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opencc-by-4.0Oct 2020View details →

Study of terminological subsystems of modern school textbooks in Russian with the help of word embedding models Word2Vec and neural networks

The aim of the project is to analyse the inventory and functioning of scientific terms and special lexemes in textbooks for secondary schools of the Russian Federation with the help of modern methods of natural language processing and deep learning. The number of terms from different fields of knowledge that a pupil should learn during secondary school studies has never been evaluated. According to the preliminary evaluations made on the basis of the Model Basic Curriculum for General and Secondary Education in 2015 only the subject "Russian language" presupposes that a pupil finishing the 11th grade of secondary school should be able to understand, recognise and use about 1000 terms and terminological combinations. Thus, taking into account the number of school subjects, the total number of special vocabulary units studied in general education schools is measured in thousands. At the same time, the comparative characteristics of the inventory and functioning of terms in textbooks for different school subjects are not studied and remain unknown. The correlation between the terminological density of the text in school textbooks for different subjects and the place occupied by these subjects in the curriculum is not clear. The traditional way of compiling lists of scientific terms is simply by gleaning them from special texts and writing down manually. If this method is reliable in terms of intellectualisation of selection principles, it cannot be applied to large data sets and does not reflect either the frequency of use of terms, or the specificity of their syntagmatic connections, or the systemic relationship between terms. The current project is aimed at filling this gap by means of 1) creating a full-text corpus of school textbooks for 5–11 classes included in the Federal List compiled by the Ministry of Education, 2) automatic extraction, stratification, and mapping of terms with the help of distribution semantics algorithms, 3) creation and training of a deep neural network capable of predicting the subject, level of education and educational topic given a group of vector representations of terms as input. The results of the research can be of fundamental interest in the perspective of terminology science development and also have practical applications in the creation of different types of educational literature. Funding: The reported study was funded by RFBR, project number 19-29-14032

opencc-by-4.0Oct 2019View details →

Dataset accompanying "SECAT: Quantifying differential protein-protein interaction states by network-centric analysis"

This repository contains input data, processing parameters and results associated with manuscript "SECAT: Quantifying differential protein-protein interaction states by network-centric analysis". Each archive contains a README.txt file that describes the contents. SECAT_scripts_data.tar.xz is an archive containing the scripts and data to generate the manuscript figures.

Kinship does not predict the structure of a shark social network

Genetic relatedness in animal societies is often a factor that drives the structure of social groups. In the marine world, most studies which have investigated this question have focused on marine mammals such as whales and dolphins. For sharks, recent studies have demonstrated preferential associations among individuals from which social communities emerge. Assortment patterns have been found according to phenotypic or behavioural traits but the role of genetic relatedness in shaping the social structure of adult shark populations has, to the best our knowledge, never been investigated. Here, we used a social network analysis crossed with DNA microsatellite genotyping to investigate the role of the genetic relatedness in the social structure of a blacktip reef shark (Carcharhinus melanopterus) population. Based on data from 156 groups of sharks, we used generalized affiliation indices to isolate social preferences from non-social associations, controlling for the contribution of sex, size, gregariousness, spatial and temporal overlap on social associations, to test for the influence of genetic relatedness on social structure. A double permutation procedure was employed to confirm our results and account for issues arising from potentially elevated type I and type II error rates. Kinship was not a predictor of associations and affiliations among sharks at the dyad or community levels as individuals tended to associate independently of the genetic relatedness among them. The lack of parental care in this species may contribute to the breakdown of family links in the population early in life, thereby preventing the formation of kin-based social networks.

