485 results on '"Johnson, Timothy P."'
Search Results
2. LISA telescope development status and flight design
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Coyle, Laura E., Matsuura, Shuji, Perrin, Marshall D., Keski-Kuha, Ritva A., Derosa, Ryan T., Boyce, Kevin R., Hadjimichael, Theodore J., Howard, Joseph M., Ivanov, Joseph M., Johnson, Timothy A., Lutter, Joshua G., Papa, Jonathan C., Sankar, Shannon R., and Weaver, Andrew
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- 2024
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3. Optical constants measurements of liquids for modeling aerosolized threats
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Guicheteau, Jason A., Howle, Christopher R., Myers, Tanya L., Lockwood, Schuyler P., Baker, Tracy, Primera-Pedrozo, Oliva M., Bernacki, Bruce E., Johnson, Timothy J., and Myers, Tanya L.
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- 2024
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4. Optimal spectral resolution for solids and liquids using FT and other infrared spectrometers: How much resolution do you really need?
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Guicheteau, Jason A., Howle, Christopher R., Myers, Tanya L., Forland, Brenda M., Hughey, Kendall D., Wilhelm, Michael J., Williams, Olivia N., Cappello, Benjamin F., Gaspar, Connor L., Myers, Tanya L., Baker, Tracy J., Sharpe, Steve, and Johnson, Timothy J.
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- 2024
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5. Deriving the infrared complex refractive indices of organic powders for optical modeling: comparison of methods
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Velez-Reyes, Miguel, Messinger, David W., Peterson, Kelly A., Bernacki, Bruce E., Saunders, Danielle L., Erickson, Jeremy D., Lockwood, Schuyler P., Johnson, Timothy J., and Myers, Tanya L.
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- 2024
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6. Dynamics of Electric Polarization and Relaxation of Ions at Humid Calcite Surfaces
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Legg, Benjamin A., Zhu, Yue, Nakouzi, Elias, Johnson, Timothy. C., and Rosso, Kevin M.
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Mobile ions at mineral surfaces can respond to an applied electric field, adopting a new distribution that effectively represents polarization of the electrical double layer. When the field is released, the ions relax to their equilibrium distribution. In both cases, the dynamics are characteristic of the interface. However, current models of electrokinetic phenomena are not sufficiently robust to accurately predict collective ion dynamics at structurally and chemically specific mineral–water interfaces. In this study, we use electrostatic force microscopy (EFM) to investigate the dynamics of ion relaxation at hydrated calcite (104) surfaces at controlled relative humidity (RH). Electrically biased probes are used to polarize the distributions of calcium and carbonate ions that are intrinsic to this interface across a range of RH values. Polarization kinetics are tracked by monitoring the tip–sample force gradient during charging, and EFM imaging is used to characterize the spatial relaxation dynamics after the applied field is released. Electrostatic finite element modeling of the sample/probe system across length-scales from nanometers to millimeters reproduces the observed stretched exponential charging response. Together, these results allow us to estimate the ion diffusivities at the interface across a wide range of RH values. These diffusivities increase by roughly 5 orders of magnitude as the RH is increased from 5 to 90%, highlighting the critical role of adsorbed water for surface ion solvation that enables ion mobility.
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- 2024
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7. Structure and Dynamics of Aqueous Electrolytes at Quartz (001) and (101) Surfaces
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Simonnin, Pauline G., Kerisit, Sebastien N., Nakouzi, Elias, Johnson, Timothy C., and Rosso, Kevin M.
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Understanding and describing reactivity at mineral–water interfaces, such as ion adsorption, the kinetics of dissolution, or surface charge development, depends on our ability to improve the accuracy of electrical double-layer (EDL) models. While molecular dynamics (MD) simulations are routinely used to investigate the structure and energetics of adsorbed ions comprising the EDL, less attention has been paid to their self-diffusion dynamics, which can uniquely inform coupling to interfacial reactions. Here, we use MD to investigate both the organization and diffusion dynamics of water and electrolyte ions (NaCl, KCl, CaCl2) on hydroxylated quartz (001) and (101) surfaces, which allow us to assess surface structural effects of corrugation and silanol density. Complementary atomic force microscopy measurements are also used to probe the interfacial solution structure. We found that the inner- versus outer-sphere complex formation depends on the cation size and charge but not necessarily on hydration energies. The participation of surface silanols in the hydration spheres of Na+and K+generally indicates their preference for inner-sphere complexation, but this is strongly dependent on the orientation of the surface considered through its influence on the organization and dynamics of adsorbed water layers. In particular, the surface orientation substantially affects the diffusive behavior of near-surface water. Na+is found to decrease the mobility of water in the first layer, consistent with the increasing frequency of hydrolysis implied by the faster quartz dissolution rates observed in experiments via the well-known salt effect. Our results are also in good agreement with the observed dissolution rate of quartz vs the surface adsorption strength measured by Dove and Nix. This study sets the stage for a forthcoming study examining how the dynamics at quartz/electrolyte interfaces are influenced by externally applied electric fields.
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- 2024
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8. Encounter rates and catch‐and‐releasemortality of steelhead in the Snake River basin
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Lubenau, William J., Johnson, Timothy R., Bowersox, Brett J., Copeland, Timothy, McCormick, Joshua L., and Quist, Michael C.
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The potential influence (i.e., impact rate) of catch‐and‐release fisheries on wild steelhead Oncorhynchus mykissis poorly understood and is a function of the abundance of wild fish, how many fish are encountered by anglers (i.e., encounter rate), and the mortality of fish that are caught and released. In Idaho, estimates of wild steelhead encounter rates have been derived using the number of wild and hatchery steelhead passing Lower Granite Dam, the number of hatchery steelhead harvested, and the number of hatchery steelhead caught and released. The method includes assumptions that hatchery and wild steelhead have equal encounter rates and catch‐and‐release mortality is 5% for wild steelhead. Here, we investigated wild and hatchery steelhead encounter rates by anglers, estimated catch‐and‐release mortality, and concatenated both aspects to examine how existing recreational steelhead fisheries influence wild steelhead mortality. We sampled, tagged, and released 1,251 spawn‐year 2020 (SY2020) and 1,956 spawn‐year 2021 (SY2021) adult steelhead at Lower Granite Dam with T‐bar anchor tags and passive integrated transponder (PIT) tags to estimate steelhead encounter rates and catch‐and‐release mortality. Differences in survival of caught steelhead and those not reported as caught were evaluated using detections at various locations (e.g., PIT arrays, weirs). Estimated encounter rates were 43.7% (95% credible interval; 28.2%, 100.0%) for wild fish and 46.7% (29.6%, 100.0%) for adipose‐clipped fish in SY2020. In SY2021, encounter rates were 47.2% (32.4%, 100.0%) for wild fish and 52.3% (37.1%, 100.0%) for adipose‐clipped fish. Based on detections of caught fish and those not reported as caught, catch‐and‐release mortality of wild steelhead was estimated to be 1.6% (0.0%, 5.2%). Wild steelhead impact rates were 0.7% (0.0%, 2.7%) in SY2020 and 0.7% (0.0%, 2.8%) in SY2021. Estimated rates of impact on wild steelhead were consistent and low across years despite major differences in the structure of the fisheries. Our results suggest assuming that encounter rates are equal between hatchery and wild steelhead, and that steelhead catch‐and‐release mortality is 5%, will likely lead to a conservative estimate of the wild steelhead impact occurring from catch‐and‐release fisheries. Impact statementWith wild steelhead numbers declining in many parts of North America, a dilemma between providing angling opportunity and wild steelhead conservation can develop. We show that encounter rate plays a larger role than mortality regarding catch‐and‐release angling on overall impact rates. Our method provides a direct, reliable estimate of encounter rates across multiple scales. With wild steelhead numbers declining in many parts of North America, a dilemma between providing angling opportunity and wild steelhead conservation can develop. We show that encounter rate plays a larger role than mortality regarding catch‐and‐release angling on overall impact rates. Our method provides a direct, reliable estimate of encounter rates across multiple scales.
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- 2024
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9. Particulate Filters for Combustion Engines to Mitigate Global Warming. Estimating the Effects of a Highly Efficient but Underutilized Tool
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Mayer, Andreas C.R., Mayer, Joerg, Wyser, Max, Legerer, Fritz, Czerwinski, Jan, Lutz, Thomas W., Johnson, Timothy V., and Jacobson, Mark Z.
