Techniques to Understand Computer Simulations: Markov Chain Analysis

The aim of this paper is to assist researchers in understanding the dynamics of simulation models that have been implemented and can be run in a computer, i.e. computer models. To do that, we start by explaining (a) that computer models are just input-output functions, (b) that every computer model can be re-implemented in many different formalisms (in particular in most programming languages), leading to alternative representations of the same input-output relation, and (c) that many computer models in the social simulation literature can be usefully represented as time-homogeneous Markov chains. Then we argue that analysing a computer model as a Markov chain can make apparent many features of the model that were not so evident before conducting such analysis. To prove this point, we present the main concepts needed to conduct a formal analysis of any time-homogeneous Markov chain, and we illustrate the usefulness of these concepts by analysing 10 well-known models in the social simulation literature as Markov chains. These models are: • Schelling\'s (1971) model of spatial segregation • Epstein and Axtell\'s (1996) Sugarscape • Miller and Page\'s (2004) standing ovation model • Arthur\'s (1989) model of competing technologies • Axelrod\'s (1986) metanorms models • Takahashi\'s (2000) model of generalized exchange • Axelrod\'s (1997) model of dissemination of culture • Kinnaird\'s (1946) truels • Axelrod and Bennett\'s (1993) model of competing bimodal coalitions • Joyce et al.\'s (2006) model of conditional association In particular, we explain how to characterise the transient and the asymptotic dynamics of these computer models and, where appropriate, how to assess the stochastic stability of their absorbing states. In all cases, the analysis conducted using the theory of Markov chains has yielded useful insights about the dynamics of the computer model under study.Computer Modelling, Simulation, Markov, Stochastic Processes, Analysis, Re-Implementation

Errors and Artefacts in Agent-Based Modelling

The objectives of this paper are to define and classify different types of errors and artefacts that can appear in the process of developing an agent-based model, and to propose activities aimed at avoiding them during the model construction and testing phases. To do this in a structured way, we review the main concepts of the process of developing such a model – establishing a general framework that summarises the process of designing, implementing, and using agent-based models. Within this framework we identify the various stages where different types of errors and artefacts may appear. Finally we propose activities that could be used to detect (and hence eliminate) each type of error or artefact.Verification, Replication, Artefact, Error, Agent-Based Modelling, Modelling Roles

Assessing the utility of statistical adjustments for imperfect detection in tropical conservation science

1. In recent years, there has been a fast development of models that adjust for imperfect detection. These models have revolutionised the analysis of field data, and their use has repeatedly demonstrated the importance of sampling design and data quality. There are, however, several practical limitations associated with the use of detectability models which restrict their relevance to tropical conservation science. 2. We outline the main advantages of detectability models, before examining their limitations associated with their applicability to the analysis of tropical communities, rare species and large-scale datasets. Finally, we discuss whether detection probability needs to be controlled before and/or after data collection. 3. Models that adjust for imperfect detection allow ecologists to assess data quality by estimating uncertainty, and to obtain adjusted ecological estimates of populations and communities. Importantly, these models have allowed informed decisions to be made about the conservation and management of target species. 4. Data requirements for obtaining unadjusted estimates are substantially lower than for detectability-adjusted estimates, which require relatively high detection/recapture probabilities and a number of repeated surveys at each location. These requirements can be difficult to meet in large-scale environmental studies where high levels of spatial replication are needed, or in the tropics where communities are composed of many naturally rare species. However, while imperfect detection can only be adjusted statistically, covariates of detection probability can also be controlled through study design. Using three study cases where we controlled for covariates of detection probability through sampling design, we show that the variation in unadjusted ecological estimates from nearly 100 species was qualitatively the same as that obtained from adjusted estimates. Finally, we discuss that the decision as to whether one should control for covariates of detection probability through study design or statistical analyses should be dependent on study objectives. 5. Synthesis and applications. Models that adjust for imperfect detection are an important part of an ecologist's toolkit, but they should not be uniformly adopted in all studies. Ecologists should never let the constraints of models dictate which questions should be pursued or how the data should be analysed, and detectability models are no exception. We argue for pluralism in scientific methods, particularly where cost-effective applied ecological science is needed to inform conservation policy at a range of different scales and in many different systems

Identification and Functional Characterization of a Novel Mutation in theNKX2-1Gene: Comparison with the Data in the Literature

