24 results
Search Results
2. Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology.
- Author
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Bonham, Kevin S. and Stefan, Melanie I.
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STEM education ,COMPUTATIONAL biology ,BIBLIOMETRICS ,SCIENCE publishing ,SCIENCE & state - Abstract
While women are generally underrepresented in STEM fields, there are noticeable differences between fields. For instance, the gender ratio in biology is more balanced than in computer science. We were interested in how this difference is reflected in the interdisciplinary field of computational/quantitative biology. To this end, we examined the proportion of female authors in publications from the PubMed and arXiv databases. There are fewer female authors on research papers in computational biology, as compared to biology in general. This is true across authorship position, year, and journal impact factor. A comparison with arXiv shows that quantitative biology papers have a higher ratio of female authors than computer science papers, placing computational biology in between its two parent fields in terms of gender representation. Both in biology and in computational biology, a female last author increases the probability of other authors on the paper being female, pointing to a potential role of female PIs in influencing the gender balance. [ABSTRACT FROM AUTHOR]
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- 2017
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3. 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
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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
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4. Ten Simple Rules for a Bioinformatics Journal Club.
- Author
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Lonsdale, Andrew, Sietsma Penington, Jocelyn, Rice, Timothy, Walker, Michael, and Dashnow, Harriet
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BIOINFORMATICS ,INFORMATION science ,COMPUTATIONAL biology ,CLUBS ,SCIENTIFIC literature ,SOCIETIES - Abstract
The article outlines the rules for a bioinformatics journal club which, according to the authors, is a great way to take in the scientific literature, keep up with developments in their field, and hone their communication and analytical skills. The rules include holding a journal club at eight in the morning, finding good articles for discussion, and expanding the roster of leaders as people join the journal club.
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- 2016
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5. Ten simple rules for measuring the impact of workshops.
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Sufi, Shoaib, Nenadic, Aleksandra, Silva, Raniere, Balzano, Melissa, Coelho, Sara, Ford, Heather, Jones, Catherine, Higgins, Vanessa, Duckles, Beth, Simera, Iveta, de Beyer, Jennifer A., Struthers, Caroline, Nurmikko-Fuller, Terhi, Bellis, Louisa, Miah, Wadud, Wilde, Adriana, Emsley, Iain, and Philippe, Olivier
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FORUMS ,RESEARCH ,DECISION making ,STRATEGIC planning ,PARTICIPATION - Abstract
Workshops are used to explore a specific topic, to transfer knowledge, to solve identified problems, or to create something new. In funded research projects and other research endeavours, workshops are the mechanism used to gather the wider project, community, or interested people together around a particular topic. However, natural questions arise: how do we measure the impact of these workshops? Do we know whether they are meeting the goals and objectives we set for them? What indicators should we use? In response to these questions, this paper will outline rules that will improve the measurement of the impact of workshops. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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6. Ten simple rules for drawing scientific comics.
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McDermott, Jason E., Partridge, Matthew, and Bromberg, Yana
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COMIC books, strips, etc. ,SCIENTIFIC terminology ,SCIENTIFIC communication ,SCIENCE journalism ,SCIENTIFIC community - Abstract
The article presents guidelines for drawing scientific comics for efficient communication of difficult ideas. Suggestions mentioned include finding the right shapes for use in conveying the appropriate message one is trying to make, making one's comics simple to convey a complicated idea easier to understand, and taking time to ensure that the details in one's comics are right.
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- 2018
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7. Ten simple rules for providing optimal administrative support to research teams.
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Garrido, Romina, Trowbridge, Casandra A., and Tamura, Nana
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RESEARCH teams ,ADMINISTRATIVE assistants ,SOCIAL learning ,PROFESSIONAL relationships ,SCIENTIFIC community ,CULTURAL pluralism ,HEBBIAN memory ,BUSINESS communication - Abstract
You can help your principal investigator on the oversight of grant rules and procedures, keeping protocols up to date, writing reports, and fulfilling requests from the Institutional Review Board (IRB). Regardless, what is important is for the administrator to be curious about science and make the effort to get a basic familiarity with the scientific discipline and academic working environment they are supporting. Although human resources, principal investigators, and lab managers are a large part of the onboarding process for a new employee, administrative staff are typically involved in the process as well. [Extracted from the article]
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- 2019
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8. Estimating influenza incidence using search query deceptiveness and generalized ridge regression.
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Priedhorsky, Reid, Daughton, Ashlynn R., Barnard, Martha, O’Connell, Fiona, and Osthus, Dave
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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]
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- 2019
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9. Ten simple rules for helping newcomers become contributors to open projects.
