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Siachos N, Lennox M, Anagnostopoulos A, Griffiths BE, Neary JM, Smith RF, Oikonomou G. Development and validation of a fully automated 2-dimensional imaging system generating body condition scores for dairy cows using machine learning. J Dairy Sci 2024; 107:2499-2511. [PMID: 37977440 DOI: 10.3168/jds.2023-23894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023]
Abstract
Monitoring body condition score (BCS) is a useful management tool to estimate the energy reserves of an individual cow or a group of cows. The aim of this study was to develop and evaluate the performance of a fully automated 2-dimensional imaging system using a machine learning algorithm to generate real-time BCS for dairy cows. Two separate datasets were used for training and testing. The training dataset included 34,150 manual BCS (MAN_BCS) assigned by 5 experienced veterinarians during 35 visits at 7 dairy farms. Ordinal regression methods and deep learning architecture were used when developing the algorithm. Subsequently, the testing dataset was used to evaluate the developed BCS prediction algorithm on 4 of the participating farms. An experienced human assessor (HA1) visited these farms and performed 8 whole-milking-herd BCS sessions. Each farm was visited twice, allowing for 30 d (±2 d) to pass between visits. The MAN_BCS assigned by HA1 were considered the ground truth data. At the end of the validation study, MAN_BCS were merged with the stored automated BCS (AI_BCS), resulting in a testing dataset of 9,657 single BCS. A total of 3,817 cows in the testing dataset were scored twice 30 d (±2 d) apart, and the change in their BCS (ΔBCS) was calculated. A subset of cows at one farm were scored twice on consecutive days to evaluate the within-observer agreement of both the human assessor and the system. The manual BCS of 2 more assessors (HA2 and HA3) were used to assess the interobserver agreement between humans. Finally, we also collected ultrasound measurements of backfat thickness (BFT) from 111 randomly selected cows with available MAN_BCS and AI_BCS. Using the testing dataset, intra- and interobserver agreement for single BCS and ΔBCS were estimated by calculating the simple percentage agreement (PA) at 3 error levels and the weighted kappa (κw) for the exact agreement. A Bland-Altman plot was constructed to visualize the systematic and proportional bias. The association between MAN_BCS and AI_BCS and the BFT was assessed with Passing-Bablok regressions. The system had an almost perfect repeatability with a κw of 0.99. The agreement between MAN_BCS and AI_BCS was substantial, with an overall κw of 0.69. The overall PA at the exact, ± 0.25-unit, and ± 0.50-unit BCS error range between MAN_BCS and AI_BCS was 44.4%, 84.6%, and 94.8%, respectively, and greater than the PA obtained between HA1 and HA3. The Bland-Altman plot revealed a minimal systematic bias of -0.09 with a proportional bias at the extreme scores. Furthermore, despite the low κw of 0.20, the overall PA at the exact and ± 0.25-unit of BCS error range between MAN_BCS and AI_BCS regarding the ΔBCS was 45.7 and 88.2%, respectively. A strong linear relationship was observed between BFT and AI_BCS (ρ = 0.75), although weaker than that between BFT and MAN_BCS (ρ = 0.91). The system was able to predict single BCS and ΔBCS with satisfactory accuracy, comparable to that obtained between trained human scorers.
