Estimation of sensitivity and specificity of bulk tank milk PCR and 2 antibody ELISA tests for herd-level diagnosis of Mycoplasma bovis infection using Bayesian latent class analysis.

Mycoplasmosis (due to infection with Mycoplasma bovis) is a serious disease of beef and dairy cattle that can adversely affect health, welfare, and productivity. Mycoplasmosis can lead to a range of often severe, clinical presentations. Mycoplasma bovis infection can present either clinically or subclinically, with the potential for recrudescence of shedding in association with stressful periods. Infection can be maintained within herds because of intermittent shedding. Mycoplasma bovis is recognized as poorly responsive to treatment, which presents a major challenge for control in infected herds. Given this, particular focus is needed on biosecurity measures to prevent introduction into uninfected herds in the first place. A robust and reliable laboratory test for surveillance is important for both herd-level prevention and control. The objective of this study was to estimate the sensitivity (Se) and specificity (Sp) of 3 diagnostic tests (1 PCR and 2 ELISA tests) on bulk tank milk (BTM), for the herd-level detection of M. bovis using Bayesian latent class analysis (BLCA). In autumn 2018, BTM samples from 11,807 herds, covering the majority of the main dairy regions in Ireland had been submitted to the Department of Agriculture testing laboratory for routine surveillance and were made available for study. A stratified random sample approach was used to select a cohort of herds for testing from this larger sample set. A final study population of 728 herds had BTM samples analyzed using a Bio-X ELISA (ELISA 1), an IDvet ELISA (ELISA 2) and a PCR test. A BLCA was conducted to estimate the Se and Sp of the 3 diagnostic tests applied to BTM for the detection of herd-level infection. An overall latent class analysis was conducted on all herds within a single population (a 3-test, 1-population model). The herds were also split into 2 populations based on herd size (small herds had <82 cattle; a 3-test, 2-population model) and separately into 3 regions in Ireland (Leinster, Munster, and Connacht/Ulster; a 3-test, 3-population model). The latent variable of interest was the herd-level M. bovis infection status. In total, 363/728 (50%) were large herds, 7 (1.0%) were positive on PCR, 88 (12%) positive on ELISA 1, and 406 (56%) positive on ELISA 2. Based on the 2-population model, the Se (95% Bayesian credible interval [BCI] was 0.03 (upper and lower limits: 0.02, 0.05), 0.22 (0.18, 0.27), and 0.94 (0.88, 0.98) for PCR, ELISA 1, and ELISA 2, respectively. The Sp (95% BCI) was 0.99 (0.99, 1.0), 0.97 (0.95, 0.99), and 0.92 (0.86, 0.97) for PCR, ELISA 1, and ELISA 2, respectively. The herd-level true prevalence was estimated at 0.43 (BCI 0.35, 0.5) for smaller herds. The true prevalence was estimated at 0.62 (BCI 0.55, 0.69) for larger herds. The true prevalence was estimated at 0.56 (BCI 0.49, 0.463) in the 1-population model. For the 3-population model, the Se (95% BCI) was 0.03 (0.02, 0.05), 0.24 (0.18, 0.29), and 0.95 (0.9, 0.98) for PCR, ELISA 1, and ELISA 2 respectively. The Sp (95% BCI) was 0.99 (0.99, 1.0), 0.98 (0.96, 0.99), and 0.88 (0.79, 0.95) for PCR, ELISA 1 and ELISA 2, respectively. The herd-level true prevalence (95% BCI) was estimated at 0.65 (0.56, 0.73), 0.38 (0.28, 0.46), and 0.53 (0.4, 0.65) for populations 1, 2, and 3 respectively. Across all 3 models, the range in true prevalence was 38% to 65% of Irish dairy herds infected with M. bovis. The operating characteristics vary substantially between tests. The IDvet ELISA had a relatively high Se (the highest Se of the 3 tests studied) but it was estimated at 0.95 at its highest in 3-test, 3-population model. This test may be an appropriate test for herd-level screening or prevalence estimation within the context of the endemically infected Irish dairy cattle population. Further work is required to optimize this test and its interpretation when applied at herd-level to offset concerns related to the lower than optimal test Sp.