Background: NKX2-1 mutations have been described in several patients with primary congenital hypothyroidism, respiratory distress, and benign hereditary chorea, which are classical manifestations of the brain-thyroid-lung syndrome (BTLS). Methods: The NKX2-1 gene was sequenced in the members of a Brazilian family with clinical features of BTLS, and a novel monoallelic mutation was identified in the affected patients. We introduced the mutation in an expression vector for the functional characterization by transfection experiments using both thyroidal and lung-specific promoters. Results: The mutation is a deletion of a cytosine at position 834 (ref. sequence NM-003317) (c.493delC) that causes a frameshift with formation of an abnormal protein from amino acid 165 and a premature stop at position 196. The last amino acid of the nuclear localization signal, the whole homeodomain, and the carboxy-terminus of NKX2-1 are all missing in the mutant protein, which has a premature stop codon at position 196 (p.Arg165Glyfs*32). The p.Arg165Glyfs*32 mutant does not bind DNA, and it is unable to transactivate the thyroglobulin (Tg) and the surfactant protein-C (SP-C) promoters. Interestingly, a dose-dependent dominant negative effect of the p.Arg165Glyfs*32 was demonstrated only on the Tg promoter, but not on the SP-C promoter. This effect was also noticed when the mutation was tested in presence of PAX8 or cofactors that synergize with NKX2-1 (P300 and TAZ). The functional effect was also compared with the data present in the literature and demonstrated that, so far, it is very difficult to establish a specific correlation among NKX2-1 mutations, their functional consequence, and the clinical phenotype of affected patients, thus suggesting that the detailed mechanisms of transcriptional regulation still remain unclear. Conclusions: We describe a novel NKX2-1 mutation and demonstrate that haploinsufficiency may not be the only explanation for BTLS. Our results indicate that NKX2-1 activity is also finely regulated in a tissue-specific manner, and additional studies are required to better understand the complexities of genotype-phenotype correlations in the NKX2-1 deficiency syndrome

The development of self-regulated learning during the pre-clinical stage of medical school: a comparison between a lecture-based and a problem based curriculum

Society expects physicians to always improve their competencies and to be up to date with developments in their field. Therefore, an important aim of medical schools is to educate future medical doctors to become self-regulated, lifelong learners. However, it is unclear if medical students become better self-regulated learners during the pre-clinical stage of medical school, and whether students develop self-regulated learning skills differently, dependent on the educational approach of their medical school. In a cross-sectional design, we investigated the development of 384 medical students’ self-regulated learning skills with the use of the Self-Regulation of Learning Self-Report Scale. Next, we compared this development in students who enrolled in two distinct medical curricula: a problem-based curriculum and a lectured-based curriculum. Analysis showed that more skills decreased than increased during the pre-clinical stage of medical school, and that the difference between the curricula was mainly caused by a decrease in the skill evaluation in the lecture-based curriculum. These findings seem to suggest that, irrespective of the curriculum, self-regulated learning skills do not develop during medical school

Rapid tests and urine sampling techniques for the diagnosis of urinary tract infection (UTI) in children under five years: a systematic review

Background: Urinary tract infection (UTI) is one of the most common sources of infection in children under five. Prompt diagnosis and treatment is important to reduce the risk of renal scarring. Rapid, cost-effective, methods of UTI diagnosis are required as an alternative to culture. Methods: We conducted a systematic review to determine the diagnostic accuracy of rapid tests for detecting UTI in children under five years of age. Results: The evidence supports the use of dipstick positive for both leukocyte esterase and nitrite (pooled LR+ = 28.2, 95% CI: 17.3, 46.0) or microscopy positive for both pyuria and bacteriuria (pooled LR+ = 37.0, 95% CI: 11.0, 125.9) to rule in UTI. Similarly dipstick negative for both LE and nitrite (Pooled LR- = 0.20, 95% CI: 0.16, 0.26) or microscopy negative for both pyuria and bacteriuria (Pooled LR- = 0.11, 95% CI: 0.05, 0.23) can be used to rule out UTI. A test for glucose showed promise in potty-trained children. However, all studies were over 30 years old. Further evaluation of this test may be useful. Conclusion: Dipstick negative for both LE and nitrite or microscopic analysis negative for both pyuria and bacteriuria of a clean voided urine, bag, or nappy/pad specimen may reasonably be used to rule out UTI. These patients can then reasonably be excluded from further investigation, without the need for confirmatory culture. Similarly, combinations of positive tests could be used to rule in UTI, and trigger further investigation

O efeito alelop?tico do ?leo neem (Azadirachta indica A. Juss) sobre a germina??o e crescimento de plantas de alface ( Lactuca sativa L.)

