Refining concepts by machine learning

DOI nefunkční (25.11.2019)In this paper we deal with machine learning methods and algorithms applied in learning simple concepts by their refining or explication. The method of refining a simple concept of an object O consists in discovering a molecular concept that defines the same or a very similar object to the object O. Typically, such a molecular concept is a professional definition of the object, for instance a biological definition according to taxonomy, or legal definition of roles, acts, etc. Our background theory is Transparent Intensional Logic (TIL). In TIL concepts are explicated as abstract procedures encoded by natural language terms. These procedures are defined as six kinds of TIL constructions. First, we briefly introduce the method of learning with a supervisor that is applied in our case. Then we describe the algorithm 'Framework' together with heuristic methods applied by it. The heuristics is based on a plausible supply of positive and negative (near-miss) examples by which learner's hypotheses are refined and adjusted. Given a positive example, the learner refines the hypothesis learnt so far, while a near-miss example triggers specialization. Our heuristic methods deal with the way refinement is applied, which includes also its special cases generalization and specialization.Web of Science23395894

Immune checkpoint inhibitor treatment and ophthalmologist consultations in patients with malignant melanoma or lung cancer—A nationwide cohort study

SIMPLE SUMMARY: Immune checkpoint inhibitors are increasingly being used for treating advanced malignant cutaneous melanoma and lung cancer. Immune-related side effects in multiple organs are common but the frequencies of ophthalmic side effects in national cohorts of unselected patients are undescribed. This study estimated frequencies of first-time ophthalmologist consultations and inflammatory conditions in consecutive patients with malignant melanoma or lung cancer treated with immune checkpoint inhibitors in Denmark from 2011–2018. The one-year risks of first-time consultation and ocular inflammation were 6% and 1%, respectively. These numbers were increased compared with patients with the same type of cancer who were not treated with immune checkpoint inhibitiors. ABSTRACT: Purpose: To estimate the frequency of first-time ocular events in patients treated with immune checkpoint inhibitors (ICI). Methods: Patients with cancer in 2011–2018 in Denmark were included and followed. The outcomes were first-time ophthalmologist consultation and ocular inflammation. One-year absolute risks of outcomes and hazard ratios were estimated. Results: 112,289 patients with cancer were included, and 2195 were treated with ICI. One year after the first ICI treatment, 6% of the patients with cancer, 5% and 8% of the lung cancer (LC) and malignant cutaneous melanoma (MM) patients, respectively, had a first-time ophthalmologist consultation. The risk of ocular inflammation was 1% (95% confidence interval (CI) 0.4–1.2). Among patients with MM, ICI was associated with ocular inflammation in women (HR 12.6 (95% CI 5.83–27.31) and men (4.87 (95% CI 1.79–13.29)). Comparing patients with and without ICI treatment, the risk of first-time ophthalmologist consultation was increased in patients with LC (HR 1.74 (95% CI 1.29–2.34) and MM (HR 3.21 (95% CI 2.31–4.44). Conclusions: The one-year risks of first-time ophthalmologist consultation and ocular inflammation were 6% and 1%, respectively, in patients treated with ICI. In patients with LC and MM, the risk was increased in patients with ICI compared with patients without ICI

Rhizobium leguminosarum HupE is a highly-specific diffusion facilitator for nickel uptake

Bacteria require nickel transporters for the synthesis of Ni-containing metalloenzymes in natural, low nickel habitats. In this work we carry out functional and topological characterization of Rhizobium leguminosarum HupE, a nickel permease required for the provision of this element for [NiFe] hydrogenase synthesis. Expression studies in the Escherichia coli nikABCDE mutant strain HYD723 revealed that HupE is a medium-affinity permease (apparent Km 227 ! 21 nM; Vmax 49 ! 21 pmol Ni2+ min"1 mg"1 bacterial dry weight) that functions as an energy-independent diffusion facilitator for the uptake of Ni(II) ions. This Ni2+ transport is not inhibited by similar cations such as Mn2+, Zn2+, or Co2+, but is blocked by Cu2+. Analysis of site-directed HupE mutants allowed the identification of several residues (H36, D42, H43, F69, E90, H130, and E133) that are essential for HupE-mediated Ni uptake in E. coli cells. By using translational fusions to reporter genes we demonstrated the presence of five transmembrane domains with a periplasmic N-terminal domain and a C-terminal domain buried in the lipid bilayer. The periplasmic N-terminal domain contributes to stability and functionality of the protei

Prevalence of the metabolic syndrome in Luxembourg according to the Joint Interim Statement definition estimated from the ORISCAV-LUX study

