Estimating the number of change-points in a two-dimensional segmentation model without penalization

In computational biology, numerous recent studies have been dedicated to the analysis of the chromatin structure within the cell by two-dimensional segmentation methods. Motivated by this application, we consider the problem of retrieving the diagonal blocks in a matrix of observations. The theoretical properties of the least-squares estimators of both the boundaries and the number of blocks proposed by L\'evy-Leduc et al. [2014] are investigated. More precisely, the contribution of the paper is to establish the consistency of these estimators. A surprising consequence of our results is that, contrary to the onedimensional case, a penalty is not needed for retrieving the true number of diagonal blocks. Finally, the results are illustrated on synthetic data.Comment: 30 pages, 8 figure

Articulatory Tradeoffs Reduce Acoustic Variability During American English /r/ Production

Acoustic and articulatory recordings reveal that speakers utilize systematic articulatory tradeoffs to maintain acoustic stability when producing the phoneme /r/. Distinct articulator configurations used to produce /r/ in various phonetic contexts show systematic tradeoffs between the cross-sectional areas of different vocal tract sections. Analysis of acoustic and articulatory variabilities reveals that these tradeoffs act to reduce acoustic variability, thus allowing large contextual variations in vocal tract shape; these contextual variations in turn apparently reduce the amount of articulatory movement required. These findings contrast with the widely held view that speaking involves a canonical vocal tract shape target for each phoneme.National Institute on Deafness and Other Communication Disorders (1R29-DC02852-02, 5R01-DC01925-04, 1R03-C2576-0l); National Science Foundation (IRI-9310518

The Iliad’s big swoon: a case of innovation within the epic tradition

In book 5 of the Iliad Sarpedon suffers so greatly from a wound that his ‘‘ψυχή leaves him’. Rather than dying, however, Sarpedon lives to fight another day. This paper investigates the phrase τὸν δὲ λίπε ψυχή in extant archaic Greek poetry to gain a sense of its traditional referentiality and better assess the meaning of Sarpedon’s swoon. Finding that all other instances of the ψυχή leaving the body signify death, it suggests that the Iliad exploits a traditional unit of utterance to flag up the importance of Sarpedon to this version of the Troy story

Strong quantum memory at resonant Fermi edges revealed by shot noise

Studies of non-equilibrium current fluctuations enable assessing correlations involved in quantum transport through nanoscale conductors. They provide additional information to the mean current on charge statistics and the presence of coherence, dissipation, disorder, or entanglement. Shot noise, being a temporal integral of the current autocorrelation function, reveals dynamical information. In particular, it detects presence of non-Markovian dynamics, i.e., memory, within open systems, which has been subject of many current theoretical studies. We report on low-temperature shot noise measurements of electronic transport through InAs quantum dots in the Fermi-edge singularity regime and show that it exhibits strong memory effects caused by quantum correlations between the dot and fermionic reservoirs. Our work, apart from addressing noise in archetypical strongly correlated system of prime interest, discloses generic quantum dynamical mechanism occurring at interacting resonant Fermi edges.Comment: 6 pages, 3 figure

The CAST Time Projection Chamber

One of the three X-ray detectors of the CAST experiment searching for solar axions is a Time Projection Chamber (TPC) with a multi-wire proportional counter (MWPC) as a readout structure. Its design has been optimized to provide high sensitivity to the detection of the low intensity X-ray signal expected in the CAST experiment. A low hardware threshold of 0.8 keV is safely set during normal data taking periods, and the overall efficiency for the detection of photons coming from conversion of solar axions is 62 %. Shielding has been installed around the detector, lowering the background level to 4.10 x 10^-5 counts/cm^2/s/keV between 1 and 10 keV. During phase I of the CAST experiment the TPC has provided robust and stable operation, thus contributing with a competitive result to the overall CAST limit on axion-photon coupling and mass.Comment: 19 pages, 11 figures and images, submitted to New Journal of Physic

Functional significance may underlie the taxonomic utility of single amino acid substitutions in conserved proteins

We hypothesized that some amino acid substitutions in conserved proteins that are strongly fixed by critical functional roles would show lineage-specific distributions. As an example of an archetypal conserved eukaryotic protein we considered the active site of ß-tubulin. Our analysis identified one amino acid substitution—ß-tubulin F224—which was highly lineage specific. Investigation of ß-tubulin for other phylogenetically restricted amino acids identified several with apparent specificity for well-defined phylogenetic groups. Intriguingly, none showed specificity for “supergroups” other than the unikonts. To understand why, we analysed the ß-tubulin Neighbor-Net and demonstrated a fundamental division between core ß-tubulins (plant-like) and divergent ß-tubulins (animal and fungal). F224 was almost completely restricted to the core ß-tubulins, while divergent ß-tubulins possessed Y224. Thus, our specific example offers insight into the restrictions associated with the co-evolution of ß-tubulin during the radiation of eukaryotes, underlining a fundamental dichotomy between F-type, core ß-tubulins and Y-type, divergent ß-tubulins. More broadly our study provides proof of principle for the taxonomic utility of critical amino acids in the active sites of conserved proteins

Understanding the Distributions of Benthic Foraminifera in the Adriatic Sea with Gradient Forest and Structural Equation Models

Abstract: In the last three decades, benthic foraminiferal ecology has been intensively investigated to improve the potential application of these marine organisms as proxies of the effects of climate change and other global change phenomena. It is still challenging to define the most important factors affecting foraminiferal communities and derived faunistic parameters. In this study, we examined the abiotic-biotic relationships of foraminiferal communities in the central-southern area of the Adriatic Sea using modern machine learning techniques. We combined gradient forest (Gf) and structural equation modeling (SEM) to test hypotheses about determinants of benthic foraminiferal assemblages. These approaches helped determine the relative effect of sizes of different environmental variables responsible for shaping living foraminiferal distributions. Four major faunal turnovers (at 13–28 m, 29–58 m, 59–215 m, and >215 m) were identified along a large bathymetric gradient (13–703 m water depth) that reflected the classical bathymetric distribution of benthic communities. Sand and organic matter (OM) contents were identified as the most relevant factors influencing the distribution of foraminifera either along the entire depth gradient or at selected bathymetric ranges. The SEM supported causal hypotheses that focused the factors that shaped assemblages at each bathymetric range, and the most notable causal relationships were direct effects of depth and indirect effects of the Gf-identified environmental parameters (i.e., sand, pollution load Index–PLI, organic matter–OM and total nitrogen–N) on foraminifera infauna and diversity. These results are relevant to understanding the basic ecology and conservation of foraminiferal communitie

Noisy Kondo impurities

The anti-ferromagnetic coupling of a magnetic impurity carrying a spin with the conduction electrons spins of a host metal is the basic mechanism responsible for the increase of the resistance of an alloy such as Cu${}_{0.998}$Fe${}_{0.002}$ at low temperature, as originally suggested by Kondo . This coupling has emerged as a very generic property of localized electronic states coupled to a continuum . The possibility to design artificial controllable magnetic impurities in nanoscopic conductors has opened a path to study this many body phenomenon in unusual situations as compared to the initial one and, in particular, in out of equilibrium situations. So far, measurements have focused on the average current. Here, we report on \textit{current fluctuations} (noise) measurements in artificial Kondo impurities made in carbon nanotube devices. We find a striking enhancement of the current noise within the Kondo resonance, in contradiction with simple non-interacting theories. Our findings provide a test bench for one of the most important many-body theories of condensed matter in out of equilibrium situations and shed light on the noise properties of highly conductive molecular devices.Comment: minor differences with published versio