Low Frequency Strain Research Articles

Efficient GPU Cloth Simulation with Non-distance Barriers and Subspace Reuse

This paper pushes the performance of cloth simulation, making the simulation interactive even for high-resolution garment models while keeping every triangle untangled. The penetration-free guarantee is inspired by the interior point method, which converts the inequality constraints to barrier potentials. We propose a major overhaul of this modality within the projective dynamics framework by leveraging an adaptive weighting mechanism inspired by barrier formulation. This approach does not depend on the distance between mesh primitives, but on the virtual life span of a collision event and thus keeps all the vertices within feasible region. Such a non-distance barrier model allows a new way to integrate collision resolution into the simulation pipeline. Another contributor to the performance boost comes from the subspace reuse strategy. This is based on the observation that low-frequency strain propagation is near orthogonal to the deformation induced by collisions or self-collisions, often of high frequency. Subspace reuse then takes care of low-frequency residuals, while high-frequency residuals can also be effectively smoothed by GPU-based iterative solvers. We show that our method outperforms existing fast cloth simulators by at least one order while producing high-quality animations of high-resolution models.

Seismic Magnitude Estimation Using Low-Frequency Strain Amplitudes Recorded by DAS Arrays at Far-Field Distances

ABSTRACT Downhole distributed acoustic sensing (DAS) data are now routinely acquired on fiber-optic cables deployed in wells for seismic imaging and microseismic monitoring. We develop a semiempirical workflow for estimating scalar seismic moment and moment magnitude of earthquakes using strain data recorded by downhole DAS arrays. At far-field distances, the time integral of axial strain is proportional to the displacement scaled by apparent slowness. Therefore, seismic moment can be directly estimated from the amplitude of the low-frequency plateau of the strain spectra divided by frequency, similar to the methodology commonly employed for far-field displacement spectra. The effect of polarization on strain amplitudes for different types of body waves is accounted for. Benefitting from the large spatial coverage provided by DAS arrays, moment estimates from multiple channels are averaged and an average radiation coefficient is assumed over the focal sphere. We validate the methods using data of microseismic events simultaneously recorded by a surface geophone array and by DAS on fiber deployed in two horizontal wells during a hydraulic fracturing experiment. For 106 microseismic events in the magnitude range ∼ −0.65 to ∼ +0.55, we find the DAS-derived magnitudes to be consistent with the magnitudes derived from the geophone array using traditional methods, with ∼95% of the magnitude estimates differing by less than ∼0.26 units. The workflow can be potentially extended to DAS arrays in vertical wells and to S waves recorded on dark fiber DAS arrays at the surface. This methodology does not require any calibration beyond knowledge of local seismic properties, and the use of the lowest possible frequencies reduces the influence of subsurface heterogeneities and the finite spatiotemporal extent of earthquake ruptures. The capacity to estimate robust seismic magnitudes from downhole DAS arrays allows improved evaluation and management of fracture growth and more effective mitigation of induced seismicity.

Interpretation of low-frequency distributed acoustic sensing data based on geomechanical models

Distributed acoustic sensing (DAS) is a technology that enables continuous, real-time measurements along the entire length of a fiber-optic cable. The low-frequency band of DAS can be used to analyze hydraulic fracture geometry and growth. In this study, the low-frequency strain waterfall plots with their corresponding pumping curves were analyzed to obtain information on fracture azimuth, propagation speed, number of fractures created in each stage, and restimulation of preexisting fractures. We also use a simple geomechanical model to predict fracture growth rates while accounting for changes in treatment parameters. As expected, the hydraulic fractures principally propagate perpendicular to the treated well, that is, parallel to the direction of maximum horizontal stress. During many stages, multiple frac hits are visible, indicating that multiple parallel fractures are created and/or reopened. Secondary fractures deviate toward the heel of the well, likely due to the cumulative stress shadow caused by previous and current stages. The presence of heart-shaped tips reveals that some stress and/or material barrier is overcome by the hydraulic fracture. The lobes of the heart are best explained by the shear stresses at 45° angles from the fracture tip instead of the tensile stresses directly ahead of the tip. Antennas ahead of the fracture hits indicate the reopening of preexisting fractures. Tails in the waterfall plots provide information on the continued opening, closing, and interaction of the hydraulic fractures within the fracture domain and stage domain corridors. The analysis of the low-frequency DAS plots thus provides in-depth insights into the rock deformation and rock-fluid interaction processes occurring close to the observation well.