The present study arises from an informal conversation with a farmer in which he reported that when mixing the leaves of neem trees (Azadirachta indica A. Juss) with cattle manure for use in the domestic orchard, the plants that received this mixture were more vigorous and less susceptible to attack by disease. Chemical inputs currently represent a significant financial cost to agriculture as well as triggering numerous contamination problems for ecosystems and humans. As a substitute for conventional agriculture, alternatives such as agroecology and organic food production have been sought. Following this precept, organic agriculture makes use of different extracts and vegetable oils as a way to boost production, either in the control of diseases and insects, or in improving the vigor and development of plants. Among the options are products derived from neem ( Azadirachta indica A. Juss ), which have been used in the ecological pest management. However, there are few studies showing the allelopathic effects of neem on germination and growth of plants such as lettuce. The objective of the present study was to evaluate the allelopathic effect of different doses of Dalneem ne neem oil ( Azadiracthta indica A. Juss ) diluted in distilled water on the germination and growth of lettuce plants ( Lactuca sativa L .) , cultivating Four Seasons of the Bionatur marca brand cultivated in different experimental systems. Three experiments were carried out. The first experiment in the laboratory, the effect of different doses (0 ml / L, 1 ml / L, 10 ml / L, 20 ml / L, 30 ml / L, 40 ml / L) was evaluated by initial screening. Neem oil on germination of lettuce seeds. In this experiment no significant changes of the neem oil were observed on the germination of lettuce seeds. Thus, a larger number of doses of neem oil (0; 0,001; 0,05; 0,1; 0,5; 1; 5; 10; 15; 20) mL of the oil / L of distilled water). In this screening, no significant changes of the neem oil were observed on the germination of lettuce seeds, although an increase in the fresh mass of the lettuce seedlings was observed at the dose of 0.5 mL / L of neem oil. From these experiments the doses (0 ml / L, 1 ml / L, 10 ml / L, 20 ml / L, 30 ml / L, 40 ml / L) used in experiments 2 and 3 were selected, the effect of neem oil on the growth of lettuce plants cultivated in trays and in pots was evaluated. In the experiments in trays and in pots, the oil of neem, in the different concentrations, was applied to the substrate with the aid of a graduated pisseta. The plants remained under treatment for 25 days. In the plants with 35 days, the chlorophyll index was evaluated using the chlorophyll meter. At the end of the experiments, the plants were collected, washed, and the root and shoot length were evaluated with the aid of a digital caliper, the fresh mass with the aid of an analytical balance and the dry mass after complete oven drying at 65?C also recorded in analytical balance. In addition, aerial part samples were macerated with potassium phosphate buffer, centrifuged and the supernatant was used to determine the concentration of soluble proteins. The data were submitted to analysis of variance and the means were compared by the Tukey test with significance of 5% of probability. When cultured in trays, neem oil applied at the dose of 1 ml / L induced an increase in shoot length, but at doses of 30 ml / L inhibited the growth of this organ in lettuce plants. The same inhibitory effect was also observed at the same doses for root growth. When lettuce plants were grown in pots, significant changes were observed only in shoot length. At the dose 1 ml of neem oil the shoot length was 14% higher when compared to the control treatment, although in the larger doses (30 and 40 mm / L of Neem oil) significant reductions were observed in the length of the aerial part of the plants of lettuce. Chlorophyll indices were not affected by the application of neem oil. In addition, an increase in protein levels was observed when lettuce plants were treated with 20 ml / L of neem oil. Therefore, the results of the present study suggest that neem oil does not affect germination, but affects the growth of lettuce plants and can be used in the management of spontaneous plants.O presente estudo surge de uma conversa informal com um agricultor em que relatou que, ao misturar as folhas das ?rvores de neem( Azadirachta indica A. Juss ) com