Sync and Swarm: Solvable Model of Nonidentical Swarmalators.

We study a model of nonidentical swarmalators, generalizations of phase oscillators that both sync in time and swarm in space. The model produces four collective states: asynchrony, sync clusters, vortexlike phase waves, and a mixed state. These states occur in many real-world swarmalator systems such as biological microswimmers, chemical nanomotors, and groups of drones. A generalized Ott-Antonsen ansatz provides the first analytic description of these states and conditions for their existence. We show how this approach may be used in studies of active matter and related disciplines.

Seroprevalence of Mycoplasma bovis in bulk milk samples in Irish dairy herds and risk factors associated with herd seropositive status.

Mycoplasma bovis is a serious disease of cattle worldwide; mastitis, pneumonia, and arthritis are particularly important clinical presentations in dairy herds. Mycoplasma bovis was first identified in Ireland in 1994, and the reporting of Mycoplasma-associated disease has substantially increased over the last 5 years. Despite the presumed endemic nature of M. bovis in Ireland, there is a paucity of data on the prevalence of infection, and the effect of this disease on the dairy industry. The aim of this observational study was to estimate apparent herd prevalence for M. bovis in Irish dairy herds using routinely collected bulk milk surveillance samples and to assess risk factors for herd seropositivity. In autumn 2018, 1,500 herds out of the 16,858 herds that submitted bulk tank milk (BTM) samples to the Department of Agriculture testing laboratory for routine surveillance were randomly selected for further testing. A final data set of 1,313 sampled herds with a BTM ELISA result were used for the analysis. Testing was conducted using an indirect ELISA kit (ID Screen Mycoplasma bovis). Herd-level risk factors were used as explanatory variables to determine potential risk factors associated with positive herd status (reflecting past or current exposure to M. bovis). A total of 588 of the 1,313 BTM samples were positive to M. bovis, providing an apparent herd prevalence of 0.45 (95% CI: 0.42, 0.47) in Irish dairy herds in autumn 2018. Multivariable analysis was conducted using logistic regression. The final model identified herd size, the number of neighboring farms, in-degree and county as statistically significant risk factors for herd BTM seropositivity to M. bovis. The results suggest a high apparent herd prevalence of seropositivity to M. bovis, and evidence that M. bovis infection is now endemic in the Irish dairy sector. In addition, risk factors identified are closely aligned to what we would expect of an infectious disease. Awareness raising and education about this important disease is warranted given the widespread nature of exposure and likely infection in Irish herds. Further work on the validation of diagnostic tests for herd-level diagnosis should be undertaken as a matter of priority.

Optimised XUV holography using spatially shaped high harmonic beams.

We present a novel method for controlling the transverse positions and relative powers of multiple high-order harmonic beams. A phase-only spatial light modulator is used to produce multiple infrared foci, the positions and intensities of which can be controlled programmably, enabling the generation and control of multiple HHG beams. To demonstrate the utility of this method we perform Fourier transform holography with separate illumination of the object and reference pinhole by a pair of HHG beams, which makes optimal use of the available photon flux. The programmable control of the spatial distribution of HHG beams demonstrated here offers new opportunities for experiments at extreme ultraviolet (XUV) wavelengths, particularly for photon intensive applications such as imaging.

Spatially resolved common-path high-order harmonic interferometry.

Spatially resolved interference is observed between high-order harmonics generated in two longitudinally separated gas targets. High-contrast modulations in the intensity of each harmonic order up to the cutoff are observed on-axis in the far field of the source as the separation between the gas targets is increased. For low-order harmonics, additional off-axis modulations are observed, which are attributed to the interference between the contributions from the long quantum trajectories from each gas target. The inherent synchronization of this setup offers the prospect for high-stability metrology of quantum states with ultrafast temporal resolutions.