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Ryder J, Smith RF, Neary JM. Postpartum longissimus dorsi muscle loss, but not back fat, is associated with resumption of postpartum ovarian activity in dairy cattle. J Dairy Sci 2023; 106:8087-8097. [PMID: 37562647 DOI: 10.3168/jds.2023-23253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/01/2023] [Indexed: 08/12/2023]
Abstract
The objectives of this observational cohort study were to assess the effect of body condition score change, back fat depth change, and muscle diameter change on the time to commencement of luteal activity and first estrus in commercial pedigree Holstein cows. A total of 140 of 200 commercial pedigree Holstein cows were enrolled in one dairy herd in Somerset, UK, over 52 wk in 2021 to 2022. The herd used 4 automatic milking machines with in-line progesterone measurement capability to determine commencement of luteal activity and time to first estrus. Cows were followed until at least 60 d postpartum, and milk progesterone was measured daily starting from 10 DIM. Body condition scoring and ultrasound measurements of back fat depth and longissimus dorsi muscle diameter were performed on cows twice, within 7 d of both calving and 60 DIM. Other explanatory variables assessed included parity, 60-d and 305-d milk yield, and subclinical ketosis (β-hydroxybutryate ≥1.2 mmol/L). Occurrence of clinical disease <60 DIM was forced into all models as a binary variable. Data were analyzed using multivariable Cox proportionate survival analyses. Muscle loss was associated with commencement of luteal activity and time to first estrus. A reduction in muscle diameter by 1.5 to 5 mm was associated with the shortest time to the start of luteal activity and first estrus. A reduction in muscle diameter >8 mm was associated with the longest times to luteal activity and first estrus. In addition to being affected by muscle loss, commencement of luteal activity was delayed by subclinical ketosis, clinical disease, and failure to gain body condition to 60 DIM. Cows that had a BCS loss of 0.25 or more between calving and 60 DIM were at least 52 ± 22% less likely to have commenced luteal activity compared with those that gained BCS. Interestingly, cows that had no change in body condition score commenced luteal activity later than those that gained body condition score. Muscle loss was associated with time to first estrus irrespective of clinical disease status. Cows that lost >8 mm of muscle diameter showed estrus behavior later than cows that lost 1.5 to 5 mm. In conclusion, our findings indicate that extensive muscle loss postpartum was associated with a delayed start to luteal activity and first estrus, irrespective of body condition change, clinical disease, and subclinical ketosis. Marginal muscle loss and a gain in body condition, however, were associated with an earlier start to luteal activity and first estrus.
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Gong X, Polsin DN, Paul R, Henderson BJ, Eggert JH, Coppari F, Smith RF, Rygg JR, Collins GW. X-Ray Diffraction of Ramp-Compressed Silicon to 390 GPa. PHYSICAL REVIEW LETTERS 2023; 130:076101. [PMID: 36867795 DOI: 10.1103/physrevlett.130.076101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/15/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Silicon (Si) exhibits a rich collection of phase transitions under ambient-temperature isothermal and shock compression. This report describes in situ diffraction measurements of ramp-compressed Si between 40 and 389 GPa. Angle-dispersive x-ray scattering reveals that Si assumes an hexagonal close-packed (hcp) structure between 40 and 93 GPa and, at higher pressure, a face-centered cubic structure that persists to at least 389 GPa, the highest pressure for which the crystal structure of Si has been investigated. The range of hcp stability extends to higher pressures and temperatures than predicted by theory.
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Surendran P, Stewart ID, Au Yeung VPW, Pietzner M, Raffler J, Wörheide MA, Li C, Smith RF, Wittemans LBL, Bomba L, Menni C, Zierer J, Rossi N, Sheridan PA, Watkins NA, Mangino M, Hysi PG, Di Angelantonio E, Falchi M, Spector TD, Soranzo N, Michelotti GA, Arlt W, Lotta LA, Denaxas S, Hemingway H, Gamazon ER, Howson JMM, Wood AM, Danesh J, Wareham NJ, Kastenmüller G, Fauman EB, Suhre K, Butterworth AS, Langenberg C. Rare and common genetic determinants of metabolic individuality and their effects on human health. Nat Med 2022; 28:2321-2332. [PMID: 36357675 PMCID: PMC9671801 DOI: 10.1038/s41591-022-02046-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 09/16/2022] [Indexed: 11/12/2022]
Abstract
Garrod's concept of 'chemical individuality' has contributed to comprehension of the molecular origins of human diseases. Untargeted high-throughput metabolomic technologies provide an in-depth snapshot of human metabolism at scale. We studied the genetic architecture of the human plasma metabolome using 913 metabolites assayed in 19,994 individuals and identified 2,599 variant-metabolite associations (P < 1.25 × 10-11) within 330 genomic regions, with rare variants (minor allele frequency ≤ 1%) explaining 9.4% of associations. Jointly modeling metabolites in each region, we identified 423 regional, co-regulated, variant-metabolite clusters called genetically influenced metabotypes. We assigned causal genes for 62.4% of these genetically influenced metabotypes, providing new insights into fundamental metabolite physiology and clinical relevance, including metabolite-guided discovery of potential adverse drug effects (DPYD and SRD5A2). We show strong enrichment of inborn errors of metabolism-causing genes, with examples of metabolite associations and clinical phenotypes of non-pathogenic variant carriers matching characteristics of the inborn errors of metabolism. Systematic, phenotypic follow-up of metabolite-specific genetic scores revealed multiple potential etiological relationships.
