Iterative data-driven forecasting of the transmission and management of SARS-CoV-2/COVID-19 using social interventions at the county-level.

The control of the initial outbreak and spread of SARS-CoV-2/COVID-19 via the application of population-wide non-pharmaceutical mitigation measures have led to remarkable successes in dampening the pandemic globally. However, with countries beginning to ease or lift these measures fully to restart activities, concern is growing regarding the impacts that such reopening of societies could have on the subsequent transmission of the virus. While mathematical models of COVID-19 transmission have played important roles in evaluating the impacts of these measures for curbing virus transmission, a key need is for models that are able to effectively capture the effects of the spatial and social heterogeneities that drive the epidemic dynamics observed at the local community level. Iterative forecasting that uses new incoming epidemiological and social behavioral data to sequentially update locally-applicable transmission models can overcome this gap, potentially resulting in better predictions and policy actions. Here, we present the development of one such data-driven iterative modelling tool based on publicly available data and an extended SEIR model for forecasting SARS-CoV-2 at the county level in the United States. Using data from the state of Florida, we demonstrate the utility of such a system for exploring the outcomes of the social measures proposed by policy makers for containing the course of the pandemic. We provide comprehensive results showing how the locally identified models could be employed for accessing the impacts and societal tradeoffs of using specific social protective strategies. We conclude that it could have been possible to lift the more disruptive social interventions related to movement restriction/social distancing measures earlier if these were accompanied by widespread testing and contact tracing. These intensified social interventions could have potentially also brought about the control of the epidemic in low- and some medium-incidence county settings first, supporting the development and deployment of a geographically-phased approach to reopening the economy of Florida. We have made our data-driven forecasting system publicly available for policymakers and health officials to use in their own locales, so that a more efficient coordinated strategy for controlling SARS-CoV-2 region-wide can be developed and successfully implemented.

Securing the Chain of Custody and Integrity of Data in a Global North-South Partnership to Monitor the Quality of Essential Medicines.

Substandard and falsified (SF) pharmaceuticals account for an estimated 10% of the pharmaceutical supply chain in low- and middle-income countries (LMICs), where a lack of regulatory and laboratory resources limits the ability to conduct effective post-market surveillance and allows SF products to penetrate the supply chain. The Distributed Pharmaceutical Analysis Laboratory (DPAL) was established in 2014 to expand testing of pharmaceutical dosage forms sourced from LMICs; DPAL is an alliance of academic institutions throughout the United States and abroad that provides high-quality, validated chemical analysis of pharmaceutical dosage forms sourced from partners in LMICs. Results from analysis are reported to relevant regulatory agencies and are used to inform purchasing decisions made by in-country stakeholders. As the DPAL program has expanded to testing more than 1,000 pharmaceutical dosage forms annually, challenges have surfaced regarding data management and sample tracking. Here, we describe a pilot project between DPAL and ARTiFACTs that applies the blockchain to organize and manage key data generated during the DPAL workflow, including a sample's progress through the workflow, its physical location, provenance of metadata, and lab reputability. Recording time and date stamps with these data will create a permanent and verifiable chain of custody for samples. This secure, distributed ledger will be linked to an easy-to-use dashboard, allowing stakeholders to view results and experimental details for each sample in real time and verify the integrity of DPAL analysis data. Introducing this blockchain-based system as a pilot will allow us to test the technology with real users analyzing real samples. Feedback from users will be recorded and necessary adjustments will be made to the system before the implementation of blockchain across all DPAL sites. Anticipated benefits of implementing the blockchain technology for managing DPAL data include efficient management for routing work, increasing throughput, creating a chain of custody for samples and their data in alignment with the distributed nature of DPAL, and using the analysis results to detect patterns of quality within and across brands of products and develop enhanced sampling techniques and best practices.

Fistula Rate after primary palatal repair with intravelarveloplasty: a retrospective three-year audit of six units (NorCleft) in the UK.

