Assessment of the Angolan (CHERRT) Mobile Laboratory Curriculum for Disaster and Pandemic Response

Introduction: As of April 5, 2020, the World Health Organization reported over one million confirmed cases and more than 62,000 confirmed coronavirus (COVID-19) deaths affecting 204 countries/ regions. The lack of COVID-19 testing capacity threatens the ability of both the United States (US) and low middle income countries (LMIC) to respond to this growing threat, The purpose of this study was to assess the effectiveness through participant self-assessment of a rapid response team (RRT) mobile laboratory curriculumMethods: We conducted a pre and post survey for the purpose of a process improvement assessment in Angola, involving 32 individuals. The survey was performed before and after a 14-day training workshop held in Luanda, Angola, in December 2019. A paired t-test was used to identify any significant change on six 7-point Likert scale questions with α< 0.05 (95% confidence interval).Results: All six of the questions –  1) “I feel confident managing a real laboratory sample test for Ebola or other highly contagious sample;” 2) “I feel safe working in the lab environment during a real scenario;” 3) “I feel as if I can appropriately manage a potentially highly contagious laboratory sample;” 4)“I feel that I can interpret a positive or negative sample during a suspected contagious outbreak;” 5) “I understand basic Biobubble/mobile laboratory concepts and procedures;” and 6) “I understand polymerase chain reaction (PCR) principles” – showed statistical significant change pre and post training. Additionally, the final two questions – “I can more effectively perform my role/position because of the training I received during this course;” and “This training was valuable”  – received high scores on the Likert scale.Conclusion: This Angolan RRT mobile laboratory training curriculum provides the nation of Angola with the confidence to rapidly respond and test at the national level a highly infectious contagion in the region and perform on-scene diagnostics. This mobile RRT laboratory provides a mobile and rapid diagnostic resource when epidemic/pandemic resource allocation may need to be prioritized based on confirmed disease prevalence

First-passage dynamics of obstructed tracer particle diffusion in one-dimensional systems

The standard setup for single-file diffusion is diffusing particles in one dimension which cannot overtake each other, where the dynamics of a tracer (tagged) particle is of main interest. In this article we generalise this system and investigate first-passage properties of a tracer particle when flanked by crowder particles which may, besides diffuse, unbind (rebind) from (to) the one-dimensional lattice with rates $k_{\rm off}$ ($k_{\rm on}$). The tracer particle is restricted to diffuse with rate $k_D$ on the lattice. Such a model is relevant for the understanding of gene regulation where regulatory proteins are searching for specific binding sites ona crowded DNA. We quantify the first-passage time distribution, $f(t)$ ($t$ is time), numerically using the Gillespie algorithm, and estimate it analytically. In terms of our key parameter, the unbinding rate $k_{\rm off}$, we study the bridging of two known regimes: (i) when unbinding is frequent the particles may effectively pass each other and we recover the standard single particle result $f(t)\sim t^{-3/2}$ with a renormalized diffusion constant, (ii) when unbinding is rare we recover well-known single-file diffusion result $f(t)\sim t^{-7/4}$. The intermediate cases display rich dynamics, with the characteristic $f(t)$-peak and the long-time power-law slope both being sensitive to $k_{\rm off}$

Critical Timescales for Burrowing in Undersea Substrates via Localized Fluidization, Demonstrated by RoboClam: A Robot Inspired by Atlantic Razor Clams

The Atlantic razor clam (Ensis directus) burrows into underwater soil by using motions of its shell to locally fluidize the surrounding substrate. The energy associated with movement through fluidized soil — characterized by a depth-independent density and viscosity — scales linearly with depth. In contrast, moving through static soil requires energy that scales with depth squared. For E. directus, this translates to a 10X reduction in the energy required to reach observed burrow depths. For engineers, localized fluidization offers a mechanically simple and purely kinematic method to dramatically reduce burrowing energy. This concept is demonstrated with RoboClam, an E. directus-inspired robot. Using a genetic algorithm to generate digging kinematics, RoboClam has achieved localized fluidization and burrowing performance comparable to that of the animal, with a linear energy-depth relationship. In this paper, we present the critical timescales and associated kinematics necessary for achieving localized fluidization, which are calculated from soil parameters and validated via RoboClam and E. directus testing.Battelle Memorial InstituteBluefin RoboticsChevron Corporatio

