Probabilistic Clustering of Time-Evolving Distance Data

We present a novel probabilistic clustering model for objects that are represented via pairwise distances and observed at different time points. The proposed method utilizes the information given by adjacent time points to find the underlying cluster structure and obtain a smooth cluster evolution. This approach allows the number of objects and clusters to differ at every time point, and no identification on the identities of the objects is needed. Further, the model does not require the number of clusters being specified in advance -- they are instead determined automatically using a Dirichlet process prior. We validate our model on synthetic data showing that the proposed method is more accurate than state-of-the-art clustering methods. Finally, we use our dynamic clustering model to analyze and illustrate the evolution of brain cancer patients over time

Asymmetries between the production of D+ and D- mesons from 500 GeV/c pi- nucleon interactions as a function of xF and pt**2

We present asymmetries between the production of D+ and D- mesons in Fermilab experiment E791 as a function of xF and pt**2. The data used here consist of 74,000 fully-reconstructed charmed mesons produced by a 500 GeV/c pi- beam on C and Pt foils. The measurements are compared to results of models which predict differences between the production of heavy-quark mesons that have a light quark in common with the beam (leading particles) and those that do not (non-leading particles). While the default models do not agree with our data, we can reach agreement with one of them, PYTHIA, by making a limited number of changes to parameters used

LipocalinPred: a SVM-based method for prediction of lipocalins

<p>Abstract</p> <p>Background</p> <p>Functional annotation of rapidly amassing nucleotide and protein sequences presents a challenging task for modern bioinformatics. This is particularly true for protein families sharing extremely low sequence identity, as for lipocalins, a family of proteins with varied functions and great diversity at the sequence level, yet conserved structures.</p> <p>Results</p> <p>In the present study we propose a SVM based method for identification of lipocalin protein sequences. The SVM models were trained with the input features generated using amino acid, dipeptide and secondary structure compositions as well as PSSM profiles. The model derived using both PSSM and secondary structure emerged as the best model in the study. Apart from achieving a high prediction accuracy (>90% in leave-one-out), lipocalinpred correctly differentiates closely related fatty acid-binding proteins and triabins as non-lipocalins.</p> <p>Conclusion</p> <p>The method offers a promising approach as a lipocalin prediction tool, complementing PROSITE, Pfam and homology modelling methods.</p

Very Low-Mass Stellar and Substellar Companions to Solar-Like Stars from MARVELS I: A Low Mass Ratio Stellar Companion to TYC 4110-01037-1 in a 79-day Orbit

TYC 4110-01037-1 has a low-mass stellar companion, whose small mass ratio and short orbital period are atypical amongst solar-like (Teff ~< 6000 K) binary systems. Our analysis of TYC 4110-01037-1 reveals it to be a moderately aged (~<5 Gyr) solar-like star having a mass of 1.07 +/- 0.08 MSun and radius of 0.99 +/- 0.18 RSun. We analyze 32 radial velocity measurements from the SDSS-III MARVELS survey as well as 6 supporting radial velocity measurements from the SARG spectrograph on the 3.6m TNG telescope obtained over a period of ~2 years. The best Keplerian orbital fit parameters were found to have a period of 78.994 +/- 0.012 days, an eccentricity of 0.1095 +/- 0.0023, and a semi-amplitude of 4199 +/- 11 m/s. We determine the minimum companion mass (if sin i = 1) to be 97.7 +/- 5.8 MJup. The system's companion to host star mass ratio, >0.087 +/- 0.003, places it at the lowest end of observed values for short period stellar companions to solar-like (Teff ~< 6000 K) stars. One possible way to create such a system would be if a triple-component stellar multiple broke up into a short period, low q binary during the cluster dispersal phase of its lifetime. A candidate tertiary body has been identified in the system via single-epoch, high contrast imagery. If this object is confirmed to be co-moving, we estimate it would be a dM4 star. We present these results in the context of our larger-scale effort to constrain the statistics of low mass stellar and brown dwarf companions to FGK-type stars via the MARVELS survey.Comment: 22 pages; accepted in A

The EGS Grading Scale For Skin And Soft Tissue Infections Is Predictive Of Poor Outcomes : A Multicenter Validation Study

Introduction: Over the last five years, the American Association for the Surgery of Trauma (AAST) has developed grading scales for Emergency General Surgery (EGS) diseases. In a prior validation study using diverticulitis, the grading scales were predictive of complications and length of stay. As EGS encompasses diverse diseases, the purpose of this study was to validate the grading scale concept against a different disease process with a higher associated mortality. We hypothesized that the grading scale would be predictive of complications, length of stay and mortality in skin and soft tissue infections (STI). Methods: This multi-institutional trial encompassed 12 centers. Data collected included demographic variables, disease characteristics and outcomes such as mortality, overall complications, hospital and ICU length of stay. The EGS scale for STI was used to grade each infection and two surgeons graded each case to evaluate inter-rater reliability. Results: 1170 patients were included in this study. Inter-rater reliability was moderate (kappa coefficient 0.472-0.642, with 64-76% agreement). Higher grades (IV and V) corresponded to significantly higher LRINEC scores when compared with lower EGS grades. Patients with grade IV and V STI had significantly increased odds of all complications, as well as ICU and overall length of stay. These associations remained significant in logistic regression controlling for age, gender, comorbidities, mental status and hospital-level volume. Grade V disease was significantly associated with mortality as well. Conclusion: This validation effort demonstrates that Grade IV and V STI are significantly predictive of complications, hospital length of stay and mortality. Though predictive ability does not improve linearly with STI grade, this is consistent with the clinical disease process, in which lower grades represent cellulitis and abscess and higher grades are invasive infections. This second validation study confirms the EGS grading scale as predictive, and easily used, in disparate disease processes

