30 results
Search Results
2. Even a good influenza forecasting model can benefit from internet-based nowcasts, but those benefits are limited.
- Author
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Osthus, Dave, Daughton, Ashlynn R., and Priedhorsky, Reid
- Subjects
INFLUENZA ,RESPIRATORY infections ,PUBLIC health ,MATHEMATICAL models of forecasting - Abstract
The ability to produce timely and accurate flu forecasts in the United States can significantly impact public health. Augmenting forecasts with internet data has shown promise for improving forecast accuracy and timeliness in controlled settings, but results in practice are less convincing, as models augmented with internet data have not consistently outperformed models without internet data. In this paper, we perform a controlled experiment, taking into account data backfill, to improve clarity on the benefits and limitations of augmenting an already good flu forecasting model with internet-based nowcasts. Our results show that a good flu forecasting model can benefit from the augmentation of internet-based nowcasts in practice for all considered public health-relevant forecasting targets. The degree of forecast improvement due to nowcasting, however, is uneven across forecasting targets, with short-term forecasting targets seeing the largest improvements and seasonal targets such as the peak timing and intensity seeing relatively marginal improvements. The uneven forecasting improvements across targets hold even when “perfect” nowcasts are used. These findings suggest that further improvements to flu forecasting, particularly seasonal targets, will need to derive from other, non-nowcasting approaches. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
3. Ten simple rules to create biological network figures for communication.
- Author
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Marai, G. Elisabeta, Pinaud, Bruno, Bühler, Katja, Lex, Alexander, and Morris, John H.
- Subjects
TELECOMMUNICATION systems ,BIOLOGICAL networks ,MEDICAL literature ,PHYSICAL sciences ,REFERENCE sources ,BIOLOGY - Abstract
Biological network figures are ubiquitous in the biology and medical literature. On the one hand, a good network figure can quickly provide information about the nature and degree of interactions between items and enable inferences about the reason for those interactions. On the other hand, good network figures are difficult to create. In this paper, we outline 10 simple rules for creating biological network figures for communication, from choosing layouts, to applying color or other channels to show attributes, to the use of layering and separation. These rules are accompanied by illustrative examples. We also provide a concise set of references and additional resources for each rule. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
4. Ten simple rules to create biological network figures for communication
- Author
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Bruno Pinaud, John H. Morris, G. Elisabeta Marai, Katja Bühler, Alexander Lex, and Lewitter, Fran
- Subjects
0301 basic medicine ,Proteomics ,Light ,Social Sciences ,Biochemistry ,Mathematical Sciences ,0302 clinical medicine ,Sociology ,Simple (abstract algebra) ,Consortia ,Medicine and Health Sciences ,Macromolecular Structure Analysis ,Blastomas ,Attention ,Protein Interaction Maps ,Biology (General) ,Neurological Tumors ,Ecology ,Physics ,Electromagnetic Radiation ,Biological Sciences ,Editorial ,Computational Theory and Mathematics ,Oncology ,Neurology ,Modeling and Simulation ,Physical Sciences ,Visual Perception ,Protein Interaction Networks ,Network Analysis ,Network analysis ,Signal Transduction ,Computer and Information Sciences ,Protein Structure ,Visible Light ,Bioinformatics ,QH301-705.5 ,Color ,Set (abstract data type) ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Data visualization ,Information and Computing Sciences ,Genetics ,Computer Graphics ,Humans ,Protein Interactions ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Information retrieval ,business.industry ,Data Visualization ,Biology and Life Sciences ,Cancers and Neoplasms ,Proteins ,Computational Biology ,030104 developmental biology ,Luminance ,business ,Protein Structure Networks ,030217 neurology & neurosurgery ,Biological network ,Glioblastoma Multiforme - Abstract
Biological network figures are ubiquitous in the biology and medical literature. On the one hand, a good network figure can quickly provide information about the nature and degree of interactions between items and enable inferences about the reason for those interactions. On the other hand, good network figures are difficult to create. In this paper, we outline 10 simple rules for creating biological network figures for communication, from choosing layouts, to applying color or other channels to show attributes, to the use of layering and separation. These rules are accompanied by illustrative examples. We also provide a concise set of references and additional resources for each rule., Author summary Biological network figures are ubiquitous in the biology and medical literature. In this paper, we outline 10 simple rules for creating biological network figures for communication, from choosing layouts, to applying color or other channels to show attributes, to the use of layering and separation.
- Published
- 2019
5. Estimating influenza incidence using search query deceptiveness and generalized ridge regression.
- Author
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Priedhorsky, Reid, Daughton, Ashlynn R., Barnard, Martha, O’Connell, Fiona, and Osthus, Dave
- Subjects
DISEASE incidence ,INFLUENZA ,SEASONAL influenza ,REGRESSION analysis ,INTERNET usage monitoring ,PHYSICAL sciences - Abstract
Seasonal influenza is a sometimes surprisingly impactful disease, causing thousands of deaths per year along with much additional morbidity. Timely knowledge of the outbreak state is valuable for managing an effective response. The current state of the art is to gather this knowledge using in-person patient contact. While accurate, this is time-consuming and expensive. This has motivated inquiry into new approaches using internet activity traces, based on the theory that lay observations of health status lead to informative features in internet data. These approaches risk being deceived by activity traces having a coincidental, rather than informative, relationship to disease incidence; to our knowledge, this risk has not yet been quantitatively explored. We evaluated both simulated and real activity traces of varying deceptiveness for influenza incidence estimation using linear regression. We found that deceptiveness knowledge does reduce error in such estimates, that it may help automatically-selected features perform as well or better than features that require human curation, and that a semantic distance measure derived from the Wikipedia article category tree serves as a useful proxy for deceptiveness. This suggests that disease incidence estimation models should incorporate not only data about how internet features map to incidence but also additional data to estimate feature deceptiveness. By doing so, we may gain one more step along the path to accurate, reliable disease incidence estimation using internet data. This capability would improve public health by decreasing the cost and increasing the timeliness of such estimates. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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- View/download PDF
