Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces

© 2016 Kontopoulos et al.Background: The term molecular cartography encompasses a family of computational methods for two-dimensional transformation of protein structures and analysis of their physicochemical properties. The underlying algorithms comprise multiple manual steps, whereas the few existing implementations typically restrict the user to a very limited set of molecular descriptors. Results: We present Structuprint, a free standalone software that fully automates the rendering of protein surface maps, given - at the very least - a directory with a PDB file and an amino acid property. The tool comes with a default database of 328 descriptors, which can be extended or substituted by user-provided ones. The core algorithm comprises the generation of a mould of the protein surface, which is subsequently converted to a sphere and mapped to two dimensions, using the Miller cylindrical projection. Structuprint is partly optimized for multicore computers, making the rendering of animations of entire molecular dynamics simulations feasible. Conclusions: Structuprint is an efficient application, implementing a molecular cartography algorithm for protein surfaces. According to the results of a benchmark, its memory requirements and execution time are reasonable, allowing it to run even on low-end personal computers. We believe that it will be of use - primarily but not exclusively - to structural biologists and computational biochemists

Long-Term Structural Health Monitoring of the Fortezza Fortress: Application of Damage Detection Techniques on Existing Cracks

Structural Health Monitoring (SHM) consists of an elaborated technique, assisting the assessment of existing structures through the detection of active or sudden damages, as well as the diagnosis of possible causes for them. Within the STORM-project [1], the SHM strategy selected for the assessment of the Venetian fortress of Fortezza in Rethymno, Greece was the continuous crack monitoring of four different existing cracks of the structure, due to their relatively large width, located at the Bastion of St. Paul’s, Prophet Elias’ and St. Luke’s as well as the Episcopal mansion. Besides the crack displacement measurements, several other environmental quantities were monitored at the weather stations, which are known to have a strong influence on the crack width. Considering the fact that most weather fluctuations have reversible effects on structural integrity, it is of great importance to recognize the environmental and operational variation of the structure, and subsequently identify any separate structural change caused by damage [2], [3]. This was achieved by employing a statistical ARX model (Auto-Regressive model with eXogenous input) [4], calibrated for each case after several months. Once this process was completed it was possible to detect possible active damage on the examined structures and estimate possible causes for them. The successful application of the methodology at the four monitored cracks provided important information about their state of damage, possible causes and early warnings in case of hazard. Over the evaluated period, it appears that the bastion of Prophet Elias is in stable condition, while the bastion of St. Luke and St. Paul are vulnerable to heavy precipitation. Moreover, the Episcopal mansion showed a destabilization response during the rainfall period, which is possible to result in the activation of an overturning mechanism

Alkali-activated cement sensors for sodium chloride monitoring

Chloride-induced corrosion of reinforced concrete costs the global economy billions of dollars every year. Despite concerted research effort, the non-invasive, continuous monitoring of sodium chloride in concrete structures is still an unsolved problem. Here, we outline a first-time demonstration of a sodium chloride sensor based on alkali-activated cements: a class of cementitious, electrolytically conductive materials which are typically used for concrete construction and repair. In this work, internal sodium chloride concentrations ranging from 0–22 wt% were measured independently of moisture contents via shifts in electrical impedance. The typical sodium chloride measurement precision was 0.85 wt%. Non-linearity of the sensor response due to signal saturation began at sodium chloride concentrations >5 wt%. We use experimental measures of ion dynamics to link this saturation to the deleterious effect of high concentrations on ion mobility. This study demonstrates sensor feasibility, and provides new experimental evidence to further our understanding of ionic conductivity mechanisms in these materials. The work will allow for the development of self-sensing repair and construction materials for locating and quantifying sodium chloride levels within concrete structures — a valuable technology for supporting concrete health monitoring and maintenance

Treatment of hemangiomas in children using a Nd:YAG laser in conjunction with ice cooling of the epidermis: techniques and results

BACKGROUND: Hemangiomas are the most common type of congenital anomaly in childhood. Although many resolve spontaneously, intervention is required when their growth could damage vital adjacent structures. Various therapeutic approaches to childhood hemangiomas with different types of laser have been described previously. The objective of this study was to determine whether the cooling of the epidermis during irradiation of hemangiomas with a Nd:YAG laser prevents thermal damage and decreases the number of sessions required to treat these lesions. METHODS: Between 1993 and 2001, 110 patients aged 3 months to 4 years, with cutaneous hemangiomas were treated with a Nd:YAG laser. The lesion was cooled with ice prior to, during, and after the irradiation. During each session the laser beam passed through the pieces of ice. The laser power was between 35–45 W with a pulse length of 2–10 seconds. RESULTS: After 6 months of follow-up, from the first session of laser treatment, total resolution was obtained in 72 (65.5%) patients. A second or third session followed in 30 out of 38 patients in which, the initial results were good, moderate, or poor. The parents of the remaining eight children refused this second session and these patients excluded from the study Complications were seen in nine (8.8%) patients. One patient had postoperative bleeding which stopped spontaneously, while atrophic scars occurred in six (5.8%) patients, and hypertrophic scars in two (1.9%) patients. CONCLUSIONS: Nd:YAG laser irradiation in conjunction with ice protection of the epidermis produces good cosmetic results for the treatment of cutaneous hemangiomas in children, and decreases the number of sessions for treatment of these lesions

XMeis3 Is Necessary for Mesodermal Hox Gene Expression and Function

Hox transcription factors provide positional information during patterning of the anteroposterior axis. Hox transcription factors can co-operatively bind with PBC-class co-factors, enhancing specificity and affinity for their appropriate binding sites. The nuclear localisation of these co-factors is regulated by the Meis-class of homeodomain proteins. During development of the zebrafish hindbrain, Meis3 has previously been shown to synergise with Hoxb1 in the autoregulation of Hoxb1. In Xenopus XMeis3 posteriorises the embryo upon ectopic expression. Recently, an early temporally collinear expression sequence of Hox genes was detected in Xenopus gastrula mesoderm (see intro. P3). There is evidence that this sequence sets up the embryo's later axial Hox expression pattern by time-space translation. We investigated whether XMeis3 is involved in regulation of this early mesodermal Hox gene expression. Here, we present evidence that XMeis3 is necessary for expression of Hoxd1, Hoxb4 and Hoxc6 in mesoderm during gastrulation. In addition, we show that XMeis3 function is necessary for the progression of gastrulation. Finally, we present evidence for synergy between XMeis3 and Hoxd1 in Hoxd1 autoregulation in mesoderm during gastrulation

Segment-Specific Neuronal Subtype Specification by the Integration of Anteroposterior and Temporal Cues

To address the question of how neuronal diversity is achieved throughout the CNS, this study provides evidence of modulation of neural progenitor cell “output” along the body axis by integration of local anteroposterior and temporal cues