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Text normalization is the task of mapping noncanonical language, typical of speech transcription and computer-mediated communication, to a standardized writing. This task is especially important for languages such as Swiss German, with strong regional variation and no written standard. In this paper, we propose a novel solution for normalizing Swiss German WhatsApp messages using the encoder–decoder neural machine translation (NMT) framework. We enhance the performance of a plain character-level NMT model with the integration of a word-level language model and linguistic features in the form of part-of-speech (POS) tags. The two components are intended to improve the performance by addressing two specific issues: the former is intended to improve the fluency of the predicted sequences, whereas the latter aims at resolving cases of word-level ambiguity. Our systematic comparison shows that our proposed solution results in an improvement over a plain NMT system and also over a comparable character-level statistical machine translation system, considered the state of the art in this task till recently. We perform a thorough analysis of the compared systems’ output, showing that our two components produce indeed the intended, complementary improvements.
The epidemiology of heritable traits whose prevalence is determined by a balance between mutation and selection is often explored through deterministic models. Here, the properties are explored by simulation of a model population followed through a sequence of closely spaced time points. Mutation and birth and death occur randomly. The condition neurofibromatosis type 1 (NF1) is used as a point of reference. Critical parameters, such as mutation rates and selection forces, are not known precisely for NF1 so speculative values based on published data from Finland and other studies are proposed.
The system of mating that maintains a general genotypic distribution among females with respect to an X-linked locus is defined. In particular, it is shown that Hardy–Weinberg proportions can be maintained with non-random mating.
Antimicrobial use in pig farming is influenced by a range of risk factors, including herd characteristics, biosecurity level, farm performance, occurrence of clinical signs and vaccination scheme, as well as farmers’ attitudes and habits towards antimicrobial use. So far, the effect of these risk factors has been explored separately. Using an innovative method called multiblock partial least-squares regression, this study aimed to investigate, in a sample of 207 farrow-to-finish farms from Belgium, France, Germany and Sweden, the relative importance of the six above mentioned categories or ‘blocks’ of risk factors for antimicrobial use in pig production. Four country separate models were developed; they showed that all six blocks provided useful contribution to explaining antimicrobial use in at least one country. The occurrence of clinical signs, especially of respiratory and nervous diseases in fatteners, was one of the largest contributing blocks in all four countries, whereas the effect of the other blocks differed between countries. In terms of risk management, it suggests that a holistic and country-specific mitigation strategy is likely to be more effective. However, further research is needed to validate our findings in larger and more representative samples, as well as in other countries.
Dietary long-chain n-3 PUFA (n-3 LCPUFA) in infancy may have long-term effects on lifestyle disease risk. The present follow-up study investigated whether maternal fish oil (FO) supplementation during lactation affected growth and blood pressure in adolescents and whether the effects differed between boys and girls. Mother–infant pairs (n 103) completed a randomised controlled trial with FO (1·5 g/d n-3 LCPUFA) or olive oil (OO) supplements during the first 4 months of lactation; forty-seven mother–infant pairs with high fish intake were followed-up for 4 months as the reference group. We also followed-up 100 children with assessment of growth, blood pressure, diet by FFQ and physical activity by 7-d accelerometry at 13·5 (sd 0·4) years of age. Dried whole-blood fatty acid composition was analysed in a subgroup (n 49). At 13 years of age, whole-blood n-3 LCPUFA, diet, physical activity and body composition did not differ between the three groups. The children from the FO group were 3·4 (95 % CI 0·2, 6·6) cm shorter (P=0·035) than those from the OO group, and tended to have less advanced puberty (P=0·068), which explained the difference in height. There was a sex-specific effect on diastolic blood pressure (Psex×group=0·020), which was driven by a 3·9 (95 % CI 0·2, 7·5) mmHg higher diastolic blood pressure in the FO compared with the OO group among boys only (P=0·041). Our results indicate that early n-3 LCPUFA intake may reduce height in early adolescence due to a delay in pubertal maturation and increase blood pressure specifically in boys, thereby tending to counteract existing sex differences.
