Chromatin segmentation based on a probabilistic model for read counts explains a large portion of the epigenome

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is an increasingly common experimental approach to generate genome-wide maps of histone modifications and to dissect the complexity of the epigenome. Here, we propose EpiCSeg: a novel algorithm that combines several histone modification maps for the segmentation and characterization of cell-type specific epigenomic landscapes. By using an accurate probabilistic model for the read counts, EpiCSeg provides a useful annotation for a considerably larger portion of the genome, shows a stronger association with validation data, and yields more consistent predictions across replicate experiments when compared to existing methods.The software is available at http://github.com/lamortenera/epicseg

Inferring nucleosome positions with their histone mark annotation from ChIP data

MOTIVATION: The nucleosome is the basic repeating unit of chromatin. It contains two copies each of the four core histones H2A, H2B, H3 and H4 and about 147 bp of DNA. The residues of the histone proteins are subject to numerous post-translational modifications, such as methylation or acetylation. Chromatin immunoprecipitiation followed by sequencing (ChIP-seq) is a technique that provides genome-wide occupancy data of these modified histone proteins, and it requires appropriate computational methods. RESULTS: We present NucHunter, an algorithm that uses the data from ChIP-seq experiments directed against many histone modifications to infer positioned nucleosomes. NucHunter annotates each of these nucleosomes with the intensities of the histone modifications. We demonstrate that these annotations can be used to infer nucleosomal states with distinct correlations to underlying genomic features and chromatin-related processes, such as transcriptional start sites, enhancers, elongation by RNA polymerase II and chromatin-mediated repression. Thus, NucHunter is a versatile tool that can be used to predict positioned nucleosomes from a panel of histone modification ChIP-seq experiments and infer distinct histone modification patterns associated to different chromatin states. AVAILABILITY: The software is available at http://epigen.molgen.mpg.de/nuchunter/. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Study of Residual Stresses from Two Machining Protocols Using an Indentation Method

Although high-speed machining offers a number of advantages over conventional machining, it is possible that the residual stress distributions generated by the former can affect the service life of the processed components. In this paper, a newly developed micro-indent method is used to evaluate different residual stress states, which were introduced in samples of AA 7075-T6 aluminum alloy milled at low and high-speed. Different surfaces were generated by varying the cutting speed in one order of magnitude, from 100 m/min to 1000 m/min. Two machining protocols, which consist of using different machine tools, were evaluated. The results show that it is possible to generate and to evaluate very small residual stresses. Finally, the values and levels obtained for normal components were analyzed in function of mechanical and thermal effects that generated the residual stresses.Fil: Diaz, Felipe Victor. Universidad Catolica de Santiago del Estero. Departamento Academico de Rafaela; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Santa Fe; ArgentinaFil: Mammana, Claudio A.. Universidad Catolica de Santiago del Estero. Departamento Academico de Rafaela; ArgentinaFil: Guidobono, Armando P.. Instituto Nacional de Tecnologia Industrial; Argentin

Productive Grasslands – The Role of Adapted Species to Increase Ecosystems Resilience

Producers are interested in diversifying grazing systems with native warm-season grasses. Climate variations may result in extreme weather events. For instance, recent studies show strong evidence pointing to an increasing frequency of flooding in the central US, due to changes in both seasonal rainfall and temperature across this region. In a constantly changing climate, adapted species play a crucial role in increasing ecosystems resilience and resistance to extreme weather events. Native grasses may be well adapted to the future changes on climatic conditions, with wide ecological amplitude and resistance under different conditions. Use of adapted warm season grasses, associated with appropriate management practices may enhance pasture ecosystem resilience, and ultimately productivity

Method to obtain nonuniformity information from field emission behavior

Copyright © 2010 American Vacuum Society / American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in Journal of Vacuum Science and Technology Part B: Microelectronics and Nanometer Structures, 28(3), Article number 441 and may be found at http://scitation.aip.org/content/avs/journal/jvstb/28/3/10.1116/1.3327928.This article describes the characterization of field emission from a planar cathode to a spherical anode with the approach curve method (ACM). In such a diode configuration the electric field strength at the cathode surface is nonuniform. This nonuniformity gives an extra degree of freedom and it allows the interpretation of the current-voltage and voltage-distance (V×d) curves in terms of nonuniformity. The authors apply the ACM to Cu emitters to explain the nonlinearity of the V×d curve in ACM measurements. This analysis provides a good insight into field emission phenomena, supporting a method for nonuniformity characterization based on field emission behavior

Determination and Analysis of Residual Stresses Induced by High Speed Milling Using a Micro-indent Method

