7,500 research outputs found
An inquiry-based learning approach to teaching information retrieval
The study of information retrieval (IR) has increased in interest and importance with the explosive growth of online information in recent years. Learning about IR within formal courses of study enables users of search engines to use
them more knowledgeably and effectively, while providing the starting point for the explorations of new researchers into novel search technologies. Although IR can be taught in a traditional manner of formal classroom instruction with students being led through the details of the subject and expected to reproduce this in assessment, the nature of IR as a topic makes it an ideal subject for inquiry-based learning approaches to teaching. In an inquiry-based learning approach students are introduced to the principles of a subject and then encouraged to develop their understanding by solving structured or open problems. Working through solutions in subsequent class discussions enables students to appreciate the availability of alternative solutions as proposed by their classmates. Following this approach students not only learn the details of IR techniques, but significantly, naturally learn to apply them in solution of problems. In doing this they not only gain an appreciation of alternative solutions to a problem, but also how to assess their relative strengths and weaknesses. Developing confidence and skills in problem solving enables student assessment to be structured around solution of problems. Thus students can be assessed on the basis of their understanding and ability to apply techniques, rather simply their skill at reciting facts. This has the additional benefit of encouraging general problem solving skills which can be of benefit in other subjects. This approach to teaching IR was successfully implemented in an undergraduate module where students were
assessed in a written examination exploring their knowledge and understanding of the principles of IR and their ability to apply them to solving problems, and a written assignment based on developing an individual research proposal
Computational Design and Elaboration of a De Novo Heterotetrameric α-Helical Protein that Selectively Binds an Emissive Abiological (Porphinato)zinc Chromophore
The first example of a computationally de novo designed protein that binds an emissive abiological chromophore is presented, in which a sophisticated level of cofactor discrimination is pre-engineered. This heterotetrameric, C(2)-symmetric bundle, A(His):B(Thr), uniquely binds (5,15-di[(4-carboxymethyleneoxy)phenyl]porphinato)zinc [(DPP)Zn] via histidine coordination and complementary noncovalent interactions. The A(2)B(2) heterotetrameric protein reflects ligand-directed elements of both positive and negative design, including hydrogen bonds to second-shell ligands. Experimental support for the appropriate formulation of [(DPP)Zn:A(His):B(Thr)](2) is provided by UV/visible and circular dichroism spectroscopies, size exclusion chromatography, and analytical ultracentrifugation. Time-resolved transient absorption and fluorescence spectroscopic data reveal classic excited-state singlet and triplet PZn photophysics for the A(His):B(Thr):(DPP)Zn protein (k(fluorescence) = 4 x 10(8) s(-1); tau(triplet) = 5 ms). The A(2)B(2) apoprotein has immeasurably low binding affinities for related [porphinato]metal chromophores that include a (DPP)Fe(III) cofactor and the zinc metal ion hemin derivative [(PPIX)Zn], underscoring the exquisite active-site binding discrimination realized in this computationally designed protein. Importantly, elements of design in the A(His):B(Thr) protein ensure that interactions within the tetra-alpha-helical bundle are such that only the heterotetramer is stable in solution; corresponding homomeric bundles present unfavorable ligand-binding environments and thus preclude protein structural rearrangements that could lead to binding of (porphinato)iron cofactors
The Power Spectrum, Bias Evolution, and the Spatial Three-Point Correlation Function
We calculate perturbatively the normalized spatial skewness, , and full
three-point correlation function (3PCF), , induced by gravitational
instability of Gaussian primordial fluctuations for a biased tracer-mass
distribution in flat and open cold-dark-matter (CDM) models. We take into
account the dependence on the shape and evolution of the CDM power spectrum,
and allow the bias to be nonlinear and/or evolving in time, using an extension
of Fry's (1996) bias-evolution model. We derive a scale-dependent,
leading-order correction to the standard perturbative expression for in
the case of nonlinear biasing, as defined for the unsmoothed galaxy and
dark-matter fields, and find that this correction becomes large when probing
positive effective power-spectrum indices. This term implies that the inferred
nonlinear-bias parameter, as usually defined in terms of the smoothed density
fields, might depend on the chosen smoothing scale. In general, we find that
the dependence of on the biasing scheme can substantially outweigh that
on the adopted cosmology. We demonstrate that the normalized 3PCF, , is an