6. Fast and near-optimal monitoring for healthcare acquired infection outbreaks.
- Author
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Adhikari, Bijaya, Lewis, Bryan, Vullikanti, Anil, Jiménez, José Mauricio, and Prakash, B. Aditya
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MEDICAL personnel ,INFECTION ,PREVENTIVE medicine ,HOSPITAL patients - Abstract
According to the Centers for Disease Control and Prevention (CDC), one in twenty five hospital patients are infected with at least one healthcare acquired infection (HAI) on any given day. Early detection of possible HAI outbreaks help practitioners implement countermeasures before the infection spreads extensively. Here, we develop an efficient data and model driven method to detect outbreaks with high accuracy. We leverage mechanistic modeling of C. difficile infection, a major HAI disease, to simulate its spread in a hospital wing and design efficient near-optimal algorithms to select people and locations to monitor using an optimization formulation. Results show that our strategy detects up to 95% of “future” C. difficile outbreaks. We design our method by incorporating specific hospital practices (like swabbing for infections) as well. As a result, our method outperforms state-of-the-art algorithms for outbreak detection. Finally, a qualitative study of our result shows that the people and locations we select to monitor as sensors are intuitive and meaningful. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
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7. Learning the structure of the world: The adaptive nature of state-space and action representations in multi-stage decision-making.
- Author
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Dezfouli, Amir and Balleine, Bernard W.
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SMART structures ,ADAPTIVE natural resource management ,NATURE ,BRAIN mapping ,COGNITIVE psychology ,DECISION making - Abstract
State-space and action representations form the building blocks of decision-making processes in the brain; states map external cues to the current situation of the agent whereas actions provide the set of motor commands from which the agent can choose to achieve specific goals. Although these factors differ across environments, it is currently unknown whether or how accurately state and action representations are acquired by the agent because previous experiments have typically provided this information a priori through instruction or pre-training. Here we studied how state and action representations adapt to reflect the structure of the world when such a priori knowledge is not available. We used a sequential decision-making task in rats in which they were required to pass through multiple states before reaching the goal, and for which the number of states and how they map onto external cues were unknown a priori. We found that, early in training, animals selected actions as if the task was not sequential and outcomes were the immediate consequence of the most proximal action. During the course of training, however, rats recovered the true structure of the environment and made decisions based on the expanded state-space, reflecting the multiple stages of the task. Similarly, we found that the set of actions expanded with training, although the emergence of new action sequences was sensitive to the experimental parameters and specifics of the training procedure. We conclude that the profile of choices shows a gradual shift from simple representations to more complex structures compatible with the structure of the world. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
8. Colony entropy—Allocation of goods in ant colonies.
- Author
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Greenwald, Efrat, Eckmann, Jean-Pierre, and Feinerman, Ofer
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INSECT societies ,ANT colonies ,HYMENOPTERA - Abstract
Allocation of goods is a key feature in defining the connection between the individual and the collective scale in any society. Both the process by which goods are to be distributed, and the resulting allocation to the members of the society may affect the success of the population as a whole. One of the most striking natural examples of a highly successful cooperative society is the ant colony which often acts as a single superorganism. In particular, each individual within the ant colony has a “communal stomach” which is used to store and share food with the other colony members by mouth to mouth feeding. Sharing food between communal stomachs allows the colony as a whole to get its food requirements and, more so, allows each individual within the colony to reach its nutritional intake target. The vast majority of colony members do not forage independently but obtain their food through secondary interactions in which food is exchanged between individuals. The global effect of this exchange is not well understood. To gain better understanding into this process we used fluorescence imaging to measure how food from a single external source is distributed and mixed within a Camponotus sanctus ant colony. Using entropic measures to quantify food-blending, we show that while collected food flows into all parts of the colony it mixes only partly. We show that mixing is controlled by the ants’ interaction rule which implies that only a fraction of the maximal potential is actually transferred. This rule leads to a robust blending process: i.e., neither the exact food volume that is transferred, nor the interaction schedule are essential to generate the global outcome. Finally, we show how the ants’ interaction rules may optimize a trade-off between fast dissemination and efficient mixing. Our results regarding the distribution of a single food source provide a baseline for future studies on distributed regulation of multiple food sources in social insect colonies. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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9. Think: Theory for Africa.
- Author
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Currin, Christopher B., Khoza, Phumlani N., Antrobus, Alexander D., Latham, Peter E., Vogels, Tim P., and Raimondo, Joseph V.
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SCIENTIFIC knowledge ,SOCIAL sciences education ,TECHNOLOGY ,COMPUTATIONAL neuroscience ,SCIENCE & state - Abstract
The article offers information on the challenging scientific problems faced by humanity. Topics discussed include information on the efforts to empower Africans to join the global neuroscience community; discussions on the BRAIN initiative in the U.S. and the Human Brain Project in Europe; and the information on the limiting factor for computational neuroscience development in Africa.
- Published
- 2019
- Full Text
- View/download PDF
10. Epidemic prevalence information on social networks can mediate emergent collective outcomes in voluntary vaccine schemes.
