Insight into the hidden bacterial diversity of Lake Balaton, Hungary

In the present study, the prokaryotic community structure of the water of Lake Balaton was investigated at the littoral region of three different points (Tihany, Balatonmáriafürdő and Keszthely) by cultivation independent methods [next-generation sequencing (NGS), specific PCRs and microscopy cell counting] to check the hidden microbial diversity of the lake. The taxon-specific PCRs did not show pathogenic bacteria but at Keszthely and Máriafürdő sites extended spectrum beta-lactamase-producing microorganisms could be detected. The bacterial as well as archaeal diversity of the water was high even when many taxa are still uncultivable. Based on NGS, the bacterial communities were dominated by Proteobacteria, Bacteroidetes and Actinobacteria, while the most frequent Archaea belonged to Woesearchaeia (Nanoarchaeota). The ratio of the detected taxa differed among the samples. Three different types of phototrophic groups appeared: Cyanobacteria (oxygenic phototrophic organisms), Chloroflexi (anaerobic, organotrophic bacteria) and the aerobic, anoxic photoheterotrophic group (AAPs). Members of Firmicutes appeared only with low abundance, and Enterobacteriales (order within Proteobacteria) were present also only in low numbers in all samples.

Molecular investigations of cat fleas (Ctenocephalides felis) provide the first evidence of Rickettsia felis in Malta and Candidatus Rickettsia senegalensis in Israel

Rickettsia felis, the causative agent of flea-borne spotted fever, occurs on all continents except Antarctica, owing to the cosmopolitan distribution of its cat flea vector. In this study, cat fleas were collected in two countries where the occurrence of R. felis was either unknown (Malta) or where accurate prevalence data were lacking (Israel). Altogether 129 fleas were molecularly analysed for the presence of rickettsial DNA. On the basis of three genetic markers, R. felis was identified in 39.5% (15/38) of the cat fleas from Malta. Sequences showed 100% identity to each other and to relevant sequences in GenBank. Among the 91 cat fleas from Israel, two (2.2%) contained the DNA of Candidatus Rickettsia senegalensis. Phylogenetically, the R. felis and Candidatus R. senegalensis identified here clustered separately (with high support) but within one clade, which was a sister group to that formed by the typhus group and spotted fever group rickettsiae. This is the first record of R. felis in Malta and of Candidatus R. senegalensis outside its formerly reported geographical range including Africa, Asia and North America.

Cost-effectiveness analysis of intensity-modulated radiation therapy with normal and hypofractionated schemes for the treatment of localised prostate cancer

The aim of our analysis was to compare the cost-effectiveness of high-dose intensity-modulated radiation therapy (IMRT) and hypofractionated intensity-modulated radiation therapy (HF-IMRT) versus conventional dose three-dimensional radiation therapy (3DCRT) for the treatment of localised prostate cancer. A Markov model was constructed to calculate the incremental quality-adjusted life years and costs. Transition probabilities, adverse events and utilities were derived from relevant systematic reviews. Microcosting in a large university hospital was applied to calculate cost vectors. The expected mean lifetime cost of patients undergoing 3DCRT, IMRT and HF-IMRT were 7,160 euros, 6,831 euros and 6,019 euros respectively. The expected quality-adjusted life years (QALYs) were 5.753 for 3DCRT, 5.956 for IMRT and 5.957 for HF-IMRT. Compared to 3DCRT, both IMRT and HF-IMRT resulted in more health gains at a lower cost. It can be concluded that high-dose IMRT is not only cost-effective compared to the conventional dose 3DCRT but, when used with a hypofractionation scheme, it has great cost-saving potential for the public payer and may improve access to radiation therapy for patients.

A horizontally polarizing liquid trap enhances the tabanid-capturing efficiency of the classic canopy trap

Host-seeking female tabanid flies, that need mammalian blood for the development of their eggs, can be captured by the classic canopy trap with an elevated shiny black sphere as a luring visual target. The design of more efficient tabanid traps is important for stock-breeders to control tabanids, since these blood-sucking insects can cause severe problems for livestock, especially for horse- and cattle-keepers: reduced meat/milk production in cattle farms, horses cannot be ridden, decreased quality of hides due to biting scars. We show here that male and female tabanids can be caught by a novel, weather-proof liquid-filled black tray laid on the ground, because the strongly and horizontally polarized light reflected from the black liquid surface attracts water-seeking polarotactic tabanids. We performed field experiments to reveal the ideal elevation of the liquid trap and to compare the tabanid-capturing efficiency of three different traps: (1) the classic canopy trap, (2) the new polarization liquid trap, and (3) the combination of the two traps. In field tests, we showed that the combined trap captures 2.4-8.2 times more tabanids than the canopy trap alone. The reason for the larger efficiency of the combined trap is that it captures simultaneously the host-seeking female and the water-seeking male and female tabanids. We suggest supplementing the traditional canopy trap with the new liquid trap in order to enhance the tabanid-capturing efficiency.

Defining the concept of 'tick repellency' in veterinary medicine

Although widely used, the term repellency needs to be employed with care when applied to ticks and other periodic or permanent ectoparasites. Repellency has classically been used to describe the effects of a substance that causes a flying arthropod to make oriented movements away from its source. However, for crawling arthropods such as ticks, the term commonly subsumes a range of effects that include arthropod irritation and consequent avoiding or leaving the host, failing to attach, to bite, or to feed. The objective of the present article is to highlight the need for clarity, to propose consensus descriptions and methods for the evaluation of various effects on ticks caused by chemical substances.

