Effective Data Sampling Strategies and Boundary Condition Constraints of Physics-Informed Neural Networks for Identifying Material Properties in Solid Mechanics

Material identification is critical for understanding the relationship between mechanical properties and the associated mechanical functions. However, material identification is a challenging task, especially when the characteristic of the material is highly nonlinear in nature, as is common in biological tissue. In this work, we identify unknown material properties in continuum solid mechanics via physics-informed neural networks (PINNs). To improve the accuracy and efficiency of PINNs, we developed efficient strategies to nonuniformly sample observational data. We also investigated different approaches to enforce Dirichlet boundary conditions as soft or hard constraints. Finally, we apply the proposed methods to a diverse set of time-dependent and time-independent solid mechanic examples that span linear elastic and hyperelastic material space. The estimated material parameters achieve relative errors of less than 1%. As such, this work is relevant to diverse applications, including optimizing structural integrity and developing novel materials

Bellybutton: Accessible and Customizable Deep-Learning Image Segmentation

The conversion of raw images into quantifiable data can be a major hurdle in experimental research, and typically involves identifying region(s) of interest, a process known as segmentation. Machine learning tools for image segmentation are often specific to a set of tasks, such as tracking cells, or require substantial compute or coding knowledge to train and use. Here we introduce an easy-to-use (no coding required), image segmentation method, using a 15-layer convolutional neural network that can be trained on a laptop: Bellybutton. The algorithm trains on user-provided segmentation of example images, but, as we show, just one or even a portion of one training image can be sufficient in some cases. We detail the machine learning method and give three use cases where Bellybutton correctly segments images despite substantial lighting, shape, size, focus, and/or structure variation across the regions(s) of interest. Instructions for easy download and use, with further details and the datasets used in this paper are available at pypi.org/project/Bellybuttonseg.Comment: 6 Pages 3 Figure

Magnetic field tuning of mechanical properties of ultrasoft PDMS-based magnetorheological elastomers for biological applications

We report tuning of the moduli and surface roughness of magnetorheological elastomers (MREs) by varying applied magnetic field. Ultrasoft MREs are fabricated using a physiologically relevant commercial polymer, SylgardTM 527, and carbonyl iron powder (CIP). We found that the shear storage modulus, Young\u27s modulus, and root-mean-square surface roughness are increased by ∼41×, ∼11×, and ∼11×, respectively, when subjected to a magnetic field strength of 95.5 kA m−1. Single fit parameter equations are presented that capture the tunability of the moduli and surface roughness as a function of CIP volume fraction and magnetic field strength. These magnetic field-induced changes in the mechanical moduli and surface roughness of MREs are key parameters for biological applications

Investigating the physical properties of transiting hot Jupiters with the 1.5-m Kuiper Telescope

We present new photometric data of 11 hot Jupiter transiting exoplanets (CoRoT-12b, HAT-P-5b, HAT-P-12b, HAT-P-33b, HAT-P-37b, WASP-2b, WASP-24b, WASP-60b, WASP-80b, WASP-103b, XO-3b) in order to update their planetary parameters and to constrain information about their atmospheres. These observations of CoRoT-12b, HAT-P-37b and WASP-60b are the first follow-up data since their discovery. Additionally, the first near-UV transits of WASP-80b and WASP-103b are presented. We compare the results of our analysis with previous work to search for transit timing variations (TTVs) and a wavelength dependence in the transit depth. TTVs may be evidence of a third body in the system and variations in planetary radius with wavelength can help constrain the properties of the exoplanet's atmosphere. For WASP-103b and XO-3b, we find a possible variation in the transit depths that may be evidence of scattering in their atmospheres. The B-band transit depth of HAT-P-37b is found to be smaller than its near-IR transit depth and such a variation may indicate TiO/VO absorption. These variations are detected from 2-4.6$\sigma$, so follow-up observations are needed to confirm these results. Additionally, a flat spectrum across optical wavelengths is found for 5 of the planets (HAT-P-5b, HAT-P-12b, WASP-2b, WASP-24b, WASP-80b), suggestive that clouds may be present in their atmospheres. We calculate a refined orbital period and ephemeris for all the targets, which will help with future observations. No TTVs are seen in our analysis with the exception of WASP-80b and follow-up observations are needed to confirm this possible detection.Comment: 18 pages, 7 figures, 9 Tables. Light Curves available online. Accepted to MNRAS (2017 August 25

Mass deworming programmes in middle childhood and adolescence

Soil-transmitted helminthes (STH) deworming programs remain among the largest public health programs in low- and lower-middle-income countries as measured by coverage. The actual scale of these programs remains unknown but substantial, with more than 1 billion donated doses of medicines effective against STHs delivered by formal programs and supplemented by widespread self-treatment and unprogrammed activities. STH infection declines worldwide likely reflect the influence of improved hygiene and sanitation associated with global declines in poverty, but it also reflects control efforts during the twentieth century that have largely eliminated STHs as a public health problem in previously endemic areas of North America (Mexico and the United States), Japan, Korea, and upper- middle-income countries throughout southern and eastern Asia. Much of the treatment targets delivery through schools and targets school-age children. STH infection associates with clinical and developmental outcomes that prove largely reversible by treatment. Both historical and contemporary trials of targeted treatment of infected individuals have also demonstrated benefit from treatment

