Clustering with shallow trees

We propose a new method for hierarchical clustering based on the optimisation of a cost function over trees of limited depth, and we derive a message--passing method that allows to solve it efficiently. The method and algorithm can be interpreted as a natural interpolation between two well-known approaches, namely single linkage and the recently presented Affinity Propagation. We analyze with this general scheme three biological/medical structured datasets (human population based on genetic information, proteins based on sequences and verbal autopsies) and show that the interpolation technique provides new insight.Comment: 11 pages, 7 figure

Protention and retention in biological systems

This paper proposes an abstract mathematical frame for describing some features of cognitive and biological time. We focus here on the so called "extended present" as a result of protentional and retentional activities (memory and anticipation). Memory, as retention, is treated in some physical theories (relaxation phenomena, which will inspire our approach), while protention (or anticipation) seems outside the scope of physics. We then suggest a simple functional representation of biological protention. This allows us to introduce the abstract notion of "biological inertia".Comment: This paper was made possible only as part of an extended collaboration with Francis Bailly (see references), a dear friend and "ma\^itre \'a penser", who contributed to the key ideas. Francis passed away in february 2008: we continue here our inspiring discussions and joint wor

Clan structure analysis and new physics signals in pp collisions at LHC

The study of possible new physics signals in global event properties in pp collisions in full phase space and in rapidity intervals accessible at LHC is presented. The main characteristic is the presence of an elbow structure in final charged particle MD's in addition to the shoulder observed at lower c.m. energies.Comment: 9 pages, talk given at Focus on Multiplicity (Bari, Italy, June 2004

Finding undetected protein associations in cell signaling by belief propagation

External information propagates in the cell mainly through signaling cascades and transcriptional activation, allowing it to react to a wide spectrum of environmental changes. High throughput experiments identify numerous molecular components of such cascades that may, however, interact through unknown partners. Some of them may be detected using data coming from the integration of a protein-protein interaction network and mRNA expression profiles. This inference problem can be mapped onto the problem of finding appropriate optimal connected subgraphs of a network defined by these datasets. The optimization procedure turns out to be computationally intractable in general. Here we present a new distributed algorithm for this task, inspired from statistical physics, and apply this scheme to alpha factor and drug perturbations data in yeast. We identify the role of the COS8 protein, a member of a gene family of previously unknown function, and validate the results by genetic experiments. The algorithm we present is specially suited for very large datasets, can run in parallel, and can be adapted to other problems in systems biology. On renowned benchmarks it outperforms other algorithms in the field.Comment: 6 pages, 3 figures, 1 table, Supporting Informatio

The effect of chronic quercetin supplementation on bone health in postmenopausal women: A double-blind placebo-controlled investigation

Currently, there is limited research investigating the effects of quercetin on bone turnover and density. Therefore, this study aimed to examine the efficacy of 90-day quercetin supplementation on bone turnover, inflammation, body composition, and physical function in postmenopausal women. Thirty-four healthy postmenopausal women (59.2 ± 7.0 yrs, 80.7 ± 15.6 kg, 29.8 ± 6.1 kg⸱m2) participated in the double-blind placebo-controlled investigation. Participants were randomly assigned to one of two groups: 500 mg of Q or 500 mg of fiber (placebo; PLB). Data collected during the pre-and post-supplementation assessments included: bone turnover (osteocalcin, P1NP, CTX), inflammation markers (IL-6, TNF-alpha, CRP), body composition, dominant handgrip strength, and timed up and go test. Independent samples t-tests were used for between-group comparisons of baseline values and the percent change for each dependent variable. A significant difference in percent change for osteocalcin (Q: 20.5±25.7; PLB: 1.3±17.2; p=0.016; d=0.89), P1NP (Q: 28.9 (6.0–57.3); PLB: 4.6 (-7.6 – 8.5); p=0.030; d=0.64), and CTX (Q: 39.0 (-10.0 – 84.6); PLB: -7.74 (-28.9 – 18.5); p=0.023; d=0.91) was found between Q and PLB, with greater increases in Q. Changes in the inflammation markers IL-6 (Q: -17.6±24.1; PLB: 2.90±31.1; p=0.045; d=0.73) and TNF-alpha (Q: -4.9± (-15.3 – [-3.2]); PLB: 1.9 (-7.8 – 4.0); p=0.021; d=0.90) between the two groups were significant. No significant changes were found between groups for CRP, body composition, and physical function (p\u3e0.05). The data suggest that Q may improve bone health status in postmenopausal women through its ability to decrease pro-inflammatory mediators and increase turnover markers

