Bio-Inspired Fluorescent Calcium Sulfate for the Conservation of Gypsum Plasterwork.

In this work, the potential of bio-inspired strategies for the synthesis of calcium sulfate (CaSO4·nH2O) materials for heritage conservation is explored. For this, a nonclassical multi-step crystallization mechanism to understand the effect of calcein- a fluorescent chelating agent with a high affinity for divalent cations- on the nucleation and growth of calcium sulfate phases is proposed. Moving from the nano- to the macro-scale, this strategy sets the basis for the design and production of fluorescent nano-bassanite (NB-C; CaSO4·0.5H2O), with application as a fully compatible consolidant for the conservation of historic plasterwork. Once applied to gypsum (CaSO4·2H2O) plaster specimens, cementation upon hydration of nano-bassanite results in a significant increase in mechanical strength, while intracrystalline occlusion of calcein in newly-formed gypsum cement improves its weathering resistance. Furthermore, under UV irradiation, the luminescence produced by calcein molecules occluded in gypsum crystals formed upon nano-bassanite hydration allows the easy identification of the newly deposited consolidant within the treated gypsum plaster without altering the substrate's appearance.

Using a smartwatch and smartphone to assess early Parkinson's disease in the WATCH-PD study.

Digital health technologies can provide continuous monitoring and objective, real-world measures of Parkinson's disease (PD), but have primarily been evaluated in small, single-site studies. In this 12-month, multicenter observational study, we evaluated whether a smartwatch and smartphone application could measure features of early PD. 82 individuals with early, untreated PD and 50 age-matched controls wore research-grade sensors, a smartwatch, and a smartphone while performing standardized assessments in the clinic. At home, participants wore the smartwatch for seven days after each clinic visit and completed motor, speech and cognitive tasks on the smartphone every other week. Features derived from the devices, particularly arm swing, the proportion of time with tremor, and finger tapping, differed significantly between individuals with early PD and age-matched controls and had variable correlation with traditional assessments. Longitudinal assessments will inform the value of these digital measures for use in future clinical trials.

Identifying and characterising sources of variability in digital outcome measures in Parkinson's disease.

Smartphones and wearables are widely recognised as the foundation for novel Digital Health Technologies (DHTs) for the clinical assessment of Parkinson's disease. Yet, only limited progress has been made towards their regulatory acceptability as effective drug development tools. A key barrier in achieving this goal relates to the influence of a wide range of sources of variability (SoVs) introduced by measurement processes incorporating DHTs, on their ability to detect relevant changes to PD. This paper introduces a conceptual framework to assist clinical research teams investigating a specific Concept of Interest within a particular Context of Use, to identify, characterise, and when possible, mitigate the influence of SoVs. We illustrate how this conceptual framework can be applied in practice through specific examples, including two data-driven case studies.

Analysis of complex, beam-sensitive materials by transmission electron microscopy and associated techniques.

We review the use of transmission electron microscopy (TEM) and associated techniques for the analysis of beam-sensitive materials and complex, multiphase systems in-situ or close to their native state. We focus on materials prone to damage by radiolysis and explain that this process cannot be eliminated or switched off, requiring TEM analysis to be done within a dose budget to achieve an optimum dose-limited resolution. We highlight the importance of determining the damage sensitivity of a particular system in terms of characteristic changes that occur on irradiation under both an electron fluence and flux by presenting results from a series of molecular crystals. We discuss the choice of electron beam accelerating voltage and detectors for optimizing resolution and outline the different strategies employed for low-dose microscopy in relation to the damage processes in operation. In particular, we discuss the use of scanning TEM (STEM) techniques for maximizing information content from high-resolution imaging and spectroscopy of minerals and molecular crystals. We suggest how this understanding can then be carried forward for in-situ analysis of samples interacting with liquids and gases, provided any electron beam-induced alteration of a specimen is controlled or used to drive a chosen reaction. Finally, we demonstrate that cryo-TEM of nanoparticle samples snap-frozen in vitreous ice can play a significant role in benchmarking dynamic processes at higher resolution. This article is part of a discussion meeting issue 'Dynamic in situ microscopy relating structure and function'.