Linguistic scope-based and biological event-based speculation and negation annotations in the BioScope and Genia Event corpora

Background

The treatment of negation and hedging in natural language processing has received much interest recently, especially in the biomedical domain. However, open access corpora annotated for negation and/or speculation are hardly available for training and testing applications, and even if they are, they sometimes follow different design principles. In this paper, the annotation principles of the two largest corpora containing annotation for negation and speculation – BioScope and Genia Event – are compared. BioScope marks linguistic cues and their scopes for negation and hedging while in Genia biological events are marked for uncertainty and/or negation.

Results

Differences among the annotations of the two corpora are thematically categorized and the frequency of each category is estimated. We found that the largest amount of differences is due to the issue that scopes – which cover text spans – deal with the key events and each argument (including events within events) of these events is under the scope as well. In contrast, Genia deals with the modality of events within events independently.

Conclusions

The analysis of multiple layers of annotation (linguistic scopes and biological events) showed that the detection of negation/hedge keywords and their scopes can contribute to determining the modality of key events (denoted by the main predicate). On the other hand, for the detection of the negation and speculation status of events within events, additional syntax-based rules investigating the dependency path between the modality cue and the event cue have to be employed.

Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

Background

Competitions in text mining have been used to measure the performance of automatic text processing solutions against a manually annotated gold standard corpus (GSC). The preparation of the GSC is time-consuming and costly and the final corpus consists at the most of a few thousand documents annotated with a limited set of semantic groups. To overcome these shortcomings, the CALBC project partners (PPs) have produced a large-scale annotated biomedical corpus with four different semantic groups through the harmonisation of annotations from automatic text mining solutions, the first version of the Silver Standard Corpus (SSC-I). The four semantic groups are chemical entities and drugs (CHED), genes and proteins (PRGE), diseases and disorders (DISO) and species (SPE). This corpus has been used for the First CALBC Challenge asking the participants to annotate the corpus with their text processing solutions.

Results

All four PPs from the CALBC project and in addition, 12 challenge participants (CPs) contributed annotated data sets for an evaluation against the SSC-I. CPs could ignore the training data and deliver the annotations from their genuine annotation system, or could train a machine-learning approach on the provided pre-annotated data. In general, the performances of the annotation solutions were lower for entities from the categories CHED and PRGE in comparison to the identification of entities categorized as DISO and SPE. The best performance over all semantic groups were achieved from two annotation solutions that have been trained on the SSC-I.

The data sets from participants were used to generate the harmonised Silver Standard Corpus II (SSC-II), if the participant did not make use of the annotated data set from the SSC-I for training purposes. The performances of the participants’ solutions were again measured against the SSC-II. The performances of the annotation solutions showed again better results for DISO and SPE in comparison to CHED and PRGE.

Conclusions

The SSC-I delivers a large set of annotations (1,121,705) for a large number of documents (100,000 Medline abstracts). The annotations cover four different semantic groups and are sufficiently homogeneous to be reproduced with a trained classifier leading to an average F-measure of 85%. Benchmarking the annotation solutions against the SSC-II leads to better performance for the CPs’ annotation solutions in comparison to the SSC-I.

Correlation between tumor-associated proteins and response to neoadjuvant treatment in patients with advanced squamous-cell esophageal cancer

BACKGROUND

Possible predictive markers of response to neoadjuvant radiochemotherapy (NRCT) of esophageal cancer have been identified.

PATIENTS AND METHODS

Patient biopsies were obtained from both tumor and normal tissue before the NRCT of locally advanced esophageal squamous cell carcinoma. Protein solutions were separated and immunoblot analysis was performed with heat shock protein (Hsp)16.2, heme-binding protein 2 (SOUL), BCL2-associated X protein (Bax), B-cell-associated leukemia protein 2 (Bcl-2) and heat shock protein 90 (Hsp90) antibodies. Following NRCT, the patients were restaged according to the Response Evaluation Criteria In Solid Tumors (RECIST). Following resections the pathological down-staging was evaluated.

RESULTS

Clinical restaging revealed a response rate of 65%. Pathological examination revealed down-staging in 30% and 25% of the cases for the T and N categories respectively. Compared to the normal esophageal mucosa, a decreased expression of Hsp16.2, Hsp90 and SOUL proteins and an increased Bax/Bcl-2 ratio was found in the responding tumors.

CONCLUSION

Hsp16,2, Hsp90 and SOUL expression and Bax/ Bcl-2 ratio correlates to the efficacy of NRCT and predict outcome in patients with locally advanced squamous-cell esophageal cancer.

Fleshflies in the flesh: epidemiology, population genetics and control of outbreaks of traumatic myiasis in the Mediterranean Basin

Although the damaging effects on healthy tissues of its developing larvae were first described in 1770, the fleshfly Wohlfahrtia magnifica remains a serious pest for the livestock industry. Wohlfahrtiosis, the severe myiasis caused by this fly, is a grave problem in terms of both the animal welfare and economic loss. This review highlights important aspects of the biology, pest status, epidemiology, population genetic structure, economics and control of W. magnifica and wohlfahrtiosis, with an emphasis on recent outbreaks in Greece and Morocco and fly population dynamics in the Mediterranean Basin. Potential areas for future studies on genetics, host tolerance, in vitro rearing, field behaviour and range expansion of the species are also discussed.