- Author
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Sharma, Anupama, Menon, Shakti N., Sasidevan, V., and Sinha, Sitabhra
- Subjects
VACCINATION ,HERD immunity ,DISEASE prevalence ,EPIDEMICS ,SOCIAL networks - Abstract
The effectiveness of a mass vaccination program can engender its own undoing if individuals choose to not get vaccinated believing that they are already protected by herd immunity. This would appear to be the optimal decision for an individual, based on a strategic appraisal of her costs and benefits, even though she would be vulnerable during subsequent outbreaks if the majority of the population argues in this manner. We investigate how voluntary vaccination can nevertheless emerge in a social network of rational agents, who make informed decisions whether to be vaccinated, integrated with a model of epidemic dynamics. The information available to each agent includes the prevalence of the disease in their local network neighborhood and/or globally in the population, as well as the fraction of their neighbors that are protected against the disease. Crucially, the payoffs governing the decision of agents vary with disease prevalence, resulting in the vaccine uptake behavior changing in response to contagion spreading. The collective behavior of the agents responding to local prevalence can lead to a significant reduction in the final epidemic size, particularly for less contagious diseases having low basic reproduction number . Near the epidemic threshold () the use of local prevalence information can result in divergent responses in the final vaccine coverage. Our results suggest that heterogeneity in the risk perception resulting from the spatio-temporal evolution of an epidemic differentially affects agents’ payoffs, which is a critical determinant of the success of voluntary vaccination schemes. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
11. Efficient algorithms to discover alterations with complementary functional association in cancer.
- Author
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Sarto Basso, Rebecca, Hochbaum, Dorit S., and Vandin, Fabio
- Subjects
CANCER genetics ,PERTURBATION theory ,PHENOTYPES ,ALGORITHMS ,COMPUTATIONAL biology - Abstract
Recent large cancer studies have measured somatic alterations in an unprecedented number of tumours. These large datasets allow the identification of cancer-related sets of genetic alterations by identifying relevant combinatorial patterns. Among such patterns, mutual exclusivity has been employed by several recent methods that have shown its effectiveness in characterizing gene sets associated to cancer. Mutual exclusivity arises because of the complementarity, at the functional level, of alterations in genes which are part of a group (e.g., a pathway) performing a given function. The availability of quantitative target profiles, from genetic perturbations or from clinical phenotypes, provides additional information that can be leveraged to improve the identification of cancer related gene sets by discovering groups with complementary functional associations with such targets. In this work we study the problem of finding groups of mutually exclusive alterations associated with a quantitative (functional) target. We propose a combinatorial formulation for the problem, and prove that the associated computational problem is computationally hard. We design two algorithms to solve the problem and implement them in our tool UNCOVER. We provide analytic evidence of the effectiveness of UNCOVER in finding high-quality solutions and show experimentally that UNCOVER finds sets of alterations significantly associated with functional targets in a variety of scenarios. In particular, we show that our algorithms find sets which are better than the ones obtained by the state-of-the-art method, even when sets are evaluated using the statistical score employed by the latter. In addition, our algorithms are much faster than the state-of-the-art, allowing the analysis of large datasets of thousands of target profiles from cancer cell lines. We show that on two such datasets, one from project Achilles and one from the Genomics of Drug Sensitivity in Cancer project, UNCOVER identifies several significant gene sets with complementary functional associations with targets. Software available at: . [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
12. Network motifs and their origins.
- Author
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Stone, Lewi, Simberloff, Daniel, and Artzy-Randrup, Yael
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SCIENCE ,DYNAMICS ,ECOLOGY ,LITERATURE ,BIOLOGY - Abstract
Author summary Modern network science is a new and exciting research field that has transformed the study of complex systems over the last 2 decades. Of particular interest is the identification of small “network motifs” that might be embedded in a larger network and that indicate the presence of evolutionary design principles or have an overly influential role on system-wide dynamics. Motifs are patterns of interconnections, or subgraphs, that appear in an observed network significantly more often than in compatible randomized networks. The concept of network motifs was introduced into Systems Biology by Milo, Alon and colleagues in 2002, quickly revolutionized the field, and it has had a huge impact in wider scientific domains ever since. Here, we argue that the same concept and tools for the detection of motifs were well known in the ecological literature decades into the last century, a fact that is generally not recognized. We review the early history of network motifs, their evolution in the mathematics literature, and their recent rediscoveries. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
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13. A simple computer vision pipeline reveals the effects of isolation on social interaction dynamics in Drosophila.
- Author
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Linneweber, Gerit A., Claeys, Annelies, Liu, Guangda, Hassan, Bassem A., Sneyders, Manu, Nicasy, Hans, Scheunders, Paul, Nath, Tanmay, De Backer, Steve, Weyn, Barbara, Guo, Zhengyu, Li, Jin, Yu, Peng, and Bengochea, Mercedes
- Subjects
ISOLATION (Philosophy) ,DROSOPHILA ,SOCIAL isolation ,FRUIT flies ,GENE expression ,CHARTS, diagrams, etc. ,ANIMAL behavior - Abstract
Isolation profoundly influences social behavior in all animals. In humans, isolation has serious effects on health and disease. Drosophila melanogaster is a powerful model to study small-scale, temporally-transient social behavior. However, longer-term analysis of large groups of flies is hampered by the lack of effective and reliable tools. We built a new imaging arena and improved the existing tracking algorithm to reliably follow a large number of flies simultaneously. Next, based on the automatic classification of touch and graph-based social network analysis, we designed an algorithm to quantify changes in the social network in response to prior social isolation. We observed that isolation significantly and swiftly enhanced individual and local social network parameters depicting near-neighbor relationships. We explored the genome-wide molecular correlates of these behavioral changes and found that whereas behavior changed throughout the six days of isolation, gene expression alterations occurred largely on day one. These changes occurred mostly in metabolic genes, and we verified the metabolic changes by showing an increase of lipid content in isolated flies. In summary, we describe a highly reliable tracking and analysis pipeline for large groups of flies that we use to unravel the behavioral, molecular and physiological impact of isolation on social network dynamics in Drosophila. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
14. Eleven quick tips for running an interdisciplinary short course for new graduate students.
- Author
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Saunders, Timothy E., He, Cynthia Y., Koehl, Patrice, Ong, L. L. Sharon, and So, Peter T. C.
