Objective Classification of Galaxy Spectra using the Information Bottleneck Method

A new method for classification of galaxy spectra is presented, based on a recently introduced information theoretical principle, the `Information Bottleneck'. For any desired number of classes, galaxies are classified such that the information content about the spectra is maximally preserved. The result is classes of galaxies with similar spectra, where the similarity is determined via a measure of information. We apply our method to approximately 6000 galaxy spectra from the ongoing 2dF redshift survey, and a mock-2dF catalogue produced by a Cold Dark Matter-based semi-analytic model of galaxy formation. We find a good match between the mean spectra of the classes found in the data and in the models. For the mock catalogue, we find that the classes produced by our algorithm form an intuitively sensible sequence in terms of physical properties such as colour, star formation activity, morphology, and internal velocity dispersion. We also show the correlation of the classes with the projections resulting from a Principal Component Analysis.Comment: submitted to MNRAS, 17 pages, Latex, with 14 figures embedde

Propagation of charged particle waves in a uniform magnetic field

This paper considers the probability density and current distributions generated by a point-like, isotropic source of monoenergetic charges embedded into a uniform magnetic field environment. Electron sources of this kind have been realized in recent photodetachment microscopy experiments. Unlike the total photocurrent cross section, which is largely understood, the spatial profiles of charge and current emitted by the source display an unexpected hierarchy of complex patterns, even though the distributions, apart from scaling, depend only on a single physical parameter. We examine the electron dynamics both by solving the quantum problem, i. e., finding the energy Green function, and from a semiclassical perspective based on the simple cyclotron orbits followed by the electron. Simulations suggest that the semiclassical method, which involves here interference between an infinite set of paths, faithfully reproduces the features observed in the quantum solution, even in extreme circumstances, and lends itself to an interpretation of some (though not all) of the rich structure exhibited in this simple problem.Comment: 39 pages, 16 figure

Paradigm of tunable clustering using binarization of consensus partition matrices (Bi-CoPaM) for gene discovery

Copyright @ 2013 Abu-Jamous et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Clustering analysis has a growing role in the study of co-expressed genes for gene discovery. Conventional binary and fuzzy clustering do not embrace the biological reality that some genes may be irrelevant for a problem and not be assigned to a cluster, while other genes may participate in several biological functions and should simultaneously belong to multiple clusters. Also, these algorithms cannot generate tight clusters that focus on their cores or wide clusters that overlap and contain all possibly relevant genes. In this paper, a new clustering paradigm is proposed. In this paradigm, all three eventualities of a gene being exclusively assigned to a single cluster, being assigned to multiple clusters, and being not assigned to any cluster are possible. These possibilities are realised through the primary novelty of the introduction of tunable binarization techniques. Results from multiple clustering experiments are aggregated to generate one fuzzy consensus partition matrix (CoPaM), which is then binarized to obtain the final binary partitions. This is referred to as Binarization of Consensus Partition Matrices (Bi-CoPaM). The method has been tested with a set of synthetic datasets and a set of five real yeast cell-cycle datasets. The results demonstrate its validity in generating relevant tight, wide, and complementary clusters that can meet requirements of different gene discovery studies.National Institute for Health Researc

Reversal of end-stage renal disease after aortic dissection using renal artery stent: a case report

BACKGROUND: Medical management is the conventional treatment for Stanford Type B aortic dissections as surgery is associated with significant morbidity and mortality. The advent of endovascular interventional techniques has revived interest in treating end-organ complications of Type B aortic dissection. We describe a patient who benefited from endovascular repair of renal artery stenosis caused by a dissection flap, which resulted in reversal of his end-stage renal disease (ESRD). CASE PRESENTATION: A 69 y/o male with a Type B aortic dissection diagnosed two months earlier was found to have a serum creatinine of 15.2 mg/dL (1343.7 μmol/L) on routine visit to his primary care physician. An MRA demonstrated a rightward spiraling aortic dissection flap involving the origins of the celiac artery, superior mesenteric artery, and both renal arteries. The right renal artery arose from the false lumen with lack of blood flow to the right kidney. The left renal artery arose from the true lumen, but an intimal dissection flap appeared to be causing an intermittent stenosis of the left renal artery with compromised blood flow to the left kidney. Endovascular reconstruction with of the left renal artery with stent placement was performed. Hemodialysis was successfully discontinued six weeks after stent placement. CONCLUSION: Percutaneous intervention provides a promising alternative for patients with Type B aortic dissections when medical treatment will not improve the likelihood of meaningful recovery and surgery entails too great a risk. Nephrologists should therefore be aggressive in the workup of ischemic renal failure associated with aortic dissection as percutaneous intervention may reverse the effects of renal failure in this population

