Exerting pulling forces in fluids by directional disassembly of microcrystalline fibres.

Biomolecular polymerization motors are biochemical systems that use supramolecular (de-)polymerization to convert chemical potential into useful mechanical work. With the intent to explore new chemomechanical transduction strategies, here we show a synthetic molecular system that can generate forces via the controlled disassembly of self-organized molecules in a crystal lattice, as they are freely suspended in a fluid. An amphiphilic monomer self-assembles into rigid, high-aspect-ratio microcrystalline fibres. The assembly process is regulated by a coumarin-based pH switching motif. The microfibre crystal morphology determines the monomer reactivity at the interface, resulting in anisotropic etching. This effect exerts a directional pulling force on microscopic beads adsorbed on the crystal surface through weak multivalent interactions. We use optical-tweezers-based force spectroscopy to extract mechanistic insights into this process, quantifying a stall force of 2.3 pN (±0.1 pN) exerted by the ratcheting mechanism produced by the disassembly of the microfibres.

Sample size estimation to substantiate freedom from disease for clustered binary data with a specific risk profile.

Disease cases are often clustered within herds or generally groups that share common characteristics. Sample size formulae must adjust for the within-cluster correlation of the primary sampling units. Traditionally, the intra-cluster correlation coefficient (ICC), which is an average measure of the data heterogeneity, has been used to modify formulae for individual sample size estimation. However, subgroups of animals sharing common characteristics, may exhibit excessively less or more heterogeneity. Hence, sample size estimates based on the ICC may not achieve the desired precision and power when applied to these groups. We propose the use of the variance partition coefficient (VPC), which measures the clustering of infection/disease for individuals with a common risk profile. Sample size estimates are obtained separately for those groups that exhibit markedly different heterogeneity, thus, optimizing resource allocation. A VPC-based predictive simulation method for sample size estimation to substantiate freedom from disease is presented. To illustrate the benefits of the proposed approach we give two examples with the analysis of data from a risk factor study on Mycobacterium avium subsp. paratuberculosis infection, in Danish dairy cattle and a study on critical control points for Salmonella cross-contamination of pork, in Greek slaughterhouses.

Viral co-infection, autoimmunity, and CSF HIV antibody profiles in HIV central nervous system escape.

Antiretroviral therapy (ART) suppresses plasma and cerebrospinal fluid (CSF) HIV replication. Neurosymptomatic (NS) CSF escape is a rare exception in which CNS HIV replication occurs in the setting of neurologic impairment. The origins of NS escape are not fully understood. We performed a case-control study of asymptomatic (AS) escape and NS escape subjects with HIV-negative subjects as controls in which we investigated differential immunoreactivity to self-antigens in the CSF of NS escape by employing neuroanatomic CSF immunostaining and massively multiplexed self-antigen serology (PhIP-Seq). Additionally, we utilized pan-viral serology (VirScan) to deeply profile the CSF anti-viral antibody response and metagenomic next-generation sequencing (mNGS) for pathogen detection. We detected Epstein-Barr virus (EBV) DNA more frequently in the CSF of NS escape subjects than in AS escape subjects. Based on immunostaining and PhIP-Seq, there was evidence for increased immunoreactivity against self-antigens in NS escape CSF. Finally, VirScan revealed several immunodominant epitopes that map to the HIV envelope and gag proteins in the CSF of AS and NS escape subjects. Whether these additional inflammatory markers are byproducts of an HIV-driven process or whether they independently contribute to the neuropathogenesis of NS escape will require further study.

Risk factors for a high somatic cell count at the first milk recording in a large sample of UK dairy herds.