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INTERDISCIPLINARY education ,GRADUATE students ,REASONING ,LIFE science education - Abstract
Quantitative reasoning and techniques are increasingly ubiquitous across the life sciences. However, new graduate researchers with a biology background are often not equipped with the skills that are required to utilize such techniques correctly and efficiently. In parallel, there are increasing numbers of engineers, mathematicians, and physical scientists interested in studying problems in biology with only basic knowledge of this field. Students from such varied backgrounds can struggle to engage proactively together to tackle problems in biology. There is therefore a need to establish bridges between those disciplines. It is our proposal that the beginning of graduate school is the appropriate time to initiate those bridges through an interdisciplinary short course. We have instigated an intensive 10-day course that brought together new graduate students in the life sciences from across departments within the National University of Singapore. The course aimed at introducing biological problems as well as some of the quantitative approaches commonly used when tackling those problems. We have run the course for three years with over 100 students attending. Building on this experience, we share 11 quick tips on how to run such an effective, interdisciplinary short course for new graduate students in the biosciences. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
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15. Costs of task allocation with local feedback: Effects of colony size and extra workers in social insects and other multi-agent systems.
- Author
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Radeva, Tsvetomira, Dornhaus, Anna, Lynch, Nancy, Nagpal, Radhika, and Su, Hsin-Hao
- Subjects
TASK analysis ,EMPLOYEES' workload ,JOB performance ,LABOR productivity ,ADAPTABILITY (Personality) ,PROBLEM solving - Abstract
Adaptive collective systems are common in biology and beyond. Typically, such systems require a task allocation algorithm: a mechanism or rule-set by which individuals select particular roles. Here we study the performance of such task allocation mechanisms measured in terms of the time for individuals to allocate to tasks. We ask: (1) Is task allocation fundamentally difficult, and thus costly? (2) Does the performance of task allocation mechanisms depend on the number of individuals? And (3) what other parameters may affect their efficiency? We use techniques from distributed computing theory to develop a model of a social insect colony, where workers have to be allocated to a set of tasks; however, our model is generalizable to other systems. We show, first, that the ability of workers to quickly assess demand for work in tasks they are not currently engaged in crucially affects whether task allocation is quickly achieved or not. This indicates that in social insect tasks such as thermoregulation, where temperature may provide a global and near instantaneous stimulus to measure the need for cooling, for example, it should be easy to match the number of workers to the need for work. In other tasks, such as nest repair, it may be impossible for workers not directly at the work site to know that this task needs more workers. We argue that this affects whether task allocation mechanisms are under strong selection. Second, we show that colony size does not affect task allocation performance under our assumptions. This implies that when effects of colony size are found, they are not inherent in the process of task allocation itself, but due to processes not modeled here, such as higher variation in task demand for smaller colonies, benefits of specialized workers, or constant overhead costs. Third, we show that the ratio of the number of available workers to the workload crucially affects performance. Thus, workers in excess of those needed to complete all tasks improve task allocation performance. This provides a potential explanation for the phenomenon that social insect colonies commonly contain inactive workers: these may be a ‘surplus’ set of workers that improves colony function by speeding up optimal allocation of workers to tasks. Overall our study shows how limitations at the individual level can affect group level outcomes, and suggests new hypotheses that can be explored empirically. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
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16. Ten simple rules for short and swift presentations.
- Author
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Lortie, Christopher J.
- Subjects
SCIENTIFIC communication ,SLIDES (Photography) ,GRAPHIC design ,SCIENCE ,COMMUNICATION - Abstract
The article offers tips on preparing short and swift scientific presentations. Since immediacy is important, preparing one primary message for the audience is suggested. Slides can be used to present a clear story by discussing one major point per slide. Using simple visuals is recommended. The style, graphical design, language and imagery of the presentation should be consistent.
- Published
- 2017
- Full Text
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17. Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.
- Author
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Hacisuleyman, Aysima and Erman, Burak
- Subjects
ALLOSTERIC proteins ,ENTROPY ,UBIQUITIN ,POLYMERASE chain reaction ,COOPERATIVE binding (Biochemistry) - Abstract
It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic property of all proteins. Here, we develop a computational method that can determine and quantify allosteric activity in any given protein. Based on Schreiber's transfer entropy formulation, our approach leads to an information transfer landscape for the protein that shows the presence of entropy sinks and sources and explains how pairs of residues communicate with each other using entropy transfer. The model can identify the residues that drive the fluctuations of others. We apply the model to Ubiquitin, whose allosteric activity has not been emphasized until recently, and show that there are indeed systematic pathways of entropy and information transfer between residues that correlate well with the activities of the protein. We use 600 nanosecond molecular dynamics trajectories for Ubiquitin and its complex with human polymerase iota and evaluate entropy transfer between all pairs of residues of Ubiquitin and quantify the binding susceptibility changes upon complex formation. We explain the complex formation propensities of Ubiquitin in terms of entropy transfer. Important residues taking part in allosteric communication in Ubiquitin predicted by our approach are in agreement with results of NMR relaxation dispersion experiments. Finally, we show that time delayed correlation of fluctuations of two interacting residues possesses an intrinsic causality that tells which residue controls the interaction and which one is controlled. Our work shows that time delayed correlations, entropy transfer and causality are the required new concepts for explaining allosteric communication in proteins. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