Breakage behavior of corn kernels subjected to repeated loadings

Studying the breakage behavior of corn kernels subjected to repeated compressive events, including at low frequency and low strain rate, are important for the development of breakage models for prediction of kernel breakage in handling and processing machines. The main purpose of this study was to identify the breakage behavior and mechanism of weakening of corn kernels under repeated loadings as affected by their moisture content and kernel thickness. Corn kernels at four moisture content levels (8.20%, 11.95%, 16.00%, 20.02%) and in four thickness ranges were subjected to repeated compressive loading between two parallel steel plates in quasi-static regime at a constant loading rate of 2 mm/min (strain rates from 4.7 × 10−3 to 1.0 × 10−2). Conducted experiments allow to observe the different grain breakage patterns, identify the crack initiation and its development, describe the weakening of kernels by changes in the total specific energy, plastic and elastic deformation energies, and the number of loading cycles to break (breakage probability) the kernels. The results indicate that the breakage models describing the damage and weakening of grains in terms of changes in the total and strain energy or changes in the stiffness can be used for understanding the effect of moisture content and thickness on breakage of corn kernels.

Malaria outbreak in Laos driven by a selective sweep for Plasmodium falciparum kelch13 R539T mutants: a genetic epidemiology analysis

Malaria outbreaks are important public health concerns that can cause resurgence in endemic regions approaching elimination. We investigated a Plasmodium falciparum outbreak in Attapeu Province, Laos, during the 2020-21 malaria season, using genomic epidemiology methods to elucidate parasite population dynamics and identify its causes. In this genetic analysis, 2164 P falciparum dried blood spot samples were collected from southern Laos between Jan 1, 2017, and April 1, 2021, which included 249 collected during the Attapeu outbreak between April 1, 2020, and April 1, 2021, by routine surveillance. Genetic barcodes obtained from these samples were used to investigate epidemiological changes underpinning the outbreak, estimate population diversity, and analyse population structure. Whole-genome sequencing data from additional historical samples were used to reconstruct the ancestry of outbreak strains using identity-by-descent analyses. The outbreak parasite populations were characterised by unprecedented loss of genetic diversity, primarily caused by rapid clonal expansion of a multidrug-resistant strain (LAA1) carrying the kelch13 Arg539Thr (R539T) mutation. LAA1 replaced kelch13 Cys580Tyr (C580Y) mutants resistant to dihydroartemisinin-piperaquine (KEL1/PLA1) as the dominant strain. LAA1 inherited 58·8% of its genome from a strain circulating in Cambodia in 2008. A secondary outbreak strain (LAA2) carried the kelch13 C580Y allele, and a genome that is essentially identical to a Cambodian parasite from 2009. A third, low-frequency strain (LAA7) was a recombinant of KEL1/PLA1 with a kelch13 R539T mutant. These results strongly suggest that the outbreak was driven by a selective sweep, possibly associated with multidrug-resistant phenotypes of the outbreak strains. Established resistant populations can circulate at low frequencies for years before suddenly overwhelming dominant strains when the conditions for selection become favourable-eg, when front-line therapies change. Genetic surveillance can support elimination by characterising key properties of outbreaks such as population diversity, drug resistance marker prevalence, and the origins of outbreak strains. Bill & Melinda Gates Foundation; The Global Fund to Fight AIDS, Tuberculosis and Malaria; Wellcome Trust. For the Lao translation of the abstract see Supplementary Materials section.