The dry period is important for the cure of existing intramammary infection (IMI) and the acquisition of new IMI. Somatic cell count (SCC) at both the last milk recording before drying off and at the first milk recording following calving can be used on farm to describe the dynamics of IMI during the dry period. The aims were to quantify the association between the main risk factors collected from milk recording data and the occurrence of a high SCC in early lactation as well as to partition the observed variation into the prevalence of high SCC in within-herd and between-herd variation. Milk recording data collected between 2004 and 2006 from 2,000 herds in England and Wales were used. Cows with an SCC ≥200,000 cells/mL were classified as high, and other cows as low. The median prevalences of the high classification were 42 and 21% at the last milk recording before drying off and the first milk recording following calving, respectively. Cows classified high or producing more milk before drying off as well as cows of greater parity or recorded in early lactation were more likely classified high at the first recording following calving. Cows from herds in which the prevalences of the high classification or the probability of remaining or becoming high over the dry period were elevated during the previous year were more likely classified as high at the first recording following calving. Half of the variability in the proportion of cows with a high SCC after calving originated at the herd level. The other half was unexplained within herd, but by between-year variability. Most cow-level predictors were important in explaining individual cow performance, but accounted for little of the overall between-herd variability. Of the predictors identified as important at the cow level, only milk yield at drying off was important in explaining the between-herd variability.

Multigenerational laboratory culture of pelagic ctenophores and CRISPR-Cas9 genome editing in the lobate Mnemiopsis leidyi.

Despite long-standing experimental interest in ctenophores due to their unique biology, ecological influence and evolutionary status, previous work has largely been constrained by the periodic seasonal availability of wild-caught animals and difficulty in reliably closing the life cycle. To address this problem, we have developed straightforward protocols that can be easily implemented to establish long-term multigenerational cultures for biological experimentation in the laboratory. In this protocol, we describe the continuous culture of the Atlantic lobate ctenophore Mnemiopsis leidyi. A rapid 3-week egg-to-egg generation time makes Mnemiopsis suitable for a wide range of experimental genetic, cellular, embryological, physiological, developmental, ecological and evolutionary studies. We provide recommendations for general husbandry to close the life cycle of Mnemiopsis in the laboratory, including feeding requirements, light-induced spawning, collection of embryos and rearing of juveniles to adults. These protocols have been successfully applied to maintain long-term multigenerational cultures of several species of pelagic ctenophores, and can be utilized by laboratories lacking easy access to the ocean. We also provide protocols for targeted genome editing via microinjection with CRISPR-Cas9 that can be completed within ~2 weeks, including single-guide RNA synthesis, early embryo microinjection, phenotype assessment and sequence validation of genome edits. These protocols provide a foundation for using Mnemiopsis as a model organism for functional genomic analyses in ctenophores.

Use of individual cow milk recording data at the start of lactation to predict the calving to conception interval.

Milk recording data collected in 2,128 dairy herds in England and Wales between 2004 and 2006 were used to predict the calving to conception intervals. The average cumulative milk production was 8,200 kg. Conception (or not) within 5 intervals measured in days (20 to 60 d, 61 to 81 d, 82 to 102 d, 103 to 123 d, 124 to 144 d) was modeled as a function of milk yields and milk constituents at the start of lactation using multilevel discrete-time survival models. Milk yield, weight and percentage of fat, protein, and lactose, and somatic cell counts on the first 2 test-days of lactation were corrected for either stage of lactation alone or stage of lactation and time of year. Five hundred and 1,628 herds, respectively, were used for parameter estimation and cross-validation. Covariates were retained in the final model if their coefficient was at least twice its standard error and their inclusion resulted in a decrease in the deviance. Overall, 73% of cows recalved. The percentage of cows that had conceived by d 20, 61, 82, 103, 124, and 145 were 0.5, 7.3, 17.9, 29.3, 38.7, and 46, respectively. The probability of conception before 145 d in milk increased with lower milk production on the second test-day, higher percentage of protein on the second test-day, and higher percentage of lactose on the first test-day. Positive associations were of a limited magnitude but nonetheless significant with the percentage of protein on the first test-day, the percentage of butterfat on the first test-day, and somatic cell count on both test-days. The model predicted the probability of conception in the cross validation data set very well. Despite the common use of fat to protein ratio as a measure of energy balance, this parameter exhibited wide variation with stage of lactation and time of the year and had a much-reduced ability to predict an early conception compared with other combinations of milk quantity and constituents.

Sampling strategies for monitoring lameness in dairy cattle.

