DifferentialRegulation: a Bayesian hierarchical approach to identify differentially regulated genes

MOTIVATION: Although transcriptomics data is typically used to analyse mature spliced mRNA, recent attention has focused on jointly investigating spliced and unspliced (or precursor-) mRNA, which can be used to study gene regulation and changes in gene expression production. Nonetheless, most methods for spliced/unspliced inference (such as RNA velocity tools) focus on individual samples, and rarely allow comparisons between groups of samples (e.g., healthy vs . diseased). Furthermore, this kind of inference is challenging, because spliced and unspliced mRNA abundance is characterized by a high degree of quantification uncertainty, due to the prevalence of multi-mapping reads, i.e., reads compatible with multiple transcripts (or genes), and/or with both their spliced and unspliced versions. RESULTS: Here, we present DifferentialRegulation , a Bayesian hierarchical method to discover changes between experimental conditions with respect to the relative abundance of unspliced mRNA (over the total mRNA). We model the quantification uncertainty via a latent variable approach, where reads are allocated to their gene/transcript of origin, and to the respective splice version. We designed several benchmarks where our approach shows good performance, in terms of sensitivity and error control, versus state-of-the-art competitors. Importantly, our tool is flexible, and works with both bulk and single-cell RNA-sequencing data. AVAILABILITY AND IMPLEMENTATION: DifferentialRegulation is distributed as a Bioconductor R package

A framework for digital sunken relief generation based on 3D geometric models

Sunken relief is a special art form of sculpture whereby the depicted shapes are sunk into a given surface. This is traditionally created by laboriously carving materials such as stone. Sunken reliefs often utilize the engraved lines or strokes to strengthen the impressions of a 3D presence and to highlight the features which otherwise are unrevealed. In other types of reliefs, smooth surfaces and their shadows convey such information in a coherent manner. Existing methods for relief generation are focused on forming a smooth surface with a shallow depth which provides the presence of 3D figures. Such methods unfortunately do not help the art form of sunken reliefs as they omit the presence of feature lines. We propose a framework to produce sunken reliefs from a known 3D geometry, which transforms the 3D objects into three layers of input to incorporate the contour lines seamlessly with the smooth surfaces. The three input layers take the advantages of the geometric information and the visual cues to assist the relief generation. This framework alters existing techniques in line drawings and relief generation, and then combines them organically for this particular purpose

A multiscale hybrid model for pro-angiogenic calcium signals in a vascular endothelial cell

Cytosolic calcium machinery is one of the principal signaling mechanisms by which endothelial cells (ECs) respond to external stimuli during several biological processes, including vascular progression in both physiological and pathological conditions. Low concentrations of angiogenic factors (such as VEGF) activate in fact complex pathways involving, among others, second messengers arachidonic acid (AA) and nitric oxide (NO), which in turn control the activity of plasma membrane calcium channels. The subsequent increase in the intracellular level of the ion regulates fundamental biophysical properties of ECs (such as elasticity, intrinsic motility, and chemical strength), enhancing their migratory capacity. Previously, a number of continuous models have represented cytosolic calcium dynamics, while EC migration in angiogenesis has been separately approached with discrete, lattice-based techniques. These two components are here integrated and interfaced to provide a multiscale and hybrid Cellular Potts Model (CPM), where the phenomenology of a motile EC is realistically mediated by its calcium-dependent subcellular events. The model, based on a realistic 3-D cell morphology with a nuclear and a cytosolic region, is set with known biochemical and electrophysiological data. In particular, the resulting simulations are able to reproduce and describe the polarization process, typical of stimulated vascular cells, in various experimental conditions.Moreover, by analyzing the mutual interactions between multilevel biochemical and biomechanical aspects, our study investigates ways to inhibit cell migration: such strategies have in fact the potential to result in pharmacological interventions useful to disrupt malignant vascular progressio

How do undergraduate medical students perceive social accountability?

Aim: The concept of social accountability within undergraduate training is embedded within the remit of medical schools. Little is known of how medical students perceive social accountability, recognize aspects of their training contributing to the development of this concept and cultivate the underpinning values. Methods: Students nearing graduation were recruited to participate in focus groups designed to explore their perceptions of social accountability, which curricular aspects had contributed to their understanding, and to investigate the implications of individual variations in training. Results: Students expressed limited appreciation of the concept of social accountability and acknowledged little explicit teaching around underpinning core concepts such as awareness of local health needs, advocacy and nurturing of altruism. However, participants recognized numerous aspects of the course and learning initiatives as impacting on their attitudes towards this concept implicitly. Conclusion: This study highlights areas of their undergraduate training that students recognize as having the greatest impact on their development into socially accountable professionals. It poses some significant challenges for health care educators in addressing unintended consequences, including an outcome-driven educational approach, in reducing students’ capacity or willingness to engage in curricular challenges often designed to embed this concept