Preface

Author Posting. © The Author(s), 2014. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 1-5, doi:10.1016/j.dsr2.2014.02.007.The Gulf of Maine (GOM) is a continental shelf sea in the northwest Atlantic, USA that supports highly-productive shellfisheries that are frequently contaminated by toxigenic Alexandrium fundyense blooms and outbreaks of paralytic shellfish poisoning (PSP), resulting in significant economic and social impacts. Additionally, an emerging threat to these resources is from blooms of toxic Pseudo-nitzschia species that produce domoic acid, the toxin responsible for amnesic shellfish poisoning (ASP). Nearshore shellfish toxins are monitored by state agencies, whereas most offshore stocks have had little or no routine monitoring. As a result, large areas of federal waters have been indefinitely closed or their shellfish beds underexploited because of the potential risk these toxins pose and the lack of scientific understanding and management tools. Patterns and dynamics of Alexandrium blooms and the resulting shellfish toxicity in nearshore waters were examined in a number of research projects, the largest being the Ecology and Oceanography of Harmful Algal Blooms (ECOHAB)-Gulf of Maine (GOM), a five-year regional program emphasizing field surveys, laboratory studies and numerical modeling. At the completion of the ECOHAB-GOM program (documented in Anderson et al., 2005), great progress was made in understanding A. fundyense blooms and resulting shellfish toxicity in nearshore waters, but there were major unknowns that still required investigation. For example, little was known about A. fundyense bloom dynamics in the waters south and east of Cape Cod, Massachusetts, and in particular, about the link between blooms in surface waters and toxicity in deep offshore shellfish. Large areas of offshore shellfish beds were off limits to harvest, including a 40,000 km2 region closed during the 2005 bloom and a much larger zone (~80,000 km2) including portions of Georges Bank was closed in 1990 after high levels of PSP toxicity were detected. In recent years, pressures were mounting from industry to open those offshore areas and to develop management strategies so that surfclam (Spisula solidissima), ocean quahog (Arctica islandica), and roe-on sea scallop (Placopecten magellanicus) fisheries could be opened. In response to these unknowns and societal needs, a new multi-investigator program, GOMTOX (Gulf of Maine Toxicity), was formulated and ultimately funded through the NOAA ECOHAB program. GOMTOX was a regional observation and modeling program that investigated the patterns and mechanisms underlying A. fundyense and Pseudo-nitzschia blooms and the resulting toxicity in shellfish in the southern GOM and its adjacent New England shelf waters, with special emphasis on the delivery pathways, mechanisms, and dynamics of offshore shellfish toxicity. The GOMTOX team of investigators included 16 principal investigators from eight institutions and, continuing in the ECOHAB-GOM tradition, strong participation from federal and state resource managers as well as representatives of the shellfish industry. This team worked together for over five years, running numerous large-scale survey cruises of Alexandrium cells and cysts, and also supporting industry cruises to collect shellfish from offshore sites including Georges Bank. Other efforts included participation in National Marine Fisheries Service surveys for shellfish (sea scallops, surfclams, and ocean quahogs), numerical modeling studies, deployment of sediment traps, and laboratory and ship-based experiments to investigate grazing and other processes that might regulate blooms and deliver toxins to shellfish in deeper waters. A smaller-scale but concurrent effort collected samples to characterize Pseudo-nitzschia species and their potential toxicity in the region.We gratefully acknowledge the support of NOAA through the ECOHAB program. Partial support for some of the studies contained herein was provided by NSF and NIEHS through the Woods Hole Center for Oceans and Human Health. Funding for J.L. Martin’s contributions from the Bay of Fundy was provided by Fisheries and Oceans Canada and NERACOOS, which is a part of the U.S. Integrated Ocean Observing System, funded in part by National Oceanic and Atmospheric Administration (NOAA)

Off-label Utilization of Antihypertensive Medications in Children

Objective— To examine off-label utilization and costs of antihypertensive drugs in children using a national sample of prescription claims. Design— Cross-sectional study. Setting— 2002 Medstat MarketScan Database, a national sample of outpatient prescription claims of children ≥18 years old enrolled in private, employer-sponsored health plans. Main Outcome Measures— Off-label use of antihypertensive drugs by patient age and costs of antihypertensives calculated as mean cost per child per 30-day fill. Results— One-half of the index antihypertensive prescription claims were off-label, based on minimum age criteria. Boys were more likely (56%) than girls (46%) to be prescribed off-label antihypertensives (p<0.001). Children aged ≥12 years were more likely to be prescribed off-label antihypertensives (53%) compared with children aged ≥5 (46%) and 6–11 years (42%, p<0.001). Off-label use varied significantly by class of antihypertensive drugs (p<0.001). Overall, off-label antihypertensives were significantly more expensive than on-label antihypertensives. Conclusions— Despite availability of often less expensive on-label alternatives for the same class of antihypertensive drugs, off-label antihypertensive drugs were prescribed frequently in children. These findings underscore the potential clinical and economic implications of common off-label prescribing, for children, their parents, physicians and payers. Originally published Ambulatory Pediatrics, Vol. 7, No. 4, July 200

