Machine learning modeling to predict causes of infectious abortions and perinatal mortalities in cattle.

A plethora of infectious and non-infectious causes of bovine abortions and perinatal mortalities (APM) have been reported in literature. However, due to financial limitations or a potential zoonotic impact, many laboratories only offer a standard analytical panel, limited to a preestablished number of pathogens. To improve the cost-efficiency of laboratory diagnostics, it could be beneficial to design a targeted analytical approach for APM cases, based on maternal and environmental characteristics associated with the prevalence of specific abortifacient pathogens. The objective of this retrospective observational study was to implement a machine learning pipeline (MLP) to predict maternal and environmental factors associated with infectious APM. Our MLP based on a greedy ensemble approach incorporated a standard tuning grid of four models, applied on a dataset of 1590 APM cases with a positive diagnosis that was achieved by analyzing an extensive set of abortifacient pathogens. Production type (dairy/beef), gestation length, and season were successfully predicted by the greedy ensemble, with a modest prediction capacity which ranged between 63 and 73 %. Besides the predictive accuracy of individual variables, our MLP hierarchically identified predictor importance causes of associated environmental/maternal characteristics of APM. For instance, in APM cases that happened in beef cows, season at APM (spring/summer) was the most important predictor with a relative importance of 24 %. Furthermore, at the last trimester of gestation Trueperella pyogenes and Neospora caninum were the most important predictors of APM with a relative importance of 22 and 17 %, respectively. Interestingly, herd size came out as the most relevant predictor for APM in multiparous dams, with a relative importance of 12 %. Based on these and other mix of predicted environmental/maternal and pathogenic potential causes, it could be concluded that implementing our MLP may be beneficial to design a more cost-effective, case-specific diagnostic approach for bovine APM cases at the diagnostic laboratory level.

Mouse models of NADK2 deficiency analyzed for metabolic and gene expression changes to elucidate pathophysiology.

NADK2 encodes the mitochondrial form of nicotinamide adenine dinucleotide (NAD) kinase, which phosphorylates NAD. Rare recessive mutations in human NADK2 are associated with a syndromic neurological mitochondrial disease that includes metabolic changes, such as hyperlysinemia and 2,4 dienoyl CoA reductase (DECR) deficiency. However, the full pathophysiology resulting from NADK2 deficiency is not known. Here, we describe two chemically induced mouse mutations in Nadk2-S326L and S330P-which cause severe neuromuscular disease and shorten lifespan. The S330P allele was characterized in detail and shown to have marked denervation of neuromuscular junctions by 5 weeks of age and muscle atrophy by 11 weeks of age. Cerebellar Purkinje cells also showed progressive degeneration in this model. Transcriptome profiling on brain and muscle was performed at early and late disease stages. In addition, metabolomic profiling was performed on the brain, muscle, liver and spinal cord at the same ages and on plasma at 5 weeks. Combined transcriptomic and metabolomic analyses identified hyperlysinemia, DECR deficiency and generalized metabolic dysfunction in Nadk2 mutant mice, indicating relevance to the human disease. We compared findings from the Nadk model to equivalent RNA sequencing and metabolomic datasets from a mouse model of infantile neuroaxonal dystrophy, caused by recessive mutations in Pla2g6. This enabled us to identify disrupted biological processes that are common between these mouse models of neurological disease, as well as those processes that are gene-specific. These findings improve our understanding of the pathophysiology of neuromuscular diseases and describe mouse models that will be useful for future preclinical studies.

A realist evaluation of a collaborative model to support research co-production in long-term care settings in England: the ExCHANGE protocol.