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Particulate filters are state-of-the-art and are used in internal combustion engines worldwide to eliminate carcinogenic nanoparticles. Health studies estimate that this prevents about one million premature deaths annually. What is less known and often neglected is their equally powerful effect on mitigating global warming. This is because these ultrafine particles form stable aerosols in the atmosphere, absorb sunlight, and heat the atmosphere due to their jet-black color. In addition, once deposited on the ground, they reduce albedo especially when deposited on ice or snow. They also thin clouds and reduce their reflectivity. In this paper, we estimate for the first time the cumulative effect of more than 300 million particulate filters currently installed globally on vehicles, showing that, while they reduce ~ 0.5 Mt of soot per year, their effect on slowing global warming is equivalent to reducing 1 Bt of CO2per year or about one-third of the CO2emissions of all European Union Member States combined. Despite its strong potential, this highly efficient, proven, and low-cost technology is not yet regarded as a priority in curbing global warming, even though it is possibly the easiest and quickest to implement. If used in retrofitting more diesel and petrol engines worldwide, it could triple the aforementioned effect. While modern internal combustion engines are on track to be replaced with zero-emission vehicles, it is also crucial, and we strongly suggest that, in the interim, all remaining internal fossil fuel combusting engines be fitted with particulate filters. Evidence is presented in this paper that the potential benefits of such retrofit on climate and human health will be impactful and lasting.
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- 2024
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10. The Dynamics of a Shavian Universe: Founding and Evolution of the John Bennett Shaw Collection at the University of Minnesota.
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JOHNSON, TIMOTHY J.
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BOOK collecting ,SHERLOCK Holmes fiction ,BOOK collectors ,AUTHORS - Published
- 2023
11. Burkholderiaspp.-based biopesticide controls wireworms (Coleoptera: Elateridae) in potatoes
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Pagani, Mika K, Johnson, Timothy B, Doughty, Hélène B, McIntyre, Kelly C, and Kuhar, Thomas P
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Wireworms (Coleoptera: Elateridae) are economically significant pests of potatoes (Solanum tuberosum), damaging the marketable portion of the crop by feeding and tunneling into tubers. While conventional potato growers use the few registered synthetic insecticides to control wireworms, certified organic growers are left with less options due to the limited effectiveness of the available insecticides. Biologically derived pesticides provide an additional alternative for both systems. Certain gram-negative proteobacteria, such as Burkholderiaspp., possess insecticidal compounds. However, very little is known about their efficacy on wireworms. From 2018 to 2021, we conducted experiments in Virginia to assess the efficacy of a Burkholderiaspp.-based commercial pesticide, Majestene, as a wireworm control in potatoes. In a lab experiment, soil drench application of this insecticide at a rate of 66 g a.i. per 1 liter resulted in 30% wireworm mortality and significantly reduced wireworm feeding damage on potato tubers. In the field, in-furrow applications of Burkholderiaspp. at a rate of 17.66 kg a.i. per ha significantly reduced wireworm damage to tubers in 2 of 7 field experiments conducted. By comparison, the commercial standard insecticide, bifenthrin, significantly reduced tuber damage in 3 of the 7 field experiments. Our study demonstrates the prospect for proteobacteria-derived insecticides for control of wireworms and potentially other soil-dwelling insects. In conclusion, findings present growers with another option to combat wireworm pressure, especially in organic systems.
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- 2023
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12. Quantifying the Impact of Electric Fields on the Local Structure and Migration of Potassium Ions at the Orthoclase (001) Surface
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Sassi, Michel, Kerisit, Sebastien N., Simonnin, Pauline G., Legg, Benjamin A., Nakouzi, Elias, Zhu, Yue, Johnson, Timothy C., and Rosso, Kevin M.
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Developing an understanding of the response of mineral/water interfaces to applied electric fields is central to detecting and interpreting signatures of interfacial processes in the subsurface. Here, we focus density functional theory calculations on understanding K+cation binding and migration across the (001) surface of orthoclase feldspar under various applied electric fields with and without surface hydration. The calculations reveal how water ligands labilize surface K+cations for migration while also increasing their sensitivity to electric field effects on the binding energy at different surface sites. The calculations also show how the direction and strength of the electric field systematically affect surface cation mobility, sorption, and hydration behavior. Specifically, electric fields directed toward the surface reduce the energy gap between the different surface potassium sites, favor hydration, and shorten K+residence time at their crystallographic site. The findings help fill a major knowledge gap in the impact of electric fields on mineral/water interface structure and dynamics more generally, featuring, in this case, a commonly found type of feldspar involved in a multitude of atmospheric and geochemical processes.
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- 2023
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13. A Cost-Effective Microfluidic Device to Teach the Principles of Electrophoresis and Electroosmosis
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Shaffer, Tyler A., Herrada, Carlos U., Walker, Avery M., Casto-Boggess, Laura D., Holland, Lisa A., Johnson, Timothy R., Jones, Megan E., and Elshamy, Yousef S.
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Electrophoresis is integral to analytical and biochemistry experiences in undergraduate education; however, fundamental principles of the method are often taught in upper-level laboratories through hands-on experiences. A laboratory activity is reported that teaches the concepts of electrophoretic mobility and electroosmotic flow. A single reuseable instrument, called a mini-E, costs 37 USD and consists of a DC power supply, a voltmeter, platinum electrodes, and a chip cast in polydimethylsiloxane. This activity uses common reagents costing only 0.02 USD per student. Experiments are devised that allow students to investigate the properties of electrophoretic flow and electroosmotic flow by separating the two commonly used food dyeing agents Brilliant Blue FCF and Allura Red AC in vinegar and in a solution of ammonium hydroxide. A dark-purple mixture of these dyes is separated into red and blue bands that are easily visualized. The migration order of the dyes differs when the separation is performed under conditions of reversed polarity and suppressed electroosmotic flow (vinegar) compared to conditions of normal polarity and active electroosmotic flow (ammonium hydroxide). When delivered to chemistry majors, students had a significant gain in their ability to apply the concepts of electroosmosis and electrophoresis to predict analyte migration. Although this activity targets upper-level chemistry content, it can also be adapted for other laboratory experiences.
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- 2023
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14. Preparation and characterization methods of thin layer samples for standoff detection
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Guicheteau, Jason A., Howle, Christopher R., Primera-Pedrozo, Oliva M., Erickson, Jeremy D., Lonergan, Charmayne E., Burton, Sarah D., Bernacki, Bruce E., Myers, Tanya L., and Johnson, Timothy J.
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- 2023
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15. Comparison of Tumescent Anesthesia Versus Pectoral Nerve Block in Bilateral Reduction Mammaplasty
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McLaughlin, Caroline M., Hughes, Alexa J., Lee, Charles C., Perez Holguin, Rolfy A., Warfield, Dennis J., Henry, Cathy R., Johnson, Timothy S., and Potochny, John D.
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- 2023
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16. Neighborhood socioeconomic change and diabetes risk: findings from the Chicago Childhood Diabetes Registry
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Grigsby-Toussaint, Diana S., Lipton, Rebecca, Chavez, Noel, Handler, Arden, Johnson, Timothy P., and Kubo, Jessica
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Diabetes -- Research -- Risk factors ,Children -- Health aspects ,Health ,University of Illinois at Chicago - Abstract
OBJECTIVE--To examine whether patterns in socioeconomic characteristics in Chicago over a 30-year period are associated with neighborhood distribution of youth diabetes risk. RESEARCH DESIGN AND METHODS--Incident cases of diabetes in [...]