The Design and Testing of RoboClam: A Machine Used to Investigate and Optimize Razor Clam-Inspired Burrowing Mechanisms for Engineering Applications

Razor clams (Ensis directus) are one of nature’s most adept burrowing organisms, able to dig to 70cm at nearly 1cm/s using only 0.21J/cm. Ensis reduces burrowing drag by using motions of its shell to fluidize a thin layer of substrate around its body. Although these shell motions have an energetic cost, moving through fluidized rather than packed soil results in exponentially lower overall energy consumption. This paper describes the design and testing of RoboClam, a device that mimics Ensis digging methods to understand the limits of razor clam-inspired burrowing, how they scale for different environments and conditions, and how they can be transferred into engineering applications. Using a genetic optimization solver, we found that RoboClam’s most efficient digging motion mimicked Ensis shell kinematics and yielded a power law relationship between digging energy and depth of n = 1.17, very close to the ideal value of n = 1. Pushing through static soil has a theoretical energy-depth power law of n = 2, which means that Ensis-inspired burrowing motions can provide exponentially higher energy efficiency and nearly depth-independent drag resistance.Battelle Memorial InstituteBluefin RoboticsChevron Corporatio

Exponential speed-up with a single bit of quantum information: Testing the quantum butterfly effect

We present an efficient quantum algorithm to measure the average fidelity decay of a quantum map under perturbation using a single bit of quantum information. Our algorithm scales only as the complexity of the map under investigation, so for those maps admitting an efficient gate decomposition, it provides an exponential speed up over known classical procedures. Fidelity decay is important in the study of complex dynamical systems, where it is conjectured to be a signature of quantum chaos. Our result also illustrates the role of chaos in the process of decoherence.Comment: 4 pages, 2 eps figure

Razor clam to RoboClam: burrowing drag reduction mechanisms and their robotic adaptation

Estimates based on the strength, size, and shape of the Atlantic razor clam (Ensis directus) indicate that the animal's burrow depth should be physically limited to a few centimeters; yet razor clams can dig as deep as 70 cm. By measuring soil deformations around burrowing E. directus, we have found the animal reduces drag by contracting its valves to initially fail, and then fluidize, the surrounding substrate. The characteristic contraction time to achieve fluidization can be calculated directly from soil properties. The geometry of the fluidized zone is dictated by two commonly-measured geotechnical parameters: coefficient of lateral earth pressure and friction angle. Calculations using full ranges for both parameters indicate that the fluidized zone is a local effect, occurring between 1–5 body radii away from the animal. The energy associated with motion through fluidized substrate—characterized by a depth-independent density and viscosity—scales linearly with depth. In contrast, moving through static soil requires energy that scales with depth squared. For E. directus, this translates to a 10X reduction in the energy required to reach observed burrow depths. For engineers, localized fluidization offers a mechanically simple and purely kinematic method to dramatically reduce energy costs associated with digging. This concept is demonstrated with RoboClam, an E. directus-inspired robot. Using a genetic algorithm to find optimal digging kinematics, RoboClam has achieved localized fluidization burrowing performance comparable to that of the animal, with a linear energy-depth relationship, in both idealized granular glass beads and E. directus' native cohesive mudflat habitat.Battelle Memorial InstituteBluefin RoboticsChevron Corporatio

Multi-Substrate Burrowing Performance and Constitutive Modeling of RoboClam: A Biomimetic Robot Based on Razor Clams

