Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Bacteria Utilizing Biphenyl, Benzoate, and Naphthalene in Long-Term Contaminated Soil

Bacteria were identified associated with biodegradation of aromatic pollutants biphenyl, benzoate, and naphthalene in a long-term polychlorinated biphenyl- and polyaromatic hydrocarbon-contaminated soil. In order to avoid biases of culture-based approaches, stable isotope probing was applied in combination with sequence analysis of 16 S rRNA gene pyrotags amplified from 13C-enriched DNA fractions. Special attention was paid to pyrosequencing data analysis in order to eliminate the errors caused by either generation of amplicons (random errors caused by DNA polymerase, formation of chimeric sequences) or sequencing itself. Therefore, sample DNA was amplified, sequenced, and analyzed along with the DNA of a mock community constructed out of 8 bacterial strains. This warranted that appropriate tools and parameters were chosen for sequence data processing. 13C-labeled metagenomes isolated after the incubation of soil samples with all three studied aromatics were largely dominated by Proteobacteria, namely sequences clustering with the genera Rhodanobacter Burkholderia, Pandoraea, Dyella as well as some Rudaea- and Skermanella-related ones. Pseudomonads were mostly labeled by 13C from naphthalene and benzoate. The results of this study show that many biphenyl/benzoate-assimilating bacteria derive carbon also from naphthalene, pointing out broader biodegradation abilities of some soil microbiota. The results also demonstrate that, in addition to traditionally isolated genera of degradative bacteria, yet-to-be cultured bacteria are important players in bioremediation. Overall, the study contributes to our understanding of biodegradation processes in contaminated soil. At the same time our results show the importance of sequencing and analyzing a mock community in order to more correctly process and analyze sequence data.
Argumentation-based reinforcement learning for robocup soccer takeaway

Reinforcement Learning (RL) is widely regarded as a generic and effective technique to learn coordinated behaviours in cooperative multi-agent systems (CMAS), but it suffers from slow convergence speed due to the huge joint action space. Incorporating domain knowledge has shown to be an effective method to tackle this problem, but little research has investigated how to propose high-quality heuristics. We consider a widely used CMAS application, RoboCup Takeaway, and use value-based argumentation to extract heuristics from conflicting domain knowledge therein.
Efficacy and effectiveness of a balance-enhancing insole.

BACKGROUND Age-related loss of foot-sole cutaneous sensation is very common and is associated with impaired balance control. This study investigated the effect of a balance-enhancing insole (designed to facilitate foot-sole sensation) on lateral gait stability and evaluated its effectiveness in daily life. METHODS Forty community-dwelling older adults (age 65-75) with moderate loss of foot-sole sensation (unrelated to neuropathy) were fitted with the same model of walking shoes. Half of the participants were assigned, at random, to wear the shoes with a facilitatory insole for 12 weeks; the other participants wore a conventional insole. A gait perturbation protocol, simulating uneven terrain, was performed at baseline and after wearing the assigned insoles for 12 weeks. Participants were tested with both types of insoles during each gait-testing session and sent in weekly postcards with information pertaining to insole comfort, hours of wear, and falls. RESULTS The facilitatory insole improved lateral stability during gait, and this benefit did not habituate after 12 weeks of wearing the insole in daily life. Nine participants who wore conventional insoles experienced one or more falls, whereas only five of the facilitatory group fell. Although there were initial reports of mild discomfort in 10 cases, all but one participant tolerated the facilitatory insole, and most indicated that they would like to continue wearing the insole on a long-term basis. CONCLUSIONS A relatively simple change in insole design can help to counter effects of age-related (non-neuropathic) decline in foot-sole sensitivity, and is a viable intervention to enhance balance control.
Modeling workplace contact networks: The effects of organizational structure, architecture, and reporting errors on epidemic predictions

Abstract Face-to-face social contacts are potentially important transmission routes for acute respiratory infections, and understanding the contact network can improve our ability to predict, contain, and control epidemics. Although workplaces are important settings for infectious disease transmission, few studies have collected workplace contact data and estimated workplace contact networks. We use contact diaries, architectural distance measures, and institutional structures to estimate social contact networks within a Swiss research institute. Some contact reports were inconsistent, indicating reporting errors. We adjust for this with a latent variable model, jointly estimating the true (unobserved) network of contacts and duration-specific reporting probabilities. We find that contact probability decreases with distance, and that research group membership, role, and shared projects are strongly predictive of contact patterns. Estimated reporting probabilities were low only for 0–5 min contacts. Adjusting for reporting error changed the estimate of the duration distribution, but did not change the estimates of covariate effects and had little effect on epidemic predictions. Our epidemic simulation study indicates that inclusion of network structure based on architectural and organizational structure data can improve the accuracy of epidemic forecasting models.
Isolation and characterization of endosulfan-degrading bacteria from contaminated agriculture soils