Prevalence of flea infestation in dogs and cats in Hungary combined with a survey of owner awareness

A survey was conducted in order to gain current information on flea species (Siphonaptera: Pulicidae) infesting dogs and cats living in urban and rural areas of Hungary, along with data on the factors that affect the presence, distribution and seasonality of infestation. In addition, owner awareness of flea infestation was evaluated. Practitioners in 13 veterinary clinics were asked to examine all dogs and cats attending the clinic and to collect fleas, when present, on 2 days in each month from December 2005 to November 2006. They also completed a questionnaire for each animal examined. A total of 319 dogs (14.1%) were found to be infested; the highest prevalence (27.1%) of infestation on dogs occurred in August and the lowest (5.4%) in May. Prevalence of fleas on cats was higher (22.9%); the highest (35.0%) and lowest (8.1%) prevalences occurred in July and April, respectively. Fleas were more prevalent in rural (387/1924 animals, 20.2%) than in urban (161/1343 animals, 12.0%) areas. Three species, Ctenocephalides felis (Bouché), Ctenocephalides canis (Curtis) and Pulex irritans L., were found. On dogs, the prevalence of C. canis alone was 53.0%, whereas that of C. felis alone was 36.0%. Only 19 specimens of P. irritans were found on 14 dogs from rural habitats only. Prevalence of C. felis only on cats was 94.3%; the remaining cats were infested with either C. canis or with mixed infestations of C. felis and C. canis. More than half (51.4%) of the owners of infested dogs and cats had not used flea control products in the past year or more, and five times as many owners in rural than urban areas had not used flea control products in the same period. Very few owners reported having attempted to kill fleas in their animals' environment; instead, they believed that fleas were acquired from other cats or dogs.

Semi-automated construction of decision rules to predict morbidities from clinical texts

OBJECTIVE In this study the authors describe the system submitted by the team of University of Szeged to the second i2b2 Challenge in Natural Language Processing for Clinical Data. The challenge focused on the development of automatic systems that analyzed clinical discharge summary texts and addressed the following question: "Who's obese and what co-morbidities do they (definitely/most likely) have?". Target diseases included obesity and its 15 most frequent comorbidities exhibited by patients, while the target labels corresponded to expert judgments based on textual evidence and intuition (separately). DESIGN The authors applied statistical methods to preselect the most common and confident terms and evaluated outlier documents by hand to discover infrequent spelling variants. The authors expected a system with dictionaries gathered semi-automatically to have a good performance with moderate development costs (the authors examined just a small proportion of the records manually). MEASUREMENTS Following the standard evaluation method of the second Workshop on challenges in Natural Language Processing for Clinical Data, the authors used both macro- and microaveraged Fbeta=1 measure for evaluation. RESULTS The authors submission achieved a microaverage F(beta=1) score of 97.29% for classification based on textual evidence (macroaverage F(beta=1) = 76.22%) and 96.42% for intuitive judgments (macroaverage F(beta=1) = 67.27%). CONCLUSIONS The results demonstrate the feasibility of the authors approach and show that even very simple systems with a shallow linguistic analysis can achieve remarkable accuracy scores for classifying clinical records on a limited set of concepts.

Morphological and mitochondrial DNA characters for identification and phylogenetic analysis of the myiasis-causing flesh fly Wohlfahrtia magnifica and its relatives, with a description of Wohlfahrtia monegrosensis sp. n. Wyatt & Hall

Wohlfahrtia magnifica (Schiner) (Diptera: Sarcophagidae) is a major cause of traumatic myiasis in livestock in Central and Eastern Europe and in countries bordering the Mediterranean. The present study explored the utility of external body characters, genitalia characters and mitochondrial DNA characters for identification of this and related species in the subfamily Paramacronychiinae. Sequence analyses of the 3' terminal 273 bp of the mitochondrial cytochrome b gene revealed two lineages of W. magnifica, one from Spain and France and the other from the rest of Eurasia, differing by only two base pairs. Phylogenetic analysis of cytochrome b showed that W. magnifica and Wohlfahrtia vigil Walker were sister species; this conclusion was not contradicted by a phylogenetic analysis of the morphological characters. Based on cytochrome b, the genetic distance between specimens of W. vigil from Europe and North America was sufficiently large to justify the recognition of more than one species. A new species, Wohlfahrtia monegrosensis, from northern Spain, was described, based on morphology and cytochrome b. A unique combination of external body characters of males or females were diagnostic for W. magnifica, the W. vigil group and Wohlfahrtia bella, but only the genitalia characters were diagnostic for all nine species studied.

Molecular genetic analysis of populations of Wohlfahrt's wound myiasis fly, Wohlfahrtia magnifica, in outbreak populations from Greece and Morocco

Wohlfahrt's wound myiasis fly, Wohlfahrtia magnifica (Schiner) (Diptera: Sarcophagidae), is the most important cause of traumatic myiasis in the southern Palaearctic region. Larval stages are obligate parasites and the wounds caused by infestations are very similar to those caused by Old and New World screwworm flies. During the last decade, W. magnifica appears to have expanded its range to parts of northern and central Morocco, and to Crete, Greece. Specimens of W. magnifica were collected in Morocco and Crete either as larvae (preserved in 80% ethanol) or as adults (dry-pinned). Comparison specimens were collected in Spain, Hungary and mainland Greece. A DNA fragment containing the 3' 715 base pairs of the mitochondrial cytochrome b gene was amplified by polymerase chain reaction from each of 132 larvae or adults of W. magnifica and the amplicons were directly sequenced and analysed phylogeographically. Twelve cytochrome b haplotypes were detected. All haplotypes from Morocco belonged to a lineage that included specimens from the Iberian peninsula, and restricted mixing of central and northern populations in Morocco was demonstrated. Cytochrome b haplotyping combined with an analysis of larval size provided clear evidence of multiple infestations of hosts in all geographical areas, with one quarter of wounds containing larvae from two to at least four females. More than 80% of specimens from Crete contained a haplotype predominating in mainland Greece and Hungary. Our survey indicated that wohlfahrtiosis was more widespread in northern and central Morocco than previously recorded by government veterinarians. However, the prevalence of wohlfahrtiosis was low (< 1%). The high genetic diversity of Moroccan populations is consistent with longterm endemicity, rather than recent introduction. Crete showed a higher prevalence of wohlfahrtiosis (< or = 15%) and less genetic diversity of W. magnifica, which is consistent with a recent introduction. The western and eastern Mediterranean lineages may have been isolated in different Pleistocene ice-age refugia, from which there has been limited post-glacial dispersal.

