Exploiting Conceptual Modeling for Searching Genomic Metadata: A Quantitative and Qualitative Empirical Study

Providing a common data model for the metadata of several heterogenous genomic data sources is hard, as they do not share any standard or agreed practice for metadata description. Two years ago we managed to discover a subset of common metadata present in most sources and to organize it as a smart genomic conceptual model (GCM); the model has been instrumental to our efforts in the development of a major software pipeline for data integration. More recently, we developed a user-friendly search interface, based on a simplified version of GCM. In this paper, we report our evaluation of the effectiveness of this new user interface. Specifically, we present the results of a compendious empirical study to answer the research question: How much is such a simple interface well-understood by a standard user? The target of this study is a mixed population, composed by biologists, bioinformaticians and computer scientists. The result of our empirical study shows that the users were successful in producing search queries starting from their natural language description, as they did it with good accuracy and small error rate. The study also shows that most users were generally satisfied; it provides indications on how to improve our search system and how to continue our effort in integration of genomic sources. We are consequently adapting the user interface, that will be soon opened to public use

Generality of shear thickening in suspensions

Suspensions are of wide interest and form the basis for many smart fluids. For most suspensions, the viscosity decreases with increasing shear rate, i.e. they shear thin. Few are reported to do the opposite, i.e. shear thicken, despite the longstanding expectation that shear thickening is a generic type of suspension behavior. Here we resolve this apparent contradiction. We demonstrate that shear thickening can be masked by a yield stress and can be recovered when the yield stress is decreased below a threshold. We show the generality of this argument and quantify the threshold in rheology experiments where we control yield stresses arising from a variety of sources, such as attractions from particle surface interactions, induced dipoles from applied electric and magnetic fields, as well as confinement of hard particles at high packing fractions. These findings open up possibilities for the design of smart suspensions that combine shear thickening with electro- or magnetorheological response.Comment: 11 pages, 9 figures, accepted for publication in Nature Material

Evolution favors protein mutational robustness in sufficiently large populations

BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar proteins can differ substantially in their robustness to mutations and capacity to evolve new functions, but it has remained unclear whether any of these differences might be due to evolutionary selection for these properties. RESULTS: Here we use laboratory experiments to demonstrate that evolution favors protein mutational robustness if the evolving population is sufficiently large. We neutrally evolve cytochrome P450 proteins under identical selection pressures and mutation rates in populations of different sizes, and show that proteins from the larger and thus more polymorphic population tend towards higher mutational robustness. Proteins from the larger population also evolve greater stability, a biophysical property that is known to enhance both mutational robustness and evolvability. The excess mutational robustness and stability is well described by existing mathematical theories, and can be quantitatively related to the way that the proteins occupy their neutral network. CONCLUSIONS: Our work is the first experimental demonstration of the general tendency of evolution to favor mutational robustness and protein stability in highly polymorphic populations. We suggest that this phenomenon may contribute to the mutational robustness and evolvability of viruses and bacteria that exist in large populations

Characterization and comparisons of microbiota in different intestinal segments between adult Chinese Shanxi Black Pigs and Large White Pigs

The carcass weight of Chinese Shanxi Black Pigs is relatively lower in comparison with that of the counterparts, i.e., Large White Pigs, although the former are resistant to harsh conditions. Since gut microflora has been recognized to play a key role in pork production, it is of interest to explore the microbial communities in different intestinal segments of pigs and its potential relatedness with host features. In this study, 16S rRNA gene amplicon sequencing, accompanied by the inter- and intra-group comparisons, was implemented to investigate the structure composition and potential functions of microbial communities of four distinct intestinal segments [duodenum (D), jejunum (J), ileum (I), and cecum (C)] between adult Chinese Shanxi Black Pigs and Large White Pigs. Comparative survey revealed that the dominant phylum in both breeds was Firmicutes, followed by Proteobacteria, and Bacteroidetes. At the genus level, Lactobacillus was predominant in all samples, and Prevotella was specifically prevalent in the cecum. Further inspection showed the differences of dominant species in the same segments between these two groups. Notably, unique taxa in C and D segments were more than that in I and J segments. Additionally, each segment was characterized by specifically enriched genera, and distinctive pathways were predicted in certain intestinal segments. In short, the findings presented a coherent picture of structure composition and predicted functionalities of gut microbiota in diverse intestinal segments of adult Chinese Shanxi Black Pigs and Large White Pigs, and extend the understanding of potential link between intestinal microbiota and their hosts

