NavMol 3.0: enabling the representation of metabolic reactions by blind users.

Summary: The representation of metabolic reactions strongly relies on visualization, which is a major barrier for blind users. The NavMol software renders the communication and interpretation of molecular structures and reactions accessible by integrating chemoinformatics and assistive technology. NavMol 3.0 provides a molecular editor for metabolic reactions. The user can start with templates of reactions and build from such cores. Atom-to-atom mapping enables changes in the reactants to be reflected in the products (and vice-versa) and the reaction centres to be automatically identified. Blind users can easily interact with the software using the keyboard and text-to-speech technology. Availability and implementation: NavMol 3.0 is free and open source under the GNU general public license (GPLv3), and can be downloaded at http://sourceforge.net/projects/navmol as a JAR file. Contact: joao@airesdesousa.com.

Gla-rich protein is involved in the cross-talk between calcification and inflammation in osteoarthritis.

Osteoarthritis (OA) is a whole-joint disease characterized by articular cartilage loss, tissue inflammation, abnormal bone formation and extracellular matrix (ECM) mineralization. Disease-modifying treatments are not yet available and a better understanding of osteoarthritis pathophysiology should lead to the discovery of more effective treatments. Gla-rich protein (GRP) has been proposed to act as a mineralization inhibitor and was recently shown to be associated with OA in vivo. Here, we further investigated the association of GRP with OA mineralization-inflammation processes. Using a synoviocyte and chondrocyte OA cell system, we showed that GRP expression was up-regulated following cell differentiation throughout ECM calcification, and that inflammatory stimulation with IL-1ß results in an increased expression of COX2 and MMP13 and up-regulation of GRP. Importantly, while treatment of articular cells with γ-carboxylated GRP inhibited ECM calcification, treatment with either GRP or GRP-coated basic calcium phosphate (BCP) crystals resulted in the down-regulation of inflammatory cytokines and mediators of inflammation, independently of its γ-carboxylation status. Our results strengthen the calcification inhibitory function of GRP and strongly suggest GRP as a novel anti-inflammatory agent, with potential beneficial effects on the main processes responsible for osteoarthritis progression. In conclusion, GRP is a strong candidate target to develop new therapeutic approaches.

Gla-rich protein acts as a calcification inhibitor in the human cardiovascular system.

OBJECTIVE: Vascular and valvular calcifications are pathological processes regulated by resident cells, and depending on a complex interplay between calcification promoters and inhibitors, resembling skeletal metabolism. Here, we study the role of the vitamin K-dependent Gla-rich protein (GRP) in vascular and valvular calcification processes. APPROACH AND RESULTS: Immunohistochemistry and quantitative polymerase chain reaction showed that GRP expression and accumulation are upregulated with calcification simultaneously with osteocalcin and matrix Gla protein (MGP). Using conformation-specific antibodies, both γ-carboxylated GRP and undercarboxylated GRP species were found accumulated at the sites of mineral deposits, whereas undercarboxylated GRP was predominant in calcified aortic valve disease valvular interstitial cells. Mineral-bound GRP, MGP, and fetuin-A were identified by mass spectrometry. Using an ex vivo model of vascular calcification, γ-carboxylated GRP but not undercarboxylated GRP was shown to inhibit calcification and osteochondrogenic differentiation through α-smooth muscle actin upregulation and osteopontin downregulation. Immunoprecipitation assays showed that GRP is part of an MGP-fetuin-A complex at the sites of valvular calcification. Moreover, extracellular vesicles released from normal vascular smooth muscle cells are loaded with GRP, MGP, and fetuin-A, whereas under calcifying conditions, released extracellular vesicles show increased calcium loading and GRP and MGP depletion. CONCLUSIONS: GRP is an inhibitor of vascular and valvular calcification involved in calcium homeostasis. Its function might be associated with prevention of calcium-induced signaling pathways and direct mineral binding to inhibit crystal formation/maturation. Our data show that GRP is a new player in mineralization competence of extracellular vesicles possibly associated with the fetuin-A-MGP calcification inhibitory system. GRP activity was found to be dependent on its γ-carboxylation status, with potential clinical relevance.

Sturgeon osteocalcin shares structural features with matrix Gla protein: evolutionary relationship and functional implications.

