Comment on "Deficiencies in molecular dynamics simulation-based prediction of protein-DNA binding free energy landscapes"

Sequence-specific DNA binding transcription factors play an essential role in the transcriptional regulation of all organisms. The development of reliable in silico methods to predict the binding affinity landscapes of transcription factors thus promises to provide rapid screening of transcription factor specificities and, at the same time, yield valuable insight into the atomistic details of the interactions driving those specificities. Recent literature has reported highly discrepant results on the current ability of state-of-the-art atomistic molecular dynamics simulations to reproduce experimental binding free energy landscapes for transcription factors. Here, we resolve one important discrepancy by noting that in the case of alchemical free energy calculations involving base pair mutations, a common convention used in improving end point convergence of mixed potentials in fact can lead to erroneous results. The underlying cause for inaccurate double free energy difference estimates is specific to the particular implementation of the alchemical transformation protocol. Using the Gromacs simulation package, which is not affected by this issue, we obtain free energy landscapes in agreement with the experimental measurements; equivalent results are obtained for a small set of test cases with a modified version of the AMBER package. Our findings provide a consistent and optimistic outlook on the current state of prediction of protein-DNA binding free energy interactions using molecular dynamics simulations and an important precaution for appropriate end point handling in a broad range of free energy calculations

Biofiltration d’un mélange de méthane et de styrène dans des biofiltres inorganiques en présence d’une solution nutritive recyclée

Le méthane (CH4), important gaz à effet de serre (GES), a des effets néfastes sur l'environnement en raison de son potentiel de réchauffement global (PRG). Toute mesure conduisant à une réduction des émissions de CH4 mérite d’être encouragée afin de limiter les effets du changement climatique sur la planète. Le procédé de biofiltration est une approche prometteuse pour l'élimination des émissions de CH4 (concentrations inférieures à 5% v/v). Les micro organismes, contenus dans le biofiltre, ont besoin de nutriments supplémentaires, qui sont généralement ajoutés sous forme d’une solution nutritive (NS). L'excès de NS, quittant le biofiltre sous forme de lixiviat, doit être traité dans des stations de traitement des eaux usées (STEP). Le méthane émis par les stations d'épuration, les sites d’enfouissement, les raffineries et les complexes pétrochimiques peut être accompagné de composés aromatiques tels que des vapeurs de styrène (C8H8). Le styrène est un composé cancérigène qui doit être traité comme un gaz résiduel. La présence d’un mélange de CH4 et de C8H8 dans un biofiltre peut entraîner certaines limitations dans les performances du bioprocédé, en raison des effets inhibiteurs du C8H8 sur la biodégradation du CH4. L'objectif principal de cette étude est de réduire la production de lixiviat et d'examiner la capacité du procédé de biofiltration lors du traitement d'un mélange de CH4 et de C8H8. Premièrement, une revue de la littérature a été effectuée sur la production de CH4 dans les stations d'épuration et les réseaux de canalisation des eaux usées, en tant que source mondiale croissante d'émissions de GES, et sur les approches potentielles permettant la bioélimination du CH4. Deuxièmement, deux biofiltres de 18 L (B1 et B2) remplis d’un garnissage inorganique ont été exploités pendant 283 jours sous un temps de résidence en fût vide (EBRT) constant de 6 min et des charges à l'entrée (IL) de CH4 de 7 à 63 g m-3 h-1. Le biofiltre B1 a été alimenté avec une NS fraîche chaque jour et B2 a été entretenu avec une NS recyclée à partir d'un réservoir de 10 L afin de réduire l’utilisation de NS (les deux biofiltres ont été alimentés avec 2 L d-1 de NS, débit volumique de 1 L min-1). Une conversion maximale de CH4 de 66% (IL de 13 g m 3 h 1) pour B1 et de 67% (IL de 30 g m 3 h 1) pour B2 a été observée. Troisièmement, quatre biofiltres à flux ascendant également remplis d’un garnissage inorganique ont été étudiés à un débit d'air constant de 3 L min-1 pour examiner l'effet du C8H8 sur la biofiltration du CH4. Différentes ILs de CH4, variant dans une plage de 7 à 60 g m 3 h 1, ont été évaluées dans ces biofiltres en utilisant des ILs constantes de C8H8 (B-ME (C8H8 IL de 0 g m 3 h 1), B-200 (C8H8 IL de 9 g m-3 h-1), B-500 (C8H8 IL de 22 g m-3 h-1) et B 700 (C8H8 IL de 32 g m-3 h-1)). Les biofiltres ont été irrigués avec une NS recyclée (débit de 1 L min-1) à partir d'un réservoir de 20 L. Des conversions de C8H8 variant entre 64 et 100% ont été obtenues en augmentant les ILs de CH4 et de C8H8 de 7 à 60 g m-3 h-1 et de 0 à 32 g m 3 h-1, respectivement. Plus de 90% du C8H8 a été éliminé dans les sections basses et centrales des biofiltres. Une étude macro-cinétique basée sur le modèle de Michaelis-Menten a confirmé qu'une inhibition non compétitive s'est produite lors de la biofiltration du mélange CH4+C8H8.Abstract: Methane (CH4), as an important greenhouse gas (GHG), has harmful effects on the environment due to its global warming potency (GWP). Any effort leading to a decline in the emission of CH4 could be a worthy step in order to prevent the planet’s climate change. Biofiltration process is a promising approach for CH4 elimination (concentrations below 5% v/v). Microorganisms in a CH4 biofilter need supplementary nutrients, which are usually added as a nutrient solution (NS). The excess NS leaves the biofilter as leachate, which has to be treated in wastewater treatment plants (WWTPs). Methane emitted from WWTPs, landfills, refineries and petrochemical complexes could be accompanied by aromatic compounds such as styrene (C8H8) vapors. Styrene is a carcinogenic compound and should be treated as a waste gas. Presence of CH4 and C8H8 as a mixture in a biofilter may result in some limits for the bioprocess’s performance, due to the inhibitory effects of C8H8 on CH4 biodegradation. The main objective of this study is to reduce the production of leachate and examine the capability of biofiltration process when treating a mixture of CH4 and C8H8. Firstly, a literature review was provided on the production of CH4 in WWTPs and sewer networks, as a growing worldwide source of GHG emission, and on the potential approaches for CH4 bioelimination. Secondly, two 18 L biofilters (B1 and B2) packed with inorganic materials were operated for 283 days under a constant empty bed residence time (EBRT) of 6 min at CH4 inlet loads (ILs) of 7 to 63 g m-3 h-1. Biofilter B1 was fed with a fresh NS every day and B2 was fed with a recycled NS from a 10 L tank in order to use less NS (both were supplied with 2 L d-1 NS, flow rate of 1 L min-1). Maximum CH4 removal efficiency (RE) of 66% (IL of 13 g m-3 h-1) for B1 and 67% (IL of 30 g m-3 h-1) for B2 was observed. Thirdly, four upflow biofilters also packed with inorganic materials were operated at a constant airflow rate of 3 L min-1 to examine the effect of C8H8 on the CH4 biofilters. Different CH4 ILs varying in the range of 7 to 60 g m-3 h-1 were evaluated in biofilters with constant flow of C8H8. B-ME (C8H8 IL of 0 g m-3 h-1), B-200 (C8H8 IL of 9 g m-3 h-1), B-500 (C8H8 IL of 22 g m-3 h-1) and B-700 (C8H8 IL of 32 g m-3 h-1) were irrigated with recycled NS (1 L d-1, flow rate of 1 L min-1) from a 20 L tank. The C8H8 REs varying between 64 and 100% were obtained at CH4 ILs increasing from 7 to 60 g m-3 h-1 and for C8H8 ILs range of 0 to 32 g m-3 h-1. More than 90% of C8H8 was removed in biofilters’ bottom and middle beds. A macrokinetic study based on the Michaelis-Menten model confirmed that an uncompetitive inhibition occurred during CH4+C8H8 biofiltration