From Nonspecific DNA–Protein Encounter Complexes to the Prediction of DNA–Protein Interactions

©2009 Gao, Skolnick. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.doi:10.1371/journal.pcbi.1000341DNA–protein interactions are involved in many essential biological activities. Because there is no simple mapping code between DNA base pairs and protein amino acids, the prediction of DNA–protein interactions is a challenging problem. Here, we present a novel computational approach for predicting DNA-binding protein residues and DNA–protein interaction modes without knowing its specific DNA target sequence. Given the structure of a DNA-binding protein, the method first generates an ensemble of complex structures obtained by rigid-body docking with a nonspecific canonical B-DNA. Representative models are subsequently selected through clustering and ranking by their DNA–protein interfacial energy. Analysis of these encounter complex models suggests that the recognition sites for specific DNA binding are usually favorable interaction sites for the nonspecific DNA probe and that nonspecific DNA–protein interaction modes exhibit some similarity to specific DNA–protein binding modes. Although the method requires as input the knowledge that the protein binds DNA, in benchmark tests, it achieves better performance in identifying DNA-binding sites than three previously established methods, which are based on sophisticated machine-learning techniques. We further apply our method to protein structures predicted through modeling and demonstrate that our method performs satisfactorily on protein models whose root-mean-square Ca deviation from native is up to 5 Å from their native structures. This study provides valuable structural insights into how a specific DNA-binding protein interacts with a nonspecific DNA sequence. The similarity between the specific DNA–protein interaction mode and nonspecific interaction modes may reflect an important sampling step in search of its specific DNA targets by a DNA-binding protein

Molecular dynamics simulations of oscillatory Couette flows with slip boundary conditions

The effect of interfacial slip on steady-state and time-periodic flows of monatomic liquids is investigated using non-equilibrium molecular dynamics simulations. The fluid phase is confined between atomically smooth rigid walls, and the fluid flows are induced by moving one of the walls. In steady shear flows, the slip length increases almost linearly with shear rate. We found that the velocity profiles in oscillatory flows are well described by the Stokes flow solution with the slip length that depends on the local shear rate. Interestingly, the rate dependence of the slip length obtained in steady shear flows is recovered when the slip length in oscillatory flows is plotted as a function of the local shear rate magnitude. For both types of flows, the friction coefficient at the liquid-solid interface correlates well with the structure of the first fluid layer near the solid wall.Comment: 31 pages, 11 figure

A Decision Support Tool for the Selection of Promoting Actions to Encourage Collaboration in Projects for the Agriculture Sector

