84 research outputs found
A systems approach to identifying correlated gene targets for the loss of colour pigmentation in plants
<p>Abstract</p> <p>Background</p> <p>The numerous diverse metabolic pathways by which plant compounds can be produced make it difficult to predict how colour pigmentation is lost for different tissues and plants. This study employs mathematical and <it>in silico </it>methods to identify correlated gene targets for the loss of colour pigmentation in plants from a whole cell perspective based on the full metabolic network of <it>Arabidopsis</it>. This involves extracting a self-contained flavonoid subnetwork from the AraCyc database and calculating feasible metabolic routes or elementary modes (EMs) for it. Those EMs leading to anthocyanin compounds are taken to constitute the anthocyanin biosynthetic pathway (ABP) and their interplay with the rest of the EMs is used to study the minimal cut sets (MCSs), which are different combinations of reactions to block for eliminating colour pigmentation. By relating the reactions to their corresponding genes, the MCSs are used to explore the phenotypic roles of the ABP genes, their relevance to the ABP and the impact their eliminations would have on other processes in the cell.</p> <p>Results</p> <p>Simulation and prediction results of the effect of different MCSs for eliminating colour pigmentation correspond with existing experimental observations. Two examples are: i) two MCSs which require the simultaneous suppression of genes DFR and ANS to eliminate colour pigmentation, correspond to observational results of the same genes being co-regulated for eliminating floral pigmentation in <it>Aquilegia </it>and; ii) the impact of another MCS requiring CHS suppression, corresponds to findings where the suppression of the early gene CHS eliminated nearly all flavonoids but did not affect the production of volatile benzenoids responsible for floral scent.</p> <p>Conclusions</p> <p>From the various MCSs identified for eliminating colour pigmentation, several correlate to existing experimental observations, indicating that different MCSs are suitable for different plants, different cells, and different conditions and could also be related to regulatory genes. Being able to correlate the predictions with experimental results gives credence to the use of these mathematical and <it>in silico </it>analyses methods in the design of experiments. The methods could be used to prioritize target enzymes for different objectives to achieve desired outcomes, especially for less understood pathways.</p
Specifying enough light to feel reassured on pedestrian footpaths
This article discusses lighting for pedestrians and how investigation of reassurance might lead toward an understanding of the right amount of light. A conventional approach is to evaluate reassurance after dark under road lighting of different illuminance: this tends to show the trivial result that higher illuminances enhance reassurance, and that alone does not enable an optimum light level to be identified. One reason is that the category rating procedure widely used is prone to stimulus range bias; experimental results are presented that demonstrate stimulus range bias in reassurance evaluations. This article also recommends alternative methods for future research. One such method is the dayâdark rating approach, which does not tend toward ever higher illuminances, and results are presented of two studies using this method
Structure Learning in Human Sequential Decision-Making
Studies of sequential decision-making in humans frequently find suboptimal performance relative to an ideal actor that has perfect knowledge of the model of how rewards and events are generated in the environment. Rather than being suboptimal, we argue that the learning problem humans face is more complex, in that it also involves learning the structure of reward generation in the environment. We formulate the problem of structure learning in sequential decision tasks using Bayesian reinforcement learning, and show that learning the generative model for rewards qualitatively changes the behavior of an optimal learning agent. To test whether people exhibit structure learning, we performed experiments involving a mixture of one-armed and two-armed bandit reward models, where structure learning produces many of the qualitative behaviors deemed suboptimal in previous studies. Our results demonstrate humans can perform structure learning in a near-optimal manner
People Efficiently Explore the Solution Space of the Computationally Intractable Traveling Salesman Problem to Find Near-Optimal Tours
Humans need to solve computationally intractable problems such as visual search, categorization, and simultaneous learning and acting, yet an increasing body of evidence suggests that their solutions to instantiations of these problems are near optimal. Computational complexity advances an explanation to this apparent paradox: (1) only a small portion of instances of such problems are actually hard, and (2) successful heuristics exploit structural properties of the typical instance to selectively improve parts that are likely to be sub-optimal. We hypothesize that these two ideas largely account for the good performance of humans on computationally hard problems. We tested part of this hypothesis by studying the solutions of 28 participants to 28 instances of the Euclidean Traveling Salesman Problem (TSP). Participants were provided feedback on the cost of their solutions and were allowed unlimited solution attempts (trials). We found a significant improvement between the first and last trials and that solutions are significantly different from random tours that follow the convex hull and do not have self-crossings. More importantly, we found that participants modified their current better solutions in such a way that edges belonging to the optimal solution (âgoodâ edges) were significantly more likely to stay than other edges (âbadâ edges), a hallmark of structural exploitation. We found, however, that more trials harmed the participants' ability to tell good from bad edges, suggesting that after too many trials the participants âran out of ideas.â In sum, we provide the first demonstration of significant performance improvement on the TSP under repetition and feedback and evidence that human problem-solving may exploit the structure of hard problems paralleling behavior of state-of-the-art heuristics
Simple large wood structures promote hydromorphological heterogeneity and benthic macroinvertebrate diversity in low-gradient rivers
This work has been carried out within the SMART Joint Doctorate Programme âScience for the MAnagement of Rivers and their Tidal systemsâ funded by the Erasmus Mundus programme of the European Union
Effect of invader removal: pollinators stay but some native plants miss their new friend
Removal of invasive species often benefits
biological diversity allowing ecosystemsâ recovery.