The widespread use of potentially harmful pesticides has recently been under scrutiny in many parts of the world. The organochlorine pesticides are one of the major chemicals responsible for the contamination and deterioration of soils and water environments especially in agricultural fields[1]. During the past 50 years, pesticides have been the essential part of the agricultural world. Although it is evident that the production and distribution of pesticides increases the quality and efficiency of the agricultural industry, the pesticides is likely to be used improperly and unreasonably[2]. Despite their benefits, pesticides are compounds that may have toxic side effects causing potential environmental risk[3]. Endosulfan (6,7,8,9,10,10-hexachloro-1,5,5a,6,9,9a-hexahydro-6, 9-methano-2,4,3-benzodioxathiepine 3-oxide), an organochlorine insecticide, is a mixture of the two isomers, αand β-endosulfan. It is a contact and stomach poison used to control chewing and sucking insects, such as Colorado beetle, flea beetle, cabbage worm aphids and leaf hopper. This insecticide is used to control insect pests of a wide range of crops, including cereals, cotton, coffee, fruits, oil seeds and vegetables[4]. In the close vicinity of agricultural fields, the contamination of atmosphere, soils, sediments, surface and rain waters, and foodstuffs by endosulfan has been documented in numerous previous studies[5]. The persistence of endosulfan in soil and water environments has been observed by different researchers under different conditions[6]. Its harmful impacts on aquatic fauna and numerous mammalian species including human beings have been reported several times in literature[7,8]. It has been reported that endosulfan is genotoxic in mammalian cells[5]. Due to the abundant usage and potential transport of endosulfan, contamination is frequently found in the environment at considerable distance from the point of application[9]. These health and environment concerns have led to an interest in degradation and detoxification of endosulfan. Detoxification of endosulfan through biological means is receiving serious attention as compared to existing methods such as incineration and landfill[10]. Biodegradation is an efficient bioremediation technique in microorganisms which grow in different ecosystems and through ARTICLE INFO ABSTRACT
Constructing Hidden Units Using Examples and Queries

While the network loading problem for 2-layer threshold nets is NP-hard when learning from examples alone (as with backpropagation), (Baum, 91) has now proved that a learner can employ queries to evade the hidden unit credit assignment problem and PAC-load nets with up to four hidden units in polynomial time. Empirical tests show that the method can also learn far more complicated functions such as randomly generated networks with 200 hidden units. The algorithm easily approximates Wieland's 2-spirals function using a single layer of 50 hidden units, and requires only 30 minutes of CPU time to learn 200-bit parity to 99.7% accuracy.
Team Synergies in Sport: Theory and Measures

Individual players act as a coherent unit during team sports performance, forming a team synergy. A synergy is a collective property of a task-specific organization of individuals, such that the degrees of freedom of each individual in the system are coupled, enabling the degrees of freedom of different individuals to co-regulate each other. Here, we present an explanation for the emergence of such collective behaviors, indicating how these can be assessed and understood through the measurement of key system properties that exist, considering the contribution of each individual and beyond These include: to (i) dimensional compression, a process resulting in independent degree of freedom being coupled so that the synergy has fewer degrees of freedom than the set of components from which it arises; (ii) reciprocal compensation, if one element do not produce its function, other elements should display changes in their contributions so that task goals are still attained; (iii) interpersonal linkages, the specific contribution of each element to a group task; and (iv), degeneracy, structurally different components performing a similar, but not necessarily identical, function with respect to context. A primary goal of our analysis is to highlight the principles and tools required to understand coherent and dynamic team behaviors, as well as the performance conditions that make such team synergies possible, through perceptual attunement to shared affordances in individual performers. A key conclusion is that teams can be trained to perceive how to use and share specific affordances, explaining how individual’s behaviors self-organize into a group synergy. Ecological dynamics explanations of team behaviors can transit beyond mere ratification of sport performance, providing a comprehensive conceptual framework to guide the implementation of diagnostic measures by sport scientists, sport psychologists and performance analysts. Complex adaptive systems, synergies, group behaviors, team sport performance, ecological dynamics, performance analysis.
What Determines the Assembly of Transcriptional Network Motifs in Escherichia coli?

