MiniBooNE and MicroBooNE Combined Fit to a 3+1 Sterile Neutrino Scenario.

This Letter presents the results from the MiniBooNE experiment within a full "3+1" scenario where one sterile neutrino is introduced to the three-active-neutrino picture. In addition to electron-neutrino appearance at short baselines, this scenario also allows for disappearance of the muon-neutrino and electron-neutrino fluxes in the Booster Neutrino Beam, which is shared by the MicroBooNE experiment. We present the 3+1 fit to the MiniBooNE electron-(anti)neutrino and muon-(anti)neutrino data alone and in combination with MicroBooNE electron-neutrino data. The best-fit parameters of the combined fit with the exclusive charged-current quasielastic analysis (inclusive analysis) are Δm^{2}=0.209 eV^{2}(0.033 eV^{2}), |U_{e4}|^{2}=0.016(0.500), |U_{µ4}|^{2}=0.500(0.500), and sin^{2}(2θ_{µe})=0.0316(1.0). Comparing the no-oscillation scenario to the 3+1 model, the data prefer the 3+1 model with a Δχ^{2}/d.o.f.=24.7/3(17.3/3), a 4.3σ(3.4σ) preference assuming the asymptotic approximation given by Wilks's theorem.

A description of interestrus and interservice intervals and associated fertility in 16 United Kingdom dairy herds.

Understanding the changes that have occurred in reproductive management and physiology of the dairy cow is necessary to reverse the trend of declining fertility. In this study we analyzed the intervals between estrus events, as detected using tail chalk, in a population of 6,092 dairy cows from 16 herds in the central United Kingdom. Intervals were categorized by absence or presence of an insemination at the first estrus event, being designated interestrus intervals and interservice intervals, respectively. Modal interestrus interval was 21 d, as has been commonly described. Interservice interval was significantly longer than interestrus interval, with a modal value of 22 d. Multivariable analysis identified explanatory variables for intervals between estrus events, with random effects modeling accounting for clustering within herds and within individual cows. Intraclass correlation coefficients indicated that herd identity has a negligible effect, whereas animal identity accounts for 9% of interval variation. Parity, days in milk, insemination at the first estrus of the interval, and interval number within lactation all affected the interval. Logistic regression modeling indicated that interval length is also associated with the outcome of pregnancy. These findings indicate that intervals following an insemination are both longer than previously described and longer than interestrus intervals with no insemination event. The data also suggest that longer interservice interval length may be more conducive to subsequent conception than shorter intervals. Several factors appear to influence interestrus events and further work is required to investigate the underlying physiological mechanisms of these phenomena.

Significant Excess of Electronlike Events in the MiniBooNE Short-Baseline Neutrino Experiment.

The MiniBooNE experiment at Fermilab reports results from an analysis of ν_{e} appearance data from 12.84×10^{20} protons on target in neutrino mode, an increase of approximately a factor of 2 over previously reported results. A ν_{e} charged-current quasielastic event excess of 381.2±85.2 events (4.5σ) is observed in the energy range 200

First Measurement of Monoenergetic Muon Neutrino Charged Current Interactions.

We report the first measurement of monoenergetic muon neutrino charged current interactions. MiniBooNE has isolated 236 MeV muon neutrino events originating from charged kaon decay at rest (K^{+}→µ^{+}ν_{µ}) at the NuMI beamline absorber. These signal ν_{µ}-carbon events are distinguished from primarily pion decay in flight ν_{µ} and ν[over ¯]_{µ} backgrounds produced at the target station and decay pipe using their arrival time and reconstructed muon energy. The significance of the signal observation is at the 3.9σ level. The muon kinetic energy, neutrino-nucleus energy transfer (ω=E_{ν}-E_{µ}), and total cross section for these events are extracted. This result is the first known-energy, weak-interaction-only probe of the nucleus to yield a measurement of ω using neutrinos, a quantity thus far only accessible through electron scattering.

A versatile apparatus for two-dimensional atomtronic quantum simulation.

We report on the implementation of a novel optical setup for generating high-resolution customizable potentials to address ultracold bosonic atoms in two dimensions. Two key features are developed for this purpose. The customizable potential is produced with a direct image of a spatial light modulator, conducted with an in-vacuum imaging system of high numerical aperture. Custom potentials are drawn over an area of 600×400 µm with a resolution of 0.9 µm. The second development is a two-dimensional planar trap for atoms with an aspect ratio of 900 and spatial extent of Rayleigh range 1.6 × 1.6 mm, providing near-ballistic in-planar movement. We characterize the setup and present a brief catalog of experiments to highlight the versatility of the system.