Statistical Clustering Performance in Pavement Condition Prediction as Decision Supporting System Tool

Mathematical methods and statistical patterns have always been considered by managers, designers and science and technology expert in order to develop technology and engineering objectives. During the development of data-gathering tools and increment of data-bases, data mining have made suitable tools in management and engineering. The assessment of roads' maintenance is highly important in order to prevent early deterioration of roads and performing maximum road capacity during the service-life. Pavement management of roads has also implemented this tool to make proper decisions and preferences of pavement repair methods, using decision tree. Through engineering management, cluster analysis is one of the basic tools of data mining and knowledge discovery and makes the decision making, easier in engineering. Data categorization is helpful for planning and is important in picking proper methods. This study was performed by using recorded data from other scientific sources considering data mining method and analyzing data with respect to statistical clustering. The results indicate that bitumen content in asphalt mix, pavement age, marshal strength and rate of passing vehicles have the most important effect on decrement of condition index of pavement, relatively. Also, the highest deterioration in asphalt happens in 5.5% and higher values of bitumen content and the progressive deteriorations take place when the pavement age exceeds 35 years

The Comparison of Aggression between Professional and Semi-Professional Male Taekwondo Athletes in Isfahan, Iran

AbstractAggression is one of the general phenomenon that athletes often directly or indirectly deal with. There are rare issues that are significant as much aggression and violence in sport. The explanation for violent behavior in humans is often the subject of research in the science of sociology. Social changes around the world in recent centuries had a significant impact on cultural structure. In this study, the researchers focused on the aggression of professional and semi-professional athletes in Taekwondo in Isfahan, Iran. The cross-sectional method was applied in this study. To analyze, we examined the relationships between predictor variables and the dependent variable or the variance criterion to explain the changes. The results shown that there was no significant difference between terms of anger and physical aggression among professional and semi-professional. On the other hand, there was meaningful differences between verbal aggression and hostility amongst participants. In addition, the amounts of aggression amongst professional players were more than semi-professional players. Keywords: Aggressive, Athlete, Iran, Isfahan, Professional, Semi-professional, Taekwond