Efficacy of treatments for polycystic ovarian syndrome management in adolescents: a systematic review and network meta-analysis

Limited evidence on treatment options for polycystic ovarian syndrome (PCOS) has led to considerable variation in healthcare practices. We aimed to compare the effects of metformin and/or oral contraceptive pills (OCPs) in combination with pioglitazone, spironolactone, flutamide, and lifestyle interventions among adolescents aged 11-19 years with PCOS. Literature searches were performed in Medline, Embase, and the Cochrane Central Register of Controlled Trials from database inception through December 2018, with no language restriction. Two reviewers screened titles and abstracts, assessed full text eligibility, and extracted information from eligible trials. Evidence was synthesized through network meta-analyses (NMA) using Bayesian random-effects approach. We identified 37 RCTs, in which 2400 patients were randomized. NMA showed no statistically important difference among all interventions to improve menstrual regulation, or body mass index. Moderate quality evidence showed hirsutism scores were reduced by multiple interventions that included single and combination medications namely; lifestyle intervention, metformin, OCP, spironolactone, pioglitazone, metformin-OCP, metformin-spironolactone, metformin-flutamide, against placebo. Moderate quality evidence showed OCP results in more dysglycaemia compared to metformin (odds ratio 2.98; 95%credible interval 1.02, 8.96), no intervention resulted in dysglycaemia reduction. In conclusion, metformin and OCP as monotherapy or in combination with other interventions compared to placebo can reduce hirsutism scores, but none of these medications lead to effective menstrual cycle regulation or weight reduction. However, the use of OCP leads to worse cardiometabolic risk factors. Further research into new treatment options is urgently needed.

opencc-by-4.0Oct 2020View details →

Hierarchical Inference With Bayesian Neural Networks: An Application to Strong Gravitational Lensing - Model Weights, Chains, BNN Samples, and Simulated Datasets

The model weights, chains, simulated datasets, and BNN samples used to produce the results shown in LSST DESC Collaboration paper "Hierarchical Inference With Bayesian Neural Networks: An Application to Strong Gravitational Lensing." All files presented here are meant for use in tandem with the python package "ovejero" (<a href="https://github.com/swagnercarena/ovejero">https://github.com/swagnercarena/ovejero</a>).

Contrasting effects of land-use changes on herbivory and pollination networks

<ol> <li>Land-use changes, one of the greatest threats to global biodiversity, can cause under-appreciated effects on ecosystems by altering the structures of interspecific interaction networks. These effects have typically been explored by evaluating interaction networks composed of a single type of interaction. Therefore, it remains unclear whether the different types of interaction networks sharing the same species respond to the same land-use changes in a similar manner.</li> <li>To compare the responses of herbivory and pollination networks to land-use changes, we investigated both types of interaction networks in semi-natural grasslands categorized into three types of agricultural land-use (abandoned, extensively managed, and intensively managed) in a Japanese agricultural landscape. We quantified the structures of the interaction networks using several indices (connectance, evenness, diversity, generality, network specialization, and robustness) and compared them among different land-use types. We conducted piecewise SEM to differentiate the direct and indirect effects of land-use changes on the network structures.</li> <li>Although both land-use changes (abandonment and intensification) led to reduced plant and insect species richness, the structures of herbivory and pollination networks showed different responses to the land-use changes. There was a marked contrast in network generality; while herbivore species were less generalized (i.e. having fewer host plant species) in fields with land-use intensification, pollinator species were less generalized in abandoned fields.</li> <li>Furthermore, the mechanisms behind the changes in interaction networks were also different between pollination and herbivory networks. The change in herbivory network generality was induced by the decrease in plant species richness, whereas the change in pollination network generality was mainly induced by the effect independent of changes in species richness and composition, which possibly reflect the less number of flowers in shaded environment.</li> <li>The present study demonstrates that agricultural land-use changes affect herbivory and pollination networks in contrasting ways and suggests the importance of assessing multiple types of interaction networks for biodiversity conservation in plant–insect systems. Our results also highlight the under-appreciated importance of maintaining habitats with an intermediate intensity of land-use.</li> </ol>

Clearcutting and selective logging have inconsistent effects on liana diversity and abundance but not on liana–tree interaction networks

