of parental religiosity and familial propinquity indicated a more modest impact on marital fertility. Couples who chose biblical names for their children had approximately 3% more children than couples relying on secular names while the presence of a potential mother-in-law in a nearby households was associated with 2% more children. Overall, our results demonstrate the need for more inclusive models of fertility behavior that include cultural and familial covariates. PMID:29720893

The impact of kin availability, parental religiosity, and nativity on fertility differentials in the late 19th-century United States.

PubMed

Hacker, J David; Roberts, Evan

2017-12-01

Most quantitative research on fertility decline in the United States ignores the potential impact of cultural and familial factors. We rely on new complete-count data from the 1880 U.S. census to construct couple-level measures of nativity/ethnicity, religiosity, and kin availability. We include these measures with a comprehensive set of demographic, economic, and contextual variables in Poisson regression models of net marital fertility to assess their relative importance. We construct models with and without area fixed effects to control for unobserved heterogeneity. All else being equal, we find a strong impact of nativity on recent net marital fertility. Fertility differentials among second generation couples relative to the native-born white population of native parentage were in most cases less than half of the differential observed among first generation immigrants, suggesting greater assimilation to native-born American childbearing norms. Our measures of parental religiosity and familial propinquity indicated a more modest impact on marital fertility. Couples who chose biblical names for their children had approximately 3% more children than couples relying on secular names while the presence of a potential mother-in-law in a nearby households was associated with 2% more children. Overall, our results demonstrate the need for more inclusive models of fertility behavior that include cultural and familial covariates.

75 FR 53939 - Magnuson-Stevens Act Provisions; Fisheries of the Northeastern United States; Northeast...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-02

... increase interactions with protected species. However, if additional nets result in greater efficiency... throughout the year, thus potentially reducing interactions with protected species. Sector vessels utilizing... Port Clyde Community Groundfish Sector, the GB Cod Fixed Gear Sector and the Tri-State Sector. 2...

Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions.

PubMed

Agarwal, Shashank; Liu, Feifan; Yu, Hong

2011-10-03

Protein-protein interaction (PPI) is an important biomedical phenomenon. Automatically detecting PPI-relevant articles and identifying methods that are used to study PPI are important text mining tasks. In this study, we have explored domain independent features to develop two open source machine learning frameworks. One performs binary classification to determine whether the given article is PPI relevant or not, named "Simple Classifier", and the other one maps the PPI relevant articles with corresponding interaction method nodes in a standardized PSI-MI (Proteomics Standards Initiative-Molecular Interactions) ontology, named "OntoNorm". We evaluated our system in the context of BioCreative challenge competition using the standardized data set. Our systems are amongst the top systems reported by the organizers, attaining 60.8% F1-score for identifying relevant documents, and 52.3% F1-score for mapping articles to interaction method ontology. Our results show that domain-independent machine learning frameworks can perform competitively well at the tasks of detecting PPI relevant articles and identifying the methods that were used to study the interaction in such articles. Simple Classifier is available at http://sourceforge.net/p/simpleclassify/home/ and OntoNorm at http://sourceforge.net/p/ontonorm/home/.

Bulk combinatorial synthesis and high throughput characterization for rapid assessment of magnetic materials: Application of laser engineered net shaping (LENS)

DOE PAGES

Geng, J.; Nlebedim, I. C.; Besser, M. F.; ...

2016-04-15

A bulk combinatorial approach for synthesizing alloy libraries using laser engineered net shaping (LENS; i.e., 3D printing) was utilized to rapidly assess material systems for magnetic applications. The LENS system feeds powders in different ratios into a melt pool created by a laser to synthesize samples with bulk (millimeters) dimensions. By analyzing these libraries with autosampler differential scanning calorimeter/thermal gravimetric analysis and vibrating sample magnetometry, we are able to rapidly characterize the thermodynamic and magnetic properties of the libraries. Furthermore, the Fe-Co binary alloy was used as a model system and the results were compared with data in the literature.

Gamma radiation exposure of accompanying persons due to Lu-177 patients

NASA Astrophysics Data System (ADS)

Kovan, Bilal; Demir, Bayram; Tuncman, Duygu; Capali, Veli; Turkmen, Cuneyt

2015-07-01

Neuroendocrine tumours (NET) are cancers usually observed and arisen in the stomach, intestine, pancreas and breathing system. Recently, radionuclide therapy applications with Lu-177 peptide compound are rapidly growing; especially effective clinical results are obtained in the treatment of well-differentiated and metastatic NET. In this treatment, Lu-177-DOTA, a beta emitter radioisotope in the radiopharmaceutical form, is given to the patient by intravenous way. Lu-177 has also gamma rays apart from beta rays. Gamma rays have 175 keV average energy and these gamma rays should be under the control in terms of radiation protection. In this study, we measured the exposure dose from the Lu-177 patient.

The water footprint of agricultural products in European river basins

NASA Astrophysics Data System (ADS)

Vanham, D.; Bidoglio, G.

2014-05-01

This work quantifies the agricultural water footprint (WF) of production (WFprod, agr) and consumption (WFcons, agr) and the resulting net virtual water import (netVWi, agr) of 365 European river basins for a reference period (REF, 1996-2005) and two diet scenarios (a healthy diet based upon food-based dietary guidelines (HEALTHY) and a vegetarian (VEG) diet). In addition to total (tot) amounts, a differentiation is also made between the green (gn), blue (bl) and grey (gy) components. River basins where the REF WFcons, agr, tot exceeds the WFprod, agr, tot (resulting in positive netVWi, agr, tot values), are found along the London-Milan axis. These include the Thames, Scheldt, Meuse, Seine, Rhine and Po basins. River basins where the WFprod, agr, tot exceeds the WFcons, agr, tot are found in Western France, the Iberian Peninsula and the Baltic region. These include the Loire, Ebro and Nemunas basins. Under the HEALTHY diet scenario, the WFcons, agr, tot of most river basins decreases (max -32%), although it was found to increase in some basins in northern and eastern Europe. This results in 22 river basins, including the Danube, shifting from being net VW importers to being net VW exporters. A reduction (max -46%) in WFcons, agr, tot is observed for all but one river basin under the VEG diet scenario. In total, 50 river basins shift from being net VW importers to being net exporters, including the Danube, Seine, Rhone and Elbe basins. Similar observations are made when only the gn + bl and gn components are assessed. When analysing only the bl component, a different river basin pattern is observed.

GFD-Net: A novel semantic similarity methodology for the analysis of gene networks.

PubMed

Díaz-Montaña, Juan J; Díaz-Díaz, Norberto; Gómez-Vela, Francisco

2017-04-01

Since the popularization of biological network inference methods, it has become crucial to create methods to validate the resulting models. Here we present GFD-Net, the first methodology that applies the concept of semantic similarity to gene network analysis. GFD-Net combines the concept of semantic similarity with the use of gene network topology to analyze the functional dissimilarity of gene networks based on Gene Ontology (GO). The main innovation of GFD-Net lies in the way that semantic similarity is used to analyze gene networks taking into account the network topology. GFD-Net selects a functionality for each gene (specified by a GO term), weights each edge according to the dissimilarity between the nodes at its ends and calculates a quantitative measure of the network functional dissimilarity, i.e. a quantitative value of the degree of dissimilarity between the connected genes. The robustness of GFD-Net as a gene network validation tool was demonstrated by performing a ROC analysis on several network repositories. Furthermore, a well-known network was analyzed showing that GFD-Net can also be used to infer knowledge. The relevance of GFD-Net becomes more evident in Section "GFD-Net applied to the study of human diseases" where an example of how GFD-Net can be applied to the study of human diseases is presented. GFD-Net is available as an open-source Cytoscape app which offers a user-friendly interface to configure and execute the algorithm as well as the ability to visualize and interact with the results(http://apps.cytoscape.org/apps/gfdnet). Copyright © 2017 Elsevier Inc. All rights reserved.

Sumoylation of the net inhibitory domain (NID) is stimulated by PIAS1 and has a negative effect on the transcriptional activity of Net.

PubMed

Wasylyk, Christine; Criqui-Filipe, Paola; Wasylyk, Bohdan

2005-01-27

Net (Elk-3, Sap-2, Erp) and the related ternary complex factors Elk-1 and Sap-1 are effectors of multiple signalling pathways at the transcriptional level and play a key role in the dynamic regulation of gene expression. Net is distinct from Elk-1 and Sap-1, in that it is a strong repressor of transcription that is converted to an activator by the Ras/Erk signalling pathway. Two autonomous repression domains of Net, the NID and the CID, mediate repression. We have previously shown that the co-repressor CtBP is implicated in repression by the CID. In this report we show that repression by the NID involves a different pathway, sumoylation by Ubc9 and PIAS1. PIAS1 interacts with the NID in the two-hybrid assay and in vitro. Ubc9 and PIAS1 stimulate sumoylation in vivo of lysine 162 in the NID. Sumoylation of lysine 162 increases repression by Net and decreases the positive activity of Net. These results increase our understanding of how one of the ternary complex factors regulates transcription, and contribute to the understanding of how different domains of a transcription factor participate in the complexity of regulation of gene expression.

Automation of Presentation Record Production Based on Rich-Media Technology Using SNT Petri Nets Theory.

PubMed

Martiník, Ivo

2015-01-01

Rich-media describes a broad range of digital interactive media that is increasingly used in the Internet and also in the support of education. Last year, a special pilot audiovisual lecture room was built as a part of the MERLINGO (MEdia-rich Repository of LearnING Objects) project solution. It contains all the elements of the modern lecture room determined for the implementation of presentation recordings based on the rich-media technologies and their publication online or on-demand featuring the access of all its elements in the automated mode including automatic editing. Property-preserving Petri net process algebras (PPPA) were designed for the specification and verification of the Petri net processes. PPPA does not need to verify the composition of the Petri net processes because all their algebraic operators preserve the specified set of the properties. These original PPPA are significantly generalized for the newly introduced class of the SNT Petri process and agent nets in this paper. The PLACE-SUBST and ASYNC-PROC algebraic operators are defined for this class of Petri nets and their chosen properties are proved. The SNT Petri process and agent nets theory were significantly applied at the design, verification, and implementation of the programming system ensuring the pilot audiovisual lecture room functionality.

Automation of Presentation Record Production Based on Rich-Media Technology Using SNT Petri Nets Theory

PubMed Central

Martiník, Ivo

2015-01-01

Rich-media describes a broad range of digital interactive media that is increasingly used in the Internet and also in the support of education. Last year, a special pilot audiovisual lecture room was built as a part of the MERLINGO (MEdia-rich Repository of LearnING Objects) project solution. It contains all the elements of the modern lecture room determined for the implementation of presentation recordings based on the rich-media technologies and their publication online or on-demand featuring the access of all its elements in the automated mode including automatic editing. Property-preserving Petri net process algebras (PPPA) were designed for the specification and verification of the Petri net processes. PPPA does not need to verify the composition of the Petri net processes because all their algebraic operators preserve the specified set of the properties. These original PPPA are significantly generalized for the newly introduced class of the SNT Petri process and agent nets in this paper. The PLACE-SUBST and ASYNC-PROC algebraic operators are defined for this class of Petri nets and their chosen properties are proved. The SNT Petri process and agent nets theory were significantly applied at the design, verification, and implementation of the programming system ensuring the pilot audiovisual lecture room functionality. PMID:26258164

Construction and Deciphering of Human Phosphorylation-Mediated Signaling Transduction Networks.

PubMed

Zhang, Menghuan; Li, Hong; He, Ying; Sun, Han; Xia, Li; Wang, Lishun; Sun, Bo; Ma, Liangxiao; Zhang, Guoqing; Li, Jing; Li, Yixue; Xie, Lu

2015-07-02

Protein phosphorylation is the most abundant reversible covalent modification. Human protein kinases participate in almost all biological pathways, and approximately half of the kinases are associated with disease. PhoSigNet was designed to store and display human phosphorylation-mediated signal transduction networks, with additional information related to cancer. It contains 11 976 experimentally validated directed edges and 216 871 phosphorylation sites. Moreover, 3491 differentially expressed proteins in human cancer from dbDEPC, 18 907 human cancer variation sites from CanProVar, and 388 hyperphosphorylation sites from PhosphoSitePlus were collected as annotation information. Compared with other phosphorylation-related databases, PhoSigNet not only takes the kinase-substrate regulatory relationship pairs into account, but also extends regulatory relationships up- and downstream (e.g., from ligand to receptor, from G protein to kinase, and from transcription factor to targets). Furthermore, PhoSigNet allows the user to investigate the impact of phosphorylation modifications on cancer. By using one set of in-house time series phosphoproteomics data, the reconstruction of a conditional and dynamic phosphorylation-mediated signaling network was exemplified. We expect PhoSigNet to be a useful database and analysis platform benefiting both proteomics and cancer studies.

Behavioural responses of females of two anopheline mosquito species to human-occupied, insecticide-treated and untreated bed nets

PubMed Central

2014-01-01

Background Insecticide-treated bed nets (ITNs), used extensively to reduce human exposure to malaria, work through physical and chemical means to block or deter host-seeking mosquitoes. Despite the importance of ITNs, very little is known about how host-seeking mosquitoes behave around occupied bed nets. As a result, evidence-based evaluations of the effects of physical damage on bed net effectiveness are not possible and there is a dearth of knowledge on which to base ITN design. Methods The dispersion of colony-raised female Anopheles gambiae and Anopheles albimanus was observed in 2-hr laboratory experiments in which up to 200 mosquitoes were released inside a mosquito-proof 3 m × 3 m tent housing a bed net arrayed with 18 30 cm × 30 cm sticky screen squares on the sides, ends and roof. Numbers of mosquitoes caught on the sticky squares were interpreted as the ‘mosquito pressure’ on that part of the net. Results Presence of a human subject in the bed net significantly increased total mosquito pressure on the net for both species and significantly re-oriented An. gambiae to the roof of the net. Anopheles albimanus pressure was greatest on the bed net roof in both host-present and no-host conditions. The effects of different human subjects in the bed net, of different ambient conditions (dry, cool conditions vs warm, humid conditions) and of bed net treatment (deltamethrin-treated or no insecticide) on mosquito pressure patterns were tested for both species. Species-specific pressure patterns did not vary greatly as a result of any of these factors though some differences were noted that may be due the size of the different human subjects. Conclusions As a result of the interaction between host-seeking responses and the convective plume from the net occupant, species-specific mosquito pressure patterns manifest more or less predictably on the bed net. This has implications for bed net design and suggests that current methods of assessing damaged bed nets, which do not take damage location into account, should be modified. PMID:25080389

Patterns of net migration by age for U.S. counties 1950-1980: the impact of increasing spatial differentiation by life cycle.

PubMed

Mueser, P R; White, M J; Tierney, J P

1988-01-01

This paper examines age patterns of net migration for US counties, arguing that the shift in the character of population redistribution will be reflected in the age structure of net migration across counties. The authors hypothesize that the increased specialization of counties with respect to activities characteristic of particular states of the life cycle would be evident in the greater dispersion of net migration rates at selected ages. For the 1950s and the 1960s, the authors used net migration estimates for US counties calculated by age, race, and sex by Gladys Bowles and colleagues. For 1970-1980, the authors constructed estimates. The study analyzed over 3000 counties or county equivalents. The results of the analysis confirm the importance of changes in age- specific patterns and provide support for the hypothesis. The increasing importance of localized amenities and an associated growth of age-specialized institutional structures across location, serves to increase concentration of net migration in certain age groups. Specifically, 1) nonmetropolitan counties become particularly attractive to migrants in their late 20s and early 30s; 2) since 1970, the dispersion of net migration rates for those over 30 have increased appreciably; 3) the degree of dispersion differs greatly across regions and is especially large among counties in the West; 4) metropolitan counties exhibit declines in the dispersion of net migration rate from the 1950s to the 1960s, which may indicate the exhaustion of the most attractive urban opportunities; and 5) since 1970, dispersion has increased, especially for rates applying to those over age 55, suggesting increased age specialization among metropolitan counties. Thus, changes in both the median rates of net migration and the dispersion of those rates are consistent with increased specialization in the age-related opportunities and services those counties provide. New patterns of net migration by age suggest that change in both the causes and effects of migration go far beyond a simple shift in the balance of population flows.

Patient portal readiness among postpartum patients in a safety net setting.

PubMed

Wieland, Daryl; Gibeau, Anne; Dewey, Caitlin; Roshto, Melanie; Frankel, Hilary

2017-07-05

Maternity patients interact with the healthcare system over an approximately ten-month interval, requiring multiple visits, acquiring pregnancy-specific education, and sharing health information among providers. Many features of a web-based patient portal could help pregnant women manage their interactions with the healthcare system; however, it is unclear whether pregnant women in safety-net settings have the resources, skills or interest required for portal adoption. In this study of postpartum patients in a safety net hospital, we aimed to: (1) determine if patients have the technical resources and skills to access a portal, (2) gain insight into their interest in health information, and (3) identify the perceived utility of portal features and potential barriers to adoption. We developed a structured questionnaire to collect demographics from postpartum patients and measure use of technology and the internet, self-reported literacy, interest in health information, awareness of portal functions, and perceived barriers to use. The questionnaire was administered in person to women in an inpatient setting. Of the 100 participants surveyed, 95% reported routine internet use and 56% used it to search for health information. Most participants had never heard of a patient portal, yet 92% believed that the portal functions were important. The two most appealing functions were to check results and manage appointments. Most participants in this study have the required resources such as a device and familiarity with the internet to access a patient portal including an interest in interacting with a healthcare institution via electronic means. Pregnancy is a critical episode of care where active engagement with the healthcare system can influence outcomes. Healthcare systems and portal developers should consider ways to tailor a portal to address the specific health needs of a maternity population including those in a safety net setting.

Salinity and light interactively affect neotropical mangrove seedlings at the leaf and whole plant levels.

PubMed

López-Hoffman, Laura; Anten, Niels P R; Martínez-Ramos, Miguel; Ackerly, David D

2007-01-01

We have studied the interactive effects of salinity and light on Avicennia germinans mangrove seedlings in greenhouse and field experiments. We hypothesized that net photosynthesis, growth, and survivorship rates should increase more with an increase in light availability for plants growing at low salinity than for those growing at high salinity. This hypothesis was supported by our results for net photosynthesis and growth. Net daily photosynthesis did increase more with increasing light for low-salinity plants than for high-salinity plants. Stomatal conductance, leaf-level transpiration, and internal CO(2) concentrations were lower at high than at low salinity. At high light, the ratio of leaf respiration to assimilation was 2.5 times greater at high than at low salinity. Stomatal limitations and increased respiratory costs may explain why, at high salinity, seedlings did not respond to increased light availability with increased net photosynthesis. Seedling mass and growth rates increased more with increasing light availability at low than at high salinity. Ratios of root mass to leaf mass were higher at high salinity, suggesting that either water or nutrient limitations may have limited seedling growth at high salinity in response to increasing light. The interactive effects of salinity and light on seedling size and growth rates observed in the greenhouse were robust in the field, despite the presence of other factors in the field--such as inundation, nutrient gradients, and herbivory. In the field, seedling survivorship was higher at low than at high salinity and increased with light availability. Interestingly, the positive effect of light on seedling survivorship was stronger at high salinity, indicating that growth and survivorship rates are decoupled. In general, this study demonstrates that environmental effects at the leaf-level also influence whole plant growth in mangroves.

Fine Mapping of the Barley Chromosome 6H Net Form Net Blotch Susceptibility Locus

PubMed Central

Richards, Jonathan; Chao, Shiaoman; Friesen, Timothy; Brueggeman, Robert

2016-01-01

Net form net blotch, caused by the necrotrophic fungal pathogen Pyrenophora teres f. teres, is a destructive foliar disease of barley with the potential to cause significant yield loss in major production regions throughout the world. The complexity of the host–parasite genetic interactions in this pathosystem hinders the deployment of effective resistance in barley cultivars, warranting a deeper understanding of the interactions. Here, we report on the high-resolution mapping of the dominant susceptibility locus near the centromere of chromosome 6H in the barley cultivars Rika and Kombar, which are putatively targeted by necrotrophic effectors from P. teres f. teres isolates 6A and 15A, respectively. Utilization of progeny isolates derived from a cross of P. teres f. teres isolates 6A × 15A harboring single major virulence loci (VK1, VK2, and VR2) allowed for the Mendelization of single inverse gene-for-gene interactions in a high-resolution population consisting of 2976 Rika × Kombar recombinant gametes. Brachypodium distachyon synteny was exploited to develop and saturate the susceptibility region with markers, delimiting it to ∼0.24 cM and a partial physical map was constructed. This genetic and physical characterization further resolved the dominant susceptibility locus, designated Spt1 (susceptibility to P. teres f. teres). The high-resolution mapping and cosegregation of the Spt1.R and Spt1.K gene/s indicates tightly linked genes in repulsion or alleles possibly targeted by different necrotrophic effectors. Newly developed barley genomic resources greatly enhance the efficiency of positional cloning efforts in barley, as demonstrated by the Spt1 fine mapping and physical contig identification reported here. PMID:27172206

A comparison of methods used to obtain age ratios of snow and Canada geese

USGS Publications Warehouse

Higgins, K.F.; Linder, R.L.; Springer, P.F.

1969-01-01

The validity of group counts, cannon-net catches, and hunter-bag checks for estimating productivity of lesser snow geese (Anser caerulescens caerulescens) and small Canada geese (Branta canadensis hutchinsii-parvipes complex) was studied at Sand Lake National Wildlife Refuge during the falls of 1965 and 1966. Age ratios of snow geese obtained from net-trapped samples were significantly higher (P < 0.01) than from group counts at the same site. Immature snow geese were shot in a significantly greater (P < 0.01) proportion than they existed in the population as determined by group counts. Cannon-net catches and hunter-bag checks of snow and Canada geese yielded age ratios which were biased because of behavioral characteristics of the geese. Immatures of both species were less wary of trap equipment and immature snow geese were more vulnerable to the gun than adults. It was believed that age ratios from group counts of snow geese were more representative of the population than those from net catches and hunter-bag checks. Sex ratios of net-trapped geese showed a preponderance of males for adult Canada and adult and immature snow geese, whereas females were predominant in the immature segment of Canada geese. Hunter selectivity of blue- or white-phase snow geese was not observed at Sand Lake Refuge. Differential vulnerability to hunting between snow and Canada geese resulted from differences m feeding-flight behavior.

Role of multidetector computed tomography in evaluating incidentally detected breast lesions.

PubMed

Moschetta, Marco; Scardapane, Arnaldo; Lorusso, Valentina; Rella, Leonarda; Telegrafo, Michele; Serio, Gabriella; Angelelli, Giuseppe; Ianora, Amato Antonio Stabile

2015-01-01

Computed tomography (CT) does not represent the primary method for the evaluation of breast lesions; however, it can detect breast abnormalities, even when performed for other reasons related to thoracic structures. The aim of this study is to evaluate the potential benefits of 320-row multidetector CT (MDCT) in evaluating and differentiating incidentally detected breast lesions by using vessel probe and 3D analysis software with net enhancement value. Sixty-two breast lesions in 46 patients who underwent 320-row chest CT examination were retrospectively evaluated. CT scans were assessed searching for the presence, location, number, morphological features, and density of breast nodules. Net enhancement was calculated by subtracting precontrast density from the density obtained by postcontrast values. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy of CT were calculated for morphological features and net enhancement. Thirty of 62 lesions were found to be malignant at histological examination and 32 were found to be benign. When morphological features were considered, the sensitivity, specificity, accuracy, PPV, and NPV of CT were 87%, 100%, 88%, 100%, and 50%, respectively. Based on net enhancement, CT reached a sensitivity, specificity, accuracy, PPV, and NPV of 100%, 94%, 97%, 94%, and 100%, respectively. MDCT allows to recognize and characterize breast lesions based on morphological features. Net enhancement can be proposed as an additional accurate feature of CT.

Net motion of acoustically levitating nano-particles: A theoretical analysis

NASA Astrophysics Data System (ADS)

Lippera, Kevin; Dauchot, Olivier; Benzaquen, Michael; Gulliver-LadHyX Collaboration

2017-11-01

A particle 2D-trapped in the nodal planed of a standing acoustic wave is prone to acoustic-phoretic motion as soon as its shape breaks polar or chiral symmetry. such a setup constitues an ideal system to study boundaryless 2D collective behavior with purely hydrodynamic long range interactions. Recent studies have indeed shown that quasi-spherical particles may undergo net propulsion, a feature partially understood theoretically in the particular case of infinite viscous boundary layers. We here extend the theoretical results of to any boundary layer thickness, by that meeting typical experimental conditions. In addition, we propose an explanation for the net spinning of the trapped particles, as observed in experiments.

Development of a Mapped Diabetes Community Program Guide for a Safety Net Population

PubMed Central

Zallman, Leah; Ibekwe, Lynn; Thompson, Jennifer W.; Ross-Degnan, Dennis; Oken, Emily

2014-01-01

Purpose Enhancing linkages between patients and community programs is increasingly recognized as a method for improving physical activity, nutrition and weight management. Although interactive mapped community program guides may be beneficial, there remains a dearth of articles that describe the processes and practicalities of creating such guides. This article describes the development of an interactive, web-based mapped community program guide at a safety net institution and the lessons learned from that process. Conclusions This project demonstrated the feasibility of creating two maps – a program guide and a population health map. It also revealed some key challenges and lessons for future work in this area, particularly within safety-net institutions. Our work underscores the need for developing partnerships outside of the health care system and the importance of employing community-based participatory methods. In addition to facilitating improvements in individual wellness, mapping community programs also has the potential to improve population health management by healthcare delivery systems such as hospitals, health centers, or public health systems, including city and state departments of health. PMID:24752180

On the design of experiments for determining ternary mixture free energies from static light scattering data using a nonlinear partial differential equation

PubMed Central

Wahle, Chris W.; Ross, David S.; Thurston, George M.

2012-01-01

We mathematically design sets of static light scattering experiments to provide for model-independent measurements of ternary liquid mixing free energies to a desired level of accuracy. A parabolic partial differential equation (PDE), linearized from the full nonlinear PDE [D. Ross, G. Thurston, and C. Lutzer, J. Chem. Phys. 129, 064106 (2008)10.1063/1.2937902], describes how data noise affects the free energies to be inferred. The linearized PDE creates a net of spacelike characteristic curves and orthogonal, timelike curves in the composition triangle, and this net governs diffusion of information coming from light scattering measurements to the free energy. Free energy perturbations induced by a light scattering perturbation diffuse along the characteristic curves and towards their concave sides, with a diffusivity that is proportional to the local characteristic curvature radius. Consequently, static light scattering can determine mixing free energies in regions with convex characteristic curve boundaries, given suitable boundary data. The dielectric coefficient is a Lyapunov function for the dynamical system whose trajectories are PDE characteristics. Information diffusion is heterogeneous and system-dependent in the composition triangle, since the characteristics depend on molecular interactions and are tangent to liquid-liquid phase separation coexistence loci at critical points. We find scaling relations that link free energy accuracy, total measurement time, the number of samples, and the interpolation method, and identify the key quantitative tradeoffs between devoting time to measuring more samples, or fewer samples more accurately. For each total measurement time there are optimal sample numbers beyond which more will not improve free energy accuracy. We estimate the degree to which many-point interpolation and optimized measurement concentrations can improve accuracy and save time. For a modest light scattering setup, a sample calculation shows that less than two minutes of measurement time is, in principle, sufficient to determine the dimensionless mixing free energy of a non-associating ternary mixture to within an integrated error norm of 0.003. These findings establish a quantitative framework for designing light scattering experiments to determine the Gibbs free energy of ternary liquid mixtures. PMID:22830693

ScaleNet: a literature-based model of scale insect biology and systematics.