BACKGROUND: Collaborative working between academic institutions and those who provide health and social care has been identified as integral in order to produce acceptable, relevant, and timely research, and for outputs to be useful and practical to implement. The ExCHANGE Collaboration aims to bring together researchers and people working, living in and visiting care homes to build capacity, share and mobilise knowledge, and identify key areas for future research. This paper describes an embedded, formative, realist and theory-driven evaluation which aims to gather information about how successful the ExCHANGE Collaboration is perceived to be in achieving its aims. An existing realist programme theory from the literature - Closer Collaboration - will be supplemented by two substantive theories: Co-production and Knowledge Brokering. This will result in an initial programme theory which will be tested by this formative evaluation to refine understanding of how the ExCHANGE Collaboration works. METHODS: The evaluation will employ mixed qualitative methods, including: analysis of documents such as feedback forms, Knowledge Broker journal/diary, event attendance records, risk and issues logs and other relevant paperwork gathered as part of project delivery; observations of events/activities; and interviews with care home providers and staff, care home residents, residents' family members, and researchers who are involved in the project (both project design/delivery, and also attendance or involvement in project activities/events). Framework Analysis will be used to interpret the data collected; analysis will be strategic, by focusing on particular key areas of importance in the developing theory of how the ExCHANGE Collaboration might achieve change. RESULTS: The results of this study are expected to be published in 2022. DISCUSSION: This evaluation will investigate how successful the ExCHANGE Collaboration is perceived to be in achieving its aims, in what way, in which contexts, and how this may differ for those involved. It will do this by testing an initial programme theory about how the collaboration works, for whom, under which circumstances, and in what way. Findings will be shared through written publication, an end of project learning event for those involved/interested in the project, and a lay summary to be made publically available.

The phase diagram of Ti-6Al-4V at high-pressures and high-temperatures.

We report results from a series of diamond-anvil-cell synchrotron x-ray diffraction and large-volume-press experiments, and calculations, to investigate the phase diagram of commercial polycrystalline high-strength Ti-6Al-4V alloy in pressure-temperature space. Up to ∼30 GPa and 886 K, Ti-6Al-4V is found to be stable in the hexagonal-close-packed, orαphase. The effect of temperature on the volume expansion and compressibility ofα-Ti-6Al-4V is modest. The martensiticα→ω(hexagonal) transition occurs at ∼30 GPa, with both phases coexisting until at ∼38-40 GPa the transition to theωphase is completed. Between 300 K and 844 K theα→ωtransition appears to be independent of temperature.ω-Ti-6Al-4V is stable to ∼91 GPa and 844 K, the highest combined pressure and temperature reached in these experiments. Pressure-volume-temperature equations-of-state for theαandωphases of Ti-6Al-4V are generated and found to be similar to pure Ti. A pronounced hysteresis is observed in theω-Ti-6Al-4V on decompression, with the hexagonal structure reverting back to theαphase at pressures below ∼9 GPa at room temperature, and at a higher pressure at elevated temperatures. Based on our data, we estimate the Ti-6Al-4Vα-ß-ωtriple point to occur at ∼900 K and 30 GPa, in good agreement with our calculations.

Baseline characteristics and comorbidities in the CAnadian REgistry for Pulmonary Fibrosis.

BACKGROUND: The CAnadian REgistry for Pulmonary Fibrosis (CARE-PF) is a multi-center, prospective registry designed to study the natural history of fibrotic interstitial lung disease (ILD) in adults. The aim of this cross-sectional sub-study was to describe the baseline characteristics, risk factors, and comorbidities of patients enrolled in CARE-PF to date. METHODS: Patients completed study questionnaires and clinical measurements at enrollment and each follow-up visit. Environmental exposures were assessed by patient self-report and comorbidities by the Charlson Comorbidity Index (CCI). Baseline characteristics, exposures, and comorbidities were described for the overall study population and for incident cases, and were compared across ILD subtypes. RESULTS: The full cohort included 1285 patients with ILD (961 incident cases (74.8%)). Diagnoses included connective tissue disease-associated ILD (33.3%), idiopathic pulmonary fibrosis (IPF) (24.7%), unclassifiable ILD (22.3%), chronic hypersensitivity pneumonitis (HP) (7.5%), sarcoidosis (3.2%), non-IPF idiopathic interstitial pneumonias (3.0%, including idiopathic nonspecific interstitial pneumonia (NSIP) in 0.9%), and other ILDs (6.0%). Patient-reported exposures were most frequent amongst chronic HP, but common across all ILD subtypes. The CCI was ≤2 in 81% of patients, with a narrow distribution and range of values. CONCLUSIONS: CTD-ILD, IPF, and unclassifiable ILD made up 80% of ILD diagnoses at ILD referral centers in Canada, while idiopathic NSIP was rare when adhering to recommended diagnostic criteria. CCI had a very narrow distribution across our cohort suggesting it may be a poor discriminator in assessing the impact of comorbidities on patients with ILD.