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Kim D, Smith RF, Ocampo IK, Coppari F, Marshall MC, Ginnane MK, Wicks JK, Tracy SJ, Millot M, Lazicki A, Rygg JR, Eggert JH, Duffy TS. Structure and density of silicon carbide to 1.5 TPa and implications for extrasolar planets. Nat Commun 2022; 13:2260. [PMID: 35477934 PMCID: PMC9046200 DOI: 10.1038/s41467-022-29762-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 03/16/2022] [Indexed: 11/10/2022] Open
Abstract
There has been considerable recent interest in the high-pressure behavior of silicon carbide, a potential major constituent of carbon-rich exoplanets. In this work, the atomic-level structure of SiC was determined through in situ X-ray diffraction under laser-driven ramp compression up to 1.5 TPa; stresses more than seven times greater than previous static and shock data. Here we show that the B1-type structure persists over this stress range and we have constrained its equation of state (EOS). Using this data we have determined the first experimentally based mass-radius curves for a hypothetical pure SiC planet. Interior structure models are constructed for planets consisting of a SiC-rich mantle and iron-rich core. Carbide planets are found to be ~10% less dense than corresponding terrestrial planets.
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Marshall MC, Millot M, Fratanduono DE, Sterbentz DM, Myint PC, Belof JL, Kim YJ, Coppari F, Ali SJ, Eggert JH, Smith RF, McNaney JM. Metastability of Liquid Water Freezing into Ice VII under Dynamic Compression. PHYSICAL REVIEW LETTERS 2021; 127:135701. [PMID: 34623849 DOI: 10.1103/physrevlett.127.135701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/23/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
The ubiquitous nature and unusual properties of water have motivated many studies on its metastability under temperature- or pressure-induced phase transformations. Here, nanosecond compression by a high-power laser is used to create the nonequilibrium conditions where liquid water persists well into the stable region of ice VII. Through our experiments, as well as a complementary theoretical-computational analysis based on classical nucleation theory, we report that the metastability limit of liquid water under nearly isentropic compression from ambient conditions is at least 8 GPa, higher than the 7 GPa previously reported for lower loading rates.
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Kraus RG, Coppari F, Fratanduono DE, Smith RF, Lazicki A, Wehrenberg C, Eggert JH, Rygg JR, Collins GW. Melting of Tantalum at Multimegabar Pressures on the Nanosecond Timescale. PHYSICAL REVIEW LETTERS 2021; 126:255701. [PMID: 34241515 DOI: 10.1103/physrevlett.126.255701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/05/2021] [Indexed: 06/13/2023]
Abstract
Tantalum was once thought to be the canonical bcc metal, but is now predicted to transition to the Pnma phase at the high pressures and temperatures expected along the principal Hugoniot. Furthermore, there remains a significant discrepancy between a number of static diamond anvil cell experiments and gas gun experiments in the measured melt temperatures at high pressures. Our in situ x-ray diffraction experiments on shock compressed tantalum show that it does not transition to the Pnma phase or other candidate phases at high pressure. We observe incipient melting at approximately 254±15 GPa and complete melting by 317±10 GPa. These transition pressures from the nanosecond experiments presented here are consistent with what can be inferred from microsecond gas gun sound velocity measurements. Furthermore, the observation of a coexistence region on the Hugoniot implies the lack of significant kinetically controlled deviation from equilibrium behavior. Consequently, we find that kinetics of phase transitions cannot be used to explain the discrepancy between static and dynamic measurements of the tantalum melt curve. Using available high pressure thermodynamic data for tantalum and our measurements of the incipient and complete melting transition pressures, we are able to infer a melting temperature 8070_{-750}^{+1250} K at 254±15 GPa, which is consistent with ambient and a recent static high pressure melt curve measurement.
