Spatio-temporal forecasting using wavelet transform-based decision trees with application to air quality and covid-19 forecasting.

We develop a new method that combines a decision tree with a wavelet transform to forecast time series data with spatial spillover effects. The method can not only improve prediction but also give good interpretability of the time series mechanism. As a feature exploration method, the wavelet transform represents information at different resolution levels, which may improve the performance of decision trees. The method is applied to simulated data, air pollution and COVID time series data sets. In the simulation, Haar, LA8, D4 and D6 wavelets are compared, with the Haar wavelet having the best performance. In the air pollution application, by using wavelet transform-based decision trees, the temporal effect of air quality index including autoregressive and seasonal effects can be described as well as the spatial correlation effect. To describe the spillover spatial effect in contiguous regions, a spatial weight is constructed to improve the modeling performance. The results show that air quality index has autoregressive, seasonal and spatial spillover effects. The wavelet transformed variables have a better forecasting performance and enhanced interpretability than the original variables. For the COVID time series of cumulative cases, spatial weighted variables are not selected which shows the lock-down policies are truly effective.

Measuring Sheep Tails: A Preliminary Study Using Length (Mm), Vulva Cover Assessment, and Number of Tail Joints.

Docking sheep tails is a long-standing practice that, when done at the recommended length, reduces the risk of flystrike. The recommended length is to cover the vulva of ewes and to a similar length in males. This length is often equated to three coccygeal joints left intact, and there are many other ways the recommended length is described by researchers, industry, and government. This study compared the observer consistency and retest consistency using three different tail length measurement methods: vulva cover assessment, length (mm), and joint palpation. The tails of 51 yearling and 48 weaner Merino ewes were assessed by two observers. Length and vulva cover assessment methods provided the most reliable results, and joint palpation was the least reliable method of tail measurement. In the sample, tails that covered the vulva of yearlings and weaners measured 57.6 mm (n = 14) and 63.7 mm (n = 30) on average, respectively, and contained two coccygeal joints (more than two coccygeal vertebrae). Tails that did not cover the vulva of yearlings and weaners measured 41.3 mm (n = 36) and 52.8 mm (n = 17) on average, respectively, and had less than two coccygeal joints. The two most reliable methods enable valid comparison to the best practice recommendations.

Contraflows and cycling safety: Evidence from 22 years of data involving 508 one-way streets.

Contraflow cycling on one-way streets is a low cost intervention that research shows can improve the cycling experience and increase participation. Evidence from several studies suggest that cyclists on contraflows have a lower crash risk. However, implementing contraflow cycling is often controversial, including in the United Kingdom (UK). In this paper we examine whether contraflow cycling on one-way streets alters crash or casualty rates for pedal cyclists. Focusing on inner London boroughs between 1998 and 2019, we identified 508 road segments where contraflow cycling was introduced on one-way streets. We identified road traffic crashes occurring within 10 m of these segments and labelled them as pre-contraflow, contraflow or contraflow removed crashes. We calculated rates using the number of crashes or casualties divided by the time exposed and generated 95 % confidence intervals using bootstrap resampling. We adjusted the rates for changes in cordon cycling volume and injury severity reporting. There were 1498 crashes involving pedal cyclists: 788 pre-contraflow, 703 contraflow and 7 following contraflow removal. There was no change in adjusted overall pedal cyclist crash or casualty rates when contraflow cycling was introduced. Proximity to a junction doubled the crash rate. The crash rate when pedal cyclists were travelling contraflow was the same as those travelling with flow. We have found no evidence that introducing contraflow cycling increases the crash or casualty rate for pedal cyclists. It is possible that such rates may indeed fall when contraflow cycling is introduced if more accurate spatio-temporal cycling volume data was available. We recommend all one-way streets are evaluated for contraflow cycling but encourage judicious junction design and recommend UK legislative change for mandatory-two-way cycling on one-way streets unless exceptional circumstances exist.

Integrated eicosanoid lipidomics and gene expression reveal decreased prostaglandin catabolism and increased 5-lipoxygenase expression in aggressive subtypes of endometrial cancer.

