Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal Structure of Cytochrome P450 (CYP105P2) from Streptomyces peucetius and Its Conformational Changes in Response to Substrate Binding

Cytochrome P450 monooxygenases (CYP, EC 1.14.14.1) belong to a large family of enzymes that catalyze the hydroxylation of various substrates. Here, we present the crystal structure of CYP105P2 isolated from Streptomyces peucetius ATCC27952 at a 2.1 Å resolution. The structure shows the presence of a pseudo-ligand molecule in the active site, which was co-purified fortuitously and is presumed to be a biphenyl derivative. Comparison with previously determined substrate-bound CYP structures showed that binding of the ligand produces large and distinctive conformational changes in α2–α3, α7–α9, and the C-terminal loop regions. This structural flexibility confirms our previous observation that CYP105P2 can accommodate a broad range of ligands. The structure complexed with a pseudo-ligand provides the first molecular view of CYP105P2–ligand interactions, and it indicates the involvement of hydrophobic residues (Pro82, Ala181, Met187, Leu189, Leu193, and Ile236) in the interactions between hydrophobic ligands and CYP105P2. These results provide useful insights into the structural changes involved in the recognition of different ligands by CYP105P2.
Control performance of active damp LCL filter of three phase PWM boost rectifier

This paper presents three methods of a three phase PWM boost rectifier connected to the grid via a single stage L filter, an undamp LCL filter and an active damp LCL filter. The first method is the simplest method uses the biggest size of single stage L filter. Although this method is straightforward, it increases the system size and weight and contains high frequency current components. The second method uses an LCL filter instead of an L filter for size and weight reduction. While size and weight can be reduced, it causes a stability problem around the resonance frequency. The last method solves all these problems by an improved control algorithm to maintain system stability. The active damp LCL filter is that it can reduce a current ripple of the system to conform to the standard. Moreover, it has a faster response than the conventional single state inductor filter. This paper presents mathematical models and implementation of the filter circuit for performance comparison. The results from a case study with 10kW load indicate that the active damping LCL filter has nearly the same performances as single stage L filter but it has small size of filter inductors, no high frequency of the current and fastest dynamic response.
IMAGE FUSION WITH EDGE PRESERVING SMOOTHING FILTER

This paper introduces fast and effective fusing of images through merging of multiple images for creating a highly information fused image . Here the edge preserving smoothing filter is used as guided filter. The fusion criterion is to minimize the different error between the fused image and input image The proposed method is based on two scale decomposition of image into a detail layer capturing small scale details and a base layer containing large scale variations in intensity. This method make full use spatial consistency for fusion of base and detail layer by using guided filter based weighted average technique.
Throughput Maximization In Multiple Antenna Communication Systems Through Quantized Rate Control

In the recent years, we have witnessed an increasing demand for the high data rate wireless communication systems. While most of the research efforts has been focused on the minimization of the packet error probability through an adaptive transmission scheme, the overall optimization of the system throughput is not well addressed. We consider the problem of throughput maximization using a quantized feedback that is an appropriate model for practical systems with limited feedback capacity. We derive the optimal quantized rate control design for general multiple transmit and multiple receive antenna systems. Moreover, an adaptive stochastic gradient search algorithm has been proposed that can efficiently find the optimal solution. It is shown that the proposed quantized rate control design with only a few bits of feedback considerably improves the throughput of a system for a given average power
Global-Scale Secure Multiparty Computation

We propose a new, constant-round protocol for multi-party computation of boolean circuits that is secure against an arbitrary number of malicious corruptions. At a high level, we extend and generalize recent work of Wang et al. in the two-party setting. Namely, we design an efficient preprocessing phase that allows the parties to generate authenticated information; we then show how to use this information to distributively construct a single "authenticated" garbled circuit that is evaluated by one party. Our resulting protocol improves upon the state-of-the-art both asymptotically and concretely. We validate these claims via several experiments demonstrating both the efficiency and scalability of our protocol: Efficiency: For three-party computation over a LAN, our protocol requires only 95 ms to evaluate AES. This is roughly a 700X improvement over the best prior work, and only 2.5X slower than the best known result in the two-party setting. In general, for n-party computation our protocol improves upon prior work (which was never implemented) by a factor of more than 230n, e.g., an improvement of 3 orders of magnitude for 5-party computation. Scalability: We successfully executed our protocol with a large number of parties located all over the world, computing (for example) AES with 128 parties across 5 continents in under 3 minutes. Our work represents the largest-scale demonstration of secure computation to date.
Construction of a new family of high efficiency bacterial expression vectors: identification of cDNA clones coding for human liver proteins.