Osteocalcin (OC) and matrix Gla protein (MGP) are considered evolutionarily related because they share key structural features, although they have been described to exert different functions. In this work, we report the identification and characterization of both OC and MGP from the Adriatic sturgeon, a ray-finned fish characterized by a slow evolution and the retention of many ancestral features. Sturgeon MGP shows a primary structure, post-translation modifications, and patterns of mRNA/protein distribution and accumulation typical of known MGPs, and it contains seven possible Gla residues that would make the sturgeon protein the most γ-carboxylated among known MGPs. In contrast, sturgeon OC was found to present a hybrid structure. Indeed, although exhibiting protein domains typical of known OCs, it also contains structural features usually found in MGPs (e.g. a putative phosphorylated propeptide). Moreover, patterns of OC gene expression and protein accumulation overlap with those reported for MGP; OC was detected in bone cells and mineralized structures but also in soft and cartilaginous tissues. We propose that, in a context of a reduced rate of evolution, sturgeon OC has retained structural features of the ancestral protein that emerged millions of years ago from the duplication of an ancient MGP gene and may exhibit intermediate functional features.

Teleost fish osteocalcin 1 and 2 share the ability to bind the calcium mineral phase.

The occurrence of a second osteocalcin (OC2) has been reported in teleost fish, where it coexists with OC1 in some species. While it has been proposed that OC2 gene originated from OC1 through the fish whole-genome duplication event, little information is available on its molecular function and physiological role. The present study brings biological data supporting the presence of OC2 in the mineral phase of teleost fish bone and its association with the mineral phase together with OC1. The occurrence of OC2 forms with different levels of phosphorylation or γ-carboxylation, and with amino acid substitutions was observed. Comparative analysis of mature peptide sequences revealed the high conservation existing between OC1 and OC2, in particular within the core γ-carboxyglutamic acid domain, and suggests that both protein forms may have the same function, i.e., binding of calcium ions or hydroxyapatite crystals.

Identification of proteins with potential osteogenic activity present in the water-soluble matrix proteins from Crassostrea gigas nacre using a proteomic approach.

Nacre, when implanted in vivo in bones of dogs, sheep, mice, and humans, induces a biological response that includes integration and osteogenic activity on the host tissue that seems to be activated by a set of proteins present in the nacre water-soluble matrix (WSM). We describe here an experimental approach that can accurately identify the proteins present in the WSM of shell mollusk nacre. Four proteins (three gigasin-2 isoforms and a cystatin A2) were for the first time identified in WSM of Crassostrea gigas nacre using 2DE and LC-MS/MS for protein identification. These proteins are thought to be involved in bone remodeling processes and could be responsible for the biocompatibility shown between bone and nacre grafts. These results represent a contribution to the study of shell biomineralization process and opens new perspectives for the development of new nacre biomaterials for orthopedic applications.

The BioVisualSpeech Serious Game with Voice Exercises for People with Parkinson's Disease with Hypokinetic Dysarthria.

People with Parkinson's disease (PD) can have dysarthria, a voice disorder that affects speech intelligibility. To fight this disorder people may resort to speech and language therapy. Unfortunately, weekly speech therapy sessions may not be enough, because to achieve and maintain good voice quality, intensive training is required. Additionally, the COVID-19 pandemic brought attention to the need for alternative speech therapy treatments that complement face-to-face appointments. Here, we propose a serious therapy game to improve voice loudness that can be used for intensive therapy or when face-to-face appointments are not possible. The game integrates three voice exercises used in speech therapy sessions for people with PD and aims to provide motivation for patients to perform the exercises on a daily basis. This application evaluates the vocal intensity, vocal frequency and maximum phonation time, offering real-time visual feedback. It also allows pathologists to customize the exercises difficulty to the needs of each patient.

Customizable Serious Speech Therapy Games with Dynamic Difficulty Adjustment for Children with Sigmatism.

Children with speech sound disorders should attend speech and language therapy and should practice the speech exercises regularly to surpass their speech difficulties. Since doing the speech exercises often may be tedious, there is the need to motivate children to practice them. During the COVID-19 pandemic, speech and language pathologists had the need to adapt their procedures to others with less physical contact. Here, we propose two serious games to motivate children with sigmatism on doing the speech exercises, which can be used at home and during face-to-face and online speech therapy sessions. The games use automatic speech recognition to classify speech productions. Visual and auditory feedback are used to help children understand their performance, and a hint system is used to help them perform the exercises correctly. A dynamic difficulty adjustment system is used to change the level of difficulty according to the child's speech performance in previous trials.

Gla-rich protein is a novel vitamin K-dependent protein present in serum that accumulates at sites of pathological calcifications.