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Sholler, Dan, Steinmacher, Igor, Ford, Denae, Averick, Mara, Hoye, Mike, and Wilson, Greg
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SOCIAL learning ,OPEN source software ,SCIENCE education ,HEBBIAN memory ,SOFTWARE engineering ,LIFE sciences ,SCIENCE & state ,HUMAN-computer interaction - Abstract
Open-source software projects are also communities of effort. "...developers who join an organization through these programs are half as likely to transition into long-term community members than developers who do not use these programs... although developers who do succeed through these programs find them valuable". 47 Fagerholm F, Guinea AS, Münch J, Borenstein J. The role of mentoring and project characteristics for onboarding in open source software projects. [Extracted from the article]
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- 2019
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10. Learning the structure of the world: The adaptive nature of state-space and action representations in multi-stage decision-making.
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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]
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- 2019
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11. Efficient algorithms to discover alterations with complementary functional association in cancer.
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Sarto Basso, Rebecca, Hochbaum, Dorit S., and Vandin, Fabio
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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
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12. Ten simple rules for organizing a webinar series.
- Author
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Fadlelmola, Faisal M., Panji, Sumir, Ahmed, Azza E., Ghouila, Amel, Akurugu, Wisdom A., Entfellner, Jean-Baka Domelevo, Souiai, Oussema, Mulder, Nicola, and null, null
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WEBINARS ,COMMUNITIES ,AUDIENCES ,EMAIL ,SOCIAL media - Abstract
The article presents ten simple rules for hosting a regular webinar series with particular emphasis on resource-constrained communities like many in Africa. Topics include aligning a webinar theme to the expectations of the audience; settling on a convenient and user friendly webinar platform; and announcing webinars through mailing lists and social media platform.
- Published
- 2019
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13. Limits on reliable information flows through stochastic populations.
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Boczkowski, Lucas, Natale, Emanuele, Feinerman, Ofer, and Korman, Amos
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BIOLOGICAL systems ,INFORMATION processing ,NOISE ,COMMUNICATION ,BIOLOGICAL networks - Abstract
Biological systems can share and collectively process information to yield emergent effects, despite inherent noise in communication. While man-made systems often employ intricate structural solutions to overcome noise, the structure of many biological systems is more amorphous. It is not well understood how communication noise may affect the computational repertoire of such groups. To approach this question we consider the basic collective task of rumor spreading, in which information from few knowledgeable sources must reliably flow into the rest of the population. We study the effect of communication noise on the ability of groups that lack stable structures to efficiently solve this task. We present an impossibility result which strongly restricts reliable rumor spreading in such groups. Namely, we prove that, in the presence of even moderate levels of noise that affect all facets of the communication, no scheme can significantly outperform the trivial one in which agents have to wait until directly interacting with the sources—a process which requires linear time in the population size. Our results imply that in order to achieve efficient rumor spread a system must exhibit either some degree of structural stability or, alternatively, some facet of the communication which is immune to noise. We then corroborate this claim by providing new analyses of experimental data regarding recruitment in Cataglyphis niger desert ants. Finally, in light of our theoretical results, we discuss strategies to overcome noise in other biological systems. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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14. Submit a Topic Page to PLOS Computational Biology and Wikipedia.
- Author
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Mietchen, Daniel, Wodak, Shoshana, Wasik, Szymon, Szostak, Natalia, and Dessimoz, Christophe
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COMPUTATIONAL biology ,AUTHORS ,READERSHIP ,ORIGIN of life - Abstract
The article offers information on the periodical's `Topic Pages' project as a way to help fill important gaps in Wikipedia's coverage of computational biology content and to credit authors for their contributions. It mentions that hypercycle theory is now more accessible not only for advanced readers, but also for ordinary people who seek knowledge on the computational aspects of the origins of life.
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- 2018
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15. Ten simple rules to create a serious game, illustrated with examples from structural biology.
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Baaden, Marc, Delalande, Olivier, Ferey, Nicolas, Pasquali, Samuela, Waldispühl, Jérôme, and Taly, Antoine
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VIDEO games ,SCIENCE ,RULES ,TEACHING ,GAMES - Abstract
The article presents simple rules for developing serious scientific videogames. One rule is that the goal of the game should be defined in a clear way in terms of science and teaching. Another rule is that equilibrium has to be created between scientific accuracy and player accessibility. Another rule is that one should let the players interact with scientific data.
