genomation: a toolkit to summarize, annotate and visualize genomic intervals

Summary: Biological insights can be obtained through computational integration of genomics data sets consisting of diverse types of information. The integration is often hampered by a large variety of existing file formats, often containing similar information, and the necessity to use complicated tools to achieve the desired results. We have built an R package, genomation, to expedite the extraction of biological information from high throughput data. The package works with a variety of genomic interval file types and enables easy summarization and annotation of high throughput data sets with given genomic annotations. Availability and implementation: The software is currently distributed under MIT artistic license and freely available at http://bioinformatics.mdc-berlin.de/genomation, and through the Bioconductor framework. Contact: [email protected], [email protected], [email protected], or [email protected]

Close binary stars in the solar-age Galactic open cluster M67

We present multi-colour time-series CCD photometry of the solar-age galactic open cluster M67 (NGC 2682). About 3600 frames spread over 28 nights were obtained with the 1.5 m Russian-Turkish and 1.2 m Mercator telescopes. High-precision observations of the close binary stars AH Cnc, EV Cnc, ES Cnc, the $\delta$ Scuti type systems EX Cnc and EW Cnc, and some long-period variables belonging to M67 are presented. Three full multi-colour light curves of the overcontact binary AH Cnc were obtained during three observing seasons. Likewise we gathered three light curves of EV Cnc, an EB-type binary, and two light curves of ES Cnc, a blue straggler binary. Parts of the light change of long-term variables S1024, S1040, S1045, S1063, S1242, and S1264 are obtained. Period variation analysis of AH Cnc, EV Cnc, and ES Cnc were done using all times of mid-eclipse available in the literature and those obtained in this study. In addition, we analyzed multi-colour light curves of the close binaries and also determined new frequencies for the $\delta$ Scuti systems. The physical parameters of the close binary stars were determined with simultaneous solutions of multi-colour light and radial velocity curves. Finally we determined the distance of M67 as 857(33) pc via binary star parameters, which is consistent with an independent method from earlier studies.Comment: 12 pages, 9 Figures, 13 Table

Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities.

The mammary epithelium depends on specific lineages and their stem and progenitor function to accommodate hormone-triggered physiological demands in the adult female. Perturbations of these lineages underpin breast cancer risk, yet our understanding of normal mammary cell composition is incomplete. Here, we build a multimodal resource for the adult gland through comprehensive profiling of primary cell epigenomes, transcriptomes, and proteomes. We define systems-level relationships between chromatin-DNA-RNA-protein states, identify lineage-specific DNA methylation of transcription factor binding sites, and pinpoint proteins underlying progesterone responsiveness. Comparative proteomics of estrogen and progesterone receptor-positive and -negative cell populations, extensive target validation, and drug testing lead to discovery of stem and progenitor cell vulnerabilities. Top epigenetic drugs exert cytostatic effects; prevent adult mammary cell expansion, clonogenicity, and mammopoiesis; and deplete stem cell frequency. Select drugs also abrogate human breast progenitor cell activity in normal and high-risk patient samples. This integrative computational and functional study provides fundamental insight into mammary lineage and stem cell biology

Investigation of optimal parameters for finite element solution of the forward problem in magnetic field tomography based on magnetoencephalography

This paper presents an investigation of optimal parameters for finite element (FE) solution of the forward problem in magnetic field tomography (MFT) brain imaging based on magnetoencephalography (MEG). It highlights detailed analyses of the main parameters involved and evaluates their optimal values for various cases of FE model solutions (e.g., steady-state, transient, etc.). In each case, a detail study of some of the main parameters and their effects on FE solution and its accuracy are carefully tested and evaluated. These parameters include: total number and size of 3D FE elements used, number and size of elements used in surface discretisation (of both white and grey matters of the brain), number and size of elements used for approximation of current sources, number of anisotropic properties used in steady-state and transient solutions, and the time steps used in transient analyses. The optimal values of these parameters in relation to solution accuracy and mesh convergence criteria have been found and presented

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Prevention of chronic rejection in mouse aortic allografts by combined treatment with CTLA4-Ig and anti-CD40 ligand monoclonal antibody