Evaluating the prevalence of lameness within herds of dairy cattle is important for management and certification purposes; however, sampling strategies that could reduce the time taken for an assessment would be valuable. The prevalence of lame and severely lame cows on 224 United Kingdom dairy farms was available for analysis. Presence of more than 1 severely lame cow on a farm was a useful indication of a lameness problem. The vast majority (80%) of the 182 farms that had > or = 1 severely lame cow present had an overall lameness prevalence >25%, whereas only 24% of the 42 farms that had no severely lame cows had an overall prevalence >25%. Information was available on individual milking order through the parlor on the day of the lameness assessment. On 37 farms where cows were housed in a group, lameness prevalence was 11.9% greater in the last third compared with the first third of the milking order. For 36 herds that were larger than 100 cows, sampling a maximum of 100 cows from the middle of the milking order produced an estimate of prevalence within 5% of the true prevalence on 83% of farms. A reasonable sampling strategy may, therefore, be to observe up to 100 cows from the middle of the milking order. Also, presence of severely lame cows at the end of milking may be useful for identifying those farms likely to benefit from further support.

Urinary incontinence in 9-16 year olds with cystic fibrosis compared to other respiratory conditions and a normal group.

BACKGROUND: Individuals with cystic fibrosis (CF) are deemed at risk of developing urinary incontinence (UI) due to repeated coughing and other factors causing increased pressure on the pelvic floor. Increased incidence of UI is recognised in women and increasingly in men and children. However, there is little comparison with normal controls and other respiratory conditions with chronic cough. Our aim was to report the incidence, degree and impact of UI in 9-16 year olds related to clinical status in CF, compared to these. METHODS: 9-16 year olds were invited to fill in a self-administered anonymous/confidential questionnaire at clinic. Data recorded were sex, age, height, weight, spirometry expressed as percentage predicted. Normal controls - age and sex only recorded. RESULTS: No significant differences were found between incidence of UI (21% CF; 22% respiratory; and 17% normal controls, P=0.43). No relationship found between respiratory or nutritional status and UI. Laughing, exercise and cough were the most common causes of UI. No difference between groups for age range, physiotherapy, breathlessness, antibiotics, urinary tract infections and menarche. Only 6% reported more than a few drops of UI. CONCLUSION: Incidence of urinary incontinence is no different between 9-16 year old girls and boys with CF, and controls.

Cow, farm, and herd management factors in the dry period associated with raised somatic cell counts in early lactation.

This study investigated cow characteristics, farm facilities, and herd management strategies during the dry period to examine their joint influence on somatic cell counts (SCC) in early lactation. Data from 52 commercial dairy farms throughout England and Wales were collected over a 2-yr period. For the purpose of analysis, cows were separated into those housed for the dry period (6,419 cow-dry periods) and those at pasture (7,425 cow-dry periods). Bayesian multilevel models were specified with 2 response variables: ln SCC (continuous) and SCC >199,000 cells/mL (binary), both within 30 d of calving. Cow factors associated with an increased SCC after calving were parity, an SCC >199,000 cells/mL in the 60 d before drying off, increasing milk yield 0 to 30 d before drying off, and reduced DIM after calving at the time of SCC estimation. Herd management factors associated with an increased SCC after calving included procedures at drying off, aspects of bedding management, stocking density, and method of pasture grazing. Posterior predictions were used for model assessment, and these indicated that model fit was generally good. The research demonstrated that specific dry-period management strategies have an important influence on SCC in early lactation.

Proton-Stabilized Photochemically Reversible E/ Z Isomerization of Spiropyrans.

Spiropyrans undergo Cspiro-O bond breaking to their ring-open protonated E-merocyanine form upon protonation and irradiation via an intermediate protonated Z-merocyanine isomer. We show that the extent of acid-induced ring opening is controlled by matching both the concentration and strength of the acid used and with strong acids full ring opening to the Z-merocyanine isomer occurs spontaneously allowing its characterization by 1H NMR spectroscopy as well as UV/vis spectroscopy, and reversible switching between Z/ E-isomerization by irradiation with UV and visible light. Under sufficiently acidic conditions, both E- and Z-isomers are thermally stable. Judicious choice of acid such that its p Ka lies between that of the E- and Z-merocyanine forms enables thermally stable switching between spiropyran and E-merocyanine forms and hence pH gating between thermally irreversible and reversible photochromic switching.