PSP toxin levels and plankton community composition and abundance in size-fractionated vertical profiles during spring/summer blooms of the toxic dinoflagellate Alexandrium fundyense in the Gulf of Maine and on Georges Bank, 2007, 2008, and 2010 : 1. Toxin levels

This paper is not subject to U.S. copyright. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 103 (2014): 329–349, doi:10.1016/j.dsr2.2013.04.013.As part of the NOAA ECOHAB funded Gulf of Maine Toxicity (GOMTOX)1 project, we determined Alexandrium fundyense abundance, paralytic shellfish poisoning (PSP) toxin composition, and concentration in quantitatively-sampled size-fractionated (20–64, 64–100, 100–200, 200–500, and >500 μm) particulate water samples, and the community composition of potential grazers of A. fundyense in these size fractions, at multiple depths (typically 1, 10, 20 m, and near-bottom) during 10 large-scale sampling cruises during the A. fundyense bloom season (May–August) in the coastal Gulf of Maine and on Georges Bank in 2007, 2008, and 2010. Our findings were as follows: (1) when all sampling stations and all depths were summed by year, the majority (94%±4%) of total PSP toxicity was contained in the 20–64 μm size fraction; (2) when further analyzed by depth, the 20–64 μm size fraction was the primary source of toxin for 97% of the stations and depths samples over three years; (3) overall PSP toxin profiles were fairly consistent during the three seasons of sampling with gonyautoxins (1, 2, 3, and 4) dominating (90.7%±5.5%), followed by the carbamate toxins saxitoxin (STX) and neosaxitoxin (NEO) (7.7%±4.5%), followed by n-sulfocarbamoyl toxins (C1 and 2, GTX5) (1.3%±0.6%), followed by all decarbamoyl toxins (dcSTX, dcNEO, dcGTX2&3) (<1%), although differences were noted between PSP toxin compositions for nearshore coastal Gulf of Maine sampling stations compared to offshore Georges Bank sampling stations for 2 out of 3 years; (4) surface cell counts of A. fundyense were a fairly reliable predictor of the presence of toxins throughout the water column; and (5) nearshore surface cell counts of A. fundyense in the coastal Gulf of Maine were not a reliable predictor of A. fundyense populations offshore on Georges Bank for 2 out of the 3 years sampled.Vangie Shue was supported through the FDA and also through the Thomas Jefferson High School for Science and Technology Mentorship Program. Research support was provided by National Oceanic and Atmospheric Administration Grant NA06NOS4780245 for the Gulf of Maine Toxicity (GOMTOX) program. BAK, DJM, and DMA were partially supported by the Woods Hole Center for Oceans and Human Health through National Science Foundation Grants OCE-0430724 and OCE-0911031 and National Institute of Environmental Health Sciences Grant 1P50-ES01274201

Structural probing of the HIV-1 polypurine tract RNA:DNA hybrid using classic nucleic acid ligands

The interactions of archetypical nucleic acid ligands with the HIV-1 polypurine tract (PPT) RNA:DNA hybrid, as well as analogous DNA:DNA, RNA:RNA and swapped hybrid substrates, were used to probe structural features of the PPT that contribute to its specific recognition and processing by reverse transcriptase (RT). Results from intercalative and groove-binding ligands indicate that the wild-type PPT hybrid does not contain any strikingly unique groove geometries and/or stacking arrangements that might contribute to the specificity of its interaction with RT. In contrast, neomycin bound preferentially and selectively to the PPT near the 5′(rA)4:(dT)4 tract and the 3′ PPT-U3 junction. Nuclear magnetic resonance data from a complex between HIV-1 RT and the PPT indicate RT contacts within the same regions highlighted on the PPT by neomycin. These observations, together with the fact that the sites are correctly spaced to allow interaction with residues in the ribonuclease H (RNase H) active site and thumb subdomain of the p66 RT subunit, suggest that despite the long cleft employed by RT to make contact with nucleic acids substrates, these sites provide discrete binding units working in concert to determine not only specific PPT recognition, but also its orientation on the hybrid structure

Hybrid Surface Patterns Mimicking the Design of the Adhesive Toe Pad of Tree Frog

Biological materials achieve directional reinforcement with oriented assemblies of anisotropic building blocks. One such example is the nanocomposite structure of keratinized epithelium on the toe pad of tree frogs, in which hexagonal arrays of (soft) epithelial cells are crossed by densely packed and oriented (hard) keratin nanofibrils. Here, a method is established to fabricate arrays of tree-frog-inspired composite micropatterns composed of polydimethylsiloxane (PDMS) micropillars embedded with polystyrene (PS) nanopillars. Adhesive and frictional studies of these synthetic materials reveal a benefit of the hierarchical and anisotropic design for both adhesion and friction, in particular, at high matrix-fiber interfacial strengths. The presence of PS nanopillars alters the stress distribution at the contact interface of micropillars and therefore enhances the adhesion and friction of the composite micropattern. The results suggest a design principle for bioinspired structural adhesives, especially for wet environments