Modification of the sterol profile in milk through feeding.

The fortification of milk with phytosterols is an increasingly common practice to enhance the sterol profile and offer consumers potential health benefits. This study investigated whether cattle feed can influence the profile of phytosterols and cholesterol in the milk produced as an alternative to direct fortification of milk. Five experiments were performed using feeds commonly used by Australian dairy farmers and selected formulated rumen-protected feeds. Statistical significances were observed for some individual plant sterols and cholesterol in milk under these differing feeding regimens compared with the respective controls. In the case of the phytosterols, where the daily recommended consumption is typically 2 g per day, the total phytosterols were <0.12 mg/100 mL of milk. An experiment using a rumen-protected feed with high phytosterol levels suggested a decreased transfer of cholesterol to the milk by as much as 20%, although further work is required to confirm these preliminary results. Overall, the study suggests that different feeding practices have minimal effect on the resulting sterol profile of the milk.

Instability of pulses in gradient reaction-diffusion systems: a symplectic approach.

In a scalar reaction-diffusion equation, it is known that the stability of a steady state can be determined from the Maslov index, a topological invariant that counts the state's critical points. In particular, this implies that pulse solutions are unstable. We extend this picture to pulses in reaction-diffusion systems with gradient nonlinearity. In particular, we associate a Maslov index to any asymptotically constant state, generalizing existing definitions of the Maslov index for homoclinic orbits. It is shown that this index equals the number of unstable eigenvalues for the linearized evolution equation. Finally, we use a symmetry argument to show that any pulse solution must have non-zero Maslov index, and hence be unstable.This article is part of the theme issue 'Stability of nonlinear waves and patterns and related topics'.

Ternary composites by an in situ hydrolytic polymerization process.

Polyamide 6/modified silica composite materials have been prepared by a coupled polymerization procedure. For this purpose, the three-component-system we presented in a previous publication, consisting of ε-aminocaproic acid (ε-ACA), ε-caprolactam (ε-CL), and 1,1',1'',1'''-silanetetrayltetrakis-(azepan-2-one) (Si(ε-CL)4), has been combined with other silicon monomers with one or two methyl groups (MeSi(ε-CL)3 and Me2Si(ε-CL)2). The simultaneous polymerization of ε-CL and silicon monomers leads to the in situ formation of silica/polysiloxane particles and the surrounding polyamide 6 matrix in one step. Moreover, 3-aminopropyltriethoxysilane has been added to the three-component-system to achieve covalent bonding between organic and inorganic phases and to inhibit agglomeration of the silica particles. Chemical structures and morphologies of the composites have been investigated by solid-state NMR and FTIR spectroscopy as well as electron microscopy and SEC measurements. Structural effects on thermal properties have been studied by DSC and TGA measurements.

Fitting of a multiphase equation of state with swarm intelligence.

Hydrocode calculations require knowledge of the variation of pressure of a material with density and temperature, which is given by the equation of state. An accurate model needs to account for discontinuities in energy, density and properties of a material across a phase boundary. When generating a multiphase equation of state the modeller attempts to balance the agreement between the available data for compression, expansion and phase boundary location. However, this can prove difficult because minor adjustments in the equation of state for a single phase can have a large impact on the overall phase diagram. This paper describes how combining statistical-mechanics-based condensed matter physics models with a stochastic analysis technique called particle swarm optimisation, yields multiphase equations of state which give good agreement with experiment over a wide range of pressure-temperature space. Aluminium and tin are used as test cases in the proof of principle described in this paper.