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- 2010
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17. 296 Effects of dietary antimicrobials on the ruminant gastrointestinal tract microbiome
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Vincent, Tyler J, Nolasco, Lester R, Suriyapha, Chaichana, Johnson, Timothy A, and Schoonmaker, Jon P
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Monensin, tylosin, and chlortetracycline (CTC) are antimicrobials frequently employed in high grain feedlot cattle diets to inhibit liver abscesses and enhance growth. However, increased public concerns regarding antibiotic resistance have created a pressing need to develop alternative strategies. A more mechanistic understanding of how antimicrobial drugs effect the microbiome in the ruminant gastrointestinal tract (GIT) may help develop effective alternatives. Therefore, the objective of this study was to determine changes in the GIT microbiome of grain-fed feedlot steers after antimicrobial drug administration. Thirty individually housed Angus x Simmental steers [body weight (BW) = 355 ± 16.8 kg] previously fed a 56% forage diet were immediately transitioned to a 93% concentrate diet and assigned to one of three treatments (10 steers/treatment): 1) control, without antibiotics, 2) 75 mg of tylosin and 200 mg of monensin per animal per day (TYLMON), and 3) 70 mg of CTC per animal per day. Fecal samples were collected on d 0, 7, 14, 28, 56, 112, and at slaughter and digesta were obtained from the rumen, jejunum, and cecum at slaughter. DNA was extracted from samples, amplified via 16S PCR, and sequenced. Jejunal samples had the least alpha diversity compared with ruminal, cecal, or fecal samples (P< 0.001). There were no differences in measures of alpha diversity in the ruminal, jejunal, or cecal digesta at slaughter (P≥ 0.10). However, overall measures of alpha diversity (Shannon entropy, observed features) in feces were greater in CTC-fed steers (P≤ 0.009) as well as in TYLMON-fed steers (P≤ 0.04) compared with control steers. Measures of alpha diversity for all treatments decreased in feces from d 0 to 7, then increased from d 7 to slaughter (time effect, (P≤ 0.001). There were no differences in fecal alpha diversity between treatment groups on d 0 (P≥ 0.50), but by d 28 both TYLMON and CTC treated steers had greater fecal alpha diversity compared with the control steers (P≤ 0.05). With regard to differential abundance, Phascolarctobacteriumand PrevotellaceaeUCG-003 were more abundant in feces of control steers relative to antimicrobial treated steers (P< 0.05). Bifidobacterium, Dorea, CAG-56, and ErysipelotrichaceaeUCG-003, were the 4 genera found to be in the greatest abundance in the feces of TYLMON-fed relative to control steers (P< 0.05). Akkermansia, Succinivibrio, and Turicbacterwere the 3 genera found to be in the greatest abundance in the feces of CTC-fed compared with control steers (P< 0.05). Taken together, these data suggest that differences in the microbiome associated with dietary antimicrobial treatment occur to a greater extent in the lower sections of the GIT, and that these changes in the microbiome occur after 28 d of feeding.
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- 2024
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18. 3 The impact of early-life cecal microbiota transplantation on injurious behaviors in egg-laying chickens
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Fu, Yuechi, Hu, Jiaying, Zhang, Huanmin, Erasmus, Marisa A, Cheng, Heng-wei, and Johnson, Timothy A
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Injurious behaviors in laying hens are a critical issue facing the poultry egg industry. Recent studies have shown that the gut microbiota influences host brain function and behavioral characteristics in humans and various animals. In laying hens, it has been reported that injurious behaviors (such as aggression, feather pecking and cannibalism) are associated with dysregulation of the microbiota-gut-brain axis. To further interrogate the role of the microbiota-gut-brain axis on bird behavior, we used two inbred layer chicken lines, 63 and 72 (line 72 displays more aggressive behavior), and transferred pooled cecal contents from either line to day of hatch chicks. Cecal microbiota transplantation (CMT) from each line was conducted once daily, by gavage, from d 1 to 10, then boosted once weekly from wk 3 to 5. We hypothesized that the cecal microbiota composition and animal behavior in recipient birds would be similar to that of their donor animals because of the microbiota-gut-brain axis. Microbial communities were compared using 16S rRNA gene amplicon sequencing, behavior was recorded in home cages as well as in paired aggression tests, and physiological measurements were taken from brain tissue and blood to measure levels of neurotransmitters and immune function. When examining the differences in the donor birds, hypothalamic serotonin and tryptophan concentrations were greater for line 63 compared with line 72 birds (P< 0.05). Plasma corticosterone, heterophil/lymphocyte ratios, and central norepinephrine concentrations were less for line 63 birds (P< 0.05). Cecal microbial diversity was not statistically different between the lines, but many bacterial taxa were differentially abundant between the two lines. After cecal transplantation, 63-CMT (recipient) birds displayed less aggressive behavior with a greater hypothalamic serotonergic activity at wk 5, similar to donor birds. Correspondingly, two amplicon sequence variants (ASVs) belonging to Lachnospiraceaeand one RuminococcaceaeUCG-005 ASV were positively correlated with the concentrations of brain tryptophan and serotonin, respectively. Along with greater aggression, 72-CMT birds seemed to have greater physical growth traits (increased body weight, ileal villus/crypt; P≤ 0.05), but decreased concentrations of brain norepinephrine and dopamine, and the greatest ileal serotonin turnover in the ileum at wk 5 (P< 0.05). ASVs belonging to Mollicutes RF39 and GCA-900066225 in 72-CMT birds were negatively correlated with the brain 5-hydroxyindoleacetic acid (5-HIAA) at wk 5, and one Bacteroides ASV was negatively correlated with plasma serotonin at wk 16. Meanwhile, 63-CMT birds potentially had better gut health and immune function (greater concentrations of ileal mucosal secretory IgA, plasma IL-10; P< 0.05). These results suggest linkages among serotonergic activity, stress response, innate immunity, and gut microbiota populations and that CMT could be a novel strategy for reducing aggressive behavior through regulating signaling along the microbiota-gut-brain axis.
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- 2024
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19. 185 Maternal live yeast supplementation protects newly weaned piglets against lipopolysaccharide challenge by regulating immune-associated milk proteins
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Fu, Yuechi, Casey, Theresa M, Johnson, Timothy A, Xie, Jun, Adeola, Olayiwola, and Ajuwon, Kolapo M
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Sow milk serves as a crucial source of nutritional, immunological, and growth-promoting components for the piglets. Our previous studies established that maternal live yeast (LY) supplementation altered the expression of antioxidant and immune-regulatory genes in the intestinal mucosa of suckling piglets. The current study aimed to investigate the effects of maternal LY supplementation during late gestation and lactation on milk proteomic profile in dams and health of offspring under lipopolysaccharide (LPS) challenge. On d 77 of gestation, 40 sows were allocated to 2 dietary treatments: without (CON) or with LY supplementation at 0.05% of diet during gestation and 0.1% during lactation. Milk samples were collected on d 0, 10, and 18 post-partum (n = 6), respectively. Within 24 h postweaning, piglets from the CON and LY groups were intraperitoneally injected with sterile saline or LPS [25 μg/kg body weight (BW)] and divided into four groups (n = 8): 1) saline + CON (CS), 2) saline + LY (YS), 3) LPS + CON (CLPS), and 4) LPS + LY (YLPS). Data were analyzed in a 2 × 2 factorial arrangement with main effects of maternal diet and immunological challenge. Rectal temperature was measured hourly for 4 h post-injection after which piglets were euthanized. Results showed that LPS increased concentrations of serum tumor necrosis factor (TNF) -α and interlekin (IL) -10 (P< 0.05) and tended to increase IL-8 in the ileal mucosa of piglets (P< 0.10). At 3 h post-injection, YLPS piglets tended to have a lower rectal temperature than CLPS piglets (P< 0.10). YLPS piglets also had decreased protein levels of TNF-α in the ileal mucosa (P< 0.05), with a tendency for greater protein abundance of E-cadherin but decreased mRNA abundance of catalase (P< 0.10) in the jejunal mucosa at 4 h post-injection (P< 0.05). In addition, YLPS piglets had less mRNA abundance of TLR2 and TLR4 in the liver than CLPS piglets (P< 0.05). With shotgun proteomics analysis, we found that milk of LY sows had more abundant proteins associated with immunity, including immunoglobulin and complement protein (Ig-like and C1q domain-containing proteins) on d 0 and d 10. Insulin-like growth factor binding protein (IGFBP) 5 was also more abundant in the d 0 milk of LY sows, whereas prostaglandin synthase was greater in d 10 and d 18 milk of CON sows. Additionally, pathway analysis showed that proteins identified in the milk of CON sows have roles in neutrophil degranulation and IL-12 signaling and production, whereas pathways associated with regulation of complement system, IGF and DHCR24 signaling, were enriched in the milk of LY sows. These results suggest that maternal LY supplementation could protect newly weaned piglets from bacteria endotoxin effect by suppressing inflammatory response, improving expression of tight junction proteins in offspring, and altering immune-associated proteins in sow milk.