Effect of Drainage and Subgrade Compaction on Pavement Frosting Performance in Construction Zone

The roughness in the construction site surrounding condition and the pavement of the paths of the workzones makes a decrease in the efficiency in executive operation. Increasing the rolling resistance due to the roughness, is one of the reasons for reducing the speed of operation and delay in that. In this study first, the fields of roughness appearance are recognized including inflation due to frost of subgrade and executive operations areas, then frost depth are calculated which is affected by the density conditions and moisture amount of workzone area’s surface. The different percentages of moisture 2, 5, 7, 15 and 20 and compaction ratio 100, 90, 75, 65 percent were considered in this study for density of workzones' top surface. Frost depth calculations are carried out in the US - Army method and by Pavem-Calc software. The results show that an increase in the density of 40 % is caused by a 25 % increase in frozen strain. Furthermore, the increase of 15 % of pavement moisture causes a 20 % increase in the frost depth and the increase of surface roughness. Statistical analyses were carried out to investigate the effectiveness of the research variables and the classification of results in the classification method of CART algorithm

Mobile-Assisted Language Learning: Practices among Iranian EFL Learners

Two hundred and fifty Iranian EFL learners participated in research into their use of mobile devices. Drawing on questionnaire and interview data, the paper examines how far the devices were embedded in the personal and professional lives of these learners, most of whom were aged 25-36. All had experience of online and distance education, and most worked in education or training. The study revealed some innovative uses of mobile devices, a selection of which is reported in this paper. The paper links the findings to wider debates about the changing relationship between learners and educational institutions, and the role of mobile devices in enabling individuals to engage in learning conversations. Data are provided on which devices were used by the learners and for what purposes, and the paper explores the implications of these findings for educators

Mobile-facilitated Time and Place among Iranian EFL Learners

Language learning is changing in a mobile technology-rich landscape and under the influence of new learner practices stemming from personal perspectives on the best places for learning and from evolving uses of available time. The key aim of this study is to conceptualize the relation between the focus of language learning and the dimensions of time and place among Iranian EFL learners. The study aims to assess what effect this might have on language learning in terms of curriculum or the design of learning activities. It draws on a survey study led by the authors, investigating how Iranian EFL learners use mobile technologies to support their learning, and particularly on interview data from the most recent project, which has focused on learners’ experiences with the use of mobile devices to support language learning. Learning activities undertaken by the interviewees were wide-ranging, with evidence of the importance of both easy learning and challenge. Specific findings relating to time and place of learning are reported. As mobile technology developments and the availability of mobile services and applications accelerate, educators and researchers need conceptual frameworks to enable them to interpret emerging learner practices. New language learning activities and services can be designed on the basis of this understanding. By reviewing individual learner experiences in learner-determined contexts, researchers and the language teaching community can work together to build up a picture of emergent practices and formulate the implications for the design of language teaching and learning now and in the future

Mobile-Assisted Language Learning: Practices among Iranian EFL Learners

Two hundred and fifty Iranian EFL learners participated in research into their use of mobile devices. Drawing on questionnaire and interview data, the paper examines how far the devices were embedded in the personal and professional lives of these learners, most of whom were aged 25-36. All had experience of online and distance education, and most worked in education or training. The study revealed some innovative uses of mobile devices, a selection of which is reported in this paper. The paper links the findings to wider debates about the changing relationship between learners and educational institutions, and the role of mobile devices in enabling individuals to engage in learning conversations. Data are provided on which devices were used by the learners and for what purposes, and the paper explores the implications of these findings for educators

Alexandria: Extensible Framework for Rapid Exploration of Social Media

The Alexandria system under development at IBM Research provides an extensible framework and platform for supporting a variety of big-data analytics and visualizations. The system is currently focused on enabling rapid exploration of text-based social media data. The system provides tools to help with constructing "domain models" (i.e., families of keywords and extractors to enable focus on tweets and other social media documents relevant to a project), to rapidly extract and segment the relevant social media and its authors, to apply further analytics (such as finding trends and anomalous terms), and visualizing the results. The system architecture is centered around a variety of REST-based service APIs to enable flexible orchestration of the system capabilities; these are especially useful to support knowledge-worker driven iterative exploration of social phenomena. The architecture also enables rapid integration of Alexandria capabilities with other social media analytics system, as has been demonstrated through an integration with IBM Research's SystemG. This paper describes a prototypical usage scenario for Alexandria, along with the architecture and key underlying analytics.Comment: 8 page