Successful pregnancy and breastfeeding in a woman with mucopolysaccharidosis type I while receiving laronidase enzyme replacement. therapy.

The authors describe the first mother-infant pair to complete an on-going, prospective, open-label, Phase 4 trial (ALIU) UU3, NCT00418821) determining the safety of laronidase enzyme replacement therapy (ERT) in pregnant women with mucopolysaccharidosis type I (MPS I) and their breastfed infants. The mother, a 32-year-old with attenuated MPS I (Scheie syndrome), received laronidase for three years and continued treatment throughout her second pregnancy and while lactating. A healthy 2.5 kg male was delivered by elective cesarean section at 37 weeks. He was breastfed for three months. No laronidase was detected in breast milk. The infant never developed anti-laronidase IgM antibodies, never had inhibitory antibody activity in a cellular uptake assay, and always had normal urinary glycosaminoglycan (GAG) levels. No drug-related adverse events were reported. At 2.5 years of age, the boy is healthy with normal growth and development. In this first prospectively monitored mother-infant pair, laronidase during pregnancy and breastfeeding was uneventful.

An objective approach to model reduction: Application to the Sirius wheat model.

An existing simulation model of wheat growth and development, Sirius, was evaluated through a systematic model reduction procedure. The model was automatically manipulated under software control to replace variables within the model structure with constants, individually and in combination. Predictions of the resultant models were compared to growth analysis observations of total biomass, grain yield, and canopy leaf area derived from 9 trials conducted in the UK and New Zealand under optimal, nitrogen limiting and drought conditions. Model performance in predicting these observations was compared in order to evaluate whether individual model variables contributed positively to the overall prediction. Of the 1 1 1 model variables considered 16 were identified as potentially redundant. Areas of the model where there was evidence of redundancy were: (a) translocation of biomass carbon to grain; (b) nitrogen physiology; (c) adjustment of air temperature for various modelled processes; (d) allowance for diurnal variation in temperature; (e) vernalisation (f) soil nitrogen mineralisation (g) soil surface evaporation. It is not suggested that these are not important processes in real crops, rather, that their representation in the model cannot be justified in the context of the analysis. The approach described is analogous to a detailed model inter-comparison although it would be better described as a model intra-comparison as it is based on the comparison of many simplified forms of the same model. The approach provides automation to increase the efficiency of the evaluation and a systematic means of increasing the rigour of the evaluation.

Posterior pharyngeal wall squamous cell carcinoma arising in a patient with dyskeratosis congenita.

OBJECTIVES: Dyskeratosis congenita is a rare, inherited bone marrow failure syndrome characterised by telomerase dysfunction. This study aimed to demonstrate the importance of recognising that this condition predisposes individuals to head and neck malignancy, and also to discuss the challenges of treatment in such individuals. CASE REPORT: We present the case of a 30-year-old man with dyskeratosis congenita, who presented with a squamous cell carcinoma of the posterior pharyngeal wall. The patient was treated successfully with surgical resection. CONCLUSION: Dyskeratosis congenita is a rare condition; however, it is vital to recognise the increased risk of upper aerodigestive tract cancers in these patients. Management of such cancers can be particularly difficult in view of the need to avoid DNA-damaging therapies such as radiotherapy.

Cervical lymphocoele: a simple solution for a complicated problem.

Spontaneous cervical lymphocoeles are extremely rare. Their surgical management can pose many challenges with the lack of clear surgical planes potentiating risks. We present the case of a patient with an extensive right-sided cervical lymphocoele. Surgical excision would have involved extensive surgery with risk to the great vessels and lungs. We describe the successful use of talc sclerotherapy in the management of this patient, who made a rapid post-operative recovery with no evidence of recurrence on follow-up. Talc sclerotherapy may be used successfully in the management of patients with cervical lymphocoeles, obviating the need for high risk surgical procedures.

Ethylene in organic synthesis. Repetitive hydrovinylation of alkenes for highly enantioselective syntheses of pseudopterosins.