PubMed

García Morales, Mayrolin; Denno, Barbara D; Miller, Douglass R; Miller, Gary L; Ben-Dov, Yair; Hardy, Nate B

2016-01-01

Scale insects (Hemiptera: Coccoidea) are small herbivorous insects found on all continents except Antarctica. They are extremely invasive, and many species are serious agricultural pests. They are also emerging models for studies of the evolution of genetic systems, endosymbiosis and plant-insect interactions. ScaleNet was launched in 1995 to provide insect identifiers, pest managers, insect systematists, evolutionary biologists and ecologists efficient access to information about scale insect biological diversity. It provides comprehensive information on scale insects taken directly from the primary literature. Currently, it draws from 23,477 articles and describes the systematics and biology of 8194 valid species. For 20 years, ScaleNet ran on the same software platform. That platform is no longer viable. Here, we present a new, open-source implementation of ScaleNet. We have normalized the data model, begun the process of correcting invalid data, upgraded the user interface, and added online administrative tools. These improvements make ScaleNet easier to use and maintain and make the ScaleNet data more accurate and extendable. Database URL: http://scalenet.info. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process

PubMed Central

Chen, Yang; Zhang, Michael Q.

2018-01-01

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. PMID:29440282

Evaluating Differential Effects Using Regression Interactions and Regression Mixture Models

ERIC Educational Resources Information Center

Van Horn, M. Lee; Jaki, Thomas; Masyn, Katherine; Howe, George; Feaster, Daniel J.; Lamont, Andrea E.; George, Melissa R. W.; Kim, Minjung

2015-01-01

Research increasingly emphasizes understanding differential effects. This article focuses on understanding regression mixture models, which are relatively new statistical methods for assessing differential effects by comparing results to using an interactive term in linear regression. The research questions which each model answers, their…

mapDIA: Preprocessing and statistical analysis of quantitative proteomics data from data independent acquisition mass spectrometry.

PubMed

Teo, Guoshou; Kim, Sinae; Tsou, Chih-Chiang; Collins, Ben; Gingras, Anne-Claude; Nesvizhskii, Alexey I; Choi, Hyungwon

2015-11-03

Data independent acquisition (DIA) mass spectrometry is an emerging technique that offers more complete detection and quantification of peptides and proteins across multiple samples. DIA allows fragment-level quantification, which can be considered as repeated measurements of the abundance of the corresponding peptides and proteins in the downstream statistical analysis. However, few statistical approaches are available for aggregating these complex fragment-level data into peptide- or protein-level statistical summaries. In this work, we describe a software package, mapDIA, for statistical analysis of differential protein expression using DIA fragment-level intensities. The workflow consists of three major steps: intensity normalization, peptide/fragment selection, and statistical analysis. First, mapDIA offers normalization of fragment-level intensities by total intensity sums as well as a novel alternative normalization by local intensity sums in retention time space. Second, mapDIA removes outlier observations and selects peptides/fragments that preserve the major quantitative patterns across all samples for each protein. Last, using the selected fragments and peptides, mapDIA performs model-based statistical significance analysis of protein-level differential expression between specified groups of samples. Using a comprehensive set of simulation datasets, we show that mapDIA detects differentially expressed proteins with accurate control of the false discovery rates. We also describe the analysis procedure in detail using two recently published DIA datasets generated for 14-3-3β dynamic interaction network and prostate cancer glycoproteome. The software was written in C++ language and the source code is available for free through SourceForge website http://sourceforge.net/projects/mapdia/.This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015 Elsevier B.V. All rights reserved.

Socioeconomic Status and Net Fertility during the Fertility Decline: A Comparative Analysis of Canada, Iceland, Sweden, Norway and the United States

PubMed Central

Dribe, Martin; Hacker, J. David; Scalone, Francesco

2014-01-01

Most previous work on the historical fertility transition has been macro-oriented, using aggregate data to examine economic correlates of demographic behaviour at regional or national levels, while much less has been done using micro data, and specifically looking at behavioural differentials among social groups. In this paper we study at the impact of socioeconomic status on net fertility during the fertility transition in five Northern American and European Countries (Canada, Iceland, Norway, Sweden and the USA). We use micro-level census data in 1900, containing information on number of children by age, occupation of the mother and father, place of residence and household context. The results show highly similar patterns across countries, with the elite and upper middle classes having considerably lower net fertility early in the transition. These patterns remain also after controlling for a range of individual and community-level fertility determinants and geographical unobserved heterogeneity. PMID:24684711

ELASTIC NET FOR COX’S PROPORTIONAL HAZARDS MODEL WITH A SOLUTION PATH ALGORITHM

PubMed Central

Wu, Yichao

2012-01-01

For least squares regression, Efron et al. (2004) proposed an efficient solution path algorithm, the least angle regression (LAR). They showed that a slight modification of the LAR leads to the whole LASSO solution path. Both the LAR and LASSO solution paths are piecewise linear. Recently Wu (2011) extended the LAR to generalized linear models and the quasi-likelihood method. In this work we extend the LAR further to handle Cox’s proportional hazards model. The goal is to develop a solution path algorithm for the elastic net penalty (Zou and Hastie (2005)) in Cox’s proportional hazards model. This goal is achieved in two steps. First we extend the LAR to optimizing the log partial likelihood plus a fixed small ridge term. Then we define a path modification, which leads to the solution path of the elastic net regularized log partial likelihood. Our solution path is exact and piecewise determined by ordinary differential equation systems. PMID:23226932

CKIP-1 suppresses odontoblastic differentiation of dental pulp stem cells via BMP2 pathway and can interact with NRP1.

PubMed

Song, Yihua; Wang, Chenfei; Gu, Zhifeng; Cao, Peipei; Huang, Dan; Feng, Guijuan; Lian, Min; Zhang, Ye; Feng, Xingmei; Gao, Zhenran

2018-05-31

Casein kinase 2 interacting protein-1 (CKIP-1) is a recently discovered intracellular regulator of bone formation, muscle cell differentiation and tumor cell proliferation. Our study aims to identify the inhibition of BMP2-Smad1/5 signaling by CKIP-1 in odontoblastic differentiation of human dental pulp stem cells (DPSCs). DPSCs infected CKIP-1 siRNA or transfected CKIP-1 full-length plasmid were cultured in odontoblastic differentiation medium or added noggin (200 ng/mL) for 21 days. We examined the effects of CKIP-1 on odontoblastic differentiation, mineralized nodules formation and interaction by western blot, real-time polymerase chain reaction (RT-PCR), alkaline phosphatase (ALP) staining, alizarin red S staining and immunoprecipitation. Firstly, we have demonstrated that CKIP-1 expression markedly decreased time-dependently along with cell odontoblastic differentiation. Indeed, the silence of CKIP-1 up-regulated odontoblastic differentiation via BMP2-Smad1/5 signaling, while CKIP-1 over-expression had a negative effect on odontoblastic differentiation of DPSCs. Furthermore, CKIP-1 could interact with Neuropilin-1 (NRP1). This work provides data that it advocates a novel perception on odontoblastic differentiation of DPSCs. Therefore, inhibiting the expression of CKIP-1 may be of great significance to the development of dental caries.

A Comparative Study on Bearing Capacity of Shallow Foundations in Sand from N and ϕ

NASA Astrophysics Data System (ADS)

Sakleshpur, V. A.; Satyanarayana Reddy, C. N. V.

2017-12-01

This work presents a comparative study on the bearing capacity of strip, square, circular footings and raft foundations in sand, estimated from the standard penetration resistance, N, and the angle of shearing resistance, ϕ. The net safe bearing capacity estimated directly from N using Teng's equation is compared with that obtained from ϕ as per IS:6403. Likewise, the net safe settlement pressure determined from IS:8009 (Part 1), based on N, is compared with that attained from the semi-empirical approach of Schmertmann et al. A parametric study quantifies the effects of the standard penetration resistance and the size and depth of foundation on the net safe bearing capacity and the net safe settlement pressure of strip, square, circular footings and raft foundations in sand. Interactive charts are prepared in terms of the standard penetration resistance to highlight the appropriate method for the benefit of civil engineers.

The Politics and Coverage of Terror: From Media Images to Public Consciousness.

ERIC Educational Resources Information Center

Wittebols, James H.

This paper presents a typology of terrorism which is grounded in how media differentially cover each type. The typology challenges some of the basic assumptions, such as that the media "allow" themselves to be exploited by terrorists and "encourage" terrorism, and the conventional wisdom about the net effects of the media's…

Have Asian American Men Achieved Labor Market Parity with White Men?

ERIC Educational Resources Information Center

Kim, ChangHwan; Sakamoto, Arthur

2010-01-01

We use the 2003 National Survey of College Graduates to investigate earnings differentials between white and Asian American men. We extend prior literature by disaggregating Asian Americans by their immigration status in relation to the U.S. educational system, and by accounting for the effects of field of study and college type. Net of the latter…

Constructing Cost-Effective and Targetable ICS Honeypots Suited for Production Networks

DTIC Science & Technology

2015-03-26

introducing Honeyd+ has a marginal impact on performance. Notable findings are that the Raspberry Pi is the preferred hosting platform for the EtherNet/IP... Raspberry Pi or Gumstix, which is a low-cost approach to replicating multiple decoys. One hidden drawback to low- interaction honeypots is the extensive time...EtherNet/IP industrial protocol. Honeyd+ is hosted on a low-cost computing platform ( Raspberry Pi running Raspbian, approximately $50) and a high-cost

Leptogenesis from spin-gravity coupling following inflation.

PubMed

Mohanty, Subhendra; Prasanna, A R; Lambiase, G

2006-02-24

The energy levels of the left- and the right-handed neutrinos are split in the background of gravitational waves generated during inflation, which, in presence of lepton-number-violating interactions, gives rise to a net lepton asymmetry at equilibrium. Lepton number violation is achieved by the same dimension five operator which gives rise to neutrino masses after electroweak symmetry breaking. A net baryon asymmetry of the same magnitude can be generated from this lepton asymmetry by electroweak sphaleron processes.

Petri Nets as Modeling Tool for Emergent Agents

NASA Technical Reports Server (NTRS)

Bergman, Marto

2004-01-01

Emergent agents, those agents whose local interactions can cause unexpected global results, require a method of modeling that is both dynamic and structured Petri Nets, a modeling tool developed for dynamic discrete event system of mainly functional agents, provide this, and have the benefit of being an established tool. We present here the details of the modeling method here and discuss how to implement its use for modeling agent-based systems. Petri Nets have been used extensively in the modeling of functional agents, those agents who have defined purposes and whose actions should result in a know outcome. However, emergent agents, those agents who have a defined structure but whose interaction causes outcomes that are unpredictable, have not yet found a modeling style that suits them. A problem with formally modeling emergent agents that any formal modeling style usually expects to show the results of a problem and the results of problems studied using emergent agents are not apparent from the initial construction. However, the study of emergent agents still requires a method to analyze the agents themselves, and have sensible conversation about the differences and similarities between types of emergent agents. We attempt to correct this problem by applying Petri Nets to the characterization of emergent agents. In doing so, the emergent properties of these agents can be highlighted, and conversation about the nature and compatibility of the differing methods of agent creation can begin.

GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response.

PubMed

Zaag, Rim; Tamby, Jean Philippe; Guichard, Cécile; Tariq, Zakia; Rigaill, Guillem; Delannoy, Etienne; Renou, Jean-Pierre; Balzergue, Sandrine; Mary-Huard, Tristan; Aubourg, Sébastien; Martin-Magniette, Marie-Laure; Brunaud, Véronique

2015-01-01

CATdb (http://urgv.evry.inra.fr/CATdb) is a database providing a public access to a large collection of transcriptomic data, mainly for Arabidopsis but also for other plants. This resource has the rare advantage to contain several thousands of microarray experiments obtained with the same technical protocol and analyzed by the same statistical pipelines. In this paper, we present GEM2Net, a new module of CATdb that takes advantage of this homogeneous dataset to mine co-expression units and decipher Arabidopsis gene functions. GEM2Net explores 387 stress conditions organized into 18 biotic and abiotic stress categories. For each one, a model-based clustering is applied on expression differences to identify clusters of co-expressed genes. To characterize functions associated with these clusters, various resources are analyzed and integrated: Gene Ontology, subcellular localization of proteins, Hormone Families, Transcription Factor Families and a refined stress-related gene list associated to publications. Exploiting protein-protein interactions and transcription factors-targets interactions enables to display gene networks. GEM2Net presents the analysis of the 18 stress categories, in which 17,264 genes are involved and organized within 681 co-expression clusters. The meta-data analyses were stored and organized to compose a dynamic Web resource. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Assessment and statistics of surgically induced astigmatism.

PubMed

Naeser, Kristian

2008-05-01

The aim of the thesis was to develop methods for assessment of surgically induced astigmatism (SIA) in individual eyes, and in groups of eyes. The thesis is based on 12 peer-reviewed publications, published over a period of 16 years. In these publications older and contemporary literature was reviewed(1). A new method (the polar system) for analysis of SIA was developed. Multivariate statistical analysis of refractive data was described(2-4). Clinical validation studies were performed. The description of a cylinder surface with polar values and differential geometry was compared. The main results were: refractive data in the form of sphere, cylinder and axis may define an individual patient or data set, but are unsuited for mathematical and statistical analyses(1). The polar value system converts net astigmatisms to orthonormal components in dioptric space. A polar value is the difference in meridional power between two orthogonal meridians(5,6). Any pair of polar values, separated by an arch of 45 degrees, characterizes a net astigmatism completely(7). The two polar values represent the net curvital and net torsional power over the chosen meridian(8). The spherical component is described by the spherical equivalent power. Several clinical studies demonstrated the efficiency of multivariate statistical analysis of refractive data(4,9-11). Polar values and formal differential geometry describe astigmatic surfaces with similar concepts and mathematical functions(8). Other contemporary methods, such as Long's power matrix, Holladay's and Alpins' methods, Zernike(12) and Fourier analyses(8), are correlated to the polar value system. In conclusion, analysis of SIA should be performed with polar values or other contemporary component systems. The study was supported by Statens Sundhedsvidenskabeligt Forskningsråd, Cykelhandler P. Th. Rasmussen og Hustrus Mindelegat, Hotelejer Carl Larsen og Hustru Nicoline Larsens Mindelegat, Landsforeningen til Vaern om Synet, Forskningsinitiativet for Arhus Amt, Alcon Denmark, and Desirée and Niels Ydes Fond.

Urban growth in Korea, 1970-1980: an application of the human ecological perspective.

PubMed

Ko, S H

1994-07-01

This study supports the ecological perspective proposed by Duncan (population, environment, organization, and technology) explaining urban population growth. Data were obtained from the 1970 and 1980 Korean Population Census and Korean Municipal Yearbook on cities with a minimum size of 20,000-50,000 people (108 cities and towns). Urban growth is most strongly influenced by indigenous labor surplus and the population potential of the city to be in contact with another city. Nine multiple regression variables explained just under 66% of the variance in urban growth. Net migration was influential among those aged 15-24 years. The extent of differentiation of industry affected net migration only among those aged 15-24 years and those aged 35-44 years. Population redistribution was more affected directly by changes in industrial organization, and migration was affected indirectly by environmental and technological effects on organization. Urban growth through migration of older age groups was affected by government expenditure on public works. Urban growth was not much affected by transportation/communication concentration, manufacturing concentration, urban labor surplus, population size, and site. Urban growth was viewed as the interaction between the unemployment rate and the urban wage, following Todaro's equilibrium models. In Korea, larger cities only grew faster during the 1960s. By the 1970s, upper middle-sized cities grew faster. Location was not a significant factor in explaining urban growth, but growth was rapid along a corridor within 100 km from Seoul and 50 km from Pusan, the second largest city in Korea. Caution was urged in interpreting Korea's ecological urban growth patterns as indicative of developing countries.

Net carbon exchange across the Arctic tundra-boreal forest transition in Alaska 1981-2000

USGS Publications Warehouse

Thompson, Catharine Copass; McGuire, A.D.; Clein, Joy S.; Chapin, F. S.; Beringer, J.

2006-01-01

Shifts in the carbon balance of high-latitude ecosystems could result from differential responses of vegetation and soil processes to changing moisture and temperature regimes and to a lengthening of the growing season. Although shrub expansion and northward movement of treeline should increase carbon inputs, the effects of these vegetation changes on net carbon exchange have not been evaluated. We selected low shrub, tall shrub, and forest tundra sites near treeline in northwestern Alaska, representing the major structural transitions expected in response to warming. In these sites, we measured aboveground net primary production (ANPP) and vegetation and soil carbon and nitrogen pools, and used these data to parameterize the Terrestrial Ecosystem Model. We simulated the response of carbon balance components to air temperature and precipitation trends during 1981-2000. In areas experiencing warmer and dryer conditions, Net Primary Production (NPP) decreased and heterotrophic respiration (R H ) increased, leading to a decrease in Net Ecosystem Production (NEP). In warmer and wetter conditions NPP increased, but the response was exceeded by an increase in R H ; therefore, NEP also decreased. Lastly, in colder and wetter regions, the increase in NPP exceeded a small decline in R H , leading to an increase in NEP. The net effect for the region was a slight gain in ecosystem carbon storage over the 20 year period. This research highlights the potential importance of spatial variability in ecosystem responses to climate change in assessing the response of carbon storage in northern Alaska over the last two decades. ?? Springer 2005.

Ariadne's Thread and Indra's Net: Reflections on Ethnography, Ethnicity, Identity, Culture, and Interaction.

ERIC Educational Resources Information Center

Moerman, Michael

1993-01-01

Defines and illustrates the main tools used in intercultural research: ethnography, ethnicity, social interaction, identity, and culture. These are the ongoing product of intersecting processes. All are social accomplishments, influenced by the context in which they occur. The anthropologist and native jointly participate in these enterprises. (17…

Effects of Diversity Experiences on Critical Thinking Skills: Who Benefits?

ERIC Educational Resources Information Center

Loes, Chad; Pascarella, Ernest; Umbach, Paul

2012-01-01

This study analyzed data from the Wabash National Study of Liberal Arts Education to estimate the unique effects of exposure to classroom diversity and involvement in interactional diversity on growth in critical thinking skills during the first year of college. Net of important confounding influences, neither classroom nor interactional diversity…

Ratchet Effects in Active Matter Systems

DOE PAGES

Reichhardt, Cynthia Jane; Reichhardt, Charles

2016-12-21

Ratchet effects can arise for single or collectively interacting Brownian particles on an asymmetric substrate when a net dc transport is produced by an externally applied ac driving force or by periodically flashing the substrate. Recently, a new class of active ratchet systems that do not require the application of external driving has been realized through the use of active matter; they are self-propelled units that can be biological or nonbiological in nature. When active materials such as swimming bacteria interact with an asymmetric substrate, a net dc directed motion can arise even without external driving, opening a wealth ofmore » possibilities such as sorting, cargo transport, or micromachine construction. We review the current status of active matter ratchets for swimming bacteria, cells, active colloids, and swarming models, focusing on the role of particle-substrate interactions. Here, we describe ratchet reversals produced by collective effects and the use of active ratchets to transport passive particles. We discuss future directions including deformable substrates or particles, the role of different swimming modes, varied particle–particle interactions, and nondissipative effects.« less

Disentangling the effects of shrubs and herbivores on tree regeneration in a dry Chaco forest (Argentina).

PubMed

Tálamo, Andrés; Barchuk, Alicia H; Garibaldi, Lucas A; Trucco, Carlos E; Cardozo, Silvana; Mohr, Federico

2015-07-01

Successful persistence of dry forests depends on tree regeneration, which depends on a balance of complex biotic interactions. In particular, the relative importance and interactive effects of shrubs and herbivores on tree regeneration are unclear. In a manipulative study, we investigated if thornless shrubs have a direct net effect, an indirect positive effect mediated by livestock, and/or an indirect negative effect mediated by small vertebrates on tree regeneration of two key species of Chaco forest (Argentina). In a spatial association study, we also explored the existence of net positive interactions from thorny and thornless shrubs. The number of Schinopsis lorentzii seedlings was highest under artificial shade with native herbivores and livestock excluded. Even excluding livestock, no seedlings were found with natural conditions (native herbivores present with natural shade or direct sunlight) at the end of the experiment. Surprisingly, seedling recruitment was not enhanced under thornless shrubs, because there was a complementary positive effect of shade and interference. Moreover, thornless shrubs had neither positive nor negative effects on regeneration of S. lorentzii. Regeneration of Aspidosperma quebracho-blanco was minimal in all treatments. In agreement with the experiment, spatial distributions of saplings of both tree species were independent of thornless shrubs, but positively associated with thorny shrubs. Our results suggest that in general thornless shrubs may have a negligible effect and thorny shrubs a net positive effect on tree regeneration in dry forests. These findings provide a conceptual framework for testing the impact of biotic interactions on seedling recruitment in other dry forests.

Quantitative prediction of repaglinide-rifampicin complex drug interactions using dynamic and static mechanistic models: delineating differential CYP3A4 induction and OATP1B1 inhibition potential of rifampicin.

PubMed

Varma, Manthena V S; Lin, Jian; Bi, Yi-An; Rotter, Charles J; Fahmi, Odette A; Lam, Justine L; El-Kattan, Ayman F; Goosen, Theunis C; Lai, Yurong

2013-05-01

Repaglinide is mainly metabolized by cytochrome P450 enzymes CYP2C8 and CYP3A4, and it is also a substrate to a hepatic uptake transporter, organic anion transporting polypeptide (OATP)1B1. The purpose of this study is to predict the dosing time-dependent pharmacokinetic interactions of repaglinide with rifampicin, using mechanistic models. In vitro hepatic transport of repaglinide, characterized using sandwich-cultured human hepatocytes, and intrinsic metabolic parameters were used to build a dynamic whole-body physiologically-based pharmacokinetic (PBPK) model. The PBPK model adequately described repaglinide plasma concentration-time profiles and successfully predicted area under the plasma concentration-time curve ratios of repaglinide (within ± 25% error), dosed (staggered 0-24 hours) after rifampicin treatment when primarily considering induction of CYP3A4 and reversible inhibition of OATP1B1 by rifampicin. Further, a static mechanistic "extended net-effect" model incorporating transport and metabolic disposition parameters of repaglinide and interaction potency of rifampicin was devised. Predictions based on the static model are similar to those observed in the clinic (average error ∼19%) and to those based on the PBPK model. Both the models suggested that the combined effect of increased gut extraction and decreased hepatic uptake caused minimal repaglinide systemic exposure change when repaglinide is dosed simultaneously or 1 hour after the rifampicin dose. On the other hand, isolated induction effect as a result of temporal separation of the two drugs translated to an approximate 5-fold reduction in repaglinide systemic exposure. In conclusion, both dynamic and static mechanistic models are instrumental in delineating the quantitative contribution of transport and metabolism in the dosing time-dependent repaglinide-rifampicin interactions.

Silk ionomers for encapsulation and differentiation of human MSCs

PubMed Central

Calabrese, Rossella; Kaplan, David L.

2012-01-01

The response of human bone marrow derived human mesenchymal stem cells (hMSCs) encapsulated in silk ionomer hydrogels was studied. Silk aqueous solutions with silk-poly-L-lysine or silk-poly-L-glutamate were formed into hydrogels via ultrasonication in situ with different net charges. hMSCs were encapsulated within the hydrogels and the impact of matrix charge was assessed over weeks in osteogenic, adipogenic and maintenance growth media. These modified silk charged polymers supported cell viability and proliferative potential, and the hMSCs were able to differentiate toward osteogenic or adipogenic lineages in the corresponding differentiation media. The silk/silk-poly-L-lysine hydrogels exhibited a positive effect on selective osteogenesis of hMSCs, inducing differentiation toward an osteogenic lineage even in the absence of osteogenic supplements, while also inhibiting adipogenesis. In contrast, silk/silk fibroin-poly-L-glutamate hydrogels supported both osteogenic and adipogenic differentiation of hMSCs when cultured under induction conditions. The results demonstrate the potential utility of silk-based ionomers in gel formats for hMSCs encapsulation and for directing hMSCs long term functional differentiation toward specific lineages. PMID:22824008

SkyNet: A Modular Nuclear Reaction Network Library

NASA Astrophysics Data System (ADS)

Lippuner, Jonas; Roberts, Luke F.

2017-12-01

Almost all of the elements heavier than hydrogen that are present in our solar system were produced by nuclear burning processes either in the early universe or at some point in the life cycle of stars. In all of these environments, there are dozens to thousands of nuclear species that interact with each other to produce successively heavier elements. In this paper, we present SkyNet, a new general-purpose nuclear reaction network that evolves the abundances of nuclear species under the influence of nuclear reactions. SkyNet can be used to compute the nucleosynthesis evolution in all astrophysical scenarios where nucleosynthesis occurs. SkyNet is free and open source, and aims to be easy to use and flexible. Any list of isotopes can be evolved, and SkyNet supports different types of nuclear reactions. SkyNet is modular so that new or existing physics, like nuclear reactions or equations of state, can easily be added or modified. Here, we present in detail the physics implemented in SkyNet with a focus on a self-consistent transition to and from nuclear statistical equilibrium to non-equilibrium nuclear burning, our implementation of electron screening, and coupling of the network to an equation of state. We also present comprehensive code tests and comparisons with existing nuclear reaction networks. We find that SkyNet agrees with published results and other codes to an accuracy of a few percent. Discrepancies, where they exist, can be traced to differences in the physics implementations.

Deep feature classification of angiomyolipoma without visible fat and renal cell carcinoma in abdominal contrast-enhanced CT images with texture image patches and hand-crafted feature concatenation.