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- 2024
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20. 72 Effect of In-feed fecal microbiota transplant on growth performance and gut microbiota dynamics of piglet subjected to post-weaning stress
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Oladele, Paul O, Richert, Brian T, and Johnson, Timothy A
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Weaning is one of the most stressful events for piglets, due to diet change from sow milk to grain-based feed. This diet change causes turnover of the gut microbial which can allow proliferation of pathogens leading to diarrhea. Antibiotics are administered to treat or prevent post-weaning diarrhea (PWD). Increased occurrence of antimicrobial resistance has increased incentives to develop viable antibiotic alternatives. PWD is most often caused by enterotoxigenic Escherichia coli. Similarly, in humans, severe diarrhea can be caused by Clostridium difficilecolonization. Use of fecal microbiota transplants (FMT) has been shown to resolve C. difficile-induced diarrhea in 80 to 90% of human cases which may suggest FMT as a potential therapeutic option for post weaning diarrhea. We previously have shown that in feed fecal microbiota transplant (FMT) improved body weight (BW) gain in newly weaned piglets but it is not clear if this benefit will be replicated in piglets subjected to weaning stress. We hypothesize that FMT (in-feed) will increase colonization efficiency, improve growth performance and reduce diarrhea incidence compared with control in piglets subjected to post weaning stress. The objective of this study was to determine the effect of In-feed FMT of diarrhea index, growth performance and gut microbiota dynamics. Piglets (n = 240) subjected to physiological and transport weaning stress were allotted to 5 treatments: In-feed FMT (FMT1), doubles dose of In-feed FMT1 (FMT2), Oral gavage (FMT3), Antibiotic (positive control), and no supplementation (negative control). The donor material was screened for enterotoxigenic E. coli(F18 and F4). FMT was carried out for 14 d. Diarrhea index was observed for the first 14 d and animal BW, and fecal microbiota was collected by rectal swab on d 0, 3, 5, 7, 14, 21, 28 and 32 for analysis of microbiota composition. DNA was extracted from fecal samples and 16S rRNA gene libraries (V4 region) were prepared for bacterial community analysis. Data were analyzed with one-way ANOVA in R. Only positive control had significantly decrease in diarrhea index and significant increase BW gain on d 14, 21, and 28 (P< 0.05) but there was no effect of FMT (P> 0.05). In conclusion, antibiotics but not FMT was efficient in alleviating the negative performance effect in piglets subjected to post-weaning stress.
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- 2024
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21. A Low-Cost and Simple Demonstration of Freezing Point Depression and Colligative Properties with Common Salts and Ice Cream
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Johnson, Timothy R., Shaffer, Tyler A., Holland, Lisa A., Veltri, Lindsay M., Lucas, John A., Elshamy, Yousef S., and Rutto, Patrick K.
- Abstract
A laboratory activity was developed to teach freezing point depression and colligative properties to introductory-level chemistry students. The laboratory uses food-grade reagents and is delivered in two units that can be taught in a single 2 hour session or two separate sessions. The total cost of the consumables is 1 USD. In the first part of this two-part activity, students perform measurements on the properties of five salt solutions to better know and understand freezing point depression. In the second part of the activity, students apply their knowledge and understanding of freezing point depression to make ice cream. The ice-cream-making experiment is delivered as a group activity to encourage reflection. Centering this experiment on ice cream allows students to connect properties described in chemistry to everyday life. The solutions used in the experiment are reusable and nonhazardous. The experiment can be implemented in a classroom, in a teaching laboratory, or at home.
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- 2022
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22. A Descriptive Analysis of Integrated Plastic Surgery Residency Program Directors in the United States
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Hughes, Alexa J., Samson, Thomas D., Henry, Cathy R., and Johnson, Timothy Shane
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- 2022
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23. Formal Reporting of Identity-Based Harassment at an Academic Medical Center: Incidence, Barriers, and Institutional Responses
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Vargas, Emily A., Cortina, Lilia M., Settles, Isis H., Brassel, Sheila T., Perumalswami, Chithra R., Johnson, Timothy R.B., and Jagsi, Reshma
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- 2022
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24. A hybrid FTIR/QCL sensing system for gas-phase kinetics using a long-path gas cell
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Harding, Kevin G., Zhang, Song, Hyun, Jae-Sang, Li, Beiwen, Dunlap, Megan K., Hughey, Kendall D., Tonkyn, Russell G., Harper, Warren W., Myers, Tanya L., and Johnson, Timothy J.
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- 2022
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25. A Data-Driven Approach to Predicting 5-Aminolevulinic Acid–Induced Fluorescence and World Health Organization Grade in Newly Diagnosed Diffuse Gliomas
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Müther, Michael, Jaber, Mohammed, Johnson, Timothy D., Orringer, Daniel A., and Stummer, Walter
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- 2022
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26. Evaluation of the effects of a smoking cessation intervention using the multilevel thresholds of change model
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Freels, Sally A., Warnecke, Richard B., Johnson, Timothy P., and Flay, Brian R.
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Smoking cessation programs -- Evaluation ,Women ,Smoking -- Care and treatment ,Law ,Social sciences - Abstract
This article examines a smoking cessation intervention which targeted females with a high school education or less. The intervention, consisting of a televised component and a written manual, was most effective within women who were precontemplative regarding quitting smoking, with the written manual being more effective than the televised component.
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- 2002
27. Method To Visualize the Intratumor Distribution and Impact of Gemcitabine in Pancreatic Ductal Adenocarcinoma by Multimodal Imaging
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Strittmatter, Nicole, Richards, Frances M., Race, Alan M., Ling, Stephanie, Sutton, Daniel, Nilsson, Anna, Wallez, Yann, Barnes, Jennifer, Maglennon, Gareth, Gopinathan, Aarthi, Brais, Rebecca, Wong, Edmond, Serra, Maria Paola, Atkinson, James, Smith, Aaron, Wilson, Joanne, Hamm, Gregory, Johnson, Timothy I., Dunlop, Charles R., Kaistha, Brajesh P., Bunch, Josephine, Sansom, Owen J., Takats, Zoltan, Andrén, Per E., Lau, Alan, Barry, Simon T., Goodwin, Richard J. A., and Jodrell, Duncan I.
- Abstract
Gemcitabine (dFdC) is a common treatment for pancreatic cancer; however, it is thought that treatment may fail because tumor stroma prevents drug distribution to tumor cells. Gemcitabine is a pro-drug with active metabolites generated intracellularly; therefore, visualizing the distribution of parent drug as well as its metabolites is important. A multimodal imaging approach was developed using spatially coregistered mass spectrometry imaging (MSI), imaging mass cytometry (IMC), multiplex immunofluorescence microscopy (mIF), and hematoxylin and eosin (H&E) staining to assess the local distribution and metabolism of gemcitabine in tumors from a genetically engineered mouse model of pancreatic cancer (KPC) allowing for comparisons between effects in the tumor tissue and its microenvironment. Mass spectrometry imaging (MSI) enabled the visualization of the distribution of gemcitabine (100 mg/kg), its phosphorylated metabolites dFdCMP, dFdCDP and dFdCTP, and the inactive metabolite dFdU. Distribution was compared to small-molecule ATR inhibitor AZD6738 (25 mg/kg), which was codosed. Gemcitabine metabolites showed heterogeneous distribution within the tumor, which was different from the parent compound. The highest abundance of dFdCMP, dFdCDP, and dFdCTP correlated with distribution of endogenous AMP, ADP, and ATP in viable tumor cell regions, showing that gemcitabine active metabolites are reaching the tumor cell compartment, while AZD6738 was located to nonviable tumor regions. The method revealed that the generation of active, phosphorylated dFdC metabolites as well as treatment-induced DNA damage primarily correlated with sites of high proliferation in KPC PDAC tumor tissue, rather than sites of high parent drug abundance.
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- 2022
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28. Learning to Speak Up: Acclimation Effects and Supreme Court Oral Argument
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Houston, Rachael, Li, Siyu, and Johnson, Timothy R.