Tensile strain and altered synovial tissue metabolism in human knee osteoarthritis

Synovium is critical for maintaining joint homeostasis and may contribute to mechanobiological responses during joint movement. We investigated mechanobiological responses of whole synovium from patients with late-stage knee osteoarthritis (OA). Synovium samples were collected during total knee arthroplasty and assigned to histopathology or cyclic 10% tensile strain loading, including (1) static (control); (2) low-frequency (0.3 Hz); and iii) high-frequency (1.0 Hz) for 30-min. After 6-h incubation, tissues were bisected for RNA isolation and immunostaining (3-nitrotyrosine; 3-NT). RNA sequencing was analyzed for differentially expressed genes and pathway enrichment. Cytokines and lactate were measured in conditioned media. Compared to controls, low-frequency strain induced enrichment of pathways related to interferon response, Fc-receptor signaling, and cell metabolism. High-frequency strain induced enrichment of pathways related to NOD-like receptor signaling, high metabolic demand, and redox signaling/stress. Metabolic and redox cell stress was confirmed by increased release of lactate into conditioned media and increased 3-NT formation in the synovial lining. Late-stage OA synovial tissue responses to tensile strain include frequency-dependent increases in inflammatory signaling, metabolism, and redox biology. Based on these findings, we speculate that some synovial mechanobiological responses to strain may be beneficial, but OA likely disturbs synovial homeostasis leading to aberrant responses to mechanical stimuli, which requires further validation.

Research Progress of Applying Distributed Fiber Optic Measurement Technology in Hydraulic Fracturing and Production Monitoring

With the exploration and development of unconventional oil and gas resources, downhole environmental monitoring and data-analysis technologies are becoming more and more important. Distributed fiber optic measurement technology, as a new monitoring technology to obtain accurate data, has a wide range of applications in hydraulic fracturing and production monitoring. It mainly includes: distributed fiber optic temperature sensors (DTSs) to monitor gas lift, identify in-flow fluid types, interpret flow profiles and monitor production enhancement operations; distributed fiber optic acoustic sensors (DASs) to monitor low frequency strain and microseismic and hydraulic fracturing operations; and distributed fiber optic stress sensors (DSSs) to characterize fractures in the near-well area, which have been well applied in the field. This paper describes the current application status of DASs and DSSs in hydraulic fracturing and production monitoring, respectively, from the principle of distributed fiber optic measurement technology. It also points out the limitations of these measurement technologies and the direction of future development. Distributed fiber optic measurement technology has been making technical breakthroughs in recent years, providing strong technical support for the development of unconventional oil and gas resources.

Large-range phase-difference sensing technology for low-frequency strain interrogation

Phase-difference sensing technology (PDST) has been applied to strain measurement, but its completeness is destroyed by the phase-difference measurement range. A scheme that can realize the completeness of the PDST for low-frequency strain interrogation is proposed. It is built on dual-interferometers and the elliptic-fitting algorithm. To break the measurement range limitation (0, π), a phase compensation setting is applied. The experimental results demonstrate that the method can obtain low-frequency strain signals, and the low-frequency signal whose phase amplitude is greater than π is recovered. The scheme is an efficient and complete method for measuring the strain of low-frequency optical fiber length, which could be applied to low-frequency seismic wave monitoring and rock deformation detection.

Influence of effective electrode coverage on the energy harvesting performance of piezoelectric cantilevers

Cantilevers are widely used for piezoelectric vibration energy harvesters (PEHs), thanks to the low resonance frequency and large mechanical strain under weak excitations. Electrode coverage optimization is essential for maximizing output power. In this study, bimorph cantilevers with segmented electrodes are developed to investigate the correlation between effective electrode coverage (EEC) and the harvesting behavior of piezoelectric cantilevers. A nonlinear electromechanical model is established using Hamilton's principle, numerically solved with the method of harmonic balance, and further validated by experimental measurements. Equivalent linear stiffness and equivalent mechanical damping ratio are firstly introduced for evaluating the equivalent effective electromechanical coupling coefficients and identifying strong and weak coupling harvesters. Both harvesters fabricated with and without proof mass behave mainly as strongly coupled systems and can obtain the maximum possible power at a very low EEC. Variation of EEC in higher range acquires almost constant maximum power on dramatically changing resistance. A comprehensive EEC design principle for acquiring the maximum output power is obtained for cantilevered PEHs. An optimal EEC obtaining the maximum effective electromechanical coupling coefficient is needed for acquiring the unique maximum power pick for weakly coupled harvesters, whereas a wide range of EEC can be used to maximize output power for harvesters those mainly behave as strongly coupled systems.