3D sunken relief generation from a single image by feature line enhancement

Sunken relief is an art form whereby the depicted shapes are sunk into a given flat plane with a shallow overall depth. In this paper, we propose an efficient sunken relief generation algorithm based on a single image by the technique of feature line enhancement. Our method starts from a single image. First, we smoothen the image with morphological operations such as opening and closing operations and extract the feature lines by comparing the values of adjacent pixels. Then we apply unsharp masking to sharpen the feature lines. After that, we enhance and smoothen the local information to obtain an image with less burrs and jaggies. Differential operations are applied to produce the perceptive relief-like images. Finally, we construct the sunken relief surface by triangularization which transforms two-dimensional information into a three-dimensional model. The experimental results demonstrate that our method is simple and efficient

Alu-Alu Recombination Underlying the First Large Genomic Deletion in GlcNAc-Phosphotransferase Alpha/Beta (GNPTAB) Gene in a MLII Alpha/Beta Patient

Mucolipidosis type II α/β is a severe, autosomal recessive lysosomal storage disorder, caused by a defect in the GNPTAB gene that codes for the α/β subunits of the GlcNAc-phosphotransferase. To date, over 100 different mutations have been identified in MLII α/β patients, but no large deletions have been reported. Here we present the first case of a large homozygous intragenic GNPTAB gene deletion (c.3435-386_3602 + 343del897) encompassing exon 19, identified in a ML II α/β patient. Long-range PCR and sequencing methodologies were used to refine the characterization of this rearrangement, leading to the identification of a 21 bp repetitive motif in introns 18 and 19. Further analysis revealed that both the 5' and 3' breakpoints were located within highly homologous Alu elements (Alu-Sz in intron 18 and Alu-Sq2, in intron 19), suggesting that this deletion has probably resulted from Alu-Alu unequal homologous recombination. RT-PCR methods were used to further evaluate the consequences of the alteration for the processing of the mutant pre mRNA GNPTAB, revealing the production of three abnormal transcripts: one without exon 19 (p.Lys1146_Trp1201del); another with an additional loss of exon 20 (p.Arg1145Serfs*2), and a third in which exon 19 was substituted by a pseudoexon inclusion consisting of a 62 bp fragment from intron 18 (p.Arg1145Serfs*16). Interestingly, this 62 bp fragment corresponds to the Alu-Sz element integrated in intron 18.This represents the first description of a large deletion identified in the GNPTAB gene and contributes to enrich the knowledge on the molecular mechanisms underlying causative mutations in ML II.This work was supported by FCT - project PIC/IC/83252/2007 (http://alfa.fct.mctes.pt/). Coutinho MF and Quental S received grants from the FCT (SFRH/BD/48103/2008; SFRH/BPD/64025/2009)

An Oscillatory Contractile Pole-Force Component Dominates the Traction Forces Exerted by Migrating Amoeboid Cells

We used principal component analysis to dissect the mechanics of chemotaxis of amoeboid cells into a reduced set of dominant components of cellular traction forces and shape changes. The dominant traction force component in wild-type cells accounted for ~40% of the mechanical work performed by these cells, and consisted of the cell attaching at front and back contracting the substrate towards its centroid (pole-force). The time evolution of this pole-force component was responsible for the periodic variations of cell length and strain energy that the cells underwent during migration. We identified four additional canonical components, reproducible from cell to cell, overall accounting for an additional ~20% of mechanical work, and associated with events such as lateral protrusion of pseudopodia. We analyzed mutant strains with contractility defects to quantify the role that non-muscle Myosin II (MyoII) plays in amoeboid motility. In MyoII essential light chain null cells the polar-force component remained dominant. On the other hand, MyoII heavy chain null cells exhibited a different dominant traction force component, with a marked increase in lateral contractile forces, suggesting that cortical contractility and/or enhanced lateral adhesions are important for motility in this cell line. By compressing the mechanics of chemotaxing cells into a reduced set of temporally-resolved degrees of freedom, the present study may contribute to refined models of cell migration that incorporate cell-substrate interactions

On the Peripheries of Planetary Urbanization: Globalizing Manaus and its Expanding Impact

In this paper I argue that global urbanism produces peripherality in ways that cannot be adequately problematized without taking into account its actual extent and geographically uneven development. Therefore, planetary urbanization needs to engage scholarly traditions attuned to regional urbanization if the discourse is to move past limitations in the urban globalization canon and its narrow focus on cities. To that end, I examine research on extensive urbanization in the Amazon region. Illustrative case studies show how attempts to globalize Manaus precipitated territorial restructuring and sociospatial change far beyond the city's boundaries. Manaus is now a more unequal city. Selective metropolitan expansion to the Rio Negro's south bank has led to the simultaneous upgrading and peripheralization of Iranduba. Yet, the building of a city-centric regional network of roadways also shaped Roraima State's transformation from isolated borderland to bypassed periphery. Moreover, financial and symbolic appropriations of standing rainforests by metropolitan conservationism marginalize remote communities even in the absence of exploitative deforestation and resource extraction. Final remarks emphasize the need for further research on the hybrid (urban—rural) conditions and functional articulations of distant-yet-impacted peripheries. Such efforts may broaden the political horizons of planetary urbanization by informing extensive contestations of entrepreneurial urbanism