Dark Matter Search in a Proton Beam Dump with MiniBooNE.

The MiniBooNE-DM Collaboration searched for vector-boson mediated production of dark matter using the Fermilab 8-GeV Booster proton beam in a dedicated run with 1.86×10^{20} protons delivered to a steel beam dump. The MiniBooNE detector, 490 m downstream, is sensitive to dark matter via elastic scattering with nucleons in the detector mineral oil. Analysis methods developed for previous MiniBooNE scattering results were employed, and several constraining data sets were simultaneously analyzed to minimize systematic errors from neutrino flux and interaction rates. No excess of events over background was observed, leading to a 90% confidence limit on the dark matter cross section parameter, Y=ε^{2}α_{D}(m_{χ}/m_{V})^{4}≲10^{-8}, for α_{D}=0.5 and for dark matter masses of 0.01

Impact of feeding and housing systems on disease incidence in dairy calves.

Contentious issues in calf rearing include milk feeding level and single versus group housing. The current study was performed on a high-producing 170 Holstein cow dairy farm to investigate the impact of nutrition and housing on disease incidence. Calves (n=100) were allocated in birth order to one of two commonly used feeding strategies. Group A calves were group housed from birth and fed ad libitum milk replacer (MR) via a computerised machine using a single teat, with weaning commencing at 63 days. Group R calves were initially housed in individual pens receiving 2.5 litres of MR twice daily via a bucket until three weeks of age when they were group housed and fed 3 litres of MR twice daily via a group trough with weaning commencing at 56 days. In total, 80 (80 per cent) calves suffered from at least one incident of disease during the period from birth to 12 weeks. Group A calves had a greater risk of disease than group R calves (diarrhoea: OR 3.86 (95 per cent CI 1.67 to 8.9); pneumonia: OR 5.80 (95 per cent CI 2.33 to 14.44)). There was a 5.1 per cent incidence of failure of passive transfer of Ig assessed via measurement of plasma total protein concentrations at 48 hours of age. It is hypothesised that the increased diarrhoea risk in group A calves was most likely associated with group housing, while the increased pneumonia risk was associated with the use of a single teat allowing increased transmission of pathogens from calf to calf.

Whole-flock, metaphylactic tilmicosin failed to eliminate contagious ovine digital dermatitis and footrot in sheep: a cluster randomised trial.

The aim of this study was to evaluate the clinical success of whole-flock systemic tilmicosin and enhanced biosecurity in eliminating active contagious ovine digital dermatitis (CODD) from sheep flocks. Thirty flocks in the UK were randomly allocated to receive either treatment as usual (as per the farmer's normal routine) or whole-flock treatment with tilmicosin, together with isolation and extended treatment of clinically affected individuals and isolation and treatment of purchased sheep during the study period. All flocks were visited once at onset of the trial to examine all sheep. One year later, all sheep were re-examined to determine the presence/absence of clinical lesions. The primary outcome was the clinical elimination of CODD from flocks. Secondary outcomes were reduction in prevalence of CODD, clinical elimination of footrot and reduction in prevalence of footrot. The analysis included 11 control flocks and 13 intervention flocks, with initially 3460 and 4686 sheep, respectively. For CODD: at follow-up, in the intervention group, 6/13 (46 per cent) flocks had a prevalence of zero compared with 1/11 (9 per cent) in the control group (P=0.12). For footrot: at follow-up, no flocks had a prevalence of zero. Therefore, the intervention is not recommended for the elimination of CODD or footrot in the UK.

Sheep and farm level factors associated with contagious ovine digital dermatitis: A longitudinal repeated cross-sectional study of sheep on six farms.