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Barden M, Smith RF, Higgins HM. The interpretation of serial Johne's disease milk antibody results is affected by test characteristics, pattern of test results and parallel bovine tuberculosis testing. Prev Vet Med 2020; 183:105134. [PMID: 32912605 DOI: 10.1016/j.prevetmed.2020.105134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 08/11/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND In the UK, quarterly Johne's disease milk antibody ELISAs (JD-mELISAs) are commonly used to classify animals which are likely to be infectious, termed "red cows". "Red cows" are classified following two positive results from the previous four tests (e.g. + - - +). All cattle are also regularly screened for bovine tuberculosis using intradermal avian and bovine tuberculin, and it is advised to maintain a 60 day interval between a tuberculosis test and JD-mELISA. AIMS To evaluate the impact of bovine tuberculosis testing on JD-mELISAs, and to quantify the impact of test specificity and "red cow" classification test pattern on the probability of infection. METHODS Four years of individual cow milk records with JD-mELISA results were collated from 735 dairy farms and matched to tuberculosis testing records. A two-level multivariable logistic regression model quantified the effect of tuberculosis testing on JD-mELISA result. The specificity and age-dependent sensitivity of a single JD-mELISA were estimated and used to calculate likelihood ratios following each test. Using Bayes' theorem, the posterior probability of infection with Johne's disease was calculated for different specificities, ages of cow, and patterns of test results. RESULTS There were increased odds of a positive JD-mELISA if it was ≤30 days (OR: 2.1) or 31-60 days (OR: 1.2) after a tuberculosis test, compared to >90 days. A larger avian skin reaction at the tuberculosis test was also associated with increased odds of a positive JD-mELISA. The proportion of cows which tested exclusively negative after their first positive JD-mELISA was higher if that JD-mELISA was ≤30 days after a tuberculosis test compared to >90 days. The posterior probability of infection reduced substantially when the test specificity was slightly reduced. In "red cows" classified following two consecutive positive tests, if the test specificity was reduced to 0.95, then the posterior probability of infection was only >95 % if the prior probability was >13 %. If the "red cow" classification was due to two non-consecutive positive tests (+ - - +), the posterior probability of infection was only >95 % if the prior probability was >43 %. CONCLUSIONS Testing for Johne's disease within 60 days of a tuberculosis test is associated with a higher chance of a positive JD-mELISA and this may reflect a reduction in the ELISA specificity. Relatively small reductions in JD-mELISA specificity can markedly reduce the posterior probability of infection which also depends on the pattern of test results which classifies "red cows".
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Rygg JR, Smith RF, Lazicki AE, Braun DG, Fratanduono DE, Kraus RG, McNaney JM, Swift DC, Wehrenberg CE, Coppari F, Ahmed MF, Barrios MA, Blobaum KJM, Collins GW, Cook AL, Di Nicola P, Dzenitis EG, Gonzales S, Heidl BF, Hohenberger M, House A, Izumi N, Kalantar DH, Khan SF, Kohut TR, Kumar C, Masters ND, Polsin DN, Regan SP, Smith CA, Vignes RM, Wall MA, Ward J, Wark JS, Zobrist TL, Arsenlis A, Eggert JH. X-ray diffraction at the National Ignition Facility. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:043902. [PMID: 32357733 DOI: 10.1063/1.5129698] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/20/2020] [Indexed: 06/11/2023]
Abstract
We report details of an experimental platform implemented at the National Ignition Facility to obtain in situ powder diffraction data from solids dynamically compressed to extreme pressures. Thin samples are sandwiched between tamper layers and ramp compressed using a gradual increase in the drive-laser irradiance. Pressure history in the sample is determined using high-precision velocimetry measurements. Up to two independently timed pulses of x rays are produced at or near the time of peak pressure by laser illumination of thin metal foils. The quasi-monochromatic x-ray pulses have a mean wavelength selectable between 0.6 Å and 1.9 Å depending on the foil material. The diffracted signal is recorded on image plates with a typical 2θ x-ray scattering angle uncertainty of about 0.2° and resolution of about 1°. Analytic expressions are reported for systematic corrections to 2θ due to finite pinhole size and sample offset. A new variant of a nonlinear background subtraction algorithm is described, which has been used to observe diffraction lines at signal-to-background ratios as low as a few percent. Variations in system response over the detector area are compensated in order to obtain accurate line intensities; this system response calculation includes a new analytic approximation for image-plate sensitivity as a function of photon energy and incident angle. This experimental platform has been used up to 2 TPa (20 Mbar) to determine the crystal structure, measure the density, and evaluate the strain-induced texturing of a variety of compressed samples spanning periods 2-7 on the periodic table.
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Jiang S, Lazicki AE, Hansen SB, Sterne PA, Grabowski P, Shepherd R, Scott HA, Smith RF, Eggert JH, Ping Y. Measurements of pressure-induced Kβ line shifts in ramp compressed cobalt up to 8 Mbar. Phys Rev E 2020; 101:023204. [PMID: 32168658 DOI: 10.1103/physreve.101.023204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 12/17/2019] [Indexed: 11/07/2022]
Abstract
We report measurements of K-shell fluorescence lines induced by fast electrons in ramp-compressed Co targets. The fluorescence emission was stimulated by fast electrons generated through short-pulse laser-solid interaction with an Al target layer. Compression up to 2.1× solid density was achieved while maintaining temperatures well below the Fermi energy, effectively removing the thermal effects from consideration. We observed small but unambiguous redshifts in the Kβ fluorescence line relative to unshifted Cu Kα. Redshifts up to 2.6 eV were found to increase with compression and to be consistent with predictions from self-consistent models based on density-functional theory.