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AbstractA long line of literature examines acclimation effects for newly confirmed U.S. Supreme Court justices. However, most of these analyses focus only on how new justices vote or write opinions. Here, we examine how they act during the one public aspect of the Court’s decision-making process—its oral arguments on the merits. In so doing, we seek to determine whether new justices speak, and interrupt their colleagues, less often than do their more senior colleagues. Using data on justices’ speaking turns and interruptions during all orally argued cases from the 1955 to 2018 terms, we find an acclimation effect exists whereby new justices are significantly less inclined to speak and interrupt their more senior colleagues. Our models also suggest gender and judicial ideology influence the extent to which new justices exhibit such effects during oral argument proceedings.
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- 2021
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29. Movement Ecology of a Potamodromous Top Predator in a Large Lake: Synchrony and Coexistence of Distinct Migratory Patterns
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Ivanova, Silviya V., Johnson, Timothy B., and Fisk, Aaron T.
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Migrations are a critical component of the life histories of many highly mobile animals. Potamodromous migrations that occur within large lakes are poorly understood for most species. This lack of understanding hampers restoration efforts and adaptive management because the movement of species and underlying patterns and mechanisms help scientists identify important habitats and quantify species’ roles in the ecosystem. This study quantified the spatiotemporal movements and migratory patterns of Lake Trout Salvelinus namaycush, an iteroparous, potamodromous predator, in eastern Lake Ontario. The lake is highly managed and supports a diverse fish community of native and nonnative species. The movements of 41 Lake Trout were quantified over 2.4 years (December 2016 to April 2019) across a large array of 196 acoustic receivers in eastern Lake Ontario. An analysis of individual movements revealed a potential annual convergence occurring in the fall at a location other than the spawning grounds, followed by a synchronized migration to spawning areas. Consistent with divergent migrations, return migration was asynchronous among individuals but consistent in timing interannually, stretching over a longer period than did prespawning movements and across multiple routes. The data suggest the existence of three groups (i.e., contingents) of Lake Trout with distinct migratory behaviors. This study provides important information on the migratory patterns and routes and a potential staging area for a potamodromous top predator population in a large lake. This information can help managers understand the potential success and implications of employing different rehabilitation strategies, such as diversifying populations of Lake Trout through selective strain stocking in large deep lakes to aid reestablishment across habitats. In addition, our results have the potential to improve community dynamics modeling, understanding of nutrient cycling, and overall ecosystem function of large lakes.
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- 2021
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30. The effect of interviewer characteristics on gatekeeper resistance in surveys of elite populations.
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Parsons, Jennifer A., Johnson, Timothy P., Warnecke, Richard B., and Kaluzny, Arnold
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Interviewing in sociology -- Research ,Professional workers -- Interviews ,Surveys -- Research - Published
- 1993
31. The scope of hospital medicine practice at night: a national survey of night shift hospitalists
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Atlas, Kathleen R., Forbes, Meggan, Riches, Jamie, Maina, Elizabeth, Lim, Richard, Johnson, Timothy, Niessen, Timothy, and Desai, Neil
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ABSTRACTIntroduction: Although in-person hospitalist presence, increasingly staffed by dedicated nocturnists, has become the norm overnight in the hospital, the scope of nocturnist practice and typical workload has not been defined. This study examines the clinical responsibilities and patient safety perceptions of hospitalists who work night shifts in the United States.Methods: In the fall of 2019, a cross-sectional, web-based survey was administered to physician and nurse practitioner/physician assistant (NP/PA) hospitalists who work night shifts. The questionnaire assessed night staffing structure, typical responsibilities, patient volume, perceptions of safety overnight, as well as demographic information. The survey was posted on the Society of Hospital Medicine (SHM) Hospital Medicine Exchange (HMX) Online Discussion Forum. Additionally, the survey was distributed by ‘snowball method’ by respondents to other night hospitalists. Responses were collected anonymously.Results: Of the 167 respondents, 157 reported working night shifts. There was at least one respondent from 32 different states. In addition to performing admissions to medicine services and covering inpatients, night hospitalists cover ICU patients, participate in RRT/Code teams and procedure teams, perform consults, participate in medical education, and take outpatient calls. Across institutions, there was a large distribution in numbers of patients covered in a night shift; however, patient volume fell into typical ranges: 5–10 admissions for physicians, 0–6 admissions for NP/PAs, and 25–75 patient cross-coverage census. When physicians perform more than five admissions per night, hospitalists were less likely to agree that they could provide safe care (88% vs. 63%, p= 0.0006).Conclusions: This is the first national study to examine the clinical responsibilities of hospitalists working overnight. Overnight responsibilities are heterogeneous across institutions. As hospitals are increasingly employing nocturnists, more research is needed to guide night staffing and optimize patient safety.
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- 2021
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32. Persistence of vaccine origin SalmonellaTyphimurium through the poultry production continuum, and development of a rapid typing scheme for their differentiation from wild type field isolates
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Johnson, Timothy J., Flores-Figueroa, Cristian, Munoz-Aguayo, Jeannette, Pinho, Glenda, and Miller, Elizabeth
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Salmonellaenterica serovar Typhimurium is one of the top Salmonellaserovars annually linked to poultry production and corresponding human illnesses. Because of this, vaccination of commercial poultry against SalmonellaTyphimurium has been a focal point in recent years. There are several commercially available SalmonellaTyphimurium vaccines available for use in poultry production. Among these are modified live vaccines, including Poulvac ST (Zoetis), Megan Egg (AviPro), and Megan Vac 1 (AviPro). In this study, analyses of 27 field isolates of SalmonellaTyphimurium from poultry sources indicated evidence for the persistence of some vaccine-origin strains through the commercial production cycle. Further analyses of 26,812 database isolates indicated vaccine-origin isolates are persisting frequently through processing, are present on retail meat products, and are even occasionally found in human patients. A novel polymerase chain reaction (PCR) was created and validated which enables simultaneous identification of Salmonellaenterica sp., the SalmonellaTyphimurium serovar, and differentiation of wild type SalmonellaTyphimurium from live attenuated vaccines involving mutations in the cya/crpor aroAgenes. The PCR was developed considering whole genome differences between the vaccines and wild type field isolates and was validated using different field isolates and recovered vaccine strains. This method enables poultry producers to rapidly determine if recovered field isolates have a vaccine origin.
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- 2024
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33. Confirmation of PNNL Quantitative Infrared Cross-Sections for Isobutane
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Johnson, Timothy J., Hughey, Kendall D., Blake, Thomas A., Sharpe, Steven W., Myers, Tanya. L., and Sams, Robert L.
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The Pacific Northwest National Laboratory (PNNL) gas-phase database is a compilation of quantitative experimental (5, 25, and 50 °C) infrared spectra of ca.500 molecules, designed for in situ, standoff or remote sensing of gases and vapors at or near atmospheric pressure. The data are characterized by calibration on both the wavenumber and intensity axes. Recent papers have called into question the PNNL intensity values for isobutane, [2-methylpropane, HC(CH3)3], suggesting discrepancies of 30–40%. In this study, we remeasure and re-examine the intensity values of isobutane using both similar and alternate methods to those used to generate the original PNNL database spectra. Indirect confirmation from literature data of homologous molecules and direct confirmation from new results confirm that for many band integrals across the isobutane spectrum, the original PNNL data are indeed accurate to within the reported 3% experimental uncertainty.