PubMed

Lee, Hansang; Hong, Helen; Kim, Junmo; Jung, Dae Chul

2018-04-01

To develop an automatic deep feature classification (DFC) method for distinguishing benign angiomyolipoma without visible fat (AMLwvf) from malignant clear cell renal cell carcinoma (ccRCC) from abdominal contrast-enhanced computer tomography (CE CT) images. A dataset including 80 abdominal CT images of 39 AMLwvf and 41 ccRCC patients was used. We proposed a DFC method for differentiating the small renal masses (SRM) into AMLwvf and ccRCC using the combination of hand-crafted and deep features, and machine learning classifiers. First, 71-dimensional hand-crafted features (HCF) of texture and shape were extracted from the SRM contours. Second, 1000-4000-dimensional deep features (DF) were extracted from the ImageNet pretrained deep learning model with the SRM image patches. In DF extraction, we proposed the texture image patches (TIP) to emphasize the texture information inside the mass in DFs and reduce the mass size variability. Finally, the two features were concatenated and the random forest (RF) classifier was trained on these concatenated features to classify the types of SRMs. The proposed method was tested on our dataset using leave-one-out cross-validation and evaluated using accuracy, sensitivity, specificity, positive predictive values (PPV), negative predictive values (NPV), and area under receiver operating characteristics curve (AUC). In experiments, the combinations of four deep learning models, AlexNet, VGGNet, GoogleNet, and ResNet, and four input image patches, including original, masked, mass-size, and texture image patches, were compared and analyzed. In qualitative evaluation, we observed the change in feature distributions between the proposed and comparative methods using tSNE method. In quantitative evaluation, we evaluated and compared the classification results, and observed that (a) the proposed HCF + DF outperformed HCF-only and DF-only, (b) AlexNet showed generally the best performances among the CNN models, and (c) the proposed TIPs not only achieved the competitive performances among the input patches, but also steady performance regardless of CNN models. As a result, the proposed method achieved the accuracy of 76.6 ± 1.4% for the proposed HCF + DF with AlexNet and TIPs, which improved the accuracy by 6.6%p and 8.3%p compared to HCF-only and DF-only, respectively. The proposed shape features and TIPs improved the HCFs and DFs, respectively, and the feature concatenation further enhanced the quality of features for differentiating AMLwvf from ccRCC in abdominal CE CT images. © 2018 American Association of Physicists in Medicine.

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process.

PubMed

Djekidel, Mohamed Nadhir; Chen, Yang; Zhang, Michael Q

2018-02-12

Polymer-based simulations and experimental studies indicate the existence of a spatial dependency between the adjacent DNA fibers involved in the formation of chromatin loops. However, the existing strategies for detecting differential chromatin interactions assume that the interacting segments are spatially independent from the other segments nearby. To resolve this issue, we developed a new computational method, FIND, which considers the local spatial dependency between interacting loci. FIND uses a spatial Poisson process to detect differential chromatin interactions that show a significant difference in their interaction frequency and the interaction frequency of their neighbors. Simulation and biological data analysis show that FIND outperforms the widely used count-based methods and has a better signal-to-noise ratio. © 2018 Djekidel et al.; Published by Cold Spring Harbor Laboratory Press.

Health safety nets can break cycles of poverty and disease: a stochastic ecological model.

PubMed

Plucinski, Mateusz M; Ngonghala, Calistus N; Bonds, Matthew H

2011-12-07

The persistence of extreme poverty is increasingly attributed to dynamic interactions between biophysical processes and economics, though there remains a dearth of integrated theoretical frameworks that can inform policy. Here, we present a stochastic model of disease-driven poverty traps. Whereas deterministic models can result in poverty traps that can only be broken by substantial external changes to the initial conditions, in the stochastic model there is always some probability that a population will leave or enter a poverty trap. We show that a 'safety net', defined as an externally enforced minimum level of health or economic conditions, can guarantee ultimate escape from a poverty trap, even if the safety net is set within the basin of attraction of the poverty trap, and even if the safety net is only in the form of a public health measure. Whereas the deterministic model implies that small improvements in initial conditions near the poverty-trap equilibrium are futile, the stochastic model suggests that the impact of changes in the location of the safety net on the rate of development may be strongest near the poverty-trap equilibrium.

Polyamines Interact with Hydroxyl Radicals in Activating Ca2+ and K+ Transport across the Root Epidermal Plasma Membranes1[W

PubMed Central

Zepeda-Jazo, Isaac; Velarde-Buendía, Ana María; Enríquez-Figueroa, René; Bose, Jayakumar; Shabala, Sergey; Muñiz-Murguía, Jesús; Pottosin, Igor I.

2011-01-01

Reactive oxygen species (ROS) are integral components of the plant adaptive responses to environment. Importantly, ROS affect the intracellular Ca2+ dynamics by activating a range of nonselective Ca2+-permeable channels in plasma membrane (PM). Using patch-clamp and noninvasive microelectrode ion flux measuring techniques, we have characterized ionic currents and net K+ and Ca2+ fluxes induced by hydroxyl radicals (OH•) in pea (Pisum sativum) roots. OH•, but not hydrogen peroxide, activated a rapid Ca2+ efflux and a more slowly developing net Ca2+ influx concurrent with a net K+ efflux. In isolated protoplasts, OH• evoked a nonselective current, with a time course and a steady-state magnitude similar to those for a K+ efflux in intact roots. This current displayed a low ionic selectivity and was permeable to Ca2+. Active OH•-induced Ca2+ efflux in roots was suppressed by the PM Ca2+ pump inhibitors eosine yellow and erythrosine B. The cation channel blockers gadolinium, nifedipine, and verapamil and the anionic channel blockers 5-nitro-2(3-phenylpropylamino)-benzoate and niflumate inhibited OH•-induced ionic currents in root protoplasts and K+ efflux and Ca2+ influx in roots. Contrary to expectations, polyamines (PAs) did not inhibit the OH•-induced cation fluxes. The net OH•-induced Ca2+ efflux was largely prolonged in the presence of spermine, and all PAs tested (spermine, spermidine, and putrescine) accelerated and augmented the OH•-induced net K+ efflux from roots. The latter effect was also observed in patch-clamp experiments on root protoplasts. We conclude that PAs interact with ROS to alter intracellular Ca2+ homeostasis by modulating both Ca2+ influx and efflux transport systems at the root cell PM. PMID:21980172

COMPUTATIONAL MODELING OF CATHODIC LIMITATIONS ON LOCALIZED CORROSION OF WETTED SS 316L, AT ROOM TEMPERATURE

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

F. Cui; F.J. Presuel-Moreno; R.G. Kelly

2005-10-13

The ability of a SS316L surface wetted with a thin electrolyte layer to serve as an effective cathode for an active localized corrosion site was studied computationally. The dependence of the total net cathodic current, I{sub net}, supplied at the repassivation potential E{sub rp} (of the anodic crevice) on relevant physical parameters including water layer thickness (WL), chloride concentration ([Cl{sup -}]) and length of cathode (Lc) were investigated using a three-level, full factorial design. The effects of kinetic parameters including the exchange current density (i{sub o,c}) and Tafel slope ({beta}{sub c}) of oxygen reduction, the anodic passive current density (i{submore » p}) (on the cathodic surface), and E{sub rp} were studied as well using three-level full factorial designs of [Cl{sup -}] and Lc with a fixed WL of 25 {micro}m. The study found that all the three parameters WL, [Cl{sup -}] and Lc as well as the interactions of Lc x WL and Lc x [Cl{sup -}] had significant impact on I{sub net}. A five-factor regression equation was obtained which fits the computation results reasonably well, but demonstrated that interactions are more complicated than can be explained with a simple linear model. Significant effects on I{sub net} were found upon varying either i{sub o,c}, {beta}{sub c}, or E{sub rp}, whereas i{sub p} in the studied range was found to have little impact. It was observed that I{sub net} asymptotically approached maximum values (I{sub max}) when Lc increased to critical minimum values. I{sub max} can be used to determine the stability of coupled localized corrosion and the critical Lc provides important information for experimental design and corrosion protection.« less

Brief narrative exposure therapy for posttraumatic stress in Iraqi refugees: a preliminary randomized clinical trial.

PubMed

Hijazi, Alaa M; Lumley, Mark A; Ziadni, Maisa S; Haddad, Luay; Rapport, Lisa J; Arnetz, Bengt B

2014-06-01

Many Iraqi refugees suffer from posttraumatic stress. Efficient, culturally sensitive interventions are needed, and so we adapted narrative exposure therapy into a brief version (brief NET) and tested its effects in a sample of traumatized Iraqi refugees. Iraqi refugees in the United States reporting elevated posttraumatic stress (N = 63) were randomized to brief NET or waitlist control conditions in a 2:1 ratio; brief NET was 3 sessions, conducted individually, in Arabic. Positive indicators (posttraumatic growth and well-being) and symptoms (posttraumatic stress, depressive, and somatic) were assessed at baseline and 2- and 4-month follow-up. Treatment participation (95.1% completion) and study retention (98.4% provided follow-up data) were very high. Significant condition by time interactions showed that those receiving brief NET had greater posttraumatic growth (d = 0.83) and well-being (d = 0.54) through 4 months than controls. Brief NET reduced symptoms of posttraumatic stress (d = -0.48) and depression (d = -0.46) more, but only at 2 months; symptoms of controls also decreased from 2 to 4 months, eliminating condition differences at 4 months. Three sessions of brief NET increased growth and well-being and led to symptom reduction in highly traumatized Iraqi refugees. This preliminary study suggests that brief NET is both acceptable and potentially efficacious in traumatized Iraqi refugees. Copyright © 2014 International Society for Traumatic Stress Studies.

Optimal management of reconfigurable manufacturing system modeling with Petri nets developed three-dimensional - RPD3D

NASA Astrophysics Data System (ADS)

Teodor, F.; Marinescu, V.; Epureanu, A.

2016-11-01

Modeling of reconfigurable manufacturing systems would have done using existing Petri net types, but the complexity and dynamics of the new manufacturing system, mainly data reconfiguration feature, required looking for a more compact representation with many variables that to model as accurately not only the normal operation of the production system but can capture and model and reconfiguration process. Thus, it was necessary to create a new class of Petri nets, called RPD3D (Developed Petri nets with three dimensional) showing the name of both lineage (new class derived from Petri nets developed, created in 2000 by Prof. Dr. Ing Vasile Marinescu in his doctoral thesis) [1], but the most important of the new features defining (transformation from one 2D model into a 3D model).The idea was to introduce the classical model of a Petri third dimension to be able to overlay multiple levels (layers) formed in 2D or 3D Petri nets that interact with each other (receiving or giving commands to enable or disable the various modules together simulating the operation of reconfigurable manufacturing systems). The aim is to present a new type of Petri nets called RPD3D - Developed Petri three-dimensional model used for optimal control and simulation of reconfigurable manufacturing systems manufacture of products such systems.

An online spacecraft environment interactions information system

NASA Technical Reports Server (NTRS)

Lauriente, Michael

1990-01-01

This paper reviews the role that EnviroNET assumes as a contemporary system that scientists and engineers can use to share information on networks that are connected globally. Advantage is being taken to use this powerful communication tool for the space community to articulate the various anomalies that our space systems are experiencing. EnviroNET is being considered as a test bed for developing an expert system for diagnosing environmentally induced anomalies for spacecraft. The various offline activities in progress toward this objective are described.

Point-Process Models of Social Network Interactions: Parameter Estimation and Missing Data Recovery

DTIC Science & Technology

2014-08-01

treating them as zero will have a de minimis impact on the results, but avoiding computing them (and computing with them) saves tremendous time. Set a... test the methods on simulated time series on artificial social networks, including some toy networks and some meant to resemble IkeNet. We conclude...the section by discussing the results in detail. In each of our tests we begin with a complete data set, whether it is real (IkeNet) or simulated. Then

DNA bending-induced phase transition of encapsidated genome in phage λ

PubMed Central

Lander, Gabriel C.; Johnson, John E.; Rau, Donald C.; Potter, Clinton S.; Carragher, Bridget; Evilevitch, Alex

2013-01-01

The DNA structure in phage capsids is determined by DNA–DNA interactions and bending energy. The effects of repulsive interactions on DNA interaxial distance were previously investigated, but not the effect of DNA bending on its structure in viral capsids. By varying packaged DNA length and through addition of spermine ions, we transform the interaction energy from net repulsive to net attractive. This allowed us to isolate the effect of bending on the resulting DNA structure. We used single particle cryo-electron microscopy reconstruction analysis to determine the interstrand spacing of double-stranded DNA encapsidated in phage λ capsids. The data reveal that stress and packing defects, both resulting from DNA bending in the capsid, are able to induce a long-range phase transition in the encapsidated DNA genome from a hexagonal to a cholesteric packing structure. This structural observation suggests significant changes in genome fluidity as a result of a phase transition affecting the rates of viral DNA ejection and packaging. PMID:23449219

Atlas of the Earth's radiation budget as measured by Nimbus-7: May 1979 to May 1980

NASA Technical Reports Server (NTRS)

Kyle, H. Lee; Hucek, Richard R.; Vallette, Brenda J.

1991-01-01

This atlas describes the seasonal changes in the Earth's radiation budget for the 13-month period, May 1979 to May 1980. It helps to illustrate the strong feedback mechanisms by which the Earth's climate interacts with the top-of-the-atmosphere insolation to modify the energy that various regions absorb from the Sun. Cloud type and cloud amount, which are linked to the surface temperature and the regional climate, are key elements in this interaction. Annual, seasonal, and monthly maps of the albedo, outgoing longwave and net radiation, noontime cloud cover, and mean diurnal surface temperatures are presented. Annual and seasonal net cloud forcing maps are also given. All of the quantities were derived from Nimbus-7 satellite measurements except for the temperatures, which were used in the cloud detection algorithm and came originally from the Air Force 3-dimensional nephanalysis dataset. The seasonal changes are described. The interaction of clouds and the radiation budget is briefly discussed.

Passing messages between biological networks to refine predicted interactions.

PubMed

Glass, Kimberly; Huttenhower, Curtis; Quackenbush, John; Yuan, Guo-Cheng

2013-01-01

Regulatory network reconstruction is a fundamental problem in computational biology. There are significant limitations to such reconstruction using individual datasets, and increasingly people attempt to construct networks using multiple, independent datasets obtained from complementary sources, but methods for this integration are lacking. We developed PANDA (Passing Attributes between Networks for Data Assimilation), a message-passing model using multiple sources of information to predict regulatory relationships, and used it to integrate protein-protein interaction, gene expression, and sequence motif data to reconstruct genome-wide, condition-specific regulatory networks in yeast as a model. The resulting networks were not only more accurate than those produced using individual data sets and other existing methods, but they also captured information regarding specific biological mechanisms and pathways that were missed using other methodologies. PANDA is scalable to higher eukaryotes, applicable to specific tissue or cell type data and conceptually generalizable to include a variety of regulatory, interaction, expression, and other genome-scale data. An implementation of the PANDA algorithm is available at www.sourceforge.net/projects/panda-net.

The Calibration Units of the KM3NeT neutrino telescope

NASA Astrophysics Data System (ADS)

Baret, B.; Keller, P.; Clark, M. Lindsey

2016-04-01

KM3NeT is a network of deep-sea neutrino telescopes to be deployed in the Mediterranean Sea that will perform neutrino astronomy and oscillation studies. It consists of three-dimensional arrays of thousands of optical modules that detect the Cherenkov light induced by charged particles resulting from the interaction of a neutrino with the surrounding medium. The performance of the neutrino telescope relies on the precise timing and positioning calibration of the detector elements. Other environmental conditions which may affect light and sound transmission, such as water temperature and salinity, must also be continuously monitored. This contribution describes the technical design of the first Calibration Unit, to be deployed on the French site as part of KM3NeT Phase 1.

Real options approach to inter-sectoral migration of U.S.farm labor

Treesearch

Gulcan Onel; Barry K. Goodwin

2014-01-01

The core of the literature on inter-sectoral labor migration is based on net present value models of investment in which individuals are assumed to migrate to take advantage of positive wage differentials. In this article, we argue that a real options approach, taken together with the adjustment costs associated with sectoral relocation, may provide a basis for...

A Multination Study of Socioeconomic Inequality in Expectations for Progression to Higher Education: The Role of Between-School Tracking and Ability Stratification

ERIC Educational Resources Information Center

Parker, Philip D.; Jerrim, John; Schoon, Ingrid; Marsh, Herbert W.

2016-01-01

Persistent inequalities in educational expectations across societies are a growing concern. Recent research has explored the extent to which inequalities in education are due to primary effects (i.e., achievement differentials) versus secondary effects (i.e., choice behaviors net of achievement). We explore educational expectations in order to…

Differential effects of canopy trimming and litter deposition on litterfall and nutrient dynamics in a wet subtropical forest

Treesearch

W.L. Silver; S.J. Hall; Grizelle Gonzalez

2014-01-01

Humid tropical forests have the highest rates of litterfall production globally, which fuels rapid nutrient recycling and high net ecosystem production. Severe storm events significantly alter patterns in litterfall mass and nutrient dynamics through a combination of canopy disturbance and litter deposition. In this study, we used a large-scale long-term manipulation...

Interactive Multimedia in University Teaching and Learning: Some Pointers to Help Promote Discussion of Design Criteria.

ERIC Educational Resources Information Center

Trevitt, Chris

This paper addresses criteria in the design and development of computer-based courseware. The term "interactive multimedia" describes both the technology and the demands placed on the user. It implies that the user becomes actively engaged with the subject, thereby improving the likelihood that net learning takes place. However, nothing…

Helping Second Language Literature Learners Overcome E-Learning Difficulties: LET-NET Team Teaching with Online Peer Interaction

ERIC Educational Resources Information Center

Wu, Pin-Hsiang Natalie; Marek, Michael W.

2013-01-01

This study presents and discusses results from an EFL second language literature program in which the instructional design included a team teaching scheme, blended learning practice, and computer-mediated peer-interaction. The team teaching plan used a Mandarin speaking English teacher and a Native English-speaking teacher collaborating and…

Trait-based diversification shifts reflect differential extinction among fossil taxa.

PubMed

Wagner, Peter J; Estabrook, George F

2014-11-18

Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models.

Space geodesy validation of the global lithospheric flow

NASA Astrophysics Data System (ADS)

Crespi, M.; Cuffaro, M.; Doglioni, C.; Giannone, F.; Riguzzi, F.

2007-02-01

Space geodesy data are used to verify whether plates move chaotically or rather follow a sort of tectonic mainstream. While independent lines of geological evidence support the existence of a global ordered flow of plate motions that is westerly polarized, the Terrestrial Reference Frame (TRF) presents limitations in describing absolute plate motions relative to the mantle. For these reasons we jointly estimated a new plate motions model and three different solutions of net lithospheric rotation. Considering the six major plate boundaries and variable source depths of the main Pacific hotspots, we adapted the TRF plate kinematics by global space geodesy to absolute plate motions models with respect to the mantle. All three reconstructions confirm (i) the tectonic mainstream and (ii) the net rotation of the lithosphere. We still do not know the precise trend of this tectonic flow and the velocity of the differential rotation. However, our results show that assuming faster Pacific motions, as the asthenospheric source of the hotspots would allow, the best lithospheric net rotation estimate is 13.4 +/- 0.7 cm yr-1. This superfast solution seems in contradiction with present knowledge on the lithosphere decoupling, but it matches remarkably better with the geological constraints than those retrieved with slower Pacific motion and net rotation estimates. Assuming faster Pacific motion, it is shown that all plates move orderly `westward' along the tectonic mainstream at different velocities and the equator of the lithospheric net rotation lies inside the corresponding tectonic mainstream latitude band (~ +/-7°), defined by the 1σ confidence intervals.

Nutrient pollution disrupts key ecosystem functions on coral reefs.

PubMed

Silbiger, Nyssa J; Nelson, Craig E; Remple, Kristina; Sevilla, Jessica K; Quinlan, Zachary A; Putnam, Hollie M; Fox, Michael D; Donahue, Megan J

2018-06-13

There is a long history of examining the impacts of nutrient pollution and pH on coral reefs. However, little is known about how these two stressors interact and influence coral reef ecosystem functioning. Using a six-week nutrient addition experiment, we measured the impact of elevated nitrate (NO - 3 ) and phosphate (PO 3- 4 ) on net community calcification (NCC) and net community production (NCP) rates of individual taxa and combined reef communities. Our study had four major outcomes: (i) NCC rates declined in response to nutrient addition in all substrate types, (ii) the mixed community switched from net calcification to net dissolution under medium and high nutrient conditions, (iii) nutrients augmented pH variability through modified photosynthesis and respiration rates, and (iv) nutrients disrupted the relationship between NCC and aragonite saturation state documented in ambient conditions. These results indicate that the negative effect of NO - 3 and PO 3- 4 addition on reef calcification is likely both a direct physiological response to nutrients and also an indirect response to a shifting pH environment from altered NCP rates. Here, we show that nutrient pollution could make reefs more vulnerable to global changes associated with ocean acidification and accelerate the predicted shift from net accretion to net erosion. © 2018 The Author(s).

SurvNet: a web server for identifying network-based biomarkers that most correlate with patient survival data.

PubMed

Li, Jun; Roebuck, Paul; Grünewald, Stefan; Liang, Han

2012-07-01

An important task in biomedical research is identifying biomarkers that correlate with patient clinical data, and these biomarkers then provide a critical foundation for the diagnosis and treatment of disease. Conventionally, such an analysis is based on individual genes, but the results are often noisy and difficult to interpret. Using a biological network as the searching platform, network-based biomarkers are expected to be more robust and provide deep insights into the molecular mechanisms of disease. We have developed a novel bioinformatics web server for identifying network-based biomarkers that most correlate with patient survival data, SurvNet. The web server takes three input files: one biological network file, representing a gene regulatory or protein interaction network; one molecular profiling file, containing any type of gene- or protein-centred high-throughput biological data (e.g. microarray expression data or DNA methylation data); and one patient survival data file (e.g. patients' progression-free survival data). Given user-defined parameters, SurvNet will automatically search for subnetworks that most correlate with the observed patient survival data. As the output, SurvNet will generate a list of network biomarkers and display them through a user-friendly interface. SurvNet can be accessed at http://bioinformatics.mdanderson.org/main/SurvNet.

Naturally occurring bioactive compounds from four repellent essential oils against Bemisia tabaci whiteflies.

PubMed

Deletre, Emilie; Chandre, Fabrice; Barkman, Barbara; Menut, Chantal; Martin, Thibaud

2016-01-01

In tropical countries, netting is an effective sustainable tool for protecting horticultural crops against Lepidoptera, although not against small pests such as Bemisia tabaci, while smaller mesh netting can be used in temperate regions. A solution is to combine a net with a repellent. Previously we identified repellent essential oils: lemongrass (Cymbopogon citratus), cinnamon (Cinnamomum zeylanicum), cumin (Cuminum cyminum) and citronella (Cymbopogon winternarius). The present study was designed to identify the active compounds of these essential oils, characterise their biological activity and examine their potential for coating nets. We investigated the efficiency and toxicity of nets dipped in different solutions. We then studied the repellent effect with an olfactometer and the irritant effect by videotracking. Geraniol and citronellol were the most promising net coatings owing to their repellent effect. The repellency, irritancy or toxicity varied with the product and concentration, and these features were independent, indicating that the repellent and the irritant/toxic mechanisms were not the same. The combined effects of these different compounds account for the bioactivity of the mixture, suggesting interactions between the compounds. This new sustainable strategy for protecting vegetable crops against whiteflies is discussed, in addition to the use of companion plants that could produce such bioactive compounds. © 2015 Society of Chemical Industry.

Neutrophils extracellular traps damage Naegleria fowleri trophozoites opsonized with human IgG.

PubMed

Contis-Montes de Oca, A; Carrasco-Yépez, M; Campos-Rodríguez, R; Pacheco-Yépez, J; Bonilla-Lemus, P; Pérez-López, J; Rojas-Hernández, S

2016-08-01

Naegleria fowleri infects humans through the nasal mucosa causing a disease in the central nervous system known as primary amoebic meningoencephalitis (PAM). Polymorphonuclear cells (PMNs) play a critical role in the early phase of N. fowleri infection. Recently, a new biological defence mechanism called neutrophil extracellular traps (NETs) has been attracting attention. NETs are composed of nuclear DNA combined with histones and antibacterial proteins, and these structures are released from the cell to direct its antimicrobial attack. In this work, we evaluate the capacity of N. fowleri to induce the liberation of NETs by human PMN cells. Neutrophils were cocultured with unopsonized or IgG-opsonized N. fowleri trophozoites. DNA, histone, myeloperoxidase (MPO) and neutrophil elastase (NE) were stained, and the formation of NETs was evaluated by confocal microscopy and by quantifying the levels of extracellular DNA. Our results showed N. fowleri induce the liberation of NETs including release of MPO and NE by human PMN cells as exposure interaction time is increased, but N. fowleri trophozoites evaded killing. However, when trophozoites were opsonized, they were susceptible to the neutrophils activity. Therefore, our study suggests that antibody-mediated PMNs activation through NET formation may be crucial for antimicrobial responses against N. fowleri. © 2016 John Wiley & Sons Ltd.

Evolution of the NET (NocA, Nlz, Elbow, TLP-1) protein family in metazoans: insights from expression data and phylogenetic analysis

PubMed Central

Pereira, Filipe; Duarte-Pereira, Sara; Silva, Raquel M.; da Costa, Luís Teixeira; Pereira-Castro, Isabel

2016-01-01

The NET (for NocA, Nlz, Elbow, TLP-1) protein family is a group of conserved zinc finger proteins linked to embryonic development and recently associated with breast cancer. The members of this family act as transcriptional repressors interacting with both class I histone deacetylases and Groucho/TLE co-repressors. In Drosophila, the NET family members Elbow and NocA are vital for the development of tracheae, eyes, wings and legs, whereas in vertebrates ZNF703 and ZNF503 are important for the development of the nervous system, eyes and limbs. Despite the relevance of this protein family in embryogenesis and cancer, many aspects of its origin and evolution remain unknown. Here, we show that NET family members are present and expressed in multiple metazoan lineages, from cnidarians to vertebrates. We identified several protein domains conserved in all metazoan species or in specific taxonomic groups. Our phylogenetic analysis suggests that the NET family emerged in the last common ancestor of cnidarians and bilaterians and that several rounds of independent events of gene duplication occurred throughout evolution. Overall, we provide novel data on the expression and evolutionary history of the NET family that can be relevant to understanding its biological role in both normal conditions and disease. PMID:27929068

Carbon dioxide flux and net primary production of a boreal treed bog: responses to warming and water table manipulations

NASA Astrophysics Data System (ADS)

Munir, T. M.; Perkins, M.; Kaing, E.; Strack, M.