Eicosanoids comprise a diverse group of bioactive lipids which orchestrate inflammation, immunity, and tissue homeostasis, and whose dysregulation has been implicated in carcinogenesis. Among the various eicosanoid metabolic pathways, studies of their role in endometrial cancer (EC) have very much been confined to the COX-2 pathway. This study aimed to determine changes in epithelial eicosanoid metabolic gene expression in endometrial carcinogenesis; to integrate these with eicosanoid profiles in matched clinical specimens; and, finally, to investigate the prognostic value of candidate eicosanoid metabolic enzymes. Eicosanoids and related mediators were profiled using liquid chromatography-tandem mass spectrometry in fresh frozen normal, hyperplastic, and cancerous (types I and II) endometrial specimens (n = 192). Sample-matched epithelia were isolated by laser capture microdissection and whole genome expression analysis was performed using microarrays. Integration of eicosanoid and gene expression data showed that the accepted paradigm of increased COX-2-mediated prostaglandin production does not apply in EC carcinogenesis. Instead, there was evidence for decreased PGE2 /PGF2α inactivation via 15-hydroxyprostaglandin dehydrogenase (HPGD) in type II ECs. Increased expression of 5-lipoxygenase (ALOX5) mRNA was also identified in type II ECs, together with proportional increases in its product, 5-hydroxyeicosatetraenoic acid (5-HETE). Decreased HPGD and elevated ALOX5 mRNA expression were associated with adverse outcome, which was confirmed by immunohistochemical tissue microarray analysis of an independent series of EC specimens (n = 419). While neither COX-1 nor COX-2 protein expression had prognostic value, low HPGD combined with high ALOX5 expression was associated with the worst overall and progression-free survival. These findings highlight HPGD and ALOX5 as potential therapeutic targets in aggressive EC subtypes. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Dietary intake in the early years and its relationship to BMI in a bi-ethnic group: the Born in Bradford 1000 study.

OBJECTIVE: To assess relationships between dietary intake at age 12, 18 and 36 months and BMI Z-scores at age 36 months in a bi-ethnic group. DESIGN: A prospective cohort study comparing cross-sectional and longitudinal data. Exposures included dietary intake at 12, 18 and 36 months (FFQ) with an outcome of BMI Z-score at age 36 months. SETTING: Born in Bradford 1000 study, Bradford, UK. SUBJECTS: Infants at age 12 months (n 722; 44 % White British, 56 % Pakistani), 18 months (n 779; 44 % White British, 56 % Pakistani) and 36 months (n 845; 45 % White British, 55 % Pakistani). RESULTS: Diet at age 12 months was not associated with BMI Z-score at age 36 months. Higher consumption of vegetables at 18 and 36 months was associated with a lower BMI Z-score at 36 months (model coefficient (95 % CI): -0·20 (-0·36, -0·03) and -0·16 (-0·31, -0·02), respectively). Higher consumption of high-fat chips at age 36 months was associated with a lower BMI Z-score at age 36 months (-0·16 (-0·32, 0·00)). Overall, White British children had higher 36-month BMI Z-scores than Pakistani children (adjusted mean difference (95 % CI): 0·21 (0·02, 0·41)). CONCLUSIONS: Our findings indicate that dietary intake at 18 and 36 months was somewhat related to BMI Z-score at age 36 months and suggest the importance of early interventions aimed at establishing healthy eating behaviours.

Lymphatic cannulation models in sheep: Recent advances for immunological and biomedical research.

Lymphatic cannulation models are useful tools for studying the immunobiology of the lymphatic system and the immunopathology of specific tissues in diseases. Sheep cannulations have been used extensively, as models for human physiology, fetal and neonatal development, human diseases, and for studies of ruminant pathobiology. The development of new and improved cannulation techniques in recent years has meant that difficult to access sites, such as mucosal associated tissues, are now more readily available to researchers. This review highlights the new approaches to cannulation and how these, in combination with advanced omics technologies, will direct future research using the sheep model.

Using Longitudinal Assessment on Extensively Managed Ewes to Quantify Welfare Compromise and Risks.

