Michaelis-Menten dynamics in protein subnetworks

To understand the behaviour of complex systems it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves memory of the past, and that the memory functions can be calculated explicitly for biochemical reaction networks made up of unary and binary reactions. However, many established network models involve also Michaelis-Menten kinetics, to describe e.g. enzymatic reactions. We show that the projection approach to subnetwork dynamics can be extended to such networks, thus significantly broadening its range of applicability. To derive the extension we construct a larger network that represents enzymes and enzyme complexes explicitly, obtain the projected equations, and finally take the limit of fast enzyme reactions that gives back Michaelis-Menten kinetics. The crucial point is that this limit can be taken in closed form. The outcome is a simple procedure that allows one to obtain a description of subnetwork dynamics, including memory functions, starting directly from any given network of unary, binary and Michaelis-Menten reactions. Numerical tests show that this closed form enzyme elimination gives a much more accurate description of the subnetwork dynamics than the simpler method that represents enzymes explicitly, and is also more efficient computationally

Differential contribution of the MTOR and MNK pathways to the regulation of mRNA translation in meiotic and postmeiotic mouse male germ cells

Translation of stored mRNAs accounts for protein synthesis during the transcriptionally inactive stages of spermatogenesis. A key step in mRNA translation is the assembly of the initiation complex EIF4F, which is regulated by the MTOR (mammalian target of rapamycin) and MNK1/2 (MAP kinase-interacting kinase 1 and 2) pathways. We investigated the expression and activity of regulatory proteins of these pathways in male germ cells at different stages of differentiation. All translation factors analyzed were expressed in germ cells throughout spermatogenesis. However, while EIF4G and PABP1 (poly[A]-binding protein 1) were more abundant in postmeiotic cells, MTOR and its target EIF4EBP1 (4E-BP1) decreased steadily during spermatogenesis. In vivo labeling showed that pachytene spermatocytes display higher rates of protein synthesis, which are partially dependent on MTOR and MNK activity. By contrast, haploid spermatids are characterized by lower levels of protein synthesis, which are independent of the activity of these pathways. Accordingly, MTOR and MNK activity enhanced formation of the EIF4F complex in pachytene spermatocytes but not in round spermatids. Moreover, external cues differentially modulated the activity of these pathways in meiotic and haploid cells. Heat shock decreased MTOR and MNK activity in pachytene spermatocytes, whereas round spermatids were much less sensitive. On the other hand, treatment with the phosphatase inhibitor okadaic acid activated MTOR and MNK in both cell types. These results indicate that translational regulation is differentially dependent on the MTOR and MNK pathways in mouse spermatocytes and spermatids and suggest that the late stages of germ cell differentiation display constitutive assembly of the translation initiation complex

Do (and say) as I say: Linguistic adaptation in human-computer dialogs

© Theodora Koulouri, Stanislao Lauria, and Robert D. Macredie. This article has been made available through the Brunel Open Access Publishing Fund.There is strong research evidence showing that people naturally align to each other’s vocabulary, sentence structure, and acoustic features in dialog, yet little is known about how the alignment mechanism operates in the interaction between users and computer systems let alone how it may be exploited to improve the efficiency of the interaction. This article provides an account of lexical alignment in human–computer dialogs, based on empirical data collected in a simulated human–computer interaction scenario. The results indicate that alignment is present, resulting in the gradual reduction and stabilization of the vocabulary-in-use, and that it is also reciprocal. Further, the results suggest that when system and user errors occur, the development of alignment is temporarily disrupted and users tend to introduce novel words to the dialog. The results also indicate that alignment in human–computer interaction may have a strong strategic component and is used as a resource to compensate for less optimal (visually impoverished) interaction conditions. Moreover, lower alignment is associated with less successful interaction, as measured by user perceptions. The article distills the results of the study into design recommendations for human–computer dialog systems and uses them to outline a model of dialog management that supports and exploits alignment through mechanisms for in-use adaptation of the system’s grammar and lexicon