Immediate reactions with glatiramer acetate: Diagnosis of allergy and desensitization protocols.

PURPOSE OF REVIEW: Diverse adverse events have been associated with administration of glatiramer acetate (GA), mainly local reactions at the injection site. Other, less frequent generalized reactions include isolated postinjection reactions and anaphylaxis, which may lead to discontinuation of GA. RECENT FINDINGS: Close collaboration between the allergy and neurology departments is needed to study adverse reactions to GA. The allergy study should include a detailed history and skin prick and intradermal tests with GA and, if possible, determination of specific IgE levels. Furthermore, the implication of other drugs should be ruled out. SUMMARY: An accurate diagnosis of reactions to GA is essential if we are to confirm or rule out allergy to GA. When an allergy diagnosis is confirmed or firmly suspected based on clinical evidence, desensitization protocols are increasingly seen as safe methods for reintroduction of GA.

Biophysical principles of choanoflagellate self-organization.

Inspired by the patterns of multicellularity in choanoflagellates, the closest living relatives of animals, we quantify the biophysical processes underlying the morphogenesis of rosette colonies in the choanoflagellate Salpingoeca rosetta We find that rosettes reproducibly transition from an early stage of 2-dimensional (2D) growth to a later stage of 3D growth, despite the underlying variability of the cell lineages. Our perturbative experiments demonstrate the fundamental importance of a basally secreted extracellular matrix (ECM) for rosette morphogenesis and show that the interaction of the ECM with cells in the colony physically constrains the packing of proliferating cells and, thus, controls colony shape. Simulations of a biophysically inspired model that accounts for the size and shape of the individual cells, the fraction of ECM, and its stiffness relative to that of the cells suffices to explain our observations and yields a morphospace consistent with observations across a range of multicellular choanoflagellate colonies. Overall, our biophysical perspective on rosette development complements previous genetic perspectives and, thus, helps illuminate the interplay between cell biology and physics in regulating morphogenesis.

Dynamics of Growth and Form in Prebiotic Vesicles.

The growth, form, and division of prebiotic vesicles, membraneous bags of fluid of varying components and shapes is hypothesized to have served as the substrate for the origin of life. The dynamics of these out-of-equilibrium structures is controlled by physicochemical processes that include the intercalation of amphiphiles into the membrane, fluid flow across the membrane, and elastic deformations of the membrane. To understand prebiotic vesicular forms and their dynamics, we construct a minimal model that couples membrane growth, deformation, and fluid permeation, ultimately couched in terms of two dimensionless parameters that characterize the relative rate of membrane growth and the membrane permeability. Numerical simulations show that our model captures the morphological diversity seen in extant precursor mimics of cellular life, and might provide simple guidelines for the synthesis of these complex shapes from simple ingredients.

Hydraulic control of mammalian embryo size and cell fate.

Size control is fundamental in tissue development and homeostasis1,2. Although the role of cell proliferation in these processes has been widely studied, the mechanisms that control embryo size-and how these mechanisms affect cell fate-remain unknown. Here we use the mouse blastocyst as a model to unravel a key role of fluid-filled lumen in the control of embryo size and specification of cell fate. We find that there is a twofold increase in lumenal pressure during blastocyst development, which translates into a concomitant increase in cell cortical tension and tissue stiffness of the trophectoderm that lines the lumen. Increased cortical tension leads to vinculin mechanosensing and maturation of functional tight junctions, which establishes a positive feedback loop to accommodate lumen growth. When the cortical tension reaches a critical threshold, cell-cell adhesion cannot be sustained during mitotic entry, which leads to trophectoderm rupture and blastocyst collapse. A simple theory of hydraulically gated oscillations recapitulates the observed dynamics of size oscillations, and predicts the scaling of embryo size with tissue volume. This theory further predicts that disrupted tight junctions or increased tissue stiffness lead to a smaller embryo size, which we verified by biophysical, embryological, pharmacological and genetic perturbations. Changes in lumenal pressure and size can influence the cell division pattern of the trophectoderm, and thereby affect cell allocation and fate. Our study reveals how lumenal pressure and tissue mechanics control embryo size at the tissue scale, which is coupled to cell position and fate at the cellular scale.