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- 2018
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16. Ten Simple Rules for a Bioinformatics Journal Club
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Michael L. Walker, Timothy Rice, Harriet Dashnow, Jocelyn Sietsma Penington, and Andrew Lonsdale
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0301 basic medicine ,Time Factors ,Economics ,Computer science ,Social Sciences ,Biologists ,Scientific literature ,Bioinformatics ,Coffee ,Attitudes (Psychology) ,Social group ,Database and Informatics Methods ,Learning and Memory ,Sociology ,Psychology ,lcsh:QH301-705.5 ,Careers ,Ecology ,Attendance ,Social Communication ,Professions ,Editorial ,Computational Theory and Mathematics ,Modeling and Simulation ,Analytical skill ,Club ,Periodicals as Topic ,Journal club ,Employment ,Research and Analysis Methods ,Peer Group ,Critical mass (sociodynamics) ,Human Learning ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Genetics ,Learning ,Humans ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Cognitive Psychology ,Biology and Life Sciences ,Relaxation (Psychology) ,Computational Biology ,Peer group ,Communications ,030104 developmental biology ,lcsh:Biology (General) ,Labor Economics ,People and Places ,Cognitive Science ,Scientists ,Population Groupings ,Neuroscience - Abstract
As science becomes increasingly interdisciplinary, we are expected to acquire both breadth of knowledge and depth of expertise. In bioinformatics, this is especially true. Keeping up to date with major techniques across multiple specialisations can be daunting, but you need not face it alone. A journal club is an excellent way to take in the scientific literature, keep up with developments in your field, and hone your communication and analytical skills. In general, a journal club is a group of people who meet regularly to discuss one or more scientific papers. The structure of such a club can vary. In the more traditional format, an individual studies a paper and then presents it to the group, usually in the form of PowerPoint slides, with time for questions. In some institutions, the journal club is for students only, designed to fulfill the requirements of a course or postgraduate program; attendance is obligatory, the scope of the literature is narrow, and the format is prescribed. The preparation of slides and a lecture may be required. Other kinds of journal clubs are just lab meetings in disguise, with the usual lab head and group members in attendance and one member nominated to present the paper. A formal style often fits well within an established academic structure—but what if your discipline is emerging? Consider the field of bioinformatics. Expertise may be spread across departments and institutions, and there may not be an obvious place or critical mass in any one lab for a traditional journal club. Research students, “pet bioinformaticians,” [1] and those interested in bioinformatics from adjoining fields all need a place to gather. We are pleased to offer an alternative structure to address this situation—an informal journal club, designed to bring together a diversity of backgrounds and career stages to discuss bioinformatics while building a network of like-minded peers. Additional benefits of such a journal club may include friendship and breakfast (see Rule 2)! We thoroughly recommend it to anyone who asks (as well as those who don’t). While this advice is drawn from our experiences in the Parkville Bioinformatics Journal Club, it is applicable to developing informal journal clubs of all disciplines. The advice contained in these rules will also help those who want to spice up their existing formal format. So don’t be a “lonely bioinformatician”[1], create a journal club! Follow these Ten Simple Rules to find out how.
- Published
- 2016
17. Short-term activity cycles impede information transmission in ant colonies.
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Richardson, Thomas O., Liechti, Jonas I., Stroeymeyt, Nathalie, Bonhoeffer, Sebastian, and Keller, Laurent
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ANT colonies ,TIME series analysis ,CIRCADIAN rhythms ,INFORMATION sharing ,ANT algorithms - Abstract
Rhythmical activity patterns are ubiquitous in nature. We study an oscillatory biological system: collective activity cycles in ant colonies. Ant colonies have become model systems for research on biological networks because the interactions between the component parts are visible to the naked eye, and because the time-ordered contact network formed by these interactions serves as the substrate for the distribution of information and other resources throughout the colony. To understand how the collective activity cycles influence the contact network transport properties, we used an automated tracking system to record the movement of all the individuals within nine different ant colonies. From these trajectories we extracted over two million ant-to-ant interactions. Time-series analysis of the temporal fluctuations of the overall colony interaction and movement rates revealed that both the period and amplitude of the activity cycles exhibit a diurnal cycle, in which daytime cycles are faster and of greater amplitude than night cycles. Using epidemiology-derived models of transmission over networks, we compared the transmission properties of the observed periodic contact networks with those of synthetic aperiodic networks. These simulations revealed that contrary to some predictions, regularly-oscillating contact networks should impede information transmission. Further, we provide a mechanistic explanation for this effect, and present evidence in support of it. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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18. Ten simple rules for short and swift presentations.
- Author
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Lortie, Christopher J.
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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.
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- 2017
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19. Ten simple rules for responsible big data research.
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Zook, Matthew, Barocas, Solon, boyd, danah, Crawford, Kate, Keller, Emily, Gangadharan, Seeta Peña, Goodman, Alyssa, Hollander, Rachelle, Koenig, Barbara A., Metcalf, Jacob, Narayanan, Arvind, Nelson, Alondra, and Pasquale, Frank
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RESEARCH ethics ,BIG data ,DATA security failures ,RESEARCH methodology ,PREVENTION - Abstract
The article discusses the results of a two-year project which aimed to provide guidance to the National Science Foundation (NSF) on how to best encourage ethical practices in scientific and engineering research involving the use of big data research methods and infrastructures. The assumption that most data represent or impact people should be used to guide one's analysis. Researchers are also encouraged to situate and contextualize data to anticipate privacy breaches and minimize harm.