Traumatic myiasis in dogs caused by Wohlfahrtia magnifica and its importance in the epidemiology of wohlfahrtiosis of livestock

In the province of Al Hoceima, northern Morocco, and on two farms in Hungary, dogs were inspected for the presence of traumatic myiasis. Nine and four infested dogs were found in Morocco and Hungary, respectively. All the larvae and adults reared from them in the laboratory were identified as Wohlfahrtia magnifica (Schiner) (Diptera: Sarcophagidae). To our knowledge, these are the first cases of wohlfahrtiosis in dogs to be reported in these countries. All infested animals lived close to livestock, where wohlfahrtiosis was endemic. Infested body sites included limbs (six cases), external genitalia (two), ears (three), nose (one) and neck (one). Developing larvae caused severe welfare problems and tissue destruction in most cases. Although the number of cases reported here is small, wohlfahrtiosis in dogs may be very important from an epidemiological perspective because farm and stray dogs can act as both reservoirs and carriers of this parasitic fly species. Therefore, education of dog owners concerning the risk factors in endemic regions is recommended in order to reduce the prevalence of wohlfahrtiosis in dogs and thereby in livestock. Both owners and veterinarians should pay regular attention to any wounds and to the natural orifices of dogs, especially during the fly seasons.

Influence of biotope on the distribution and peak activity of questing ixodid ticks in Hungary

In order to update the occurrence of hard tick species in Hungary, 3442 questing ticks were collected from the vegetation by the dragging/flagging method in 37 different places in the country, between March and June of 2007. Ixodes ricinus (L.) turned out to be ubiquitous. Dermacentor marginatus (Schulzer) was absent from sampling sites in the southwestern part of the country, but in most places was concomitant and contemporaneous with Dermacentor reticulatus (Fabricius). These two species, as well as I. ricinus, occurred up to an altitude of 900-1000 m a.s.l. Haemaphysalis inermis (Birula) and Haemaphysalis concinna (Koch) were not confined to any parts of the country, unlike Haemaphysalis punctata (Canestrini & Fanzago) which was found in only one region. The local prevalence of the latter species was also significantly lower than those of the former two in the same habitat (fringes of meadows, paths in forests). Dermacentor spp. and H. inermis were represented only by adults. In most species females were collected more frequently than males, except in H. concinna and H. punctata. Temporal differences between the peak activity of I. ricinus and Dermacentor spp. on dry pastures appeared to equalize on meadows in mountain forests, and a similar phenomenon was observed for the three Haemaphysalis spp. when collected along forest paths with fresh, green vegetation.

The BioScope corpus: biomedical texts annotated for uncertainty, negation and their scopes

Background

Detecting uncertain and negative assertions is essential in most BioMedical Text Mining tasks where, in general, the aim is to derive factual knowledge from textual data. This article reports on a corpus annotation project that has produced a freely available resource for research on handling negation and uncertainty in biomedical texts (we call this corpus the BioScope corpus).

Results

The corpus consists of three parts, namely medical free texts, biological full papers and biological scientific abstracts. The dataset contains annotations at the token level for negative and speculative keywords and at the sentence level for their linguistic scope. The annotation process was carried out by two independent linguist annotators and a chief linguist – also responsible for setting up the annotation guidelines – who resolved cases where the annotators disagreed. The resulting corpus consists of more than 20.000 sentences that were considered for annotation and over 10% of them actually contain one (or more) linguistic annotation suggesting negation or uncertainty.

Conclusion

Statistics are reported on corpus size, ambiguity levels and the consistency of annotations. The corpus is accessible for academic purposes and is free of charge. Apart from the intended goal of serving as a common resource for the training, testing and comparing of biomedical Natural Language Processing systems, the corpus is also a good resource for the linguistic analysis of scientific and clinical texts.

Automatic construction of rule-based ICD-9-CM coding systems

BACKGROUND

In this paper we focus on the problem of automatically constructing ICD-9-CM coding systems for radiology reports. ICD-9-CM codes are used for billing purposes by health institutes and are assigned to clinical records manually following clinical treatment. Since this labeling task requires expert knowledge in the field of medicine, the process itself is costly and is prone to errors as human annotators have to consider thousands of possible codes when assigning the right ICD-9-CM labels to a document. In this study we use the datasets made available for training and testing automated ICD-9-CM coding systems by the organisers of an International Challenge on Classifying Clinical Free Text Using Natural Language Processing in spring 2007. The challenge itself was dominated by entirely or partly rule-based systems that solve the coding task using a set of hand crafted expert rules. Since the feasibility of the construction of such systems for thousands of ICD codes is indeed questionable, we decided to examine the problem of automatically constructing similar rule sets that turned out to achieve a remarkable accuracy in the shared task challenge.

RESULTS

Our results are very promising in the sense that we managed to achieve comparable results with purely hand-crafted ICD-9-CM classifiers. Our best model got a 90.26% F measure on the training dataset and an 88.93% F measure on the challenge test dataset, using the micro-averaged F beta=1 measure, the official evaluation metric of the International Challenge on Classifying Clinical Free Text Using Natural Language Processing. This result would have placed second in the challenge, with a hand-crafted system achieving slightly better results.