On Biomineralization: Enzymes Switch on Mesocrystal Assembly.

Cellular machineries guide the bottom-up pathways toward crystal superstructures based on the transport of inorganic precursors and their precise integration with organic frameworks. The biosynthesis of mesocrystalline spines entails concerted interactions between biomolecules and inorganic precursors; however, the bioinorganic interactions and interfaces that regulate material form and growth as well as the selective emergence of structural complexity in the form of nanostructured crystals are not clear. By investigating mineral nucleation under the regulation of recombinant proteins, we show that SpSM50, a matrix protein of the sea urchin spine, stabilizes mineral precursors via vesicle-confinement, a function conferred by a low-complexity, disordered region. Site-specific proteolysis of this domain by a collagenase initiates phase transformation of the confined mineral phase. The residual C-type lectin domain molds the fluidic mineral precursor into hierarchical mesocrystals identical to structural crystal modules constituting the biogenic mineral. Thus, the regulatory functions of proteolytic enzymes can guide biomacromolecular domain constitutions and interfaces, in turn determining inorganic phase transformations toward hybrid materials as well as integrating organic and inorganic components across hierarchical length scales. Bearing striking resemblance to biogenic mineralization, these hybrid materials recruit bioinorganic interactions which elegantly intertwine nucleation and crystallization phenomena with biomolecular structural dynamics, hence elucidating a long-sought key of how nature can orchestrate complex biomineralization processes.

"On demand" triggered crystallization of CaCO3 from solute precursor species stabilized by the water-in-oil microemulsion.

Can we control the crystallization of solid CaCO3 from supersaturated aqueous solutions and thus mimic a natural process predicted to occur in living organisms that produce biominerals? Here we show how we achieved this by confining the reaction between Ca2+ and CO32- ions to the environment of nanosized water cores of water-in-oil microemulsions, in which the reaction between the ions is controlled by the intermicellar exchange processes. Using a combination of in situ small-angle X-ray scattering, high-energy X-ray diffraction, and low-dose liquid-cell scanning transmission electron microscopy, we elucidate how the presence of micellar interfaces leads to the formation of a solute CaCO3 phase/species that can be stabilized for extended periods of time inside micellar water nano-droplets. The nucleation and growth of any solid CaCO3 polymorph, including the amorphous phase, from such nano-droplets is prevented despite the fact that the water cores in the used microemulsion are highly supersaturated with respect to all known calcium carbonate solid phases. On the other hand the presence of the solute CaCO3 phase inside of the water cores decreases the rigidity of the micellar surfactant/water interface, which promotes the aggregation of micelles and the formation of large (>2 µm in diameter) globules. The actual precipitation and crystallization of solid CaCO3 could be triggered "on-demand" through the targeted removal of the organic-inorganic interface and hence the destabilization of globules carrying the CaCO3 solute.

Organ size control via hydraulically gated oscillations.

Hollow vesicular tissues of various sizes and shapes arise in biological organs such as ears, guts, hearts, brains and even entire organisms. Regulating their size and shape is crucial for their function. Although chemical signaling has been thought to play a role in the regulation of cellular processes that feed into larger scales, it is increasingly recognized that mechanical forces are involved in the modulation of size and shape at larger length scales. Motivated by a variety of examples of tissue cyst formation and size control that show simultaneous growth and size oscillations, we create a minimal theoretical framework for the growth and dynamics of a soft, fluid-permeable, spherical shell. We show that these shells can relieve internal pressure by bursting intermittently, shrinking and re-growing, providing a simple mechanism by which hydraulically gated oscillations can regulate size. To test our theory, we develop an in vitro experimental set-up to monitor the growth and oscillations of a hollow tissue spheroid growing freely or when confined. A simple generalization of our theory to account for irreversible deformations allows us to explain the time scales and the amplitudes of oscillations in terms of the geometry and mechanical properties of the tissue shells. Taken together, our theory and experimental observations show how soft hydraulics can regulate the size of growing tissue shells.