Supervivencia intracelular de cepas de Mycobacterium bovis de alta y baja frecuencia probado en un modelo de macrófagos bovinos

Bovine tuberculosis is a disease caused by Mycobacterium bovis that affects cattle and other species, including humans. Mycobacterium bovis resides mainly in macrophages, so bacilli survival within macrophages is related to virulence. Isolation and strain identification are important for disease control. However, little is known about virulence of the circulating strains in cattle populations. Therefore, the aim of this study was to compare the intracellular survival of Mycobacterium bovis strains with high and low frequency genotypes in cattle in Mexico. Four high frequency genotypes and four low frequency genotypes were identified and subjected to intracellular survival assays in bovine macrophages. Results showed that the phagocytosis proportion was approximately 63 % for all strains. There were no significant differences in the average Colony Forming Units (CFUs) in phagocytosis and survival between the high and low frequency groups; however, when the CFU average of phagocytosis was compared with the survival, significant differences were found in both groups. In intracellular growth, a significant difference was observed between low and high frequency strains, and between low frequency strains. Finally, the intracellular growth average of the groups was analyzed showing no significant difference. These results suggest that the frequency of the genotype in cattle population is not related to the intracellular survival and the virulence of the M. bovis strains.

Intracellular invasion ability of Streptococcus agalactiae among non-invasive isolates from human adults and companion animals in Japan

ObjectiveThis study evaluated the cell invasion ability (CIA) of Streptococcus agalactiae isolates from humans and companion animals and clarified the relationship between CIA populations and their microbiological features. MethodsHuman-origin and companion animal-origin isolates were collected along with host information. We measured CIA using human-lineage colon cancer epithelium (Caco-2) and keratinocyte (HaCaT) cell lines, via virulence-associated gene profiling (bca-rib-bac-lmb-cylE-hylB-pavA-pilB-spb1-srtC1-brpA), capsular genotyping, multilocus sequence typing, and antimicrobial resistance (AMR) phenotyping/genotyping. Significant differences in data regarding CIA into epithelium and keratinocytes and those of isolates from different hosts were assessed. We analyzed the association of CIA populations with the virulence genotypes, capsular genotypes, sequence types/clonal complexes, and AMR phenotypes/genotypes. ResultsA comparative analysis was performed between human (n = 15) and canine (n = 17) non-invasive isolates. There was a difference in CIA data between Caco-2 and HaCaT cells using human and animal isolates. For percent invasion ability into Caco-2 cells, we designated values ≥ 0.1 as high-frequency CIA and values < 0.1 as low-frequency CIA. Fourteen isolates harbored high-frequency and 18 isolates harbored low-frequency strains. There was no association between the high-frequency population and the virulence genotypes, capsular genotypes, sequence types/clonal complexes, and AMR phenotypes/genotypes. ConclusionThis is the first report assessing the invasion ability of S. agalactiae into HaCaT and Caco-2 cells. Our observations suggest that S. agalactiae is more capable of entering Caco-2 rather than HaCaT.

Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome.