This study examined variation in the welfare of extensively managed ewes and potential welfare risks. A total of 100 Merino ewes (aged 2-4 years) were individually identified and examined at three key stages: pregnancy, lactation and weaning. Eight animal-based welfare measures were used to assess welfare: flight distance, body condition score (BCS), fleece condition, skin lesions, tail length, dag score, lameness and mastitis. Data were analysed by ANOVA and McNemar's statistics. Overall, the average BCS of the group was in agreement with industry recommendations. However, a number of animals were classified with inadequate condition (either too thin or too fat) across the three observation periods. The presence of heavy dags was greatest at mid-lactation (87%, P < 0.0001), lameness was greatest at weaning (14%, P = 0.01), clinical mastitis was 1% annually, and five ewes were lost from the study. Ewes had better health at mid-pregnancy compared to mid-lactation and weaning. The main welfare issues identified were under and over feeding, ewe mortality, lameness, ecto-parasites (flystrike) and mastitis, all of which have the potential to be reduced with improved management practices. Future welfare assessment programs must consider that significant variation in on-farm welfare will occur in extensively managed systems and this needs to be accounted for when evaluating farms.

A statistical method for analysing cospeciation in tritrophic ecology using electrical circuit theory.

We introduce a new method to test efficiently for cospeciation in tritrophic systems. Our method utilises an analogy with electrical circuit theory to reduce higher order systems into bitrophic data sets that retain the information of the original system. We use a sophisticated permutation scheme that weights interactions between two trophic layers based on their connection to the third layer in the system. Our method has several advantages compared to the method of Mramba et al. [Mramba, L. K., S. Barber, K. Hommola, L. A. Dyer, J. S. Wilson, M. L. Forister and W. R. Gilks (2013): "Permutation tests for analyzing cospeciation in multiple phylogenies: applications in tri-trophic ecology," Stat. Appl. Genet. Mol. Biol., 12, 679-701.]. We do not require triangular interactions to connect the three phylogenetic trees and an easily interpreted p-value is obtained in one step. Another advantage of our method is the scope for generalisation to higher order systems and phylogenetic networks. The performance of our method is compared to the methods of Hommola et al. [Hommola, K., J. E. Smith, Y. Qiu and W. R. Gilks (2009): "A permutation test of host-parasite cospeciation," Mol. Biol. Evol., 26, 1457-1468.] and Mramba et al. [Mramba, L. K., S. Barber, K. Hommola, L. A. Dyer, J. S. Wilson, M. L. Forister and W. R. Gilks (2013): "Permutation tests for analyzing cospeciation in multiple phylogenies: applications in tri-trophic ecology," Stat. Appl. Genet. Mol. Biol., 12, 679-701.] at the bitrophic and tritrophic level, respectively. This was achieved by evaluating type I error and statistical power. The results show that our method produces unbiased p-values and has comparable power overall at both trophic levels. Our method was successfully applied to a dataset of leaf-mining moths, parasitoid wasps and host plants [Lopez-Vaamonde, C., H. Godfray, S. West, C. Hansson and J. Cook (2005): "The evolution of host use and unusual reproductive strategies in achrysocharoides parasitoid wasps," J. Evol. Biol., 18, 1029-1041.], at both the bitrophic and tritrophic levels.

Adaptation of Chain Event Graphs for use with Case-Control Studies in Epidemiology.

Case-control studies are used in epidemiology to try to uncover the causes of diseases, but are a retrospective study design known to suffer from non-participation and recall bias, which may explain their decreased popularity in recent years. Traditional analyses report usually only the odds ratio for given exposures and the binary disease status. Chain event graphs are a graphical representation of a statistical model derived from event trees which have been developed in artificial intelligence and statistics, and only recently introduced to the epidemiology literature. They are a modern Bayesian technique which enable prior knowledge to be incorporated into the data analysis using the agglomerative hierarchical clustering algorithm, used to form a suitable chain event graph. Additionally, they can account for missing data and be used to explore missingness mechanisms. Here we adapt the chain event graph framework to suit scenarios often encountered in case-control studies, to strengthen this study design which is time and financially efficient. We demonstrate eight adaptations to the graphs, which consist of two suitable for full case-control study analysis, four which can be used in interim analyses to explore biases, and two which aim to improve the ease and accuracy of analyses. The adaptations are illustrated with complete, reproducible, fully-interpreted examples, including the event tree and chain event graph. Chain event graphs are used here for the first time to summarise non-participation, data collection techniques, data reliability, and disease severity in case-control studies. We demonstrate how these features of a case-control study can be incorporated into the analysis to provide further insight, which can help to identify potential biases and lead to more accurate study results.