- Published
- 2017
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20. Entropy Transfer between Residue Pairs and Allostery in Proteins: Quantifying Allosteric Communication in Ubiquitin.
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Hacisuleyman, Aysima and Erman, Burak
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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
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21. 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
22. Ten Simple Rules for Curating and Facilitating Small Workshops.
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McInerny, Greg J.
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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
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23. High-Degree Neurons Feed Cortical Computations.
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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.
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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
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24. Transmission delays and frequency detuning can regulate information flow between brain regions
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Aref Pariz, Ingo Fischer, Claudio R. Mirasso, Alireza Valizadeh, Agencia Estatal de Investigación (España), Ministerio de Economía y Competitividad (España), European Commission, and Ministerio de Ciencia e Innovación (España)
- Subjects
0301 basic medicine ,Information transfer ,Computer science ,Social Sciences ,Phase Determination ,0302 clinical medicine ,Sociology ,Animal Cells ,Biology (General) ,Information exchange ,Phase response curve ,Neurons ,Soil Perturbation ,Ecology ,Artificial neural network ,Oscillation ,Functional connectivity ,Brain ,Computational Theory and Mathematics ,Modeling and Simulation ,Connectome ,Crystallographic Techniques ,Engineering and Technology ,Cellular Types ,Network Analysis ,Research Article ,Signal Transduction ,Computer and Information Sciences ,Neural Networks ,QH301-705.5 ,Models, Neurological ,Soil Science ,Research and Analysis Methods ,Topology ,03 medical and health sciences ,Cellular and Molecular Neuroscience ,Quality (physics) ,Genetics ,Information flow (information theory) ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Quantitative Biology::Neurons and Cognition ,Biology and Life Sciences ,Cell Biology ,Communications ,Signaling Networks ,030104 developmental biology ,Transmission (telecommunications) ,Cellular Neuroscience ,Signal Processing ,Earth Sciences ,Cognitive Science ,030217 neurology & neurosurgery ,Neuroscience - Abstract
[Abstract] Brain networks exhibit very variable and dynamical functional connectivity and flexible configurations of information exchange despite their overall fixed structure. Brain oscillations are hypothesized to underlie time-dependent functional connectivity by periodically changing the excitability of neural populations. In this paper, we investigate the role of the connection delay and the detuning between the natural frequencies of neural populations in the transmission of signals. Based on numerical simulations and analytical arguments, we show that the amount of information transfer between two oscillating neural populations could be determined by their connection delay and the mismatch in their oscillation frequencies. Our results highlight the role of the collective phase response curve of the oscillating neural populations for the efficacy of signal transmission and the quality of the information transfer in brain networks., [Author summary] Collective dynamics in brain networks are characterized by a coordinated activity of their constituent neurons that lead to brain oscillations. Many evidences highlight the role that brain oscillations play in signal transmission, the control of the effective communication between brain areas, and the integration of information processed by different specialized regions. Oscillations periodically modulate the excitability of neurons and determine the response of those areas receiving the signals. Based on the communication through coherence (CTC) theory, the adjustment of the phase difference between local oscillations of connected areas can specify the timing of exchanged signals and therefore, the efficacy of the communication channels. In this respect, an important factor is the delay in the transmission of signals from one region to another that affects the phase difference and timing, and consequently the impact of the signals. Despite this delay plays an essential role in CTC theory, its role has been mostly overlooked in previous studies. In this manuscript, we concentrate on the role that the connection delay and the oscillation frequency of the populations play in the signal transmission, and consequently in the effective connectivity, between two brain areas. Through extensive numerical simulations, as well as analytical results with reduced models, we show that these parameters have two essential impacts on the effective connectivity of neural networks: First, that the populations advancing in phase to others do not necessarily play the role of the information source; and second, that the amount and direction of information transfer dependents on the oscillation frequency of the populations., The work of AP, IF and CM was partially supported by the Spanish State Research Agency, through the Severo Ochoa and Maria de Maeztu Program for Centers and Units of Excellence in R&D (MDM-2017-0711) and the MINECO (Spain) through project TEC2016-80063-C3 (AEI/FEDER, UE). IF and CM acknowledge support from the Ministerio de Ciencia e Innovación through projects PID2019-111537GB-C21/AEI/10.13039/501100011033 and PID2019-111537GB-C22/AEI/10.13039/501100011033, respectively.
- Published
- 2021
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