Cow, farm, and management factors during the dry period that determine the rate of clinical mastitis after calving.

The purpose of the research was to investigate cow characteristics, farm facilities, and herd management strategies during the dry period to examine their joint influence on the rate of clinical mastitis after calving. Data were collected over a 2-yr period from 52 commercial dairy farms throughout England and Wales. Cows were separated for analysis into those housed for the dry period (8,710 cow-dry periods) and those at pasture (9,964 cow-dry periods). Multilevel models were used within a Bayesian framework with 2 response variables, the occurrence of a first case of clinical mastitis within the first 30 d of lactation and time to the first case of clinical mastitis during lactation. A variety of cow and herd management factors were identified as being associated with an increased rate of clinical mastitis and these were found to occur throughout the dry period. Significant cow factors were increased parity and at least one somatic cell count > or = 200,000 cells/mL in the 90 d before drying off. A number of management factors related to hygiene were significantly associated with an increased rate of clinical mastitis. These included measures linked to the administration of dry-cow treatments and management of the early and late dry-period accommodation and calving areas. Other farm factors associated with a reduced rate of clinical mastitis were vaccination with a leptospirosis vaccine, selection of dry-cow treatments for individual cows within a herd rather than for the herd as a whole, routine body condition scoring of cows at drying off, and a pasture rotation policy of grazing dry cows for a maximum of 2 wk before allowing the pasture to remain nongrazed for a period of 4 wk. Models demonstrated a good ability to predict the farm incidence rate of clinical mastitis in a given year, with model predictions explaining over 85% of the variability in the observed data. The research indicates that specific dry-period management strategies have an important influence on the rate of clinical mastitis during the next lactation.

Early-life risk factors identified for owner-reported feline overweight and obesity at around two years of age.

Obesity is considered the second most common health problem in pet cats in developed countries. This study used prospective data from a longitudinal study of pet cats ('C.L.A.W.S.', www.bristol.ac.uk/vetscience/claws) to identify early-life risk factors for feline overweight/obesity occurring at around two years of age. Data were collected via five owner-completed questionnaires (for cats aged two-six months, six months, 12 months, 18 months and two years respectively) completed between May 2011 and April 2015. Owner-reported body condition scores (BCS) of cats at age two years, assessed using images from the 9-point BCS system (Laflamme, 1997), were categorised into a dichotomous variable: overweight/obese (BCS 6-9) and not overweight (BCS 1-5) and used as the dependent variable. Of the 375 cats with owner-reported BCS, 25.3% were overweight or obese at two years of age. Multivariable logistic regression models were built using stepwise forward-selection. To account for potential hierarchical clustering due to multi-cat households two-level random intercept models were considered but clustering had no impact on the analysis. Models were compared using Wald tests. Six factors were significantly associated with overweight/obesity at two years of age: being overweight or obese at one year of age (OR=10.6, 95%CI 4.4-25.3); owner belief that BCS 7 was the ideal weight (OR=33.2, 95%CI 8.5-129.4), or that BCS represented overweight cats but they would not be concerned if their cat were classified in this category (OR=2.7, 95%CI 1.2-6.2), at questionnaire five completion; vets advising owners that the cat should lose weight, or making no comment on their weight, between one and two years of age (OR=12.1, 95%CI 3.2-44.9 and OR=3.9, 95%CI 1.5-10.3 respectively); owners giving their cat treats when they "felt happy" with them at 18 months of age (OR=2.7, 95%CI 1.0 - 7.3); feeding ≥250g wet food daily between two and six months of age (OR=2.7, 95%CI 1.2-5.9), and feeding dry food as the only or major part (>50%) of the diet at two years of age (OR=2.1, 95%CI 1.0-4.2). These findings have the potential to reduce the current high prevalence of a widespread problem by informing preventive advice, and as such improving the health and welfare of pet cats.

Chirality controlled responsive self-assembled nanotubes in water.