Contagious ovine digital dermatitis (CODD) is a cause of severe lameness in sheep in the UK currently affecting approximately 50% of farms. Six farms were studied in North Wales to investigate (1) the prevalence dynamics of CODD, (2) the association between sheep with CODD and potential risk factors and (3) the impact of CODD on lameness in sheep. The farms were visited at approximately two-month intervals between June 2012 and October 2013 and 6515 sheep were examined. The mean sheep level prevalence of CODD varied between farms (2.5-11.9%). Within farms, prevalence may increase in the late summer/early autumn and after housing. Environmental risk factors included larger flocks, lowland pasture, lush pasture and poached pasture. Co-infection of a foot with footrot was strongly associated with CODD in that foot (OR: 7.7 95% CI: 3.9-15.5 P<0.001) but negatively associated with co-infection of a foot with interdigital dermatitis (OR: 0.04 95% CI: 0.02-0.1 P<0.001). Reinfection with CODD was observed in 78 individual sheep but there was no re-infection at foot level. Lameness on all farms reduced during the study and seasonal changes in lameness followed similar patterns to those for CODD. Infection with CODD leads to a greater increase in locomotion score compared to footrot or interdigital dermatitis and CODD lesion grade was strongly associated with being lame. Sheep with CODD in more than one foot were more likely to be lame (OR: 25.0 95% CI: 12.5-49.9 P<0.001) than those with just one foot affected (OR:10.0 95% CI: 8.6-11.6 P<0.001). The biggest risk factor for CODD is co-infection with footrot and therefore control of footrot should help reduce the risk of CODD on affected farms. Furthermore environmental risk factors for CODD are similar to those for footrot adding weight for control strategies that target both diseases in tandem. The routine repeated gathering of sheep for the purposes of treating all lame sheep might be an effective control strategy for lameness on some sheep farms. Effective systemic immunity to CODD in sheep appears to be lacking, as 78 sheep were observed to be re-infected with CODD during the survey. However, there is epidemiological evidence that there may be some local immunity within the foot warranting further investigation.

The gastrointestinal tract as a potential infection reservoir of digital dermatitis-associated treponemes in beef cattle and sheep.

Digital dermatitis (DD) is an important cause of lameness in dairy cattle worldwide. It has now been reported in beef cattle and also sheep (contagious ovine digital dermatitis [CODD]). Three Treponema phylogroups are consistently isolated from lesions, Treponema medium-like, Treponema phagedenis-like, and Treponema pedis. The gastrointestinal (GI) tract and feces are suggested sites of treponemal infection in dairy cattle; however, isolation of DD-associated treponemes from these areas has previously failed. This study surveyed gingival tissues, rectal tissues, and feces of beef cattle and sheep for the molecular presence (PCR) and isolation of the three cultivable DD-treponeme phylogroups. Of the sheep gingival (n = 40) and rectal (n = 40) tissues, 1/40 gingival tissues was positive for DD-associated treponemes (T. pedis), as were 3/40 rectal tissues (one containing T. medium-like and two containing T. pedis). No DD-associated treponeme DNA was amplified from beef cattle rectal tissues (n = 40); however, 4/40 beef gingival tissues were positive for DD-associated treponemes (all containing T. phagedenis-like). A T. phagedenis-like DD-associated treponeme was isolated from the rectal tissue of a CODD symptomatic sheep. Beef cattle (n = 41) and sheep (n = 79) feces failed to amplify DD-associated Treponema DNA. Twenty-two treponemes were isolated from sheep feces; however, upon phylogenetic analysis, these clustered with the considered nonpathogenic treponemes. This study detected DD-associated treponemes in the GI tract tissues of sheep and beef cattle and successfully isolated a DD-associated treponeme from ruminant rectal tissue. This gives evidence that the GI tract is an important infection reservoir of DD-associated treponemes in multiple DD-infected species.

Husbandry, health and biosecurity of the smallholder and pet pig population in England.

Three hundred and thirteen pet and smallholder pig owners in England responded to an online questionnaire regarding husbandry and healthcare of their pigs. There was a lack of knowledge of the legislation regarding Department for Environment, Food and Rural Affairs (DEFRA) registration, animal movements and feeding of domestic food waste. Only 83.8 per cent of respondents had registered their pigs with DEFRA, while 17.7 per cent were not familiar with the movement regulations, and 23.9 per cent were feeding their pigs with household scraps. Contact with veterinary surgeons may be positively associated with DEFRA registration, legal feeding practices and knowledge of vaccination. Furthermore, the veterinary surgeon was considered to be the primary source of husbandry and healthcare knowledge. This paper identifies the pet and smallholder pig population as a potential risk for the incursion and spread of infectious disease, while highlighting the need for improved owner education.

A molecular epidemiology of treponemes in beef cattle digital dermatitis lesions and comparative analyses with sheep contagious ovine digital dermatitis and dairy cattle digital dermatitis lesions.