The purpose of this work is to determine and analyze residual stress normal components and anisotropy degrees introduced by high-speed milling in specimens of AA 6082-T6 and AA 7075-T6 aluminum alloys. At each machined sample, the climb and conventional cutting zones were evaluated and compared. This paper includes a comprehensive study of thermal and mechanical effects associated with the residual stress introduction. For normal components determination, an optimized micro-indent method was used. Each measurement sequence from this approach was performed using a high accuracy measuring machine and classified according to thermal deviations measured. The residual displacements were determined with an absolute error down to ±300 nm. The normal components analysis allowed to infer the strong influence of the rolling process previous to high-speed milling and besides, the stress levels associated with thermal effects (higher in AA 7075-T6). Finally, the lower residual stress anisotropy degrees in both materials observed in the conventional cutting zone would indicate more homogenous local plastic stretching in this region for all planar directions.Fil: Vottero, S.. Universidad Tecnológica Nacional. Facultad Regional Rafaela; ArgentinaFil: Diaz, Felipe Victor. Universidad Tecnológica Nacional. Facultad Regional Rafaela; ArgentinaFil: Mammana, Claudio Alejandro. Universidad Tecnológica Nacional. Facultad Regional Rafaela; ArgentinaFil: Guidobono, A.. Instituto Nacional de Tecnología Industrial; Argentin

Detection of prions in skin punch biopsies of Creutzfeldt–Jakob disease patients

Prion real-time quaking-induced conversion (RT-QuIC) is an ultrasensitive assay detecting pathological aggregates of misfolded prion protein in biospecimens. We studied 71 punch biopsy skin samples of 35 patients with Creutzfeldt–Jakob disease (CJD), including five assessed in vitam. The results confirmed the high value of skin prion RT-QuIC for CJD diagnosis (89% sensitivity and 100% specificity) and support its use in clinical practice. Preliminary data based on a limited number of cases suggest that prion-seeding activity in the skin varies according to the prion strain, being higher in sporadic CJD subtypes linked to the V2 strain (VV2 and MV2K) than in typical CJDMM1

Buccal mucosa is a promising graft in Peyronie's disease surgery. Our experience and a brief literature review on autologous grafting materials

AIM: Peyronie's Disease (PD) is an under reported acquired benign condition that, at the moment, is not curable with medical therapy. Surgery represent the gold standard of treatment. Surgical approaches are several and they consist in "plication techniques" or plaque incision/excision with grafting of resulting albuginea defect. Among grafting procedures, albuginea defect substitution with autologous materials demonstrated over the years not inferior results respect to heterologous grafts. Buccal mucosa graft (BMG) is not usually emphasized in many review articles and clinical series are yet limited. METHODS: We present our experience with seventeen plaque incision procedures and BMG in surgical correction of complex penile curvatures due to PD performed in a period of 30 months. Our analyses was focused on buccal mucosa graft characteristics as major determinant of the surgical success. We also conducted a brief literature review on autologous grafting materials used in reconstructive penile surgery for PD. RESULTS: Our cosmetics and functional results consists in a 100% of functional penile straightening with no relapses and 5,8% of de novo erectile dysfunction. Mean age was 56.4 years, mean follow-up of 22.5 (6-36) months. No complications graft related were observed. Operative time was 115.3 minutes in mean. Over 94% of patients referred they were "really much better" and "much better" satisfied based on PGI-I questionnaire administrated at the last follow- up visit. CONCLUSION: BMG is revealing as an optimal choice for reconstructive surgery in PD. Anatomical characteristics consisting in the great elasticity, the quick integration time and the easy harvesting technique lead to high cosmetics and functional success rate, without omitting economical and invasiveness aspects

The first observed stellar occultations by the irregular satellite Phoebe (Saturn IX) and improved rotational period

peer reviewedWe report six stellar occultations by Phoebe (Saturn IX), an irregular satellite of Saturn, obtained between mid-2017 and mid-2019. The 2017 July 6 event was the first stellar occultation by an irregular satellite ever observed. The occultation chords were compared to a 3D shape model of the satellite obtained from Cassini observations. The rotation period available in the literature led to a sub-observer point at the moment of the observed occultations where the chords could not fit the 3D model. A procedure was developed to identify the correct sub-observer longitude. It allowed us to obtain the rotation period with improved precision compared to the currently known value from literature. We show that the difference between the observed and the predicted sub-observer longitude suggests two possible solutions for the rotation period. By comparing these values with recently observed rotational light curves and single- chord stellar occultations, we can identify the best solution for Phoebe's rotational period as 9.27365 ± 0.00002 h. From the stellar occultations, we also obtained six geocentric astrometric positions in the ICRS as realized by the Gaia DR2 with uncertainties at the 1-mas level