The concept of using chirality to dictate dimensions and to store chiral information in self-assembled nanotubes in a fully controlled manner is presented. We report a photoresponsive amphiphile that co-assembles with its chiral counterpart to form nanotubes and demonstrate how chirality can be used to effect the formation of either micrometer long, achiral nanotubes or shorter (∼300 nm) chiral nanotubes that are bundled. The nature of these assemblies is studied using a variety of spectroscopic and microscopic techniques and it is shown that the tubes can be disassembled with light, thereby allowing the chiral information to be erased.

Seasonal variation of bulk milk somatic cell counts in UK dairy herds: investigations of the summer rise.

Individual cow somatic cell count (SCC) patterns were explored over a one year period in 33 dairy herds to investigate the reason for a summer rise in bulk milk somatic cell counts (BMSCC). Cow test day somatic cell counts were categorised according to the magnitude of change since the previous test day reading, to examine which categories were responsible for the summer increase. Multilevel models using Markov chain Monte Carlo methods were specified to estimate the number of somatic cells/ml produced by different cell count categories. Stage of lactation and parity were accounted for in the models. There was an increase in the proportion of cows that remained above 200,000 cells/ml for two consecutive recordings in summer and this group of cows were responsible for 70.8% of the increase in somatic cells/ml produced from May to September compared with October to March. There was no evidence that a greater new infection rate (somatic cell counts moving from below 100,000 cells/ml to over 200,000 cells/ml) contributed to the increased summer bulk milk somatic cell counts. There was no indication that a general small increase in all somatic cell counts played an important role in the increased summer somatic cell counts. Markov chain Monte Carlo methods provided a valuable and flexible platform for parameter estimation in reasonably complex multilevel models.

Sequential sampling: a novel method in farm animal welfare assessment.

Lameness in dairy cows is an important welfare issue. As part of a welfare assessment, herd level lameness prevalence can be estimated from scoring a sample of animals, where higher levels of accuracy are associated with larger sample sizes. As the financial cost is related to the number of cows sampled, smaller samples are preferred. Sequential sampling schemes have been used for informing decision making in clinical trials. Sequential sampling involves taking samples in stages, where sampling can stop early depending on the estimated lameness prevalence. When welfare assessment is used for a pass/fail decision, a similar approach could be applied to reduce the overall sample size. The sampling schemes proposed here apply the principles of sequential sampling within a diagnostic testing framework. This study develops three sequential sampling schemes of increasing complexity to classify 80 fully assessed UK dairy farms, each with known lameness prevalence. Using the Welfare Quality herd-size-based sampling scheme, the first 'basic' scheme involves two sampling events. At the first sampling event half the Welfare Quality sample size is drawn, and then depending on the outcome, sampling either stops or is continued and the same number of animals is sampled again. In the second 'cautious' scheme, an adaptation is made to ensure that correctly classifying a farm as 'bad' is done with greater certainty. The third scheme is the only scheme to go beyond lameness as a binary measure and investigates the potential for increasing accuracy by incorporating the number of severely lame cows into the decision. The three schemes are evaluated with respect to accuracy and average sample size by running 100 000 simulations for each scheme, and a comparison is made with the fixed size Welfare Quality herd-size-based sampling scheme. All three schemes performed almost as well as the fixed size scheme but with much smaller average sample sizes. For the third scheme, an overall association between lameness prevalence and the proportion of lame cows that were severely lame on a farm was found. However, as this association was found to not be consistent across all farms, the sampling scheme did not prove to be as useful as expected. The preferred scheme was therefore the 'cautious' scheme for which a sampling protocol has also been developed.

A Bayesian micro-simulation to evaluate the cost-effectiveness of interventions for mastitis control during the dry period in UK dairy herds.