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Fratanduono DE, Smith RF, Ali SJ, Braun DG, Fernandez-Pañella A, Zhang S, Kraus RG, Coppari F, McNaney JM, Marshall MC, Kirch LE, Swift DC, Millot M, Wicks JK, Eggert JH. Probing the Solid Phase of Noble Metal Copper at Terapascal Conditions. PHYSICAL REVIEW LETTERS 2020; 124:015701. [PMID: 31976690 DOI: 10.1103/physrevlett.124.015701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Ramp compression along a low-temperature adiabat offers a unique avenue to explore the physical properties of materials at the highest densities of their solid form, a region inaccessible by single shock compression. Using the National Ignition Facility and OMEGA laser facilities, copper samples were ramp compressed to peak pressures of 2.30 TPa and densities of nearly 30 g/cc, providing fundamental information regarding the compressibility and phase of copper at pressures more than 5 times greater than previously explored. Through x-ray diffraction measurements, we find that the ambient face-centered-cubic structure is preserved up to 1.15 TPa. The ramp compression equation-of-state measurements shows that there are no discontinuities in sound velocities up to 2.30 TPa, suggesting this phase is likely stable up to the peak pressures measured, as predicted by first-principal calculations. The high precision of these quasiabsolute measurements enables us to provide essential benchmarks for advanced computational studies on the behavior of dense monoatomic materials under extreme conditions that constitute a stringent test for solid-state quantum theory. We find that both density-functional theory and the stabilized jellium model, which assumes that the ionic structure can be replaced by an ionic charge distribution by constant positive-charge background, reproduces our data well. Further, our data could serve to establish new international secondary scales of pressure in the terapascal range that is becoming experimentally accessible with advanced static and dynamic compression techniques.
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Heighway PG, Sliwa M, McGonegle D, Wehrenberg C, Bolme CA, Eggert J, Higginbotham A, Lazicki A, Lee HJ, Nagler B, Park HS, Rudd RE, Smith RF, Suggit MJ, Swift D, Tavella F, Remington BA, Wark JS. Nonisentropic Release of a Shocked Solid. PHYSICAL REVIEW LETTERS 2019; 123:245501. [PMID: 31922830 DOI: 10.1103/physrevlett.123.245501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 09/09/2019] [Indexed: 06/10/2023]
Abstract
We present molecular dynamics simulations of shock and release in micron-scale tantalum crystals that exhibit postbreakout temperatures far exceeding those expected under the standard assumption of isentropic release. We show via an energy-budget analysis that this is due to plastic-work heating from material strength that largely counters thermoelastic cooling. The simulations are corroborated by experiments where the release temperatures of laser-shocked tantalum foils are deduced from their thermal strains via in situ x-ray diffraction and are found to be close to those behind the shock.
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Coppari F, Smith RF, Thorn DB, Rygg JR, Liedahl DA, Kraus RG, Lazicki A, Millot M, Eggert JH. Optimized x-ray sources for x-ray diffraction measurements at the Omega Laser Facility. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2019; 90:125113. [PMID: 31893795 DOI: 10.1063/1.5111878] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
The use of x-ray diffraction (XRD) measurements in laser-driven dynamic compression experiments at high-power laser facilities is becoming increasingly common. Diffraction allows one to probe in situ the transformations occurring at the atomic level at extreme conditions of pressure, temperature, and time scale. In these measurements, the x-ray source is generated by irradiation of a solid foil. Under certain laser drive conditions, quasimonochromatic He-α radiation is generated. Careful analysis of the x-ray source plasma spectra reveals that this radiation is not a single line emission and that monochromaticity is highly dependent on the laser irradiance. In this work, we analyze how the spectra emitted by laser-irradiated copper, germanium, and iron foils at the Omega Laser vary depending on different laser drive conditions and discuss the implications for XRD experiments.