Submarine volcanic morphology of the western Galapagos based on EM300 bathymetry and MR1 side-scan sonar

Author Posting. © American Geophysical Union, 2007. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 8 (2007): Q03010, doi:10.1029/2006GC001464.A compilation of high-resolution EM300 multibeam bathymetric and existing MR1 side-scan sonar data was used to investigate the volcanic morphology of the flanks of the western Galápagos Islands. The data portray an assortment of constructional volcanic features on the shallow to deep submarine flanks of Fernandina, Isabela, and Santiago Islands, including rift zones and groups of cones that are considered to be the primary elements in constructing the archipelagic apron. Ten submarine rift zones were mapped, ranging in length from 5 to 20 km, comparable in length to western Canary Island rift zones but significantly shorter than Hawaiian submarine rift zones. A detailed analysis of the northwestern Fernandina submarine rift, including calculated magnetization from a surface-towed magnetic study, suggests that the most recent volcanism has focused at the shallow end of the rift. Small submarine volcanic cones with various morphologies (e.g., pointed, cratered, and occasionally breached) are common in the submarine western Galápagos both on rift zones and on the island flanks where no rifts are present. At depths greater than ∼3000 m, large lava flow fields in regions of low bathymetric relief have been previously identified as a common seafloor feature in the western Galápagos by Geist et al. (2006); however, their source(s) remained enigmatic. The new EM300 data show that a number of the deep lava flows originate from small cones along the mid-lower portion of the NW submarine rift of Fernandina, suggesting that the deep flows owe their origin, at least in part, to submarine rift zone volcanism.Data collected on TN188 was funded by NSF grant OCE0326148 and NOAA grant NA04OAR460009 to S.M.W. Support for data collected on previous multibeam and MR1 cruises was provided by NSF grants OCE9811504 and OCE0002461 (D.J.F.)

Crystal structure of the ferritin from the hyperthermophilic archaeal anaerobe Pyrococcus furiosus

The crystal structure of the ferritin from the archaeon, hyperthermophile and anaerobe Pyrococcus furiosus (PfFtn) is presented. While many ferritin structures from bacteria to mammals have been reported, until now only one was available from archaea, the ferritin from Archaeoglobus fulgidus (AfFtn). The PfFtn 24-mer exhibits the 432 point-group symmetry that is characteristic of most ferritins, which suggests that the 23 symmetry found in the previously reported AfFtn is not a common feature of archaeal ferritins. Consequently, the four large pores that were found in AfFtn are not present in PfFtn. The structure has been solved by molecular replacement and refined at 2.75-Å resolution to R = 0.195 and Rfree = 0.247. The ferroxidase center of the aerobically crystallized ferritin contains one iron at site A and shows sites B and C only upon iron or zinc soaking. Electron paramagnetic resonance studies suggest this iron depletion of the native ferroxidase center to be a result of a complexation of iron by the crystallization salt. The extreme thermostability of PfFtn is compared with that of eight structurally similar ferritins and is proposed to originate mostly from the observed high number of intrasubunit hydrogen bonds. A preservation of the monomer fold, rather than the 24-mer assembly, appears to be the most important factor that protects the ferritin from inactivation by heat

Asymmetries Between the Production of Ds- and Ds+ Mesons from 500 GeV/c pi- Nucleon Interactions as Functions of x_F and square of p_t

This paper presents measurements of the production of Ds- mesons relative to Ds+ mesons as functions of x_F and square of p_t for a sample of 2445 Ds decays to phi pi. The Ds mesons were produced in Fermilab experiment E791 with 500 GeV/c pi- mesons incident on one platinum and four carbon foil targets. The acceptance-corrected integrated asymmetry in the x_F range -0.1 to 0.5 for Ds+- mesons is 0.032 +- 0.022 +- 0.022, consistent with no net asymmetry. The results, as functions of x_F and square of p_t, are compared to predictions and to the large production asymmetry observed for D+- mesons in the same experiment. These comparisons support the hypothesis that production asymmetries come from the fragmentation process and not from the charm quark production itself.Comment: Latex file (11 pages) and three eps files for figures This paper has been accepted for publication by Physics Letters

Asymmetries in the production of lambda zero, cascade minus, and omega minus hyperons in 500 GeV/c pi minus-Nucleon Interactions

Using data from Fermilab fixed-target experiment E791, we have measured particle-antiparticle production asymmetries for lambda zero, cascade minus, and omega minus hyperons in pi minus-nucleon interactions at 500 GeV/c. The asymmetries are measured as functions of Feynman-x (x_F) and pt^2 over the ranges of -0.12 GE x_F LE 0.12 and 0 GE pt^2 LE 4 (GeV/c)^2. We find substantial asymmetries, even at x_F = 0. We also observe leading-particle- type asymmetries which qualitatively agree with theoretical predictions.Comment: 15 pages, including 5 figures and 2 tables. To be submitted to Phys. Lett.