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- 2021
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34. 277 Effect of Mode of Delivery of Fecal Microbiota Transplants on Growth Performance and Gut Microbiome in Weaning Piglets
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Oladele, Paul, Dong, Wenxuan, Richert, Brian T, and Johnson, Timothy A
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Weaning is one of the most stressful events for piglets, due to diet change from sow milk to grain-based feed. This diet change causes turnover of the gut microbial which can allow proliferation of pathogens leading to diarrhea. Antibiotics are administered to treat or prevent post-weaning diarrhea (PWD). Increased occurrence of antimicrobial resistance has increased incentives to develop viable antibiotic alternatives. Previous studies have shown that fecal microbiota transplant (FMT) reduced diarrhea incidence and improved body weight gain in piglets. However, one barrier to FMT adoption in swine production is that FMT are generally given via oral gavage, which is difficult and labor intensive for large swine operations. For FMT to be a viable option in swine management, a simple method is needed to administer the transplant. The objective of this study was to determine the effect of three methods of FMT administration (oral, rectal and lyophilized in-feed) on growth performance, diarrhea incidence and gut microbiome. We hypothesize that FMT (in-feed and rectal) will increase colonization efficiency, improve growth performance and reduce diarrhea incidence compared with control. Weaned male piglets (n = 40) were allotted to 4 treatments at 10 piglets per treatment (no FMT - Control, Oral gavage - FMT1, rectal gavage - FMT2 and lyophilized in-feed – FMT3). Feces from 12-week-old pigs, screened for pathogens, was donor material. The study lasted nine days and FMT was for five days. Diarrhea incidences and body weight were observed for the first week. Fecal samples were collected on days 0, 2, 5 and 7. Five piglets per group were sacrificed on day 4 and the remaining on day 8. Cecal and colon contents were collected from the sacrificed piglets. DNA was extracted from fecal and digesta samples and 16S rRNA gene libraries (V4 region) were prepared for bacterial community analysis. Data were analyzed with one-way ANOVA in R. All FMT groups had significantly greater body weight on day 3 (P< 0.05) and average daily gain between day 0 – 3 (P< 0.05) compared with control but there was no difference between FMT groups. There was no effect of FMT on average daily feed intake and diarrhea incidence. Only FMT3 had greater alpha diversity (Observed features and Faith’s phylogenetic diversity) on day 5 (P< 0.05) compared with control, but there was no difference in beta diversity between FMT groups. There was decreased abundance of 27 ASVs (amplicon sequence variant) and increased abundance of 30 ASVs in increased in FMT3 compared with control on day 5. In conclusion, the three FMT groups has similar colonization pattern but there was no difference in diarrhea incidence. FMT3 (lyophilized in-feed) altered overall community structure of piglets and modulated individual taxa.
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- 2023
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35. 54 Impact of Ileal Indigestible Protein on Nitrogen Excretion and Fecal Microbiota may be Greater Compared with Total Protein Concentration of Diets in Growing Pigs
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Sung, Jung Yeol, Johnson, Timothy A, Ragland, Darryl, and Adeola, Olayiwola
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The effect of changes in dietary ileal indigestible protein concentration may be more influential in the amount of nitrogen flowing to the large intestine compared with changes in total dietary protein concentration. For this reason, we hypothesized that an increase in dietary ileal indigestible protein concentration induces an increase in hindgut nitrogen utilization and nitrogen excretion and a shift in fecal microbiota in growing pigs, when compared with pigs given a high total protein diet. Three diets were prepared: 1) standard protein diet based on corn and soybean meal, 2) high-indigestible protein diet in which autoclaved soybean meal replaced normal soybean meal in the first diet, and 3) high protein diet where the inclusion rate of soybean meal was greater than that of the other diets. T-cannulated barrows (n = 18; initial BW = 63.4 ± 8.0 kg) were allotted to the 3 diets in a randomized complete block design with BW as a blocking factor. Pigs were individually housed in pens and the experiment lasted for 23 days. On d 7 and 21, fecal samples were collected by rectal massage for microbiota analysis. Grab samples of feces were collected on d 20 and 21, and ileal digesta were collected on d 22 and 23 for the determination of energy and nitrogen utilization. Energy and nitrogen utilization data were analyzed using the MIXED procedure of SAS using a pig as the experimental unit and a model that included diet as a fixed variable and block as a random variable. For microbiome analysis, R was used. Alpha and beta diversity metrics were analyzed and the difference in abundance of the genus was determined using the DESeq2 function. The high-indigestible protein diet achieved decreased apparent ileal digestibility of nitrogen and resulted in greater ileal indigestible nitrogen concentration (P< 0.05). Apparent total tract digestibility of nitrogen was less (P< 0.05), and correspondingly fecal nitrogen concentration and daily fecal nitrogen output were greater (P< 0.05) in the high-indigestible protein diet. Apparent post-ileal digestibility and hindgut disappearance of nitrogen and gross energy were the greatest (P< 0.05) in the high protein diet. Beta diversity metrics of feces in the high-indigestible protein diet on d 21 were different (q < 0.05) from those in the other two diets, which indicates a shift in fecal microbiota. According to the DESeq2 results, the direction of the microbiota shift induced by the high-indigestible protein diet may have reduced hindgut fiber utilization. In conclusion, an increase in dietary ileal indigestible protein increased nitrogen excretion and shifted fecal microbial communities but did not increase hindgut nitrogen utilization.
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- 2023
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36. Combining spectroscopic ellipsometry with transmission spectroscopy to derive accurate optical constants for organic materials
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Guicheteau, Jason A., Howle, Chris R., Yokosuk, Michael O., Tiwald, Thomas E., Saunders, Danielle L., Blake, Thomas A., Johnson, Timothy J., and Myers, Tanya L.
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- 2021
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37. Experimental and modeling investigation of binary liquid mixtures
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Guicheteau, Jason A., Howle, Chris R., Bradley, Ashley M., Bernacki, Bruce E., Smith, Steven C., Primera-Pedrozo, Oliva M., Tonkyn, Russell G., Johnson, Timothy J., and Myers, Tanya L.
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- 2021
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38. Challenges to detection: humidity as a spur to chemical agent change
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Guicheteau, Jason A., Howle, Chris R., Saunders, Danielle L., Mo, Kai-For, Tonkyn, Russell G., Banach, Catherine A., Fraga, Carlos G., Szecsody, James E., Cappello, Benjamin F., Johnson, Timothy J., and Myers, Tanya L.
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- 2021
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39. Hydrolysis of methylphosphonic anhydride solid to methylphosphonic acid probed by Raman and infrared reflectance spectroscopies
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Myers, Tanya L., Saunders, Danielle L., Szecsody, James E., Tonkyn, Russell G., Mo, Kai-For, Cappello, Benjamin F., Banach, Catherine A., Fraga, Carlos G., and Johnson, Timothy J.
- Abstract
Much is still unknown about the mechanisms and rates of environmental degradation of organophosphorous pesticides and agents. In this study we focus on the degradation of one organophosphorous compound, namely solid methylphosphonic anhydride [CH3P(O)OHOP(O)OHCH3, MPAN] and its rate of conversion to methylphosphonic acid (MPA) viaheterogeneous hydrolysis. Pure MPAN was synthesized and loaded in open sample cups placed inside exposure chambers containing saturated salt solutions to control the relative humidity (RH). The reaction was monitored in the sample cup at various times using both infrared hemispherical reflectance (HRF) spectroscopy and Raman spectroscopy. Calibrated HRF and Raman spectra of both pure reagents as well as gravimetrically prepared mixtures were used to quantify the concentrations of MPAN and MPA throughout the reaction. Results show both HRF and Raman spectroscopies are convenient non-invasive methods for detection of solid chemicals as long as a large area is sampled to average out any spatial inhomogeneities that occur on the sample surface and minimal phase changes occur during the course of the reaction. The samples for the 54 and 75% RH studies showed significant deliquescence, and the liquid water had to be removed prior to measurement; this effect led to differences in the sample form, such that the calibration spectra were no longer valid for quantitative analysis using HRF spectroscopy. Raman spectroscopy, on the other hand, proved to be less sensitive to these effects and provided better estimation of the MPAN and MPA concentrations. The MPAN degradation rate displayed a very strong dependence on relative humidity: at room temperature the reaction showed 50% conversion of the MPAN in 761 ± 54 h at 33% RH, 33 ± 4 h at 43% RH, 17 ± 2 h at 54% RH and just 7 ± 1 h at 75% RH.
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- 2021
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40. Absolute Band Intensity of the Iodine Monochloride Fundamental Mode for Infrared Sensing and Quantitative Analysis
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Hughey, Kendall D., Bradley, Ashley M., Tonkyn, Russell G., Felmy, Heather M., Blake, Thomas A., Bryan, Samuel A., Johnson, Timothy J., and Lines, Amanda M.