Protein sequences bound to mineral surfaces persist into deep time.

Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites of Laetoli (3.8 Ma) and Olduvai Gorge (1.3 Ma) in Tanzania. By tracking protein diagenesis back in time we find consistent patterns of preservation, demonstrating authenticity of the surviving sequences. Molecular dynamics simulations of struthiocalcin-1 and -2, the dominant proteins within the eggshell, reveal that distinct domains bind to the mineral surface. It is the domain with the strongest calculated binding energy to the calcite surface that is selectively preserved. Thermal age calculations demonstrate that the Laetoli and Olduvai peptides are 50 times older than any previously authenticated sequence (equivalent to ~16 Ma at a constant 10°C).

Synergistic Biomineralization Phenomena Created by a Combinatorial Nacre Protein Model System.

In the nacre or aragonite layer of the mollusk shell, proteomes that regulate both the early stages of nucleation and nano-to-mesoscale assembly of nacre tablets from mineral nanoparticle precursors exist. Several approaches have been developed to understand protein-associated mechanisms of nacre formation, yet we still lack insight into how protein ensembles or proteomes manage nucleation and crystal growth. To provide additional insights, we have created a proportionally defined combinatorial model consisting of two nacre-associated proteins, C-RING AP7 (shell nacre, Haliotis rufescens) and pseudo-EF hand PFMG1 (oyster pearl nacre, Pinctada fucata), whose individual in vitro mineralization functionalities are well-documented and distinct from one another. Using scanning electron microscopy, flow cell scanning transmission electron microscopy, atomic force microscopy, Ca(II) potentiometric titrations, and quartz crystal microbalance with dissipation monitoring quantitative analyses, we find that both nacre proteins are functionally active within the same mineralization environments and, at 1:1 molar ratios, synergistically create calcium carbonate mesoscale structures with ordered intracrystalline nanoporosities, extensively prolong nucleation times, and introduce an additional nucleation event. Further, these two proteins jointly create nanoscale protein aggregates or phases that under mineralization conditions further assemble into protein-mineral polymer-induced liquid precursor-like phases with enhanced ACC stabilization capabilities, and there is evidence of intermolecular interactions between AP7 and PFMG1 under these conditions. Thus, a combinatorial model system consisting of more than one defined biomineralization protein dramatically changes the outcome of the in vitro biomineralization process.

SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences.

DNA-binding proteins control many fundamental biological processes such as transcription, recombination and replication. A major goal is to decipher the role that DNA sequence plays in orchestrating the binding and activity of such regulatory proteins. To address this goal, it is useful to rationally design DNA sequences with desired numbers, affinities and arrangements of protein binding sites. However, removing binding sites from DNA is computationally non-trivial since one risks creating new sites in the process of deleting or moving others. Here we present an online binding site removal tool, SiteOut, that enables users to design arbitrary DNA sequences that entirely lack binding sites for factors of interest. SiteOut can also be used to delete sites from a specific sequence, or to introduce site-free spacers between functional sequences without creating new sites at the junctions. In combination with commercial DNA synthesis services, SiteOut provides a powerful and flexible platform for synthetic projects that interrogate regulatory DNA. Here we describe the algorithm and illustrate the ways in which SiteOut can be used; it is publicly available at https://depace.med.harvard.edu/siteout/.

Semiconductor-Metal Nanofloret Hybrid Structures by Self-Processing Synthesis.