Understanding the effects of forest management on lianas and their interaction with trees is an important step towards effective forest management. Our study therefore aimed at quantifying the patterns of liana diversity and abundance, and liana-tree interaction network structure in response to logging disturbance in a moist semi-deciduous forest in Ghana. We sampled lianas (diameter at 1.3 m ≥ 1 cm) and their host trees (diameter at breast height ≥ 5 cm) in 90 20 × 20 m plots among three forest management regimes: clearcut-logged, selectively-logged and old-growth forests. Liana species diversity and abundance in the selectively-logged forest was similar to that of the old-growth forest, while that in clearcut-logged forest was significantly lower than both above-mentioned forest types. Liana-tree interaction networks showed anti-nested structure, which is a form of nonrandom community organization. There were significant modularity and degree of specialization, but no significant connectance in the network structure. Largely, most of the species were peripherals, while a few species acted as structurally important species (i.e. module hubs, network hubs and connectors) in the three networks. A different set of species acted as structurally important species in the different forest management regimes. Our findings call for a re-examination of clearcutting logging in forest management in view of its negative effects on lianas, and we recommend prioritizing important modules in liana-tree network for future conservation.

Intermedia agenda-setting networks

We investigate the impact of noise and topology on opinion diversity in social networks. We do so by extending well-established models of opinion dynamics to a stochastic setting where agents are subject both to assimilative forces by their local social interactions, as well as to idiosyncratic factors preventing their population from reaching consensus. We model the latter to account for both scenarios where noise is entirely exogenous to peer influence and cases where it is instead endogenous, arising from the agents' desire to maintain some uniqueness in their opinions. We derive a general analytical expression for opinion diversity, which holds for any network and depends on the network's topology through its spectral properties alone. Using this expression, we find that opinion diversity decreases as communities and clusters are broken down. We test our predictions against data describing empirical influence networks between major news outlets and find that incorporating our measure in linear models for the sentiment expressed by such sources on a variety of topics yields a notable improvement in terms of explanatory power.

opencc-by-4.0Nov 2020View details →

A sermon by any other name? The pseudo-Augustinian S. App. 121 and its medieval textual network

The Latin sermons preached by the Fathers of the Early Church – Augustine, Gregory, Leo – and their contemporaries had a dynamic and complex medieval afterlife. Throughout the Middle Ages, they circulated in manuscript form, usually as part of collections of patristic preaching. Both the collections and the sermons themselves were heavily manipulated as part of their medieval reception. Additionally, they circulated alongside (and became intertwined with) an enormous corpus of pseudo-epigraphic sermons that were attributed to one of the authoritative Fathers but of which the origin, whether Late-Antique or Medieval, is uncertain. The ERC-funded PASSIM project (2019-2023) aims at charting and analysing the complex interrelations between the manuscripts transmitting patristic sermon collections, and between the texts they contain, through the development of a database and web application. In due course, these digital tools will grant access to the corpus’ complex research tradition, manuscript transmission and textual relations. In doing so, the PASSIM project strives to open up new research avenues for the study of the reception of Latin patristic sermons in medieval manuscripts. In addition to traditional list views, we aim to include in the PASSIM web application various types of network visualisations, presenting at a glance the manuscript transmission of a sermon, the building blocks of a collection, the spread of author attributions, the popularity of a sermon over time etc. In this paper, we want to focus on network visualisations of textual overlap between sermons. Specifically, we will explore the challenges inherent in creating a serviceable network of a sermon’s textual relations that is not dependent upon a full textual analysis of the relevant texts. We want to point the user in the right direction without saying the final word on the subject. As a testcase, we will use the pseudo-Augustinian sermon S. App. 121, an anonymous text derived from various models, which also served as a model for later sermons. Moving from the conceptual to the concrete, our paper will explore the possibilities and challenges of visualisations for networks of texts, contributing as such to the accessibility of the complex corpus of patristic preaching and to the development of the PASSIM database.

opencc-by-4.0Nov 2020View details →

Social (-ecological) network analysis in environmental governance - central publications, important concepts and areas of application data collected in January 2019

Social and Social-Ecological Network Analysis (S(E)NA) have recently emerged as new methods in the environmental governance (EG) literature. By investigating networks of connections between actors, S(E)NA advances the understanding of who is involved in EG and how. We provide an overview of the EG literature applying S(E)NA and respective metrics of 1) a citation network analysis, 2) topic detection methods and 3) a similarity network analysis. 20 publications occupy central positions as sources, storers or bridges of knowledge in the citation network. While we see S(E)NA applied in diverse resource contexts, these are mainly discussed on the local spatial level, with a focus on “policy” or “collaboration”. We discover that “power structures” and “the production of knowledge” are themes influencing the whole field.