The Atlantic razor clam (Ensis directus) reduces burrowing drag by using motions of its shell to fluidize a thin layer of substrate around its body. We have developed RoboClam, a robot that digs using the same mechanisms as Ensis, to explore how localized fluidization burrowing can be extended to engineering applications. In this work we present burrowing performance results of RoboClam in two distinctly different substrates: ideally granular 1mm soda lime glass beads and cohesive ocean mudflat soil. Using a genetic algorithm to optimize RoboClam’s kinematics, the machine was able to burrow in both substrates with a power law relationship between digging energy and depth of n = 1.17. Pushing through static soil has a theoretical energy-depth power law of n = 2, which means that Ensis-inspired burrowing motions can provide exponentially higher energy efficiency. We propose a theoretical constitutive model that describes how a fluidized region should form around a contracting body in virtually any type of saturated soil. The model predicts fluidization to be a relatively local effect, extending only two to three characteristic lengths away from the body, depending on friction angle and coefficient of lateral earth pressure, two commonly measured soil parameters.Battelle Memorial InstituteBluefin RoboticsChevron Corporatio

Overprinting orogenic events, ductile extrusion and strain partitioning during Caledonian transpression, NW Mainland Shetland

A 3.6 km thick stack of mid-crustal deformed Precambrian rocks is associated with the North Roe Nappe (NRN) and Walls Boundary Fault in the northernmost Scottish Caledonides on NW Mainland Shetland. The greenschist- to amphibolite-facies rocks display unusually complex and heterogeneous combinations of coaxial and non-coaxial transpressional deformation. Previously published isotopic dating, together with new detailed field mapping and microstructural characterisation show that the NRN preserves a record of Neoarchaean, Neoproterozoic (Knoydartian) and Ordovician-Silurian (Caledonian) overprinting deformation and metamorphism. Neoarchaean events in the Uyea Gneiss Complex located in its footwall are reworked by younger events in the overlying nappe pile. The main ductile fabrics were formed during Caledonian top-to-the W/NW thrusting and top-to-the N sinistral shearing, with subordinate regions of top- to-the E extensional and NNE-SSW dextral shearing. In lower parts of the NRN, these different kinematic domains are texturally indistinguishable and overprinting relationships are absent. At higher levels, top-to-the-W/NW thrust-related fabrics are consistently overprinted by top-to-the-N/NE sinistral shearing. The highly partitioned transpressional deformation shows similarities with equivalent rocks of the Moine Nappe in NW Scotland

Evaluation of FTIR Spectroscopy as a diagnostic tool for lung cancer using sputum

BACKGROUND: Survival time for lung cancer is poor with over 90% of patients dying within five years of diagnosis primarily due to detection at late stage. The main objective of this study was to evaluate Fourier transform infrared spectroscopy (FTIR) as a high throughput and cost effective method for identifying biochemical changes in sputum as biomarkers for detection of lung cancer. METHODS: Sputum was collected from 25 lung cancer patients in the Medlung observational study and 25 healthy controls. FTIR spectra were generated from sputum cell pellets using infrared wavenumbers within the 1800 to 950 cm(-1 )"fingerprint" region. RESULTS: A panel of 92 infrared wavenumbers had absorbances significantly different between cancer and normal sputum spectra and were associated with putative changes in protein, nucleic acid and glycogen levels in tumours. Five prominent significant wavenumbers at 964 cm(-1), 1024 cm(-1), 1411 cm(-1), 1577 cm(-1 )and 1656 cm(-1 )separated cancer spectra from normal spectra into two distinct groups using multivariate analysis (group 1: 100% cancer cases; group 2: 92% normal cases). Principal components analysis revealed that these wavenumbers were also able to distinguish lung cancer patients who had previously been diagnosed with breast cancer. No patterns of spectra groupings were associated with inflammation or other diseases of the airways. CONCLUSIONS: Our results suggest that FTIR applied to sputum might have high sensitivity and specificity in diagnosing lung cancer with potential as a non-invasive, cost-effective and high-throughput method for screening. TRIAL REGISTRATION: ClinicalTrials.gov: NCT0089926