Transcriptional networks are constituted by a collection of building blocks known as network motifs. Why do motifs appear? An adaptive model of motif emergence was recently questioned in favor of neutralist scenarios. Here, we provide a new picture of motif assembly in Escherichia coli which partially clarifies these contrasting explanations. This is based on characterizing the linkage between motifs and sensing or response specificity of their constituent transcriptional factors (TFs). We find that sensing specificity influences the distribution of autoregulation, while the tendency of a TF to establish feed-forward loops (FFLs) depends on response specificity, i.e., regulon size. Analysis of the latter pattern reveals that coregulation between large regulon-size TFs is common under a network neutral model, leading to the assembly of a great number of FFLs and bifans. In addition, neutral exclusive regulation also leads to a collection of single input modules -the fourth basic motif. On the whole, and even under the conservative neutralist scenario considered, a substantial group of regulatory structures revealed adaptive. These structures visibly function as fully-fledged working units.
Variable Selection for Partially Linear Models With Measurement Errors

This article focuses on variable selection for partially linear models when the covariates are measured with additive errors. We propose two classes of variable selection procedures, penalized least squares and penalized quantile regression, using the nonconvex penalized principle. The first procedure corrects the bias in the loss function caused by the measurement error by applying the so-called correction-for-attenuation approach, whereas the second procedure corrects the bias by using orthogonal regression. The sampling properties for the two procedures are investigated. The rate of convergence and the asymptotic normality of the resulting estimates are established. We further demonstrate that, with proper choices of the penalty functions and the regularization parameter, the resulting estimates perform asymptotically as well as an oracle procedure as proposed by Fan and Li. Choice of smoothing parameters is also discussed. Finite sample performance of the proposed variable selection procedures is assessed by Monte Carlo simulation studies. We further illustrate the proposed procedures by an application.
A Multidisciplinary Approaches of Big Data and Data Science Using Hadoop and Map Reduce

Data Science and Big Data have an important role among the modern science and emerging technology. Infact, we can say that these are the two side of the same coin. Data Science is establishing basic foundations to become a profession. The data science community can follow a road map for how data science can be more useful for various social and commercial sectors. Today we are surrounding by data like oxygen. The growth of data first presented challenges to cutting edge businesses such as Google, yahoo, Amazon, Microsoft, Face book, twitter etc. Keywords— Big Data, Data Science, Hadoop, Map Reduce, Data Security, Privacy.
Free Edge Lengths in Plane Graphs

We study the impact of metric constraints on the realizability of planar graphs. Let G be a subgraph of a planar graph H (where H is the “host” of G). The graph G is free in H if for every choice of positive lengths for the edges of G, the host H has a planar straight-line embedding that realizes these lengths; and G is extrinsically free in H if all constraints on the edge lengths of G depend on G only, irrespective of additional edges of the host H. We characterize the planar graphs G that are free in every host H, G⊆H\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$G\subseteq H$$\end{document}, and all the planar graphs G that are extrinsically free in every host H, G⊆H\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$G\subseteq H$$\end{document}. The case of cycles G=Ck\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$G=C_k$$\end{document} provides a new version of the celebrated carpenter’s rule problem. Even though cycles Ck\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$C_k$$\end{document}, k≥4\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$k\ge 4$$\end{document}, are not extrinsically free in all triangulations, it turns out that “nondegenerate” edge lengths are always realizable, where the edge lengths are considered degenerate if the cycle can be flattened (into a line) in two different ways. Separating triangles, and separating cycles in general, play an important role in our arguments. We show that every star is free in a 4-connected triangulation (which has no separating triangle).
VLBI observations of weak sources using fast frequency switching

We have developed a new phase referencing technique for high frequency VLBI observations. In conventional phase referencing, one interleaves short scans on a nearby phase calibrator between the target source observations. In fast frequency switching described here, one observes the target source continuously while switching rapidly between the target frequency and a lower reference frequency. We demonstrate that the technique allows phase calibration almost reaching the thermal noise limit and present the first detection of the AGN in the FR I radio galaxy NGC 4261 at 86 GHz. Although point-like, this is the weakest source ever detected with VLBI at this frequency.
Formation of filopodia-like bundles in vitro from a dendritic network

We report the development and characterization of an in vitro system for the formation of filopodia-like bundles. Beads coated with actin-related protein 2/3 (Arp2/3)–activating proteins can induce two distinct types of actin organization in cytoplasmic extracts: (1) comet tails or clouds displaying a dendritic array of actin filaments and (2) stars with filament bundles radiating from the bead. Actin filaments in these bundles, like those in filopodia, are long, unbranched, aligned, uniformly polar, and grow at the barbed end. Like filopodia, star bundles are enriched in fascin and lack Arp2/3 complex and capping protein. Transition from dendritic to bundled organization was induced by depletion of capping protein, and add-back of this protein restored the dendritic mode. Depletion experiments demonstrated that star formation is dependent on Arp2/3 complex. This poses the paradox of how Arp2/3 complex can be involved in the formation of both branched (lamellipodia-like) and unbranched (filopodia-like) actin structures. Using purified proteins, we showed that a small number of components are sufficient for the assembly of filopodia-like bundles: Wiskott-Aldrich syndrome protein (WASP)–coated beads, actin, Arp2/3 complex, and fascin. We propose a model for filopodial formation in which actin filaments of a preexisting dendritic network are elongated by inhibition of capping and subsequently cross-linked into bundles by fascin.
The HomeCar organiser: designing for blurring home-car boundaries