Zinc-modified nanopolymers improve the quality of resin-dentin bonded interfaces

Introduction: Demineralized collagen fibers at the hybrid layer are susceptible to degradation. Remineralization may aid to improve bond longevity. Objectives: The aim of the present study was to infiltrate zinc and calcium-loaded polymeric nanoparticles into demineralized dentin to facilitate hybrid layer remineralization. Materials and methods: Zinc or calcium-loaded polymeric nanoparticles were infiltrated into etched dentin, and Single Bond Adhesive was applied. Bond strength was tested after 24 h and 6 months storage. Nanomechanical properties, dyeassisted confocal laser microscopy, and Masson’s trichrome staining evaluation were performed to assess for the hybrid layer morphology, permeability, and remineralization ability after 24 h and 3 months. Data were analyzed by ANOVA and Student–Newman–Keuls multiple comparisons tests (p < 0.05). Results: Immediate bond strength was not affected by nanoparticles infiltration (25 to 30 MPa), while after 6 months, bond strengths were maintained (22 to 24 MPa). After 3 months, permeability occurred only in specimens in which nanoparticles were not infiltrated. Dentin remineralization, at the bottom of the hybrid layer, was observed in all groups. After microscopy analysis, zinc-loaded nanoparticles were shown to facilitate calcium deposition throughout the entire hybrid layer. Young’s modulus at the hybrid layer increased from 2.09 to 3.25 GPa after 3 months, in specimens with zinc nanoparticles; meanwhile, these values were reduced from 1.66 to 0.49 GPa, in the control group. Conclusion: Infiltration of polymeric nanoparticles into demineralized dentin increased long-term bond strengths. Zinc-loaded nanoparticles facilitate dentin remineralization within the complete resin–dentin interface. Clinical relevance: Resin–dentin bond longevity and dentin remineralization at the hybrid layer were facilitated by zincloaded nanoparticles.This work was supported by a grant, MINECO/FEDER MAT2014-52036-P

Epidemiology and pattern of resistance of gram-negative bacteria isolated from blood samples in hospitalized patients: A single center retrospective analysis from southern italy

Background: Blood culturing remains the mainstream tool to inform an appropriate treatment in hospital-acquired bloodstream infections and to diagnose any bacteremia. Methods: A retrospective investigation on the prevalence of Gram-negative bacteria (GNB) and their resistance in hospitalized patients by age, sex, and units from blood cultures (BCs) was conducted from January 2018 to April 2020 at Sant’Elia hospital, Caltanissetta, southern Italy. We divided the patient age range into four equal intervals. Results: Multivariate demographic and microbiological variables did not show an association between bacteria distributions and gender and age. The distribution by units showed a higher prevalence of Klebsiella pneumoniae and Acinetobacter baumannii in the intensive care unit (ICU) and Escherichia coli in the non-intensive care units (non-ICUs). The analysis of antibiotic resistance showed that E. coli was susceptible to a large class of antibiotics such as carbapenem and trimethoprim-sulfamethoxazole. K. pneumoniae showed a significant susceptibility to colistin, tigecycline, and trimethoprim-sulfamethoxazole. From the survival analysis, patients with E. coli had a higher survival rate. Conclusions: The authors stress the importance of the implementation of large community-level programs to prevent E. coli bacteremia. K. pneumoniae and E. coli susceptibility patterns to antibiotics, including in the prescription patterns of general practitioners, suggest that the local surveillance and implementation of educational programs remain essential measures to slow down the spread of resistance and, consequently, increase the antibiotic lifespan

A human-centered design methodology to enhance the usability, human factors, and user experience of connected health systems: a three-phase methodology.

peer-reviewedDesign processes such as human-centered design, which involve the end user throughout the product development and testing process, can be crucial in ensuring that the product meets the needs and capabilities of the user, particularly in terms of safety and user experience. The structured and iterative nature of human-centered design can often present a challenge when design teams are faced with the necessary, rapid, product development life cycles associated with the competitive connected health industry. We wanted to derive a structured methodology that followed the principles of human-centered design that would allow designers and developers to ensure that the needs of the user are taken into account throughout the design process, while maintaining a rapid pace of development. In this paper, we present the methodology and its rationale before outlining how it was applied to assess and enhance the usability, human factors, and user experience of a connected health system known as the Wireless Insole for Independent and Safe Elderly Living (WIISEL) system, a system designed to continuously assess fall risk by measuring gait and balance parameters associated with fall risk. We derived a three-phase methodology. In Phase 1 we emphasized the construction of a use case document. This document can be used to detail the context of use of the system by utilizing storyboarding, paper prototypes, and mock-ups in conjunction with user interviews to gather insightful user feedback on different proposed concepts. In Phase 2 we emphasized the use of expert usability inspections such as heuristic evaluations and cognitive walkthroughs with small multidisciplinary groups to review the prototypes born out of the Phase 1 feedback. Finally, in Phase 3 we emphasized classical user testing with target end users, using various metrics to measure the user experience and improve the final prototypes. We report a successful implementation of the methodology for the design and development of a system for detecting and predicting falls in older adults. We describe in detail what testing and evaluation activities we carried out to effectively test the system and overcome usability and human factors problems. We feel this methodology can be applied to a wide variety of connected health devices and systems. We consider this a methodology that can be scaled to different-sized projects accordingly.PUBLISHEDpeer-reviewe

U-PHOS Project: Development of a Large Diameter Pulsating Heat Pipe Experiment on board REXUS 22