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Briggs R, Coppari F, Gorman MG, Smith RF, Tracy SJ, Coleman AL, Fernandez-Pañella A, Millot M, Eggert JH, Fratanduono DE. Measurement of Body-Centered Cubic Gold and Melting under Shock Compression. PHYSICAL REVIEW LETTERS 2019; 123:045701. [PMID: 31491279 DOI: 10.1103/physrevlett.123.045701] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Indexed: 06/10/2023]
Abstract
We combined laser shock compression with in situ x-ray diffraction to probe the crystallographic state of gold (Au) on its principal shock Hugoniot. Au has long been recognized as an important calibration standard in diamond anvil cell experiments due to the stability of its face-centered cubic (fcc) structure to extremely high pressures (P >600 GPa at 300 K). This is in contrast to density functional theory and first principles calculations of the high-pressure phases of Au that predict a variety of fcc-like structures with different stacking arrangements at intermediate pressures. In this Letter, we probe high-pressure and high-temperature conditions on the shock Hugoniot and observe fcc Au at 169 GPa and the first evidence of body-centered cubic (bcc) Au at 223 GPa. Upon further compression, the bcc phase is observed in coexistence with liquid scattering as the Hugoniot crosses the Au melt curve before 322 GPa. The results suggest a triple point on the Au phase diagram that lies very close to the principal shock Hugoniot near ∼220 GPa.
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Coleman AL, Gorman MG, Briggs R, McWilliams RS, McGonegle D, Bolme CA, Gleason AE, Fratanduono DE, Smith RF, Galtier E, Lee HJ, Nagler B, Granados E, Collins GW, Eggert JH, Wark JS, McMahon MI. Identification of Phase Transitions and Metastability in Dynamically Compressed Antimony Using Ultrafast X-Ray Diffraction. PHYSICAL REVIEW LETTERS 2019; 122:255704. [PMID: 31347883 DOI: 10.1103/physrevlett.122.255704] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Indexed: 06/10/2023]
Abstract
Ultrafast x-ray diffraction at the LCLS x-ray free electron laser has been used to resolve the structural behavior of antimony under shock compression to 59 GPa. Antimony is seen to transform to the incommensurate, host-guest phase Sb-II at ∼11 GPa, which forms on nanosecond timescales with ordered guest-atom chains. The high-pressure bcc phase Sb-III is observed above ∼15 GPa, some 8 GPa lower than in static compression studies, and mixed Sb-III/liquid diffraction are obtained between 38 and 59 GPa. An additional phase which does not exist under static compression, Sb-I^{'}, is also observed between 8 and 12 GPa, beyond the normal stability field of Sb-I, and resembles Sb-I with a resolved Peierls distortion. The incommensurate Sb-II high-pressure phase can be recovered metastably on release to ambient pressure, where it is stable for more than 10 ns.
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Gorman MG, Coleman AL, Briggs R, McWilliams RS, McGonegle D, Bolme CA, Gleason AE, Galtier E, Lee HJ, Granados E, Śliwa M, Sanloup C, Rothman S, Fratanduono DE, Smith RF, Collins GW, Eggert JH, Wark JS, McMahon MI. Femtosecond diffraction studies of solid and liquid phase changes in shock-compressed bismuth. Sci Rep 2018; 8:16927. [PMID: 30446720 PMCID: PMC6240068 DOI: 10.1038/s41598-018-35260-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/28/2018] [Indexed: 11/09/2022] Open
Abstract
Bismuth has long been a prototypical system for investigating phase transformations and melting at high pressure. Despite decades of experimental study, however, the lattice-level response of Bi to rapid (shock) compression and the relationship between structures occurring dynamically and those observed during slow (static) compression, are still not clearly understood. We have determined the structural response of shock-compressed Bi to 68 GPa using femtosecond X-ray diffraction, thereby revealing the phase transition sequence and equation-of-state in unprecedented detail for the first time. We show that shocked-Bi exhibits a marked departure from equilibrium behavior - the incommensurate Bi-III phase is not observed, but rather a new metastable phase, and the Bi-V phase is formed at significantly lower pressures compared to static compression studies. We also directly measure structural changes in a shocked liquid for the first time. These observations reveal new behaviour in the solid and liquid phases of a shocked material and give important insights into the validity of comparing static and dynamic datasets.
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Polsin DN, Fratanduono DE, Rygg JR, Lazicki A, Smith RF, Eggert JH, Gregor MC, Henderson BH, Delettrez JA, Kraus RG, Celliers PM, Coppari F, Swift DC, McCoy CA, Seagle CT, Davis JP, Burns SJ, Collins GW, Boehly TR. Erratum: Measurement of Body-Centered-Cubic Aluminum at 475 GPa [Phys. Rev. Lett. 119, 175702 (2017)]. PHYSICAL REVIEW LETTERS 2018; 120:029902. [PMID: 29376685 DOI: 10.1103/physrevlett.120.029902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Indexed: 06/07/2023]
Abstract
This corrects the article DOI: 10.1103/PhysRevLett.119.175702.