We present a synthetic strategy that takes advantage of the inherent asymmetry exhibited by semiconductor nanowires prepared by Au-catalyzed chemical vapor deposition (CVD). The metal-semiconductor junction is used for activating etch, deposition, and modification steps localized to the tip area using a wet-chemistry approach. The hybrid nanostructures obtained for the coinage metals Cu, Ag, and Au resemble the morphology of grass flowers, termed here Nanofloret hybrid nanostructures consisting of a high aspect ratio SiGe nanowire (NW) with a metallic nanoshell cap. The synthetic method is used to prepare hybrid nanostructures in one step by triggering a programmable cascade of events that is autonomously executed, termed self-processing synthesis. The synthesis progression was monitored by ex situ transmission electron microscopy (TEM), in situ scanning transmission electron microscopy (STEM) and inductively coupled plasma mass spectrometry (ICP-MS) analyses to study the mechanistic reaction details of the various processes taking place during the synthesis. Our results indicate that the synthesis involves distinct processing steps including localized oxide etch, metal deposition, and process termination. Control over the deposition and etching processes is demonstrated by several parameters: (i) etchant concentration (water), (ii) SiGe alloy composition, (iii) reducing agent, (iv) metal redox potential, and (v) addition of surfactants for controlling the deposited metal grain size. The NF structures exhibit broad plasmonic absorption that is utilized for demonstrating surface-enhanced Raman scattering (SERS) of thiophenol monolayer. The new type of nanostructures feature a metallic nanoshell directly coupled to the crystalline semiconductor NW showing broad plasmonic absorption.

Simulations show that virus assembly and budding are facilitated by membrane microdomains.

For many viruses, assembly and budding occur simultaneously during virion formation. Understanding the mechanisms underlying this process could promote biomedical efforts to block viral propagation and enable use of capsids in nanomaterials applications. To this end, we have performed molecular dynamics simulations on a coarse-grained model that describes virus assembly on a fluctuating lipid membrane. Our simulations show that the membrane can promote association of adsorbed subunits through dimensional reduction, but it also introduces thermodynamic and kinetic effects that can inhibit complete assembly. We find several mechanisms by which membrane microdomains, such as lipid rafts, reduce these effects, and thus, enhance assembly. We show how these predicted mechanisms can be experimentally tested. Furthermore, the simulations demonstrate that assembly and budding depend crucially on the system dynamics via multiple timescales related to membrane deformation, protein diffusion, association, and adsorption onto the membrane.

A tunable coarse-grained model for ligand-receptor interaction.

Cell-surface receptors are the most common target for therapeutic drugs. The design and optimization of next generation synthetic drugs require a detailed understanding of the interaction with their corresponding receptors. Mathematical approximations to study ligand-receptor systems based on reaction kinetics strongly simplify the spatial constraints of the interaction, while full atomistic ligand-receptor models do not allow for a statistical many-particle analysis, due to their high computational requirements. Here we present a generic coarse-grained model for ligand-receptor systems that accounts for the essential spatial characteristics of the interaction, while allowing statistical analysis. The model captures the main features of ligand-receptor kinetics, such as diffusion dependence of affinity and dissociation rates. Our model is used to characterize chimeric compounds, designed to take advantage of the receptor over-expression phenotype of certain diseases to selectively target unhealthy cells. Molecular dynamics simulations of chimeric ligands are used to study how selectivity can be optimized based on receptor abundance, ligand-receptor affinity and length of the linker between both ligand subunits. Overall, this coarse-grained model is a useful approximation in the study of systems with complex ligand-receptor interactions or spatial constraints.

Mechanisms of budding of nanoscale particles through lipid bilayers.

We examine the budding of a nanoscale particle through a lipid bilayer using molecular dynamics simulations, free energy calculations, and an elastic theory, with the aim of determining the extent to which equilibrium elasticity theory can describe the factors that control the mechanism and efficiency of budding. The particle is a smooth sphere which experiences attractive interactions to the lipid head groups. Depending on the parameters, we observe four classes of dynamical trajectories: particle adhesion to the membrane, stalled partially wrapped states, budding followed by scission, and membrane rupture. In most regions of parameter space we find that the elastic theory agrees nearly quantitatively with the simulated phase behavior as a function of adhesion strength, membrane bending rigidity, and particle radius. However, at parameter values near the transition between particle adhesion and budding, we observe long-lived partially wrapped states which are not captured by existing elastic theories. These states could constrain the accessible system parameters for those enveloped viruses or drug delivery vehicles which rely on exo- or endocytosis for membrane transport.

