Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural Insight into the Tetramerization of an Iterative Ketoreductase SiaM through Aromatic Residues in the Interfaces

In the biosynthesis of polyketides, ketoreductases (KRs) are an important group of enzymes that determine the chiralities of the carbon backbones. SiaM is a special member of this group that can recognize substrates with different lengths and can be used iteratively. Here we report the crystal structure of SiaM. Structural analysis indicates that the overall structure resembles those of other KRs. However, significant disparity can be found in the conserved LDD motif that is replaced with IRD motif in SiaM. The isoleucine and aspartic acid residues take similar orientations as leucine and aspartic acid in the conserved LDD motif, while the arginine residue points out towards the solvent. PISA analysis shows that SiaM forms a tetramer. Several aromatic residues are found in the interfaces, which have aromatic stacking interactions with the aromatic residues in the neighboring protomers. Mutagenesis studies performed on the aromatic residues show that these sites are important for maintaining the structural integrity of SiaM. However, the aromatic residues contribute differently to the enzymatic activity. In the N-terminal interface, the aromatic residues can be replaced with leucine without affecting the enzymatic activity while, in the other interface, such mutations abolish the enzymatic activity.
INS/GPS integrated navigation for wheeled agricultural robot based on sigma-point Kalman Filter

This paper describes a numerical robust and computational efficient square-root central difference Kalman filter (SRCDKF) and put it into the application of state estimation of Inertial Navigation System (INS)/GPS integrated navigation for wheeled agricultural robot to overcome the flaws exist in EKF (Extended Kalman Filter). A standard INS mechanization with quaternion form attitude expression is introduced and a GPS antenna position compensated observation model is used. Based on the model above, both EKF and SRCDKF are implemented, and their performances are compared through simulation under several situations. Results indicate that the SRCDKF is much more robust and superior than EKF in the existence of large initial heading errors, short period of GPS outrage and low-cost IMU (Inertial Measurement Unit). It based a good foundation for the accurate and robust control of the agricultural robot.
Framing and the health policy process: a scoping review

Framing research seeks to understand the forces that shape human behaviour in the policy process. It assumes that policy is a social construct and can be cast in a variety of ways to imply multiple legitimate value considerations. Frames provide the cognitive means of making sense of the social world, but discordance among them forms the basis of policy contestation. Framing, as both theory and method, has proven to generate considerable insight into the nature of policy debates in a variety of disciplines. Despite its salience for understanding health policy debates; however, little is known about the ways frames influence the health policy process. A scoping review using the Arksey and O’Malley framework was conducted. The literature on framing in the health sector was reviewed using nine health and social science databases. Articles were included that explicitly reported theory and methods used, data source(s), at least one frame, frame sponsor and evidence of a given frame’s effect on the health policy process. A total of 52 articles, from 1996 to 2014, and representing 12 countries, were identified. Much of the research came from the policy studies/political science literature (n = 17) and used a constructivist epistemology. The term ‘frame’ was used as a label to describe a variety of ideas, packaged as values, social problems, metaphors or arguments. Frames were characterized at various levels of abstraction ranging from general ideological orientations to specific policy positions. Most articles presented multiple frames and showed how actors advocated for them in a highly contested political process. Framing is increasingly an important, yet overlooked aspect of the policy process. Further analysis on frames, framing processes and frame conflict can help researchers and policymakers to understand opaque and highly charged policy issues, which may facilitate the resolution of protracted policy controversies.
A patch-based sparse representation for sketch recognition

Categorizing free-hand human sketches has profound implications in applications such as human computer interaction and image retrieval. The task is non-trivial due to the iconic nature of sketches, signified by large variances in both appearance and structure when compared with photographs. One of the most fundamental problems is how to effectively describe a sketch image. Many existing descriptors, such as histogram of oriented gradients (HOG) and shape context (SC), have achieved great success. Moreover, some works have attempted to design features specifically engineered for sketches, such as symmetric-aware flip invariant sketch histogram (SYM-FISH). We present a novel patch-based sparse representation (PSR) for describing sketch image and it is evaluated under a sketch recognition framework. Extensive experiments on a large scale human drawn sketch dataset demonstrate the effectiveness of the proposed method.
Personalizing communication about trust

Agents in open multi-agent systems must deal with the difficult problem of selecting interaction partners in the face of uncertainty about their behaviour. This is especially problematic if they have to interact with an agent they have not interacted with before. In this case they can turn to their peers for information about this potential partner. However, in scenarios where agents may be evaluated according to many different criteria for many different purposes, their peers' evaluations may be mismatched with regards to their own expectations. In this paper we present a novel method, using an argumentation framework, that allows agents to discuss and adapt their trust model. This allows agents to provide, and receive, personalized trust evaluations, better suited to the agent in need, as is shown in a prototypical experiment.
Hands-On Analysis and Illustration: Interactive Exploratory Visualization of Vector Fields