2014-09-01

Mid-latitude treed bogs are significant carbon (C) stocks and are highly sensitive to global climate change. In a dry continental treed bog, we compared three sites; control, recent (1-3 years; experimental) and older drained (10-13 years; drained) with water levels at 38, 74 and 120 cm below the surface, respectively. At each site we measured carbon dioxide (CO2) fluxes and tree root respiration (Rr) (across hummock-hollow microtopography of the forest floor) and net primary production (NPP) of trees during the growing seasons (May to October) of 2011-2013. The carbon (C) balance was calculated by adding net CO2 exchange of the forest floor (NEff-Rr) to the NPP of the trees. From cooler and wetter 2011 to driest and warmest 2013, The control site was a~C sink of 92, 70 and 76 g m-2, experimental site was a C source of 14, 57 and 135 g m-2, and drained site was a progressively smaller source of 26, 23 and 13 g m-2, respectively. Although all microforms at the experimental site had large net CO2 emissions, the longer-term drainage and deeper water level at the drained site resulted in the replacement of mosses with vascular plants (shrubs) at the hummocks and lichens at the hollows leading to the highest CO2 uptake at drained hummocks and significant losses at hollows. The tree NPP was highest at the drained site. We also quantified the impact of climatic warming at all water table treatments by equipping additional plots with open-top chambers (OTCs) that caused a passive warming on average of ∼1 °C and differential air warming of ∼6 °C (at mid-day full sun) across the study years. Warming significantly enhanced the shrub growth and CO2 sink function of the drained hummocks (exceeding the cumulative respiration losses at hollows induced by the lowered water level × warming). There was an interaction of water level with warming across hummocks that resulted in largest net CO2 uptake at warmed drained hummocks. Thus in 2013, the warming treatment enhanced the sink function of control by 13 g m-2, reduced the source function of experimental by 10 g m-2, and significantly enhanced the sink function of the drained site by 73 g m-2. Therefore, drying and warming in continental bogs is expected to initially accelerate C losses via respiration but persistent drought and warming is expected to restore the peatland's original C sink function as a result of transitional shift of vegetation between the microforms and increased NPP of trees over time.

Moisture sorption isotherms and thermodynamic properties of bovine leather

NASA Astrophysics Data System (ADS)

Fakhfakh, Rihab; Mihoubi, Daoued; Kechaou, Nabil

2018-04-01

This study was aimed at the determination of bovine leather moisture sorption characteristics using a static gravimetric method at 30, 40, 50, 60 and 70 °C. The curves exhibit type II behaviour according to the BET classification. The sorption isotherms fitting by seven equations shows that GAB model is able to reproduce the equilibrium moisture content evolution with water activity for moisture range varying from 0.02 to 0.83 kg/kg d.b (0.9898 < R2 < 0.999). The sorption isotherms exhibit hysteresis effect. Additionally, sorption isotherms data were used to determine the thermodynamic properties such as isosteric heat of sorption, sorption entropy, spreading pressure, net integral enthalpy and entropy. Net isosteric heat of sorption and differential entropy were evaluated through direct use of moisture isotherms by applying the Clausius-Clapeyron equation and used to investigate the enthalpy-entropy compensation theory. Both sorption enthalpy and entropy for desorption increase to a maximum with increasing moisture content, and then decrease sharply with rising moisture content. Adsorption enthalpy decreases with increasing moisture content. Whereas, adsorption entropy increases smoothly with increasing moisture content to a maximum of 6.29 J/K.mol. Spreading pressure increases with rising water activity. The net integral enthalpy seemed to decrease and then increase to become asymptotic. The net integral entropy decreased with moisture content increase.

A rop net and removable walkway used to quantitatively sample fishes over wetland surfaces in the dwarf mangrove of the Southern Everglades

USGS Publications Warehouse

Lorenz, J.J.; McIvor, C.C.; Powell, G.V.N.; Frederick, P.C.

1997-01-01

We describe a 9 m2 drop net and removable walkways designed to quantify densities of small fishes in wetland habitats with low to moderate vegetation density. The method permits the collection of small, quantitative, discrete samples in ecologically sensitive areas by combining rapid net deployment from fixed sites with the carefully contained use of the fish toxicant rotenone. This method requires very little contact with the substrate, causes minimal alteration to the habitat being sampled, samples small fishes in an unbiased manner, and allows for differential sampling of microhabitats within a wetland. When used in dwarf red mangrove (Rhizophora mangle) habitat in southern Everglades National Park and adjacent areas (September 1990 to March 1993), we achieved high recovery efficiencies (78–90%) for five common species <110 mm in length. We captured 20,193 individuals of 26 species. The most abundant fishes were sheepshead minnowCyprinodon variegatus, goldspotted killifishFloridichthys carpio, rainwater killifishLucania parva, sailfin mollyPoecilia latipinna, and the exotic Mayan cichlidCichlasoma urophthalmus. The 9 m2 drop net and associated removable walkways are versatile and can be used in a variety of wetland types, including both interior and coastal wetlands with either herbaceous or woody vegetation.

Developmental switching in Physarum polycephalum: Petri net analysis of single cell trajectories of gene expression indicates responsiveness and genetic plasticity of the Waddington quasipotential landscape

NASA Astrophysics Data System (ADS)

Werthmann, Britta; Marwan, Wolfgang

2017-11-01

The developmental switch to sporulation in Physarum polycephalum is a phytochrome-mediated far-red light-induced cell fate decision that synchronously encompasses the entire multinucleate plasmodial cell and is associated with extensive reprogramming of the transcriptome. By repeatedly taking samples of single cells after delivery of a light stimulus pulse, we analysed differential gene expression in two mutant strains and in a heterokaryon of the two strains all of which display a different propensity for making the cell fate decision. Multidimensional scaling of the gene expression data revealed individually different single cell trajectories eventually leading to sporulation. Characterization of the trajectories as walks through states of gene expression discretized by hierarchical clustering allowed the reconstruction of Petri nets that model and predict the observed behavior. Structural analyses of the Petri nets indicated stimulus- and genotype-dependence of both, single cell trajectories and of the quasipotential landscape through which these trajectories are taken. The Petri net-based approach to the analysis and decomposition of complex cellular responses and of complex mutant phenotypes may provide a scaffold for the data-driven reconstruction of causal molecular mechanisms that shape the topology of the quasipotential landscape.

The selective PI3Kα inhibitor BYL719 as a novel therapeutic option for neuroendocrine tumors: Results from multiple cell line models

PubMed Central

Rentsch, Jakob; Freitag, Helma; Detjen, Katharina; Briest, Franziska; Möbs, Markus; Weissmann, Victoria; Siegmund, Britta; Auernhammer, Christoph J.; Aristizabal Prada, Elke Tatjana; Lauseker, Michael; Grossman, Ashley; Exner, Samantha; Fischer, Christian; Grötzinger, Carsten

2017-01-01

Background/Aims The therapeutic options for metastatic neuroendocrine tumors (NETs) are limited. As PI3K signaling is often activated in NETs, we have assessed the effects of selective PI3Kp110α inhibition by the novel agent BYL719 on cell viability, colony formation, apoptosis, cell cycle, signaling pathways, differentiation and secretion in pancreatic (BON-1, QGP-1) and pulmonary (H727) NET cell lines. Methods Cell viability was investigated by WST-1 assay, colony formation by clonogenic assay, apoptosis by caspase3/7 assay, the cell cycle by FACS, cell signaling by Western blot analysis, expression of chromogranin A and somatostatin receptors 1/2/5 by RT-qPCR, and chromogranin A secretion by ELISA. Results BYL719 dose-dependently decreased cell viability and colony formation with the highest sensitivity in BON-1, followed by H727, and lowest sensitivity in QGP-1 cells. BYL719 induced apoptosis and G0/G1 cell cycle arrest associated with increased p27 expression. Western blots showed inhibition of PI3K downstream targets to a varying degree in the different cell lines, but IGF1R activation. The most sensitive BON-1 cells displayed a significant, and H727 cells a non-significant, GSK3 inhibition after BYL719 treatment, but these effects do not appear to be mediated through the IGF1R. In contrast, the most resistant QGP-1 cells showed no GSK3 inhibition, but a modest activation, which would partially counteract the other anti-proliferative effects. Accordingly, BYL719 enhanced neuroendocrine differentiation with the strongest effect in BON-1, followed by H727 cells indicated by induction of chromogranin A and somatostatin receptor 1/2 mRNA-synthesis, but not in QGP-1 cells. In BON-1 and QGP-1 cells, the BYL719/everolimus combination was synergistic through simultaneous AKT/mTORC1 inhibition, and significantly increased somatostatin receptor 2 transcription compared to each drug separately. Conclusion Our results suggest that the agent BYL719 could be a novel therapeutic approach to the treatment of NETs that may sensitize NET cells to somatostatin analogs, and that if there is resistance to its action this may be overcome by combination with everolimus. PMID:28800359

The selective PI3Kα inhibitor BYL719 as a novel therapeutic option for neuroendocrine tumors: Results from multiple cell line models.

PubMed

Nölting, Svenja; Rentsch, Jakob; Freitag, Helma; Detjen, Katharina; Briest, Franziska; Möbs, Markus; Weissmann, Victoria; Siegmund, Britta; Auernhammer, Christoph J; Aristizabal Prada, Elke Tatjana; Lauseker, Michael; Grossman, Ashley; Exner, Samantha; Fischer, Christian; Grötzinger, Carsten; Schrader, Jörg; Grabowski, Patricia

2017-01-01

The therapeutic options for metastatic neuroendocrine tumors (NETs) are limited. As PI3K signaling is often activated in NETs, we have assessed the effects of selective PI3Kp110α inhibition by the novel agent BYL719 on cell viability, colony formation, apoptosis, cell cycle, signaling pathways, differentiation and secretion in pancreatic (BON-1, QGP-1) and pulmonary (H727) NET cell lines. Cell viability was investigated by WST-1 assay, colony formation by clonogenic assay, apoptosis by caspase3/7 assay, the cell cycle by FACS, cell signaling by Western blot analysis, expression of chromogranin A and somatostatin receptors 1/2/5 by RT-qPCR, and chromogranin A secretion by ELISA. BYL719 dose-dependently decreased cell viability and colony formation with the highest sensitivity in BON-1, followed by H727, and lowest sensitivity in QGP-1 cells. BYL719 induced apoptosis and G0/G1 cell cycle arrest associated with increased p27 expression. Western blots showed inhibition of PI3K downstream targets to a varying degree in the different cell lines, but IGF1R activation. The most sensitive BON-1 cells displayed a significant, and H727 cells a non-significant, GSK3 inhibition after BYL719 treatment, but these effects do not appear to be mediated through the IGF1R. In contrast, the most resistant QGP-1 cells showed no GSK3 inhibition, but a modest activation, which would partially counteract the other anti-proliferative effects. Accordingly, BYL719 enhanced neuroendocrine differentiation with the strongest effect in BON-1, followed by H727 cells indicated by induction of chromogranin A and somatostatin receptor 1/2 mRNA-synthesis, but not in QGP-1 cells. In BON-1 and QGP-1 cells, the BYL719/everolimus combination was synergistic through simultaneous AKT/mTORC1 inhibition, and significantly increased somatostatin receptor 2 transcription compared to each drug separately. Our results suggest that the agent BYL719 could be a novel therapeutic approach to the treatment of NETs that may sensitize NET cells to somatostatin analogs, and that if there is resistance to its action this may be overcome by combination with everolimus.

Neutrophil extracellular traps can activate alternative complement pathways.

PubMed

Wang, H; Wang, C; Zhao, M-H; Chen, M

2015-09-01

The interaction between neutrophils and activation of alternative complement pathway plays a pivotal role in the pathogenesis of anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV). ANCAs activate primed neutrophils to release neutrophil extracellular traps (NETs), which have recently gathered increasing attention in the development of AAV. The relationship between NETs and alternative complement pathway has not been elucidated. The current study aimed to investigate the relationship between NETs and alternative complement pathway. Detection of components of alternative complement pathway on NETs in vitro was assessed by immunostain and confocal microscopy. Complement deposition on NETs were detected after incubation with magnesium salt ethyleneglycol tetraacetic acid (Mg-EGTA)-treated human serum. After incubation of serum with supernatants enriched in ANCA-induced NETs, levels of complement components in supernatants were measured by enzyme-linked immunosorbent assay (ELISA). Complement factor B (Bb) and properdin deposited on NETs in vitro. The deposition of C3b and C5b-9 on NETs incubated with heat-inactivated normal human serum (Hi-NHS) or EGTA-treated Hi-NHS (Mg-EGTA-Hi-NHS) were significantly less than that on NETs incubated with NHS or EGTA-treated NHS (Mg-EGTA-NHS). NETs induced by ANCA could activate the alternative complement cascade in the serum. In the presence of EGTA, C3a, C5a and SC5b-9 concentration decreased from 800·42 ± 244·81 ng/ml, 7·68 ± 1·50 ng/ml, 382·15 ± 159·75 ng/ml in the supernatants enriched in ANCA induced NETs to 479·07 ± 156·2 ng/ml, 4·86 ± 1·26 ng/ml, 212·65 ± 44·40 ng/ml in the supernatants of DNase I-degraded NETs (P < 0·001, P = 0·008, P < 0·001, respectively). NETs could activate the alternative complement pathway, and might thus participate in the pathogenesis of AAV. © 2015 British Society for Immunology.

Imaging of Chemokine Receptor 4 Expression in Neuroendocrine Tumors - a Triple Tracer Comparative Approach.

PubMed

Werner, Rudolf A; Weich, Alexander; Higuchi, Takahiro; Schmid, Jan S; Schirbel, Andreas; Lassmann, Michael; Wild, Vanessa; Rudelius, Martina; Kudlich, Theodor; Herrmann, Ken; Scheurlen, Michael; Buck, Andreas K; Kropf, Saskia; Wester, Hans-Jürgen; Lapa, Constantin

2017-01-01

C-X-C motif chemokine receptor 4 (CXCR4) and somatostatin receptors (SSTR) are overexpressed in gastro-entero-pancreatic neuroendocrine tumors (GEP-NET). In this study, we aimed to elucidate the feasibility of non-invasive CXCR4 positron emission tomography/computed tomography (PET/CT) imaging in GEP-NET patients using [ 68 Ga]Pentixafor in comparison to 68 Ga-DOTA-D-Phe-Tyr3-octreotide ([ 68 Ga]DOTATOC) and 18 F-fluorodeoxyglucose ([ 18 F]FDG). Twelve patients with histologically proven GEP-NET (3xG1, 4xG2, 5xG3) underwent [ 68 Ga]DOTATOC, [ 18 F]FDG, and [ 68 Ga]Pentixafor PET/CT for staging and planning of the therapeutic management. Scans were analyzed on a patient as well as on a lesion basis and compared to immunohistochemical staining patterns of CXCR4 and somatostatin receptors SSTR2a and SSTR5. [ 68 Ga]Pentixafor visualized tumor lesions in 6/12 subjects, whereas [ 18 F]FDG revealed sites of disease in 10/12 and [ 68 Ga]DOTATOC in 11/12 patients, respectively. Regarding sensitivity, SSTR-directed PET was the superior imaging modality in all G1 and G2 NET. CXCR4-directed PET was negative in all G1 NET. In contrast, 50% of G2 and 80% of G3 patients exhibited [ 68 Ga]Pentixafor-positive tumor lesions. Whereas CXCR4 seems to play only a limited role in detecting well-differentiated NET, increasing receptor expression could be non-invasively observed with increasing tumor grade. Thus, [ 68 Ga]Pentixafor PET/CT might serve as non-invasive read-out for evaluating the possibility of CXCR4-directed endoradiotherapy in advanced dedifferentiated SSTR-negative tumors.

Net mineral requirements for growth of Saanen goat kids in early life are similar among genders.

PubMed

Mendonça, A N; Härter, C J; Souza, S F; Oliveira, D; Boaventura Neto, O; Biagioli, B; Resende, K T; Teixeira, I A M A

2017-02-01

The current mineral requirements for growing goat kids are based on sheep and cattle studies without differentiating between the stages of development or gender. The aims of this study were to determine the net requirements for growth of Ca, P, Mg, Na and K of Saanen goat kids during the initial stages of growth and to analyse the effect of gender on the net requirements for growth of these macrominerals. Eighteen female, 19 intact male and 10 castrated male Saanen goat kids were studied. The kids were selected applying a completely randomized design and slaughtered when their body weight (BW) reached approximately 5, 10 and 15 kg to determine the mineral requirements for growth at these stages. The net mineral requirements for growth were similar among genders. The goat kids had slightly increased net requirements of Ca, P and Mg for growth with increasing BW from 5 to 15 kg. The net requirements for growth of Ca, P, Mg, Na and K ranged from 9.61 to 9.67 g/kg of BW gain, 7.14 to 7.56 g/kg of BW gain, 0.34 to 0.37 g/kg of BW gain, 1.26 to 1.13 g/kg of BW gain, 1.88 to 1.82 g/kg of BW gain as the animals grew from 5 to 15 kg respectively. In conclusion, when formulating diets for Saanen goat kids in early growth stage mineral levels do not need to adjusted based on gender. Journal of Animal Physiology and Animal Nutrition © 2016 Blackwell Verlag GmbH.

What clinicians are asking pathologists when dealing with lung neuroendocrine neoplasms?

PubMed

Pelosi, Giuseppe; Fabbri, Alessandra; Cossa, Mara; Sonzogni, Angelica; Valeri, Barbara; Righi, Luisella; Papotti, Mauro

2015-11-01

Lung neuroendocrine tumors (NET) are currently classified in resection specimens according to four histological categories, namely typical carcinoid (TC), atypical carcinoid (AC), large-cell neuroendocrine carcinoma (LCNEC) and small cell carcinoma (SCC). Diagnostic criteria have remained unchanged in the 2015 WHO classification, which has ratified the wide acceptance and popularity of such terminology in the pathologists׳ and clinicians׳ community. A unifying umbrella of NE morphology and differentiation has been recognized in lung NET, which has pushed to enter an unique box of invasive tumors along with diffuse idiopathic pulmonary NE cell hyperplasia (DIPNECH) as a pre-invasive lesion with a potential toward the development of carcinoids. However, uncertainties remain in the terminology of lung NET upon small samples, where Ki-67 antigen could play some role to avoid misdiagnosing carcinoids as high-grade NE tumors. Epidemiologic, clinical and genetic traits support a biological three-tier over a pathology four-tier model, according to which TC are low malignancy tumors, AC intermediate malignancy tumors and LCNEC/SCC high malignancy tumors with no significant differences in survival among them. Inconsistencies in diagnostic reproducibility, troubles in the therapy of AC and LCNEC, and limitations to histology within the same tumor category argue in favor of a global re-thinking of lung NET where a grading system could play a role. This review outlines three main key questions in the field of lung NET: (A) unbiased diagnoses, (B) the role of Ki-67 and tumor grading, and (C) management of predictive markers. Answers are still inconclusive, thus additional research is required to improve our understanding on lung NET. Copyright © 2015 Elsevier Inc. All rights reserved.

Dynamic Network-Based Relevance Score Reveals Essential Proteins and Functional Modules in Directed Differentiation

PubMed Central

Wu, Chia-Chou; Lin, Che

2015-01-01

The induction of stem cells toward a desired differentiation direction is required for the advancement of stem cell-based therapies. Despite successful demonstrations of the control of differentiation direction, the effective use of stem cell-based therapies suffers from a lack of systematic knowledge regarding the mechanisms underlying directed differentiation. Using dynamic modeling and the temporal microarray data of three differentiation stages, three dynamic protein-protein interaction networks were constructed. The interaction difference networks derived from the constructed networks systematically delineated the evolution of interaction variations and the underlying mechanisms. A proposed relevance score identified the essential components in the directed differentiation. Inspection of well-known proteins and functional modules in the directed differentiation showed the plausibility of the proposed relevance score, with the higher scores of several proteins and function modules indicating their essential roles in the directed differentiation. During the differentiation process, the proteins and functional modules with higher relevance scores also became more specific to the neuronal identity. Ultimately, the essential components revealed by the relevance scores may play a role in controlling the direction of differentiation. In addition, these components may serve as a starting point for understanding the systematic mechanisms of directed differentiation and for increasing the efficiency of stem cell-based therapies. PMID:25977693

Development and pilot evaluation of an Internet-facilitated cognitive-behavioral intervention for maternal depression.

PubMed

Sheeber, Lisa B; Seeley, John R; Feil, Edward G; Davis, Betsy; Sorensen, Erik; Kosty, Derek B; Lewinsohn, Peter M

2012-10-01

Develop and pilot an Internet-facilitated cognitive-behavioral treatment intervention for depression, tailored to economically disadvantaged mothers of young children. Mothers (N = 70) of children enrolled in Head Start, who reported elevated levels of depressive symptoms, were randomized to either the 8-session, Internet-facilitated intervention (Mom-Net) or delayed intervention/facilitated treatment-as-usual (DI/TAU). Outcomes were measured using the Beck Depression Inventory (BDI-II; Beck, Steer, & Brown, 1996); the Patient Health Questionnaire 9 (PHQ-9; Spitzer et al., 1999), Behavioral Observations of Parent-Child Interactions using the Living in Family Environments coding system (LIFE; Hops, Davis, & Longoria, 1995); the Dyadic Parent-Child Interaction Coding Systems (DPICS; Eyberg, Nelson, Duke, & Boggs, 2005); the Parent Behavior Inventory (PBI; Lovejoy, Weis, O'Hare, & Rubin, 1999); and the Parenting Sense of Competence scale (PSOC; Gibaud-Wallston & Wandersman, 1978). Mom-Net demonstrated high levels of feasibility as indicated by low attrition and high program usage and satisfaction ratings. Participants in the Mom-Net condition demonstrated significantly greater reduction in depression, the primary outcome, at the level of both symptoms and estimates of criteria-based diagnoses over the course of the intervention. They also demonstrated significantly greater improvement on a questionnaire measure of parent satisfaction and efficacy as well as on both questionnaire and observational indices of harsh parenting behavior. Initial results suggest that the Mom-Net intervention is feasible and efficacious as a remotely delivered intervention for economically disadvantaged mothers. (PsycINFO Database Record (c) 2012 APA, all rights reserved).

Agent-based modeling of the immune system: NetLogo, a promising framework.

PubMed

Chiacchio, Ferdinando; Pennisi, Marzio; Russo, Giulia; Motta, Santo; Pappalardo, Francesco

2014-01-01

Several components that interact with each other to evolve a complex, and, in some cases, unexpected behavior, represents one of the main and fascinating features of the mammalian immune system. Agent-based modeling and cellular automata belong to a class of discrete mathematical approaches in which entities (agents) sense local information and undertake actions over time according to predefined rules. The strength of this approach is characterized by the appearance of a global behavior that emerges from interactions among agents. This behavior is unpredictable, as it does not follow linear rules. There are a lot of works that investigates the immune system with agent-based modeling and cellular automata. They have shown the ability to see clearly and intuitively into the nature of immunological processes. NetLogo is a multiagent programming language and modeling environment for simulating complex phenomena. It is designed for both research and education and is used across a wide range of disciplines and education levels. In this paper, we summarize NetLogo applications to immunology and, particularly, how this framework can help in the development and formulation of hypotheses that might drive further experimental investigations of disease mechanisms.

Plant-plant interactions in the restoration of Mediterranean drylands

NASA Astrophysics Data System (ADS)

Valdecantos, Alejandro; Fuentes, David; Smanis, Athanasios

2014-05-01

Plant-plant interactions are complex and dependent of both local abiotic features of the ecosystem and biotic relationships with other plants and animals. The net result of these interactions may be positive, negative or neutral resulting in facilitation, competition or neutralism, respectively (role of phylogeny). It has been proposed that competition is stronger between those individuals that share functional traits than between unrelated ones. The relative interaction effect of one plant on a neighbour may change in relation to resource availability - especially water in drylands. In addition, plants develop above and belowground biomass with time increasing the level and, eventually, changing the intensity and/or the direction of the interaction. In the framework of the restoration of degraded drylands, many studies have focused on the positive (nurse) effects of adult trees, shrubs and even grasses on artificially planted seedlings by improving the microclimate or providing protection against herbivores, but little is known about the interactions between seedlings of different life traits planted together under natural field conditions. In 2010 we established planting plots in two contrasted sites under semiarid Mediterranean climate and introduced one year old seedlings in different combinations of three species, two shrubs (Olea europaea and Pistacia lentiscus) and one grass (Stipa tenacissima). Half of the planting holes in each site were implemented with low-cost ecotechnological inputs to increase water availability by forcing runoff production and promoting deep infiltration (small plastic fabric + dry well). This resulted in four levels of abiotic stress. Biotic interactions were assessed by monitoring seedling survival and growth for three years after planting. The Relative Interaction Index (RII) of S. tenacissima on O. europaea was almost flat and close to 0 along the stress gradient since the beginning of the study suggesting limited interaction. Pistacia lentiscus showed facilitation on O. europaea in the most stressed situations and competition under the most favourable ones. We also observed mutual negative net effects between S. tenacissima and P. lentiscus as abiotic stress increased but with different sign of the slopes of RII with time: positive in the grass and negative in the shrub as plants become bigger in the most stressed conditions. These net effects and their temporal dynamics are discussed according to the specific life traits of the studied species as well as the implications for the restoration of semiarid lands.

CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components.

PubMed

Heberle, Henry; Carazzolle, Marcelo Falsarella; Telles, Guilherme P; Meirelles, Gabriela Vaz; Minghim, Rosane

2017-09-13

The advent of "omics" science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organization of biological pathways. Biomolecular interaction networks, or graphs, are simple abstract representations where the components of a cell (e.g. proteins, metabolites etc.) are represented by nodes and their interactions are represented by edges. An appropriate visualization of data is crucial for understanding such networks, since pathways are related to functions that occur in specific regions of the cell. The force-directed layout is an important and widely used technique to draw networks according to their topologies. Placing the networks into cellular compartments helps to quickly identify where network elements are located and, more specifically, concentrated. Currently, only a few tools provide the capability of visually organizing networks by cellular compartments. Most of them cannot handle large and dense networks. Even for small networks with hundreds of nodes the available tools are not able to reposition the network while the user is interacting, limiting the visual exploration capability. Here we propose CellNetVis, a web tool to easily display biological networks in a cell diagram employing a constrained force-directed layout algorithm. The tool is freely available and open-source. It was originally designed for networks generated by the Integrated Interactome System and can be used with networks from others databases, like InnateDB. CellNetVis has demonstrated to be applicable for dynamic investigation of complex networks over a consistent representation of a cell on the Web, with capabilities not matched elsewhere.

Impact of biodiversity-climate futures on primary production and metabolism in a model benthic estuarine system.

PubMed

Hicks, Natalie; Bulling, Mark T; Solan, Martin; Raffaelli, Dave; White, Piran C L; Paterson, David M

2011-02-14

Understanding the effects of anthropogenically-driven changes in global temperature, atmospheric carbon dioxide and biodiversity on the functionality of marine ecosystems is crucial for predicting and managing the associated impacts. Coastal ecosystems are important sources of carbon (primary production) to shelf waters and play a vital role in global nutrient cycling. These systems are especially vulnerable to the effects of human activities and will be the first areas impacted by rising sea levels. Within these coastal ecosystems, microalgal assemblages (microphytobenthos: MPB) are vital for autochthonous carbon fixation. The level of in situ production by MPB mediates the net carbon cycling of transitional ecosystems between net heterotrophic or autotrophic metabolism. In this study, we examine the interactive effects of elevated atmospheric CO(2) concentrations (370, 600, and 1000 ppmv), temperature (6°C, 12°C, and 18°C) and invertebrate biodiversity on MPB biomass in experimental systems. We assembled communities of three common grazing invertebrates (Hydrobia ulvae, Corophium volutator and Hediste diversicolor) in monoculture and in all possible multispecies combinations. This experimental design specifically addresses interactions between the selected climate change variables and any ecological consequences caused by changes in species composition or richness. The effects of elevated CO(2) concentration, temperature and invertebrate diversity were not additive, rather they interacted to determine MPB biomass, and overall this effect was negative. Diversity effects were underpinned by strong species composition effects, illustrating the importance of individual species identity. Overall, our findings suggest that in natural systems, the complex interactions between changing environmental conditions and any associated changes in invertebrate assemblage structure are likely to reduce MPB biomass. Furthermore, these effects would be sufficient to affect the net metabolic balance of the coastal ecosystem, with important implications for system ecology and sustainable exploitation.

