The integration of morphological design and topology optimization to enhance the visual quality of electricity pylons

Purpose: This paper aims to enhance the visual quality of artificial above-ground structures, like pylons, masts, and towers of infrastructures and facilities, through a systematic design method for their morphological and structural optimization. Design/methodology/approach: The method achieves the functional and aesthetic goals based on the application of computer-aided tools. In particular, this is achieved according to three key steps: • Morphological development of landscape-related symbolism, environment, or culture and social needs. • Topology optimization of the design concept to reduce the structural weight and its visual impact. • Engineering of the resulting optimized structure. Practical implications: As a case study, the method is used for designing electricity pylons for the coastal territory of a Mediterranean European country, such as Italy. Citizens were involved during the identification phase of a symbolic shape for the concept development and during the final assessment phase. Research limitations/implications: The engineering phase has been performed by assembling standard lattice components with welded connections. Even if the use of this truss-like structure should lead to a minimum cost, the developed structure employs an additional 15%–20% of trusses and sheet metal covers the final cost is higher than a standard lattice pylon. Findings: The result is a structure with enhanced visual quality according to the international guidelines and fully complying with mandatory and functional requirements, such as regulatory and industrial feasibility, as well as those arising from social components. Originality/value: The method shows its potential in defining a custom design for lightweight structures with enhanced visual quality regarding the critical situation discussed here. The method considers both the subjective perception of citizens and their priorities and the landscape where the structures will be installed

Artificial intelligence methods enhance the discovery of RNA interactions

Understanding how RNAs interact with proteins, RNAs, or other molecules remains a challenge of main interest in biology, given the importance of these complexes in both normal and pathological cellular processes. Since experimental datasets are starting to be available for hundreds of functional interactions between RNAs and other biomolecules, several machine learning and deep learning algorithms have been proposed for predicting RNA-RNA or RNA-protein interactions. However, most of these approaches were evaluated on a single dataset, making performance comparisons difficult. With this review, we aim to summarize recent computational methods, developed in this broad research area, highlighting feature encoding and machine learning strategies adopted. Given the magnitude of the effect that dataset size and quality have on performance, we explored the characteristics of these datasets. Additionally, we discuss multiple approaches to generate datasets of negative examples for training. Finally, we describe the best-performing methods to predict interactions between proteins and specific classes of RNA molecules, such as circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs), and methods to predict RNA-RNA or RNA-RBP interactions independently of the RNA type

Vasoactive intestinal peptide, whose receptor-mediated signalling may be defective in alopecia areata, provides protection from hair follicle immune privilege collapse

Background: Alopecia areata (AA) is an autoimmune disorder whose pathogenesis involves the collapse of the relative immune privilege (IP) of the hair follicle (HF). Given that vasoactive intestinal peptide (VIP) is an immunoinhibitory neuropeptide released by perifollicular sensory nerve fibres, which play a role in IP maintenance, it may modulate human HF-IP and thus be therapeutically relevant for AA. Objectives: To answer the following questions: Do human HFs express VIP receptors, and does their stimulation protect from or restore experimentally induced HF-IP collapse? Is VIP signalling defective in AA HFs?. Methods: Firstly, VIP and VIP receptor (VPAC1, VPAC2) expression in human scalp HFs and AA skin was assessed. In HF organ culture, we then explored whether VIP treatment can restore and/or protect from interferon-γ-induced HF-IP collapse, assessing the expression of the key IP markers by quantitative (immuno-)histomorphometry. Results: Here we provide the first evidence that VIP receptors are expressed in the epithelium of healthy human HFs at the gene and protein level. Furthermore, VIP receptor protein expression, but not VIP+ nerve fibres, is significantly downregulated in lesional hair bulbs of patients with AA, suggesting defects in VIP receptor-mediated signalling. Moreover, we show that VIP protects the HF from experimentally induced IP collapse in vitro, but does not fully restore it once collapsed. Conclusions: These pilot data suggest that insufficient VIP receptor-mediated signalling may contribute to impairing HF-IP in patients with AA, and that VIP is a promising candidate ‘HF-IP guardian’ that may be therapeutically exploited to inhibit the progression of AA lesions.</p

Systemic immunity is required for effective cancer immunotherapy

Immune responses involve coordination across cell types and tissues. However, studies in cancer immunotherapy have focused heavily on local immune responses in the tumor microenvironment. To investigate immune activity more broadly, we performed an organism-wide study in genetically engineered cancer models using mass cytometry. We analyzed immune responses in several tissues after immunotherapy by developing intuitive models for visualizing single-cell data with statistical inference. Immune activation was evident in the tumor and systemically shortly after effective therapy was administered. However, during tumor rejection, only peripheral immune cells sustained their proliferation. This systemic response was coordinated across tissues and required for tumor eradication in several immunotherapy models. An emergent population of peripheral CD4 T cells conferred protection against new tumors and was significantly expanded in patients responding to immunotherapy. These studies demonstrate the critical impact of systemic immune responses that drive tumor rejection