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Iodine monochloride (ICl) is a potential off-gas product of molten salt reactors; monitoring this heteronuclear diatomic molecule is of great interest for both environmental and safety purposes. In this paper, we investigate the possibility of infrared monitoring of ICl by measuring the far-infrared absorption cross section of its fundamental band near 381 cm–1. We have performed quantitative studies of the neat gas in a 20 cm cell at 25, 35, 50, and 70 °C at multiple pressures up to ∼9 Torr and investigated the temperature and pressure dependencies of the band’s infrared cross section. Quantitative measurements were problematic due to sample adhesion to the cell walls and windows as well as reactions/possible hydrolysis of ICl to form HCl gas. Effects were mitigated by measuring only the neat gas, using short measurement times, and subtracting out the partial pressure of the HCl(g). The integrated band strength is shown to be temperature independent and was found to be equal to 9.1 × 10–19(cm2/molecule) cm–1. As expected, the temperature dependence of the band profile showed only a small effect over this limited temperature range. We have also investigated using the absorption data along with inverse least squares multivariate methods for the quantitative monitoring of ICl effluent concentrations under different scenarios using infrared (standoff) sensing and compare these results with traditional Beer’s law (univariate) techniques.
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- 2020
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41. Correlation between Venous Thromboembolism Risk and Venous Congestion in Microvascular Reconstruction of the Lower Extremity
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Parham, Christopher S., Shen, Chan, Pennock, Michael M., Henderson, Stacy R., Kulaylat, Audrey S., and Johnson, Timothy S.
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- 2020
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42. Multicenter evaluation of parametric response mapping as an indicator of bronchiolitis obliterans syndrome after hematopoietic stem cell transplantation
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Cheng, Guang‐Shing, Selwa, Katherine E., Hatt, Charles, Ram, Sundaresh, Fortuna, Aleksa B., Guerriero, Margaret, Himelhoch, Ben, McAree, Daniel, Hoffman, Timothy C., Brisson, Joseph, Nazareno, Ryan, Bloye, Kiernan, Johnson, Timothy D., Remberger, Mats, Mattsson, Jonas, Vummidi, Dharshan, Kazerooni, Ella E., Lama, Vibha N., Galban, Stefanie, Boeckh, Michael, Yanik, Gregory A., and Galban, Craig J.
- Abstract
Parametric response mapping (PRM) is a novel computed tomography (CT) technology that has shown potential for assessment of bronchiolitis obliterans syndrome (BOS) after hematopoietic stem cell transplantation (HCT). The primary aim of this study was to evaluate whether variations in image acquisition under real‐world conditions affect the PRM measurements of clinically diagnosed BOS. CT scans were obtained retrospectively from 72 HCT recipients with BOS and graft‐versus‐host disease from Fred Hutchinson Cancer Research Center, Karolinska Institute, and the University of Michigan. Whole lung volumetric scans were performed at inspiration and expiration using site‐specific acquisition and reconstruction protocols. PRM and pulmonary function measurements were assessed. Patients with moderately severe BOS at diagnosis (median forced expiratory volume at 1 second [FEV1] 53.5% predicted) had similar characteristics between sites. Variations in site‐specific CT acquisition protocols had a negligible effect on the PRM‐derived small airways disease (SAD), that is, BOS measurements. PRM‐derived SAD was found to correlate with FEV1% predicted and FEV1/ forced vital capacity (R= −0.236, P= .046; and R= −0.689, P< .0001, respectively), which suggests that elevated levels in the PRM measurements are primarily affected by BOS airflow obstruction and not CT scan acquisition parameters. Based on these results, PRM may be applied broadly for post‐HCT diagnosis and monitoring of BOS. Parametric response mapping, a potential indicator of bronchiolitis obliterans syndrome following hematopoietic cell transplant, was examined in a multicenter setting and is shown to be applicable using a variety of high resolution CT scan techniques.
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- 2020
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43. Next-generation sequencing implicates oncogenic roles for p53 and JAK/STAT signaling in microcystic adnexal carcinomas
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Chan, May P., Plouffe, Komal R., Liu, Chia-Jen, Palanisamy, Nallasivam, Carskadon, Shannon, Zhao, Lili, Nazarian, Rosalynn M., Durham, Alison B., Johnson, Timothy M., Andea, Aleodor A., Patel, Rajiv M., Lowe, Lori, Fullen, Douglas R., Brown, Noah A., Tomlins, Scott A., Udager, Aaron M., and Harms, Paul W.
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Microcystic adnexal carcinoma is a locally aggressive sweat gland carcinoma characterized by its infiltrative growth and histopathologic overlap with benign adnexal tumors, often posing challenges to both diagnosis and management. Understanding the molecular underpinnings of microcystic adnexal carcinoma may allow for more accurate diagnosis and identify potential targetable oncogenic drivers. We characterized 18 microcystic adnexal carcinomas by targeted, multiplexed PCR-based DNA next-generation sequencing of the coding sequence of over 400 cancer-relevant genes. The majority of cases had relatively few (<8) prioritized somatic mutations, and lacked an ultraviolet (UV) signature. The most recurrent mutation was TP53inactivation in four (22%) tumors. Frame-preserving insertions affecting the kinase domain of JAK1were detected in three (17%) cases, and were nonoverlapping with TP53mutations. Seven (39%) cases demonstrated copy number gain of at least one oncogene. By immunohistochemistry, p53 expression was significantly higher in microcystic adnexal carcinomas with TP53mutations compared with those without such mutations and syringomas. Similarly, phospho-STAT3 expression was significantly higher in microcystic adnexal carcinomas harboring JAK1kinase insertions compared with those with wild-type JAK1and syringomas. In conclusion, microcystic adnexal carcinomas are molecularly heterogeneous tumors, with inactivated p53 or activated JAK/STAT signaling in a subset. Unlike most other nonmelanoma skin cancers involving sun-exposed areas, most microcystic adnexal carcinomas lack evidence of UV damage, and hence likely originate from a relatively photo-protected progenitor population in the dermis. These findings have implications for the biology, diagnosis, and treatment of microcystic adnexal carcinomas, including potential for therapeutic targeting of p53 or the JAK/STAT pathway in advanced tumors.
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- 2020
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44. Quantitative far-infrared band strengths of iodine monochloride (ICl), a molten salt off-gas product
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Guicheteau, Jason A., Howle, Chris R., Hughey, Kendall D., Bradley, Ashley M., Felmy, Heather M., Clifford, Andrew J., Cox, Richard M., Lines, Amanda M., Bryan, Samuel A., and Johnson, Timothy J.
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- 2020
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45. The Influence of Item Characteristics on Acquiescence among Latino Survey Respondents
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Davis, Rachel E., Lee, Sunghee, Johnson, Timothy P., Conrad, Frederick, Resnicow, Ken, Thrasher, James F., Mesa, Anna, and Peterson, Karen E.
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Acquiescence is often defined as the systematic selection of agreeable (“strongly agree”) or affirmative (“yes”) responses to survey items, regardless of item content or directionality. This definition implies that acquiescence is immune to item characteristics; however, the influence of item characteristics on acquiescence remains largely unexplored. We examined the influence of eight item characteristics on acquiescence in a telephone survey of 400 Latinos and non-Latino Whites: qualified wording, mental comparisons, negated wording, unfamiliar terms, ambiguous wording, knowledge accessibility, item length, and polysyllabic wording. Negated and ambiguous wording was associated with reduced acquiescence for the full sample as well as subsamples stratified by ethnicity and sociodemographic characteristics. This effect was strongest among younger, more educated, and non-Latino white respondents. No other item characteristics had a significant influence on respondent acquiescence. Findings from this study suggest that acquiescence may be affected by interactions between respondent and item characteristics.
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- 2020
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46. Near real-time intraoperative brain tumor diagnosis using stimulated Raman histology and deep neural networks
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Hollon, Todd C., Pandian, Balaji, Adapa, Arjun R., Urias, Esteban, Save, Akshay V., Khalsa, Siri Sahib S., Eichberg, Daniel G., D’Amico, Randy S., Farooq, Zia U., Lewis, Spencer, Petridis, Petros D., Marie, Tamara, Shah, Ashish H., Garton, Hugh J. L., Maher, Cormac O., Heth, Jason A., McKean, Erin L., Sullivan, Stephen E., Hervey-Jumper, Shawn L., Patil, Parag G., Thompson, B. Gregory, Sagher, Oren, McKhann, Guy M., Komotar, Ricardo J., Ivan, Michael E., Snuderl, Matija, Otten, Marc L., Johnson, Timothy D., Sisti, Michael B., Bruce, Jeffrey N., Muraszko, Karin M., Trautman, Jay, Freudiger, Christian W., Canoll, Peter, Lee, Honglak, Camelo-Piragua, Sandra, and Orringer, Daniel A.