Importance of the dry period with respect to mastitis control is now well established although the precise interventions that reduce the risk of acquiring intramammary infections during this time are not clearly understood. There are very few intervention studies that have measured the clinical efficacy of specific mastitis interventions within a cost-effectiveness framework so there remains a large degree of uncertainty about the impact of a specific intervention and its costeffectiveness. The aim of this study was to use a Bayesian framework to investigate the cost-effectiveness of mastitis controls during the dry period. Data were assimilated from 77 UK dairy farms that participated in a British national mastitis control programme during 2009-2012 in which the majority of intramammary infections were acquired during the dry period. The data consisted of clinical mastitis (CM) and somatic cell count (SCC) records, herd management practices and details of interventions that were implemented by the farmer as part of the control plan. The outcomes used to measure the effectiveness of the interventions were i) changes in the incidence rate of clinical mastitis during the first 30days after calving and ii) the rate at which cows gained new infections during the dry period (measured by SCC changes across the dry period from <200,000cells/ml to >200,000cells/ml). A Bayesian one-step microsimulation model was constructed such that posterior predictions from the model incorporated uncertainty in all parameters. The incremental net benefit was calculated across 10,000 Markov chain Monte Carlo iterations, to estimate the cost-benefit (and associated uncertainty) of each mastitis intervention. Interventions identified as being cost-effective in most circumstances included selecting dry-cow therapy at the cow level, dry-cow rations formulated by a qualified nutritionist, use of individual calving pens, first milking cows within 24h of calving and spreading bedding evenly in dry-cow yards. The results of this study highlighted the efficacy of specific mastitis interventions in UK conditions which, when incorporated into a costeffectiveness framework, can be used to optimize decision making in mastitis control. This intervention study provides an example of how an intuitive and clinically useful Bayesian approach can be used to form the basis of an on-farm decision support tool.

Interferon fever: absence of human leukocytic pyrogen response to recombinant alpha-interferon.

A sensitive in vitro assay for generation of human leukocytic pyrogen has been used to study the pathogenesis of fever accompanying administration of human alpha-interferon. Unlike other potent pyrogens, two recombinant interferon preparations tested over a wide concentration range did not stimulate release of leukocytic pyrogen. This result suggests that interferon may cause fever by a novel mechanism not dependent on leukocytic pyrogen.

Exceeding tertiary standards with a pond/reed bed system in Norway.

At Vidaråsen in Norway sewage from a community consisting of 160 people, including a dairy, a food processing workshop, a bakery and a laundry is treated using a pond/reed bed system. The system consists of sludge settlement, pre-treatment surface/vertical-flow constructed wetlands, a 5 m deep enhanced facultative pond, three stabilization ponds, a planted sand filter and finally two horizontal-flow constructed wetlands filled with lightweight aggregate (Filtralite-P). The enhanced facultative pond and the primary stabilization pond are equipped with Flowform-cascades, which provide year-round aeration, rhythmical treatment and mixing of wastewater in the ponds. Treatment performance during the first five years has been high and unaffected by harsh winter conditions. Average phosphorus discharge from the system is 0.25 mg/l with total nitrogen 4 mg/l, total organic carbon (TOC) 5 mg/l and thermo-tolerant coliforms < 100/100 ml. The system is ecologically diverse and supports abundant populations of higher aquatic life such as ducks, amphibians and carp.

Assessing changes in the UK pet cat and dog populations: numbers and household ownership.

The main aim of this study was to replicate methodology used to estimate the size of the UK pet cat and dog populations in 2006 and the proportion of households owning cats/dogs in 2007, to produce updated data to compare trends in ownership and population sizes. A cross-sectional study design was used to collect telephone interview data from 3155 households in the UK. 2011 UK human census data were used to predict the size of the cat and dog populations owned by households in the UK in 2011. Of the households, 23 per cent (714/3155) owned one or more cats and 30 per cent (940/3155) owned one or more dogs. There was some overlap in pet ownership with 7 per cent (210/3155) of households owning both one or more cats and one or more dogs. There was a small but significant decrease in the proportion of households that owned one or more cats in 2011 compared with 2007, with no change in the proportion owning dogs. However, overall, the total number of cats and dogs that were estimated to be owned by UK households did not change significantly between 2006 and 2011. The estimated size (and 95% CIs) of the pet cat and dog populations in the UK in 2011 was 10,114,764 cats (9,138,603-11,090,924) and 11,599,824 dogs (10,708,070-12,491,578).