ABSTRACT: BACKGROUND: The prevalence of the metabolic syndrome (MS) has been determined in many countries worldwide but never in Luxembourg. This research aimed to 1) establish the gender- and age-specific prevalence of MS and its components in the general adult population of Luxembourg, according to the most recent Joint Interim Statement (JIS) definition, by using both the high and low cut-off points to define abdominal obesity, and 2) compare and assess the degree of agreement with the Revised National Cholesterol Education Programme-Adult Treatment Panel III (R-ATPIII) and the International Diabetes Federation (IDF) definitions. METHODS: A representative stratified random sample of 1349 European subjects, aged 18-69 years, participated to ORISCAV-LUX survey. Logistic regression and odds ratios (OR) were used to study MS prevalence with respect to gender and age. The Framingham risk score (FRS) to predict the 10-year coronary heart disease (CHD) risk was calculated to compare the proportion of MS cases below or above 20%, according to both high and low waist circumference (WC) thresholds. Cohen's kappa coefficient (kappa) was utilized to measure the degree of agreement between MS definitions. RESULTS: The prevalence of the MS defined by the JIS was 28.0% and 24.7% when using the low (94/80) and the high (102/88) WC cut-off points, respectively. The prevalence was significantly higher in men than in women (OR = 2.6 and 2.3 for the low and high WC thresholds), as were all components of the MS except abdominal obesity measured by both thresholds. It also increased with age (OR values in age categories ranging from 2.7 to 28 when compared to the younger subjects for low WC and from 3.3 to 31 for the high WC cut-offs). The 10-year predicted risk of CHD by FRS did not depend on the threshold used. Globally, excellent agreement was observed between the three definitions of MS (kappa= 0.89), in particular between JIS and IDF (kappa = 0.93). Agreement was significantly higher in women than in men, and differed between age groups. CONCLUSION: Regardless of the definition used, the adult population of Luxembourg reveals a high MS prevalence. Our findings contribute to build evidence regarding the definitive construct of the MS, to help selecting the waist circumference thresholds for Europid populations, and to support the need to revise the guidelines for abdominal obesity levels

Violence against civilians and access to health care in North Kivu, Democratic Republic of Congo: three cross-sectional surveys

ABSTRACT

The treasure vault can be opened: large-scale genome skimming works well using herbarium and silica gel dried material

Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications

Postglacial species arrival and diversity buildup of northern ecosystems took millennia

What drives ecosystem buildup, diversity, and stability? We assess species arrival and ecosystem changes across 16 millennia by combining regional-scale plant sedimentary ancient DNA from Fennoscandia with near-complete DNA and trait databases. We show that postglacial arrival time varies within and between plant growth forms. Further, arrival times were mainly predicted by adaptation to temperature, disturbance, and light. Major break points in ecological trait diversity were seen between 13.9 and 10.8 calibrated thousand years before the present (cal ka BP), as well as break point in functional diversity at 12.0 cal ka BP, shifting from a state of ecosystem buildup to a state where most habitat types and biotic ecosystem components were in place. Trait and functional diversity stabilized around 8 cal ka BP, after which both remained stable, although changes in climate took place and species inflow continued. Our ecosystem reconstruction indicates a millennial-scale time phase of formation to reach stable and resilient levels of diversity and functioning.publishedVersio

Contentores, corpos e topologias: Uma análise integral da coleção arqueológica de Pampa Grande (Salta, Argentina)

A partir del análisis de la colección arqueológica de Pampa Grande (Salta, Argentina) se indagan diversos contenedores (animales, cerámicos, vegetales) en tanto cuerpos, junto a las operaciones topológicas que dan sentido a los mismos en contextos funerarios. Metodología: análisis de la colección arqueológica y documentación asociada junto a antecedentes bibliográficos. Conclusiones: se proponen otros vínculos y efectividades epistémicas para los contenedores lógicos de Pampa Grande a partir de movimientos (romper, voltear, combinar, asentar, envolver) que habilitan nuevos aspectos topo-lógicos tras o hacia la muerte, alterando sus capacidades afectivas y potencialidades.Originalidad: este artículo pretende aportar una nueva mirada sobre diversos elementos que conforman una colección arqueológica y que suelen ordenarse según la especialidad del investigador, antes que seguir las conexiones que el material mismo sugiere. Así, este trabajo aporta una red relacional alternativa que vincula diversos cuerpos contenedores desde un abordaje topológico que permite ir más allá de nuestra usual mirada académica sobre los mismos.From the analysis of the archaeological collection at Pampa Grande (Salta, Argentina) different containers (animals, ceramics, vegetables) are explored as bodies, together with the topological operations that confer meaning to them in funerary contexts. Methodology: Analysis of the archaeological collection and associated documentation together with bibliographical background. Conclusions: Other links and epistemic effectivities are proposed for the logical containers of Pampa Grande based on movements (breaking, turning, combining, settling, wrapping) that enable new topological aspects after or towards death, altering their affective capacities and potentialities. Originality: This article aims to provide a new look at the various elements that make up an archaeological collection and that are usually ordered according to the specialty of the researcher, rather than following the connections that the material itself suggests. Thus, this work provides an alternative relational network that links different container bodies from a topological approach that allows us to go beyond our usual academic view of them.A partir da análise da coleção arqueológica de Pampa Grande (Salta, Argentina), são questionados diversos contentores (animais, cerâmicos, vegetais) de corpos, junto às operações topológicas que lhes dão sentido em contextos funerários. Metodologia: análise da coleção arqueológica e documentação associada junto a antecedentes bibliográficos. Conclusões: propõem-se outros vínculos e efetividades epistêmicas para os contentores lógicos de Pampa Grande a partir de movimentos (quebrar, virar, combinar, assentar, envolver) que permitem novos aspectos topológicos após a morte ou em direção a ela, alterando suas capacidades afetivas e potencialidades. Originalidade: este artigo pretende contribuir com uma nova visão sobre diversos elementos que conformam uma coleção arqueológica e que costumam ser organizados segundo a especialidade do pesquisador, antes que seguir as conexões que o material em si sugere. Assim, este trabalho contribui com uma rede relacional alternativa que vincula diversos corpos contentores a partir de uma abordagem topológica que possibilita ir mais além da nosso usual olhar acadêmico sobre eles.Fil: Lema, Veronica Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Antropología de Córdoba. Universidad Nacional de Córdoba. Facultad de Filosofía y Humanidades. Instituto de Antropología de Córdoba; Argentin