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Polsin DN, Fratanduono DE, Rygg JR, Lazicki A, Smith RF, Eggert JH, Gregor MC, Henderson BH, Delettrez JA, Kraus RG, Celliers PM, Coppari F, Swift DC, McCoy CA, Seagle CT, Davis JP, Burns SJ, Collins GW, Boehly TR. Measurement of Body-Centered-Cubic Aluminum at 475 GPa. PHYSICAL REVIEW LETTERS 2017; 119:175702. [PMID: 29219452 DOI: 10.1103/physrevlett.119.175702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Indexed: 06/07/2023]
Abstract
Nanosecond in situ x-ray diffraction and simultaneous velocimetry measurements were used to determine the crystal structure and pressure, respectively, of ramp-compressed aluminum at stress states between 111 and 475 GPa. The solid-solid Al phase transformations, fcc-hcp and hcp-bcc, are observed at 216±9 and 321±12 GPa, respectively, with the bcc phase persisting to 475 GPa. The high-pressure crystallographic texture of the hcp and bcc phases suggests close-packed or nearly close-packed lattice planes remain parallel through both transformations.
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Spaulding DK, McWilliams RS, Jeanloz R, Eggert JH, Celliers PM, Hicks DG, Collins GW, Smith RF. Erratum: Evidence for a Phase Transition in Silicate Melt at Extreme Pressure and Temperature Conditions [Phys. Rev. Lett. 108, 065701 (2012)]. PHYSICAL REVIEW LETTERS 2017; 119:139903. [PMID: 29341693 DOI: 10.1103/physrevlett.119.139903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Indexed: 06/07/2023]
Abstract
This corrects the article DOI: 10.1103/PhysRevLett.108.065701.
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Fergani C, Routly JE, Jones DN, Pickavance LC, Smith RF, Dobson H. KNDy neurone activation prior to the LH surge of the ewe is disrupted by LPS. Reproduction 2017. [PMID: 28630099 DOI: 10.1530/rep-17-0191] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the ewe, steroid hormones act on the hypothalamic arcuate nucleus (ARC) to initiate the GnRH/LH surge. Within the ARC, steroid signal transduction may be mediated by estrogen receptive dopamine-, β-endorphin- or neuropeptide Y (NPY)-expressing cells, as well as those co-localising kisspeptin, neurokinin B (NKB) and dynorphin (termed KNDy). We investigated the time during the follicular phase when these cells become activated (i.e., co-localise c-Fos) relative to the timing of the LH surge onset and may therefore be involved in the surge generating mechanism. Furthermore, we aimed to elucidate whether these activation patterns are altered after lipopolysaccharide (LPS) administration, which is known to inhibit the LH surge. Follicular phases of ewes were synchronised by progesterone withdrawal and blood samples were collected every 2 h. Hypothalamic tissue was retrieved at various times during the follicular phase with or without the administration of LPS (100 ng/kg). The percentage of activated dopamine cells decreased before the onset of sexual behaviour, whereas activation of β-endorphin decreased and NPY activation tended to increase during the LH surge. These patterns were not disturbed by LPS administration. Maximal co-expression of c-Fos in dynorphin immunoreactive neurons was observed earlier during the follicular phase, compared to kisspeptin and NKB, which were maximally activated during the surge. This indicates a distinct role for ARC dynorphin in the LH surge generation mechanism. Acute LPS decreased the percentage of activated dynorphin and kisspeptin immunoreactive cells. Thus, in the ovary-intact ewe, KNDy neurones are activated prior to the LH surge onset and this pattern is inhibited by the administration of LPS.