Violent Interaction Detection in Video Based on Deep Learning

NASA Astrophysics Data System (ADS)

Zhou, Peipei; Ding, Qinghai; Luo, Haibo; Hou, Xinglin

2017-06-01

Violent interaction detection is of vital importance in some video surveillance scenarios like railway stations, prisons or psychiatric centres. Existing vision-based methods are mainly based on hand-crafted features such as statistic features between motion regions, leading to a poor adaptability to another dataset. En lightened by the development of convolutional networks on common activity recognition, we construct a FightNet to represent the complicated visual violence interaction. In this paper, a new input modality, image acceleration field is proposed to better extract the motion attributes. Firstly, each video is framed as RGB images. Secondly, optical flow field is computed using the consecutive frames and acceleration field is obtained according to the optical flow field. Thirdly, the FightNet is trained with three kinds of input modalities, i.e., RGB images for spatial networks, optical flow images and acceleration images for temporal networks. By fusing results from different inputs, we conclude whether a video tells a violent event or not. To provide researchers a common ground for comparison, we have collected a violent interaction dataset (VID), containing 2314 videos with 1077 fight ones and 1237 no-fight ones. By comparison with other algorithms, experimental results demonstrate that the proposed model for violent interaction detection shows higher accuracy and better robustness.

Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction.

PubMed

Yang, Yang; Yu, Haibo; York, Darrin; Cui, Qiang; Elstner, Marcus

2007-10-25

The standard self-consistent-charge density-functional-tight-binding (SCC-DFTB) method (Phys. Rev. B 1998, 58, 7260) is derived by a second-order expansion of the density functional theory total energy expression, followed by an approximation of the charge density fluctuations by charge monopoles and an effective damped Coulomb interaction between the atomic net charges. The central assumptions behind this effective charge-charge interaction are the inverse relation of atomic size and chemical hardness and the use of a fixed chemical hardness parameter independent of the atomic charge state. While these approximations seem to be unproblematic for many covalently bound systems, they are quantitatively insufficient for hydrogen-bonding interactions and (anionic) molecules with localized net charges. Here, we present an extension of the SCC-DFTB method to incorporate third-order terms in the charge density fluctuations, leading to chemical hardness parameters that are dependent on the atomic charge state and a modification of the Coulomb scaling to improve the electrostatic treatment within the second-order terms. These modifications lead to a significant improvement in the description of hydrogen-bonding interactions and proton affinities of biologically relevant molecules.

Integrating evidence-based practices for increasing cancer screenings in safety net health systems: a multiple case study using the Consolidated Framework for Implementation Research.

PubMed

Liang, Shuting; Kegler, Michelle C; Cotter, Megan; Emily, Phillips; Beasley, Derrick; Hermstad, April; Morton, Rentonia; Martinez, Jeremy; Riehman, Kara

2016-08-02

Implementing evidence-based practices (EBPs) to increase cancer screenings in safety net primary care systems has great potential for reducing cancer disparities. Yet there is a gap in understanding the factors and mechanisms that influence EBP implementation within these high-priority systems. Guided by the Consolidated Framework for Implementation Research (CFIR), our study aims to fill this gap with a multiple case study of health care safety net systems that were funded by an American Cancer Society (ACS) grants program to increase breast and colorectal cancer screening rates. The initiative funded 68 safety net systems to increase cancer screening through implementation of evidence-based provider and client-oriented strategies. Data are from a mixed-methods evaluation with nine purposively selected safety net systems. Fifty-two interviews were conducted with project leaders, implementers, and ACS staff. Funded safety net systems were categorized into high-, medium-, and low-performing cases based on the level of EBP implementation. Within- and cross-case analyses were performed to identify CFIR constructs that influenced level of EBP implementation. Of 39 CFIR constructs examined, six distinguished levels of implementation. Two constructs were from the intervention characteristics domain: adaptability and trialability. Three were from the inner setting domain: leadership engagement, tension for change, and access to information and knowledge. Engaging formally appointed internal implementation leaders, from the process domain, also distinguished level of implementation. No constructs from the outer setting or individual characteristics domain differentiated systems by level of implementation. Our study identified a number of influential CFIR constructs and illustrated how they impacted EBP implementation across a variety of safety net systems. Findings may inform future dissemination efforts of EBPs for increasing cancer screening in similar settings. Moreover, our analytic approach is similar to previous case studies using CFIR and hence could facilitate comparisons across studies.

Children's schemes for anticipating the validity of nets for solids

NASA Astrophysics Data System (ADS)

Wright, Vince; Smith, Ken

2017-09-01

There is growing acknowledgement of the importance of spatial abilities to student achievement across a broad range of domains and disciplines. Nets are one way to connect three-dimensional shapes and their two-dimensional representations and are a common focus of geometry curricula. Thirty-four students at year 6 (upper primary school) were interviewed on two occasions about their anticipation of whether or not given nets for the cube- and square-based pyramid would fold to form the target solid. Vergnaud's ( Journal of Mathematical Behavior, 17(2), 167-181, 1998, Human Development, 52, 83-94, 2009) four characteristics of schemes were used as a theoretical lens to analyse the data. Successful schemes depended on the interaction of operational invariants, such as strategic choice of the base, rules for action, particularly rotation of shapes, and anticipations of composites of polygons in the net forming arrangements of faces in the solid. Inferences were rare. These data suggest that students need teacher support to make inferences, in order to create transferable schemes.

SchNet - A deep learning architecture for molecules and materials

NASA Astrophysics Data System (ADS)

Schütt, K. T.; Sauceda, H. E.; Kindermans, P.-J.; Tkatchenko, A.; Müller, K.-R.

2018-06-01

Deep learning has led to a paradigm shift in artificial intelligence, including web, text, and image search, speech recognition, as well as bioinformatics, with growing impact in chemical physics. Machine learning, in general, and deep learning, in particular, are ideally suitable for representing quantum-mechanical interactions, enabling us to model nonlinear potential-energy surfaces or enhancing the exploration of chemical compound space. Here we present the deep learning architecture SchNet that is specifically designed to model atomistic systems by making use of continuous-filter convolutional layers. We demonstrate the capabilities of SchNet by accurately predicting a range of properties across chemical space for molecules and materials, where our model learns chemically plausible embeddings of atom types across the periodic table. Finally, we employ SchNet to predict potential-energy surfaces and energy-conserving force fields for molecular dynamics simulations of small molecules and perform an exemplary study on the quantum-mechanical properties of C20-fullerene that would have been infeasible with regular ab initio molecular dynamics.

Cross race comparisons between SES health gradients among African-American and white women at mid-life

PubMed Central

Salsberry, Pamela J.

2014-01-01

This study explored how multiple indicators of socioeconomic status (SES) inform understanding of race differences in the magnitude of health gains associated with higher SES. The study sample, 1268 African-American women and 2066 white women, was drawn from the National Longitudinal Surveys of Youth 1979. The outcome was the Physical Components Summary from the SF-12 assessed at age 40. Ordinary least squares regressions using education, income and net worth fully interacted with race were conducted. Single measure gradients tended to be steeper for whites than African-Americans, partly because “sheepskin” effects of high school and college graduation were higher for whites and low income and low net worth whites had worse health than comparable African-Americans. Conditioning on multiple measures of SES eliminated race disparities in health benefits of education and net worth, but not income. A discussion of current public policies that affect race disparities in levels of education, income and net wealth is provided. PMID:24632052

Multi-focus and multi-level techniques for visualization and analysis of networks with thematic data

NASA Astrophysics Data System (ADS)

Cossalter, Michele; Mengshoel, Ole J.; Selker, Ted

2013-01-01

Information-rich data sets bring several challenges in the areas of visualization and analysis, even when associated with node-link network visualizations. This paper presents an integration of multi-focus and multi-level techniques that enable interactive, multi-step comparisons in node-link networks. We describe NetEx, a visualization tool that enables users to simultaneously explore different parts of a network and its thematic data, such as time series or conditional probability tables. NetEx, implemented as a Cytoscape plug-in, has been applied to the analysis of electrical power networks, Bayesian networks, and the Enron e-mail repository. In this paper we briefly discuss visualization and analysis of the Enron social network, but focus on data from an electrical power network. Specifically, we demonstrate how NetEx supports the analytical task of electrical power system fault diagnosis. Results from a user study with 25 subjects suggest that NetEx enables more accurate isolation of complex faults compared to an especially designed software tool.

Thermal adaptation of net ecosystem exchange

DOE PAGES

Yuan, W.; Luo, Y.; Liang, S.; ...

2011-06-06

Thermal adaptation of gross primary production and ecosystem respiration has been well documented over broad thermal gradients. However, no study has examined their interaction as a function of temperature, i.e. the thermal responses of net ecosystem exchange of carbon (NEE). Here in this study, we constructed temperature response curves of NEE against temperature using 380 site-years of eddy covariance data at 72 forest, grassland and shrubland ecosystems located at latitudes ranging from ~29° N to 64° N. The response curves were used to define two critical temperatures: transition temperature (T b) at which ecosystem transfer from carbon source to sinkmore » and optimal temperature (T o) at which carbon uptake is maximized. T b was strongly correlated with annual mean air temperature. T o was strongly correlated with mean temperature during the net carbon uptake period across the study ecosystems. Our results imply that the net ecosystem exchange of carbon adapts to the temperature across the geographical range due to intrinsic connections between vegetation primary production and ecosystem respiration.« less

Using fuzzy logic to integrate neural networks and knowledge-based systems

NASA Technical Reports Server (NTRS)

Yen, John

1991-01-01

Outlined here is a novel hybrid architecture that uses fuzzy logic to integrate neural networks and knowledge-based systems. The author's approach offers important synergistic benefits to neural nets, approximate reasoning, and symbolic processing. Fuzzy inference rules extend symbolic systems with approximate reasoning capabilities, which are used for integrating and interpreting the outputs of neural networks. The symbolic system captures meta-level information about neural networks and defines its interaction with neural networks through a set of control tasks. Fuzzy action rules provide a robust mechanism for recognizing the situations in which neural networks require certain control actions. The neural nets, on the other hand, offer flexible classification and adaptive learning capabilities, which are crucial for dynamic and noisy environments. By combining neural nets and symbolic systems at their system levels through the use of fuzzy logic, the author's approach alleviates current difficulties in reconciling differences between low-level data processing mechanisms of neural nets and artificial intelligence systems.

Thermal adaptation of net ecosystem exchange

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

Yuan, W.; Luo, Y.; Liang, S.

Thermal adaptation of gross primary production and ecosystem respiration has been well documented over broad thermal gradients. However, no study has examined their interaction as a function of temperature, i.e. the thermal responses of net ecosystem exchange of carbon (NEE). Here in this study, we constructed temperature response curves of NEE against temperature using 380 site-years of eddy covariance data at 72 forest, grassland and shrubland ecosystems located at latitudes ranging from ~29° N to 64° N. The response curves were used to define two critical temperatures: transition temperature (T b) at which ecosystem transfer from carbon source to sinkmore » and optimal temperature (T o) at which carbon uptake is maximized. T b was strongly correlated with annual mean air temperature. T o was strongly correlated with mean temperature during the net carbon uptake period across the study ecosystems. Our results imply that the net ecosystem exchange of carbon adapts to the temperature across the geographical range due to intrinsic connections between vegetation primary production and ecosystem respiration.« less

Stochasticity and Spatial Interaction Govern Stem Cell Differentiation Dynamics

NASA Astrophysics Data System (ADS)

Smith, Quinton; Stukalin, Evgeny; Kusuma, Sravanti; Gerecht, Sharon; Sun, Sean X.

2015-07-01

Stem cell differentiation underlies many fundamental processes such as development, tissue growth and regeneration, as well as disease progression. Understanding how stem cell differentiation is controlled in mixed cell populations is an important step in developing quantitative models of cell population dynamics. Here we focus on quantifying the role of cell-cell interactions in determining stem cell fate. Toward this, we monitor stem cell differentiation in adherent cultures on micropatterns and collect statistical cell fate data. Results show high cell fate variability and a bimodal probability distribution of stem cell fraction on small (80-140 μm diameter) micropatterns. On larger (225-500 μm diameter) micropatterns, the variability is also high but the distribution of the stem cell fraction becomes unimodal. Using a stochastic model, we analyze the differentiation dynamics and quantitatively determine the differentiation probability as a function of stem cell fraction. Results indicate that stem cells can interact and sense cellular composition in their immediate neighborhood and adjust their differentiation probability accordingly. Blocking epithelial cadherin (E-cadherin) can diminish this cell-cell contact mediated sensing. For larger micropatterns, cell motility adds a spatial dimension to the picture. Taken together, we find stochasticity and cell-cell interactions are important factors in determining cell fate in mixed cell populations.

Inheritance of silicate differentiation during lunar origin by giant impact

NASA Technical Reports Server (NTRS)

Warren, Paul H.

1992-01-01

It is pointed out that the implication of the popular giant impact model of lunar origin (e.g., Hartmann and Davis, 1975; Cameron and Ward, 1976; Stevenson, 1987) is that any depth-related silicate differentiation within the impactor (and/or the earth) at the time of the impact must be partly inherited by the preferentially peripheral matter that forms the moon. This paper presents calculations of the magnitude of the net differentiation of the protolunar matter for a variety of elements and scenarios, with different assumptions regarding the geometries of the 'sampled' peripheral zones, the relative proportions of the earth-derived to impactor-derived matter in the final moon, and the degree to which the impactor mantle had crystallized prior to the giant impact. It is shown that these differention effects constrain the overall plausibility of the giant impact hypothesis.

Differentiated Staffing and Non-Teamed Organizational Structures as They Affect Elementary School Teacher-Pupil Interaction.

ERIC Educational Resources Information Center

Petrie, Thomas A.; And Others

A study was conducted of the differences in the frequency of selected student-teacher interaction in differentiated staffs and in non-teamed schools. The interaction processes studied were synthesized from Erikson's four stages of childhood: student behaviors--information processing, choice-making, reflection, problem solving, and procedures or…

Steric and electrostatic surface forces on sulfonated PEG graft surfaces with selective albumin adsorption.

PubMed

Bremmell, Kristen E; Britcher, Leanne; Griesser, Hans J

2013-06-01

Addition of ionized terminal groups to PEG graft layers may cause additional interfacial forces to modulate the net interfacial interactions between PEG graft layers and proteins. In this study we investigated the effect of terminal sulfonate groups, characterizing PEG-aldehyde (PEG-CHO) and sulfonated PEG (PEG-SO3) graft layers by XPS and colloid probe AFM interaction force measurements as a function of ionic strength, in order to determine surface forces relevant to protein resistance and models of bio-interfacial interaction of such graft coatings. On the PEG-CHO surface the measured interaction force does not alter with ionic strength, typical of a repulsive steric barrier coating. An analogous repulsive interaction force of steric origin was also observed on the PEG-SO3 graft coating; however, the net interaction force changed with ionic strength. Interaction forces were modelled by steric and electrical double layer interaction theories, with fitting to a scaling theory model enabling determination of the spacing and stretching of the grafted chains. Albumin, fibrinogen, and lysozyme did not adsorb on the PEG-CHO coating, whereas the PEG graft with terminal sulfonate groups showed substantial adsorption of albumin but not fibrinogen or lysozyme from 0.15 M salt solutions. Under lower ionic strength conditions albumin adsorption was again minimized as a result of the increased electrical double-layer interaction observed with the PEG-SO3 modified surface. This unique and unexpected adsorption behaviour of albumin provides an alternative explanation to the "negative cilia" model used by others to rationalize observed thromboresistance on PEG-sulfonate coatings. Copyright © 2013 Elsevier B.V. All rights reserved.

Developing and Implementing an Interactive End-of-Life Education Module Using Raptivity and iSpring: Lessons Learned

ERIC Educational Resources Information Center

Lewis-Pierre, LaToya; Aziza, Khitam

2017-01-01

The 21st century nurse is a forward-thinking individual who is expected to deliver holistic nursing care. Multigenerational learners are seeking degrees and the new Net generation learner will reflect the majority of the workforce. Thus, the integration of a multilevel interactive classroom is instrumental in facilitating the student's knowledge…

Trends in Information Technology and Future Prospects with Regard to Transforming Classroom Interaction.

ERIC Educational Resources Information Center

Hashem, Mahboub E.; Crawford, Christopher B.; Strohkirch, C. Sue

Educators have conquered e-mail and surfing the net; now they are striving to provide quality distance education. Classes often form discussion groups and use listservs to facilitate interaction. A discussion group is little more than a mailing list. Messages can be mailed to the list address and are copied to each person on that mailing list. The…

Computational studies of sequence-specific driving forces in peptide self-assembly

NASA Astrophysics Data System (ADS)

Jeon, Joohyun

Peptides are biopolymers made from various sequences of twenty different types of amino acids, connected by peptide bonds. There are practically an infinite number of possible sequences and tremendous possible combinations of peptide-peptide interactions. Recently, an increasing number of studies have shown a stark variety of peptide self-assembled nanomaterials whose detailed structures depend on their sequences and environmental factors; these have end uses in medical and bio-electronic applications, for example. To understand the underlying physics of complex peptide self-assembly processes and to delineate sequence specific effects, in this study, I use various simulation tools spanning all-atom molecular dynamics to simple lattice models and quantify the balance of interactions in the peptide self-assembly processes. In contrast to the existing view that peptides' aggregation propensities are proportional to the net sequence hydrophobicity and inversely proportional to the net charge, I show the more nuanced effects of electrostatic interactions, including the cooperative effects between hydrophobic and electrostatic interactions. Notably, I suggest rather unexpected, yet important roles of entropies in the small scale oligomerization processes. Overall, this study broadens our understanding of the role of thermodynamic driving forces in peptide self-assembly.

Do π-conjugative effects facilitate SN2 reactions?

PubMed

Wu, Chia-Hua; Galabov, Boris; Wu, Judy I-Chia; Ilieva, Sonia; Schleyer, Paul von R; Allen, Wesley D

2014-02-26

Rigorous quantum chemical investigations of the SN2 identity exchange reactions of methyl, ethyl, propyl, allyl, benzyl, propargyl, and acetonitrile halides (X = F(-), Cl(-)) refute the traditional view that the acceleration of SN2 reactions for substrates with a multiple bond at Cβ (carbon adjacent to the reacting Cα center) is primarily due to π-conjugation in the SN2 transition state (TS). Instead, substrate-nucleophile electrostatic interactions dictate SN2 reaction rate trends. Regardless of the presence or absence of a Cβ multiple bond in the SN2 reactant in a series of analogues, attractive Cβ(δ(+))···X(δ(-)) interactions in the SN2 TS lower net activation barriers (E(b)) and enhance reaction rates, whereas repulsive Cβ(δ(-))···X(δ(-)) interactions increase E(b) barriers and retard SN2 rates. Block-localized wave function (BLW) computations confirm that π-conjugation lowers the net activation barriers of SN2 allyl (1t, coplanar), benzyl, propargyl, and acetonitrile halide identity exchange reactions, but does so to nearly the same extent. Therefore, such orbital interactions cannot account for the large range of E(b) values in these systems.

The influence of health policy and market factors on the hospital safety net.

PubMed

Bazzoli, Gloria J; Lindrooth, Richard C; Kang, Ray; Hasnain-Wynia, Romana

2006-08-01

To examine how the financial pressures resulting from the Balanced Budget Act (BBA) of 1997 interacted with private sector pressures to affect indigent care provision. American Hospital Association Annual Survey, Area Resource File, InterStudy Health Maintenance Organization files, Current Population Survey, and Bureau of Primary Health Care data. We distinguished core and voluntary safety net hospitals in our analysis. Core safety net hospitals provide a large share of uncompensated care in their markets and have large indigent care patient mix. Voluntary safety net hospitals provide substantial indigent care but less so than core hospitals. We examined the effect of financial pressure in the initial year of the 1997 BBA on uncompensated care for three hospital groups. Data for 1996-2000 were analyzed using approaches that control for hospital and market heterogeneity. All urban U.S. general acute care hospitals with complete data for at least 2 years between 1996 and 2000, which totaled 1,693 institutions. Core safety net hospitals reduced their uncompensated care in response to Medicaid financial pressure. Voluntary safety net hospitals also responded in this way but only when faced with the combined forces of Medicaid and private sector payment pressures. Nonsafety net hospitals did not exhibit similar responses. Our results are consistent with theories of hospital behavior when institutions face reductions in payment. They raise concern given continuing state budget crises plus the focus of recent federal deficit reduction legislation intended to cut Medicaid expenditures.

Shared decision making in the safety net: where do we go from here?

PubMed

Bouma, Angelique B; Tiedje, Kristina; Poplau, Sara; Boehm, Deborah H; Shah, Nilay D; Commers, Matthew J; Linzer, Mark; Montori, Victor M

2014-01-01

Shared decision making (SDM) is an interactive process between clinicians and patients in which both share information, deliberate together, and make clinical decisions. Clinics serving safety net patients face special challenges, including fewer resources and more challenging work environments. The use of SDM within safety net institutions has not been well studied. We recruited a convenience sample of 15 safety net primary care clinicians (13 physicians, 2 nurse practitioners). Each answered a 9-item SDM questionnaire and participated in a semistructured interview. From the transcribed interviews and questionnaire data, we identified themes and suggestions for introducing SDM into a safety net environment. Clinicians reported only partially fulfilling the central components of SDM (sharing information, deliberating, and decision making). Most clinicians expressed interest in SDM by stating that they "selected a treatment option together" with patients (8 of 15 in strong or complete agreement), but only a minority (3 of 15) "thoroughly weighed the different treatment options" together with patients. Clinicians attributed this gap to many barriers, including time pressure, overwhelming visit content, patient preferences, and lack of available resources. All clinicians believed that lack of time made it difficult to practice SDM. To increase use of SDM in the safety net, efficient SDM interventions designed for this environment, team care, and patient engagement in SDM will need further development. Future studies should focus on adapting SDM to safety net settings and determine whether SDM can reduce health care disparities.

MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis.

PubMed

Lee, Dong-Yup; Yun, Hongsoek; Park, Sunwon; Lee, Sang Yup

2003-11-01

MetaFluxNet is a program package for managing information on the metabolic reaction network and for quantitatively analyzing metabolic fluxes in an interactive and customized way. It allows users to interpret and examine metabolic behavior in response to genetic and/or environmental modifications. As a result, quantitative in silico simulations of metabolic pathways can be carried out to understand the metabolic status and to design the metabolic engineering strategies. The main features of the program include a well-developed model construction environment, user-friendly interface for metabolic flux analysis (MFA), comparative MFA of strains having different genotypes under various environmental conditions, and automated pathway layout creation. http://mbel.kaist.ac.kr/ A manual for MetaFluxNet is available as PDF file.

Differential Susceptibility to Long-Term Effects of Quality of Child Care on Externalizing Behavior in Adolescence?

ERIC Educational Resources Information Center

Belsky, Jay; Pluess, Michael

2012-01-01

Much research on the quality of child care reveals it--in the case of low-quality child care--to be related to poorer child functioning, net of confounding factors, perhaps especially in the case of cognitive-linguistic performance. Recent work using data from the National Institute of Child Health and Human Development (NICHD) Study of Early…

Small Private Online Research: A Proposal for A Numerical Methods Course Based on Technology Use and Blended Learning

ERIC Educational Resources Information Center

Cepeda, Francisco Javier Delgado

2017-01-01

This work presents a proposed model in blended learning for a numerical methods course evolved from traditional teaching into a research lab in scientific visualization. The blended learning approach sets a differentiated and flexible scheme based on a mobile setup and face to face sessions centered on a net of research challenges. Model is…

Incidentally Detected Thyroid Follicular Neoplasm on Somatostatin Receptor Imaging and Post-therapy Scan.

PubMed

Sood, Apurva; Singh, Harpreet; Sood, Ashwani; Basher, Rajender Kumar; Mittal, Bhagwant Rai

2017-01-01

Peptide receptor radionuclide therapy (PRRT) either using Lu-177 or Y-90 peptide radiopharmaceuticals has emerged as promising treatment modality in patients with inoperable metastatic neuroendocrine tumour (NET) including medullary thyroid cancer, because of overexpression of somatostatin receptor 2 (sstr-2) on these cells. The several investigators have used PRRT in non-iodine avid differentiated thyroid cancer patients with limited success, where other treatment modalities have failed, probably due to faint sstr-2 expression in these lesions. However Hurthle cell neoplasms being predominantly non-iodine avid lesions have shown sstr-2 over-expression. The present case of inoperable NET patient imaged and treated with radiolabelled somatostatin analogue showed incidentally detected thyroid lesion highlighting the its importance in imaging and treatment in these type of thyroid malignancies.

Incidentally Detected Thyroid Follicular Neoplasm on Somatostatin Receptor Imaging and Post-therapy Scan

PubMed Central

Sood, Apurva; Singh, Harpreet; Sood, Ashwani; Basher, Rajender Kumar; Mittal, Bhagwant Rai

2017-01-01

Peptide receptor radionuclide therapy (PRRT) either using Lu-177 or Y-90 peptide radiopharmaceuticals has emerged as promising treatment modality in patients with inoperable metastatic neuroendocrine tumour (NET) including medullary thyroid cancer, because of overexpression of somatostatin receptor 2 (sstr-2) on these cells. The several investigators have used PRRT in non-iodine avid differentiated thyroid cancer patients with limited success, where other treatment modalities have failed, probably due to faint sstr-2 expression in these lesions. However Hurthle cell neoplasms being predominantly non-iodine avid lesions have shown sstr-2 over-expression. The present case of inoperable NET patient imaged and treated with radiolabelled somatostatin analogue showed incidentally detected thyroid lesion highlighting the its importance in imaging and treatment in these type of thyroid malignancies. PMID:28680210

Production of Extracellular Traps against Aspergillus fumigatus In Vitro and in Infected Lung Tissue Is Dependent on Invading Neutrophils and Influenced by Hydrophobin RodA

PubMed Central

Aimanianda, Vishukumar; Nietzsche, Sandor; Thywißen, Andreas; Jeron, Andreas; Latgé, Jean-Paul; Brakhage, Axel A.; Gunzer, Matthias

2010-01-01

Aspergillus fumigatus is the most important airborne fungal pathogen causing life-threatening infections in immunocompromised patients. Macrophages and neutrophils are known to kill conidia, whereas hyphae are killed mainly by neutrophils. Since hyphae are too large to be engulfed, neutrophils possess an array of extracellular killing mechanisms including the formation of neutrophil extracellular traps (NETs) consisting of nuclear DNA decorated with fungicidal proteins. However, until now NET formation in response to A. fumigatus has only been demonstrated in vitro, the importance of neutrophils for their production in vivo is unclear and the molecular mechanisms of the fungus to defend against NET formation are unknown. Here, we show that human neutrophils produce NETs in vitro when encountering A. fumigatus. In time-lapse movies NET production was a highly dynamic process which, however, was only exhibited by a sub-population of cells. NETosis was maximal against hyphae, but reduced against resting and swollen conidia. In a newly developed mouse model we could then demonstrate the existence and measure the kinetics of NET formation in vivo by 2-photon microscopy of Aspergillus-infected lungs. We also observed the enormous dynamics of neutrophils within the lung and their ability to interact with and phagocytose fungal elements in situ. Furthermore, systemic neutrophil depletion in mice almost completely inhibited NET formation in lungs, thus directly linking the immigration of neutrophils with NET formation in vivo. By using fungal mutants and purified proteins we demonstrate that hydrophobin RodA, a surface protein making conidia immunologically inert, led to reduced NET formation of neutrophils encountering Aspergillus fungal elements. NET-dependent killing of Aspergillus-hyphae could be demonstrated at later time-points, but was only moderate. Thus, these data establish that NET formation occurs in vivo during host defence against A. fumigatus, but suggest that it does not play a major role in killing this fungus. Instead, NETs may have a fungistatic effect and may prevent further spreading. PMID:20442864

Production of extracellular traps against Aspergillus fumigatus in vitro and in infected lung tissue is dependent on invading neutrophils and influenced by hydrophobin RodA.