CONCLUSIONS

Our results demonstrate that hand-crafted systems - which proved to be successful in ICD-9-CM coding - can be reproduced by replacing several laborious steps in their construction with machine learning models. These hybrid systems preserve the favourable aspects of rule-based classifiers like good performance, and their development can be achieved rapidly and requires less human effort. Hence the construction of such hybrid systems can be feasible for a set of labels one magnitude bigger, and with more labeled data.

The strength of co-authorship in gene name disambiguation

Background

A biomedical entity mention in articles and other free texts is often ambiguous. For example, 13% of the gene names (aliases) might refer to more than one gene. The task of Gene Symbol Disambiguation (GSD) – a special case of Word Sense Disambiguation (WSD) – is to assign a unique gene identifier for all identified gene name aliases in biology-related articles. Supervised and unsupervised machine learning WSD techniques have been applied in the biomedical field with promising results. We examine here the utilisation potential of the fact – one of the special features of biological articles – that the authors of the documents are known through graph-based semi-supervised methods for the GSD task.

Results

Our key hypothesis is that a biologist refers to each particular gene by a fixed gene alias and this holds for the co-authors as well. To make use of the co-authorship information we decided to build the inverse co-author graph on MedLine abstracts. The nodes of the inverse co-author graph are articles and there is an edge between two nodes if and only if the two articles have a mutual author. We introduce here two methods using distances (based on the graph) of abstracts for the GSD task. We found that a disambiguation decision can be made in 85% of cases with an extremely high (99.5%) precision rate just by using information obtained from the inverse co-author graph. We incorporated the co-authorship information into two GSD systems in order to attain full coverage and in experiments our procedure achieved precision of 94.3%, 98.85%, 96.05% and 99.63% on the human, mouse, fly and yeast GSD evaluation sets, respectively.

Conclusion

Based on the promising results obtained so far we suggest that the co-authorship information and the circumstances of the articles' release (like the title of the journal, the year of publication) can be a crucial building block of any sophisticated similarity measure among biological articles and hence the methods introduced here should be useful for other biomedical natural language processing tasks (like organism or target disease detection) as well.

Prevalence of Setaria equina microfilaraemia in horses in Hungary

Peripheral blood samples were collected randomly from 195 horses in various parts of Hungary, and the presence of microfilariae was evaluated by the Knott technique. On the basis of morphological identification 18 of the horses (9.2 per cent) were infected with Setaria equina, and the infection was confirmed in 10 animals by pcr and sequencing. The level of microfilaraemia was between 1 and 1138 larvae in 2 ml of blood. There was no correlation between the time of sampling or the sex of the animals (stallions versus mares) and the prevalence of infection, but the prevalence decreased with age. There was a significant association between the prevalence of microfilaraemia and the presence of still waters; positive samples were collected either in the region of Lake Balaton, the largest lake in the country, or at places with nearby ponds.

Serological evidence for Babesia canis infection of horses and an endemic focus of B. caballi in Hungary

In order to evaluate the seroconversion of horses to Babesia caballi and B. canis in Hungary, blood samples were collected from 371 animals on 23 different locations of the country. The presence of antibodies to B. caballi was screened with a competitive ELISA. All 29 positive samples came from one region (the Hortobágy). The prevalence of infection did not show correlation with sexes, and reached 100% in the age group of 2-5 years. Babesia canis-specific antibodies were demonstrated by IFAT in 6.74% of animals kept in 7 regions. The titres were low or medium level (1:40 to 1:160), indicating that the horses had previously been exposed to this piroplasm, but their infection must have been limited. The highest seropositivity rate was observed in the age group of 3-4 years, and males (stallions and geldings) were significantly more frequently infected than females. However, neither B. caballi nor B. canis could be identified in the peripheral blood samples of infected horses by PCR. Since most of the B. caballi-positive horses remained negative in the B. canis IFAT, whereas seroconversion solely to B. canis was detected in several regions of the country, serological cross-reaction between the two species can be discounted. This is the first serological evidence of horses being naturally infected with B. canis, supporting the view that piroplasms are less host specific than previously thought.

State-of-the-art anonymization of medical records using an iterative machine learning framework

OBJECTIVE

The anonymization of medical records is of great importance in the human life sciences because a de-identified text can be made publicly available for non-hospital researchers as well, to facilitate research on human diseases. Here the authors have developed a de-identification model that can successfully remove personal health information (PHI) from discharge records to make them conform to the guidelines of the Health Information Portability and Accountability Act.

DESIGN

We introduce here a novel, machine learning-based iterative Named Entity Recognition approach intended for use on semi-structured documents like discharge records. Our method identifies PHI in several steps. First, it labels all entities whose tags can be inferred from the structure of the text and it then utilizes this information to find further PHI phrases in the flow text parts of the document.

MEASUREMENTS

Following the standard evaluation method of the first Workshop on Challenges in Natural Language Processing for Clinical Data, we used token-level Precision, Recall and F(beta=1) measure metrics for evaluation.

RESULTS

Our system achieved outstanding accuracy on the standard evaluation dataset of the de-identification challenge, with an F measure of 99.7534% for the best submitted model.

CONCLUSION

We can say that our system is competitive with the current state-of-the-art solutions, while we describe here several techniques that can be beneficial in other tasks that need to handle structured documents such as clinical records.

Seroprevalence of canine babesiosis in Hungary suggesting breed predisposition

Six hundred fifty-one blood samples were collected from urban and rural dogs in various parts of Hungary to measure antibody levels to Babesia canis with indirect fluorescent antibody test. Thirty-seven (5.7%) of the sera showed positivity with titers between 1:80 and 1:10,240. Seroconverted dogs were found in 13 locations of the country. It is concluded that canine babesiosis is becoming more prevalent in Eastern Hungary. Seropositivity increased then declined with age, reaching a maximum in case of 3.1- to 5-year-old dogs. Prevalence of antibodies to B. canis was significantly higher among german shepherds and komondors. This suggests a genetic predisposition of german shepherd dogs to chronic babesiosis (carrier status) with long-term maintenance of their seropositivity. On the other hand, heavy-coated komondors are phenotypically more suitable for repeated exposure to ticks, potentially infected with B. canis. This is the first report on the seroprevalence of canine babesiosis in Hungary.

