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1.
Background
The transmission networks of Plasmodium vivax characterize how the parasite transmits from one location to another, which are informative and insightful for public health policy makers to accurately predict the patterns of its geographical spread. However, such networks are not apparent from surveillance data because P. vivax transmission can be affected by many factors, such as the biological characteristics of mosquitoes and the mobility of human beings. Here, we pay special attention to the problem of how to infer the underlying transmission networks of P. vivax based on available tempo-spatial patterns of reported cases.Methodology
We first define a spatial transmission model, which involves representing both the heterogeneous transmission potential of P. vivax at individual locations and the mobility of infected populations among different locations. Based on the proposed transmission model, we further introduce a recurrent neural network model to infer the transmission networks from surveillance data. Specifically, in this model, we take into account multiple real-world factors, including the length of P. vivax incubation period, the impact of malaria control at different locations, and the total number of imported cases.Principal Findings
We implement our proposed models by focusing on the P. vivax transmission among 62 towns in Yunnan province, People''s Republic China, which have been experiencing high malaria transmission in the past years. By conducting scenario analysis with respect to different numbers of imported cases, we can (i) infer the underlying P. vivax transmission networks, (ii) estimate the number of imported cases for each individual town, and (iii) quantify the roles of individual towns in the geographical spread of P. vivax.Conclusion
The demonstrated models have presented a general means for inferring the underlying transmission networks from surveillance data. The inferred networks will offer new insights into how to improve the predictability of P. vivax transmission. 相似文献2.
Prados-Torres A Poblador-Plou B Calderón-Larrañaga A Gimeno-Feliu LA González-Rubio F Poncel-Falcó A Sicras-Mainar A Alcalá-Nalvaiz JT 《PloS one》2012,7(2):e32190
Objectives
The primary objective of this study was to identify the existence of chronic disease multimorbidity patterns in the primary care population, describing their clinical components and analysing how these patterns change and evolve over time both in women and men. The secondary objective of this study was to generate evidence regarding the pathophysiological processes underlying multimorbidity and to understand the interactions and synergies among the various diseases.Methods
This observational, retrospective, multicentre study utilised information from the electronic medical records of 19 primary care centres from 2008. To identify multimorbidity patterns, an exploratory factor analysis was carried out based on the tetra-choric correlations between the diagnostic information of 275,682 patients who were over 14 years of age. The analysis was stratified by age group and sex.Results
Multimorbidity was found in all age groups, and its prevalence ranged from 13% in the 15 to 44 year age group to 67% in those 65 years of age or older. Goodness-of-fit indicators revealed sample values between 0.50 and 0.71. We identified five patterns of multimorbidity: cardio-metabolic, psychiatric-substance abuse, mechanical-obesity-thyroidal, psychogeriatric and depressive. Some of these patterns were found to evolve with age, and there were differences between men and women.Conclusions
Non-random associations between chronic diseases result in clinically consistent multimorbidity patterns affecting a significant proportion of the population. Underlying pathophysiological phenomena were observed upon which action can be taken both from a clinical, individual-level perspective and from a public health or population-level perspective. 相似文献3.
Background
The present study sought to investigate the associations between workplace social capital and hazardous drinking (HD) among Chinese rural-urban migrant workers (RUMW).Methods
A cross sectional study with a multi-stage stratified sampling procedure was conducted in Shanghai during July 2012 to January 2013. In total, 5,318 RUMWs from 77 workplaces were involved. Work-place social capital was assessed using a validated and psychometrically tested eight-item measure. The Chinese version of Alcohol Use Disorders Identification Test (AUDIT) was used to assess hazardous drinking. Control variables included gender, age, marital status, education level, salary, and current smoking. Multilevel logistic regression analysis was conducted to test whether individual- and workplace-level social capital was associated with hazardous drinking.Results
Overall, the prevalence of HD was 10.6%. After controlling for individual-level socio-demographic and lifestyle variables, compared to workers in the highest quartile of individual-level social capital, the odds of HD for workers in the three bottom quartiles were 1.13(95%CI: 1.04–1.23), 1.17(95%CI: 1.05–1.56) and 1.26(95%CI: 1.13–1.72), respectively. However, contrary to hypothesis, there was no relationship between workplace-level social capital and hazardous drinking.Conclusions
Higher individual-level social capital may protect against HD among Chinese RUMWs. Interventions to build individual social capital among RUMWs in China may help reduce HD among this population. 相似文献4.