18. The Virtuous Cycle of a Data Ecosystem.
- Author
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Voytek, Bradley
- Subjects
INFORMATION sharing ,BIG data ,DATA mining ,AGGREGATION (Statistics) ,META-analysis - Abstract
The article discusses the virtuous cycle of a data ecosystem. Topics include the increasing creation of digital data of all types, the benefits of data sharing which include data remixing and combining, bias minimization and meta-analysis, and the growth of data collection techniques along with data aggregation and mining algorithms.
- Published
- 2016
- Full Text
- View/download PDF
19. Targeted pandemic containment through identifying local contact network bottlenecks
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Chris T. Bauch, Di Wang, Shenghao Yang, Priyabrata Senapati, and Kimon Fountoulakis
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FOS: Computer and information sciences ,Viral Diseases ,Facebook ,Computer science ,Epidemiology ,Distributed computing ,Social Sciences ,01 natural sciences ,Systems Science ,Oregon ,Medical Conditions ,Sociology ,Agent-Based Modeling ,Medicine and Health Sciences ,Centrality ,Biology (General) ,Computer Networks ,0303 health sciences ,education.field_of_study ,Ecology ,Simulation and Modeling ,Quebec ,Social Communication ,Computer Science - Social and Information Networks ,Infectious Diseases ,Computational Theory and Mathematics ,Social Networks ,Modeling and Simulation ,Convex optimization ,Physical Sciences ,Network Analysis ,Algorithms ,Research Article ,Physics - Physics and Society ,Computer and Information Sciences ,QH301-705.5 ,Population ,FOS: Physical sciences ,Physics and Society (physics.soc-ph) ,Research and Analysis Methods ,Models, Biological ,Bottleneck ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,0103 physical sciences ,Genetics ,Humans ,Computer Simulation ,Quantitative Biology - Populations and Evolution ,010306 general physics ,education ,Molecular Biology ,Pandemics ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Social and Information Networks (cs.SI) ,Simulation modeling ,Populations and Evolution (q-bio.PE) ,COVID-19 ,Covid 19 ,Flow network ,Communications ,Transmission (telecommunications) ,Flow (mathematics) ,FOS: Biological sciences ,Social Media ,Mathematics - Abstract
Decision-making about pandemic mitigation often relies upon simulation modelling. Models of disease transmission through networks of contacts--between individuals or between population centres--are increasingly used for these purposes. Real-world contact networks are rich in structural features that influence infection transmission, such as tightly-knit local communities that are weakly connected to one another. In this paper, we propose a new flow-based edge-betweenness centrality method for detecting bottleneck edges that connect nodes in contact networks. In particular, we utilize convex optimization formulations based on the idea of diffusion with p-norm network flow. Using simulation models of COVID-19 transmission through real network data at both individual and county levels, we demonstrate that targeting bottleneck edges identified by the proposed method reduces the number of infected cases by up to 10% more than state-of-the-art edge-betweenness methods. Furthermore, the proposed method is orders of magnitude faster than existing methods., Comment: 38 pages, 21 figures
- Published
- 2021
20. Ten Simple Rules for Curating and Facilitating Small Workshops.
- Author
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McInerny, Greg J.
- Subjects
FORUMS ,WORKSHOPS (Facilities) -- Design & construction ,RESEARCH ,TOPIC & comment (Grammar) ,DISCUSSION ,TIME perspective ,INTERACTION model (Communication) - Abstract
The article discusses the creation of good workshops which could be in a diverse form and fit different goals. This is needed for exploring a single research topic, initiation of working group, and interdisciplinary collaborations. It requires attendees, timetables, and interactions. Topics discussed processes in facilitating workshops including assessment on past success and failures, developing of workshop name, and preparing for speakers speech.
- Published
- 2016
- Full Text
- View/download PDF
21. Disease Surveillance on Complex Social Networks.
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Herrera, Jose L., Srinivasan, Ravi, Brownstein, John S., Galvani, Alison P., and Meyers, Lauren Ancel
- Subjects
PUBLIC health ,SOCIAL dating ,DATING (Social customs) ,NETWORK society ,SOCIAL networks - Abstract
As infectious disease surveillance systems expand to include digital, crowd-sourced, and social network data, public health agencies are gaining unprecedented access to high-resolution data and have an opportunity to selectively monitor informative individuals. Contact networks, which are the webs of interaction through which diseases spread, determine whether and when individuals become infected, and thus who might serve as early and accurate surveillance sensors. Here, we evaluate three strategies for selecting sensors—sampling the most connected, random, and friends of random individuals—in three complex social networks—a simple scale-free network, an empirical Venezuelan college student network, and an empirical Montreal wireless hotspot usage network. Across five different surveillance goals—early and accurate detection of epidemic emergence and peak, and general situational awareness—we find that the optimal choice of sensors depends on the public health goal, the underlying network and the reproduction number of the disease (R
0 ). For diseases with a low R0 , the most connected individuals provide the earliest and most accurate information about both the onset and peak of an outbreak. However, identifying network hubs is often impractical, and they can be misleading if monitored for general situational awareness, if the underlying network has significant community structure, or if R0 is high or unknown. Taking a theoretical approach, we also derive the optimal surveillance system for early outbreak detection but find that real-world identification of such sensors would be nearly impossible. By contrast, the friends-of-random strategy offers a more practical and robust alternative. It can be readily implemented without prior knowledge of the network, and by identifying sensors with higher than average, but not the highest, epidemiological risk, it provides reasonably early and accurate information. [ABSTRACT FROM AUTHOR]- Published