Canine neosporosis in Hungary: screening for seroconversion of household, herding and stray dogs

In order to assess the seroprevalence of canine neosporosis 651 blood samples were collected from 586 household, 41 herding and 24 stray dogs, at small animal clinics in four large cities and other places of Hungary. Nineteen (2.9%) showed positivity in the IFAT with titres between 1:80 and 1:10240. Two dogs with high titres of antibodies to Neospora caninum had neuromuscular signs (imbalance, tremor) and a further one developed papulomatous, ulcerative and necrotizing dermatitis. There was no correlation between titers and age, sex, breed or keeping place. Although more male dogs had antibodies to N. caninum than females in case of both household and herding dogs, this association was not significant. No breed predisposition was observed. However, dogs with seroconversion were significantly more prevalent among rural (6%) than among urban dogs (1%), indicating that dogs in the countryside may have contact with or access to potentially infected offal from cattle and other intermediate hosts more frequently than those in large cities. Furthermore, significantly more herding dogs (29.3%) had antibodies to N. caninum than household dogs (1.2%), confirming the association between the occurrence of neosporosis and dog keeping on farms. The 12 dogs found seropositive among herding ones lived on 6 farms, on 5 of which seropositive cattle were also identified. This is the first report on the prevalence of N. caninum infection in dogs in Hungary.

Wohlfahrtiosis in sheep and the role of dicyclanil in its prevention

Wohlfahrtia magnifica is the main agent of traumatic myiasis in the southern Palaearctic zone. It was recorded in outbreak situations in Crete, Greece, for the first time in 1999, causing widespread production losses and considerable concern in the livestock sectors. Most commonly applied curative insecticides, organophosphates and pyrethroids, can kill larvae of W. magnifica, but they do not provide long-term protection from infestation or re-infestation, which would facilitate wound healing. The objective of the present work was to study the seasonal dynamics of sheep wohlfahrtiosis in Crete and to determine the prophylactic efficacy of dicyclanil, an insect growth regulator, against natural infestations by larvae of W. magnifica. Six sheep flocks were studied, three from a semi-intensive husbandry system and three from an extensive husbandry system. Two flocks were kept as untreated controls and also were used to study the disease dynamics. Dicyclanil was strategically applied just to males and young non-milking females in four treatment flocks; milking females in these flocks were not treated. The untreated flocks demonstrated seasonal patterns in case numbers that were associated with changes in climate and husbandry activities, especially reproduction and shearing. Cases were most common on the genitalia (60%) and a greater proportion of males than females were infested. The prophylactic efficacy of dicyclanil in males was up to 91.3% over the entire trial period. Hence the incidence in treated males at 22 weeks, when final infestations were recorded, was 5-10% compared to 45-55% in untreated controls. Moreover, the application of dicyclanil to a limited number of animals per flock (males and non-milking females=c. 15-20% of the flock) significantly reduced the incidence of wohlfahrtiosis even in the untreated animals. Hence, final overall incidences in the treated flocks ranged from 4.5 to 5.5% compared to 13.3-13.4% in the control flocks.

Evaluation of efficacy of entomopathogenic nematodes against larvae of Lucilia sericata (Meigen, 1826) (Diptera: Calliphoridae)

The blowfly Lucilia sericata (Meigen, 1826) (Diptera: Calliphoridae) is the primary agent of cutaneous myiasis of sheep in northern Europe, southern Africa, Australia and New Zealand. As the application of chemicals has several disadvantages, alternative control measures of traumatic myiasis of livestock must be developed. In this study, the use of entomopathogenic nematodes (EPNs) as potential biocontrol agents against second instar larvae of Lucilia sericata was considered. The following nematode species were tested: Heterorhabditis bacteriophora (IS 5, HHU 1, Hmol, HNC 1, HAZ 36, Hbrecon, HHU 2, HAZ 29, HHP 88, HHU 3, HHU 4 and HGua), Steinernema intermedia, NC513 strain of S. glaserii, S. anomali, S. riobrave, Steinernema sp. and 5 strains of S. feltiae (22, Vija Norway, HU 1, scp, and IS 6). None of the examined EPN species or strains showed larvicidal efficacy at 37 degrees C (no killing effect was observed in the case of the two heat-tolerant strains--H. bacteriophora and S.feltiae) against L. sericata larvae. At lower temperatures (20 degrees C and 25 degrees C) only strains of S. feltiae were found to be active. The overall odds ratios calculated for L. sericata maggots to contract S. feltiae nematode infection show significant (p < 0.05) effect only in the case of strains HU 1, 22 and IS 6. In the case of strains HU 1 and 22 parasitic forms of S. feltiae could be detected in the dead larvae of L. sericata. Strain IS 6 (and also Vija Norway at 20 degrees C) penetrated and killed fly larvae, but only adult forms of the nematode occurred in the cadavers.

