Enabling Semantic Data Access for Toxicological Risk Assessment

Experimental effort and animal welfare are concerns when exploring the effects a compound has on an organism. Appropriate methods for extrapolating chemical effects can further mitigate these challenges. In this paper we present the efforts to (i) (pre)process and gather data from public and private sources, varying from tabular files to SPARQL endpoints, (ii) integrate the data and represent them as a knowledge graph with richer semantics. This knowledge graph is further applied to facilitate the retrieval of the relevant data for a ecological risk assessment task, extrapolation of effect data, where two prediction techniques are developed

Prediction of Adverse Biological Effects of Chemicals Using Knowledge Graph Embeddings

We have created a knowledge graph based on major data sources used in ecotoxicological risk assessment. We have applied this knowledge graph to an important task in risk assessment, namely chemical effect prediction. We have evaluated nine knowledge graph embedding models from a selection of geometric, decomposition, and convolutional models on this prediction task. We show that using knowledge graph embeddings can increase the accuracy of effect prediction with neural networks. Furthermore, we have implemented a fine-tuning architecture which adapts the knowledge graph embeddings to the effect prediction task and leads to a better performance. Finally, we evaluate certain characteristics of the knowledge graph embedding models to shed light on the individual model performance

Deaths due to differentiated thyroid cancer: A 46-year perspective

From 1940 to 1986, a total of 798 patients were treated for differentiated thyroid carcinoma. One hundred and seventy-two patients died during the follow-up period: 42 (24.4%) patients from thyroid cancer, 14 (8.1%) from other causes with extensive thyroid cancer present, 75 (43.6%) with no thyroid cancer, and 41 (23.8%) with an unknown status of thyroid cancer . Of the 42 patients dying due to thyroid cancer, 15 were male and 27, female. Mean age at diagnosis was 48.3±17.7 years with one-third of patients age 45 or younger at the time of the initial diagnosis. The primary tumors were large (>4 cm) and 59.5% of the patients had local invasion and/or cervical metastasis. Distant metastases were present in 9 (21.4%) patients at the time of diagnosis . Surgical therapy included total thyroidectomy (72.1%) and limited or radical neck dissection (69.4%). Radioactive iodine ( 131 I) was used to treat residual cancer and/or distant metastasis in 73.8% of the patients. External radiation therapy was used to treat locally advanced or recurrent disease in 52.3% of the patients. Distant metastases and local recurrence were identified earlier in patients with follicular thyroid cancer whose survival time and disease-free interval were significantly shorter ( p < 0.001) than that of patients with papillary neoplasms. However, the survival and disease-free intervals were often very long in both papillary and follicular thyroid cancer deaths . Onset of differentiated thyroid cancer before the age of 40 years does not preclude serious sequelae and death. Since no known histopathologic features can consistently predict outcome, we continue to advocate aggressive treatment of all patients with differentiated thyroid cancer . Entre 1940 et 1986, 798 patients au total ont été traités pour un cancer différencié de la thyroïde. Cent-soixant-douze patients sont morts par la suite: 42 (24.4%) de leur cancer, 14 (8.1%) d'une autre cause alors que des signes d'extension du cancer étaient présents, 75 (43.6%) d'une autre cause sans signe de cancer, et 41 (23.8%) sans qu'on ait pu connaître le stade du cancer. Des 42 patients morts de leur cancer, il y avait 15 hommes et 27 femmes. L'âge moyen au moment du diagnostic était de 48.3±17.7 ans: un tiers des patients avait 45 ans ou moins au moment du diagnostic. Les tumeurs primitives avaient plus de 4 cm et 59.5% des patients présentaient un envahissement local et/ou une métastase cervicale. Les métastases à distance ont été détectées chez 9 (21.4%) patients au moment du diagnostic. Une thyroïdectomie totale a été effectuée chez 72.1% des patients, associée à un curage cervical limité ou radical chez 69.4% des patients. Chez 73.8% des patients on a traité le tissu cancéreux résiduel et/ou des métastases à distance par de l'I 131. La radiothérapie a été utilisée pour traiter les patients présentant une extension importante ou une récidive chez 52.3% des patients. Des métastases à distance et des récidives ont été identifiées précocement chez les patients ayant un cancer folliculaire. Dans ce groupe de patients, la survie et l'intervalle de temps sans maladie étaient significativement plus courts ( p <0.001) que chez les patients ayant un cancer papillaire. Il faut cependant noter que la survie et l'intervalle de temps sans maladie étaient très longs dans les 2 groupes de patients. La découverte d'un cancer différencié de la thyroïde avant l'âge de 40 ans n'est pas un facteur pronostique particulier. Puisqu'il n'y pas de facteur histologique permettant de prévoir l'évolution, nous continuons de préconiser un traitement agressif chez tout patient présentant un cancer différencié de la thyroïde. En el período 1940–1986, un total de 798 pacientes recibieron tratamiento para carcinoma tiroideo; 172 murieron en el curso del seguimiento: 42 (24.4%) por cancer tiroideo, 14 (8.1%) por otras causas pero con presencia de extenso cáncer tiroideo, 75 (43.6%) libres de cáncer tiroideo, y 41 (23.8%) con estado desconocido en cuanto al cancer tiroideo.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41283/1/268_2005_Article_BF01655866.pd