PubMed

Bruns, Sandra; Kniemeyer, Olaf; Hasenberg, Mike; Aimanianda, Vishukumar; Nietzsche, Sandor; Thywissen, Andreas; Jeron, Andreas; Latgé, Jean-Paul; Brakhage, Axel A; Gunzer, Matthias

2010-04-29

Aspergillus fumigatus is the most important airborne fungal pathogen causing life-threatening infections in immunocompromised patients. Macrophages and neutrophils are known to kill conidia, whereas hyphae are killed mainly by neutrophils. Since hyphae are too large to be engulfed, neutrophils possess an array of extracellular killing mechanisms including the formation of neutrophil extracellular traps (NETs) consisting of nuclear DNA decorated with fungicidal proteins. However, until now NET formation in response to A. fumigatus has only been demonstrated in vitro, the importance of neutrophils for their production in vivo is unclear and the molecular mechanisms of the fungus to defend against NET formation are unknown. Here, we show that human neutrophils produce NETs in vitro when encountering A. fumigatus. In time-lapse movies NET production was a highly dynamic process which, however, was only exhibited by a sub-population of cells. NETosis was maximal against hyphae, but reduced against resting and swollen conidia. In a newly developed mouse model we could then demonstrate the existence and measure the kinetics of NET formation in vivo by 2-photon microscopy of Aspergillus-infected lungs. We also observed the enormous dynamics of neutrophils within the lung and their ability to interact with and phagocytose fungal elements in situ. Furthermore, systemic neutrophil depletion in mice almost completely inhibited NET formation in lungs, thus directly linking the immigration of neutrophils with NET formation in vivo. By using fungal mutants and purified proteins we demonstrate that hydrophobin RodA, a surface protein making conidia immunologically inert, led to reduced NET formation of neutrophils encountering Aspergillus fungal elements. NET-dependent killing of Aspergillus-hyphae could be demonstrated at later time-points, but was only moderate. Thus, these data establish that NET formation occurs in vivo during host defence against A. fumigatus, but suggest that it does not play a major role in killing this fungus. Instead, NETs may have a fungistatic effect and may prevent further spreading.

Understanding the digital divide in the clinical setting: the technology knowledge gap experienced by US safety net patients during teleretinal screening.

PubMed

George, Sheba; Moran, Erin; Fish, Allison; Ogunyemi, Lola

2013-01-01

Differential access to everyday technology and healthcare amongst safety net patients is associated with low technological and health literacies, respectively. These low rates of literacy produce a complex patient "knowledge gap" that influences the effectiveness of telehealth technologies. To understand this "knowledge gap", six focus groups (2 African-American and 4 Latino) were conducted with patients who received teleretinal screenings in U.S. urban safety-net settings. Findings indicate that patients' "knowledge gap" is primarily produced at three points: (1) when patients' preexisting personal barriers to care became exacerbated in the clinical setting; (2) through encounters with technology during screening; and (3) in doctor-patient follow-up. This "knowledge gap" can produce confusion and fear, potentially affecting patients' confidence in quality of care and limiting their disease management ability. In rethinking the digital divide to include the consequences of this knowledge gap faced by patients in the clinical setting, we suggest that patient education focus on both their disease and specific telehealth technologies deployed in care delivery.

Classical ROS-dependent and early/rapid ROS-independent release of Neutrophil Extracellular Traps triggered by Leishmania parasites.

PubMed

Rochael, Natalia C; Guimarães-Costa, Anderson B; Nascimento, Michelle T C; DeSouza-Vieira, Thiago S; Oliveira, Matheus P; Garcia e Souza, Luiz F; Oliveira, Marcus F; Saraiva, Elvira M

2015-12-17

Neutrophil extracellular traps (NETs) extruded from neutrophils upon activation are composed of chromatin associated with cytosolic and granular proteins, which ensnare and kill microorganisms. This microbicidal mechanism named classical netosis has been shown to dependent on reactive oxygen species (ROS) generation by NADPH oxidase and also chromatin decondensation dependent upon the enzymes (PAD4), neutrophil elastase (NE) and myeloperoxidase (MPO). NET release also occurs through an early/rapid ROS-independent mechanism, named early/rapid vital netosis. Here we analyze the role of ROS, NE, MPO and PAD4 in the netosis stimulated by Leishmania amazonensis promastigotes in human neutrophils. We demonstrate that promastigotes induce a classical netosis, dependent on the cellular redox imbalance, as well as by a chloroamidine sensitive and elastase activity mechanism. Additionally, Leishmania also induces the early/rapid NET release occurring only 10 minutes after neutrophil-parasite interaction. We demonstrate here, that this early/rapid mechanism is dependent on elastase activity, but independent of ROS generation and chloroamidine. A better understanding of both mechanisms of NET release, and the NETs effects on the host immune system modulation, could support the development of new potential therapeutic strategies for leishmaniasis.

Estimating net solar radiation using Landsat Thematic Mapper and digital elevation data

NASA Technical Reports Server (NTRS)

Dubayah, R.

1992-01-01

A radiative transfer algorithm is combined with digital elevation and satellite reflectance data to model spatial variability in net solar radiation at fine spatial resolution. The method is applied to the tall-grass prairie of the 16 x 16 sq km FIFE site (First ISLSCP Field Experiment) of the International Satellite Land Surface Climatology Project. Spectral reflectances as measured by the Landsat Thematic Mapper (TM) are corrected for atmospheric and topographic effects using field measurements and accurate 30-m digital elevation data in a detailed model of atmosphere-surface interaction. The spectral reflectances are then integrated to produce estimates of surface albedo in the range 0.3-3.0 microns. This map of albedo is used in an atmospheric and topographic radiative transfer model to produce a map of net solar radiation. A map of apparent net solar radiation is also derived using only the TM reflectance data, uncorrected for topography, and the average field-measured downwelling solar irradiance. Comparison with field measurements at 10 sites on the prairie shows that the topographically derived radiation map accurately captures the spatial variability in net solar radiation, but the apparent map does not.

An Agro-Climatological Early Warning Tool Based on the Google Earth Engine to Support Regional Food Security Analysis

NASA Astrophysics Data System (ADS)

Landsfeld, M. F.; Daudert, B.; Friedrichs, M.; Morton, C.; Hegewisch, K.; Husak, G. J.; Funk, C. C.; Peterson, P.; Huntington, J. L.; Abatzoglou, J. T.; Verdin, J. P.; Williams, E. L.

2015-12-01

The Famine Early Warning Systems Network (FEWS NET) focuses on food insecurity in developing nations and provides objective, evidence based analysis to help government decision-makers and relief agencies plan for and respond to humanitarian emergencies. The Google Earth Engine (GEE) is a platform provided by Google Inc. to support scientific research and analysis of environmental data in their cloud environment. The intent is to allow scientists and independent researchers to mine massive collections of environmental data and leverage Google's vast computational resources to detect changes and monitor the Earth's surface and climate. GEE hosts an enormous amount of satellite imagery and climate archives, one of which is the Climate Hazards Group Infrared Precipitation with Stations dataset (CHIRPS). The CHIRPS dataset is land based, quasi-global (latitude 50N-50S), 0.05 degree resolution, and has a relatively long term period of record (1981-present). CHIRPS is on a continuous monthly feed into the GEE as new data fields are generated each month. This precipitation dataset is a key input for FEWS NET monitoring and forecasting efforts. FEWS NET intends to leverage the GEE in order to provide analysts and scientists with flexible, interactive tools to aid in their monitoring and research efforts. These scientists often work in bandwidth limited regions, so lightweight Internet tools and services that bypass the need for downloading massive datasets to analyze them, are preferred for their work. The GEE provides just this type of service. We present a tool designed specifically for FEWS NET scientists to be utilized interactively for investigating and monitoring for agro-climatological issues. We are able to utilize the enormous GEE computing power to generate on-the-fly statistics to calculate precipitation anomalies, z-scores, percentiles and band ratios, and allow the user to interactively select custom areas for statistical time series comparisons and predictions.

Cyclic occurrence of fire and its role in carbon dynamics along an edaphic moisture gradient in longleaf pine ecosystems.

PubMed

Whelan, Andrew; Mitchell, Robert; Staudhammer, Christina; Starr, Gregory

2013-01-01

Fire regulates the structure and function of savanna ecosystems, yet we lack understanding of how cyclic fire affects savanna carbon dynamics. Furthermore, it is largely unknown how predicted changes in climate may impact the interaction between fire and carbon cycling in these ecosystems. This study utilizes a novel combination of prescribed fire, eddy covariance (EC) and statistical techniques to investigate carbon dynamics in frequently burned longleaf pine savannas along a gradient of soil moisture availability (mesic, intermediate and xeric). This research approach allowed us to investigate the complex interactions between carbon exchange and cyclic fire along the ecological amplitude of longleaf pine. Over three years of EC measurement of net ecosystem exchange (NEE) show that the mesic site was a net carbon sink (NEE = -2.48 tonnes C ha(-1)), while intermediate and xeric sites were net carbon sources (NEE = 1.57 and 1.46 tonnes C ha(-1), respectively), but when carbon losses due to fuel consumption were taken into account, all three sites were carbon sources (10.78, 7.95 and 9.69 tonnes C ha(-1) at the mesic, intermediate and xeric sites, respectively). Nonetheless, rates of NEE returned to pre-fire levels 1-2 months following fire. Consumption of leaf area by prescribed fire was associated with reduction in NEE post-fire, and the system quickly recovered its carbon uptake capacity 30-60 days post fire. While losses due to fire affected carbon balances on short time scales (instantaneous to a few months), drought conditions over the final two years of the study were a more important driver of net carbon loss on yearly to multi-year time scales. However, longer-term observations over greater environmental variability and additional fire cycles would help to more precisely examine interactions between fire and climate and make future predictions about carbon dynamics in these systems.

Cyclic Occurrence of Fire and Its Role in Carbon Dynamics along an Edaphic Moisture Gradient in Longleaf Pine Ecosystems

PubMed Central

Whelan, Andrew; Mitchell, Robert; Staudhammer, Christina; Starr, Gregory

2013-01-01

Fire regulates the structure and function of savanna ecosystems, yet we lack understanding of how cyclic fire affects savanna carbon dynamics. Furthermore, it is largely unknown how predicted changes in climate may impact the interaction between fire and carbon cycling in these ecosystems. This study utilizes a novel combination of prescribed fire, eddy covariance (EC) and statistical techniques to investigate carbon dynamics in frequently burned longleaf pine savannas along a gradient of soil moisture availability (mesic, intermediate and xeric). This research approach allowed us to investigate the complex interactions between carbon exchange and cyclic fire along the ecological amplitude of longleaf pine. Over three years of EC measurement of net ecosystem exchange (NEE) show that the mesic site was a net carbon sink (NEE = −2.48 tonnes C ha−1), while intermediate and xeric sites were net carbon sources (NEE = 1.57 and 1.46 tonnes C ha−1, respectively), but when carbon losses due to fuel consumption were taken into account, all three sites were carbon sources (10.78, 7.95 and 9.69 tonnes C ha−1 at the mesic, intermediate and xeric sites, respectively). Nonetheless, rates of NEE returned to pre-fire levels 1–2 months following fire. Consumption of leaf area by prescribed fire was associated with reduction in NEE post-fire, and the system quickly recovered its carbon uptake capacity 30–60 days post fire. While losses due to fire affected carbon balances on short time scales (instantaneous to a few months), drought conditions over the final two years of the study were a more important driver of net carbon loss on yearly to multi-year time scales. However, longer-term observations over greater environmental variability and additional fire cycles would help to more precisely examine interactions between fire and climate and make future predictions about carbon dynamics in these systems. PMID:23335986

Ski can negatively regulates macrophage differentiation through its interaction with PU.1

PubMed Central

Ueki, N; Zhang, L; Haymann, MJ

2010-01-01

In the hematopoietic cell system, the oncoprotein Ski dramatically affects growth and differentiation programs, in some cases leading to malignant leukemia. However, little is known about the interaction partners or signaling pathways involved in the Ski-mediated block of differentiation in hematopoietic cells. Here we show that Ski interacts with PU.1, a lineage-specific transcription factor essential for terminal myeloid differentiation, and thereby represses PU.1-dependent transcriptional activation. Consistent with this, Ski inhibits the biological function of PU.1 to promote myeloid cells to differentiate into macrophage colony-stimulating factor receptor (M-CSFR)-positive macrophages. Using a Ski mutant deficient in PU.1 binding, we demonstrate that Ski–PU.1 interaction is critical for Ski's ability to repress PU.1-dependent transcription and block macrophage differentiation. Furthermore, we provide evidence that Ski-mediated repression of PU.1 is due to Ski's ability to recruit histone deacetylase 3 to PU.1 bound to DNA. Since inactivation of PU.1 is closely related to the development of myeloid leukemia and Ski strongly inhibits PU.1 function, we propose that aberrant Ski expression in certain types of myeloid cell lineages might contribute to leukemogenesis. PMID:17621263

Rb Loss and KRAS Mutation Are Predictors of the Response to Platinum-Based Chemotherapy in Pancreatic Neuroendocrine Neoplasm with Grade 3: A Japanese Multicenter Pancreatic NEN-G3 Study.

PubMed

Hijioka, Susumu; Hosoda, Waki; Matsuo, Keitaro; Ueno, Makoto; Furukawa, Masayuki; Yoshitomi, Hideyuki; Kobayashi, Noritoshi; Ikeda, Masafumi; Ito, Tetsuhide; Nakamori, Shoji; Ishii, Hiroshi; Kodama, Yuzo; Morizane, Chigusa; Okusaka, Takuji; Yanagimoto, Hiroaki; Notohara, Kenji; Taguchi, Hiroki; Kitano, Masayuki; Yane, Kei; Maguchi, Hiroyuki; Tsuchiya, Yoshiaki; Komoto, Izumi; Tanaka, Hiroki; Tsuji, Akihito; Hashigo, Syunpei; Kawaguchi, Yoshiaki; Mine, Tetsuya; Kanno, Atsushi; Murohisa, Go; Miyabe, Katsuyuki; Takagi, Tadayuki; Matayoshi, Nobutaka; Yoshida, Tsukasa; Hara, Kazuo; Imamura, Masayuki; Furuse, Junji; Yatabe, Yasushi; Mizuno, Nobumasa

2017-08-15

Purpose: Patients with pancreatic neuroendocrine neoplasm grade-3 (PanNEN-G3) show variable responses to platinum-based chemotherapy. Recent studies indicated that PanNEN-G3 includes well-differentiated neuroendocrine tumor with G3 (NET-G3). Here, we examined the clinicopathologic and molecular features of PanNEN-G3 and assessed the responsiveness to chemotherapy and survival. Experimental Design: A total of 100 patients with PanNEN-G3 were collected from 31 institutions, and after central review characteristics of each histologic subtype [NET-G3 vs. pancreatic neuroendocrine carcinoma (NEC-G3)] were analyzed, including clinical, radiological, and molecular features. Factors that correlate with response to chemotherapy and survival were assessed. Results: Seventy patients analyzed included 21 NETs-G3 (30%) and 49 NECs-G3 (70%). NET-G3 showed lower Ki67-labeling index (LI; median 28.5%), no abnormal Rb expression (0%), and no mutated KRAS (0%), whereas NEC-G3 showed higher Ki67-LI (median 80.0%), Rb loss (54.5%), and KRAS mutations (48.7%). Chemotherapy response rate (RR), platinum-based chemotherapy RR, and prognosis differed significantly between NET-G3 and NEC-G3. Chemotherapeutic outcomes were worse in NET-G3 ( P < 0.001). When we stratified PanNEN-G3 with Rb and KRAS , PanNENs-G3 with Rb loss and those with mutated KRAS showed significantly higher RRs to platinum-based chemotherapy than those without (Rb loss, 80% vs. normal Rb, 24%, P = 0.006; mutated KRAS , 77% versus wild type, 23%, P = 0.023). Rb was a predictive marker of response to platinum-based chemotherapy even in NEC-G3 ( P = 0.035). Conclusions: NET-G3 and NEC-G3 showed distinct clinicopathologic characteristics. Notably, NET-G3 does not respond to platinum-based chemotherapy. Rb and KRAS are promising predictors of response to platinum-based chemotherapy for PanNEN-G3, and Rb for NEC-G3. Clin Cancer Res; 23(16); 4625-32. ©2017 AACR . ©2017 American Association for Cancer Research.

Symbiotic Cell Differentiation and Cooperative Growth in Multicellular Aggregates

PubMed Central

Yamagishi, Jumpei F; Saito, Nen; Kaneko, Kunihiko

2016-01-01

As cells grow and divide under a given environment, they become crowded and resources are limited, as seen in bacterial biofilms and multicellular aggregates. These cells often show strong interactions through exchanging chemicals, as evident in quorum sensing, to achieve mutualism and division of labor. Here, to achieve stable division of labor, three characteristics are required. First, isogenous cells differentiate into several types. Second, this aggregate of distinct cell types shows better growth than that of isolated cells without interaction and differentiation, by achieving division of labor. Third, this cell aggregate is robust with respect to the number distribution of differentiated cell types. Indeed, theoretical studies have thus far considered how such cooperation is achieved when the ability of cell differentiation is presumed. Here, we address how cells acquire the ability of cell differentiation and division of labor simultaneously, which is also connected with the robustness of a cell society. For this purpose, we developed a dynamical-systems model of cells consisting of chemical components with intracellular catalytic reaction dynamics. The reactions convert external nutrients into internal components for cellular growth, and the divided cells interact through chemical diffusion. We found that cells sharing an identical catalytic network spontaneously differentiate via induction from cell-cell interactions, and then achieve division of labor, enabling a higher growth rate than that in the unicellular case. This symbiotic differentiation emerged for a class of reaction networks under the condition of nutrient limitation and strong cell-cell interactions. Then, robustness in the cell type distribution was achieved, while instability of collective growth could emerge even among the cooperative cells when the internal reserves of products were dominant. The present mechanism is simple and general as a natural consequence of interacting cells with limited resources, and is consistent with the observed behaviors and forms of several aggregates of unicellular organisms. PMID:27749898

Synthesis, characterization and monoamine transporter activity of the new psychoactive substance mexedrone and its N-methoxy positional isomer, N-methoxymephedrone

PubMed Central

McLaughlin, Gavin; Morris, Noreen; Kavanagh, Pierce V.; Power, John D.; Dowling, Geraldine; Twamley, Brendan; O'Brien, John; Talbot, Brian; Walther, Donna; Partilla, John S.; Baumann, Michael H.; Brandt, Simon D.

2017-01-01

3-Methoxy-2-(methylamino)-1-(4-methylphenyl)propan-1-one (mexedrone) appeared in 2015 and was advertised by UK Internet retailers as a non-controlled mephedrone derivative (2-(methylamino)-1-(4-methylphenyl)propan-1-one), which was of particular interest to countries who operate generic drugs legislation. This study describes the synthesis and analytical characterization of mexedrone and the differentiation from its isomer, N-methoxymephedrone, which was predicted to be a suitable candidate before the identity of mexedrone was revealed. A full analytical characterization is described using various chromatographic, spectroscopic and mass spectrometric platforms and X-ray crystal structure analysis. The analytical data obtained for a vendor sample were consistent with the synthesized mexedrone reference standard and analytical differentiation between the mexedrone and N-methoxymephedrone positional isomers was achieved. Furthermore, α-chloromethylmephedrone was identified as a by-product during mexedrone synthesis. All three substances were also studied for their uptake and releasing properties at dopamine transporters (DAT), norepinephrine transporters (NET) and serotonin transporters (SERT) using in vitro monoamine transporter assays in rat brain synaptosomes and compared to mephedrone. Mexedrone was a weak non-selective uptake blocker with IC50 values in the low μM range. It was also devoid of releasing activity at DAT and NET but displayed weak releasing activity at SERT (EC50= 2.5 μM). The isomer N-methoxymephedrone was found to be a weak uptake blocker at DAT, NET and SERT, as well as a fully efficacious substrate-type releasing agent across all three transporters with EC50 values in the low micromolar range. The synthesis by-product α-chloromethylmephedrone was inactive in all assays. PMID:27524685

CD133 expression in well-differentiated pancreatic neuroendocrine tumors: a potential predictor of progressive clinical courses.

PubMed

Sakai, Yasuhiro; Hong, Seung-Mo; An, Soyeon; Kim, Joo Young; Corbeil, Denis; Karbanová, Jana; Otani, Kyoko; Fujikura, Kohei; Song, Ki-Byung; Kim, Song Cheol; Akita, Masayuki; Nanno, Yoshihide; Toyama, Hirochika; Fukumoto, Takumi; Ku, Yonson; Hirose, Takanori; Itoh, Tomoo; Zen, Yoh

2017-03-01

The present study aimed to elucidate whether the stemness molecule, CD133, is expressed in well-differentiated pancreatic neuroendocrine tumors (PanNETs; World Health Organization grades 1 and 2) and establish its clinical relevance using 2 separate cohorts. In the first series (n = 178) in which tissue microarrays were available, immunohistochemistry revealed that CD133 was expressed in 14 cases (8%). CD133+ PanNETs had higher TNM stages (P < .01), more frequent lymphovascular invasion (P = .01), and higher recurrence rates (P = .01). In the second cohort (n = 56), the expression of CD133 and CK19 was examined in whole tissue sections. CD133 and CK19 were positive in 10 (18%) and 36 (64%) cases, respectively. CD133 expression correlated with higher pT scores (P < .01), the presence of microscopic venous infiltration (P = .03), and shorter disease-free periods (P < .01). When cases were divided into grade 1 and 2 neoplasms, patients with CD133+ PanNET continued to have shorter disease-free periods than did those with CD133- tumors in both groups (P < .01 and P = .02, respectively). Although CK19+ cases had shorter disease-free periods than did CK19- cases in the whole cohort (P = .02), this difference was less apparent in subanalyses of grade 1 and 2 cases. CD133 expression also appeared to be an independent predictive factor for tumor recurrence in a multivariate analysis (P = .018). The CD133 phenotype was identical between primary and metastatic foci in 17 of 18 cases from which tissues of metastatic deposits were available. In conclusion, the combination of CD133 phenotyping and World Health Organization grading may assist in stratifying patients in terms of the risk of progressive clinical courses. Copyright © 2016 Elsevier Inc. All rights reserved.

Synthesis, characterization and monoamine transporter activity of the new psychoactive substance mexedrone and its N-methoxy positional isomer, N-methoxymephedrone.

PubMed

McLaughlin, Gavin; Morris, Noreen; Kavanagh, Pierce V; Power, John D; Dowling, Geraldine; Twamley, Brendan; O'Brien, John; Talbot, Brian; Walther, Donna; Partilla, John S; Baumann, Michael H; Brandt, Simon D

2017-03-01

3-Methoxy-2-(methylamino)-1-(4-methylphenyl)propan-1-one (mexedrone) appeared in 2015 and was advertised by UK Internet retailers as a non-controlled mephedrone derivative (2-(methylamino)-1-(4-methylphenyl)propan-1-one), which was of particular interest to countries who operate generic drugs legislation. This study describes the synthesis and analytical characterization of mexedrone and the differentiation from its isomer, N-methoxymephedrone, which was predicted to be a suitable candidate before the identity of mexedrone was revealed. A full analytical characterization is described using various chromatographic, spectroscopic and mass spectrometric platforms and X-ray crystal structure analysis. The analytical data obtained for a vendor sample were consistent with the synthesized mexedrone reference standard and analytical differentiation between the mexedrone and N-methoxymephedrone positional isomers was achieved. Furthermore, α-chloromethylmephedrone was identified as a by-product during mexedrone synthesis. All three substances were also studied for their uptake and releasing properties at dopamine transporters (DAT), norepinephrine transporters (NET) and serotonin transporters (SERT) using in vitro monoamine transporter assays in rat brain synaptosomes and compared to mephedrone. Mexedrone was a weak non-selective uptake blocker with IC 50 values in the low μM range. It was also devoid of releasing activity at DAT and NET but displayed weak releasing activity at SERT (EC 50  = 2.5 μM). The isomer N-methoxymephedrone was found to be a weak uptake blocker at DAT, NET and SERT, as well as a fully efficacious substrate-type releasing agent across all three transporters with EC 50 values in the low micromolar range. The synthesis by-product α-chloromethylmephedrone was inactive in all assays. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Temperature response of denitrification rate and greenhouse gas production in agricultural river marginal wetland soils.

PubMed

Bonnett, S A F; Blackwell, M S A; Leah, R; Cook, V; O'Connor, M; Maltby, E

2013-05-01

Soils are predicted to exhibit significant feedback to global warming via the temperature response of greenhouse gas (GHG) production. However, the temperature response of hydromorphic wetland soils is complicated by confounding factors such as oxygen (O2 ), nitrate (NO3-) and soil carbon (C). We examined the effect of a temperature gradient (2-25 °C) on denitrification rates and net nitrous oxide (N2 O), methane (CH4 ) production and heterotrophic respiration in mineral (Eutric cambisol and Fluvisol) and organic (Histosol) soil types in a river marginal landscape of the Tamar catchment, Devon, UK, under non-flooded and flooded with enriched NO3- conditions. It was hypothesized that the temperature response is dependent on interactions with NO3--enriched flooding, and the physicochemical conditions of these soil types. Denitrification rate (mean, 746 ± 97.3 μg m(-2)  h(-1) ), net N2 O production (mean, 180 ± 26.6 μg m(-2)  h(-1) ) and net CH4 production (mean, 1065 ± 183 μg m(-2)  h(-1) ) were highest in the organic Histosol, with higher organic matter, ammonium and moisture, and lower NO3- concentrations. Heterotrophic respiration (mean, 127 ± 4.6 mg m(-2)  h(-1) ) was not significantly different between soil types and dominated total GHG (CO2 eq) production in all soil types. Generally, the temperature responses of denitrification rate and net N2 O production were exponential, whilst net CH4 production was unresponsive, possibly due to substrate limitation, and heterotrophic respiration was exponential but limited in summer at higher temperatures. Flooding with NO3- increased denitrification rate, net N2 O production and heterotrophic respiration, but a reduction in net CH4 production suggests inhibition of methanogenesis by NO3- or N2 O produced from denitrification. Implications for management and policy are that warming and flood events may promote microbial interactions in soil between distinct microbial communities and increase denitrification of excess NO3- with N2 O production contributing to no more than 50% of increases in total GHG production. © 2013 Blackwell Publishing Ltd.