E. M. Nicholls (1927–2011) was a humanist, medical practitioner, human biologist, geneticist and, above all, a teacher, as well as a husband and father. He believed that he had made a fundamental contribution to the two-hit model of cancer formation. This hypothesis is associated with retinoblastoma, in particular. Nicholls presented it through his observations on neurofibromatosis. He received little credit for what he believed was his most original contribution to medical science. This note attempts to redress the balance in his favor.
Disease prevention through biosecurity measures is believed to be an important factor for improvement of the overall health status in animal production. This study aimed at assessing the levels of implementation of biosecurity measures in pig production in four European Union (EU) countries and to describe possible associations between the biosecurity level and farm and production characteristics. A cross-sectional study was conducted in 232 farrow-to-finish pig herds in Belgium, France, Germany and Sweden between December 2012 and December 2013. The biosecurity status in each of these herds was described and quantified by using the risk-based scoring tool Biocheck.UGentTM (www.biocheck.ugent.be). Production and management characteristics, obtained from the herd management system and by interviewing the farmer, were analysed for their association with the biosecurity level. A causal path was designed to study statistical associations. The results showed that there was substantial room for improvement in the biosecurity status on many pig farms. Significant differences (P<0.01) both in internal and external biosecurity levels were observed between countries. The external biosecurity status, combining all measures taken to prevent disease introduction into the herd, was highest in Germany and lowest in France. The internal biosecurity status, combining all measures taken to prevent within herd disease transmission, was highest in Sweden and lowest, with a large variation, in Belgium. External biosecurity scores were in general higher compared to internal biosecurity scores. The number of pathogens vaccinated against was significantly associated with internal biosecurity status, suggesting an overall more preventive approach towards the risk of disease transmission. A higher external biosecurity was associated with more weaned piglets per sow per year. Furthermore also the weaning age and the mortality till weaning were highly associated with the number of weaned piglets per sow per year. The negative association observed between the biosecurity level and the estimated frequency of treatment against certain clinical signs of disease as a proxy for disease incidence is consistent with the hypothesis that a higher biosecurity level results in healthier animals. These findings promote an improved biosecurity status at pig farms and are of relevance in the discussion on alternative ways to keep animals healthy with a reduced necessity of antimicrobials; Prevention is better than cure!
The objective was to investigate the association between early and late maternal smoking during pregnancy on offspring body mass index (BMI). We undertook a retrospective cohort study using linked records from the Women’s and Children’s Health Network in South Australia. Among a cohort of women delivering a singleton, live-born infants between January 2000 and December 2005 (n=7658), 5961 reported not smoking during pregnancy, 297 reported quitting smoking during the first trimester of pregnancy, and 1400 reported continued smoking throughout pregnancy. Trained nurses measured the height and weight of the children at preschool visits in a state-wide surveillance programme. The main outcome measure was age- and sex-specific BMI z-score. At 4 to 5 years, mean (s.d.) BMI z-score was 0.40 (1.05), 0.60 (1.07) and 0.65 (1.18) in children of mothers who reported never smoking, quitting smoking and continued smoking during pregnancy, respectively. Compared with the group of non-smokers, both quitting smoking and continued smoking were associated with an increase in child BMI z-score of 0.15 (95% confidence interval: 0.01–0.29) and 0.21 (0.13–0.29), respectively. A significant dose–response relationship was also observed between the number of cigarettes smoked per day on average during the second half of pregnancy and the increase in offspring BMI z-score (P<0.001). In conclusion, any maternal smoking in pregnancy, even if mothers quit, is associated with an increase in offspring BMI at 4 to 5 years of age.