Supplementary material 10 from: Tomaskinova J, Dicks L, Collier M, Geneletti D, Grace M, Longato D, Sadula R, Stoev P, Sapundzhieva A, Balzan MV (2020) Capacity-building and networking events for nature-based solutions and re-naturing in Malta. Research Ideas and Outcomes 6: e60893. https://doi.org/10.3897/rio.6.e60893

How can we save bees through sustainable farming

Supplementary material 8 from: Tomaskinova J, Dicks L, Collier M, Geneletti D, Grace M, Longato D, Sadula R, Stoev P, Sapundzhieva A, Balzan MV (2020) Capacity-building and networking events for nature-based solutions and re-naturing in Malta. Research Ideas and Outcomes 6: e60893. https://doi.org/10.3897/rio.6.e60893

Nature-based solutions: not just a city thing!

Supplementary material 7 from: Tomaskinova J, Dicks L, Collier M, Geneletti D, Grace M, Longato D, Sadula R, Stoev P, Sapundzhieva A, Balzan MV (2020) Capacity-building and networking events for nature-based solutions and re-naturing in Malta. Research Ideas and Outcomes 6: e60893. https://doi.org/10.3897/rio.6.e60893

Nature-based solutions and environmental justice

Supplementary material 6 from: Tomaskinova J, Dicks L, Collier M, Geneletti D, Grace M, Longato D, Sadula R, Stoev P, Sapundzhieva A, Balzan MV (2020) Capacity-building and networking events for nature-based solutions and re-naturing in Malta. Research Ideas and Outcomes 6: e60893. https://doi.org/10.3897/rio.6.e60893

Designing NbS in cities: What do planners need to know?

Supplementary material 5 from: Tomaskinova J, Dicks L, Collier M, Geneletti D, Grace M, Longato D, Sadula R, Stoev P, Sapundzhieva A, Balzan MV (2020) Capacity-building and networking events for nature-based solutions and re-naturing in Malta. Research Ideas and Outcomes 6: e60893. https://doi.org/10.3897/rio.6.e60893

The ecological foundations: biodiversity and its relationship to ecological function

Supplementary material 4 from: Tomaskinova J, Dicks L, Collier M, Geneletti D, Grace M, Longato D, Sadula R, Stoev P, Sapundzhieva A, Balzan MV (2020) Capacity-building and networking events for nature-based solutions and re-naturing in Malta. Research Ideas and Outcomes 6: e60893. https://doi.org/10.3897/rio.6.e60893

Using evidence in decision-making

Supplementary material 3 from: Tomaskinova J, Dicks L, Collier M, Geneletti D, Grace M, Longato D, Sadula R, Stoev P, Sapundzhieva A, Balzan MV (2020) Capacity-building and networking events for nature-based solutions and re-naturing in Malta. Research Ideas and Outcomes 6: e60893. https://doi.org/10.3897/rio.6.e60893

Ecosystem services in Polish urban areas

Supplementary material 1 from: Tomaskinova J, Dicks L, Collier M, Geneletti D, Grace M, Longato D, Sadula R, Stoev P, Sapundzhieva A, Balzan MV (2020) Capacity-building and networking events for nature-based solutions and re-naturing in Malta. Research Ideas and Outcomes 6: e60893. https://doi.org/10.3897/rio.6.e60893

Biodiversity, green infrastructure and ecosystem services: an introduction

Supplementary material 2 from: Tomaskinova J, Dicks L, Collier M, Geneletti D, Grace M, Longato D, Sadula R, Stoev P, Sapundzhieva A, Balzan MV (2020) Capacity-building and networking events for nature-based solutions and re-naturing in Malta. Research Ideas and Outcomes 6: e60893. https://doi.org/10.3897/rio.6.e60893

Identification of trees in a Maltese urban context