In vitro rearing of the screwworm fly Wohlfahrtia magnifica

Wohlfahrtia magnifica (Schiner) (Diptera: Sarcophagidae) is the main agent of traumatic myiasis in many European, African and Asian countries. Although it can be reared in vivo without technical difficulty, such rearing presents ethical problems. Studies were therefore made of in vitro rearing to facilitate development of laboratory colonies that could be used in a wide range of biological, physiological and applied studies of W. magnifica, particularly in the long period of the year when natural populations of the fly are unavailable for study. Parental colonies of W. magnifica were established from larvae collected from natural infestations of sheep and cattle in central Hungary. First stage larvae were harvested from gravid females and were reared in groups of 5-20 on one of six artificial diets. The diets were based on various combinations of five to seven of eight ingredients: water, agar, blood (heparinized or dried), ground meat, egg yolk, low-fat milk powder, yeast and 10% formol. The larvae were incubated on the diets at 37 degrees C. There was no mortality of first stage larvae, which appeared to feed together in foci, in a natural manner. However, during the second stage, and especially after renewal of diet associated with disturbance of the larvae, many larvae began to disperse, crawling over the surface of the media and feeding less intensively. Mortality of larvae during all larval stadia was 64-98%, compared to 33% in batches of third stage larvae collected from natural infestations. The mean weights of puparia from artificial diets ranged from 38.7 to 59.3 mg, compared to 92.2 mg of puparia from larvae collected from natural infestations. There was a high mortality in the pupal stage, from 61 to 100%. Only a maximum of 6% of first stage larvae were successfully reared to the adult stage. Further studies are needed to identify factors present or absent in the diets that contributed to the present poor development of W. magnifica in vitro.

Long-term follow-up study with repetitive transcranial magnetic stimulation (rTMS) in Parkinson's disease

Several studies have claimed the effectiveness of repetitive transcranial magnetic stimulation (rTMS) in Parkinson's disease (PD). The rTMS therapy has to be repeated regularly to achieve a permanent effect but the side effects of long-term administration of low frequency rTMS are not known. Further, there is no information about its influence on the development of Parkinson's disease. Two different groups of patients with PD were compared in a retrospective study for 3 years. The first group (A) was treated with drugs, the second group (B) was treated with drugs + rTMS (1 Hz, 0.6 T, 100 stimuli per day for 7 days using a round coil). rTMS was repeated at least twice each year for 3 years. Symptoms of PD were assessed using the Graded Rating Scale. Although at the onset of the study group B patients had greater disease severity and were receiving higher doses of levodopa, this group (receiving rTMS) showed no deterioration in these parameters, whereas those in group A receiving drugs alone showed a marked deterioration. Hoehn-Yahr (H-Y) stages at the onset of the study and 3 years later were: group A: 1.93 +/- 0.75, 3.03 +/- 1.01; group B: 2.50 +/- 0.83, 2.45 +/- 0.62. The dose of levodopa (mg/day) was at the onset of trial and 3 years later was: group A: 124.4 +/- 144.0, 555.5 +/- 247.2; group B: 287.7 +/- 217.1, 333.4 +/- 181.0. The yearly increment in the scores was: group A: 1.308 +/- 0.307 (P < 0.001), group B: 0.642 +/- 0.389 (P < 0.1). Accordingly, this retrospective study using regularly repeated rTMS with 1 Hz for 7 days, at least twice yearly for 3 years, significantly slowed the development of Parkinson's disease. Unwanted side effects were not observed during the 3 years.

Fly larvicidal activity in the faeces of cattle and pigs treated with endectocide products

Bioassays were conducted to study the effect of a single therapeutic dose of injectable ivermectin, doramectin or moxidectin given to cattle and pigs and excreted in their faeces, against larvae of the housefly, Musca domestica L. (Diptera: Muscidae). Five cattle were treated with each of the test products. Cattle faecal samples were collected before treatment and on days 1, 2, 3, 6, 10, 16, 20, 23 and 28 after treatment. Three groups of pigs, each comprising 12-14 pregnant sows and gilts, were used in the experiment. Pig faeces was collected from each group before treatment and on days 1, 3, 5, 7, 9, 11, 13, 15 and 20 after treatment. Thirty, first-stage larvae were placed into 100 g of faeces. Five replicates were examined for each time-point and for each endectocide group. Evaluation was based on the number of larvae surviving to adult emergence. Low numbers of adults emerged from samples taken from cattle 1 day after treatment, indicating that ivermectin and doramectin were rapidly excreted in the faeces and affected the development of the house fly. A larvicidal effect of both drugs in cattle faeces was present for a period of about 3-4 weeks and lasted a few days longer in cattle treated with doramectin than with ivermectin. In cattle, the larvicidal activity of moxidectin was first observed in faecal samples collected 2 days post-treatment; however, it killed fewer larvae than the other two drugs. The larvicidal effect of moxidectin subsequently decreased. Ivermectin and doramectin exhibited a pronounced larvicidal effect against the house fly in the faeces of pigs. The effect of doramectin was of longer duration. Moxidectin gave the weakest larvicidal effect in pig faeces. The main difference between the results obtained for the two livestock species is that peak toxicity occurred relatively later and for a shorter duration in pig than in cattle faeces.