Bovine digital dermatitis (BDD) is an infective foot disease commonly reported in dairy cattle where Treponema are considered as the primary causative infectious agents. There still remains little definitive information on the etiology of BDD in beef cattle suggesting further investigations are warranted. Beef BDD lesions (n=34) and healthy beef foot tissues (n=38) were analysed by PCR for three BDD-associated Treponema phylogroups and also for Dichelobacter nodosus and Fusobacterium necrophorum. Spirochete culture was attempted on all BDD lesion samples. One or more BDD-associated Treponema phylogroups were detected in 100% of beef BDD lesions. "Treponema medium/Treponema vincentii-like", "Treponema phagedenis-like" and Treponema pedis spirochetes were identified in 27/34 (79%), 31/34 (91%) and 24/34 (71%) of BDD lesions, respectively. No BDD-associated treponeme DNA was amplified from beef healthy foot tissues. D. nodosus and F. necrophorum were present in 24/34 (71%) and 15/34 (44%) of lesions and 10/38 (26%) and 12/38 (32%) of healthy foot tissues, respectively. Twenty spirochetes were isolated from beef BDD lesions; 19 were representatives of the three BDD-associated Treponema phylogroups. One spirochete isolate shared less than 97% 16S rRNA gene similarity to the three cultivable BDD-associated Treponema phylogroups and therefore may represent a novel taxa of Treponema. Upon comparison, sheep contagious ovine digital dermatitis (CODD), dairy cattle and beef cattle BDD lesions appear to have extremely similar bacteriological data and therefore provides evidence of a shared etiopathogenesis posing concerns for cross-species transmission.

Identification and quantification of factors affecting neonatal immunological transfer in dairy calves in the UK.

The object of the study was to quantify the prevalence of failure of passive transfer in UK dairy farms and to identify variables that had a significant impact on the rate of immunological transfer. In a six-month study of 444 calvings from seven UK dairy farms, 26 per cent of calves failed to receive adequate immunoglobulin transfer as judged by a plasma total protein (pTP) concentration less than 5.6 g/dl. Colostrum immunoglobulin concentration, indirectly measured using Brix refractometry, showed wide variations with samples ranging from 10.3 to 34.7 Brix units. Thirty-seven per cent of samples were below the suggested cut-off Brix score for colostrum quality of 22 per cent. Potential associations between covariates and plasma protein concentration were investigated using multiple linear regression models. The covariate with the greatest impact on the pTP concentration was the farm on which the calf was born (P<0.05). A significant but small association was demonstrated between colostrum immunoglobulin concentration and calf pTP concentration (P<0.01). Multiple linear regression models suggested that the time of colostrum collection after calving, parity of the dam, and the individual farm were associated with the Brix measurements (P<0.05). This study suggested that veterinary review of colostrum protocols on farm with emphasis on prompt collection and dosing after calving remains a simple and effective measure to improve passive transfer and thus calf health on UK dairy farms.

Clinical and radiographic features of contagious ovine digital dermatitis and a novel lesion grading system.

Contagious ovine digital dermatitis (CODD) is an infectious foot disease of sheep causing severe lameness. Diagnosis is currently made using broad anecdotal descriptions. The aim of this study was to systematically and formally describe the clinical presentation of the disease in terms of (1) a lesion grading system; (2) associated radiographic changes and (3) severity of associated lameness. A five-point lesion grading system was developed and applied to 908 sheep affected by CODD from six farms. Sheep with lesions typical of each grade were euthanased and their feet radiographed. Radiographic abnormalities including soft tissue and bony changes were evident in feet with lesions graded 2-5. In order to quantify the welfare impact of CODD, all the 908 sheep were locomotion scored. Five hundred and eighty-five (64.5% (95% CI 61.4% to 67.6%)) were lame. The locomotion score for affected sheep increased with worsening pathological changes. Once healing had begun the locomotion score decreased. In conclusion the five-point grading system may be used to clinically describe stages of CODD lesions. The radiographic changes revealed examples of deeper pathological changes and there was a strong association between the lesion grading system and locomotion score in affected sheep.

A practical tool for locomotion scoring in sheep: reliability when used by veterinary surgeons and sheep farmers.

A four-point locomotion scoring tool for sheep was developed and tested on 10 general practice veterinary surgeons (VS) and 10 sheep farmers. Thirty-four video clips of sheep displaying different locomotion scores were recorded and randomly assorted. Following a set period of training using four other video clips typical of the four locomotion scores, participants then scored the 34 test clips. The participants repeated the training and the exercise one month later. There were high levels of intraobserver repeatability: weighted κ (κW) 0.81 for VS and 0.83 for farmers. There was no difference in intraobserver repeatability between vets and farmers (Wilcoxon signed rank P=0.8). When considering the overall distribution of scores within the video package, there were high levels of interobserver repeatability: mean κW 0.73 for VS and 0.72 for farmers. However, the repeatability for the individual locomotion scores was only fair to moderate. It is therefore recommended that when observations are repeated on different occasions they are made by the same observer.