Learning Through Chain Event Graphs: The Role of Maternal Factors in Childhood Type 1 Diabetes.

Chain event graphs (CEGs) are a graphical representation of a statistical model derived from event trees. They have previously been applied to cohort studies but not to case-control studies. In this paper, we apply the CEG framework to a Yorkshire, United Kingdom, case-control study of childhood type 1 diabetes (1993-1994) in order to examine 4 exposure variables associated with the mother, 3 of which are fully observed (her school-leaving-age, amniocenteses during pregnancy, and delivery type) and 1 with missing values (her rhesus factor), while incorporating previous type 1 diabetes knowledge. We conclude that the unknown rhesus factor values were likely to be missing not at random and were mainly rhesus-positive. The mother's school-leaving-age and rhesus factor were not associated with the diabetes status of the child, whereas having at least 1 amniocentesis procedure and, to a lesser extent, birth by cesarean delivery were associated; the combination of both procedures further increased the probability of diabetes. This application of CEGs to case-control data allows for the inclusion of missing data and prior knowledge, while investigating associations in the data. Communication of the analysis with the clinical expert is more straightforward than with traditional modeling, and this approach can be applied retrospectively or when assumptions for traditional analyses are not held.

Development of an ovine efferent mammary lymphatic cannulation model with minimal tissue damage.

BACKGROUND: Two mammary lymphatic cannulation models in sheep have been described with minimal use in the past 50 years. The purpose of this study was to investigate a new surgical technique to allow long term monitoring of mammary lymph flow and composition from the mammary glands, with rapid ewe recovery and minimal complications post-surgery. RESULTS: We developed a modified methodology for cannulating the efferent mammary lymphatic from the mammary lymph node with minimum tissue damage. Compared to the previous models, our method required only a small incision on the aponeurosis of the external abdominal oblique muscles and thus reduced the difficulties in suturing the aponeurosis. It allowed for lymph collection and assessment for at least one week post-surgery with concurrent milk collection. CONCLUSION: This method allows for good ewe recovery post-surgery and in vivo sampling of efferent mammary lymph from the mammary lymph nodes in real-time and comparison with milk parameters.

Molecular epidemiology of an outbreak of clinical mastitis in sheep caused by Mannheimia haemolytica.

The aetiology and epidemiology of outbreaks of clinical mastitis in sheep under extensive pastoral conditions are incompletely understood. The objective of this study was to conduct a detailed investigation of a clinical mastitis outbreak that affected more than 10% of 230 at-risk ewes on a sheep and grain producing property in south east Australia during drought conditions in 2009. Milk samples were collected aseptically from all affected ewes and plated on sheep blood agar for bacterial identification. M. haemolytica was isolated from 80% of the samples that yielded cultivable microorganisms and thus was the main microorganism responsible for the outbreak. Analysis of the restriction endonuclease cleavage patterns of the isolates using pulsed field gel electrophoresis revealed some evidence of clonality, suggesting the possibility of horizontal transmission, but there was also considerable diversity between the clusters of closely related isolates. Multilocus sequence typing of the M. haemolytica isolates revealed most of the isolates belonged to ST1 with no association between the PFGE and MLST fingerprints of the isolates. Resistance to neomycin, streptomycin and sulphafurazole was detected in some of the isolates, but they were all susceptible to penicillin, ampicillin, ceftiofur, amoxycillin/clavulanic acid, ciprofloxacin, tetracycline, erythromycin and trimethoprim. This is the first published record of a comparison of the strains of M. haemolytica involved in a clinical mastitis outbreak in sheep and demonstrates the importance of this pathogen in sheep production systems, particularly during adverse climatic conditions and increased stocking rate.