Association between airborne pollen and epidemic asthma in Madrid, Spain: a case-control study.

BACKGROUND Despite the fact that airborne pollen is an important factor in precipitating asthma attacks, its implication in increases of epidemic asthma in usual meteorological conditions has not been reported. A study was undertaken to estimate the relationship between various types of aeroallergens and seasonal epidemic asthma in the region of Madrid, Spain. METHODS A case-control study was carried out in individuals aged 4-79 years who received emergency healthcare for asthma during 2001 in a base hospital covering a population of 750 000 inhabitants of Madrid. A skin prick test was performed with grass pollen, plantain pollen, olive pollen, cypress pollen, plane tree pollen, dust mites and Alternaria and the prevalence of skin reactivity was compared between subjects with asthma requiring emergency care for asthma within (cases) and outside (controls) the seasonal epidemic period. Data were analysed using logistic regression adjusting for age and sex. RESULTS The response rate was 61.7% for cases (n=95) and 51.6% for controls (n=146). The OR of sensitisation to grass pollen for cases compared with controls was 9.9 (95% CI 4.5 to 21.5); plantain pollen: 4.5 (95% CI 2.5 to 8.2); olive pollen: 7.3 (95% CI 3.5 to 15.2); plane tree pollen: 3.6 (95% CI 2.0 to 6.4); cypress pollen: 3.5 (95% CI 2.0 to 6.2); dust mites: 1.1 (95% CI 0.6 to 1.9); Alternaria: 0.9 (95% CI 0.5 to 1.9). The association with grasses was maintained after adjusting simultaneously for the remaining aeroallergens (OR 5.0 (95% CI 1.5 to 16.4)); this was the only one that retained statistical significance (p=0.007). CONCLUSIONS These results suggest that allergy to pollen, particularly grass pollen, is associated with the epidemic increase in asthma episodes during the months of May and June in the Madrid area of Spain.

Acoustic voice analysis in different phonetic contexts after larynx radiotherapy for T1 vocal cord carcinoma.

INTRODUCTION: Radiotherapy for early vocal cord carcinoma affects quality of voice. Nevertheless, most patients refer to having a high satisfaction level with their voice. The few acoustic studies on quality of voice have been performed only in prolonged vowel production, which is not a usual speech situation. The present study has been done with the aim of establishing which phonetic situations reflect a greater alteration in voice production related to irradiation. MATERIAL AND METHODS: Eighteen male patients irradiated for Tis-T1 vocal cord carcinoma and a control group of 31 non-irradiated subjects were included in a study of acoustic voice analysis. This analysis was performed one year after radiotherapy. Patients and control group voices were tape recorded in extended vowel production, oral reading of a standard paragraph, spontaneous speech and in a song. Acoustic analysis was performed by a Kay Elemetric's Computerized Speech Lab (model CSL #4300). Fundamental frequency, jitter, shimmer and harmonics-to-noise ratio were obtained in both groups. Statistical test: Lin concordance coefficient and Pearson's correlation coefficient, Student's t-test and ROC curves. RESULTS: Concordance and correlation studies did not allow selection of any subgroup in acoustic parameters and different acoustic situations. Acoustic parameters had higher median values in irradiated patients. Student's t-test showed significant differences for fundamental frequency in sustained vowel production and spontaneous speech; for jitter there was statistical significance in all the acoustic situations and for shimmer in oral reading and song. Jitter showed a cut-off of 2.02% with a sensitivity of 89% and specificity of 97% in classifying irradiated and non-irradiated groups. The ROC curve for jitter correctly classified 94% of subjects into irradiated or non-irradiated groups. CONCLUSIONS: The present study showed that jitter obtained from spontaneous speech was the most relevant parameter in discriminating voice in irradiated patients by acoustic analysis. Jitter in spontaneous speech is in need of more analysis in bigger series and in more advanced stages of larynx cancer as its relevance has been demonstrated.