Host-associated microbiomes can be critical for the health and proper development of animals and plants. The answers to many fundamental questions regarding the modes of acquisition and microevolution of microbiome communities remain to be established. Deciphering strain-level dynamics is essential to fully understand how microbial communities evolve, but the forces shaping the strain-level dynamics of microbial communities remain largely unexplored, mostly because of methodological issues and cost. Here, we used targeted strain-level deep sequencing to uncover the strain dynamics within a host-associated microbial community using the honey bee gut microbiome as a model system. Our results revealed that amplicon sequencing of conserved protein-coding gene regions using species-specific primers is a cost-effective and accurate method for exploring strain-level diversity. In fact, using this method we were able to confirm strain-level results that have been obtained from whole-genome shotgun sequencing of the honey bee gut microbiome but with a much higher resolution. Importantly, our deep sequencing approach allowed us to explore the impact of low-frequency strains (i.e., cryptic strains) on microbiome dynamics. Results show that cryptic strain diversity is not responsible for the observed variations in microbiome composition across bees. Altogether, the findings revealed new fundamental insights regarding strain dynamics of host-associated microbiomes.IMPORTANCE The factors driving fine-scale composition and dynamics of gut microbial communities are poorly understood. In this study, we used metagenomic amplicon deep sequencing to decipher the strain dynamics of two key members of the honey bee gut microbiome. Using this high-throughput and cost-effective approach, we were able to confirm results from previous large-scale whole-genome shotgun (WGS) metagenomic sequencing studies while also gaining additional insights into the community dynamics of two core members of the honey bee gut microbiome. Moreover, we were able to show that cryptic strains are not responsible for the observed variations in microbiome composition across bees.

Optimizing strain energy extraction from multi-beam piezoelectric devices for heavy haul freight cars

Heavy haul trains used to transport commodities are generally very long and operated by a single individual. Owing to high noise levels from the rolling stock displacement, the driver cannot notice failures in the compartments. It is practically impossible to visually inspect the wagons located far from the locomotive. Sensors that can measure in-train forces may improve the train’s operation, indicating potential failures and preventing accidents and derailments. However, the freight cars employed in most of the railroads are not equipped with electric power sources, making inspections unlikely. Therefore, an energy harvesting system must be developed for the sensors to avoid the need for periodic battery charging or replacement. As a high level of kinetic energy is present in the rolling stock, a vibration energy harvester (VEH) system is an acceptable alternative. Among VEH devices, multi-beam piezoelectric materials used in planar zigzag (PZ) or orthogonal spiral outer fixed (OSo) configurations can be effective alternatives. These can be powered by low-frequency strains readily available in the freight cars. This study investigates the optimum geometries of PZ and OSo aiming to increase the generated power and minimize the structure mass with a focus on their application to ore wagons. Among the optimum solutions, the OSo geometry generates the maximum power, up to 20.93 mW, which is sufficient to feed some critical devices. Conversely, the PZ configurations present the highest energy density, up to 16.595 mW/kg(m s−2)2, which allows for a more suitable solution to be combined in serial and/or parallel pack configurations.

Use of single and double fractional Kelvin–Voigt model on viscoelastic elastomer

Dielectric elastomer actuators also known as DEAs are widely used as soft actuators. In order to control such actuators its mechanical properties are needed. Since viscoelastic materials are mainly used as a base for DEAs, an appropriate mathematical model is needed to get appropriate control parameters. Viscoelastic elastomers have very complex mechanical characteristics. They exhibit a combination of behaviors of solid material and liquid. Usually, solid materials exhibit elasticity up to a certain point. Liquids exhibits viscosity. They change their shape regardless on the stress applied on it and do not regain their original shape. Viscoelastic materials exhibit both behaviors at once. However, the ratio between elasticity and viscosity depends on the material being used. The use of fractional Kelvin–Voigt model can be of great help in determining the elastic and/or viscous material properties. Even more, a comparison between single and double fractional Kelvin–Voigt models will be given for low frequency strain ranges. It will be shown that viscoelastic mechanical properties are frequency dependent. At the end a least-square method is introduced for determination of optimal parameters for both models. This study can be used as a guidance for viscoelastic material parameter identification either for single or double fractional Kelvin–Voigt model. Both models can be further used in control theory with fractional derivatives to obtain proper control parameters since they are easily transferable to Laplace domain.