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Briggs R, Gorman MG, Coleman AL, McWilliams RS, McBride EE, McGonegle D, Wark JS, Peacock L, Rothman S, Macleod SG, Bolme CA, Gleason AE, Collins GW, Eggert JH, Fratanduono DE, Smith RF, Galtier E, Granados E, Lee HJ, Nagler B, Nam I, Xing Z, McMahon MI. Ultrafast X-Ray Diffraction Studies of the Phase Transitions and Equation of State of Scandium Shock Compressed to 82 GPa. PHYSICAL REVIEW LETTERS 2017; 118:025501. [PMID: 28128621 DOI: 10.1103/physrevlett.118.025501] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Indexed: 06/06/2023]
Abstract
Using x-ray diffraction at the Linac Coherent Light Source x-ray free-electron laser, we have determined simultaneously and self-consistently the phase transitions and equation of state (EOS) of the lightest transition metal, scandium, under shock compression. On compression scandium undergoes a structural phase transition between 32 and 35 GPa to the same bcc structure seen at high temperatures at ambient pressures, and then a further transition at 46 GPa to the incommensurate host-guest polymorph found above 21 GPa in static compression at room temperature. Shock melting of the host-guest phase is observed between 53 and 72 GPa with the disappearance of Bragg scattering and the growth of a broad asymmetric diffraction peak from the high-density liquid.
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Coyne LA, Latham SM, Williams NJ, Dawson S, Donald IJ, Pearson RB, Smith RF, Pinchbeck GL. Understanding the culture of antimicrobial prescribing in agriculture: a qualitative study of UK pig veterinary surgeons. J Antimicrob Chemother 2016; 71:3300-3312. [PMID: 27516473 PMCID: PMC5079303 DOI: 10.1093/jac/dkw300] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 06/18/2016] [Accepted: 06/24/2016] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES The use of antimicrobials in food-producing animals has been linked with the emergence of antimicrobial resistance in bacterial populations, with consequences for animal and public health. This study explored the underpinning drivers, motivators and reasoning behind prescribing decisions made by veterinary surgeons working in the UK pig industry. METHODS A qualitative interview study was conducted with 21 veterinary surgeons purposively selected from all UK pig veterinary surgeons. Thematic analysis was used to analyse transcripts. RESULTS Ensuring optimum pig health and welfare was described as a driver for antimicrobial use by many veterinary surgeons and was considered a professional and moral obligation. Veterinary surgeons also exhibited a strong sense of social responsibility over the need to ensure that antimicrobial use was responsible. A close relationship between management practices, health and economics was evident, with improvements in management commonly identified as being potential routes to reduce antimicrobial usage; however, these were not always considered economically viable. The relationship with clients was identified as being a source of professional stress for practitioners due to pressure from farmers requesting antimicrobial prescriptions, and concern over poor compliance of antimicrobial administration by some farmers. CONCLUSIONS The drivers behind prescribing decisions by veterinary surgeons were complex and diverse. A combination of education, improving communication between veterinary surgeons and farmers, and changes in regulations, in farm management and in consumer/retailer demands may all be needed to ensure that antimicrobial prescribing is optimal and to achieve significant reductions in use.
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Vignes RM, Ahmed MF, Eggert JH, Fisher AC, Kalantar DH, Masters ND, Smith CA, Smith RF. TARDIS-C: A target diagnostic for measuring material structure at high pressure. ACTA ACUST UNITED AC 2016. [DOI: 10.1088/1742-6596/717/1/012115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Gorman MG, Briggs R, McBride EE, Higginbotham A, Arnold B, Eggert JH, Fratanduono DE, Galtier E, Lazicki AE, Lee HJ, Liermann HP, Nagler B, Rothkirch A, Smith RF, Swift DC, Collins GW, Wark JS, McMahon MI. Direct Observation of Melting in Shock-Compressed Bismuth With Femtosecond X-ray Diffraction. PHYSICAL REVIEW LETTERS 2015; 115:095701. [PMID: 26371663 DOI: 10.1103/physrevlett.115.095701] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Indexed: 06/05/2023]
Abstract
The melting of bismuth in response to shock compression has been studied using in situ femtosecond x-ray diffraction at an x-ray free electron laser. Both solid-solid and solid-liquid phase transitions are documented using changes in discrete diffraction peaks and the emergence of broad, liquid scattering upon release from shock pressures up to 14 GPa. The transformation from the solid state to the liquid is found to occur in less than 3 ns, very much faster than previously believed. These results are the first quantitative measurements of a liquid material obtained on shock release using x-ray diffraction, and provide an upper limit for the time scale of melting of bismuth under shock loading.
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James CD, Jeynes C, Barradas NP, Clifton L, Dalgliesh RM, Smith RF, Sankey SW, Hutchings LR, Thompson RL. Modifying polyester surfaces with incompatible polymer additives. REACT FUNCT POLYM 2015. [DOI: 10.1016/j.reactfunctpolym.2015.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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