We present techniques to interactively explore representations of 2D vector fields. Through a set of simple hand postures used on large, touch-sensitive displays, our approach allows individuals to custom-design glyphs (arrows, lines, etc.) that best reveal patterns of the underlying dataset. Interactive exploration of vector fields is facilitated through freedom of glyph placement, glyph density control, and animation. The custom glyphs can be applied individually to probe specific areas of the data but can also be applied in groups to explore larger regions of a vector field. Repositionable sources from which glyphs—animated according to the local vector field—continue to emerge are used to examine the vector field dynamically. The combination of these techniques results in an engaging visualization with which the user can rapidly explore and analyze varying types of 2D vector fields, using a virtually infinite number of custom-designed glyphs.
Future Generations: Further Problems

There are three kinds of choice. Different Number Choices affect both the number and the identities of future people. Same Number Choices affect the identities of future people, but do not affect their number. Same People Choices affect neither. Different Number Choices raise well-known problems. Less wellknown are the problems raised by Same Number Choices. Both are discussed above by Gregory Kavka. ' I shall continue this discussion. 2
What to Expect from Transiting Multiplanet Systems

Abstract So far radial velocity measurements have discovered ~25 stars to host multiple planets. The statistics imply that many of the known hosts of transiting planets should have additional planets, yet none have been solidly detected. They will be soon, via complementary search methods of RV, transit-time variations of the known planet, and transits of the additional planet. When they are found, what can transit measurements add to studies of multiplanet dynamical evolution? First, mutual inclinations become measurable, for comparison to the solar system's disk-like configuration. Such measurements will give important constraints to planet-planet scattering models, just as the radial velocity measurements of eccentricity have done. Second, the Rossiter-McLaughlin effect measures stellar obliquity, which can be modified by two-planet dynamics with a tidally evolving inner planet. Third, transit-time variations are exquisitely sensitive to planets in mean motion resonance. Two planets differentially migrating in the disk can establish such resonances, and tidal evolution of the planets can break them, so the configuration and frequency of these resonances as a function of planetary parameters will constrain these processes.
THE WEAK LENSING SIGNAL AND THE CLUSTERING OF BOSS GALAXIES. II. ASTROPHYSICAL AND COSMOLOGICAL CONSTRAINTS

We perform a joint analysis of the abundance, the clustering, and the galaxy–galaxy lensing signal of galaxies measured from Data Release 11 of the Sloan Digital Sky Survey III Baryon Oscillation Spectroscopic Survey in our companion paper, Miyatake et al. The lensing signal was obtained by using the shape catalog of background galaxies from the Canada France Hawaii Telescope Legacy Survey, which was made publicly available by the CFHTLenS collaboration, with an area overlap of about 105 deg2. We analyze the data in the framework of the halo model in order to fit halo occupation parameters and cosmological parameters (Ω m ? > and &sgr; 8 ? > ) to these observables simultaneously, and thus break the degeneracy between galaxy bias and cosmology. Adopting a flat ΛCDM cosmology with priors on Ω b h 2 ? > , n s ? > , and h from the analysis of WMAP 9 yr data, we obtain constraints on the stellar mass–halo mass relation of galaxies in our sample. Marginalizing over the halo occupation distribution parameters and a number of other nuisance parameters in our model, we obtain Ω m = 0.310 − 0.020 + 0.019 ? > and &sgr; 8 = 0.785 − 0.044 + 0.044 ? > (68% confidence). We demonstrate the robustness of our results with respect to sample selection and a variety of systematics such as the halo off-centering effect and possible incompleteness in our sample. Our constraints are consistent, complementary, and competitive with those obtained using other independent probes of these cosmological parameters. The cosmological analysis is the first of its kind to be performed at a redshift as high as 0.53.
A perturbation method for the numerical solution of the Bernoulli problem

We consider the numerical solution of the free boundary Bernoulli problem by employing level set formulations. Using a perturbation technique, we derive a second order method that leads to a fast iteration solver. The iteration procedure is adapted in order to work in the case of topology changes. Various numerical experiments confirm the efficiency of the derived numerical method.
Patch-clamp studies of isolated mouse olfactory receptor neurons

