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

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

Chemical and vibratory signals used in alarm communication in the termite Reticulitermes flavipes (Rhinotermitidae)

Termites have evolved diverse defence strategies to protect themselves against predators, including a complex alarm communication system based on vibroacoustic and/or chemical signals. In reaction to alarm signals, workers and other vulnerable castes flee away while soldiers, the specialized colony defenders, actively move toward the alarm source. In this study, we investigated the nature of alarm communication in the pest Reticulitermes flavipes. We found that workers and soldiers of R. flavipes respond to various danger stimuli using both vibroacoustic and chemical alarm signals. Among the danger stimuli, the blow of air triggered the strongest response, followed by crushed soldier head and light flash. The crushed soldier heads, which implied the alarm pheromone release, had the longest-lasting effect on the group behaviour, while the responses to other stimuli decreased quickly. We also found evidence of a positive feedback, as the release of alarm pheromones increased the vibratory communication among workers and soldiers. Our study demonstrates that alarm modalities are differentially expressed between castes, and that the response varies according to the nature of stimuli

Nlgn4 knockout induces network hypo-excitability in juvenile mouse somatosensory cortex in vitro

Neuroligins (Nlgns) are postsynaptic cell adhesion molecules that form transynaptic complexes with presynaptic neurexins and regulate synapse maturation and plasticity. We studied the impact of the loss of Nlgn4 on the excitatory and inhibitory circuits in somatosensory cortical slices of juvenile mice by electrically stimulating these circuits using a multi-electrode array and recording the synaptic input to single neurons using the patch-clamp technique. We detected a decreased network response to stimulation in both excitatory and inhibitory circuits of Nlgn4 knock-out animals as compared to wild-type controls, and a decreased excitation-inhibition ratio. These data indicate that Nlgn4 is involved in the regulation of excitatory and inhibitory circuits and contributes to a balanced circuit response to stimulation

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

VGLL2-NCOA2 leverages developmental programs for pediatric sarcomagenesis

Clinical sequencing efforts are rapidly identifying sarcoma gene fusions that lack functional validation. An example is the fusion of transcriptional coactivators, VGLL2-NCOA2, found in infantile rhabdomyosarcoma. To delineate VGLL2-NCOA2 tumorigenic mechanisms and identify therapeutic vulnerabilities, we implement a cross-species comparative oncology approach with zebrafish, mouse allograft, and patient samples. We find that VGLL2-NCOA2 is sufficient to generate mesenchymal tumors that display features of immature skeletal muscle and recapitulate the human disease. A subset of VGLL2-NCOA2 zebrafish tumors transcriptionally cluster with embryonic somitogenesis and identify VGLL2-NCOA2 developmental programs, including a RAS family GTPase, ARF6. In VGLL2-NCOA2 zebrafish, mouse, and patient tumors, ARF6 is highly expressed. ARF6 knockout suppresses VGLL2-NCOA2 oncogenic activity in cell culture, and, more broadly, ARF6 is overexpressed in adult and pediatric sarcomas. Our data indicate that VGLL2-NCOA2 is an oncogene that leverages developmental programs for tumorigenesis and that reactivation or persistence of ARF6 could represent a therapeutic opportunity