Lane Yoder 《PloS one》2010,5(2)
Background
Two previous articles proposed an explicit model of how the brain processes information by its organization of synaptic connections. The family of logic circuits was shown to generate neural correlates of complex psychophysical phenomena in different sensory systems.Methodology/Principal Findings
Here it is shown that the most cost-effective architectures for these networks produce correlates of electrophysiological brain phenomena and predict major aspects of the anatomical structure and physiological organization of the neocortex. The logic circuits are markedly efficient in several respects and provide the foundation for all of the brain''s combinational processing of information.Conclusions/Significance
At the local level, these networks account for much of the physical structure of the neocortex as well its organization of synaptic connections. Electronic implementations of the logic circuits may be more efficient than current electronic logic arrays in generating both Boolean and fuzzy logic. 相似文献5.
Rocío Rodríguez-López Armando Reyes-Palomares Francisca Sánchez-Jiménez Miguel ángel Medina 《BMC bioinformatics》2014,15(1)
Background
Several types of genetic interactions in humans can be directly or indirectly associated with the causal effects of mutations. These interactions are usually based on their co-associations to biological processes, coexistence in cellular locations, coexpression in cell lines, physical interactions and so on. In addition, pathological processes can present similar phenotypes that have mutations either in the same genomic location or in different genomic regions. Therefore, integrative resources for all of these complex interactions can help us prioritize the relationships between genes and diseases that are most deserving to be studied by researchers and physicians.Results
PhenUMA is a web application that displays biological networks using information from biomedical and biomolecular data repositories. One of its most innovative features is to combine the benefits of semantic similarity methods with the information taken from databases of genetic diseases and biological interactions. More specifically, this tool is useful in studying novel pathological relationships between functionally related genes, merging diseases into clusters that share specific phenotypes or finding diseases related to reported phenotypes.Conclusions
This framework builds, analyzes and visualizes networks based on both functional and phenotypic relationships. The integration of this information helps in the discovery of alternative pathological roles of genes, biological functions and diseases. PhenUMA represents an advancement toward the use of new technologies for genomics and personalized medicine.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0375-1) contains supplementary material, which is available to authorized users. 相似文献6.
Background
Understanding social interactions requires the ability to accurately interpret conspecifics'' actions, sometimes only on the basis of subtle body language analysis. Here we address an important issue that has not yet received much attention in social neuroscience, that of an interaction between two agents. We attempted to isolate brain responses to two individuals interacting compared to two individuals acting independently.Methodology/Principal Findings
We used minimalistic point-light displays to depict the characters, as they provide the most straightforward way to isolate mechanisms used to extract information from motion per se without any interference with other visual information. Functional magnetic resonance imaging (fMRI) method was used to determine which brain regions were recruited during the observation of two interacting agents, mimicking everyday social scenes. While the mirror and mentalizing networks are rarely concurrently active, we found that both of them might be needed to catch the social intentions carried by whole-body motion.Conclusions/Significance
These findings shed light on how motor cognition contributes to social cognition when social information is embedded in whole-body motion only. Finally, the approach described here provides a valuable and original tool for investigating the brain networks responsible for social understanding, in particular in psychiatric disorders. 相似文献7.
Background
Spatial structure across fragmented landscapes can enhance regional population persistence by promoting local “rescue effects.” In small, vulnerable populations, where chance or random events between individuals may have disproportionately large effects on species interactions, such local processes are particularly important. However, existing theory often only describes the dynamics of metapopulations at regional scales, neglecting the role of multispecies population dynamics within habitat patches.Findings
By coupling analysis across spatial scales we quantified the interaction between local scale population regulation, regional dispersal and noise processes in the dynamics of experimental host-parasitoid metapopulations. We find that increasing community complexity increases negative correlation between local population dynamics. A potential mechanism underpinning this finding was explored using a simple population dynamic model.Conclusions
Our results suggest a paradox: parasitism, whilst clearly damaging to hosts at the individual level, reduces extinction risk at the population level. 相似文献8.
Background
Networks of single interaction types, such as plant-pollinator mutualisms, are biodiversity’s “building blocks”. Yet, the structure of mutualistic and antagonistic networks differs, leaving no unified modeling framework across biodiversity’s component pieces.Methods/Principal Findings
We use a one-dimensional “niche model” to predict antagonistic and mutualistic species interactions, finding that accuracy decreases with the size of the network. We show that properties of the modeled network structure closely approximate empirical properties even where individual interactions are poorly predicted. Further, some aspects of the structure of the niche space were consistently different between network classes.Conclusions/Significance
These novel results reveal fundamental differences between the ability to predict ecologically important features of the overall structure of a network and the ability to predict pair-wise species interactions. 相似文献9.