esterco bovino, para uso no pomar dom?stico, as plantas que receberam esta mistura se mostraram mais vigorosas e menos suscet?veis aos ataques por doen?as. Os insumos qu?micos representam atualmente um significativo custo financeiro para a agricultura al?m de desencadear in?meros problemas de contamina??o para os ecossistemas e aos humanos. Dessa forma, em substitui??o a agricultura convencional tem se buscado alternativas tais como a agroecologia e produ??o org?nica de alimentos. Seguindo este preceito, a agricultura org?nica faz uso de diferentes extratos e ?leos vegetais como forma de potencializar a produ??o, seja no controle de doen?as e insetos, ou na melhoria do vigor e desenvolvimento das plantas. Dentre as op??es est?o os produtos derivados do neem ( Azadirachta indica A. Juss ), os quais vem sendo utilizados no manejo ecol?gico de pragas. No entanto, s?o escassos os estudos mostrando os efeitos alelop?ticos do neem sobre a germina??o e crescimento de plantas tal como a alface. Assim, o objetivo do presente estudo foi avaliar o efeito alelop?tico de diferentes doses de ?leo de neem da marca Dalneem?(Ec) dilu?dos em ?gua destilada sobre a germina??o e crescimento de plantas de alface( Lactuca sativa L.), cultivar Quatro Esta??es da marca Bionatur? cultivada em diferentes sistemas experimentais. Para isso foram realizados tr?s experimentos. O primeiro experimento em laborat?rio, avaliou-se atrav?s de uma triagem inicial o efeito de diferentes doses (0 ml/L, 1 ml/L, 10 ml/L, 20 ml/L, 30 ml/L, 40 ml/L) de ?leo de neem na germina??o de sementes de alface. Em tal experimento n?o foram observadas altera??es significativas do ?leo de neem sobre a germina??o de sementes de alface. Assim, em uma segunda triagem, ainda em laborat?rio, foi utilizada um n?mero mais amplo de doses de ?leo de neem (0; 0,001; 0,05; 0,1; 0,5; 1; 5; 10; 15; 20) mL do ?leo/ por L de ?gua destilada). Neste screening foram observadas altera??es significativas do ?leo de neem sobre a germina??o das sementes de alface, embora um incremento na massa fresca das pl?ntulas de alface tenha sido observado na dose de 0,5 mL/L de ?leo de neem. A partir destes experimentos foram selecionadas as doses (0 ml/L, 1 ml/L, 10 ml/L, 20 ml/L, 30 ml/L, 40 ml/L) de ?leo de neem dissolvidos em ?gua destilada utilizadas nos experimentos em bandeja e nos vasos, o ?leo foi aplicado ao substrato com o aux?lio de uma pisseta graduada, avaliou-se o efeito do ?leo de neem sobre o crescimento de plantas de alface cultivadas. As plantas permaneceram sob tratamento durante 25 dias. Nas plantas com 35 dias foi realizada a avalia??o do ?ndice de clorofila, utilizando o aparelho clorofil?metro. Ao final dos experimentos, as plantas foram coletadas, lavadas, sendo avaliado o comprimento da raiz e parte a?rea com o aux?lio de um paqu?metro digital, a massa fresca com o aux?lio de uma balan?a anal?tica e a massa seca ap?s secagem completa em estufa a 65?C tamb?m registrada em balan?a anal?tica. Al?m disso, amostras de parte a?rea foram maceradas com tamp?o fosfato de pot?ssio, centrifugadas e o sobrenadante foi utilizado para a determina??o da concentra??o de prote?nas sol?veis. Os dados foram submetidos ? an?lise de vari?ncia e as m?dias foram comparadas pelo teste de Tukey com signific?ncia de 5 % de probabilidade. Quando cultivadas em bandejas, o ?leo de neem aplicado na dose de 1 ml/L induziu um incremento no comprimento da parte a?rea, mas nas doses a partir de 30 ml/L inibiu o crescimento deste ?rg?o em plantas de alface. O mesmo efeito inibit?rio foi tamb?m observado nas mesmas doses para o crescimento de ra?zes. Quando as plantas de alface foram cultivadas em vasos, altera??es significativas foram observadas somente quanto ao comprimento da parte a?rea. Na dose 1 ml de ?leo de neem o comprimento da parte a?rea foi 14% maior quando comparado ao tratamento controle, embora nas doses maiores (30 e 40 mm/L de ?leo de Neem) foram observadas redu??es significativas no comprimento da parte a?rea das plantas de alface. Os ?ndices de clorofila n?o sofreram altera??es pela aplica??o do ?leo de neem. Al?m disso, um incremento nos n?veis de prote?nas foi observado quando plantas de alface foram tratadas com 20 ml/L de ?leo de neem. Portanto, os resultados do presente estudo sugerem que o ?leo de neem n?o altera a germina??o, mas afeta o crescimento de plantas de alface, podendo o mesmo ser utilizado no manejo de plantas espont?neas