Ubiquitous computing is having an important impact on family life with a wide range of technologies supporting and creating the need for connected and smarter homes. In particular, mobile devices are allowing families to connect activities across spaces, which include the home and the car. This paper presents a new design concept -- the HomeCar Organiser -- which is a connected system that enables families to coordinate schedules, activities and artifacts between the home and activities placed in the car. The design of HomeCar Organiser was informed by an empirical ethnographic study of family car travel practices in the UK over one and a half years. The study motivated us to consider how routine practices of everyday life are negotiated through and in the car while supported by a range of technologies.
RNA Structure Refinement using the ERRASER-Phenix pipeline

The final step of RNA crystallography involves the fitting of coordinates into electron density maps. The large number of backbone atoms in RNA presents a difficult and tedious challenge, particularly when experimental density is poor. The ERRASER-Phenix pipeline can improve an initial set of RNA coordinates automatically based on a physically realistic model of atomic-level RNA interactions. The pipeline couples diffraction-based refinement in Phenix with the Rosetta-based real-space refinement protocol ERRASER (Enumerative Real-Space Refinement ASsisted by Electron density under Rosetta). The combination of ERRASER and Phenix can improve the geometrical quality of RNA crystallographic models while maintaining or improving the fit to the diffraction data (as measured by Rfree). Here we present a complete tutorial for running ERRASER-Phenix through the Phenix GUI, from the command-line, and via an application in the Rosetta On-line Server that Includes Everyone (ROSIE).
Applicability of compressive sensing on three-dimensional terahertz imagery for in-depth object defect detection and recognition using a dedicated semisupervised image processing methodology

Abstract. The quality control of composite multilayered materials and structures using nondestructive tests is of high interest for numerous applications in the aerospace and aeronautics industry. One of the established nondestructive methods uses microwaves to reveal defects inside a three-dimensional (3-D) object. Recently, there has been a tendency to extrapolate this method to higher frequencies (going to the subterahertz spectrum) which could lead to higher resolutions in the obtained 3-D images. Working at higher frequencies reveals challenges to deal with the increased data rate and to efficiently and effectively process and evaluate the obtained 3-D imagery for defect detection and recognition. To deal with these two challenges, we combine compressive sensing (for data rate reduction) with a dedicated image processing methodology for a fast, accurate, and robust quality evaluation of the object under test. We describe in detail the used methodology and evaluate the obtained results using subterahertz data acquired of two calibration samples with a frequency modulated continuous wave system. The applicability of compressive sensing within this context is discussed as well as the quality of the image processing methodology dealing with the reconstructed images.
Lower Incidence of Thrombus Formation With Cryoenergy Versus Radiofrequency Catheter Ablation

Background—Radiofrequency (RF) catheter ablation is limited by thromboembolic complications. The objective of this study was to compare the incidence and characteristics of thrombi complicating RF and cryoenergy ablation, a novel technology for the catheter-based treatment of arrhythmias. Methods and Results—Ablation lesions (n=197) were performed in 22 mongrel dogs at right atrial, right ventricular, and left ventricular sites preselected by a randomized factorial design devised to compare RF ablation with cryocatheter configurations of varying sizes (7F and 9F), cooling rates (−1°C/s, −5°C/s, and −20°C/s) and target temperatures (−55°C and −75°C). Animals were pretreated with acetylsalicylic acid and received intraprocedural intravenous unfractionated heparin. Seven days after ablation, the incidence of thrombus formation was significantly higher with RF than with cryoablation (75.8% versus 30.1%, P =0.0005). In a multiple regression model, RF energy remained an independent predictor of thrombus formation compared with cryoenergy (OR, 5.6; 95% CI, 1.7, 18.1;P =0.0042). Thrombus volume was also significantly greater with RF than with cryoablation (median, 2.8 versus 0.0 mm3;P <0.0001). More voluminous thrombi were associated with larger RF lesions, but cryolesion dimensions were not predictive of thrombus size. Conclusions—RF energy is significantly more thrombogenic than cryoenergy, with a higher incidence of thrombus formation and larger thrombus volumes. The extent of hyperthermic tissue injury is positively correlated with thrombus bulk, whereas cryoenergy lesion size does not predict thrombus volume, most likely reflecting intact tissue ultrastructure with endothelial cell preservation.