Mineralization of soft tissues is an abnormal process that occurs in any body tissue and can greatly increase morbidity and mortality. Vitamin K-dependent (VKD) proteins play a crucial role in these processes; matrix Gla protein is considered one of the most relevant physiological inhibitors of soft tissue calcification know to date. Several studies have suggested that other, still unknown, VKD proteins might also be involved in soft tissue calcification pathologies. We have recently identified in sturgeon a new VKD protein, Gla-rich protein (GRP), which contains the highest ratio between number of Gla residues and size of the mature protein so far identified. Although mainly expressed in cartilaginous tissues of sturgeon, in rat GRP is present in both cartilage and bone. We now show that GRP is a circulating protein that is also expressed and accumulated in soft tissues of rats and humans, including the skin and vascular system in which, when affected by pathological calcifications, GRP accumulates at high levels at sites of mineral deposition, indicating an association with calcification processes. The high number of Gla residues and consequent mineral binding affinity properties strongly suggest that GRP may directly influence mineral formation, thereby playing a role in processes involving connective tissue mineralization.

User Experience of Interactive Technologies for People With Dementia: Comparative Observational Study.

BACKGROUND: Serious games (SGs) are used as complementary approaches to stimulate patients with dementia. However, many of the SGs use out-of-the-shelf technologies that may not always be suitable for such populations, as they can lead to negative behaviors, such as anxiety, fatigue, and even cybersickness. OBJECTIVE: This study aims to evaluate how patients with dementia interact and accept 5 out-of-the-shelf technologies while completing 10 virtual reality tasks. METHODS: A total of 12 participants diagnosed with dementia (mean age 75.08 [SD 8.07] years, mean Mini-Mental State Examination score 17.33 [SD 5.79], and mean schooling 5.55 [SD 3.30]) at a health care center in Portugal were invited to participate in this study. A within-subject experimental design was used to allow all participants to interact with all technologies, such as HTC VIVE, head-mounted display (HMD), tablet, mouse, augmented reality (AR), leap motion (LM), and a combination of HMD with LM. Participants' performance was quantified through behavioral and verbal responses, which were captured through video recordings and written notes. RESULTS: The findings of this study revealed that the user experience using technology was dependent on the patient profile; the patients had a better user experience when they use technologies with direct interaction configuration as opposed to indirect interaction configuration in terms of assistance required (P=.01) and comprehension (P=.01); the participants did not trigger any emotional responses when using any of the technologies; the participants' performance was task-dependent; the most cost-effective technology was the mouse, whereas the least cost-effective was AR; and all the technologies, except for one (HMD with LM), were not exposed to external hazards. CONCLUSIONS: Most participants were able to perform tasks using out-of-the-shelf technologies. However, there is no perfect technology, as they are not explicitly designed to address the needs and skills of people with dementia. Here, we propose a set of guidelines that aim to help health professionals and engineers maximize user experience when using such technologies for the population with dementia.

Statistical modeling of intrinsic structures in impacts sounds.

This paper presents a statistical data-driven method for learning intrinsic structures of impact sounds. The method applies principal and independent component analysis to learn low-dimensional representations that model the distribution of both the time-varying spectral and amplitude structure. As a result, the method is able to decompose sounds into a small number of underlying features that characterize acoustic properties such as ringing, resonance, sustain, decay, and onsets. The method is highly flexible and makes no a priori assumptions about the physics, acoustics, or dynamics of the objects. In addition, by modeling the underlying distribution, the method can capture the natural variability of ensembles of related impact sounds.

Removal of chromium from electroplating industry effluents by ion exchange resins.

Effluent discharged from the chromium electroplating industry contains a large number of metals, including chromium, copper, nickel, zinc, manganese and lead. The ion exchange process is an alternative technique for application in the treatment of industrial wastewater containing heavy metals and indeed it has proven to be very promising in the removal and recovery of valuable species. The main objective of the present work is to evaluate the performance of commercial ion exchange resins for removing chromium trivalent from industrial effluents, and for this purpose two resins were tested: a chelating exchange resin (Diaion CR11) and a weak cationic resin (Amberlite IRC86). In order to evaluate the sorption capacity of the resins some equilibrium experiments were carried out, being the temperature and pH the main variables considered. The chromium solutions employed in the experiments were synthetic solutions and industrial effluents. In addition, a transient test was also performed as an attempt to understand the kinetic behaviour of the process.

Insights into the association of Gla-rich protein and osteoarthritis, novel splice variants and γ-carboxylation status.