Our aim was to evaluate the rate of fistulation after one-stage palatal repair by intravelarveloplasty in the NorCleft Cleft Services (Scotland and Northern England), this being a primary outcome measure after repair of a cleft palate. We designed a retrospective, three-year clinical audit of six cleft units in the UK, and retrospectively reviewed the casenotes of babies with cleft palate born in 2006-2008 who were treated by intravelarveloplasty. We recorded type of cleft and procedure, including lateral relieving incisions, and our main outcome measure was the presence of a fistula behind the incisive foramen at 3 years of age, or a history of repair of a fistula. A total of 743 patients had cleft palates, but 69 (9%) were excluded (because they had not been operated on, or had not been reviewed by the age of 3 years, or their records were unavailable). A total of 626 patients had had a Sommerlad intravelarveloplasty repair, and 48 had had mixed procedures including Veau-Wardill-Kilner, Furlow, or two-stage repairs, and were not studied further. Eighty-seven (14%) who had had intravelarvoloplasty had a fistula behind the incisive foramen. There was no significant difference in age at time of repair between those who developed a fistula and those who did not (p=0.65). The fistula rate of 14% is comparable with that of Sommerlad. The fistula rate was higher in patients who had had lateral releasing incisions (58/275, 21%) or who had bilateral cleft palate (16/63, 25%). To our knowledge this is the largest review of the fistula rate in patients who had primary palatal repair using the intravelarveloplasty technique in the UK, and shows significant correlation between lateral releasing incisions and formation of a fistula, except in the unilateral cleft lip and palate group (p=0.12).

saltPAD: A New Analytical Tool for Monitoring Salt Iodization in Low Resource Settings.

We created a paper test card that measures a common iodizing agent, iodate, in salt. To test the analytical metrics, usability, and robustness of the paper test card when it is used in low resource settings, the South African Medical Research Council and GroundWork performed independent validation studies of the device. The accuracy and precision metrics from both studies were comparable. In the SAMRC study, more than 90% of the test results (n=1704) were correctly classified as corresponding to adequately or inadequately iodized salt. The cards are suitable for market and household surveys to determine whether salt is adequately iodized. Further development of the cards will improve their utility for monitoring salt iodization during production.

Interventions for the treatment of keratocystic odontogenic tumours.

BACKGROUND: The keratocystic odontogenic tumours (KCOTs) account for between about 2% and 11% of all jaw cysts and can occur at any age. They are more common in males than females with a male:female ratio of approximately 2:1. Although they are benign, KCOTs are locally very aggressive and have a tendency to recur after treatment. Reported recurrence rates range from 3% to 60%. The traditional method for the treatment of most KCOTs is surgical enucleation. However, due to the lining of the cyst being delicate and the fact that they frequently recur, this method alone is not sufficient. Adjunctive surgical treatment has been proposed in addition to the surgical enucleation, such as removal of the peripheral bone (ostectomy) or resection of the cyst with surrounding bone (en-bloc) resection. Other adjunctive treatments proposed are: cryotherapy (freezing) with liquid nitrogen and the use of the fixative Carnoy's solution placed in the cyst cavity after enucleation; both of which attempt to address residual tissue to prevent recurrence. OBJECTIVES: To assess the available evidence comparing the effectiveness of interventions for the treatment of KCOTs. SEARCH METHODS: We searched the following electronic databases: the Cochrane Oral Health Group Trials Register (to 17 March 2015), the Cochrane Central Register of Controlled Trials (CENTRAL) (The Cochrane Library, 2015, Issue 2), MEDLINE via Ovid (1946 to 17 March 2015) and EMBASE via Ovid (1980 to 17 March 2015). We searched the US National Institutes of Health Trials Register (http://clinicaltrials.gov) and the WHO Clinical Trials Registry Platform for ongoing trials. No restrictions were placed on the language or date of publication when searching the electronic databases. SELECTION CRITERIA: Randomised controlled trials comparing one modality of intervention with another with or without adjunctive treatment for the treatment of KCOTs. Adults, over the age of 18 with a validated diagnosis of solitary KCOTs arising in the jaw bones of the maxilla or mandible. Patients with known Gorlin syndrome were to be excluded. DATA COLLECTION AND ANALYSIS: Review authors screened trials for inclusion. Full papers were obtained for relevant and potentially relevant trials. If data had been extracted, it would have been synthesised using the fixed-effect model, if substantial clinical diversity were identified between studies we planned to use the random-effects model with studies grouped by action provided there were four or more studies included in the meta-analysis, and we would have explored the heterogeneity between the included studies. MAIN RESULTS: No randomised controlled trials that met the inclusion criteria were identified. AUTHORS' CONCLUSIONS: There are no published randomised controlled trials relevant to this review question, therefore no conclusions could be reached about the effectiveness or otherwise of the interventions considered in this review. There is a need for well designed and conducted randomised controlled trials to evaluate treatments for KCOTs.