Glycotope structures and intramolecular affinity factors of plant lectins for Tn/T antigens

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Interacting mindreaders

Could interacting mindreaders be in a position to know things which they would be unable to know if they were manifestly passive observers? This paper argues that they could. Mindreading is sometimes reciprocal: the mindreader's target reciprocates by taking the mindreader as a target for mindreading. The paper explains how such reciprocity can significantly narrow the range of possible interpretations of behaviour where mindreaders are, or appear to be, in a position to interact. A consequence is that revisions and extensions are needed to standard theories of the evidential basis of mindreading. The view also has consequences for understanding how abilities to interact combined with comparatively simple forms of mindreading may explain the emergence, in evolution or development, of sophisticated forms of social cognition

Migrant participation in Norwegian health care. A qualitative study using key informants

Background Little is known about how migrants adapt to first-world public health systems. In Norway, patients are assigned a registered general practitioner (RGP) to provide basic care and serve as gatekeeper for other medical services. Objectives: To explore determinants of migrant compliance with the RGP scheme and obstacles that migrants may experience. Methods: Individuals in leadership positions within migrant organizations for the 13 largest migrant populations in Norway in 2008 participated in this qualitative study. Semi-structured interviews, with migrants serving as key informants, were used to elucidate possible challenges migrant patients face in navigating the local primary health-care system. Conversations were structured using an interview guide covering the range of challenges that migrant patients meet in the health-care system. Results: According to informants, integration into the RGP scheme and adequacy of patient-physician communication varies according to duration of stay in Norway, the patient's country of origin, the reason for migration, health literacy, intention to establish permanent residence in Norway, language proficiency, and comprehension of information received about the health system. Informants noted as obstacles: doctor-patient interaction patterns, conflicting ideas about the role of the doctor, and language and cultural differences. In addressing noted obstacles, one strategy would be to combine direct intervention by migrant associations with indirect intervention via the public-health system

Isolation and characterization of a novel 2-sec-butylphenol-degrading bacterium Pseudomonas sp. strain MS-1

A novel bacterium capable of utilizing 2-sec-butylphenol as the sole carbon and energy source, Pseudomonas sp. strain MS-1, was isolated from freshwater sediment. Within 30 h, strain MS-1 completely degraded 1.5 mM 2-sec-butylphenol in basal salt medium, with concomitant cell growth. A pathway for the metabolism of 2-sec-butylphenol by strain MS-1 was proposed on the basis of the identification of 3 internal metabolites—3-sec-butylcatechol, 2-hydroxy-6-oxo-7-methylnona-2,4-dienoic acid, and 2-methylbutyric acid—by gas chromatography-mass spectrometry analysis. Strain MS-1 degraded 2-sec-butylphenol through 3-sec-butylcatechol along a meta-cleavage pathway. Degradation experiments with various alkylphenols showed that the degradability of alkylphenols by strain MS-1 depended strongly on the position (ortho ≫ meta = para) of the alkyl substitute, and that strain MS-1 could degrade 2-alkylphenols with various sized and branched alkyl chain (o-cresol, 2-ethylphenol, 2-n-propylphenol, 2-isopropylphenol, 2-sec-butylphenol, and 2-tert-butylphenol), as well as a dialkylphenol (namely, 6-tert-butyl-m-cresol)

Persistent Chlamydia Pneumoniae serology is related to decline in lung function in women but not in men. Effect of persistent Chlamydia pneumoniae infection on lung function

<p>Abstract</p> <p>Background</p> <p><it>Chlamydia pneumoniae </it>(C pn) infection causes an acute inflammation in the respiratory system that may become persistent, but little is known about the long-term respiratory effects of C pn infections. Aim: To estimate the long term respiratory effects of C pn with change in forced expiratory volume in one second (FEV₁) and forced vital capacity (FVC) as a main outcome variable.</p> <p>Methods</p> <p>The study comprised of 1109 subjects (500 men and 609 women, mean age 28 ± 6 years) that participated in the Reykjavik Heart Study of the Young. Spirometry and blood samples for measurements of IgG antibodies for C pn were done at inclusion and at the end of the follow-up period (mean follow-up time 27 ± 4 years).</p> <p>Results</p> <p>Having IgG against C pn at both examinations was significantly associated to a larger decrease in FEV₁(6 mL/year) and FVC (7 mL/year) in women but not in men. In women the association between C pn and larger FEV₁decline was only found in women that smoked at baseline where having C pn IgG was associated with 10 mL/year decline compared to smokers without C pn IgG. These results were still significant after adjustment for age, smoking and change in body weight.</p> <p>Conclusion</p> <p>Our results indicate that persistent C pn serology is related to increased decline in lung function in women but not in men. This effect was, however, primarily found in smoking women. This study is a further indication that the pathophysiological process leading to lung impairment may differ between men and women.</p