The upper respiratory tract is a natural reservoir of haemolytic Mannheimia species associated with ovine mastitis.

Lamb suckling has been suggested to be an important way of infecting a ewe's udder with different bacteria, including Mannheimia haemolytica. To test the potential role of lambs in transferring Mannheimia species to the ewe's udder, the restriction endonuclease cleavage patterns of isolates obtained from nasopharyngeal swabs were compared with those obtained from cases of mastitis. Sterile cotton swabs were used to collect nasopharyngeal samples from 50 ewes and 36 lambs from three flocks. M. haemolytica and Mannheimia glucosida as well as haemolytic Mannheimia ruminalis-like organisms were detected in the upper respiratory tract of lambs and ewes. Comparison of the restriction endonuclease cleavage patterns of the isolates suggested that the M. haemolytica isolates obtained from different milk samples from ewes with mastitis were more clonal than those obtained from the nasal swabs. However, some nasal isolates within both Mannheimia species had restriction endonuclease cleavage patterns identical to those obtained from milk samples from ewes with mastitis, indicating that lambs may have a role in transferring these organisms to the udder. More clonality was observed between the M. glucosida isolates than between M. haemolytica isolates.

Genetic diversity of Mycoplasma arginini isolates based on multilocus sequence typing.

The contribution of Mycoplasma arginini to mycoplasmosis in small ruminants remains unclear because it is recovered from both healthy and diseased animals. In order to gain a better understanding of any relationships between isolates from different sites and different geographical locations, we developed a method for genotyping M. arginini using multilocus sequence typing (MLST). A MLST scheme based on five housekeeping genes was used to characterize M. arginini isolates from flocks of sheep and goats. A high level of genetic variability was detected between strains and within herds.

Human Wound Infection with Mannheimia glucosida following Lamb Bite.

Mannheimia spp. are veterinary pathogens that can cause mastitis and pneumonia in domestic cattle and sheep. While Mannheimia glucosida can be found as normal flora in oral and respiratory mucosa in sheep, there have been no reported cases of human infection with this organism.

Sequence diversity, cytotoxicity and antigenic similarities of the leukotoxin of isolates of Mannheimia species from mastitis in domestic sheep.

Species within the genus Mannheimia are among the most important causes of ovine mastitis. Isolates of these species can express leukotoxin A (LktA), a primary virulence factor of these bacteria. To examine the significance of variation in the LktA, the sequences of the lktA genes in a panel of isolates from cases of ovine mastitis were compared. The cross-neutralising capacities of rat antisera raised against LktA of one Mannheimia glucosida, one haemolytic Mannheimia ruminalis, and two Mannheimia haemolytica isolates were also examined to assess the effect that variation in the lktA gene can have on protective immunity against leukotoxins with differing sequences. The lktA nucleotide distance between the M. haemolytica isolates was greater than between the M. glucosida isolates, with the M. haemolytica isolates divisible into two groups based on their lktA sequences. Comparison of the topology of phylogenetic trees of 16S rDNA and lktA sequences revealed differences in the relationships between some isolates, suggesting horizontal gene transfer. Cross neutralisation data obtained with monospecific anti-LktA rat sera were used to derive antigenic similarity coefficients for LktA from the four Mannheimia species isolates. Similarity coefficients indicated that LktA of the two M. haemolytica isolates were least similar, while LktA from M. glucosida was most similar to those for one of the M. haemolytica isolates and the haemolytic M. ruminalis isolate. The results suggested that vaccination with the M. glucosida leukotoxin would generate the greatest cross-protection against ovine mastitis caused by Mannheimia species with these alleles.

Permutation tests for analyzing cospeciation in multiple phylogenies: applications in tri-trophic ecology.