Long Timestep Molecular Dynamics on the Graphical Processing Unit.

Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD simulations. In particular, we discuss new methods to calculate the needed terms in LTMD as well as issues germane to a GPU implementation. The resulting code, implemented in the OpenMM MD library, can achieve a significant 6-fold speed increase, leading to MD simulations on the order of 5 µs/day using implicit solvent models.

Modelling platelet-blood flow interaction using the subcellular element Langevin method.

In this paper, a new three-dimensional modelling approach is described for studying fluid-viscoelastic cell interaction, the subcellular element Langevin (SCEL) method, with cells modelled by subcellular elements (SCEs) and SCE cells coupled with fluid flow and substrate models by using the Langevin equation. It is demonstrated that: (i) the new method is computationally efficient, scaling as (N) for N SCEs; (ii) cell geometry, stiffness and adhesivity can be modelled by directly relating parameters to experimentally measured values; (iii) modelling the fluid-platelet interface as a surface leads to a very good correlation with experimentally observed platelet flow interactions. Using this method, the three-dimensional motion of a viscoelastic platelet in a shear blood flow was simulated and compared with experiments on tracking platelets in a blood chamber. It is shown that the complex platelet-flipping dynamics under linear shear flows can be accurately recovered with the SCEL model when compared with the experiments. All experimental details and electronic supplementary material are archived at http://biomath.math.nd.edu/scelsupplementaryinformation/.

Study of elastic collisions of Myxococcus xanthus in swarms.

In very low density situations where a single myxobacterial cell is isolated from direct contact with other cells, the slime capsule interaction with the substrate or slime tracks on the substrate produce a viscous drag that results in a smooth gliding motion. Viscoelastic interactions of myxobacteria cells in a low-density domain close to the edge of a swarm are studied using a combination of a cell-based three-dimensional computational model and cell-tracking experiments. The model takes into account the flexible nature of Myxococcus xanthus as well as the effects of adhesion between cells arising from the interaction of the capsular polysaccharide covering two cells in contact with each other. New image and dynamic cell curvature analysis algorithms are used to track and measure the change in cell shapes that occur as flexible cells undergo significant bending during collisions resulting in direct calibration of the model parameters. Like aspect-ratio and directional reversals, the flexibility of cells and the adhesive cell-cell and cell-substrate interactions of M. xanthus play an important role in smooth gliding and more efficient swarming.

Modeling conformational ensembles of slow functional motions in Pin1-WW.

Protein-protein interactions are often mediated by flexible loops that experience conformational dynamics on the microsecond to millisecond time scales. NMR relaxation studies can map these dynamics. However, defining the network of inter-converting conformers that underlie the relaxation data remains generally challenging. Here, we combine NMR relaxation experiments with simulation to visualize networks of inter-converting conformers. We demonstrate our approach with the apo Pin1-WW domain, for which NMR has revealed conformational dynamics of a flexible loop in the millisecond range. We sample and cluster the free energy landscape using Markov State Models (MSM) with major and minor exchange states with high correlation with the NMR relaxation data and low NOE violations. These MSM are hierarchical ensembles of slowly interconverting, metastable macrostates and rapidly interconverting microstates. We found a low population state that consists primarily of holo-like conformations and is a "hub" visited by most pathways between macrostates. These results suggest that conformational equilibria between holo-like and alternative conformers pre-exist in the intrinsic dynamics of apo Pin1-WW. Analysis using MutInf, a mutual information method for quantifying correlated motions, reveals that WW dynamics not only play a role in substrate recognition, but also may help couple the substrate binding site on the WW domain to the one on the catalytic domain. Our work represents an important step towards building networks of inter-converting conformational states and is generally applicable.

Interventions for the treatment of keratocystic odontogenic tumours (KCOT, odontogenic keratocysts (OKC)).

