Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images

Motivation: Recently, confocal light sheet microscopy has enabled high-throughput acquisition of whole mouse brain 3D images at the micron scale resolution. This poses the unprecedented challenge of creating accurate digital maps of the whole set of cells in a brain. Results: We introduce a fast and scalable algorithm for fully automated cell identification. We obtained the whole digital map of Purkinje cells in mouse cerebellum consisting of a set of 3D cell center coordinates. The method is accurate and we estimated an F(1) measure of 0.96 using 56 representative volumes, totaling 1.09 GVoxel and containing 4138 manually annotated soma centers. Availability and implementation: Source code and its documentation are available at http://bcfind.dinfo.unifi.it/. The whole pipeline of methods is implemented in Python and makes use of Pylearn2 and modified parts of Scikit-learn. Brain images are available on request. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Dynamic regulation of Ero1 and peroxiredoxin 4 localization in the secretory pathway

In the early secretory compartment (ESC), a network of chaper- ones and enzymes assists oxidative folding of nascent proteins. Ero1 flavoproteins oxidize protein disulfide isomerase (PDI), gen- erating H2O2 as a byproduct. Peroxiredoxin 4 (Prx4) can utilize luminal H2O2 to oxidize PDI, thus favoring oxidative folding while limiting oxidative stress. Interestingly, neither ER oxidase contains known ER retention signal(s), raising the question of how cells pre- vent their secretion. Here we show that the two proteins share sim- ilar intracellular localization mechanisms. Their secretion is pre- vented by sequential interactions with PDI and ERp44, two resident proteins of the ESC-bearing KDEL-like motifs. PDI binds preferentially Ero1 , whereas ERp44 equally retains Ero1 and Prx4. The different binding properties of Ero1 and Prx4 increase the robustness of ER redox homeostasis

Dead or Alive? Long-term evolution of SN 2015bh (SNhunt275)

This is the final version of the article. It first appeared from Oxford University Press via http://dx.doi.org/10.1093/mnras/stw2253Supernova (SN) 2015bh (or SNhunt275) was discovered in NGC 2770 on 2015 February with an absolute magnitude of M$_r$ ~ −13.4 mag, and was initially classified as an SN impostor. Here, we present the photometric and spectroscopic evolution of SN 2015bh from discovery to late phases (~1 yr after). In addition, we inspect archival images of the host galaxy up to ~21 yr before discovery, finding a burst ~1 yr before discovery, and further signatures of stellar instability until late 2014. Later on, the luminosity of the transient slowly increases, and a broad light-curve peak is reached after about three months. We propose that the transient discovered in early 2015 could be a core-collapse SN explosion. The pre-SN luminosity variability history, the long-lasting rise and faintness first light-curve peak suggests that the progenitor was a very massive, unstable and blue star, which exploded as a faint SN because of severe fallback of material. Later on, the object experiences a sudden brightening of 3 mag, which results from the interaction of the SN ejecta with circumstellar material formed through repeated past mass-loss events. Spectroscopic signatures of interaction are however visible at all epochs. A similar chain of events was previously proposed for the similar interacting SN 2009ip.European Research Council under the European Union's Seventh Framework Programme, Science and Technology Facilities Counci

Violent behavior of patients living in psychiatric residential facilities: A comparison of male patients with different violence histories

People with severe mental disorders and a history of violence are often seen as a difficult-to-manage segment of the population. In addition, this group is usually characterized by a high risk of crime recidivism, and poor compliance with community and aftercare programs. To investigate a sample of male patients living in Residential Facilities (RFs) with a history of violent behavior against people and to compare their characteristics with those of never-violent residents; to analyze the associations between aggressive behaviors in the last two years and a history of previous violence; and, to assess the predictors of aggressive behaviors. This study is part of a prospective observational cohort study which involved 23 RFs in Northern Italy. A comprehensive set of sociodemographic, clinical, and treatment-related information was gathered, and standardized assessments were administered to each participant. Also a detailed assessment of aggressive behaviors in the past two years was carried out. The study involved 268 males: 81 violent and 187 never-violent. Compared to never-violent patients, violent patients were younger, with a higher proportion of personality disorders, and have displayed an increased number of aggressive behaviors in the last two years. The presence of a history of violent behavior in the past significantly increases the probability of committing aggressive acts in the future

The effect of service satisfaction and spiritual well-being on the quality of life of patients with schizophrenia.

Quality of life (QOL) has been considered an important outcome measure in psychiatric research and determinants of QOL have been widely investigated. We aimed at detecting predictors of QOL at baseline and at testing the longitudinal interrelations of the baseline predictors with QOL scores at a 1-year follow-up in a sample of patients living in Residential Facilities (RFs). Logistic regression models were adopted to evaluate the association between WHOQoL-Bref scores and potential determinants of QOL. In addition, all variables significantly associated with QOL domains in the final logistic regression model were included by using the Structural Equation Modeling (SEM). We included 139 patients with a diagnosis of schizophrenia spectrum. In the final logistic regression model level of activity, social support, age, service satisfaction, spiritual well-being and symptoms' severity were identified as predictors of QOL scores at baseline. Longitudinal analyses carried out by SEM showed that 40% of QOL follow-up variability was explained by QOL at baseline, and significant indirect effects toward QOL at follow-up were found for satisfaction with services and for social support. Rehabilitation plans for people with schizophrenia living in RFs should also consider mediators of change in subjective QOL such as satisfaction with mental health services

Luminous Red Novae: Stellar Mergers or Giant Eruptions?

We present extensive datasets for a class of intermediate-luminosity optical transients known as luminous red novae. They show double-peaked light curves, with an initial rapid luminosity rise to a blue peak (at -13 to -15 mag), which is followed by a longer-duration red peak that sometimes is attenuated, resembling a plateau. The progenitors of three of them (NGC 4490-2011OT1, M 101-2015OT1, and SNhunt248), likely relatively massive blue to yellow stars, were also observed in a pre-eruptive stage when their luminosity was slowly increasing. Early spectra obtained during the first peak show a blue continuum with superposed prominent narrow Balmer lines, with P Cygni profiles. Lines of Fe II are also clearly observed, mostly in emission. During the second peak, the spectral continuum becomes much redder, H alpha is barely detected, and a forest of narrow metal lines is observed in absorption. Very late-time spectra (similar to 6 months after blue peak) show an extremely red spectral continuum, peaking in the infrared (IR) domain. H alpha is detected in pure emission at such late phases, along with broad absorption bands due to molecular overtones (such as TiO, VO). We discuss a few alternative scenarios for luminous red novae. Although major instabilities of single massive stars cannot be definitely ruled out, we favour a common envelope ejection in a close binary system, with possibly a final coalescence of the two stars. The similarity between luminous red novae and the outburst observed a few months before the explosion of the Type IIn SN 2011ht is also discussed

Progranulin Gene Variability and Plasma Levels in Bipolar Disorder and Schizophrenia

Basing on the assumption that frontotemporal lobar degeneration (FTLD), schizophrenia and bipolar disorder (BPD) might share common aetiological mechanisms, we analyzed genetic variation in the FTLD risk gene progranulin (GRN) in a German population of patients with schizophrenia (n = 271) or BPD (n = 237) as compared with 574 age-, gender- and ethnicity-matched controls. Furthermore, we measured plasma progranulin levels in 26 German BPD patients as well as in 61 Italian BPD patients and 29 matched controls