High-level association of bovine digital dermatitis Treponema spp. with contagious ovine digital dermatitis lesions and presence of Fusobacterium necrophorum and Dichelobacter nodosus.

Contagious ovine digital dermatitis (CODD) is an important foot disease in sheep, with significant animal welfare and economic implications. It is thought that CODD emerged from bovine digital dermatitis (BDD) via treponemal bacteria. With wildlife species such as elk now suffering a CODD-like disease, it is imperative to clarify these disease etiologies. A large investigation into treponemal association with CODD is warranted. CODD lesions (n = 58) and healthy sheep foot tissues (n = 56) were analyzed by PCR for the three BDD-associated Treponema phylogroups and two other lameness-associated bacteria, Dichelobacter nodosus and Fusobacterium necrophorum. Spirochete culture was also attempted on CODD lesions. "Treponema medium/Treponema vincentii-like," "Treponema phagedenis-like," and Treponema pedis spirochetes were identified in 39/58 (67%), 49/58 (85%), and 41/58 (71%) of CODD lesions, respectively. One or more BDD-associated Treponema phylogroups were detected in 100% of CODD lesions. Healthy foot tissues did not amplify BDD-associated Treponema phylogroup DNA. D. nodosus and F. necrophorum were present in 34/58 (59%) and 41/58 (71%) of CODD lesions and 22/56 (39%) and 5/56 (9%) of healthy foot tissues, respectively. Thirty-two spirochetes were isolated from CODD lesions, with representatives clustering with, and indistinguishable from, each of the three BDD-associated Treponema phylogroups based on 16S rRNA gene comparisons. This study for the first time demonstrates a high-level association for BDD treponeme phylogroups in CODD and their absence from healthy tissues, supporting the hypothesis that BDD treponemes play a primary causative role in CODD and confirming that the specific PCR assays are an effective differential diagnostic tool for CODD.

Contagious ovine digital dermatitis: an emerging disease.

The novel sheep disease, contagious ovine digital dermatitis (CODD) was first described in the UK in 1997. The disease is characterised by severe lameness associated with initial inflammation at the coronary band, followed by progressive separation of the hoof capsule from the underlying tissue. On microbiological examination, treponeme bacteria have been frequently isolated from cases of CODD, including treponemes phylogenetically identical to those associated with bovine digital dermatitis (BDD). Dichelobacter nodosus and Fusobacterium necrophorum have also been isolated from CODD lesions although their role in the pathogenesis remains uncertain. While epidemiological data indicate that the prevalence of CODD is increasing in the UK, the routes of transmission and associated risk factors have not been clearly elucidated. Evidenced-based treatment trials indicate that parenteral administration of long-acting amoxicillin is an efficacious treatment for CODD, while anecdotal evidence suggests other antibiotics, given locally and/or parenterally, may also be beneficial. Further microbiological and epidemiological research is urgently required to develop sustainable control strategies, including the development of vaccines and appropriate biosecurity and farm management protocols. In this review current knowledge of the clinical, aetiological, and epidemiological aspects of CODD is assessed as well as approaches to its control.

Presence of digital dermatitis treponemes on cattle and sheep hoof trimming equipment.

Digital dermatitis (DD) is an infectious foot disease causing severe lameness in dairy cattle (worldwide) and sheep (UK). This study investigated whether DD Treponema phylogroups can be present on equipment used to trim ruminant hooves and, therefore, consider this trimming equipment as a possible vector for the transmission of DD. Equipment was tested after being used to trim DD symptomatic and asymptomatic cattle and sheep hooves, and subsequently after disinfection of equipment. After trimming, 'Treponema medium/Treponema vincentii-like', 'Treponema phagedenis-like' and 'Treponema denticola/T putidum-like' DD spirochaetes, were shown to be present on 23/37 (62%), 21/37 (57%) and 20/37 (54%) of knives, respectively. After disinfection, detection rates for the DD treponemes were 9/37 (24%), 6/37 (16%) and 3/37 (8%), respectively. Following culture of a swab, an isolate belonging to the T phagedenis-like spirochaetes was identified from a knife sample after trimming a DD positive cow. No isolates were obtained from knife samples after disinfection. This new data has, for the first time, identified treponemes in the farm environment, and highlighted disinfection of hoof trimming equipment between animals and between farms, as a logical precaution to limit the spread of DD.