- 2016
- Full Text
- View/download PDF
22. How to Estimate Epidemic Risk from Incomplete Contact Diaries Data?
- Author
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Mastrandrea, Rossana and Barrat, Alain
- Subjects
RISK factors of epidemics ,PROXIMITY detectors ,COMMUNICABLE diseases ,HETEROGENEITY ,PROFILE descriptions (Education) - Abstract
Social interactions shape the patterns of spreading processes in a population. Techniques such as diaries or proximity sensors allow to collect data about encounters and to build networks of contacts between individuals. The contact networks obtained from these different techniques are however quantitatively different. Here, we first show how these discrepancies affect the prediction of the epidemic risk when these data are fed to numerical models of epidemic spread: low participation rate, under-reporting of contacts and overestimation of contact durations in contact diaries with respect to sensor data determine indeed important differences in the outcomes of the corresponding simulations with for instance an enhanced sensitivity to initial conditions. Most importantly, we investigate if and how information gathered from contact diaries can be used in such simulations in order to yield an accurate description of the epidemic risk, assuming that data from sensors represent the ground truth. The contact networks built from contact sensors and diaries present indeed several structural similarities: this suggests the possibility to construct, using only the contact diary network information, a surrogate contact network such that simulations using this surrogate network give the same estimation of the epidemic risk as simulations using the contact sensor network. We present and compare several methods to build such surrogate data, and show that it is indeed possible to obtain a good agreement between the outcomes of simulations using surrogate and sensor data, as long as the contact diary information is complemented by publicly available data describing the heterogeneity of the durations of human contacts. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
23. Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability.
- Author
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Schiffthaler, Bastian, Kostadima, Myrto, null, null, Delhomme, Nicolas, and Rustici, Gabriella
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DATA analysis ,COMPUTER software reusability ,TRAINING manuals ,TECHNICAL manuals ,LEARNING ability - Abstract
The advancement of high-throughput sequencing (HTS) technologies and the rapid development of numerous analysis algorithms and pipelines in this field has resulted in an unprecedentedly high demand for training scientists in HTS data analysis. Embarking on developing new training materials is challenging for many reasons. Trainers often do not have prior experience in preparing or delivering such materials and struggle to keep them up to date. A repository of curated HTS training materials would support trainers in materials preparation, reduce the duplication of effort by increasing the usage of existing materials, and allow for the sharing of teaching experience among the HTS trainers’ community. To achieve this, we have developed a strategy for materials’ curation and dissemination. Standards for describing training materials have been proposed and applied to the curation of existing materials. A Git repository has been set up for sharing annotated materials that can now be reused, modified, or incorporated into new courses. This repository uses Git; hence, it is decentralized and self-managed by the community and can be forked/built-upon by all users. The repository is accessible at . [ABSTRACT FROM AUTHOR]
- Published
- 2016
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24. High-Degree Neurons Feed Cortical Computations.
- Author
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Timme, Nicholas M., Ito, Shinya, Myroshnychenko, Maxym, Nigam, Sunny, Shimono, Masanori, Yeh, Fang-Chin, Hottowy, Pawel, Litke, Alan M., and Beggs, John M.
- Subjects
NEURONS ,HIGHER nervous activity ,INFORMATION resources ,COMPUTATIONAL mechanics ,MULTIVARIATE analysis - Abstract
Recent work has shown that functional connectivity among cortical neurons is highly varied, with a small percentage of neurons having many more connections than others. Also, recent theoretical developments now make it possible to quantify how neurons modify information from the connections they receive. Therefore, it is now possible to investigate how information modification, or computation, depends on the number of connections a neuron receives (in-degree) or sends out (out-degree). To do this, we recorded the simultaneous spiking activity of hundreds of neurons in cortico-hippocampal slice cultures using a high-density 512-electrode array. This preparation and recording method combination produced large numbers of neurons recorded at temporal and spatial resolutions that are not currently available in any in vivo recording system. We utilized transfer entropy (a well-established method for detecting linear and nonlinear interactions in time series) and the partial information decomposition (a powerful, recently developed tool for dissecting multivariate information processing into distinct parts) to quantify computation between neurons where information flows converged. We found that computations did not occur equally in all neurons throughout the networks. Surprisingly, neurons that computed large amounts of information tended to receive connections from high out-degree neurons. However, the in-degree of a neuron was not related to the amount of information it computed. To gain insight into these findings, we developed a simple feedforward network model. We found that a degree-modified Hebbian wiring rule best reproduced the pattern of computation and degree correlation results seen in the real data. Interestingly, this rule also maximized signal propagation in the presence of network-wide correlations, suggesting a mechanism by which cortex could deal with common random background input. These are the first results to show that the extent to which a neuron modifies incoming information streams depends on its topological location in the surrounding functional network. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
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25. The Development of Audio-Visual Integration for Temporal Judgements.
- Author
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Adams, Wendy J.