Olfactory receptor neurons isolated from embryonic, neonatal, and adult mice were studied using the patch-clamp technique. Several distinct types of ion channels were characterized in patches of membrane from the neuronal soma and the dendritic knob of receptor neurons, including a 130-pS Ca++-activated K+ channel with voltage-dependent kinetics, an 80-pS Ca++-activated K+ channel with voltage-insensitive kinetics, a 25- pS K+ channel with properties similar to inward rectifiers, and a 40-pS K+ channel that was activated and then inactivated by rapid depolarization. Evidence of large-conductance (greater than 200 pS) Cl- channels, which were Ca++ insensitive and increasingly active at depolarizing membrane potentials, and voltage-activated Ca++ channels (16 pS) was also obtained. From K+ channel activity recorded from cell- attached patches, the intracellular [Ca++] was inferred to be below 0.1 microM, and the membrane potential was inferred to be approximately -50 mV. The receptor neurons had high input resistances, and action potentials could be elicited by picoampere amounts of depolarizing current. The receptor neurons responded to applied odorant molecules and to forskolin with increases in membrane conductance. These results provide a description of the membrane properties of olfactory receptor neurons and a basis for understanding their electrical activity and response to odorants.
Polynomial real root isolation by differentiation

A new algorithm is described, for the isolation of the real roots of a real polynomial. This algorithm utilizes the sequence of derivatives of the given polynomial, relying on Rolle's theorem and a tangent construction to decide whether an interval contains two roots or none. The algorithm is carefully compared, both analytically and empirically, with an algorithm based on Sturm's theorem, and is found to be significantly faster in general. It also requires less memory, and produces isolating intervals for the derivatives as a cost-free by-product.
Creativity among entrepreneurship students: comparing engineering and business education

As creativity is increasingly recognised as a vital component of entrepreneurship, researchers and educators struggle to reform enterprise pedagogy. To help in this effort, we use a personality test and open-ended interviews to explore creativity between two groups of entrepreneurship masters' students: one at a business school and one at an engineering school. The findings indicate that both groups had high creative potential, but that engineering students channelled this into practical and incremental efforts whereas the business students were more speculative and had a clearer market focus. The findings are drawn on to make some suggestions for entrepreneurship education.
Sub-Astronomical Unit Structure of the Near-Infrared Emission from AB Aurigae

We present near-infrared, long-baseline, interferometric observations of AB Aurigae, a well-known Herbig Ae/Be star, obtained with the Infrared Optical Telescope Array. The near-infrared emission from this source has been spatially resolved for the first time, and the observations indicate a characteristic diameter of 5 mas for the emission, corresponding to 0.7 AU at the distance of AB Aur. The data appear to be most consistent with models in which the circumstellar material around AB Aurigae lies in a flattened structure with a central large hole or optically thin region of radius about 0.3 AU.
Negative selection algorithm for monitoring processes with large number of variables

Chemical processes are being more heavily instrumented leading to larger and larger number of variables to monitor. Developing models for process monitoring using this colossal amount of data in a high dimensional space of process variables is a difficult task. In the recent times, immune system inspired Negative Selection Algorithm (NSA) has been gaining much attention for fault detection. Generally, the entire set of process variables is provided as input without pre-selection and as the number of variables becomes large, the monitoring performance of NSA reduces drastically. In this paper we propose a metric based on Bhattacharyya distance to measure the extent of similarity of a particular fault operation w.r. t normal in the space of any subset of variables. Then using this similarity metric, a scheme is proposed to systematically identify a smaller set of key variables for a particular fault. We also demonstrate through the benchmark Tennessee Eastman challenge process that NSA performs significantly better in the fault specific space of key variables.
The SweDat Project and Swedia Database for Phonetic and Acoustic Research

The project described here may be seen as a continuation of an earlier project, SweDia 2000, aimed at transforming the database collected in that project to a full-fledged e-science database. The database consists of recordings of Swedish dialects from 107 locations in Sweden and Swedish speaking parts of Finland. The goal of the present project is to make the material searchable in a flexible and simple way to make it available to a much wider sector of the research community than is the case at present. The database will be accessible over the Internet via user-friendly interfaces specifically designed for this type of data. Other more specialized research interfaces will also be designed to facilitate phonetic acoustic research and orientation of the database.
The Sensory Histidine Kinases TorS and EvgS Tend to Form Clusters in Escherichia coli Cells