[EN] Development and innovation agencies promote consortiums of agricultural stakeholders to collaborate in the proposal of projects for public calls. To achieve this partnerships, these agencies should select between different promoting actions to be performed with two objectives: maximize the number of project proposals presented and minimize the resources invested. To support agencies with these decisions, a computer tool based on a multi-objective integer linear programming model is proposed. To deal with the two objectives the weighting sum method is implemented. The model is validated in different scenarios by means a realistic case of an agency in Brittany (France). The results show the conflict between the two objectives considered and the dependency of the solutions on the scenarios defined. As a conclusion it can be stated that: 1) decision-makers should be careful in defining the weights of each objective and 2) the impact of the different promoting actions on the level of stakeholders¿ participation should be precisely estimated.The authors acknowledge the support of the project 691249, RUCAPS: "Enhancing and implementing knowledge based ICT solutions within high risk and uncertain conditions for agriculture production systems", funded by the European Union¿s research and innovation programme under the H2020 Marie Sk¿odowska-Curie Actions.Alemany Díaz, MDM.; Alarcón Valero, F.; Pérez Perales, D.; Guyon, C. (2020). A Decision Support Tool for the Selection of Promoting Actions to Encourage Collaboration in Projects for the Agriculture Sector. IFIP Advances in Information and Communication Technology. 598:534-545. https://doi.org/10.1007/978-3-030-62412-5_44S534545598European Comission Funded Programs. https://ec.europa.eu/programmes/horizon2020Zoie, C., Radulescu, M.: Decision analysis for the project selection problem under risk. IFAC Proc. 34(8), 445–450 (2001)Sadi-Nezhad, S.: A state-of-art survey on project selection using MCDM techniques. J. Project Manage. 2, 1–10 (2017)Caballero, H.C., Chopra, S., Schmidt, E.K.: Project portfolio selection using mathematical programming and optimization methods. In: Paper presented at PMI® Global Congress 2012–North America, Vancouver, British Columbia, Canada, Newtown Square, PA, Project Management Institute (2012)Ahmad, B., Haq, I.: Project selection techniques, relevance and applications in Pakistan. Int. J. Technol. Res. 4, 52–60 (2016)Inuiguchi, M., Ramı́k, J.: Possibilistic linear programming: a brief review of fuzzy mathematical programming and a comparison with stochastic programming in portfolio selection problem. Fuzzy Sets Syst. 111(1), 3–28 (2000)Stewart, R., Mohamed, S.: IT/IS projects selection using multi-criteria utility theory. Log. Inf. Manage. 15(4), 254–270 (2002)Alzober, W., Yaakub, A.R.: Integrated model for MCDM: selection contractor in Malaysian construction industry. In: Applied Mechanics and Materials 548, pp. 1587–1595. Trans Tech Publications (2014)Adhikary, P., Roy, P.K., Mazumdar, A.: Optimal renewable energy project selection: a multi-criteria optimization technique approach. Global J. Pure Appl. Math. 11(5), 3319–3329 (2015)Strang, K.D.: Portfolio selection methodology for a nuclear project. Project Manage. J. 42(2), 81–93 (2011)Benjamin, C.O.: A linear goal-programming model for public-sector project selection. J. Oper. Res. Soc. 36(1), 13–23 (1985)Coronado, J.R., Pardo-Mora, E.M., Valero, M.: A multi-objective model for selection of projects to finance new enterprise SMEs in Colombia. J. Ind. Eng. Manage. 4(3), 407–417 (2011)Mat, N.A.C., Cheung, Y.: Partner selection: criteria for successful collaborative network. In: 20th Australian Conference on Information Systems, pp. 631–641 (2009)Camarinha-Matos, L.M., Afsarmanesh, H.: Collaborative Networks. In: Wang, K., Kovacs, G.L., Wozny, M., Fang, M. (eds.) PROLAMAT 2006. IIFIP, vol. 207, pp. 26–40. Springer, Boston, MA (2006). https://doi.org/10.1007/0-387-34403-9_4Paixão, M., Sbragia, R., Kruglianskas, I.: Factors for selecting partners in innovation projects–evidences from alliances in the Brazilian petrochemical leader. Rev. Admin. Innov. São Paulo 11(2), 241–272 (2014)Duisters, D., Duysters, G., de Man, A.P.: The partner selection process: steps, effectiveness, governance. Ann. Hematol. 2, 7–25 (2011)Zhang, X.: Criteria for selecting the private-sector partner in public-private partnerships. J. Constr. Eng. Manage. 131(6), 631–644 (2005

China's economic co-operation related investment:an investigation of its direction and some implications for outward investment

Chinese firms undertake large scale contracted projects in a number of countries under the auspices of economic cooperation. While there are suggestions that these activities are an extension of China's soft power aimed at facilitating Chinese foreign direct investment (FDI) in those countries, often for access to natural resources, there is no systematic analysis of this in the literature. In this paper, we examine China's economic cooperation related investment (ECI) over time. Our results suggest that the pattern of investment is indeed explained well by factors that are used in the stylised literature to explain directional patterns of outward FDI. They also demonstrate that the (positive) relationship between Chinese ECI and the recipient countries' natural resource richness is not economically meaningful. Finally, while there is some support for the popular wisdom that China is willing to do business with countries with weak political rights, the evidence suggests that, ceteris paribus, its ECI is more likely to flow to countries with low corruption levels and, by extension, better institutions

Regional innovation and spillover effects of foreign direct investment in China: a threshold approach

Using a data set on twenty-nine Chinese provinces for the period 1985–2008, this paper establishes a threshold model to analyse the relationship between spillover effects of foreign direct investment (FDI) and regional innovation in China. There is clear evidence of double-threshold effects of regional innovation on productivity spillovers from FDI. Specifically, only when the level of regional innovation reaches the minimum innovation threshold will FDI in the region begin to produce positive productivity spillovers. Furthermore, positive productivity spillovers from FDI will be substantial only when the level of regional innovation attains a higher threshold. The double threshold divides Chinese provinces into three super-regions in terms of innovation, with most provinces positioned within the middle-level innovation super-region. Policy implications are discussed