503 research outputs found
An analysis of simple computational strategies to facilitate the design of functional molecular information processors
BACKGROUND: Biological macromolecules (DNA, RNA and proteins) are capable of processing physical or chemical inputs to generate outputs that parallel conventional Boolean logical operators. However, the design of functional modules that will enable these macromolecules to operate as synthetic molecular computing devices is challenging. RESULTS: Using three simple heuristics, we designed RNA sensors that can mimic the function of a seven-segment display (SSD). Ten independent and orthogonal sensors representing the numerals 0 to 9 are designed and constructed. Each sensor has its own unique oligonucleotide binding site region that is activated uniquely by a specific input. Each operator was subjected to a stringent in silico filtering. Random sensors were selected and functionally validated via ribozyme self cleavage assays that were visualized via electrophoresis. CONCLUSIONS: By utilising simple permutation and randomisation in the sequence design phase, we have developed functional RNA sensors thus demonstrating that even the simplest of computational methods can greatly aid the design phase for constructing functional molecular devices. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1297-x) contains supplementary material, which is available to authorized users
Understanding the limits to generalizability of experimental evolutionary models.
Post print version of article deposited in accordance with SHERPA RoMEO guidelines. The final definitive version is available online at: http://www.nature.com/nature/journal/v455/n7210/abs/nature07152.htmlGiven the difficulty of testing evolutionary and ecological theory in situ, in vitro model systems are attractive alternatives; however, can we appraise whether an experimental result is particular to the in vitro model, and, if so, characterize the systems likely to behave differently and understand why? Here we examine these issues using the relationship between phenotypic diversity and resource input in the T7-Escherichia coli co-evolving system as a case history. We establish a mathematical model of this interaction, framed as one instance of a super-class of host-parasite co-evolutionary models, and show that it captures experimental results. By tuning this model, we then ask how diversity as a function of resource input could behave for alternative co-evolving partners (for example, E. coli with lambda bacteriophages). In contrast to populations lacking bacteriophages, variation in diversity with differences in resources is always found for co-evolving populations, supporting the geographic mosaic theory of co-evolution. The form of this variation is not, however, universal. Details of infectivity are pivotal: in T7-E. coli with a modified gene-for-gene interaction, diversity is low at high resource input, whereas, for matching-allele interactions, maximal diversity is found at high resource input. A combination of in vitro systems and appropriately configured mathematical models is an effective means to isolate results particular to the in vitro system, to characterize systems likely to behave differently and to understand the biology underpinning those alternatives
Measurement of Exclusive B Decays to Final States Containing a Charmed Baryon
Using data collected by the CLEO detector in the Upsilon(4S) region, we
report new measurements of the exclusive decays of B mesons into final states
of the type Lambda_c^+ p-bar n(pi), where n=0,1,2,3. We find signals in modes
with one, two and three pions and an upper limit for the two body decay
Lambda_c^+ pbar. We also make the first measurements of exclusive decays of B
mesons to Sigma_c p-bar n(pi), where n=0,1,2. We find signals in modes with one
and two pions and an upper limit for the two body decay Sigma_c p-bar.