In this report we highlight the significant potential of ethylene as a reagent for the introduction of a vinyl group with excellent stereoselectivity at three different stages in the synthesis of a broad class of natural products, best exemplified by syntheses of pseudopterosins. The late-stage applications of the asymmetric hydrovinylation reaction further illustrate the compatibility of the catalyst with complex functional groups. We also show that, depending on the choice of the catalyst, it is possible to either enhance or even completely reverse the inherent diastereoselectivity in the reactions of advanced chiral intermediates. This should enable the synthesis of diastereomeric analogs of several classes of medicinally relevant compounds that are not readily accessible by the existing methods, which depend on 'substrate control' for the installation of many of the chiral centers, especially in molecules of this class.

The use of the reamer-irrigator-aspirator to harvest mesenchymal stem cells.

The scarcity of mesenchymal stem cells (MSCs) in iliac crest bone marrow aspirate (ICBMA), and the expense and time in culturing cells, has led to the search for alternative harvest sites. The reamer-irrigation-aspirator (RIA) provides continuous irrigation and suction during reaming of long bones. The aspirated contents pass via a filter, trapping bony fragments, before moving into a 'waste' bag from which MSCs have been previously isolated. We examined the liquid and solid phases, performed a novel digestion of the solid phase, and made a comparative assessment in terms of number, phenotype and differentiation capacity with matched ICBMA. The solid fraction from the filtrate was digested for 60 minutes at 37° C with collagenase. Enumeration was performed via the colony-forming unit fibroblast (CFU-F) assay. Passage (P2) cells were differentiated towards osteogenic, adipogenic and chondrogenic lineages, and their phenotypes assessed using flow cytometry (CD33, CD34, CD45, CD73, CD90, and CD105). MSCs from the RIA phases were able to differentiate at least as well as those from ICBMA, and all fractions had phenotypes consistent with other established sources. The median number of colonies for the three groups was: ICBMA = 8.5 (2 to 86), RIA-liquid = 19.5 (4 to 90), RIA-solid = 109 (67 to 200) per 200 µl. The mean total yield of cells for the three groups was: ICBMA = 920 (0 to 4275), RIA-liquid = 114,983 (16,500 to 477,750), RIA-solid = 12,785 (7210 to 28 475). The RIA filtrate contains large numbers of MSCs that could potentially be extracted without enzymatic digestion and used for bone repair without prior cell expansion.

Antibody responses following administration of a Cryptosporidium parvum rCP15/60 vaccine to pregnant cattle.

Cryptosporidium parvum is a zoonotic Apicomplexa-protozoan pathogen that causes gastroenteritis and diarrhea in mammals worldwide. Globally, C. parvum is ubiquitous on dairy operations and is the pathogen most commonly diagnosed in association with calf diarrhea. Here, we describe the antibody response in 20 pregnant cows to a recombinant C. parvum oocyst surface protein (rCP15/60) vaccine compared with 20 controls, and the antibody response in 19 calves fed the rCP15/60-immune colostrum from these vaccinated cows compared with 20 control calves. Cows vaccinated with rCP15/60 produced a significantly greater antibody response compared to controls (p<0.0001) and this response was strongly associated with the subsequent level of colostral antibody (r=0.82, p<0.0001). Calves fed rCP15/60-immune colostrum showed a dose-dependent absorption of antibody, also associated with colostral antibody levels (r=0.83, p<0.0001). Currently, drug therapy against cryptosporidiosis is limited making development of an effective vaccine attractive. This report describes the first stages in development of a C. parvum rCP15/60 vaccine designed to confer passive protection to calves against cryptosporidiosis.

Bone-turnover markers in fracture healing.