However, it is important to assess the functional roles
that invaders may have established in their new areas
to avoid unexpected results from species elimination.
Invasive animal-pollinated plants may affect the
plantâpollination interactions by changing pollinator
availability and/or behaviour in the community. Thus,
removal of an invasive plant may have important
effects on pollinator community that may then be
reflected positive or negatively on the reproductive
success of native plants. The objective of this study
was to assess the effect of removing Oxalis pescaprae,
an invasive weed widely spread in the
Mediterranean basin, on plantâpollinator interactions
and on the reproductive success of co-flowering native
plants. For this, a disturbed area in central Portugal,
where this species is highly abundant, was selected.
Visitation rates, natural pollen loads, pollen tube
growth and natural fruit set of native plants were
compared in the presence of O. pes-caprae and after
manual removal of their flowers. Our results showed a
highly resilient pollination network but also revealed
some facilitative effects of O. pes-caprae on the
reproductive success of co-flowering native plants.
Reproductive success of the native plants seems to
depend not only on the number and diversity of floral
visitors, but also on their efficiency as pollinators. The
information provided on the effects of invasive species
on the sexual reproductive success of natives is
essential for adequate management of invaded areas.This work is financed by FEDER funds through the
COMPETE Program and by Portuguese Foundation for Science
and Technology (FCT) funds in the ambit of the project PTDC/
BIA-BIC/110824/2009, by CRUP AccžoËes Integradas Luso-
Espanholas 2010 with the project E10/10, by MCI-Programa de
InternacionalizacioÂŽn de la I ? D (PT2009-0068) and by the
Spanish DGICYT (CGL2009-10466), FEDER funds from the
European Union, and the Xunta de Galicia (INCITE09-
3103009PR). FCT also supported the work of S. Castro (FCT/
BPD/41200/2007) and J. Costa (CB/C05/2009/209; PTDC/
BIA-BIC/110824/2009). The work of V. Ferrero was supported
by the FundacioÂŽn RamoÂŽn Areces
A case of behavioural diversification in male floral function â the evolution of thigmonastic pollen presentation
The authors gratefully acknowledge funding provided by an Else-Neumann-Stipendium (http://www.fu-berlin.de/sites/promovieren/drs/nachwuchs/nachwuchs/nafoeg.html), Deutscher Akademischer Austausch Dienst (DAAD) and botconsult GmbH at different stages of data acquisition. We thank Tobias Grass, Joana Bergmann and Franziska Weber (Freie UniversitÀt Berlin) for help with data collection in the field and in the greenhouse. Nicole Schmandt, Federico Luebert, Juliana Chacón and Dietmar Quant (UniversitÀt Bonn) provided help in the molecular laboratory and the edition of the molecular dataset. We furthermore thank Markus Ackermann (Koblenz) for providing photographs, Philipp Klein (Berlin) for editing the video and Katy Jones (Berlin) for helpful comments on an earlier version of the manuscript. Rafael Acuña has been supported by the ALECOSTA scholarship program. Coverage of the article processing charge by the German Research Foundation via the Open Access Publication Fund of the Freie UniversitÀt Berlin is gratefully acknowledged.Peer reviewedPublisher PD
Improved functionalization of oleic acid-coated iron oxide nanoparticles for biomedical applications
Superparamagnetic iron oxide nanoparticles
can providemultiple benefits for biomedical applications
in aqueous environments such asmagnetic separation or
magnetic resonance imaging. To increase the colloidal
stability and allow subsequent reactions, the introduction
of hydrophilic functional groups onto the particlesâ
surface is essential. During this process, the original
coating is exchanged by preferably covalently bonded
ligands such as trialkoxysilanes. The duration of the
silane exchange reaction, which commonly takes more
than 24 h, is an important drawback for this approach. In
this paper, we present a novel method, which introduces
ultrasonication as an energy source to dramatically
accelerate this process, resulting in high-quality waterdispersible nanoparticles around 10 nmin size. To prove
the generic character, different functional groups were
introduced on the surface including polyethylene glycol
chains, carboxylic acid, amine, and thiol groups. Their
colloidal stability in various aqueous buffer solutions as
well as human plasma and serum was investigated to
allow implementation in biomedical and sensing
applications.status: publishe
A922 Sequential measurement of 1 hour creatinine clearance (1-CRCL) in critically ill patients at risk of acute kidney injury (AKI)
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