A survey of nearshore areas in the Vestfold Hills, Antarctica, using high-resolution multibeam swath bathymetry provided both a detailed digital bathymetric model and information on sediment acoustic backscatter. Combined with underwater video transects and sediment sampling, these data were used to identify and map geomorphic units. Six geomorphic units identified in the survey region include: rocky outcrops, basins, pediments, valleys, scarps and embayments. In addition to geomorphic units, the data revealed sedimentary features that provide insights into post-glacial sediment transport and erosion in the area. Ice keel pits and scours are common, and sea floor channels, scour depressions and sand ribbons indicate transport and deposition by wind-driven currents and oceanographic circulation. Gullies and sediment lobes observed on steep slopes indicate mass movement of sediment. Some of these processes have not been directly observed to date, but their effectiveness in shaping the modern sea floor is clearly indicated by the sea floor mapping data. The embayments preserve a mantle of boulder sand probably deposited by cold-based glaciers which were flanked by faster-flowing ice in adjoining regions.
The Hardy–Weinberg (HW) principle explains how random mating (RM) can produce and maintain a population in equilibrium, that is, with constant genotypic proportions. When proportions diverge from HW form, it is of interest to estimate the fixation index F, which reflects the degree of divergence. Starting from a sample of genotypic counts, a mixed procedure gives first the orthodox estimate of gene frequency q and then a Bayesian estimate of F, based on a credible prior distribution of F, which is described here.
Human salmonellosis linked to contact with live poultry is an increasing public health concern. In 2012, eight unrelated outbreaks of human salmonellosis linked to live poultry contact resulted in 517 illnesses. In July 2012, PulseNet, a national molecular surveillance network, reported a multistate cluster of a rare strain of Salmonella Braenderup infections which we investigated. We defined a case as infection with the outbreak strain, determined by pulsed-field gel electrophoresis, with illness onset from 25 July 2012–27 February 2013. Ill persons and mail-order hatchery (MOH) owners were interviewed using standardized questionnaires. Traceback and environmental investigations were conducted. We identified 48 cases in 24 states. Twenty-six (81%) of 32 ill persons reported live poultry contact in the week before illness; case-patients named 12 different MOHs from eight states. The investigation identified hatchery D as the ultimate poultry source. Sampling at hatchery D yielded the outbreak strain. Hatchery D improved sanitation procedures and pest control; subsequent sampling failed to yield Salmonella. This outbreak highlights the interconnectedness of humans, animals, and the environment and the importance of industry knowledge and involvement in solving complex outbreaks. Preventing these infections requires a ‘One Health’ approach that leverages expertise in human, animal, and environmental health.
Avian influenza virus (AIV) is an important zoonotic pathogen, resulting in global human morbidity and mortality and substantial economic losses to the poultry industry. Poultry and wild birds have transmitted AIV to humans, most frequently subtypes H5 and H7, but also different strains and subtypes of H6, H9, and H10. Determining which birds are AIV reservoirs can help identify human populations that have a high risk of infection with these viruses due to occupational or recreational exposure to the reservoir species. To assess the prevalence of AIV in tropical birds, from 2010 to 2014, we sampled 40 099 birds at 32 sites in Central Africa (Cameroon, Central African Republic, Congo-Brazzaville, Gabon) and West Africa (Benin, Côte d'Ivoire, Togo). In Central Africa, detection rates by real-time RT–PCR were 16·6% in songbirds (eight passerine families, n = 1257), 16·4% in kingfishers (family Alcedinidae, n = 73), 8·2% in ducks (family Anatidae, n = 564), and 3·65% in chickens (family Phasianidae, n = 1042). Public health authorities should educate human cohorts that have high exposure to these bird populations about AIV and assess their adherence to biosecurity practices, including Cameroonian farmers who raise small backyard flocks.