Analytic curves in algebraic varieties over number fields

We establish algebraicity criteria for formal germs of curves in algebraic varieties over number fields and apply them to derive a rationality criterion for formal germs of functions, which extends the classical rationality theorems of Borel-Dwork and P\'olya-Bertrandias valid over the projective line to arbitrary algebraic curves over a number field. The formulation and the proof of these criteria involve some basic notions in Arakelov geometry, combined with complex and rigid analytic geometry (notably, potential theory over complex and $p$-adic curves). We also discuss geometric analogues, pertaining to the algebraic geometry of projective surfaces, of these arithmetic criteria.Comment: 55 pages. To appear in "Algebra, Arithmetic, and Geometry: In Honor of Y.i. Manin", Y. Tschinkel & Yu. Manin editors, Birkh\"auser, 200

Continuous-Wave Second-Harmonic Generation in Orientation-Patterned Gallium Phosphide Waveguides at Telecom Wavelengths

A new process to produce orientation-patterned gallium phosphide (OP-GaP) on GaAs with almost perfectly parallel domain boundaries is presented. Taking advantage of the chemical selectivity between phosphides and arsenides, OP-GaP is processed into suspended shallow-ridge waveguides. Efficient second-harmonic generation from telecom wavelengths is achieved in both Type-I and Type-II polarisation configurations. The highest observed conversion efficiency is 200% W–1 cm–2, with a bandwidth of 2.67 nm in a 1 mm-long waveguide. The variation of the conversion efficiency with wavelength closely follows a squared cardinal sine function, in excellent agreement with theory, confirming the good uniformity of the poling period over the entire length of the waveguide

The Effect of Quercetin on Bone Turnover Markers, Inflammatory Markers, and Bone Mineral Density in Postmenopausal Women: A Double-Blind Placebo-Controlled Investigation

Maintaining optimal bone health prevents major bone disorders (e.g., osteoporosis) and prolongs longevity. Quercetin is a plant-based flavonoid that is suggested to have anti-inflammatory effects and may improve bone health. PURPOSE: To investigate the effects of quercetin supplementation over 90-days on prominent bone turnover markers (BTMs), inflammatory markers, bone mineral density (BMD), body composition, and physical functioning in postmenopausal women. METHODS: Thirty-three healthy, nonosteoporotic, postmenopausal women (59.2±7.0 years) participated in a double-blind, placebo-controlled investigation. Participants were randomized into one of two supplement groups: 1) 500 mg of quercetin (QUE) once daily or 2) 500 mg of methylcellulose (placebo; PLB) once daily. Pre- and post-testing visits included assessments of BTMs (i.e., osteocalcin [OC], procollagen type-I N-terminal propeptide [PINP], and type-I collagen cross-linked C-terminal telopeptide [CTX]), inflammatory markers (i.e., interleukin [IL]-6, tumor necrosis factor-alpha [TNF-a], and C-reactive protein [CRP]), BMD measurements, body composition measurements (i.e., body fat percentage), and physical function. RESULTS: The QUE group increased OC (p=0.016; d=0.89), PINP (p=0.030; d=0.64), and CTX (p=0.023; d=0.91) levels and decreased IL-6 (p=0.045; d=0.73) and TNF-a (p=0.021; d=0.90) levels compared to PLB. CRP (p=0.448; d=0.34), BMD, body composition, and physical function remained unchanged. CONCLUSION: The results indicate that QUE may maintain optimal bone health by mediating bone formation and decreasing pro-inflammatory cytokines

Reverse Engineering Gene Networks with ANN: Variability in Network Inference Algorithms

Motivation :Reconstructing the topology of a gene regulatory network is one of the key tasks in systems biology. Despite of the wide variety of proposed methods, very little work has been dedicated to the assessment of their stability properties. Here we present a methodical comparison of the performance of a novel method (RegnANN) for gene network inference based on multilayer perceptrons with three reference algorithms (ARACNE, CLR, KELLER), focussing our analysis on the prediction variability induced by both the network intrinsic structure and the available data. Results: The extensive evaluation on both synthetic data and a selection of gene modules of "Escherichia coli" indicates that all the algorithms suffer of instability and variability issues with regards to the reconstruction of the topology of the network. This instability makes objectively very hard the task of establishing which method performs best. Nevertheless, RegnANN shows MCC scores that compare very favorably with all the other inference methods tested. Availability: The software for the RegnANN inference algorithm is distributed under GPL3 and it is available at the corresponding author home page (http://mpba.fbk.eu/grimaldi/regnann-supmat