BACKGROUND: The keratocystic odontogenic tumours (KCOTs) account for between about 2% and 11% of all jaw cysts and can occur at any age. They are more common in males than females with a male:female ratio of approximately 2:1. Although they are benign, KCOTs are locally very aggressive and have a tendency to recur after treatment, reported recurrence rates range from 3% to 60%. The traditional method for the treatment of most KCOTs is surgical enucleation. However, due to the lining of the cyst being delicate and the fact that they frequently recur, this method alone is not sufficient. Adjunctive surgical treatment has been proposed in addition to the surgical enucleation, such as removal of the peripheral bone (ostectomy) or resection of the cyst with surrounding bone (en-bloc) resection. Other adjunctive treatments proposed are: cryotherapy (freezing) with liquid nitrogen and the use of the fixative Carnoy's solution placed in the cyst cavity after enucleation; both of which attempt to address residual tissue to prevent recurrence. OBJECTIVES: To assess the available evidence comparing the effectiveness of surgical interventions and adjuncts for the treatment of KCOTs. SEARCH STRATEGY: Databases searched were: the Cochrane Oral Health Group's Trials Register (to 28th July 2010), CENTRAL (The Cochrane Library 2010, Issue 3), MEDLINE (from 1950 to 28th July 2010), and EMBASE (from 1980 to 28th July 2010). The reference lists of all trials identified were cross checked for additional trials. There were no language restrictions and several articles were translated. SELECTION CRITERIA: Randomised controlled trials comparing one modality of surgical intervention with another with or without adjunctive treatment for the treatment of KCOTs. Adults, over the age of 18 with a validated diagnosis of solitary KCOTs arising in the jaw bones of the maxilla or mandible. Patients with known Gorlin syndrome were to be excluded. DATA COLLECTION AND ANALYSIS: Review authors screened trials for inclusion. Full papers were obtained for relevant and potentially relevant trials. If data had been extracted, it would have been synthesised using the fixed-effect model, if substantial clinical diversity were identified between studies we planned to use the random-effects model with studies grouped by action provided there were four or more studies included in the meta-analysis, and we would have explored the heterogeneity between the included studies. MAIN RESULTS: No randomised controlled trials that met the inclusion criteria were identified. AUTHORS' CONCLUSIONS: There are no published randomised controlled trials relevant to this review question, therefore no conclusions could be reached about the effectiveness or otherwise of the interventions considered in this review. There is a need for well designed and conducted randomised controlled trials to evaluate treatments for KCOTs.

MDLab: a molecular dynamics simulation prototyping environment.

Molecular dynamics (MD) simulation involves solving Newton's equations of motion for a system of atoms, by calculating forces and updating atomic positions and velocities over a timestep Deltat. Despite the large amount of computing power currently available, the timescale of MD simulations is limited by both the small timestep required for propagation, and the expensive algorithm for computing pairwise forces. These issues are currently addressed through the development of efficient simulation methods, some of which make acceptable approximations and as a result can afford larger timesteps. We present MDLab, a development environment for MD simulations built with Python which facilitates prototyping, testing, and debugging of these methods. MDLab provides constructs which allow the development of propagators, force calculators, and high level sampling protocols that run several instances of molecular dynamics. For computationally demanding sampling protocols which require testing on large biomolecules, MDL includes an interface to the OpenMM libraries of Friedrichs et al. which execute on graphical processing units (GPUs) and achieve considerable speedup over execution on the CPU. As an example of an interesting high level method developed in MDLab, we present a parallel implementation of the On-The-Fly string method of Maragliano and Vanden-Eijnden. MDLab is available at http://mdlab.sourceforge.net.

A separable shadow Hamiltonian hybrid Monte Carlo method.