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Intraoperative diagnosis is essential for providing safe and effective care during cancer surgery1. The existing workflow for intraoperative diagnosis based on hematoxylin and eosin staining of processed tissue is time, resource and labor intensive2,3. Moreover, interpretation of intraoperative histologic images is dependent on a contracting, unevenly distributed, pathology workforce4. In the present study, we report a parallel workflow that combines stimulated Raman histology (SRH)5–7, a label-free optical imaging method and deep convolutional neural networks (CNNs) to predict diagnosis at the bedside in near real-time in an automated fashion. Specifically, our CNNs, trained on over 2.5 million SRH images, predict brain tumor diagnosis in the operating room in under 150 s, an order of magnitude faster than conventional techniques (for example, 20–30 min)2. In a multicenter, prospective clinical trial (n= 278), we demonstrated that CNN-based diagnosis of SRH images was noninferior to pathologist-based interpretation of conventional histologic images (overall accuracy, 94.6% versus 93.9%). Our CNNs learned a hierarchy of recognizable histologic feature representations to classify the major histopathologic classes of brain tumors. In addition, we implemented a semantic segmentation method to identify tumor-infiltrated diagnostic regions within SRH images. These results demonstrate how intraoperative cancer diagnosis can be streamlined, creating a complementary pathway for tissue diagnosis that is independent of a traditional pathology laboratory.
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- 2020
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47. Protein kinase C-α is upregulated by IMP1 in melanoma and is linked to poor survival
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Mahapatra, Lily, Andruska, Neal, Mao, Chengjian, Gruber, Stephen B., Johnson, Timothy M., Fullen, Douglass R., Raskin, Leon, and Shapiro, David J.
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The oncofetal mRNA-binding protein, IMP1 or insulin-like growth factor-2 mRNA-binding protein 1 (IGF2BP1), promotes the overexpression of several oncogenic proteins by binding to and stabilizing their mRNAs. IMP1 is frequently overexpressed in melanoma and is associated with a poor prognosis, but the full spectrum of IMP1 target transcripts remains unknown. Here, we report the identification of protein kinase C-α (PKCα), as a novel molecular target of IMP1. Overexpression of IMP1 resulted in increased levels of PKCα, while RNAi knockdown of IMP1 resulted in decreased PKCα mRNA stability, PKCα protein levels, and MAPK/ERK activation. In addition to IMP1 acting as a positive regulator of PKCα mRNA, we also report the identification of miR-340 as a negative regulator of PKCα mRNA. In melanoma cancer cells, inhibition of miR-340 led to increased PKCα protein levels. PKCα plays important roles in numerous signaling pathways including the MAPK/ERK signaling pathway. PKCα activates RAF1, which in turn activates MEK1, and activates downstream transcriptional targets of MAPK through activation of JNK signaling. Together, these pathways provide a way to activate MAPK signaling downstream of BRAF and MEK1 inhibitors, which are commonly used to treat melanoma. Analysis of 117 melanoma tumors samples showed that overexpression of PKCα is associated with poorer overall survival. In patients harboring BRAFV600Eor NRAS mutations, PKCα overexpression is associated with an 11-fold increased risk of death. Thus, PKCα mRNA is a novel target of IMP1, which is commonly overexpressed in melanoma and is linked to poorer overall survival.
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- 2019
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48. Antibiotic Resistance Genes in Freshwater Trout Farms in a Watershed in Chile
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Bueno, Irene, Travis, Dominic, Gonzalez‐Rocha, Gerardo, Alvarez, Julio, Lima, Celia, Benitez, Cristián Garcia, Phelps, Nicholas B.D., Wass, Britta, Johnson, Timothy J., Zhang, Qian, Ishii, Satoshi, and Singer, Randall S.
- Abstract
Point sources such as wastewater treatment plants, terrestrial agriculture, and aquaculture may release antibiotic residues, antibiotic resistant bacteria, and antibiotic resistance genes (ARGs) into aquatic ecosystems. However, there is a lack of quantitative studies attributing environmental ARG abundance to specific sources. The goal of this study was to evaluate the role of freshwater trout farms in the release and dissemination of ARGs into the environment. Sediment samples upstream and downstream from five rainbow trout farms were collected over time in southern Chile. A microfluidic quantitative polymerase chain reaction approach was used to quantify an ARG array covering different mechanisms of resistance, and data were analyzed using principal component analysis (PCA) and linear mixed regression models. Surveys were also conducted to obtain information about management practices, including antibiotic use, at the farms. Florfenicol and oxytetracycline were used at these farms, although at different rates. A total of 93 samples were analyzed. In the PCA, strB, sul1, sul2, qacG, tet(A), tet(B), tet(C), tet(W), and floRgrouped together. A statistically significant increase in abundance of qacG, strB, sul1, and several tetgenes was found downstream from the farms compared with upstream sites, and retention ponds had the highest ARG abundance at each site. Antibiotic resistance gene levels returned to baseline at an average distance of 132.7 m downstream from the farms. Although results from this study indicate an influence of trout farms on the presence of ARGs in the immediate environment, the extent of their contribution to ARG dissemination is unknown and deserves further investigation. Point sources contribute to antimicrobial resistance (AMR) in the environment.Antibiotic resistance genes (ARG) were quantified in river sediment samples.Freshwater trout farms in southern Chile increased ARG abundance in the watershed.The extent of the contribution of the trout farms on ARG dissemination is uncertain.Epidemiological methods are needed to attribute environmental AMR to specific point sources.
- Published
- 2019
- Full Text
- View/download PDF
49. A free spectroscopic databank of optical constants for use in optics education and modeling: complex refractive index data n and k from 1.0 to 25 μm
- Author
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Poulin-Girard, Anne-Sophie, Shaw, Joseph A., Oeck, Ashley M., Tonkyn, Russell G., Loring, John S., Banach, Catherine A., Francis, Ryan M., Burton, Sarah D., Bernacki, Bruce E., Smith, Steven C., Su, Yin-Fong, Szecsody, James E., Saunders, Danielle L., Myers, Tanya L., and Johnson, Timothy J.
- Published
- 2019
- Full Text
- View/download PDF
50. Stabilization of O–O Bonds by d0Cations in Li4+xNi1–xWO6(0 ≤ x≤ 0.25) Rock Salt Oxides as the Origin of Large Voltage Hysteresis
- Author
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Taylor, Zoe N., Perez, Arnaud J., Coca-Clemente, José A., Braga, Filipe, Drewett, Nicholas E., Pitcher, Michael J., Thomas, William J., Dyer, Matthew S., Collins, Christopher, Zanella, Marco, Johnson, Timothy, Day, Sarah, Tang, Chiu, Dhanak, Vinod R., Claridge, John B., Hardwick, Laurence J., and Rosseinsky, Matthew J.
- Abstract
Multinary lithium oxides with the rock salt structure are of technological importance as cathode materials in rechargeable lithium ion batteries. Current state-of-the-art cathodes such as LiNi1/3Mn1/3Co1/3O2rely on redox cycling of earth-abundant transition-metal cations to provide charge capacity. Recently, the possibility of using the oxide anion as a redox center in Li-rich rock salt oxides has been established as a new paradigm in the design of cathode materials with enhanced capacities (>200 mAh/g). To increase the lithium content and access electrons from oxygen-derived states, these materials typically require transition metals in high oxidation states, which can be easily achieved using d0cations. However, Li-rich rock salt oxides with high valent d0cations such as Nb5+and Mo6+show strikingly high voltage hysteresis between charge and discharge, the origin of which is uninvestigated. In this work, we study a series of Li-rich compounds, Li4+xNi1–xWO6(0 ≤ x≤ 0.25) adopting two new and distinct cation-ordered variants of the rock salt structure. The Li4.15Ni0.85WO6(x = 0.15) phase has a large reversible capacity of 200 mAh/g, without accessing the Ni3+/Ni4+redox couple, implying that more than two-thirds of the capacity is due to anionic redox, with good cyclability. The presence of the 5d0W6+cation affords extensive (>2 V) voltage hysteresis associated with the anionic redox. We present experimental evidence for the formation of strongly stabilized localized O–O single bonds that explain the energy penalty required to reduce the material upon discharge. The high valent d0cation associates localized anion–anion bonding with the anion redox capacity.
- Published
- 2019
- Full Text
- View/download PDF
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