A comparison of Lucitraps and sticky targets for sampling the blowfly Lucilia sericata

The Lucitrap (Miazma Pty Ltd, Queensland, Australia) combined with a synthetic odour bait, Lucilure (Miazma Pty Ltd, Queensland, Australia), is a commercially available trap for sampling and control of Lucilia cuprina (Wiedemann) in Australia. It was tested in Hungary against Lucilia sericata (Meigen) (Diptera: Calliphoridae), a cause of sheep strike throughout temperate Europe. The standard Lucitrap was tested against black or yellow sticky target traps. Both trap types were baited with either Lucilure or liver and 10% w/v sodium sulphide solution. With Lucilure as bait, L. sericata were caught on sticky traps but not in Lucitraps. With liver and sodium sulphide as bait, sticky traps caught 500-1500 times more L. sericata than Lucitraps. An adhesive sheet fitted to the top of a Lucitrap captured 30-300 times more L. sericata then were captured inside an unaltered Lucitrap. Direct observation of metallic green calliphorids (92.1% L. sericata) alighting on Lucitraps indicated that most flies stayed for a short while (modal class 2-4 s) and only a few stayed longer, to an observed maximum of 28 s. Flies explored a mean of 1.5 entry holes (range 0-7) during a visit but only 6% entered the trap. Size of L. sericata was not a physical barrier to Lucitrap entry, because many larger species were captured. However, L. sericata captured inside Lucitraps were significantly smaller than those captured on sticky traps, demonstrating that size was of behavioural importance. The data demonstrate that the Lucitrap is not effective as a trap for L. sericata in Hungary, due mainly to a failure of flies to enter the trap in large numbers. In Australia and South Africa, L. sericata is commonly caught in Lucitraps baited with Lucilure, although L. cuprina is more numerous. Our study highlights the potential for diversity of fly behaviour between different geographical populations of the same species. Such diversity can have a significant effect on the functioning of systems for fly sampling and control, when these systems depend for their success on certain behavioural responses of the target species.

Application of pressurized liquid extraction technology to pharmaceutical solid dosage form analysis

The technique of pressurized liquid extraction has been evaluated for the extraction of active ingredients from pharmaceutical dosage forms using montelukast sodium oral chewable tablets as a model. The extraction method was optimized for the number of extraction cycles, extraction time, extraction solvent composition and temperature. Samples were extracted using two cycles of water for 2 min with a cell temperature of 40 degrees C and a pressure of 1.0 x 10(4) kPa, to disintegrate the tablet, followed by three cycles of methanol for 3 min at 70 degrees C and 1.0 x 10(4) kPa, to solubilize montelukast sodium. The method demonstrated an extraction efficiency of 98.2% of label claim and an RSD of 1.3% (n=10), as compared to 97.6% and an RSD of 0.9% obtained using a validated mechanical extraction method.

Swelling of mitochondria induced by juvenile hormone in larval salivary glands of Drosophila melanogaster

Treatment of Drosophila larval salivary glands with juvenile hormone or its analogues leads to ultrastructural changes of mitochondria that mimic those seen after application of uncouplers of oxidative phosphorylation. This alteration of mitochondria, also known as swelling, is manifested in strong dilatation of their intercristae space. The mitochondrial response of salivary glands to juvenile hormone is restricted to collum cells that are known to be ultrastructurally and functionally different from transitional and corpus cells and may reflect their specialization in energy metabolism and water/ion balance. Morphological change of mitochondria and about a fivefold increase in cytochrome c oxidase activity in response to juvenile hormone appear to be a consequence of uncoupling of oxidative phosphorylation. We have noticed no significant difference of the responses in Methoprene, the juvenile hormone resistant mutant, suggesting that this action of juvenile hormone may be mediated via a mechanism different from that using nuclear transcription factors. The "uncoupling" effect is caused also by juvenile hormone analogues which are considered inactive in producing morphogenetic effects in Drosophila. Mitochondrial response is independent of transcription and translation, as revealed by the use of RNA and protein synthesis inhibitors. Given these data together, we reasoned that the protonophoric/uncoupling effect of juvenile hormone is a cell type specific nongenomic response to this lipophilic ligand and contrasts with widely accepted notions about nuclear action of juvenile hormone.

Traumatic myiasis of horses caused by Wohlfahrtia magnifica

A survey was carried out in three stud farms with grazing animals, in order to gather data on the prevalence and clinical manifestation of, and the fly species involved in, traumatic myiasis of horses in Hungary. This parasitic disease was recorded in each farm. On the whole, 9.0% (14) of the inspected horses were infested with fly larvae. The affected horses had one infested lesion only, located at the mucosa of the vulva or the vaginal vestibule. The clinical symptoms depended on the age of infestation. Wohlfahrtia magnifica (Diptera: Sarcophagidae) was the only myiasis-causing fly species identified. It was assumed that unknown volatile chemicals might be responsible for the attraction of gravid females to the undamaged vulvar region. These odours are supposed to be produced during different physiological and/or pathological events associated with oestrus, prolonged puerperal period or inflammation of tissues. Daily inspection of grazing horses and early treatment of the affected areas are needed to avert significant damage to the infested horses.

Traumatic myiasis of geese in Hungary

Five geese flocks were surveyed to gather data on the prevalence and clinical manifestation of traumatic myiasis and the fly species involved. Myiasis was recorded in all the flocks and the total number of infested geese was 26 (ca. 0.1% of the total numbers). The first cases were observed at the end of May, the last ones in August. Most birds (16/26) were infested in August. Each affected goose had only one lesion, which was located more frequently on the wings (14/26) than on any other body. In seven geese, Wohlfahrtia magnifica (Diptera: Sarcophagidae) was the only myiasis-causing species. In these cases the detransformed mean number of larvae per wound was 18.1 (range 5-40). Lucilia sericata (Diptera: Calliphoridae) was found to be solely responsible for the lesions of 12 birds, with detransformed mean of 94.0 (range 2-893) larvae per goose. The larvae of this species appeared to be generally less invasive than those of W. magnifica, but in three cases they were also deeply embedded in the wounds. In seven geese larvae of both fly species developed together in and around the wounds. With the exception of one lesion, there were more larvae of W. magnifica (detransformed mean of 21.8 with a range of 1-55) than that of L. sericata (detransformed mean of 11.2 with a range of 2-61) in these mixed infections. Predisposing conditions for development of traumatic myiasis in geese included plucking of feathers, other injuries and bacterial infections (e.g. inflammation of the phallus).