Background
Allometric studies have shown that individual growth rate is inversely related to body size across a broad spectrum of organisms that vary greatly in size. Fewer studies have documented such patterns within species. No data exist directly documenting the influence of colony size on growth rate for microscopic, colonial organisms.Methodology/Principal Findings
To determine if similar negative relationships between growth rate and size hold for colonial organisms, we developed a technique for measuring the growth of individual colonies of a bloom-forming, toxic cyanobacterium, Microcystis aeruginosa using microscopy and digital image analysis. For five out of six genotypes of M. aeruginosa isolated from lakes in Michigan and Alabama, we found significant negative relationships between colony size and growth rate. We found large intraspecific variation in both the slope of these relationships and in the growth rate of colonies at a standard size. In addition, growth rate estimates for individual colonies were generally consistent with population growth rates measured using standard batch culture.Conclusions/Significance
Given that colony size varies widely within populations, our results imply that natural populations of colonial phytoplankton exist as a mosaic of individuals with widely varying ecological attributes (since size strongly affects growth rate, grazing mortality, and migration speed). Quantifying the influence of colony size on growth rate will permit development of more accurate, predictive models of ecological interactions (e.g., competition, herbivory) and their role in the proliferation of harmful algal blooms, in addition to increasing our understanding about why these interactions vary in strength within and across environments. 相似文献10.
Background
Many patients with chronic kidney disease (CKD) suffer from fatigue caused by anemia, but that anemia can be reversed. Successful treatment can be measured as a decrease in fatigue and an increase in energy or vitality, particularly on the vitality (VT) subscale of the SF-36. Changes in VT scores are most commonly interpreted in terms of minimally important differences or standardized effect sizes, but neither a minimally important difference nor a standardized effect size provides information about how patients’ activities are affected. Therefore, we analyzed the association between differences in VT scores and a variable that is meaningful to patients and to society the frequency of going out.Study Design
Questionnaire survey. Analyses of differences among participants at bseline, and analyses of differences within participants over time.Setting and Participants
CKD patients who were not on dialysis and were involved in a study of anti-anemia therapy.Predictor
VT scores.Outcome
Frequency of going out.Measurements
VT scores and the frequency of going out.Results
At baseline, higher VT scores and younger age were associated with going out more often, while sex and the presence of diabetic nephropathy were not associated with the frequency of going out. Greater changes in VT scores over time were associated with greater changes in the frequency of going out, in univariate and multivariate analyses.Conclusions
At baseline, VT was associated with the frequency of going out. Increases in VT were also associated with increases in the frequency of going out. These results show how VT scores can be linked to daily activities that are important to individual patients and to society. 相似文献11.
Background
Understanding protein complexes is important for understanding the science of cellular organization and function. Many computational methods have been developed to identify protein complexes from experimentally obtained protein-protein interaction (PPI) networks. However, interaction information obtained experimentally can be unreliable and incomplete. Reconstructing these PPI networks with PPI evidences from other sources can improve protein complex identification.Results
We combined PPI information from 6 different sources and obtained a reconstructed PPI network for yeast through machine learning. Some popular protein complex identification methods were then applied to detect yeast protein complexes using the new PPI networks. Our evaluation indicates that protein complex identification algorithms using the reconstructed PPI network significantly outperform ones on experimentally verified PPI networks.Conclusions
We conclude that incorporating PPI information from other sources can improve the effectiveness of protein complex identification. 相似文献12.
Background and Aims
Functional–structural plant models (FSPMs) simulate biological processes at different spatial scales. Methods exist for multiscale data representation and modification, but the advantages of using multiple scales in the dynamic aspects of FSPMs remain unclear. Results from multiscale models in various other areas of science that share fundamental modelling issues with FSPMs suggest that potential advantages do exist, and this study therefore aims to introduce an approach to multiscale modelling in FSPMs.Methods
A three-part graph data structure and grammar is revisited, and presented with a conceptual framework for multiscale modelling. The framework is used for identifying roles, categorizing and describing scale-to-scale interactions, thus allowing alternative approaches to model development as opposed to correlation-based modelling at a single scale. Reverse information flow (from macro- to micro-scale) is catered for in the framework. The methods are implemented within the programming language XL.Key Results
Three example models are implemented using the proposed multiscale graph model and framework. The first illustrates the fundamental usage of the graph data structure and grammar, the second uses probabilistic modelling for organs at the fine scale in order to derive crown growth, and the third combines multiscale plant topology with ozone trends and metabolic network simulations in order to model juvenile beech stands under exposure to a toxic trace gas.Conclusions
The graph data structure supports data representation and grammar operations at multiple scales. The results demonstrate that multiscale modelling is a viable method in FSPM and an alternative to correlation-based modelling. Advantages and disadvantages of multiscale modelling are illustrated by comparisons with single-scale implementations, leading to motivations for further research in sensitivity analysis and run-time efficiency for these models. 相似文献13.