Tularemia is a contagious infectious disease due to Francisiella tularensis that can cause serious clinical manifestations and significant mortality if untreated. Although the frequency and significance of the disease has diminished over the last decades in Central Europe, over the past few years, there is new evidence suggesting that tularemia has re-emerged worldwide. To know the real epidemiology of the disease is at the root of correct control measures. In order to evaluate whether tularemia is re-emerging in Italy, data on mortality and morbidity (obtained by the National Institute of Statistics; ISTAT), Italian cases described in the scientific literature and data concerning hospitalizations for tularemia (obtained by the National Hospital Discharge Database) were analysed. From 1979 to 2010, ISTAT reported 474 cases and no deaths. The overall number of cases obtained from the literature review was at least 31% higher than that reported by ISTAT. Moreover, the number of cases reported by ISTAT was 3·5 times smaller than hospitalized cases. In Italy tularemia is sporadic, rarely endemic and self-limiting; but, although the trend of reported tularemia does not support the hypothesis of a re-emerging disease, the study demonstrates a wide underreporting of the disease. The real frequency of the disease should be carefully investigated and taken into account in order to implement specific prevention measures.
Balamuthia mandrillaris is an emerging cause of encephalitis in humans. The transmission dynamics are poorly understood due to the high fatality rate and the sporadic nature of cases. Seventy-two soil samples were collected from beaches and the banks of lagoons, rivers, ponds, mineral springs and streams from across Jamaica and assayed for the presence of B. mandrillaris. Seventy-nine sites were sampled and the mitochondrial 16S rDNA gene of B. mandrillaris was amplified and sequenced to confirm the presence of the amoeba. One isolate of B. mandrillaris was recovered from soil from mineral spring which hosts an informal therapeutic mud bath business. Although B. mandrillaris is less frequently isolated from soil than other free-living amoebae, rubbing mud containing the organism onto the skin increases the likelihood of exposure and infection. This first report on the isolation of B. mandrillaris in the Caribbean and its presence in soil where human contact is likely warrants further investigation using serological methods to elucidate exposure patterns.
The bacterium Francisella tularensis causes the vector-borne zoonotic disease tularemia, and may infect a wide range of hosts including invertebrates, mammals and birds. Transmission to humans occurs through contact with infected animals or contaminated environments, or through arthropod vectors. Tularemia has a broad geographical distribution, and there is evidence which suggests local emergence or re-emergence of this disease in Europe. This review was developed to provide an update on the geographical distribution of F. tularensis in humans, wildlife, domestic animals and vector species, to identify potential public health hazards, and to characterize the epidemiology of tularemia in Europe. Information was collated on cases in humans, domestic animals and wildlife, and on reports of detection of the bacterium in arthropod vectors, from 38 European countries for the period 1992–2012. Multiple international databases on human and animal health were consulted, as well as published reports in the literature. Tularemia is a disease of complex epidemiology that is challenging to understand and therefore to control. Many aspects of this disease remain poorly understood. Better understanding is needed of the epidemiological role of animal hosts, potential vectors, mechanisms of maintenance in the different ecosystems, and routes of transmission of the disease.
Nipah virus (NiV) is a recently emerged zoonotic virus that causes severe disease in humans. The reservoir hosts for NiV, bats of the genus Pteropus (known as flying-foxes) are found across the Asia-Pacific including Australia. While NiV has not been detected in Australia, evidence for NiV infection has been found in flying-foxes in some of Australia's closest neighbours. A qualitative risk assessment was undertaken to assess the risk of NiV establishing in Australian flying-foxes through flying-fox movements from nearby regions. Events surrounding the emergence of new diseases are typically uncertain and in this study an expert opinion workshop was used to address gaps in knowledge. Given the difficulties in combining expert opinion, five different combination methods were analysed to assess their influence on the risk outcome. Under the baseline scenario where the median was used to combine opinions, the risk was estimated to be very low. However, this risk increased when the mean and linear opinion pooling combination methods were used. This assessment highlights the effects that different methods for combining expert opinion have on final risk estimates and the caution needed when interpreting these outcomes given the high degree of uncertainty in expert opinion. This work has provided a flexible model framework for assessing the risk of NiV establishment in Australian flying-foxes through bat movements which can be updated when new data become available.