On reminder effects, drop-outs and dominance: evidence from an online experiment on charitable giving

We present the results of an experiment that (a) shows the usefulness of screening out drop-outs and (b) tests whether different methods of payment and reminder intervals affect charitable giving. Following a lab session, participants could make online donations to charity for a total duration of three months. Our procedure justifying the exclusion of drop-outs consists in requiring participants to collect payments in person flexibly and as known in advance and as highlighted to them later. Our interpretation is that participants who failed to collect their positive payments under these circumstances are likely not to satisfy dominance. If we restrict the sample to subjects who did not drop out, but not otherwise, reminders significantly increase the overall amount of charitable giving. We also find that weekly reminders are no more effective than monthly reminders in increasing charitable giving, and that, in our three months duration experiment, standing orders do not increase giving relative to one-off donations

Systems biology via redescription and ontologies (I): finding phase changes with applications to malaria temporal data

Biological systems are complex and often composed of many subtly interacting components. Furthermore, such systems evolve through time and, as the underlying biology executes its genetic program, the relationships between components change and undergo dynamic reorganization. Characterizing these relationships precisely is a challenging task, but one that must be undertaken if we are to understand these systems in sufficient detail. One set of tools that may prove useful are the formal principles of model building and checking, which could allow the biologist to frame these inherently temporal questions in a sufficiently rigorous framework. In response to these challenges, GOALIE (Gene ontology algorithmic logic and information extractor) was developed and has been successfully employed in the analysis of high throughput biological data (e.g. time-course gene-expression microarray data and neural spike train recordings). The method has applications to a wide variety of temporal data, indeed any data for which there exist ontological descriptions. This paper describes the algorithms behind GOALIE and its use in the study of the Intraerythrocytic Developmental Cycle (IDC) of Plasmodium falciparum, the parasite responsible for a deadly form of chloroquine resistant malaria. We focus in particular on the problem of finding phase changes, times of reorganization of transcriptional control

Identifying discrete behavioural types: A re-analysis of public goods game contributions by hierarchical clustering

We propose a framework for identifying discrete behavioural types in experimental data. We re-analyse data from six previous studies of public goods voluntary contributions games. Using hierarchical clustering analysis, we construct a typology of behaviour based on a simi- larity measure between strategies. We identify four types with distinct sterotypical behaviours, which together account for about 90% of participants. Compared to previous approaches, our method produces a classification in which different types are more clearly distinguished in terms of strategic behaviour and the resulting economic implications

The structure of the PapD-PapGII pilin complex reveals an open and flexible P5 pocket

P pili are hairlike polymeric structures that mediate binding of uropathogenic Escherichia coli to the surface of the kidney via the PapG adhesin at their tips. PapG is composed of two domains: a lectin domain at the tip of the pilus followed by a pilin domain that comprises the initial polymerizing subunit of the 1,000-plus-subunit heteropolymeric pilus fiber. Prior to assembly, periplasmic pilin domains bind to a chaperone, PapD. PapD mediates donor strand complementation, in which a beta strand of PapD temporarily completes the pilin domain's fold, preventing premature, nonproductive interactions with other pilin subunits and facilitating subunit folding. Chaperone-subunit complexes are delivered to the outer membrane usher where donor strand exchange (DSE) replaces PapD's donated beta strand with an amino-terminal extension on the next incoming pilin subunit. This occurs via a zip-in-zip-out mechanism that initiates at a relatively accessible hydrophobic space termed the P5 pocket on the terminally incorporated pilus subunit. Here, we solve the structure of PapD in complex with the pilin domain of isoform II of PapG (PapGIIp). Our data revealed that PapGIIp adopts an immunoglobulin fold with a missing seventh strand, complemented in parallel by the G1 PapD strand, typical of pilin subunits. Comparisons with other chaperone-pilin complexes indicated that the interactive surfaces are highly conserved. Interestingly, the PapGIIp P5 pocket was in an open conformation, which, as molecular dynamics simulations revealed, switches between an open and a closed conformation due to the flexibility of the surrounding loops. Our study reveals the structural details of the DSE mechanism

Acute Complex Type A Dissection associated with peripheral malperfusion syndrome treated with a staged approach guided by lactate levels

Acute type A aortic dissection can be complicated by visceral malperfusion and is associated with a significant surgical morbidity and mortality. We describe a case of successful management of a complex acute type A dissection with mesenteric and lower limb ischemia treated with endovascular thoracic stenting and femoro-femoral crossover bypass grafting followed by aortic arch repair. To accomplish this, we applied a staged therapeutic approach using serial lactate measurements to assess the adequacy of peripheral perfusion and metabolic status prior to surgical repair of the proximal dissection