Roland Wiest Eugenio Abela John Missimer Gerhard Schroth Christian W. Hess Matthias Sturzenegger Danny J. J. Wang Bruno Weder Andrea Federspiel 《PloS one》2014,9(9)
Background
Unilateral ischemic stroke disrupts the well balanced interactions within bilateral cortical networks. Restitution of interhemispheric balance is thought to contribute to post-stroke recovery. Longitudinal measurements of cerebral blood flow (CBF) changes might act as surrogate marker for this process.Objective
To quantify longitudinal CBF changes using arterial spin labeling MRI (ASL) and interhemispheric balance within the cortical sensorimotor network and to assess their relationship with motor hand function recovery.Methods
Longitudinal CBF data were acquired in 23 patients at 3 and 9 months after cortical sensorimotor stroke and in 20 healthy controls using pulsed ASL. Recovery of grip force and manual dexterity was assessed with tasks requiring power and precision grips. Voxel-based analysis was performed to identify areas of significant CBF change. Region-of-interest analyses were used to quantify the interhemispheric balance across nodes of the cortical sensorimotor network.Results
Dexterity was more affected, and recovered at a slower pace than grip force. In patients with successful recovery of dexterous hand function, CBF decreased over time in the contralesional supplementary motor area, paralimbic anterior cingulate cortex and superior precuneus, and interhemispheric balance returned to healthy control levels. In contrast, patients with poor recovery presented with sustained hypoperfusion in the sensorimotor cortices encompassing the ischemic tissue, and CBF remained lateralized to the contralesional hemisphere.Conclusions
Sustained perfusion imbalance within the cortical sensorimotor network, as measured with task-unrelated ASL, is associated with poor recovery of dexterous hand function after stroke. CBF at rest might be used to monitor recovery and gain prognostic information. 相似文献14.
Purpose
To investigate whether social interactions in friendship networks influence the following weight-related behaviors of adolescents: exercising regularly, playing an active sport, hours of TV/Video viewing, sleeping six or fewer hours, eating breakfast on weekdays, frequency of eating at fast food restaurants, eating five servings of fruits/vegetables daily, and consuming calorie-dense snacks.Method
Data from a nationally representative sample of adolescents are used to examine the association between peer and individual weight-related behaviors. Evidence from multivariate regression analysis controlling for an extensive list of individual- and family-level factors as well as school-level unobserved heterogeneity is obtained.Results
We find a significant positive association between individuals'' and friends'' behaviors in terms of sports, exercise and fast food consumption. The estimated associations are robust to controls for individual- and family-level factors, unobserved heterogeneity at the school level and our attempts to account for non-random peer selection.Conclusions
The social transmission of weight-related behaviors is a viable explanation for the spread of obesity in friendship networks documented in recent research. Traditional weight reduction interventions may be fruitfully complemented with strategies that focus on harnessing peer support to modify behaviors. 相似文献15.
Andrew Schoenrock Bahram Samanfar Sylvain Pitre Mohsen Hooshyar Ke Jin Charles A Phillips Hui Wang Sadhna Phanse Katayoun Omidi Yuan Gui Md Alamgir Alex Wong Fredrik Barren?s Mohan Babu Mikael Benson Michael A Langston James R Green Frank Dehne Ashkan Golshani 《BMC bioinformatics》2014,15(1)
Background
Our knowledge of global protein-protein interaction (PPI) networks in complex organisms such as humans is hindered by technical limitations of current methods.Results
On the basis of short co-occurring polypeptide regions, we developed a tool called MP-PIPE capable of predicting a global human PPI network within 3 months. With a recall of 23% at a precision of 82.1%, we predicted 172,132 putative PPIs. We demonstrate the usefulness of these predictions through a range of experiments.Conclusions
The speed and accuracy associated with MP-PIPE can make this a potential tool to study individual human PPI networks (from genomic sequences alone) for personalized medicine.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0383-1) contains supplementary material, which is available to authorized users. 相似文献16.