CoryneRegNet 4.0 – A reference database for corynebacterial gene regulatory networks

PubMed Central

Baumbach, Jan

2007-01-01

Background Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression) and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the way for the genome-wide analysis of transcriptional regulatory networks. The large-scale reconstruction of these networks allows the in silico analysis of cell behavior in response to changing environmental conditions. We previously published CoryneRegNet, an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum. Results Now we introduce CoryneRegNet release 4.0, which integrates data on the gene regulatory networks of 4 corynebacteria, 2 mycobacteria and the model organism Escherichia coli K12. As the previous versions, CoryneRegNet provides a web-based user interface to access the database content, to allow various queries, and to support the reconstruction, analysis and visualization of regulatory networks at different hierarchical levels. In this article, we present the further improved database content of CoryneRegNet along with novel analysis features. The network visualization feature GraphVis now allows the inter-species comparisons of reconstructed gene regulatory networks and the projection of gene expression levels onto that networks. Therefore, we added stimulon data directly into the database, but also provide Web Service access to the DNA microarray analysis platform EMMA. Additionally, CoryneRegNet now provides a SOAP based Web Service server, which can easily be consumed by other bioinformatics software systems. Stimulons (imported from the database, or uploaded by the user) can be analyzed in the context of known transcriptional regulatory networks to predict putative contradictions or further gene regulatory interactions. Furthermore, it integrates protein clusters by means of heuristically solving the weighted graph cluster editing problem. In addition, it provides Web Service based access to up to date gene annotation data from GenDB. Conclusion The release 4.0 of CoryneRegNet is a comprehensive system for the integrated analysis of procaryotic gene regulatory networks. It is a versatile systems biology platform to support the efficient and large-scale analysis of transcriptional regulation of gene expression in microorganisms. It is publicly available at . PMID:17986320

Net Metering | State, Local, and Tribal Governments | NREL

Science.gov Websites

research organizations have explored this question by conducting solar cost-benefit studies. Program Design Sequencing for State Distributed PV Policies: A Quantitative Analysis of Policy Impacts and Interactions

Division of Labor in Biofilms: the Ecology of Cell Differentiation.

PubMed

van Gestel, Jordi; Vlamakis, Hera; Kolter, Roberto

2015-04-01

The dense aggregation of cells on a surface, as seen in biofilms, inevitably results in both environmental and cellular heterogeneity. For example, nutrient gradients can trigger cells to differentiate into various phenotypic states. Not only do cells adapt physiologically to the local environmental conditions, but they also differentiate into cell types that interact with each other. This allows for task differentiation and, hence, the division of labor. In this article, we focus on cell differentiation and the division of labor in three bacterial species: Myxococcus xanthus, Bacillus subtilis, and Pseudomonas aeruginosa. During biofilm formation each of these species differentiates into distinct cell types, in some cases leading to cooperative interactions. The division of labor and the cooperative interactions between cell types are assumed to yield an emergent ecological benefit. Yet in most cases the ecological benefits have yet to be elucidated. A notable exception is M. xanthus, in which cell differentiation within fruiting bodies facilitates the dispersal of spores. We argue that the ecological benefits of the division of labor might best be understood when we consider the dynamic nature of both biofilm formation and degradation.

Heterocellular interaction enhances recruitment of {alpha} and {beta}-catenins and ZO-2 into functional gap-junction complexes and induces gap junction-dependant differentiation of mammary epithelial cells

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

Talhouk, Rabih S.; Mroue, Rana; Mokalled, Mayssa

2008-11-01

Gap junctions (GJ) are required for mammary epithelial differentiation. Using epithelial (SCp2) and myoepithelial-like (SCg6) mouse-derived mammary cells, the role of heterocellular interaction in assembly of GJ complexes and functional differentiation ({beta}-casein expression) was evaluated. Heterocellular interaction is critical for {beta}-casein expression, independent of exogenous basement membrane or cell anchoring substrata. Functional differentiation of SCp2, co-cultured with SCg6, is more sensitive to GJ inhibition relative to homocellular SCp2 cultures differentiated by exogenous basement membrane. Connexin (Cx)32 and Cx43 levels were not regulated across culture conditions; however, GJ functionality was enhanced under differentiation-permissive conditions. Immunoprecipitation studies demonstrated association of junctional complexmore » components ({alpha}-catenin, {beta}-catenin and ZO-2) with Cx32 and Cx43, in differentiation conditions, and additionally with Cx30 in heterocellular cultures. Although {beta}-catenin did not shuttle between cadherin and GJ complexes, increased association between connexins and {beta}-catenin in heterocellular cultures was observed. This was concomitant with reduced nuclear {beta}-catenin, suggesting that differentiation in heterocellular cultures involves sequestration of {beta}-catenin in GJ complexes.« less

MetNetAPI: A flexible method to access and manipulate biological network data from MetNet

PubMed Central

2010-01-01

Background Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. Results MetNetAPI is a versatile Application Programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only. Conclusions An API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at http://www.metnetonline.org/api. PMID:21083943

Simulation of a Petri net-based model of the terpenoid biosynthesis pathway.

PubMed

Hawari, Aliah Hazmah; Mohamed-Hussein, Zeti-Azura

2010-02-09

The development and simulation of dynamic models of terpenoid biosynthesis has yielded a systems perspective that provides new insights into how the structure of this biochemical pathway affects compound synthesis. These insights may eventually help identify reactions that could be experimentally manipulated to amplify terpenoid production. In this study, a dynamic model of the terpenoid biosynthesis pathway was constructed based on the Hybrid Functional Petri Net (HFPN) technique. This technique is a fusion of three other extended Petri net techniques, namely Hybrid Petri Net (HPN), Dynamic Petri Net (HDN) and Functional Petri Net (FPN). The biological data needed to construct the terpenoid metabolic model were gathered from the literature and from biological databases. These data were used as building blocks to create an HFPNe model and to generate parameters that govern the global behaviour of the model. The dynamic model was simulated and validated against known experimental data obtained from extensive literature searches. The model successfully simulated metabolite concentration changes over time (pt) and the observations correlated with known data. Interactions between the intermediates that affect the production of terpenes could be observed through the introduction of inhibitors that established feedback loops within and crosstalk between the pathways. Although this metabolic model is only preliminary, it will provide a platform for analysing various high-throughput data, and it should lead to a more holistic understanding of terpenoid biosynthesis.

Monoamine Oxidase A (MAOA) and Catechol-O-Methyltransferase (COMT) Gene Polymorphisms Interact with Maternal Parenting in Association with Adolescent Reactive Aggression but not Proactive Aggression: Evidence of Differential Susceptibility.

PubMed

Zhang, Wenxin; Cao, Cong; Wang, Meiping; Ji, Linqin; Cao, Yanmiao

2016-04-01

To date, whether and how gene-environment (G × E) interactions operate differently across distinct subtypes of aggression remains untested. More recently, in contrast with the diathesis-stress hypothesis, an alternative hypothesis of differential susceptibility proposes that individuals could be differentially susceptible to environments depending on their genotypes in a "for better and for worse" manner. The current study examined interactions between monoamine oxidase A (MAOA) T941G and catechol-O-methyltransferase (COMT) Val158Met polymorphisms with maternal parenting on two types of aggression: reactive and proactive. Moreover, whether these potential G × E interactions would be consistent with the diathesis-stress versus the differential susceptibility hypothesis was tested. Within the sample of 1399 Chinese Han adolescents (47.2 % girls, M age = 12.32 years, SD = 0.50), MAOA and COMT genes both interacted with positive parenting in their associations with reactive but not proactive aggression. Adolescents with T alleles/TT homozygotes of MAOA gene or Met alleles of COMT gene exhibited more reactive aggression when exposed to low positive parenting, but less reactive aggression when exposed to high positive parenting. These findings provide the first evidence for distinct G × E interaction effects on reactive versus proactive aggression and lend further support for the differential susceptibility hypothesis.

Trait-based diversification shifts reflect differential extinction among fossil taxa

PubMed Central

Wagner, Peter J.; Estabrook, George F.

2014-01-01

Evolution provides many cases of apparent shifts in diversification associated with particular anatomical traits. Three general models connect these patterns to anatomical evolution: (i) elevated net extinction of taxa bearing particular traits, (ii) elevated net speciation of taxa bearing particular traits, and (iii) elevated evolvability expanding the range of anatomies available to some species. Trait-based diversification shifts predict elevated hierarchical stratigraphic compatibility (i.e., primitive→derived→highly derived sequences) among pairs of anatomical characters. The three specific models further predict (i) early loss of diversity for taxa retaining primitive conditions (elevated net extinction), (ii) increased diversification among later members of a clade (elevated net speciation), and (iii) increased disparity among later members in a clade (elevated evolvability). Analyses of 319 anatomical and stratigraphic datasets for fossil species and genera show that hierarchical stratigraphic compatibility exceeds the expectations of trait-independent diversification in the vast majority of cases, which was expected if trait-dependent diversification shifts are common. Excess hierarchical stratigraphic compatibility correlates with early loss of diversity for groups retaining primitive conditions rather than delayed bursts of diversity or disparity across entire clades. Cambrian clades (predominantly trilobites) alone fit null expectations well. However, it is not clear whether evolution was unusual among Cambrian taxa or only early trilobites. At least among post-Cambrian taxa, these results implicate models, such as competition and extinction selectivity/resistance, as major drivers of trait-based diversification shifts at the species and genus levels while contradicting the predictions of elevated net speciation and elevated evolvability models. PMID:25331898

Substrate binding stoichiometry and kinetics of the norepinephrine transporter.

PubMed

Schwartz, Joel W; Novarino, Gaia; Piston, David W; DeFelice, Louis J

2005-05-13

The human norepinephrine (NE) transporter (hNET) attenuates neuronal signaling by rapid NE clearance from the synaptic cleft, and NET is a target for cocaine and amphetamines as well as therapeutics for depression, obsessive-compulsive disorder, and post-traumatic stress disorder. In spite of its central importance in the nervous system, little is known about how NET substrates, such as NE, 1-methyl-4-tetrahydropyridinium (MPP+), or amphetamine, interact with NET at the molecular level. Nor do we understand the mechanisms behind the transport rate. Previously we introduced a fluorescent substrate similar to MPP+, which allowed separate and simultaneous binding and transport measurement (Schwartz, J. W., Blakely, R. D., and DeFelice, L. J. (2003) J. Biol. Chem. 278, 9768-9777). Here we use this substrate, 4-(4-(dimethylamino)styrl)-N-methyl-pyridinium (ASP+), in combination with green fluorescent protein-tagged hNETs to measure substrate-transporter stoichiometry and substrate binding kinetics. Calibrated confocal microscopy and fluorescence correlation spectroscopy reveal that hNETs, which are homomultimers, bind one substrate molecule per transporter subunit. Substrate residence at the transporter, obtained from rapid on-off kinetics revealed in fluorescence correlation spectroscopy, is 526 micros. Substrate residence obtained by infinite dilution is 1000 times slower. This novel examination of substrate-transporter kinetics indicates that a single ASP+ molecule binds and unbinds thousands of times before being transported or ultimately dissociated from hNET. Calibrated fluorescent images combined with mass spectroscopy give a transport rate of 0.06 ASP+/hNET-protein/s, thus 36,000 on-off binding events (and 36 actual departures) occur for one transport event. Therefore binding has a low probability of resulting in transport. We interpret these data to mean that inefficient binding could contribute to slow transport rates.

The Impact of PD-L1 Expression in Patients with Metastatic GEP-NETs

PubMed Central

Kim, Seung Tae; Ha, Sang Yun; Lee, Sujin; Ahn, Soomin; Lee, Jeeyun; Park, Se Hoon; Park, Joon Oh; Lim, Ho Yeong; Kang, Won Ki; Kim, Kyoung-Mee; Park, Young Suk

2016-01-01

Programmed death-ligand 1 (PD-L1), which is expressed on many cancer cells, interacts with PD1 expressed on the surface of T cells, inhibiting the T cells and blocking the antitumor immune response. Expression of PD-L1 in gastroenteropancreatic neuroendocrine tumors (GEP-NETs) has not been studied. We investigated the impact of PD-L1 expression in 32 patients with metastatic GEP-NET. The expression of PD-L1 was evaluated using an anti-PD-L1 immunohistochemistry (IHC) antibody optimized for staining of formalin-fixed paraffin-embedded (FFPE) tissue samples. The correlation between PD-L1 and clinicopathological data including survival and response to systemic treatments was analyzed. Primary sites were 24 foregut-derived GEP-NETs, including stomach (n=1), duodenum (n=2), biliary tract (n=7), and pancreas (n=14), and 8 hindgut-derived GEP-NETs of the distal colon and rectum. Among the 32 patients with metastatic GEP-NET analyzed in this study, 7 (21.9%) had expression of PD-L1 in tumor tissues. Expression of PD-L1 was significantly associated with high-grade WHO classification (grade 3) (p=0.008) but not with gender, primary site, and number of metastatic sites (p>0.05). The status of PD-L1 expression was statistically associated with progression-free survival (PFS) for first-line systemic treatment (p=0.047). Moreover, the status of PD-L1 expression could significantly predict overall survival (p=0.037). The expression of PD-L1 was associated with higher WHO tumor grade (grade 3) in metastatic GEP-NETs. PD-L1 expression had both predictive and prognostic value for survival of patients with metastatic GEP-NETs. PMID:26958083

Gene and environment interaction: is the differential susceptibility hypothesis relevant for obesity?

PubMed Central

Dalle Molle, Roberta; Fatemi, Hajar; Dagher, Alain; Levitan, Robert D.; Silveira, Patricia P.; Dubé, Laurette

2017-01-01

The differential susceptibility model states that a given genetic variant is associated with an increased risk of pathology in negative environments but greater than average resilience in enriched ones. While this theory was first implemented in psychiatric-genetic research, it may also help us to unravel the complex ways that genes and environments interact to influence feeding behavior and obesity. We reviewed evidence on gene vs. environment interactions that influence obesity development, aiming to support the applicability of the differential susceptibility model for this condition, and propose that various environmental “layers” relevant for human development should be considered when bearing the differential susceptibility model in mind. Mother-child relationship, socioeconomic status and individual's response are important modifiers of BMI and food intake when interacting with gene variants, “for better and for worse”. While only a few studies to date have investigated obesity outcomes using this approach, we propose that the differential susceptibility hypothesis is in fact highly applicable to the study of genetic and environmental influences on feeding behavior and obesity risk. PMID:28024828

A Method for Overcoming the Problem of Concept-Scale Interaction in Semantic Differential Research

ERIC Educational Resources Information Center

Bynner, John; Romney, David

1972-01-01

Data collected in a study of hospital staff attitudes to drug addicts and other types of patients are used to illustrate the problem of concept-scale interaction in semantic differential research. (Authors)

The effect of changes in hospital reimbursement on nurse staffing decisions at safety net and nonsafety net hospitals.

PubMed

Lindrooth, Richard C; Bazzoli, Gloria J; Needleman, Jack; Hasnain-Wynia, Romana

2006-06-01

The financial savings from the Balanced Budget Act (BBA) are attractive to policy makers, but such savings come at a cost. We measure changes in nurse staffing at hospitals related to potential declines in reimbursement through the BBA. Following Hadley, Zuckerman, and Feder (1989), we define a fiscal pressure index (FPI) to measure the differential effect of the BBA. We estimate the effect of the FPI on the number of full-time equivalent registered nurses (RN) and licensed practical nurses (LPN) per adjusted patient day using American Hospital Association (AHA) data of a panel of hospitals from 1996 to 2001. The AHA data are combined with the Area Resource Files and health maintenance organizations penetration data. We control for hospital heterogeneity using fixed effects. All urban short-term general hospitals that responded to the staffing and uncompensated care questions in the AHA survey between 1996 and 2001. We define safety net hospitals as those with a high ratio of uncompensated costs to total hospital expenses (see, e.g., Zuckerman et al. 2001). We find that the nonsafety net hospitals that were most susceptible to the provisions of the BBA experienced a decline in RN staffing ratios about twice the rate of the nonsafety net hospitals that were least susceptible to the BBA. We are unable to detect an effect of the BBA on staffing at safety net hospitals. RN and LPN staffing levels per adjusted patient day declined, on average, between 1996 and 2001. Within the context of the general decline, we find that RN staffing per adjusted patient day declined even more at nonsafety net hospitals that were most susceptible to lower reimbursement related to the BBA. Thus, there was a small but statistically significant incremental effect of potential BBA losses on RN staffing at hospitals that were expected to be affected most. This incremental decline represented about a 6 percent increase in nurse workload that in isolation might not affect quality. Nevertheless, the BBA contributed to the contemporaneous trends toward higher nurse workloads that could have deleterious effects on quality. In contrast, safety net hospitals did not respond to the provisions of the BBA by reducing staffing ratios. This conclusion is tempered by the fact that we have few safety net hospitals in the sample.

An applied test of the social learning theory of deviance to college alcohol use.

PubMed

DeMartino, Cynthia H; Rice, Ronald E; Saltz, Robert

2015-04-01

Several hypotheses about influences on college drinking derived from the social learning theory of deviance were tested and confirmed. The effect of ethnicity on alcohol use was completely mediated by differential association and differential reinforcement, whereas the effect of biological sex on alcohol use was partially mediated. Higher net positive reinforcements to costs for alcohol use predicted increased general use, more underage use, and more frequent binge drinking. Two unexpected finding were the negative relationship between negative expectations and negative experiences, and the substantive difference between nondrinkers and general drinkers compared with illegal or binge drinkers. The discussion considers implications for future campaigns based on Akers's deterrence theory.

Student-Content Interactions in Online Courses: The Role of Question Prompts in Facilitating Higher-Level Engagement with Course Content

ERIC Educational Resources Information Center

Ertmer, Peggy A.; Sadaf, Ayesha; Ertmer, David J.

2011-01-01

This study examined the relationships among question types and levels and students' subsequent responses/interactions in online discussion forums. Question prompts were classified both by type, as outlined by Andrews ("POD Q J Prof Organ Dev Net Higher Education" 2(34):129-163, 1980), and by levels of critical thinking, as outlined by Bloom…

Passing Messages between Biological Networks to Refine Predicted Interactions

PubMed Central

Glass, Kimberly; Huttenhower, Curtis; Quackenbush, John; Yuan, Guo-Cheng

2013-01-01

Regulatory network reconstruction is a fundamental problem in computational biology. There are significant limitations to such reconstruction using individual datasets, and increasingly people attempt to construct networks using multiple, independent datasets obtained from complementary sources, but methods for this integration are lacking. We developed PANDA (Passing Attributes between Networks for Data Assimilation), a message-passing model using multiple sources of information to predict regulatory relationships, and used it to integrate protein-protein interaction, gene expression, and sequence motif data to reconstruct genome-wide, condition-specific regulatory networks in yeast as a model. The resulting networks were not only more accurate than those produced using individual data sets and other existing methods, but they also captured information regarding specific biological mechanisms and pathways that were missed using other methodologies. PANDA is scalable to higher eukaryotes, applicable to specific tissue or cell type data and conceptually generalizable to include a variety of regulatory, interaction, expression, and other genome-scale data. An implementation of the PANDA algorithm is available at www.sourceforge.net/projects/panda-net. PMID:23741402

Diffusing colloidal probes of protein-carbohydrate interactions.

PubMed

Eichmann, Shannon L; Meric, Gulsum; Swavola, Julia C; Bevan, Michael A

2013-02-19

We present diffusing colloidal probe measurements of weak, multivalent, specific protein-polysaccharide interactions mediated by a competing monosaccharide. Specifically, we used integrated evanescent wave and video microscopy methods to monitor the three-dimensional Brownian excursions of conconavilin A (ConA) decorated colloids interacting with dextran-functionalized surfaces in the presence of glucose. Particle trajectories were interpreted as binding lifetime histograms, binding isotherms, and potentials of mean force. Binding lifetimes and isotherms showed clear trends of decreasing ConA-dextran-specific binding with increasing glucose concentration, consistent with expectations. Net potentials were accurately captured by superposition of a short-range, glucose-independent ConA-dextran repulsion and a longer-range, glucose-dependent dextran bridging attraction modeled as a harmonic potential. For glucose concentrations greater than 100 mM, the net ConA-dextran potential was found to have only a nonspecific repulsion, similar to that of bovine serum albumin (BSA) decorated colloids over dextran determined in control experiments. Our results demonstrate the first use of optical microscopy methods to quantify the connections between potentials of mean force and the binding behavior of ConA-decorated colloids on dextran-functionalized surfaces.

Competition and cooperation among similar representations: toward a unified account of facilitative and inhibitory effects of lexical neighbors.

PubMed

Chen, Qi; Mirman, Daniel

2012-04-01

One of the core principles of how the mind works is the graded, parallel activation of multiple related or similar representations. Parallel activation of multiple representations has been particularly important in the development of theories and models of language processing, where coactivated representations (neighbors) have been shown to exhibit both facilitative and inhibitory effects on word recognition and production. Researchers generally ascribe these effects to interactive activation and competition, but there is no unified explanation for why the effects are facilitative in some cases and inhibitory in others. We present a series of simulations of a simple domain-general interactive activation and competition model that is broadly consistent with more specialized domain-specific models of lexical processing. The results showed that interactive activation and competition can indeed account for the complex pattern of reversals. Critically, the simulations revealed a core computational principle that determines whether neighbor effects are facilitative or inhibitory: strongly active neighbors exert a net inhibitory effect, and weakly active neighbors exert a net facilitative effect.

The NetLogger Toolkit V2.0

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

Gunter, Dan; Lee, Jason; Stoufer, Martin

2003-03-28

The NetLogger Toolkit is designed to monitor, under actual operating conditions, the behavior of all the elements of the application-to-application communication path in order to determine exactly where time is spent within a complex system Using NetLogger, distnbuted application components are modified to produce timestamped logs of "interesting" events at all the critical points of the distributed system Events from each component are correlated, which allov^ one to characterize the performance of all aspects of the system and network in detail. The NetLogger Toolkit itself consists of four components an API and library of functions to simplify the generation ofmore » application-level event logs, a set of tools for collecting and sorting log files, an event archive system, and a tool for visualization and analysis of the log files In order to instrument an application to produce event logs, the application developer inserts calls to the NetLogger API at all the critical points in the code, then links the application with the NetLogger library All the tools in the NetLogger Toolkit share a common log format, and assume the existence of accurate and synchronized system clocks NetLogger messages can be logged using an easy-to-read text based format based on the lETF-proposed ULM format, or a binary format that can still be used through the same API but that is several times faster and smaller, with performance comparable or better than binary message formats such as MPI, XDR, SDDF-Binary, and PBIO. The NetLogger binary format is both highly efficient and self-describing, thus optimized for the dynamic message construction and parsing of application instrumentation. NetLogger includes an "activation" API that allows NetLogger logging to be turned on, off, or modified by changing an external file This IS useful for activating logging in daemons/services (e g GndFTP server). The NetLogger reliability API provides the ability to specify backup logging locations and penodically try to reconnect broken TCP pipe. A typical use for this is to store data on local disk while net is down. An event archiver can log one or more incoming NetLogger streams to a local disk file (netlogd) or to a mySQL database (netarchd). We have found exploratory, visual analysis of the log event data to be the most useful means of determining the causes of performance anomalies The NetLogger Visualization tool, niv, has been developed to provide a flexible and interactive graphical representation of system-level and application-level events.« less

A Value Chain Analysis of ghost nets in the Arafura Sea: identifying trans-boundary stakeholders, intervention points and livelihood trade-offs.

PubMed

Butler, J R A; Gunn, R; Berry, H L; Wagey, G A; Hardesty, B D; Wilcox, C

2013-07-15

Lost or discarded fishing nets are a significant component of marine debris which has trans-boundary impacts in large marine ecosystems. Such 'ghost nets' cause the by-catch of marine fauna and require retrieval from coastlines where they wash up. Identifying the causes of discarded nets and feasible intervention points requires analysis of a complex value chain and the stakeholders within it, yet no studies have attempted this. In this paper we combine Value Chain Analysis, commonly applied to understand value-adding for a commodity, with elements of Life Cycle Assessment and social network analysis to examine the drivers, stakeholders, economic, environmental and social costs and benefits in the life of a trawl net. We use the Arafura Sea as a case study, which is shared by Indonesia, Papua New Guinea and Australia, and is the focus of a Trans-boundary Diagnostic Assessment (TDA) within the Arafura-Timor Seas Ecosystem Action program (ATSEA). We follow a trawl net through four sub-systems: manufacture of webbing in South Korea, fishing and loss by an Indonesian vessel, retrieval as ghost net on the northern Australian coastline by Indigenous rangers, and disposal or re-cycling as 'GhostNet Art' by Indigenous artists. Primary stakeholders along the value chain incur economic and social benefits, and economic and environmental costs. There is an anomaly in the chain between Indonesian fishermen and Indigenous rangers, artists and communities due to the lack of market linkages between these primary stakeholders. The first 'nexus of influence' where reductions in net losses and environmental costs can be achieved is through interactions between GhostNets Australia, the World Wide Fund for Nature and the Australian Government, which can influence Indonesian fishery management institutions and fishing crews. The second nexus is via the international art market which by publicising GhostNet Art can raise awareness amongst fish consumers about the impacts of ghost nets, and hence influence Indonesian fishing companies. GhostNets Australia is a key bridging organisation in the network, linking stakeholders across scales and sub-systems. Feasible preventative interventions are discussed to rectify the anomaly in the value chain. The importance of GhostNets Australia and ATSEA in the evolving adaptive co-management and trans-boundary governance of fisheries is highlighted. However, the prevention of ghost nets will result in trade-offs in benefits for the livelihoods of primary stakeholders. The utility of the method for analysing marine debris in TDAs, and ATSEA in particular, is discussed. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

Channel water balance and exchange with subsurface flow along a mountain headwater stream in Montana, United States

USGS Publications Warehouse

Payn, R.A.; Gooseff, M.N.; McGlynn, B.L.; Bencala, K.E.; Wondzell, S.M.