Measurements of these modes shed light on the mechanisms involved in B decays
to baryons.Comment: 11 pages postscript, also available through
http://w4.lns.cornell.edu/public/CLNS, submitted to PR
Measurement of the Masses and Widths of the Sigma_c^++ and Sigma_c^0 Charmed Baryons
Using data recorded by the CLEO II and CLEO II.V detector configurations at
CESR, we report new measurements of the masses of the Sigma_c^{++} and
Sigma_c^0 charmed baryons, and the first measurements of their intrinsic
widths. We find M(Sigma_c^{++}) - M(Lambda_c^+) = 167.4 +- 0.1 +- 0.2 MeV,
Gamma(Sigma_c^{++}) = 2.3 +- 0.2 +- 0.3 MeV, and M(Sigma_c^0) - M(Lambda_c^+) =
167.2 +- 0.1 +- 0.2 MeV, Gamma(Sigma_c^0) = 2.5 +- 0.2 +- 0.3 MeV, where the
uncertainties are statistical and systematic, respectively.Comment: 9 pages postscript, also available through
http://w4.lns.cornell.edu/public/CLNS, submitted to PRD, Rapid
Communications. Reference [13] correcte
Bolus characteristics based on Magnetic Resonance Angiography
BACKGROUND: A detailed contrast bolus propagation model is essential for optimizing bolus-chasing Computed Tomography Angiography (CTA). Bolus characteristics were studied using bolus-timing datasets from Magnetic Resonance Angiography (MRA) for adaptive controller design and validation. METHODS: MRA bolus-timing datasets of the aorta in thirty patients were analyzed by a program developed with MATLAB. Bolus characteristics, such as peak position, dispersion and bolus velocity, were studied. The bolus profile was fit to a convolution function, which would serve as a mathematical model of bolus propagation in future controller design. RESULTS: The maximum speed of the bolus in the aorta ranged from 5–13 cm/s and the dwell time ranged from 7–13 seconds. Bolus characteristics were well described by the proposed propagation model, which included the exact functional relationships between the parameters and aortic location. CONCLUSION: The convolution function describes bolus dynamics reasonably well and could be used to implement the adaptive controller design
Evidence for the Decay
We present a search for the ``wrong-sign'' decay D0 -> K+ pi- pi+ pi- using 9
fb-1 of e+e- collisions on and just below the Upsilon(4S) resonance. This decay
can occur either through a doubly Cabibbo-suppressed process or through mixing
to a D0bar followed by a Cabibbo-favored process. Our result for the
time-integrated wrong-sign rate relative to the decay D0 -> K- pi+ pi- pi+ is
(0.0041 +0.0012-0.0011(stat.) +-0.0004(syst.))x(1.07 +-0.10)(phase space),
which has a statistical significance of 3.9 standard deviations.Comment: 9 pages postscript, also available through
http://w4.lns.cornell.edu/public/CLNS, submitted to PR
Observation of Exclusive barB --> D(*) K*- Decays
We report the first observation of the exclusive decays \bar B\to
D^{(*)}K^{*-}, using 9.66 x 10^{6} B\bar{B} pairs collected at the \Upsilon(4S)
with the CLEO detector. We measure the following branching fractions: {\cal
B}(B^- -> D^0 K^{*-})=(6.1 +- 1.6 +-1.7)x10^{-4}, {\cal B}(\bar{B^0} ->
D^+K^{*-})=(3.7 +- 1.5 +- 1.0) x 10^{-4}, {\cal B}(\bar{B^0} ->
D^{*+}K^{*-})=(3.8 +- 1.3 +- 0.8) x 10^{-4} and {\cal B}(B^- --> D^{*0}
K^{*-})=(7.7 +- 2.2 +- 2.6) x 10^{-4}. The \bar B ->D^*K^{*-} branching ratios
are the averages of those corresponding to the 00 and 11 helicity states. The
errors shown are statistical and systematic, respectively.Comment: 9 pages postscript, also available through
http://w4.lns.cornell.edu/public/CLNS, Published in
Phys.Rev.Lett.88:101803,200
Search for the Decay
We report on a search for the radiative decay U(1S) -> gamma + eta' in 61.3
pb^-1 of data taken with the CLEO II detector at the Cornell Electron Storage
Ring. Three decay chains were investigated, all involving eta' -> pi+ pi- +
eta, followed by eta -> gamma + gamma, eta -> pi0 + pi0 + pi0, or eta -> pi+ +
pi- + pi0. We find no candidate events in any of the three cases and set a
combined upper limit of 1.6 x 10^-5 at 90% C.L., significantly smaller than the
previous limit. We compare our result to other radiative U(1S) decays, to
radiative J/psi decays, and to theoretical predictions.Comment: 9 pages postscript, also available through
http://w4.lns.cornell.edu/public/CLNS, submitted to PR
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