Background
Compartmentalization and nestedness are common patterns in ecological networks. The aim of this study was to elucidate some of the processes shaping these patterns in a well resolved network of host/pathogen interactions.Methology/Principal Findings
Based on a long-term (1972–2005) survey of forest health at the regional scale (all French forests; 15 million ha), we uncovered an almost fully connected network of 51 tree taxa and 157 parasitic fungal species. Our analyses revealed that the compartmentalization of the network maps out the ancient evolutionary history of seed plants, but not the ancient evolutionary history of fungal species. The very early divergence of the major fungal phyla may account for this asymmetric influence of past evolutionary history. Unlike compartmentalization, nestedness did not reflect any consistent phylogenetic signal. Instead, it seemed to reflect the ecological features of the current species, such as the relative abundance of tree species and the life-history strategies of fungal pathogens. We discussed how the evolution of host range in fungal species may account for the observed nested patterns.Conclusion/Significance
Overall, our analyses emphasized how the current complexity of ecological networks results from the diversification of the species and their interactions over evolutionary times. They confirmed that the current architecture of ecological networks is not only dependant on recent ecological processes. 相似文献17.
Background
HIV-related outcomes may be affected by biological sex and by pregnancy. Including women in general and pregnant women in particular in HIV-related research is important for generalizability of findings.Objective
To characterize representation of pregnant and non-pregnant women in HIV-related research conducted in general populations.Data Sources
All HIV-related articles published in fifteen journals from January to March of 2011. We selected the top five journals by 2010 impact factor, in internal medicine, infectious diseases, and HIV/AIDS.Study Eligibility Criteria
HIV-related studies reporting original research on questions applicable to both men and women of reproductive age were considered; studies were excluded if they did not include individual-level patient data.Study appraisal and synthesis methods.
Articles were doubly reviewed and abstracted; discrepancies were resolved through consensus. We recorded proportion of female study participants, whether pregnant women were included or excluded, and other key factors.Results
In total, 2014 articles were published during this period. After screening, 259 articles were included as original HIV-related research reporting individual-level data; of these, 226 were determined to be articles relevant to both men and women of reproductive age. In these articles, women were adequately represented within geographic region. The vast majority of published articles, 183/226 (81%), did not mention pregnancy (or related issues); still fewer included pregnant women (n=33), reported numbers of pregnant women (n=19), or analyzed using pregnancy status (n=9).Limitations
Data were missing for some key variables, including pregnancy. The time period over which published works were evaluated was relatively short.Conclusions and implications of key findings.
The under-reporting and inattention to pregnancy in the HIV literature may reduce policy-makers’ ability to set evidence-based policy around HIV/AIDS care for pregnant women and women of child-bearing age. 相似文献18.
Background
Radial intra- and interlaminar connections form a basic microcircuit in primary auditory cortex (AI) that extracts acoustic information and distributes it to cortical and subcortical networks. Though the structure of this microcircuit is known, we do not know how the functional connectivity between layers relates to laminar processing.Methodology/Principal Findings
We studied the relationships between functional connectivity and receptive field properties in this columnar microcircuit by simultaneously recording from single neurons in cat AI in response to broadband dynamic moving ripple stimuli. We used spectrotemporal receptive fields (STRFs) to estimate the relationship between receptive field parameters and the functional connectivity between pairs of neurons. Interlaminar connectivity obtained through cross-covariance analysis reflected a consistent pattern of information flow from thalamic input layers to cortical output layers. Connection strength and STRF similarity were greatest for intralaminar neuron pairs and in supragranular layers and weaker for interlaminar projections. Interlaminar connection strength co-varied with several STRF parameters: feature selectivity, phase locking to the stimulus envelope, best temporal modulation frequency, and best spectral modulation frequency. Connectivity properties and receptive field relationships differed for vertical and horizontal connections.Conclusions/Significance
Thus, the mode of local processing in supragranular layers differs from that in infragranular layers. Therefore, specific connectivity patterns in the auditory cortex shape the flow of information and constrain how spectrotemporal processing transformations progress in the canonical columnar auditory microcircuit. 相似文献19.
Background
Simple models inspired by processes shaping consumer-resource interactions have helped to establish the primary processes underlying the organization of food webs, networks of trophic interactions among species. Because other ecological interactions such as mutualisms between plants and their pollinators and seed dispersers are inherently based in consumer-resource relationships we hypothesize that processes shaping food webs should organize mutualistic relationships as well.Methodology/Principal Findings
We used a likelihood-based model selection approach to compare the performance of food web models and that of a model designed for mutualisms, in reproducing the structure of networks depicting mutualistic relationships. Our results show that these food web models are able to reproduce the structure of most of the mutualistic networks and even the simplest among the food web models, the cascade model, often reproduce overall structural properties of real mutualistic networks.Conclusions/Significance
Based on our results we hypothesize that processes leading to feeding hierarchy, which is a characteristic shared by all food web models, might be a fundamental aspect in the assembly of mutualisms. These findings suggest that similar underlying ecological processes might be important in organizing different types of interactions. 相似文献20.