Development and validation of a fully automated 2-dimensional imaging system generating body condition scores for dairy cows using machine learning.

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.

Postpartum longissimus dorsi muscle loss, but not back fat, is associated with resumption of postpartum ovarian activity in dairy cattle.

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 (ß-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.

X-Ray Diffraction of Ramp-Compressed Silicon to 390 GPa.

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.

Structure and density of silicon carbide to 1.5 TPa and implications for extrasolar planets.

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.

Metastability of Liquid Water Freezing into Ice VII under Dynamic Compression.

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.

Melting of Tantalum at Multimegabar Pressures on the Nanosecond Timescale.

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.

Establishing gold and platinum standards to 1 terapascal using shockless compression.

New techniques are advancing the frontier of high-pressure physics beyond 1 terapascal, leading to new discoveries and offering stringent tests for condensed-matter theory and advanced numerical methods. However, the ability to absolutely determine the pressure state remains challenging, and well-calibrated pressure-density reference materials are required. We conducted shockless dynamic compression experiments at the National Ignition Facility and the Z machine to obtain quasi-absolute, high-precision, pressure-density equation-of-state data for gold and platinum. We derived two experimentally constrained pressure standards to terapascal conditions. Establishing accurate experimental determinations of extreme pressure will facilitate better connections between experiments and theory, paving the way toward improving our understanding of material response to these extreme conditions.

Metastability of diamond ramp-compressed to 2 terapascals.

Carbon is the fourth-most prevalent element in the Universe and essential for all known life. In the elemental form it is found in multiple allotropes, including graphite, diamond and fullerenes, and it has long been predicted that even more structures can exist at pressures greater than those at Earth's core1-3. Several phases have been predicted to exist in the multi-terapascal regime, which is important for accurate modelling of the interiors of carbon-rich exoplanets4,5. By compressing solid carbon to 2 terapascals (20 million atmospheres; more than five times the pressure at Earth's core) using ramp-shaped laser pulses and simultaneously measuring nanosecond-duration time-resolved X-ray diffraction, we found that solid carbon retains the diamond structure far beyond its regime of predicted stability. The results confirm predictions that the strength of the tetrahedral molecular orbital bonds in diamond persists under enormous pressure, resulting in large energy barriers that hinder conversion to more-stable high-pressure allotropes1,2, just as graphite formation from metastable diamond is kinetically hindered at atmospheric pressure. This work nearly doubles the highest pressure at which X-ray diffraction has been recorded on any material.

The interpretation of serial Johne's disease milk antibody results is affected by test characteristics, pattern of test results and parallel bovine tuberculosis testing.

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".

X-ray diffraction at the National Ignition Facility.

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.

Measurements of pressure-induced Kß line shifts in ramp compressed cobalt up to 8 Mbar.

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 Kß 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.

Putative ß-Barrel Outer Membrane Proteins of the Bovine Digital Dermatitis-Associated Treponemes: Identification, Functional Characterization, and Immunogenicity.

Bovine digital dermatitis (BDD), an infectious disease of the bovine foot with a predominant treponemal etiology, is a leading cause of lameness in dairy and beef herds worldwide. BDD is poorly responsive to antimicrobial therapy and exhibits a relapsing clinical course; an effective vaccine is therefore urgently sought. Using a reverse vaccinology approach, the present study surveyed the genomes of the three BDD-associated Treponema phylogroups for putative ß-barrel outer membrane proteins and considered their potential as vaccine candidates. Selection criteria included the presence of a signal peptidase I cleavage site, a predicted ß-barrel fold, and cross-phylogroup homology. Four candidate genes were overexpressed in Escherichia coli BL21(DE3), refolded, and purified. Consistent with their classification as ß-barrel OMPs, circular-dichroism spectroscopy revealed the adoption of a predominantly ß-sheet secondary structure. These recombinant proteins, when screened for their ability to adhere to immobilized extracellular matrix (ECM) components, exhibited a diverse range of ligand specificities. All four proteins specifically and dose dependently adhered to bovine fibrinogen. One recombinant protein was identified as a candidate diagnostic antigen (disease specificity, 75%). Finally, when adjuvanted with aluminum hydroxide and administered to BDD-naive calves using a prime-boost vaccination protocol, these proteins were immunogenic, eliciting specific IgG antibodies. In summary, we present the description of four putative treponemal ß-barrel OMPs that exhibit the characteristics of multispecific adhesins. The observed interactions with fibrinogen may be critical to host colonization and it is hypothesized that vaccination-induced antibody blockade of these interactions will impede treponemal virulence and thus be of therapeutic value.

Probing the Solid Phase of Noble Metal Copper at Terapascal Conditions.

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.

Measurement of Body-Centered Cubic Gold and Melting under Shock Compression.

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.

Identification of Phase Transitions and Metastability in Dynamically Compressed Antimony Using Ultrafast X-Ray Diffraction.

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.

Nonisentropic Release of a Shocked Solid.

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.

Optimized x-ray sources for x-ray diffraction measurements at the Omega Laser Facility.

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.

Femtosecond diffraction studies of solid and liquid phase changes in shock-compressed bismuth.

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.

Antimicrobial use practices, attitudes and responsibilities in UK farm animal veterinary surgeons.

Increasing levels of antimicrobial resistance in human and veterinary medicine have raised concerns around the issue of overprescribing and the indiscriminate use of antimicrobials. Their use in food producing animals is under scrutiny due to the perceived risk from the zoonotic transfer of resistant pathogens from animals to humans. This study aimed to explore UK veterinary surgeons antimicrobial prescribing behaviours, their attitudes to antimicrobial resistance and their perceptions of responsibility of antimicrobial use in pigs through a questionnaire study on a census sample of 261 veterinary surgeons in England, Wales and Scotland who had a clinical caseload which included commercial pigs. The questionnaire had a useable response rate of 34.1% (n = 61/179) in eligible veterinary surgeons. Overall, veterinary surgeons reported personal confidence that their prescribing decisions were responsible however, there was concern that the prescribing behaviours of other veterinary surgeons and physicians in human medicine may be less responsible; a sociological concept known as 'othering'. In parallel, veterinary surgeons seldom identified that treatment failure was a consequence of antimicrobial resistance in their own clinical caseload, however they considered it an issue for other veterinary surgeons and for human prescribers. Veterinary surgeons consulted a wide spectrum of resources on antimicrobial use in pigs which, on occasion, contained conflicting guidance on what was defined as responsible prescribing. The decision over whether or not to prescribe an antimicrobial was influenced by numerous factors relating to the veterinary surgeons' experience and the clinical situation presented, but maintaining pig welfare was a high priority. There was a shared desire to seek alternative methods to prevent disease to antimicrobial use, however the use of diagnostics to support prescribing decisions was an infrequently reported behaviour and could play a more significant role in prescriber decisions if more cost effective and rapid tests were available. Future interventions to optimise antimicrobial use in pigs needs to focus on the evolution of antimicrobial use practices in a changing political and scientific landscape whilst also considering individual motivations and justifications for use.