382. Virulence in Candida glabrata Is Not Attenuated by FKS Mutations but Associated With the Frequency of Cells With Distinct Morphology

BackgroundEchinocandins are the first-line treatment for C. glabrata; however, echinocandin resistance is increasingly reported. Acquired FKS-mediated echinocandin resistance has been associated with the upregulation of chitin synthesis and attenuated fitness and virulence in C. albicans; however, conflicting data are reported in C. glabrata. Here, the influence of FKS mutations on fitness, virulence, morphology, and cell wall chitin was assessed among clinical strains of C. glabrata.MethodsThree sets of isogenic paired strains consisting of an index-WT and persistent-FKS mutant (S663P), two un-paired FKS mutant strains (S663F and S629P), and a WT reference strain (CBS138) were included. Growth kinetics were measured over 24 hours in 96-well microplate containing liquid RPMI. After overnight growth in RPMI and staining with a chitin-specific fluorescent marker, morphology, and chitin were assessed at the single-cell level utilizing high-content imaging technique. Virulence was evaluated in Galleria mellonella larvae by injecting 107 cells/larvae. Mortality was assessed daily for 5 days.ResultsSignificant differences in growth kinetics, frequency of morphologic phenotypes within the cell populations (nonbudding, single-bud, multiple-buds), and virulence were observed between strains obtained from different patients (P < 0.05 for each). However, no difference was observed between paired index-WT and persistent-FKS S663P mutants. Compared with index-WT and the CBS138 reference strain, FKS mutant isolates (S663P, S629P, and S663F) had significantly elevated cell wall chitin content (P < 0.05). Neither chitin content, the presence of an FKS mutation, nor in vitro growth characteristics were found to be associated with virulence. Virulence was strongly correlated with the frequency of multi-bud cells within the population however, with 5-day post-injection survival rates of 4% vs. 28% for high-frequency (>12% multi-bud cells) and low-frequency strains, respectively (P < 0.001).ConclusionAcquired FKS-mediated echinocandin resistance induced significant alterations in cell wall chitin content but was not observed to attenuate fitness or virulence. Virulence was highly associated with the frequency of cells with distinct morphology.Disclosures N. D. Beyda, Astellas: Grant Investigator and Scientific Advisor, Consulting fee and Research grant.

Modeling of polyurethane/lead zirconate titanate composites for vibration energy harvesting

Collecting the vibration energy existing in the surrounding environment and its transformation to a useful electrical energy in order to supply ultra-low power systems remains an emerging and promising technology. During the last decades, most of research efforts dealt with energy-harvesting technology using piezoelectric ceramics. However, those materials are stiff and limited in mechanical strain abilities. In addition, they lose their stiffness and piezoelectricity at high levels of mechanical strain. Thus, they are unsuitable for many applications in which low frequency and high strain level are required. However, electrostrictive polymers are lightweight, very flexible, have low manufacturing costs and are easy to mould into any desired shapes. These special properties led to them being considered as potential actuators. However, it is not well known that these materials also can be used for mechanical-to-electrical energy harvesting. In this research paper, electromechanical characterization of polymer/lead zirconate titanate composites was extended. The first part develops the analytical model predicting the energy harvested by polyurethane/PZT composites from electrical and mechanical properties of their constituent materials. Indeed, this model was based on the approach of representing the experimental setup with an equivalent electrical scheme. The second part focuses on the assessment of model performance by comparison between predicted and observed values. As a result, good agreements were observed between the two sets of data; in addition, the model could be used to optimize the choice of constituent materials. The last part concerns the contribution of both the electrostrictive effect and piezoelectric effect in electrical powers harvested by PU/PZT composites.

Carstensen’s contributions to shear stress in strain and tissues

Some of Edwin Carstensen's final papers considered elastographic shear waves, which had opened up a new set of questions regarding stress and strain in tissues. Carstensen, from his commanding perspective overlooking nearly 70 years of fields and waves in tissues, could uniquely make the following statement: “At present, no consensus group has undertaken a systematic evaluation of the biological effects of low-frequency strains…Thanks to developments in the field of elastography over the last two decades, we now have the tools needed to measure low-frequency strains in tissues directly…Despite the fundamental importance of strain in bioeffects, no bioeffects investigators to our knowledge have taken advantage of these techniques. In fact, strain is rarely mentioned in the bioeffects literature” (Carstensen et al., “Biological effects of low-frequency shear strain: physical descriptors,” Ultrasound Med Biol 42(1)1-15, 2016). Indeed, with this topic, his “voyage of exploration and illumination” had truly come full circle, returning to some earlier questions but under new circumstances. We explore the deep issues Carstensen uncovered, including special forms of shear waves, the implications of Ostreicher's work, tissue viscoelastic response to shear stresses, and the inherent puzzles of linear hysteresis models.