Biochemical markers of bone-turnover have long been used to complement the radiological assessment of patients with metabolic bone disease. Their implementation in daily clinical practice has been helpful in the understanding of the pathogenesis of osteoporosis, the selection of the optimal dose and the understanding of the progression of the onset and resolution of treatment. Since they are derived from both cortical and trabecular bone, they reflect the metabolic activity of the entire skeleton rather than that of individual cells or the process of mineralisation. Quantitative changes in skeletal-turnover can be assessed easily and non-invasively by the measurement of bone-turnover markers. They are commonly subdivided into three categories; 1) bone-resorption markers, 2) osteoclast regulatory proteins and 3) bone-formation markers. Because of the rapidly accumulating new knowledge of bone matrix biochemistry, attempts have been made to use them in the interpretation and characterisation of various stages of the healing of fractures. Early knowledge of the individual progress of a fracture could help to avoid delayed or nonunion by enabling modification of the host's biological response. The levels of bone-turnover markers vary throughout the course of fracture repair with their rates of change being dependent on the size of the fracture and the time that it will take to heal. However, their short-term biological variability, the relatively low bone specificity exerted, given that the production and destruction of collagen is not limited to bone, as well as the influence of the host's metabolism on their concentration, produce considerable intra- and inter-individual variability in their interpretation. Despite this, the possible role of bone-turnover markers in the assessment of progression to union, the risks of delayed or nonunion and the impact of innovations to accelerate fracture healing must not be ignored.

Influence of chronic dietary carbohydrate supplementation on plasma cytokine responses to exercise.

This study examined the influence of 28 days of dietary carbohydrate (CHO) supplementation on plasma cytokine responses to cycle ergometry. Sixteen highly trained male cyclists and triathletes (age: 30.6+/-5.6 y; VO2max: 64.8+/-4.7 mL x kg(-1) x min(-1); mean+/-SD) participated in the study. One group (n=8) consumed a higher-CHO (8.5+/-1.7 g x kg(-1) body mass.day (-1)) diet for 28 days; a second group (n=8) consumed a moderate-CHO diet (5.3+/-0.4 g x kg (-1) x day (-1)). Total daily energy intakes were similar between the two groups. Cytokine responses to cycle ergometry were assessed prior to and again following the dietary intervention period. The cycle ergometry protocol involved 100 min steady state cycling at 70% VO2max followed by a time trial of approximately 30 min. Athletes were provided with 15 mL x kg (-1) x h (-1) of water during each trial. Blood samples were collected pre-, immediately post- and 1 h post-exercise for determination of plasma glucose and pro-inflammatory (IL-6, IL-8) and anti-inflammatory (IL-10, IL-1ra) cytokine concentrations. Cytokine responses to cycle ergometry were not substantially altered following the 28-day higher-CHO diet. In contrast, following the 28-day moderate-CHO diet, there were approximately 30-50% reductions (p=0.08-0.11) in anti-inflammatory cytokine responses post-exercise. These findings suggest that increased dietary CHO content alone does not effectively attenuate the pro-inflammatory cytokine response to exercise, however, there may be a small reduction in the anti-inflammatory cytokine response.

The development and performance of a rapid-access neurovascular (TIA) assessment clinic in a rural hospital setting.

INTRODUCTION: Following the withdrawal of acute medical services from rural Angus, a rapid-access Neurovascular (TIA) Clinic was established at Stracathro Hospital in December 2003. Referral protocols were agreed with Angus Primary Care. We measured the performance of this clinic over its first two years against national standards outlined by Quality Improvement Scotland (2005). METHODS: In a retrospective study between 1st December 2003 and 30th November 2005, patient demographics, waiting times, investigation results, diagnoses, and secondary prevention issues were analysed. Challenges presented by a rural setting were also examined, RESULTS: By November 2005, from a total of 355 patients, 79% were seen within 7 days and 98% within 14 days of clinic referral. Pre-clinic bloods were increasingly done in general practice. All patients had CT head and carotid NIVA scans performed on the day of clinic attendance. A high positive diagnostic yield from CT scanning was obtained in the first year of the clinic, and a significant proportion of patients had new secondary drug prevention treatment recommended. Organisational and transport difficulties were addressed and overcome. DISCUSSION: Developing a rapid-access neurovascular clinic in a rural setting is achievable, and waiting times approaching national standard targets are possible. A TIA clinic can identify rapidly those with cerebrovascular disease, allowing commencement of appropriate secondary prevention therapy.