Stable marriage with general preferences

We propose a generalization of the classical stable marriage problem. In our model, the preferences on one side of the partition are given in terms of arbitrary binary relations, which need not be transitive nor acyclic. This generalization is practically well-motivated, and as we show, encompasses the well studied hard variant of stable marriage where preferences are allowed to have ties and to be incomplete. As a result, we prove that deciding the existence of a stable matching in our model is NP-complete. Complementing this negative result we present a polynomial-time algorithm for the above decision problem in a significant class of instances where the preferences are asymmetric. We also present a linear programming formulation whose feasibility fully characterizes the existence of stable matchings in this special case. Finally, we use our model to study a long standing open problem regarding the existence of cyclic 3D stable matchings. In particular, we prove that the problem of deciding whether a fixed 2D perfect matching can be extended to a 3D stable matching is NP-complete, showing this way that a natural attempt to resolve the existence (or not) of 3D stable matchings is bound to fail.Comment: This is an extended version of a paper to appear at the The 7th International Symposium on Algorithmic Game Theory (SAGT 2014

Prokaryotic expression, purification and immunogenicity analysis of CpsD protein from Streptococcus iniae

Streptococcus iniae is a major cause of serious bacterial infections in both fish and human beings. Capsular polysaccharide (CPS) of S. iniae is vital to evade phagocytic clearance of the host and serves as an important protective antigen of S. iniae infection in aquatic animals. The CpsD gene was determined to be highly conservative in capsule polysaccharide operon. Prokaryotic expression of the CpsD gene of a clinical isolate of S. iniae from channel catfish and immunogenic examination of the recombinant protein were first described in this essay. The recombinant protein was expressed in the form of inclusion bodies (IBs). Induction conditions in Escherichia coli were optimized with 0.6mM Isopropyl β-D-1-Thiogalactopyranoside at 37°C for 5h after the culture mid-log phase in Luria Bertani (LB) medium. The recombinant protein CpsD was thus expressed and purified by immobilized metal affinity chromatography (IMAC), yielding approximate 582.47 mg the protein per liter culture. Western blot analysis showed that the purified CpsD had reactogenicity. It will possibly reveal more details of capsule synthesis and capsule regulation during various stages of the S. iniae infectious process

Popular matchings in the marriage and roommates problems

Popular matchings have recently been a subject of study in the context of the so-called House Allocation Problem, where the objective is to match applicants to houses over which the applicants have preferences. A matching M is called popular if there is no other matching M′ with the property that more applicants prefer their allocation in M′ to their allocation in M. In this paper we study popular matchings in the context of the Roommates Problem, including its special (bipartite) case, the Marriage Problem. We investigate the relationship between popularity and stability, and describe efficient algorithms to test a matching for popularity in these settings. We also show that, when ties are permitted in the preferences, it is NP-hard to determine whether a popular matching exists in both the Roommates and Marriage cases

Charged-Lepton-Flavour Violation in the CMSSM in View of the Muon Anomalous Magnetic Moment

We use the BNL E821 measurement of g - 2, the anomalous magnetic moment of the muon, to normalize, within a supersymmetric GUT framework, constrained MSSM (CMSSM) predictions for processes that violate charged-lepton flavour conservation, including mu to e gamma, mu to e conversion and K^0_L to mu e. We illustrate our analysis with two examples of lepton mass matrix textures motivated by data on neutrino oscillations. We find that mu to e gamma may well occur at a rate within one or two (two or three) orders of magnitude of the present experimental upper limit if g - 2 is within the one- (two-)standard deviation range indicated by E821. We also find that mu to e conversion is likely to occur at rate measurable by MECO, and there is a chance that K^0_L to mu e may be observable in an experiment using an intense proton source.Comment: 14 pages, 3 eps figure

Effect of stress-triaxiality on void growth in dynamic fracture of metals: a molecular dynamics study

The effect of stress-triaxiality on growth of a void in a three dimensional single-crystal face-centered-cubic (FCC) lattice has been studied. Molecular dynamics (MD) simulations using an embedded-atom (EAM) potential for copper have been performed at room temperature and using strain controlling with high strain rates ranging from 10^7/sec to 10^10/sec. Strain-rates of these magnitudes can be studied experimentally, e.g. using shock waves induced by laser ablation. Void growth has been simulated in three different conditions, namely uniaxial, biaxial, and triaxial expansion. The response of the system in the three cases have been compared in terms of the void growth rate, the detailed void shape evolution, and the stress-strain behavior including the development of plastic strain. Also macroscopic observables as plastic work and porosity have been computed from the atomistic level. The stress thresholds for void growth are found to be comparable with spall strength values determined by dynamic fracture experiments. The conventional macroscopic assumption that the mean plastic strain results from the growth of the void is validated. The evolution of the system in the uniaxial case is found to exhibit four different regimes: elastic expansion; plastic yielding, when the mean stress is nearly constant, but the stress-triaxiality increases rapidly together with exponential growth of the void; saturation of the stress-triaxiality; and finally the failure.Comment: 35 figures, which are small (and blurry) due to the space limitations; submitted (with original figures) to Physical Review B. Final versio