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SENSORIMOTOR integration ,PERCEPTUAL-motor processes ,SENSORY processing disorder ,SENSES - Abstract
Adults combine information from different sensory modalities to estimate object properties such as size or location. This process is optimal in that (i) sensory information is weighted according to relative reliability: more reliable estimates have more influence on the combined estimate and (ii) the combined estimate is more reliable than the component uni-modal estimates. Previous studies suggest that optimal sensory integration does not emerge until around 10 years of age. Younger children rely on a single modality or combine information using inappropriate sensory weights. Children aged 4–11 and adults completed a simple audio-visual task in which they reported either the number of beeps or the number of flashes in uni-modal and bi-modal conditions. In bi-modal trials, beeps and flashes differed in number by 0, 1 or 2. Mutual interactions between the sensory signals were evident at all ages: the reported number of flashes was influenced by the number of simultaneously presented beeps and vice versa. Furthermore, for all ages, the relative strength of these interactions was predicted by the relative reliabilities of the two modalities, in other words, all observers weighted the signals appropriately. The degree of cross-modal interaction decreased with age: the youngest observers could not ignore the task-irrelevant modality—they fully combined vision and audition such that they perceived equal numbers of flashes and beeps for bi-modal stimuli. Older observers showed much smaller effects of the task-irrelevant modality. Do these interactions reflect optimal integration? Full or partial cross-modal integration predicts improved reliability in bi-modal conditions. In contrast, switching between modalities reduces reliability. Model comparison suggests that older observers employed partial integration, whereas younger observers (up to around 8 years) did not integrate, but followed a sub-optimal switching strategy, responding according to either visual or auditory information on each trial. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
26. Robust Brain-Machine Interface Design Using Optimal Feedback Control Modeling and Adaptive Point Process Filtering.
- Author
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Shanechi, Maryam M., Orsborn, Amy L., and Carmena, Jose M.
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BRAIN-computer interfaces ,FEEDBACK control systems ,KALMAN filtering ,DECODERS (Electronics) ,MOTOR ability testing ,NEUROLOGIC examination - Abstract
Much progress has been made in brain-machine interfaces (BMI) using decoders such as Kalman filters and finding their parameters with closed-loop decoder adaptation (CLDA). However, current decoders do not model the spikes directly, and hence may limit the processing time-scale of BMI control and adaptation. Moreover, while specialized CLDA techniques for intention estimation and assisted training exist, a unified and systematic CLDA framework that generalizes across different setups is lacking. Here we develop a novel closed-loop BMI training architecture that allows for processing, control, and adaptation using spike events, enables robust control and extends to various tasks. Moreover, we develop a unified control-theoretic CLDA framework within which intention estimation, assisted training, and adaptation are performed. The architecture incorporates an infinite-horizon optimal feedback-control (OFC) model of the brain’s behavior in closed-loop BMI control, and a point process model of spikes. The OFC model infers the user’s motor intention during CLDA—a process termed intention estimation. OFC is also used to design an autonomous and dynamic assisted training technique. The point process model allows for neural processing, control and decoder adaptation with every spike event and at a faster time-scale than current decoders; it also enables dynamic spike-event-based parameter adaptation unlike current CLDA methods that use batch-based adaptation on much slower adaptation time-scales. We conducted closed-loop experiments in a non-human primate over tens of days to dissociate the effects of these novel CLDA components. The OFC intention estimation improved BMI performance compared with current intention estimation techniques. OFC assisted training allowed the subject to consistently achieve proficient control. Spike-event-based adaptation resulted in faster and more consistent performance convergence compared with batch-based methods, and was robust to parameter initialization. Finally, the architecture extended control to tasks beyond those used for CLDA training. These results have significant implications towards the development of clinically-viable neuroprosthetics. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
27. Evolution of Cooperation in Social Dilemmas on Complex Networks.
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Iyer, Swami and Killingback, Timothy
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COOPERATION ,DILEMMA -- Social aspects ,NATURAL selection ,MATHEMATICAL models ,INTERGROUP relations - Abstract
Cooperation in social dilemmas is essential for the functioning of systems at multiple levels of complexity, from the simplest biological organisms to the most sophisticated human societies. Cooperation, although widespread, is fundamentally challenging to explain evolutionarily, since natural selection typically favors selfish behavior which is not socially optimal. Here we study the evolution of cooperation in three exemplars of key social dilemmas, representing the prisoner’s dilemma, hawk-dove and coordination classes of games, in structured populations defined by complex networks. Using individual-based simulations of the games on model and empirical networks, we give a detailed comparative study of the effects of the structural properties of a network, such as its average degree, variance in degree distribution, clustering coefficient, and assortativity coefficient, on the promotion of cooperative behavior in all three classes of games. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
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28. Social Norms of Cooperation in Small-Scale Societies.
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Santos, Fernando P., Santos, Francisco C., and Pacheco, Jorge M.