Hybrid Monte Carlo (HMC) is a rigorous sampling method that uses molecular dynamics (MD) as a global Monte Carlo move. The acceptance rate of HMC decays exponentially with system size. The shadow hybrid Monte Carlo (SHMC) was previously introduced to reduce this performance degradation by sampling instead from the shadow Hamiltonian defined for MD when using a symplectic integrator. SHMC's performance is limited by the need to generate momenta for the MD step from a nonseparable shadow Hamiltonian. We introduce the separable shadow Hamiltonian hybrid Monte Carlo (S2HMC) method based on a formulation of the leapfrog/Verlet integrator that corresponds to a separable shadow Hamiltonian, which allows efficient generation of momenta. S2HMC gives the acceptance rate of a fourth order integrator at the cost of a second-order integrator. Through numerical experiments we show that S2HMC consistently gives a speedup greater than two over HMC for systems with more than 4000 atoms for the same variance. By comparison, SHMC gave a maximum speedup of only 1.6 over HMC. S2HMC has the additional advantage of not requiring any user parameters beyond those of HMC. S2HMC is available in the program PROTOMOL 2.1. A Python version, adequate for didactic purposes, is also in MDL (http://mdlab.sourceforge.net/s2hmc).

Normal mode partitioning of Langevin dynamics for biomolecules.

We propose a novel normal mode multiple time stepping Langevin dynamics integrator called NML. The aim is to approximate the kinetics or thermodynamics of a biomolecule by a reduced model based on a normal mode decomposition of the dynamical space. Our basis set uses the eigenvectors of a mass reweighted Hessian matrix calculated with a biomolecular force field. This particular choice has the advantage of an ordering according to the eigenvalues, which have a physical meaning of being the square of the mode frequency. Low frequency eigenvalues correspond to more collective motions, whereas the highest frequency eigenvalues are the limiting factor for the stability of the integrator. In NML, the higher frequency modes are overdamped and relaxed near their energy minimum while respecting the subspace of low frequency dynamical modes. Our numerical results confirm that both sampling and rates are conserved for an implicitly solvated alanine dipeptide model, with only 30% of the modes propagated, when compared to the full model. For implicitly solvated systems, NML gives a twofold improvement in efficiency over plain Langevin dynamics for sampling a small 22 atom (alanine dipeptide) model and in excess of an order of magnitude for sampling an 882 atom (bovine pancreatic trypsin inhibitor) model, with good scaling with system size subject to the number of modes propagated. NML has been implemented in the open source software PROTOMOL.

Accelerating the replica exchange method through an efficient all-pairs exchange.

The authors accelerate the replica exchange method through an efficient all-pairs replica exchange. A proof of detailed balance is shown along with an analytical estimate of the enhanced exchange efficiency. The new method provides asymptotically four fold speedup of conformation traversal for replica counts of 8 and larger with typical exchange rates. Experimental tests using the blocked alanine dipeptide demonstrate the method's correctness and show an approximate sampling efficiency improvement of 100% according to potential energy cumulative averages and an ergodic measure. An explicitly solvated PIN1 WW domain system of 4958 atoms is sampled using our new method, yielding a cluster sampling rate almost twice that of the single exchange near neighbor implementation. Computational software and scripts along with input and output data sets are available at.

Making a good impression: (a 'how to' paper on dental alginate).

Approximately 20,000 impressions are made with alginate annually at the University Dental Hospital of Manchester alone, and countless more wherever clinical dentistry is practised. A proportion of these are considered unsatisfactory for clinical use. The reason for these 'failures' is often poor operator technique, rather than an inherent problem of the material. With improved handling of the material and better clinical technique, failures can be avoided. This paper provides an overview of the use of alginate impression material in clinical dentistry.

The canonical ensemble via symplectic integrators using Nosé and Nosé-Poincaré chains.

Simulations that sample from the canonical ensemble can be generated by the addition of a single degree of freedom, provided that the system is ergodic, as described by Nosé with subsequent modifications by Hoover to allow sampling in real time. Nosé-Hoover dynamics is not ergodic for small or stiff systems and the addition of auxiliary thermostats is needed to overcome this deficiency. Nosé-Hoover dynamics, like its derivatives, does not have a Hamiltonian structure, precluding the use of symplectic integrators which are noted for their long term stability and structure preservation. As an alternative to Nosé-Hoover, the Hamiltonian Nosé-Poincaré method was proposed by Bond, Laird, and Leimkuhler [J. Comput. Phys. 151, 114 (1999)], but the straightforward addition of thermostatting chains does not sample from the canonical ensemble. In this paper a method is proposed whereby additional thermostats can be applied to a Hamiltonian system while retaining sampling from the canonical ensemble. This technique has been used to construct thermostatting chains for the Nosé and Nosé-Poincaré methods.