ESTIMATING GENOME-WIDE COPY NUMBER USING ALLELE SPECIFIC MIXTURE MODELS

Genomic changes such as copy number alterations are thought to be one of the major underlying causes of human phenotypic variation among normal and disease subjects [23,11,25,26,5,4,7,18]. These include chromosomal regions with so-called copy number alterations: instead of the expected two copies, a section of the chromosome for a particular individual may have zero copies (homozygous deletion), one copy (hemizygous deletions), or more than two copies (amplifications). The canonical example is Down syndrome which is caused by an extra copy of chromosome 21. Identification of such abnormalities in smaller regions has been of great interest, because it is believed to be an underlying cause of cancer. More than one decade ago comparative genomic hybridization (CGH)technology was developed to detect copy number changes in a high-throughput fashion. However, this technology only provides a 10 MB resolution which limits the ability to detect copy number alterations spanning small regions. It is widely believed that a copy number alteration as small as one base can have significant downstream effects, thus microarray manufacturers have developed technologies that provide much higher resolution. Unfortunately, strong probe effects and variation introduced by sample preparation procedures have made single-point copy number estimates too imprecise to be useful. CGH arrays use a two-color hybridization, usually comparing a sample of interest to a reference sample, which to some degree removes the probe effect. However, the resolution is not nearly high enough to provide single-point copy number estimates. Various groups have proposed statistical procedures that pool data from neighboring locations to successfully improve precision. However, these procedure need to average across relatively large regions to work effectively thus greatly reducing the resolution. Recently, regression-type models that account for probe-effect have been proposed and appear to improve accuracy as well as precision. In this paper, we propose a mixture model solution specifically designed for single-point estimation, that provides various advantages over the existing methodology. We use a 314 sample database, constructed with public datasets, to motivate and fit models for the conditional distribution of the observed intensities given allele specific copy numbers. With the estimated models in place we can compute posterior probabilities that provide a useful prediction rule as well as a confidence measure for each call. Software to implement this procedure will be available in the Bioconductor oligo packagehttp://www.bioconductor.org)

Entropy-Corrected New Agegraphic Dark Energy Model in Horava-Lifshitz Gravity

In this work, we have considered the entropy-corrected new agegraphic dark energy (ECNADE) model in Horava-Lifshitz gravity in FRW universe. We have discussed the correspondence between ECNADE and other dark energy models such as DBI-essence,Yang-Mills dark energy, Chameleon field, Non-linear electrodynamics field and hessence dark energy in the context of Horava-Lifshitz gravity and reconstructed the potentials and the dynamics of the scalar field theory which describe the ECNADE.Comment: 12 page

PRDM3 attenuates pancreatitis and pancreatic tumorigenesis by regulating inflammatory response

Pancreatic ductal adenocarcinoma (PDAC) is associated with metaplastic changes in the pancreas but the transcriptional program underlying these changes is incompletely understood. The zinc finger transcription factor, PRDM3, is lowly expressed in normal pancreatic acini and its expression increases during tumorigenesis. Although PRDM3 promotes proliferation and migration of PDAC cell lines, the role of PRDM3 during tumor initiation from pancreatic acinar cells in vivo is unclear. In this study, we showed that high levels of PRDM3 expression in human pancreas was associated with pancreatitis, and well-differentiated but not poorly differentiated carcinoma. We examined PRDM3 function in pancreatic acinar cells during tumor formation and pancreatitis by inactivating Prdm3 using a conditional allele (Ptf1a(CreER);Prdm3(flox/flox) mice) in the context of oncogenic Kras expression and supraphysiological cerulein injections, respectively. In Prdm3-deficient mice, Kras(G12D)-driven preneoplastic lesions were more abundant and progressed to high-grade precancerous lesions more rapidly. This is consistent with our observations that low levels of PRDM3 in human PDAC was correlated significantly with poorer survival in patient. Moreover, loss of Prdm3 in acinar cells elevated exocrine injury, enhanced immune cell activation and infiltration, and greatly increased acinar-to-ductal cell reprogramming upon cerulein-induced pancreatitis. Whole transcriptome analyses of Prdm3 knockout acini revealed that pathways involved in inflammatory response and Hif-1 signaling were significantly upregulated in Prdm3-depleted acinar cells. Taken together, our results suggest that Prdm3 favors the maintenance of acinar cell homeostasis through modulation of their response to inflammation and oncogenic Kras activation, and thus plays a previously unexpected suppressive role during PDAC initiation