Bovine Herpes Virus Type 1 (BoHV-1) seroprevalence, risk factor and Bovine Viral Diarrhoea (BVD) co-infection analysis from Ireland.

Surveillance of endemic pathogens is essential for disease control, providing an evidence base for policy and advice. Bovine Herpes Virus Type 1 (BoHV-1), the causative agent of Infectious Bovine Rhinotracheitis (IBR), has been found to have high seroprevalence within the Irish cattle population. The aim of the present study was to establish seroprevalence levels for culled cattle in Ireland aged < 30 months and to establish whether BVD exposure and other factors was associated with BoHV-1 exposure. We employed random effects logit models coupled with repeated bootstrap sampling to provide robust estimates. The final dataset contained results for 5273 animals tested over two study years, 2018 and 2020. The animal-level seroprevalence of BoHV-1 was 21.43% (1130/5273; 95%CI: 20.32-22.53%). Univariable analysis suggested that BoHV-1 seropositivity risk was associated with BVDV serodiagnosis status, age, sex, year sampled, herd type, herd-size, and metrics of movement into the herd. Final random-effects multivariable models suggested increased risk associated with increasing herd size of the last herd, movements made by animals during the previous year, and the year the animal was sampled. Despite BVDV status and sex being retained in the final model, repeated bootstrap sampling of the regression model to estimate biased-corrected 95%CI suggested that these associations were not robust. The overall apparent prevalence of BoHV-1 exposure for culled cattle in Ireland declined in 2020 relative to 2018 (from 23.32 to 17.61%). Herd-size and the movement of animals were found to be important factors associated with animal-level risk, but there was less statistical support for sex-based or BVDV status associations.

Pulse compression with time-domain optimized chirped mirrors.

Dispersive optical interference coatings (chirped mirrors - CMs) are designed by computer optimization of an analytically calculated initial multilayer. Traditionally, the relevant properties of the CM (reflectance and the frequency-dependence of the phase shift upon reflection) are optimized to match frequency-domain targets. We propose a novel target function that quantifies directly the capability of a multilayer to control the temporal shape of the reflected optical pulse. Employing this time-domain analysis/optimization one can design dispersive multilayers having air as medium of incidence and supporting the generation of pulses with durations in the sub-5-fs-range, as demonstrated in a proof-of-principle compression experiment.

Quantal breathing frequency variation in halothane anaesthetised neonatal rats.

We examined the changes in cardioventilatory synchronisation and breathing frequency variability that occur during early postnatal development in anaesthetised rats. Five-minute periods of heart rate and inspiratory timing data were recorded from 26 halothane anaesthetised, spontaneously breathing rats aged 2-14 days. The presence of cardioventilatory synchronisation was determined by examining the timing relationship between inspiratory onset and the preceding ECG R waves. We observed synchronisation at all ages, and the degree of synchronisation present (measured as the Shannon entropy of the interval between inspiration and the immediately preceding R wave) did not correlate with age. Frequent apnoeas were observed in the respiratory frequency time series. The duration of these apnoeas was close to either one or two times the duration of the immediately preceding breath. We suggest that these "dropped breaths" may be the consequence of a resetting of the respiratory oscillator just prior to initiation of the breath, or a gating process beneath the oscillator that intermittently blocks the mechanical initiation of breaths. Dropped breaths were seen commonly in rats up to 11 days of age, but rarely in 11-14-day old rats, and were not associated with the presence or absence of cardioventilatory synchronisation.

Dietary status of trained female cyclists.