ill-behaved quantity, and instead investigate , the variance-normalized
3PCF. The configuration dependence of shows similarly strong
sensitivities to the bias scheme as , but also exhibits significant
dependence on the form of the CDM power spectrum. Though the degeneracy of
with respect to the cosmological parameters and constant linear- and
nonlinear-bias parameters can be broken by the full configuration dependence of
, neither statistic can distinguish well between evolving and non-evolving
bias scenarios. We show that this can be resolved, in principle, by considering
the redshift dependence of .Comment: 41 pages, including 12 Figures. To appear in The Astrophysical
Journal, Vol. 521, #
Probing Primordial Non-Gaussianity with Large-Scale Structure
We consider primordial non-Gaussianity due to quadratic corrections in the
gravitational potential parametrized by a non-linear coupling parameter fnl. We
study constraints on fnl from measurements of the galaxy bispectrum in redshift
surveys. Using estimates for idealized survey geometries of the 2dF and SDSS
surveys and realistic ones from SDSS mock catalogs, we show that it is possible
to probe |fnl|~100, after marginalization over bias parameters. We apply our
methods to the galaxy bispectrum measured from the PSCz survey, and obtain a
2sigma-constraint |fnl|< 1800. We estimate that an all sky redshift survey up
to z~1 can probe |fnl|~1. We also consider the use of cluster abundance to
constrain fnl and find that in order to be sensitive to |fnl|~100, cluster
masses need to be determined with an accuracy of a few percent, assuming
perfect knowledge of the mass function and cosmological parameters.Comment: 15 pages, 7 figure
Improving the mass determination of Galactic Cepheids
We have selected a sample of Galactic Cepheids for which accurate estimates
of radii, distances, and photometric parameters are available. The comparison
between their pulsation masses, based on new Period-Mass-Radius (PMR)
relations, and their evolutionary masses, based on both optical and NIR
Color-Magnitude (CM) diagrams, suggests that pulsation masses are on average of
the order of 10% smaller than the evolutionary masses. Current pulsation masses
show, at fixed radius, a strongly reduced dispersion when compared with values
published in literature.The increased precision in the pulsation masses is due
to the fact that our predicted PMR relations based on nonlinear, convective
Cepheid models present smaller standard deviations than PMR relations based on
linear models. At the same time, the empirical radii of our Cepheid sample are
typically accurate at the 5% level. Our evolutionary mass determinations are
based on stellar models constructed by neglecting the effect of mass-loss
during the He burning phase. Therefore, the difference between pulsation and
evolutionary masses could be intrinsic and does not necessarily imply a problem
with either evolutionary and/or nonlinear pulsation models. The marginal
evidence of a trend in the difference between evolutionary and pulsation masses
when moving from short to long-period Cepheids is also briefly discussed. The
main finding of our investigation is that the long-standing Cepheid mass
discrepancy seems now resolved at the 10% level either if account for canonical
or mild convective core overshooting evolutionary models.Comment: 14 pages, 4 postscript figures, accepted for publication on ApJ
Letter
Long range neutrino forces in the cosmic relic neutrino background
Neutrinos mediate long range forces among macroscopic bodies in vacuum. When
the bodies are placed in the neutrino cosmic background, these forces are
modified. Indeed, at distances long compared to the scale , the relic
neutrinos completely screen off the 2-neutrino exchange force, whereas for
small distances the interaction remains unaffected.Comment: 8 pages, 2 figure
Accurate quantification of apoptosis progression and toxicity using a dielectrophoretic approach
A loss of ability of cells to undergo apoptosis (programmed cell death, whereby the cell ceases to function and destroys itself) is commonly associated with cancer, and many anti-cancer interventions aim to restart the process. Consequently, the accurate quantification of apoptosis is essential in understanding the function and performance of new anti-cancer drugs. Dielectrophoresis has previously been demonstrated to detect apoptosis more rapidly than other methods, and is low-cost, label-free and rapid, but has previously been unable to accurately quantify cells through the apoptotic process because cells in late apoptosis disintegrate, making cell tracking impossible. In this paper we use a novel method based on light absorbance and multi-population tracking to quantify the progress of apoptosis, benchmarking against conventional assays including MTT, trypan blue and Annexin-V. Analyses are performed on suspension and adherent cells, and using two apoptosis-inducing agents. IC50 measurements compared favourably to MTT and were superior to trypan blue, whilst also detecting apoptotic progression faster than Annexin-V
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