Microorganisms use multiple two-component sensory systems to detect changes in their environment and elicit physiological responses. Despite their wide spread and importance, the intracellular organization of two-component sensory proteins in bacteria remains little investigated. A notable exception is the well-studied clustering of the chemoreceptor-kinase complexes that mediate chemotaxis behaviour. However, these chemosensory complexes differ fundamentally from other systems, both structurally and functionally. Therefore, studying the organization of typical sensory kinases in bacteria is essential for understanding the general role of receptor clustering in bacterial sensory signalling. Here, by studying mYFP-tagged sensory kinases in Escherichia coli, we show that the tagged TorS and EvgS sensors have a clear tendency for self-association and clustering. These sensors clustered even when expressed at a level of a few hundred copies per cell. Moreover, the mYFP-tagged response regulator TorR showed clear TorS-dependent clustering, indicating that untagged TorS sensors also tend to form clusters. We also provide evidence for the functionality of these tagged sensors. Experiments with truncated TorS or EvgS proteins suggested that clustering of EvgS sensors depends on the cytoplasmic part of the protein, whereas clustering of TorS sensors can be potentially mediated by the periplasmic/transmembrane domain. Overall, these findings support the notion that sensor clustering plays a role in bacterial sensory signalling beyond chemotaxis.
Opus: University of Bath Online Publication Store Modification of Standard Cmos Technology for Cell-based Biosensors

NOTICE: this is the author's version of a work that was accepted for publication in Biosensors and Bioelectronics. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was This version is made available in accordance with publisher policies. Please cite only the published version using the reference above. Abstract We present an electrode based on complementary metal oxide semiconductor (CMOS) technology that can be made fully biocompatible and chemically inert using a simple, low-cost and non-specialised process. Since these devices are based on ubiquitous CMOS technology, the integrated circuits can be readily developed to include appropriate amplifiers, filters and wireless subsystems, thus reducing the complexity and cost of external systems. The unprocessed CMOS aluminium electrodes are modified using anodisation and plating techniques which do not require intricate and expensive semiconductor processing equipment and can be performed on the bench-top as a clean-room environment is not required. The resulting transducers are able to detect both the fast electrical activity of neurons and the slow changes in Manuscript Click here to view linked References 2 impedance of growing and dividing cells. By using standard semiconductor fabrication techniques and well-established technologies, the approach can form the basis of cell-based biosensors and transducers for high throughput drug discovery assays, neuroprosthetics and as a basic research tool in biosciences. The technology is equally applicable to other biosensors that require noble metal or nanoporous microelectrodes.
A New Approach for Resolving Conflicts in Actionable Behavioral Rules

Knowledge is considered actionable if users can take direct actions based on such knowledge to their advantage. Among the most important and distinctive actionable knowledge are actionable behavioral rules that can directly and explicitly suggest specific actions to take to influence (restrain or encourage) the behavior in the users' best interest. However, in mining such rules, it often occurs that different rules may suggest the same actions with different expected utilities, which we call conflicting rules. To resolve the conflicts, a previous valid method was proposed. However, inconsistency of the measure for rule evaluating may hinder its performance. To overcome this problem, we develop a new method that utilizes rule ranking procedure as the basis for selecting the rule with the highest utility prediction accuracy. More specifically, we propose an integrative measure, which combines the measures of the support and antecedent length, to evaluate the utility prediction accuracies of conflicting rules. We also introduce a tunable weight parameter to allow the flexibility of integration. We conduct several experiments to test our proposed approach and evaluate the sensitivity of the weight parameter. Empirical results indicate that our approach outperforms those from previous research.
Cortistatin, a new antiinflammatory peptide with therapeutic effect on lethal endotoxemia

Cortistatin is a recently discovered cyclic neuropeptide related to somatostatin that has emerged as a potential endogenous antiinflammatory factor based on its production by and binding to immune cells. Because human septic shock involves excessive inflammatory cytokine production, we investigated the effect of cortistatin on the production of inflammatory mediators and its therapeutic action in various murine models of endotoxemia. Cortistatin down-regulated the production of inflammatory mediators by endotoxin-activated macrophages. The administration of cortistatin protected against lethality after cecal ligation and puncture, or injection of bacterial endotoxin or Escherichia coli, and prevented the septic shock-associated histopathology, such as infiltration of inflammatory cells and intravascular disseminated coagulation in various target organs. The therapeutic effect of cortistatin was mediated by decreasing the local and systemic levels of a wide spectrum of inflammatory mediators, including cytokines, chemokines, and acute phase proteins. The combined use of cortistatin and other antiinflammatory peptides was very efficient treating murine septic shock. This work provides the first evidence of cortistatin as a new immunomodulatory factor with the capacity to deactivate the inflammatory response. Cortistatin represents a potential multistep therapeutic agent for human septic shock, to be used in combination with other immunomodulatory agents or as a complement to other therapies.