Dietary status was evaluated in eight highly trained female cyclists. Each cyclist kept a 3-day weighed food record. Diets were analyzed for nutrient content using a computerized software package. Blood was also obtained and evaluated for hemoglobin, hematocrit, and albumin. For an athletic group, the cyclists' diets were found to be low in energy (85% RDA) and carbohydrate (4.4 gm/kg body weight per day). Mean daily dietary intakes were well below the RDAs for folacin (76% RDA), magnesium (81%), iron (59%), and zinc (48%). In addition, more than one-third of the cyclists failed to consume 67% of the RDA for the following micronutrients: pyridoxine, folacin, cobalamin, vitamin E, magnesium, iron, and zinc. Hemoglobin (135 gm/L), hematocrit (0.39), and albumin (45 gm/L) values were all normal, although most hemoglobin values were in the lower 50% of normal range. Foods such as meats, poultry, fish, beans, peas, and nuts were low or absent from the diets of most athletes. Dietary quality in this group of female cyclists could have been greatly improved with the addition of more of those foods. These athletes could benefit from nutrition education and diet counseling.

Alterations in dietary carbohydrate, protein, and fat intake and mood state in trained female cyclists.

Seven highly trained female cyclists (age 22 +/- 5 yr, height 165 +/- 6 cm, weight 60 +/- 5 kg, VO2max 55 +/- 6 ml.min-1.kg-1, mean +/- SD) consumed, for 1 wk each, isocaloric diets containing varying levels of carbohydrate, protein, and fat designated as low carbohydrate (LCHO), moderate carbohydrate (MCHO), and high carbohydrate (HCHO). Diets were administered in random order, and each subject consumed all three diet treatments. At the end of each weekly diet treatment, subjects rode on a cycle ergometer at 80% VO2max until fatigued. Cyclists continued light training during the diet treatments. Following each diet treatment and immediately prior to the fatiguing cycle ergometer ride, cyclists completed a Profile of Mood States (POMS) questionnaire. The POMS yields measures of tension (T), depression (D), anger (A), vigor (V), fatigue (F), and confusion (C), as well as providing a total mood score (TMS). Results indicated that subjects on LCHO had significantly (P less than or equal to 0.05) greater T, D, A, and TMS and less V compared with MCHO and HCHO. There were no significant differences between MCHO and HCHO. In the present study, LCHO in conjunction with training and exercise adversely affected the mood state of trained female cyclists as compared with MCHO and HCHO diets.

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Simple technique for generating trains of ultrashort pulses.

A simple method for generating trains of high-contrast femtosecond pulses is proposed and demonstrated: a linearly polarized, frequency-chirped laser pulse is passed through a multiple-order wave plate and a linear polarizer. It is shown theoretically that this arrangement forms a train of laser pulses, and in experiments the production of a train of approximately 100 pulses, each of 200 fs duration, is demonstrated. In combination with an acousto-optic programmable dispersive filter this technique could be used to generate and control pulse trains with chirped spacing. Pulse trains of this type have widespread applications in ultrafast optics.

Generation of a train of ultrashort pulses from a compact birefringent crystal array.

A linear array of n calcite crystals is shown to allow the generation of a high contrast (>10:1) train of 2(n) high energy (>100 microJ) pulses from a single ultrafast laser pulse. Advantage is taken of the pulse-splitting properties of a single birefringent crystal, where an incident laser pulse can be split into two pulses with orthogonal polarizations and equal intensity, separated temporally in proportion to the thickness of the crystal traversed and the difference in refractive indices of the two optic axes. In the work presented here an array of seven calcite crystals of sequentially doubled thickness is used to produce a train of 128 pulses, each of femtosecond duration. Readily versatile properties such as the number of pulses in the train and variable mark-space ratio are realized from such a setup.

Accidental hypothermia: a review of 62 cases.

A retrospective review of all patients seen in an urban city-county emergency department over a 32-month period with a primary or associated diagnosis of hypothermia was performed using the emergency department encounter form and the inpatient chart of 62 cases (59 patients) with core temperatures of 35 C (95 F) or below. With this relatively large population, a general conclusion was reached about the presentation and natural history of this interesting entity. This permitted a defensible treatment regimen which is currently employed a this institution and which is offered for institutions in similar settings. The variance in clinical signs, laboratory values, electrocardiographic findings and complications encountered in this study are detailed against the background of a review of the findings of the current literature.