Damping of carbon fibre and flax fibre angle-ply composite laminates

The damping behaviour of continuous carbon fibre and flax fibre reinforced polymer (CFRP and FFRP) composites was studied by comparing angle-ply laminates. Using logarithmic decrement measurements, dynamic mechanical analysis and vibration beam measurements, the damping was described as the specific damping capacity ψ in order to compare data using the different methods.Our results show approximately 2–3 times better damping of FFRP compared to CFRP at low frequency and low strain. We show that the damping of both materials increases with increasing angle-ply orientation below 300Hz. While the matrix and interface seems to contribute mainly to damping at lower frequencies, the fibre shows an increasing contribution with ψ = 64.4% for unidirectional FFRP at 1259Hz in the 5th mode of vibration, without a notable change in the elastic modulus. This work demonstrates that the FFRP may be simultaneously stiff and efficient at damping.

Geophysical monitoring of subsurface contamination in two-phase porous media

We have explored a new technology based on using low-frequency strain attenuation data to monitor the infiltration of contaminants into two-fluid phase porous materials. The attenuation mechanism is related to the loss of energy due to the hysteresis of resistance to meniscus movement (changes in surface tension and wettability) when a pore containing two fluids is stressed at very low frequencies. This phenomenon was verified in our laboratory experiments and applied to a field study near Maricopa, Arizona. In the field study we conducted controlled experiments with the aim of detecting and monitoring the infiltration of a contaminant – a biosurfactant – into groundwater. Three sets of geophysical instruments, each consisting of a 3-component seismometer and a tiltmeter, were installed near an irrigation site. The experiment lasted about 3years with controlled irrigations of initially water only and then water with contaminant into the vadose zone. We used naturally occurring signals of microseisms for our seismic sources and solid Earth tides as sources for the tilt signals.To process the tilt data we extracted the tidal signal from the raw data, and then compared the measured tidal signals with site-specific theoretical data. Changes in tidal signals indicate a strong anomaly associated with the irrigation when a 150ppm concentration of a biosurfactant was present. No such anomaly was detected when only water was used. Further data processing with an automated procedure shows that the anomalies still persisted. Furthermore, the microseismic results from the seismic data suggest that there may also be a detectable anomaly.

Primer ID ultra-deep sequencing reveals dynamics of drug resistance-associated variants in breakthrough hepatitis C viruses: relevance to treatment outcome and resistance screening.

Use of direct-acting antiviral drugs (DAAs) that target HCV may be hampered by the rapid selection of viral strains that harbour drug resistance-associated variants (RAVs). These RAVs are often associated with a fitness cost and tend to occur on low-frequency strains within treatment-naive subjects. To address the clinical relevance of low frequency RAVs in the setting of DAAs, this study utilized a Primer ID ultra-deep sequencing approach to mitigate PCR errors and bias to accurately quantify viral sequences in subjects that failed DAA treatment. Subjects were enrolled in the follow-up study P05063, and had previous treatment with boceprevir and all had detectable RAVs at virological failure (VF) based on Sanger-based population sequencing. Twelve subjects had three time points available: baseline, VF and follow-up (median 830.5 days). Viral RNA was amplified using unique primer identifiers (Primer IDs) and sequenced using 454 ultra-deep sequencing. The sequencing strategy used in this study improved the detection of clinically relevant low frequency strains bearing RAVs compared to population sequencing and showed that these strains can persist for up to 2 years post-treatment failure. Strains carrying multiple RAVs were common in breakthrough viruses. Putative compensatory mutations were identified. The Primer ID ultra-deep sequencing approach identifies RAVs that can reduce drug sensitivity at levels below the detection threshold for population sequencing. The approach also removes PCR errors and biases, suggesting this sequencing strategy should become the standard approach by which to perform temporal quasispecies studies and resistance screening. ClinicalTrials.gov NCT00689390.