Carotid Ultrasound Boundary Study (CUBS): An Open Multicenter Analysis of Computerized Intima–Media Thickness Measurement Systems and Their Clinical Impact

Common carotid intima–media thickness (CIMT) is a commonly used marker for atherosclerosis and is often computed in carotid ultrasound images. An analysis of different computerized techniques for CIMT measurement and their clinical impacts on the same patient data set is lacking. Here we compared and assessed five computerized CIMT algorithms against three expert analysts’ manual measurements on a data set of 1088 patients from two centers. Inter- and intra-observer variability was assessed, and the computerized CIMT values were compared with those manually obtained. The CIMT measurements were used to assess the correlation with clinical parameters, cardiovascular event prediction through a generalized linear model and the Kaplan–Meier hazard ratio. CIMT measurements obtained with a skilled analyst's segmentation and the computerized segmentation were comparable in statistical analyses, suggesting they can be used interchangeably for CIMT quantification and clinical outcome investigation. To facilitate future studies, the entire data set used is made publicly available for the community at http://dx.doi.org/10.17632/fpv535fss7.1

MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions

Analysis of protein–ligand complexes and recognition of spatially conserved physico-chemical properties is important for the prediction of binding and function. Here, we present two webservers for multiple alignment and recognition of binding patterns shared by a set of protein structures. The first webserver, MultiBind (http://bioinfo3d.cs.tau.ac.il/MultiBind), performs multiple alignment of protein binding sites. It recognizes the common spatial chemical binding patterns even in the absence of similarity of the sequences or the folds of the compared proteins. The input to the MultiBind server is a set of protein-binding sites defined by interactions with small molecules. The output is a detailed list of the shared physico-chemical binding site properties. The second webserver, MAPPIS (http://bioinfo3d.cs.tau.ac.il/MAPPIS), aims to analyze protein–protein interactions. It performs multiple alignment of protein–protein interfaces (PPIs), which are regions of interaction between two protein molecules. MAPPIS recognizes the spatially conserved physico-chemical interactions, which often involve energetically important hot-spot residues that are crucial for protein–protein associations. The input to the MAPPIS server is a set of protein-protein complexes. The output is a detailed list of the shared interaction properties of the interfaces

Insights into the complex regulation of rpoS in Borrelia burgdorferi

Co-ordinated regulation of gene expression is required for the transmission and survival of Borrelia burgdorferi in different hosts. The sigma factor RpoS (σS), as regulated by RpoN (σ54), has been shown to regulate key virulence factors (e.g. OspC) required for these processes. As important, multiple signals (e.g. temperature, pH, cell density, oxygen) have been shown to increase the expression of σS-dependent genes; however, little is known about the signal transduction mechanisms that modulate the expression of rpoS. In this report we show that: (i) rpoS has a σ54-dependent promoter that requires Rrp2 to activate transcription; (ii) Rrp2Δ123, a constitutively active form of Rrp2, activated σ54-dependent transcription of rpoS/P-lacZ reporter constructs in Escherichia coli; (iii) quantitative reverse transcription polymerase chain reaction (QRT-PCR) experiments with reporter cat constructs in B. burgdorferi indicated that Rrp2 activated transcription of rpoS in an enhancer-independent fashion; and finally, (iv) rpoN is required for cell density- and temperature-dependent expression of rpoS in B. burgdorferi, but histidine kinase Hk2, encoded by the gene immediately upstream of rrp2, is not essential. Based on these findings, a model for regulation of rpoS has been proposed which provides mechanisms for multiple signalling pathways to modulate the expression of the σS regulon in B. burgdorferi

Landscape of coordinated immune responses to H1N1 challenge in humans

Influenza is a significant cause of morbidity and mortality worldwide. Here we show changes in the abundance and activation states of more than 50 immune cell subsets in 35 individuals over 11 time points during human A/California/2009 (H1N1) virus challenge monitored using mass cytometry along with other clinical assessments. Peak change in monocyte, B cell, and T cell subset frequencies coincided with peak virus shedding, followed by marked activation of T and NI&lt; cells. Results led to the identification of C038 as a critical regulator of plasmacytoid dendritic cell function in response to influenza virus. Machine learning using study-derived clinical parameters and single-cell data effectively classified and predicted susceptibility to infection. The coordinated immune cell dynamics defined in this study provide a framework for identifying novel correlates of protection in the evaluation of future influenza therapeutics