U-PHOS Project aims to analyse and characterise the behaviour of a large diameter Pulsating Heat Pipe (PHP) on board REXUS 22 sounding rocket. A PHP is a passive thermal control device consisting of a serpentine capillary tube, evacuated, partially filled with a working fluid and finally sealed. In this configuration, the liquid and vapour phases are randomly distributed in the form of liquid slugs and vapour plugs. The heat is efficiently transported by means of the self-sustained oscillatory fluid motion driven by the phase change phenomena. On ground conditions, a small diameter is required in order to obtain a confined slug flow regime. In milli-gravity conditions, buoyancy forces become less intense and the PHP diameter may be increased still maintaining the slug/plug flow configuration typical of the PHP operation. Consequently, the PHP heat power capability may be increased too. U-PHOS aims at proving that a Large Diameter PHP effectively works in milli-g conditions by characterizing its thermal response during a sounding rocket flight. The actual PHP tube is made of aluminum (3 mm inner diameter, filled with FC-72), heated at the evaporator by a compact electrical resistance, cooled at the condenser by a Phase Change Material (PCM) embedded in a metallic foam. The tube wall temperatures are recorded by means of Fibre Bragg Grating (FBG) sensors; the local fluid pressure is acquired by means of a pressure transducer. The present work intends to report the actual status of the project, focusing in particular on the experiment improvements with respect to the previous campaign

Antibacterial and Bonding Properties of Universal Adhesive Dental Polymers Doped with Pyrogallol

This study investigated the antibacterial activity, bond strength to dentin (SBS), and ultra-morphology of the polymer–dentin interface of experimental adhesive systems doped with pyrogallol (PY), which is a ubiquitous phenolic moiety that is present in flavonoids and polyphenols. A universal adhesive containing 4-META and 10-MDP was used in this study. PY behaves as an antioxidant and anti-cancerogenic agent and it was incorporated into the adhesive at different concentrations (0.5 and 1 wt.%). The antibacterial activity and SBS were analyzed and the results were statistically analyzed. The ultra-morphology of the polymer–dentin interface was assessed using scanning electron microscopy (SEM). At 24 h, a lower antibacterial activity was observed for the control adhesive compared to those with 0.5% and 1% PY. No difference was seen in SBS between the three groups at 24 h. After 6 months, the SBS of the 0.5% PY adhesive was significantly lower than the other tested adhesives. The specimens created with 1% PY adhesive presented a higher bond strength at six months compared with that found at 24 h. No morphological differences were found at the polymer–dentin interfaces of the tested adhesives. Pyrogallol may be incorporated into modern universal adhesive systems to preserve the polymer–dentin bonding interface and confer a certain degree of antibacterial activity.</jats:p

Computerized general practice based networks yield comparable performance with sentinel data in monitoring epidemiological time-course of influenza-like illness and acute respiratory illness

<p>Abstract</p> <p>Background</p> <p>Computerized morbidity registration networks might serve as early warning systems in a time where natural epidemics such as the H₁N₁flu can easily spread from one region to another.</p> <p>Methods</p> <p>In this contribution we examine whether general practice based broad-spectrum computerized morbidity registration networks have the potential to act as a valid surveillance instrument of frequently occurring diseases. We compare general practice based computerized data assessing the frequency of influenza-like illness (ILI) and acute respiratory infections (ARI) with data from a well established case-specific sentinel network, the European Influenza Surveillance Scheme (EISS). The overall frequency and trends of weekly ILI and ARI data are compared using both networks.</p> <p>Results</p> <p>Detection of influenza-like illness and acute respiratory illness occurs equally fast in EISS and the computerized network. The overall frequency data for ARI are the same for both networks, the overall trends are similar, but the increases and decreases in frequency do not occur in exactly the same weeks. For ILI, the overall rate was slightly higher for the computerized network population, especially before the increase of ILI, the overall trend was almost identical and the increases and decreases occur in the same weeks for both networks.</p> <p>Conclusions</p> <p>Computerized morbidity registration networks are a valid tool for monitoring frequent occurring respiratory diseases and the detection of sudden outbreaks.</p

A Hidden Feedback in Signaling Cascades Is Revealed

Cycles involving covalent modification of proteins are key components of the intracellular signaling machinery. Each cycle is comprised of two interconvertable forms of a particular protein. A classic signaling pathway is structured by a chain or cascade of basic cycle units in such a way that the activated protein in one cycle promotes the activation of the next protein in the chain, and so on. Starting from a mechanistic kinetic description and using a careful perturbation analysis, we have derived, to our knowledge for the first time, a consistent approximation of the chain with one variable per cycle. The model we derive is distinct from the one that has been in use in the literature for several years, which is a phenomenological extension of the Goldbeter-Koshland biochemical switch. Even though much has been done regarding the mathematical modeling of these systems, our contribution fills a gap between existing models and, in doing so, we have unveiled critical new properties of this type of signaling cascades. A key feature of our new model is that a negative feedback emerges naturally, exerted between each cycle and its predecessor. Due to this negative feedback, the system displays damped temporal oscillations under constant stimulation and, most important, propagates perturbations both forwards and backwards. This last attribute challenges the widespread notion of unidirectionality in signaling cascades. Concrete examples of applications to MAPK cascades are discussed. All these properties are shared by the complete mechanistic description and our simplified model, but not by previously derived phenomenological models of signaling cascades