There is a need for a reliable statistical test which is appropriate for assessing cospeciation of more than two phylogenies. We have developed an algorithm using a permutation method that can be used to test for and infer tri-trophic evolutionary relationships of organisms given both their phylogenies and pairwise interactions. An overall statistic has been developed based on the dominant eigenvalue of a covariance matrix, and compared to values of the statistic computed when tree labels are permuted. The resulting overall p-value is used to test for the presence or absence of cospeciation in a tri-trophic system. If cospeciation is detected, we propose new test statistics based on partial correlations to uncover more details about the relationships between multiple phylogenies. One of the strengths of our method is that it allows more parasites than hosts or more hosts than parasites, with multiple associations and more than one parasite attached to a host (or one parasite attached to multiple hosts). The new method does not require any parametric assumptions of the distribution of the data, and unlike the old methods, which utilize several pairwise steps, the overall statistic used is obtained in one step. We have applied our method to two published datasets where we obtained detailed information about the strength of associations among species with calculated partial p-values and one overall p-value from the dominant eigenvalue test statistic. Our permutation method produces reliable results with a clear procedure and statistics applied in an intuitive manner. Our algorithm is useful in testing evidence for three-way cospeciation in multiple phylogenies with tri-trophic associations and determining which phylogenies are involved in cospeciation.

BAYESIAN ALIGNMENT OF SIMILARITY SHAPES.

We develop a Bayesian model for the alignment of two point configurations under the full similarity transformations of rotation, translation and scaling. Other work in this area has concentrated on rigid body transformations, where scale information is preserved, motivated by problems involving molecular data; this is known as form analysis. We concentrate on a Bayesian formulation for statistical shape analysis. We generalize the model introduced by Green and Mardia for the pairwise alignment of two unlabeled configurations to full similarity transformations by introducing a scaling factor to the model. The generalization is not straight-forward, since the model needs to be reformulated to give good performance when scaling is included. We illustrate our method on the alignment of rat growth profiles and a novel application to the alignment of protein domains. Here, scaling is applied to secondary structure elements when comparing protein folds; additionally, we find that one global scaling factor is not in general sufficient to model these data and, hence, we develop a model in which multiple scale factors can be included to handle different scalings of shape components.

Molecular epidemiology of Mannheimia haemolytica and Mannheimia glucosida associated with ovine mastitis.

While Mannheimia haemolytica and Mannheimia glucosida have been recognized as causes of intramammary infection in sheep, there has been no investigation of the epidemiology of the strains involved. Pulsed field gel electrophoresis was used to study the molecular epidemiology of isolates of these 2 species associated with ovine mastitis. Ten distinct strains were recognized among 12 M. haemolytica isolates, and 7 distinct strains among 13 M. glucosida isolates. The results demonstrate a high diversity of isolates with the ability to cause ovine mastitis. However, the presence of some identical isolates may suggest the possibility of horizontal transmission of these species in some flocks, possibly through lamb sucking, and/or differences in the capacity of some isolates to cause mastitis in sheep.

Predicting phenolic acid absorption in Caco-2 cells: a theoretical permeability model and mechanistic study.

There is a considerable need to rationalize the membrane permeability and mechanism of transport for potential nutraceuticals. The aim of this investigation was to develop a theoretical permeability equation, based on a reported descriptive absorption model, enabling calculation of the transcellular component of absorption across Caco-2 monolayers. Published data for Caco-2 permeability of 30 drugs transported by the transcellular route were correlated with the descriptors 1-octanol/water distribution coefficient (log D, pH 7.4) and size, based on molecular mass. Nonlinear regression analysis was used to derive a set of model parameters a', ß', and b' with an integrated molecular mass function. The new theoretical transcellular permeability (TTP) model obtained a good fit of the published data (R² = 0.93) and predicted reasonably well (R² = 0.86) the experimental apparent permeability coefficient (P(app)) for nine non-training set compounds reportedly transported by the transcellular route. For the first time, the TTP model was used to predict the absorption characteristics of six phenolic acids, and this original investigation was supported by in vitro Caco-2 cell mechanistic studies, which suggested that deviation of the P(app) value from the predicted transcellular permeability (P(app)(trans)) may be attributed to involvement of active uptake, efflux transporters, or paracellular flux.