Background. In this study, using a murine model of aortic allotransplantation, the role of blockade of signaling through CD28/B7 and CD40/CD40 ligand costimulatory pathways in the evolvement of posttransplant vasculopathy was examined. Methods. Aortic allografts were transplanted across C57BL/10J (H2b)→C3H (H2(k)) strain combinations. Transient or more stable blockade of second signaling was achieved by either a single injection or multiple injections of CTLA4-Ig fusion protein (200 μg/dose i.p.) and/or anti-CD40 ligand (CD40L) monoclonal antibody (250 μg i.m.). At day 30 after transplantation, the grafts were harvested for histopathological and immunohistochemical examination. Results. Similar to allografts of untreated animals, aortic allografts obtained from recipients treated with either CTLA4-Ig or anti-CD40L monoclonal antibody alone exhibited marked narrowing of the lumen primarily due to concentric intimal thickening caused by proliferation of α-smooth muscle actin-positive cells. Contemporaneous treatment, however, with either a single injection or multiple injections of CTLA4-Ig and anti-CD40L monoclonal antibody resulted in marked diminution of intimal thickening. Interestingly, concurrent prolonged inhibition of CD28/B7 and CD40/ CD40L pathways resulted in complete abrogation of the development of posttransplant arteriopathy. Conclusion. These data suggest that a more stable disruption of signaling through costimulatory pathways may be required to obviate the development of posttransplant vasculopathy

The nature and persistence of the effects of posthypnotic suggestions on food preferences: The final report of an online study

The persistence of food preferences, which are crucial for diet-related decisions, is a significant obstacle to changing unhealthy eating behavior. To overcome this obstacle, the current study investigates whether posthypnotic suggestions (PHSs) can enhance food-related decisions by measuring food choices and subjective ratings. After assessing hypnotic susceptibility in Session 1, at the beginning of Session 2, a PHS was delivered aiming to increase the desirability of healthy food items (e.g., vegetables and fruit). After the termination of hypnosis, a set of two tasks was administrated twice, once when the PHS was activated and once deactivated in counterbalanced order. The task set consisted of rating 170 pictures of food items, followed by an online supermarket where participants were instructed to select enough food from the same item pool for a fictitious week of quarantine. After 1 week, Session 3 mimicked Session 2 without renewed hypnosis induction to assess the persistence of the PHS effects. The Bayesian hierarchical modeling results indicate that the PHS increased preferences and choices of healthy food items without altering the influence of preferences in choices. In contrast, for unhealthy food items, not only both preferences and choices were decreased due to the PHS, but also their relationship was modified. That is, although choices became negatively biased against unhealthy items, preferences played a more dominant role in unhealthy choices when the PHS was activated. Importantly, all effects persisted over 1 week, qualitatively and quantitatively. Our results indicate that although the PHS affected healthy choices through resolve, i.e., preferred more and chosen more, unhealthy items were probably chosen less impulsively through effortful suppression. Together, besides the translational importance of the current results for helping the obesity epidemic in modern societies, our results contribute theoretically to the understanding of hypnosis and food choices.Peer Reviewe

Soil ecosystem services of the under different uses in the Colombian Amazonia

Agroforestry systems (AFs), where agricultural and livestock crops are associated with woody plants, are known as sustainable systems, that conserve biodiversity and improve the provision of ecosystem services without compromising productivity. This work focuses mainly on cacao AFs, which have been related to different ecosystem services in tropical regions. Especially, our study focuses on the ability of the cacao AFs to improve soil ecosystem services in the Colombian Amazon region. We focused on soil ecosystems ecosystem services in the Colombian Amazonia because: of the social importance of cacao production system in the study region, specifically within the post conflict context; the lack of knowledge on the capacity of cacao AFs to offer soil ecosystem services in the study zone and its capacity in restoring ecosystem services in degraded soils. Aim The objective of our work was to evaluate the soil quality in different cacao agroforestry systems in the Colombian Amazonia, and to compare these evaluated soil quality of soil quality in Forest and Pasture. Material and methods The study was conducted at the Macagual Amazon Research Center, located west of the Colombian Amazon. We evaluated soil quality in four types of AFs Cacao, presenting different establishment, composition and structural characteristics; but also in a plot of native forest composed of characteristic species of the area, and in a plot of pasture composed of grasses. In the different plot of each land use, we evaluated the diversity of macrofauna, the morphology of aggregate, the physical properties and the soil chemistry. We summarized these variables in a General Indicator of Soil Quality GISQ, characterizing soil quality in the different land uses. Major results and Conclusion It was found that the level of intensification among land uses (Bosque>AFs>Pasture) affects the decrease of the macrofauna populations, which was related to soil compaction (physical properties). Chemical fertility improved with the establishment of AFs influenced by the application of amendments and organic fertilizers. When establishing agroforestry systems from pasture areas at a certain level of degradation, the GISQ scale was found to increase by 42%. Our results indicate that AFs practices can definitely be used as a restoration strategy, for the recovery of degraded areas