SCOPE: Gla-rich protein (GRP) is a vitamin K dependent protein, characterized by a high density of γ-carboxylated Glu residues, shown to accumulate in mouse and sturgeon cartilage and at sites of skin and vascular calcification in humans. Therefore, we investigated the involvement of GRP in pathological calcification in osteoarthritis (OA). METHODS AND RESULTS: Comparative analysis of GRP patterning at transcriptional and translational levels was performed between controls and OA patients. Using a RT-PCR strategy we unveiled two novel splice variants in human-GRP-F5 and F6-potentially characterized by the loss of full γ-carboxylation and secretion functional motifs. GRP-F1 is shown to be the predominant splice variant expressed in mouse and human adult tissues, particularly in OA cartilage, while an overexpressing human cell model points it as the major γ-carboxylated isoform. Using validated conformational antibodies detecting carboxylated or undercarboxylated GRP (c/uc GRP), we have demonstrated cGRP accumulation in controls, whereas ucGRP was the predominant form in OA-affected tissues, colocalizing at sites of ectopic calcification. CONCLUSION: Overall, our results indicate the predominance of GRP-F1, and a clear association of ucGRP with OA cartilage and synovial membrane. Levels of vitamin K should be further assessed in these patients to determine its potential therapeutic use as a supplement in OA treatment.

Gla-rich protein is a potential new vitamin K target in cancer: evidences for a direct GRP-mineral interaction.

Gla-rich protein (GRP) was described in sturgeon as a new vitamin-K-dependent protein (VKDP) with a high density of Gla residues and associated with ectopic calcifications in humans. Although VKDPs function has been related with γ-carboxylation, the Gla status of GRP in humans is still unknown. Here, we investigated the expression of recently identified GRP spliced transcripts, the γ-carboxylation status, and its association with ectopic calcifications, in skin basal cell and breast carcinomas. GRP-F1 was identified as the predominant splice variant expressed in healthy and cancer tissues. Patterns of γ-carboxylated GRP (cGRP)/undercarboxylated GRP (ucGRP) accumulation in healthy and cancer tissues were determined by immunohistochemistry, using newly developed conformation-specific antibodies. Both GRP protein forms were found colocalized in healthy tissues, while ucGRP was the predominant form associated with tumor cells. Both cGRP and ucGRP found at sites of microcalcifications were shown to have in vitro calcium mineral-binding capacity. The decreased levels of cGRP and predominance of ucGRP in tumor cells suggest that GRP may represent a new target for the anticancer potential of vitamin K. Also, the direct interaction of cGRP and ucGRP with BCP crystals provides a possible mechanism explaining GRP association with pathological mineralization.

Evaluation of chelating ion-exchange resins for separating Cr(III) from industrial effluents.

In this study two chelating resins containing iminodiacetic acid groups (Amberlite IRC 748 and Diaion CR 11) and a chelating resin based on sulfonic and diphosphonic acid groups (Diphonix) were investigated in order to separate Cr(III) from industrial effluents produced in hard and decorative electroplating. Samples of two industrial plants were characterized during a period of about one year and a half in terms of the metals content (Cr, Cu, Na, Ca, Fe and Ni), Total Suspended Solids (TSS), Total Dissolved Solids (TDS), Chemical Oxygen Demand (COD) and pH. Some of the physical properties of the resins, namely the moisture content, apparent density, intraparticle porosity and the particle size distribution were also evaluated. To quantify the sorption capacity of the resins, batch experiments were performed using synthetic solutions of Cr(III), as well as solutions of Fe in the case of Diphonix. The Langmuir and Langmuir-Freundlich isotherms enabled a good description of the ion-exchange equilibrium data, and the maximum sorption capacity determined for Amberlite and Diaion was 3.6 mequiv./g(dry resin). For Diphonix that parameter was 3.4 mequiv./g(dry resin). The Diphonix resin exhibits a high selectivity for transition metals (Fe, Ni) over the chromium trivalent. Therefore, it was screened as the most suitable for selectively removing those metal impurities from chromium electroplating effluents. For this resin, the sorption capacity is strongly dependent on the initial pH of the solution. Though, high regeneration efficiencies of Diphonix for stripping Cr(III) were found by using a mixture of NaOH/H(2)O(2). The mathematical model tested for describing the dynamics of the process allowed a good fitting to the experimental data and enabled the estimation of effective pore diffusivity of Cr(III). The saturations of Diphonix with industrial effluents demonstrated that the breakthrough capacity of the resin is affected by the presence of other species in solution, such as Fe and Ni. Nevertheless, these effluents may be treated with this resin, being possible to separate Cr(III) from other transition metallic ions in solution.