2009-01-01

Channel water balances of contiguous reaches along streams represent a poorly understood scale of stream-subsurface interaction. We measured reach water balances along a headwater stream in Montana, United States, during summer base flow recessions. Reach water balances were estimated from series of tracer tests in 13 consecutive reaches delineated evenly along a 2.6 km valley segment. For each reach, we estimated net change in discharge, gross hydrologic loss, and gross hydrologic gain from tracer dilution and mass recovery. Four series of tracer tests were performed during relatively high, intermediate, and low base flow conditions. The relative distribution of channel water along the stream was strongly related to a transition in valley structure, with a general increase in gross losses through the recession. During tracer tests at intermediate and low flows, there were frequent substantial losses of tracer mass (>10%) that could not be explained by net loss in flow over the reach, indicating that many of the study reaches were concurrently losing and gaining water. For example, one reach with little net change in discharge exchanged nearly 20% of upstream flow with gains and losses along the reach. These substantial bidirectional exchanges suggest that some channel interactions with subsurface flow paths were not measurable by net change in flow or transient storage of recovered tracer. Understanding bidirectional channel water balances in stream reaches along valleys is critical to an accurate assessment of stream solute fate and transport and to a full assessment of exchanges between the stream channel and surrounding subsurface.

Channel water balance and exchange with subsurface flow along a mountain headwater stream in Montana, United States

USGS Publications Warehouse

Payn, R.A.; Gooseff, M.N.; McGlynn, B.L.; Bencala, K.E.; Wondzell, S.M.

2009-01-01

Channel water balances of contiguous reaches along streams represent a poorly understood scale of stream-subsurface interaction. We measured reach water balances along a headwater stream in Montana, United States, during summer base flow recessions. Reach water balances were estimated from series of tracer tests in 13 consecutive reaches delineated evenly along a 2.6 km valley segment. For each reach, we estimated net change in discharge, gross hydrologic loss, and gross hydrologic gain from tracer dilution and mass recovery. Four series of tracer tests were performed during relatively high, intermediate, and low base flow conditions. The relative distribution of channel water along the stream was strongly related to a transition in valley structure, with a general increase in gross losses through the recession. During tracer tests at intermediate and low flows, there were frequent substantial losses of tracer mass (>10%) that could not be explained by net loss in flow over the reach, indicating that many of the study reaches were concurrently losing and gaining water. For example, one reach with little net change in discharge exchanged nearly 20% of upstream flow with gains and losses along the reach. These substantial bidirectional exchanges suggest that some channel interactions with subsurface flow paths were not measurable by net change in flow or transient storage of recovered tracer. Understanding bidirectional channel water balances in stream reaches along valleys is critical to an accurate assessment of stream solute fate and transport and to a full assessment of exchanges between the stream channel and surrounding subsurface. Copyright 2009 by the American Geophysical Union.

Differentiation-dependent rearrangements of actin filaments and microtubules hinder apical endocytosis in urothelial cells.

PubMed

Tratnjek, Larisa; Romih, Rok; Kreft, Mateja Erdani

2017-08-01

During differentiation, superficial urothelial cells (UCs) of the urinary bladder form the apical surface, which is almost entirely covered by urothelial plaques containing densely packed uroplakin particles. These urothelial plaques are the main structural components of the blood-urine permeability barrier in the urinary bladder. We have shown previously that endocytosis from the apical plasma membrane decreases during urothelial cell differentiation. Here, we investigated the role of actin filament and microtubule rearrangements in apical endocytosis of differentiating UCs cells using hyperplastic and normoplastic porcine urothelial models. Partially differentiated normal porcine UCs contained actin filaments in the subapical cytoplasm, while microtubules had a net-like appearance. In highly differentiated UCs, actin filaments mostly disappeared from the subapical cytoplasm and microtubules remained as a thin layer close to the apical plasma membrane. Inhibition of actin filament formation with cytochalasin-D in partially differentiated UCs caused a decrease in apical endocytosis. Depolymerisation of microtubules with nocodazole did not prevent endocytosis of the endocytotic marker WGA into the subapical cytoplasm; however, it abolished WGA transport to endolysosomal compartments in the central cytoplasm. Cytochalasin-D or nocodazole treatment did not significantly change apical endocytosis in highly differentiated UCs. In conclusion, we showed that the physiological differentiation-dependent or chemically induced redistribution and reorganization of actin filaments and microtubules impair apical endocytosis in UCs. Importantly, reduced apical endocytosis due to cytoskeletal rearrangements in highly differentiated UCs, together with the formation of rigid urothelial plaques, reinforces the barrier function of the urothelium.

Free-fermion descriptions of parafermion chains and string-net models

NASA Astrophysics Data System (ADS)

Meichanetzidis, Konstantinos; Turner, Christopher J.; Farjami, Ashk; Papić, Zlatko; Pachos, Jiannis K.

2018-03-01

Topological phases of matter remain a focus of interest due to their unique properties: fractionalization, ground-state degeneracy, and exotic excitations. While some of these properties can occur in systems of free fermions, their emergence is generally associated with interactions between particles. Here, we quantify the role of interactions in general classes of topological states of matter in one and two spatial dimensions, including parafermion chains and string-net models. Surprisingly, we find that certain topological states can be exactly described by free fermions, while others saturate the maximum possible distance from their optimal free-fermion description [C. J. Turner et al., Nat. Commun. 8, 14926 (2017), 10.1038/ncomms14926]. Our work opens the door to understanding the complexity of topological models by establishing new types of fermionization procedures to describe their low-energy physics, thus making them amenable to experimental realizations.

Strangeness at high temperatures: from hadrons to quarks.

PubMed

Bazavov, A; Ding, H-T; Hegde, P; Kaczmarek, O; Karsch, F; Laermann, E; Maezawa, Y; Mukherjee, Swagato; Ohno, H; Petreczky, P; Schmidt, C; Sharma, S; Soeldner, W; Wagner, M

2013-08-23

Appropriate combinations of up to fourth order cumulants of net strangeness fluctuations and their correlations with net baryon number and electric charge fluctuations, obtained from lattice QCD calculations, have been used to probe the strangeness carrying degrees of freedom at high temperatures. For temperatures up to the chiral crossover, separate contributions of strange mesons and baryons can be well described by an uncorrelated gas of hadrons. Such a description breaks down in the chiral crossover region, suggesting that the deconfinement of strangeness takes place at the chiral crossover. On the other hand, the strangeness carrying degrees of freedom inside the quark gluon plasma can be described by a weakly interacting gas of quarks only for temperatures larger than twice the chiral crossover temperature. In the intermediate temperature window, these observables show considerably richer structures, indicative of the strongly interacting nature of the quark gluon plasma.

Integrated Autopilot/Autothrottle Based on a Total Energy Control Concept: Design and Evaluation of Additional Autopilot Modes

NASA Technical Reports Server (NTRS)

Bruce, Kevin R.

1988-01-01

An integrated autopilot/autothrottle system was designed using a total energy control design philosophy. This design ensures that the system can differentiate between maneuvers requiring a change in thrust to accomplish a net energy change, and those maneuvers which only require elevator control to redistribute energy. The system design, the development of the system, and a summary of simulation results are defined.

Discovering causal signaling pathways through gene-expression patterns

PubMed Central

Parikh, Jignesh R.; Klinger, Bertram; Xia, Yu; Marto, Jarrod A.; Blüthgen, Nils

2010-01-01

High-throughput gene-expression studies result in lists of differentially expressed genes. Most current meta-analyses of these gene lists include searching for significant membership of the translated proteins in various signaling pathways. However, such membership enrichment algorithms do not provide insight into which pathways caused the genes to be differentially expressed in the first place. Here, we present an intuitive approach for discovering upstream signaling pathways responsible for regulating these differentially expressed genes. We identify consistently regulated signature genes specific for signal transduction pathways from a panel of single-pathway perturbation experiments. An algorithm that detects overrepresentation of these signature genes in a gene group of interest is used to infer the signaling pathway responsible for regulation. We expose our novel resource and algorithm through a web server called SPEED: Signaling Pathway Enrichment using Experimental Data sets. SPEED can be freely accessed at http://speed.sys-bio.net/. PMID:20494976

Characterization and Molecular Interpretation of the Photosynthetic Traits of Lonicera confusa in Karst Environment

PubMed Central

Gan, Lu; Fu, Chunhua; Zhang, Libin; Yu, Longjiang; Li, Maoteng

2014-01-01

Lonicera confusa was a medical plant which could adapt to the Ca-rich environment in the karst area of China. The photosynthesis, relative chlorophyll content,differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) of L. confusa that cultivated in calcareous and sandstone soils were investigated. The results showed that the relative chlorophyll content and net photosynthesis rate of L. confusa in calcareous soil are much higher than that planted in sandstone soil, the higher content of calcium might play a role in keeping the chloroplast from harm and showed higher photosynthesis rate. The transpiration and stomata conductance were decreased in calcareous soil, which might result from the closure of stomata. The GeneFishing and proteomic results showed that the expression of DEGs and DEPs were critical for photosynthesis and stomata closure, such as RuBisCO, photosynthetic electron transfer c and malate dehydrogenase varied in the leaves of L. confusa that cultivated in different soils. These DEGs or DEPs were further found to be directly or indirectly regulated by calcium sensor proteins. This study enriched our knowledge of the molecular mechanism of high net photosynthesis rate and lower transpiration of L. confusa that cultivated in the calcareous soil in some degree. PMID:24959829

Modeling and Simulation of Metallurgical Process Based on Hybrid Petri Net

NASA Astrophysics Data System (ADS)

Ren, Yujuan; Bao, Hong

2016-11-01

In order to achieve the goals of energy saving and emission reduction of iron and steel enterprises, an increasing number of modeling and simulation technologies are used to research and analyse metallurgical production process. In this paper, the basic principle of Hybrid Petri net is used to model and analyse the Metallurgical Process. Firstly, the definition of Hybrid Petri Net System of Metallurgical Process (MPHPNS) and its modeling theory are proposed. Secondly, the model of MPHPNS based on material flow is constructed. The dynamic flow of materials and the real-time change of each technological state in metallurgical process are simulated vividly by using this model. The simulation process can implement interaction between the continuous event dynamic system and the discrete event dynamic system at the same level, and play a positive role in the production decision.

IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity

PubMed Central

Hu, Yang; Yang, Haixiu; Zhou, Chen; Sun, Jie; Zhou, Meng

2016-01-01

Increasing evidence indicated that long non-coding RNAs (lncRNAs) were involved in various biological processes and complex diseases by communicating with mRNAs/miRNAs each other. Exploiting interactions between lncRNAs and mRNA/miRNAs to lncRNA functional similarity (LFS) is an effective method to explore function of lncRNAs and predict novel lncRNA-disease associations. In this article, we proposed an integrative framework, IntNetLncSim, to infer LFS by modeling the information flow in an integrated network that comprises both lncRNA-related transcriptional and post-transcriptional information. The performance of IntNetLncSim was evaluated by investigating the relationship of LFS with the similarity of lncRNA-related mRNA sets (LmRSets) and miRNA sets (LmiRSets). As a result, LFS by IntNetLncSim was significant positively correlated with the LmRSet (Pearson correlation γ2=0.8424) and LmiRSet (Pearson correlation γ2=0.2601). Particularly, the performance of IntNetLncSim is superior to several previous methods. In the case of applying the LFS to identify novel lncRNA-disease relationships, we achieved an area under the ROC curve (0.7300) in experimentally verified lncRNA-disease associations based on leave-one-out cross-validation. Furthermore, highly-ranked lncRNA-disease associations confirmed by literature mining demonstrated the excellent performance of IntNetLncSim. Finally, a web-accessible system was provided for querying LFS and potential lncRNA-disease relationships: http://www.bio-bigdata.com/IntNetLncSim. PMID:27323856

IntNetLncSim: an integrative network analysis method to infer human lncRNA functional similarity.

PubMed

Cheng, Liang; Shi, Hongbo; Wang, Zhenzhen; Hu, Yang; Yang, Haixiu; Zhou, Chen; Sun, Jie; Zhou, Meng

2016-07-26

Increasing evidence indicated that long non-coding RNAs (lncRNAs) were involved in various biological processes and complex diseases by communicating with mRNAs/miRNAs each other. Exploiting interactions between lncRNAs and mRNA/miRNAs to lncRNA functional similarity (LFS) is an effective method to explore function of lncRNAs and predict novel lncRNA-disease associations. In this article, we proposed an integrative framework, IntNetLncSim, to infer LFS by modeling the information flow in an integrated network that comprises both lncRNA-related transcriptional and post-transcriptional information. The performance of IntNetLncSim was evaluated by investigating the relationship of LFS with the similarity of lncRNA-related mRNA sets (LmRSets) and miRNA sets (LmiRSets). As a result, LFS by IntNetLncSim was significant positively correlated with the LmRSet (Pearson correlation γ2=0.8424) and LmiRSet (Pearson correlation γ2=0.2601). Particularly, the performance of IntNetLncSim is superior to several previous methods. In the case of applying the LFS to identify novel lncRNA-disease relationships, we achieved an area under the ROC curve (0.7300) in experimentally verified lncRNA-disease associations based on leave-one-out cross-validation. Furthermore, highly-ranked lncRNA-disease associations confirmed by literature mining demonstrated the excellent performance of IntNetLncSim. Finally, a web-accessible system was provided for querying LFS and potential lncRNA-disease relationships: http://www.bio-bigdata.com/IntNetLncSim.

The Influence of Health Policy and Market Factors on the Hospital Safety Net

PubMed Central

Bazzoli, Gloria J; Lindrooth, Richard C; Kang, R ay; Hasnain-Wynia, R omana

2006-01-01

Objective To examine how the financial pressures resulting from the Balanced Budget Act (BBA) of 1997 interacted with private sector pressures to affect indigent care provision. Data Sources/Study Setting American Hospital Association Annual Survey, Area Resource File, InterStudy Health Maintenance Organization files, Current Population Survey, and Bureau of Primary Health Care data. Study Design We distinguished core and voluntary safety net hospitals in our analysis. Core safety net hospitals provide a large share of uncompensated care in their markets and have large indigent care patient mix. Voluntary safety net hospitals provide substantial indigent care but less so than core hospitals. We examined the effect of financial pressure in the initial year of the 1997 BBA on uncompensated care for three hospital groups. Data for 1996–2000 were analyzed using approaches that control for hospital and market heterogeneity. Data Collection/Extraction Methods All urban U.S. general acute care hospitals with complete data for at least 2 years between 1996 and 2000, which totaled 1,693 institutions. Principal Findings Core safety net hospitals reduced their uncompensated care in response to Medicaid financial pressure. Voluntary safety net hospitals also responded in this way but only when faced with the combined forces of Medicaid and private sector payment pressures. Nonsafety net hospitals did not exhibit similar responses. Conclusions Our results are consistent with theories of hospital behavior when institutions face reductions in payment. They raise concern given continuing state budget crises plus the focus of recent federal deficit reduction legislation intended to cut Medicaid expenditures. PMID:16899001

Evaluating differential effects using regression interactions and regression mixture models

PubMed Central

Van Horn, M. Lee; Jaki, Thomas; Masyn, Katherine; Howe, George; Feaster, Daniel J.; Lamont, Andrea E.; George, Melissa R. W.; Kim, Minjung

2015-01-01

Research increasingly emphasizes understanding differential effects. This paper focuses on understanding regression mixture models, a relatively new statistical methods for assessing differential effects by comparing results to using an interactive term in linear regression. The research questions which each model answers, their formulation, and their assumptions are compared using Monte Carlo simulations and real data analysis. The capabilities of regression mixture models are described and specific issues to be addressed when conducting regression mixtures are proposed. The paper aims to clarify the role that regression mixtures can take in the estimation of differential effects and increase awareness of the benefits and potential pitfalls of this approach. Regression mixture models are shown to be a potentially effective exploratory method for finding differential effects when these effects can be defined by a small number of classes of respondents who share a typical relationship between a predictor and an outcome. It is also shown that the comparison between regression mixture models and interactions becomes substantially more complex as the number of classes increases. It is argued that regression interactions are well suited for direct tests of specific hypotheses about differential effects and regression mixtures provide a useful approach for exploring effect heterogeneity given adequate samples and study design. PMID:26556903

Differential CLE peptide perception by plant receptors implicated from structural and functional analyses of TDIF-TDR interactions

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

Li, Zhijie; Chakraborty, Sayan; Xu, Guozhou

Tracheary Element Differentiation Inhibitory Factor (TDIF) belongs to the family of post-translationally modified CLE (CLAVATA3/embryo surrounding region (ESR)-related) peptide hormones that control root growth and define the delicate balance between stem cell proliferation and differentiation in SAM (shoot apical meristem) or RAM (root apical meristem). In Arabidopsis, Tracheary Element Differentiation Inhibitory Factor Receptor (TDR) and its ligand TDIF signaling pathway is involved in the regulation of procambial cell proliferation and inhibiting its differentiation into xylem cells. Here we present the crystal structures of the extracellular domains (ECD) of TDR alone and in complex with its ligand TDIF resolved at 2.65more » Åand 2.75 Å respectively. These structures provide insights about the ligand perception and specific interactions between the CLE peptides and their cognate receptors. Our in vitro biochemical studies indicate that the interactions between the ligands and the receptors at the C-terminal anchoring site provide conserved binding. While the binding interactions occurring at the N-terminal anchoring site dictate differential binding specificities between different ligands and receptors. Our studies will open different unknown avenues of TDR-TDIF signaling pathways that will enhance our knowledge in this field highlighting the receptor ligand interaction, receptor activation, signaling network, modes of action and will serve as a structure function relationship model between the ligand and the receptor for various similar leucine-rich repeat receptor-like kinases (LRR-RLKs).« less

Local and global anatomy of antibody-protein antigen recognition.

PubMed

Wang, Meryl; Zhu, David; Zhu, Jianwei; Nussinov, Ruth; Ma, Buyong

2018-05-01

Deciphering antibody-protein antigen recognition is of fundamental and practical significance. We constructed an antibody structural dataset, partitioned it into human and murine subgroups, and compared it with nonantibody protein-protein complexes. We investigated the physicochemical properties of regions on and away from the antibody-antigen interfaces, including net charge, overall antibody charge distributions, and their potential role in antigen interaction. We observed that amino acid preference in antibody-protein antigen recognition is entropy driven, with residues having low side-chain entropy appearing to compensate for the high backbone entropy in interaction with protein antigens. Antibodies prefer charged and polar antigen residues and bridging water molecules. They also prefer positive net charge, presumably to promote interaction with negatively charged protein antigens, which are common in proteomes. Antibody-antigen interfaces have large percentages of Tyr, Ser, and Asp, but little Lys. Electrostatic and hydrophobic interactions in the Ag binding sites might be coupled with Fab domains through organized charge and residue distributions away from the binding interfaces. Here we describe some features of antibody-antigen interfaces and of Fab domains as compared with nonantibody protein-protein interactions. The distributions of interface residues in human and murine antibodies do not differ significantly. Overall, our results provide not only a local but also a global anatomy of antibody structures. Copyright © 2017 John Wiley & Sons, Ltd.

Protein Charge and Mass Contribute to the Spatio-temporal Dynamics of Protein-Protein Interactions in a Minimal Proteome

PubMed Central

Xu, Yu; Wang, Hong; Nussinov, Ruth; Ma, Buyong

2013-01-01

We constructed and simulated a ‘minimal proteome’ model using Langevin dynamics. It contains 206 essential protein types which were compiled from the literature. For comparison, we generated six proteomes with randomized concentrations. We found that the net charges and molecular weights of the proteins in the minimal genome are not random. The net charge of a protein decreases linearly with molecular weight, with small proteins being mostly positively charged and large proteins negatively charged. The protein copy numbers in the minimal genome have the tendency to maximize the number of protein-protein interactions in the network. Negatively charged proteins which tend to have larger sizes can provide large collision cross-section allowing them to interact with other proteins; on the other hand, the smaller positively charged proteins could have higher diffusion speed and are more likely to collide with other proteins. Proteomes with random charge/mass populations form less stable clusters than those with experimental protein copy numbers. Our study suggests that ‘proper’ populations of negatively and positively charged proteins are important for maintaining a protein-protein interaction network in a proteome. It is interesting to note that the minimal genome model based on the charge and mass of E. Coli may have a larger protein-protein interaction network than that based on the lower organism M. pneumoniae. PMID:23420643

The role of particle-to-cell interactions in dictating nanoparticle aided magnetophoretic separation of microalgal cells.

PubMed

Toh, Pey Yi; Ng, Bee Wah; Ahmad, Abdul Latif; Chieh, Derek Chan Juinn; Lim, JitKang

2014-11-07

Successful application of a magnetophoretic separation technique for harvesting biological cells often relies on the need to tag the cells with magnetic nanoparticles. This study investigates the underlying principle behind the attachment of iron oxide nanoparticles (IONPs) onto microalgal cells, Chlorella sp. and Nannochloropsis sp., in both freshwater and seawater, by taking into account the contributions of various colloidal forces involved. The complex interplay between van der Waals (vdW), electrostatic (ES) and Lewis acid-base interactions (AB) in dictating IONP attachment was studied under the framework of extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) analysis. Our results showed that ES interaction plays an important role in determining the net interaction between the Chlorella sp. cells and IONPs in freshwater, while the AB and vdW interactions play a more dominant role in dictating the net particle-to-cell interaction in high ionic strength media (≥100 mM NaCl), such as seawater. XDLVO predicted effective attachment between cells and surface functionalized IONPs (SF-IONPs) with an estimated secondary minimum of -3.12 kT in freshwater. This prediction is in accordance with the experimental observation in which 98.89% of cells can be magnetophoretically separated from freshwater with SF-IONPs. We have observed successful magnetophoretic separation of microalgal cells from freshwater and/or seawater for all the cases as long as XDLVO analysis predicts particle attachment. For both the conditions, no pH adjustment is required for particle-to-cell attachment.

Warming and drought reduce temperature sensitivity of nitrogen transformations.

PubMed

Novem Auyeung, Dolaporn S; Suseela, Vidya; Dukes, Jeffrey S

2013-02-01

Shifts in nitrogen (N) mineralization and nitrification rates due to global changes can influence nutrient availability, which can affect terrestrial productivity and climate change feedbacks. While many single-factor studies have examined the effects of environmental changes on N mineralization and nitrification, few have examined these effects in a multifactor context or recorded how these effects vary seasonally. In an old-field ecosystem in Massachusetts, USA, we investigated the combined effects of four levels of warming (up to 4 °C) and three levels of precipitation (drought, ambient, and wet) on net N mineralization, net nitrification, and potential nitrification. We also examined the treatment effects on the temperature sensitivity of net N mineralization and net nitrification and on the ratio of C mineralization to net N mineralization. During winter, freeze-thaw events, snow depth, and soil freezing depth explained little of the variation in net nitrification and N mineralization rates among treatments. During two years of treatments, warming and altered precipitation rarely influenced the rates of N cycling, and there was no evidence of a seasonal pattern in the responses. In contrast, warming and drought dramatically decreased the apparent Q10 of net N mineralization and net nitrification, and the warming-induced decrease in apparent Q10 was more pronounced in ambient and wet treatments than the drought treatment. The ratio of C mineralization to net N mineralization varied over time and was sensitive to the interactive effects of warming and altered precipitation. Although many studies have found that warming tends to accelerate N cycling, our results suggest that warming can have little to no effect on N cycling in some ecosystems. Thus, ecosystem models that assume that warming will consistently increase N mineralization rates and inputs of plant-available N may overestimate the increase in terrestrial productivity and the magnitude of an important negative feedback to climate change. © 2012 Blackwell Publishing Ltd.

Mass distribution of free insecticide-treated nets do not interfere with continuous net distribution in Tanzania

PubMed Central

2014-01-01

Background To protect the most vulnerable groups from malaria (pregnant women and infants) the Tanzanian Government introduced a subsidy (voucher) scheme in 2004, on the basis of a public-private partnership. These vouchers are provided to pregnant women at their first antenatal care visit and mothers of infants at first vaccination. The vouchers are redeemed at registered retailers for a long-lasting insecticidal net against the payment of a modest top-up price. The present work analysed a large body of data from the Tanzanian National Voucher Scheme, focusing on interactions with concurrent mass distribution campaigns of free nets. Methods In an ecologic study involving all regions of Tanzania, voucher redemption data for the period 2007 2011, as well as data on potential determinants of voucher redemption were analysed. The four outcome variables were: pregnant woman and infant voucher redemption rates, use of treated bed nets by all household members and by under- five children. Each of the outcomes was regressed with selected determinants, using a generalized estimating equation model and accounting for regional data clustering. Results There was a consistent improvement in voucher redemption rates over the selected time period, with rates >80% in 2011. The major determinants of redemption rates were the top-up price paid by the voucher beneficiary, the retailer- clinic ratio, and socio-economic status. Improved redemption rates after 2009 were most likely due to reduced top-up prices (following a change in policy). Redemption rates were not affected by two major free net distribution campaigns. During this period, there was a consistent improvement in net use across all the regions, with rates of up to 75% in 2011. Conclusion The key components of the National Treated Nets Programme (NATNETS) seem to work harmoniously, leading to a high level of net use in the entire population. This calls for the continuation of this effort in Tanzania and for emulation by other countries with endemic malaria. PMID:24884786

Mass distribution of free insecticide-treated nets do not interfere with continuous net distribution in Tanzania.

PubMed

Eze, Ikenna C; Kramer, Karen; Msengwa, Amina; Mandike, Renata; Lengeler, Christian

2014-05-27

To protect the most vulnerable groups from malaria (pregnant women and infants) the Tanzanian Government introduced a subsidy (voucher) scheme in 2004, on the basis of a public-private partnership. These vouchers are provided to pregnant women at their first antenatal care visit and mothers of infants at first vaccination. The vouchers are redeemed at registered retailers for a long-lasting insecticidal net against the payment of a modest top-up price. The present work analysed a large body of data from the Tanzanian National Voucher Scheme, focusing on interactions with concurrent mass distribution campaigns of free nets. In an ecologic study involving all regions of Tanzania, voucher redemption data for the period 2007-2011, as well as data on potential determinants of voucher redemption were analysed. The four outcome variables were: pregnant woman and infant voucher redemption rates, use of treated bed nets by all household members and by under- five children. Each of the outcomes was regressed with selected determinants, using a generalized estimating equation model and accounting for regional data clustering. There was a consistent improvement in voucher redemption rates over the selected time period, with rates >80% in 2011. The major determinants of redemption rates were the top-up price paid by the voucher beneficiary, the retailer- clinic ratio, and socio-economic status. Improved redemption rates after 2009 were most likely due to reduced top-up prices (following a change in policy). Redemption rates were not affected by two major free net distribution campaigns. During this period, there was a consistent improvement in net use across all the regions, with rates of up to 75% in 2011. The key components of the National Treated Nets Programme (NATNETS) seem to work harmoniously, leading to a high level of net use in the entire population. This calls for the continuation of this effort in Tanzania and for emulation by other countries with endemic malaria.