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SOCIAL norms ,SOCIAL control ,NORMALIZATION (Sociology) ,ORGANIZATIONAL behavior ,COMPUTATIONAL biology - Abstract
Indirect reciprocity, besides providing a convenient framework to address the evolution of moral systems, offers a simple and plausible explanation for the prevalence of cooperation among unrelated individuals. By helping someone, an individual may increase her/his reputation, which may change the pre-disposition of others to help her/him in the future. This, however, depends on what is reckoned as a good or a bad action, i.e., on the adopted social norm responsible for raising or damaging a reputation. In particular, it remains an open question which social norms are able to foster cooperation in small-scale societies, while enduring the wide plethora of stochastic affects inherent to finite populations. Here we address this problem by studying the stochastic dynamics of cooperation under distinct social norms, showing that the leading norms capable of promoting cooperation depend on the community size. However, only a single norm systematically leads to the highest cooperative standards in small communities. That simple norm dictates that only whoever cooperates with good individuals, and defects against bad ones, deserves a good reputation, a pattern that proves robust to errors, mutations and variations in the intensity of selection. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
29. Ten simple rules for partnering with K-12 teachers to support broader impact goals
- Author
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Louise S. Mead, Kristin M. Bass, Alexa Warwick, Frieda Reichsman, and Angela Kolonich
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0301 basic medicine ,Evolutionary Genetics ,Science and Technology Workforce ,Biomedical Research ,Social Sciences ,Careers in Research ,Science education ,0302 clinical medicine ,Learning and Memory ,Sociology ,ComputingMilieux_COMPUTERSANDEDUCATION ,Psychology ,Cooperative Behavior ,Biology (General) ,Grade level ,Simple (philosophy) ,Schools ,Ecology ,Professional development ,Research Personnel ,Professions ,Science research ,Editorial ,Computational Theory and Mathematics ,Modeling and Simulation ,Physical Sciences ,Educational Status ,Engineering ethics ,Human learning ,Science Policy ,QH301-705.5 ,Science ,Materials Science ,Schoolchildren ,Biology ,Education ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Human Learning ,Genetics ,Humans ,Learning ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Evolutionary Biology ,Cognitive Psychology ,Biology and Life Sciences ,Teachers ,030104 developmental biology ,Science Education ,People and Places ,Cognitive Science ,Scientists ,Population Groupings ,School Teachers ,030217 neurology & neurosurgery ,Professional expertise ,Neuroscience - Abstract
Contributing to broader impacts is an important aspect of scientific research. Engaging practicing K-12 teachers as part of a research project can be an effective approach for addressing broader impacts requirements of grants, while also advancing researcher and teacher professional growth. Our focus is on leveraging teachers' professional expertise to develop science education materials grounded in emerging scientific research. In this paper, we describe ten simple rules for planning, implementing, and evaluating teacher engagement to support the broader impact goals of your research project. These collaborations can lead to the development of instructional materials or activities for students in the classroom or provide science research opportunities for teachers. We share our successes and lessons learned while collaborating with high school biology teachers to create technology-based, instructional materials developed from basic biological research. The rules we describe are applicable across teacher partnerships at any grade level in that they emphasize eliciting and respecting teachers' professionalism and expertise.
- Published
- 2020
30. Simulated epidemics in an empirical spatiotemporal network of 50,185 sexual contacts
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Luis E. C. Rocha, Petter Holme, and Fredrik Liljeros
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Male ,Human immunodeficiency virus (HIV) ,Public Health and Epidemiology/Infectious Diseases ,medicine.disease_cause ,law.invention ,Disease Outbreaks ,Models ,law ,Econometrics ,Sociology ,Biology (General) ,Ecology ,Statistical ,Transmission (mechanics) ,Sexual Partners ,Computational Theory and Mathematics ,Modeling and Simulation ,Physical Sciences ,Probability distribution ,Female ,Brazil ,Network analysis ,Research Article ,Sexual network ,Physics - Physics and Society ,QH301-705.5 ,Sexually Transmitted Diseases ,FOS: Physical sciences ,Topology (electrical circuits) ,Prostitution ,Physics and Society (physics.soc-ph) ,Network topology ,Models, Biological ,Physics/Interdisciplinary Physics ,Cellular and Molecular Neuroscience ,Genetics ,medicine ,Infectious Diseases/Sexually Transmitted Diseases ,Humans ,Fysik ,Computer Simulation ,Quantitative Biology - Populations and Evolution ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Simulation ,Sex work ,Internet ,Models, Statistical ,Populations and Evolution (q-bio.PE) ,Biological ,Sex Work ,FOS: Biological sciences ,Public Health and Epidemiology/Epidemiology - Abstract
Sexual contact patterns, both in their temporal and network structure, can influence the spread of sexually transmitted infections (STI). Most previous literature has focused on effects of network topology; few studies have addressed the role of temporal structure. We simulate disease spread using SI and SIR models on an empirical temporal network of sexual contacts in high-end prostitution. We compare these results with several other approaches, including randomization of the data, classic mean-field approaches, and static network simulations. We observe that epidemic dynamics in this contact structure have well-defined, rather high epidemic thresholds. Temporal effects create a broad distribution of outbreak sizes, even if the per-contact transmission probability is taken to its hypothetical maximum of 100%. In general, we conclude that the temporal correlations of our network accelerate outbreaks, especially in the early phase of the epidemics, while the network topology (apart from the contact-rate distribution) slows them down. We find that the temporal correlations of sexual contacts can significantly change simulated outbreaks in a large empirical sexual network. Thus, temporal structures are needed alongside network topology to fully understand the spread of STIs. On a side note, our simulations further suggest that the specific type of commercial sex we investigate is not a reservoir of major importance for HIV., Author Summary Human sexual contacts form a spatiotemporal network—the underlying structure over which sexually transmitted infections (STI) spread. By understanding the structure of this system we can better understand the dynamics of STIs. So far, there has been much focus on the static network structure of sexual contacts. In this paper, we extend this approach and also address temporal effects in a special type of sexual network—that of Internet-mediated prostitution. We analyze reported sexual contacts, probably the largest record of such, from a Brazilian Internet community where sex buyers rate their encounters with escorts. First, we thoroughly investigated disease spread in this dynamic sexual network. We found that the temporal correlations in this system would accelerate disease spread, especially at shorter time scales, whereas geographical effects would slow down an outbreak. More specifically, we found that this contact structure could sustain more contagious diseases, like human papillomavirus, but not HIV. These results highlight the importance of prostitution in the global dynamics of STIs.
- Published
- 2011
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