Construction of a family of bacterial expression vectors, pEX1‐3, is described. These vectors are derived from a cro‐lacZ gene fusion plasmid which expresses large quantities of fusion protein under the control of the PR promoter of bacteriophage lambda. A polylinker has been engineered into the 3′ end of the lacZ gene in all three translational reading frames, and stop signals for transcription and translation inserted, so that any open reading frame DNA may be expressed as a hybrid beta‐galactosidase protein. cDNA fragments cloned in these vectors can be detected with an efficiency of greater than 1 in 3, thus enabling the detection of rare cDNA molecules. In addition, the low solubility of hybrid proteins leads to a rapid isolation procedure allowing antibodies of pre‐determined specificity to be made against expressed regions of cloned DNA. We describe the cloning of albumin and complement C9 genes from a human cDNA library using polyclonal and monoclonal antibodies.
A necessary and sufficient condition for determining the girth of quasi-cyclic LDPC codes

The parity-check matrix of a quasi-cyclic low- density parity-check (QC-LDPC) code can be compactly represented by a polynomial parity-check matrix. By using this compact representation, we derive a necessary and sufficient condition for determining the girth of QC-LDPC codes in a systematic way. The new condition avoids an explicit enumeration of cycles for determining the girth of codes, and thus can be well employed to generate QC-LDPC codes with large girth.
Tensor distance based multilinear multidimensional scaling for image and video analysis

This paper presents a novel dimensionality reduction technique named Tensor Distance based Multilinear Multidimensional Scaling (TD-MMDS). First, we propose a new distance metric called Tensor Distance (TD) to build a relationship graph of data points with high-order. Then we employ an iterative strategy to sequentially learn the transformation matrices that can best keep pair-wise TDs of the high-order data in the low-dimensional embedded space. By integrating both tensor distance and tensor embedding, TD-MMDS provides a uniform framework of tensor based dimensionality reduction, which preserves the intrinsic structure of high-order data through the whole learning procedure. Experiments on standard image and video datasets validate the effectiveness of the proposed TD-MMDS.
Social E-Atmospherics in Practice (or Not): A French and Turkish Web Designers' Perspectives

Little is known about the development of social e-atmospherics. And yet, e-atmospherics have motivated an emerging body of research which reports that both better layouts and 'recognized' atmospherics encourage consumers to modify their shopping habits. While the literature has analyzed mainly the functional (design) aspect of e-atmospherics, little has been done in terms of linking its characteristics to social (co-) creation. This paper attempts to redress the imbalance by exploring the anatomy from a website designer perspective of the social dimension of design in relation to e-atmospherics, which includes factors such as the aesthetic design of space and the influence of visual cues as a socially constructed meaning. We identify the challenges that web designers as social agents, who interact within intangible social reference sets, restricted by social standards, value, beliefs, status and duties, face daily within their work. We aim to review the current understanding of the importance and voluntary integration of social cues displayed by web designers from a mature market and an emerging market, and provides an analysis based recommendation towards the development of an integrated e-social atmospheric framework. Results report exploratory findings from questionnaires with 10 French and 16 Turkish web designers. These allow us to re-interpret the web designers' reality regarding social e-atmospherics. We contend that by comprehending (before any consumer/client input) social capital, daily micro practices, habits and routine of designers, a deeper understanding of social e-atmospherics possible functions in the future will be unpacked.
Remodeling of U2-U6 snRNA helix I during pre-mRNA splicing by Prp16 and the NineTeen Complex protein Cwc2

Removal of intron regions from pre-messenger RNA (pre-mRNA) requires spliceosome assembly with pre-mRNA, then subsequent spliceosome remodeling to allow activation for the two steps of intron removal. Spliceosome remodeling is carried out through the action of DExD/H-box ATPases that modulate RNA–RNA and protein–RNA interactions. The ATPase Prp16 remodels the spliceosome between the first and second steps of splicing by catalyzing release of first step factors Yju2 and Cwc25 as well as destabilizing U2-U6 snRNA helix I. How Prp16 destabilizes U2-U6 helix I is not clear. We show that the NineTeen Complex (NTC) protein Cwc2 displays genetic interactions with the U6 ACAGAGA, the U6 internal stem loop (ISL) and the U2-U6 helix I, all RNA elements that form the spliceosome active site. We find that one function of Cwc2 is to stabilize U2-U6 snRNA helix I during splicing. Cwc2 also functionally cooperates with the NTC protein Isy1/NTC30. Mutation in Cwc2 can suppress the cold sensitive phenotype of the prp16-302 mutation indicating a functional link between Cwc2 and Prp16. Specifically the prp16-302 mutation in Prp16 stabilizes Cwc2 interactions with U6 snRNA and destabilizes Cwc2 interactions with pre-mRNA, indicating antagonistic functions of Cwc2 and Prp16. We propose that Cwc2 is a target for Prp16-mediated spliceosome remodeling during pre-mRNA splicing.
Long-term performance modelling of a combined energy generation system

The installation of the combined energy generation system at West Beacon Farm, Loughborough, Leicestershire commenced in 1988, since when it has steadily grown in both generating capacity and operating complexity. It now consists of three electrical generating sources: two 25kW fixed speed horizontal axis wind turbines, a 6kWp photovoltaic array consisting of both monocrystalline and polycrystalline cells and a 15kW combined heat and power unit which also provides 38kW of thermal energy. Electricity is stored in a 184kWh lead acid battery, and also imported and exported from the grid. Previous research on the system was limited, due to lack of detailed system information and time. Therefore the aim of this research project has been to develop a more detailed and accurate computer model of the system that enables the present operating strategy to be evaluated, together with the effects on the system of changing this strategy. The outcome will be to optimize the generating cost and to provide a model with the flexibility to investigate the conditions in other hybrid systems. [Continues. ]
Opportunistic Routing in Dynamic Ad Hoc Networks: the OPRAH protocol

This paper describes the opportunistic routing in dynamic ad hoc networks, the OPRAH protocols, which uses the air interface to find a more optimal path for each packet in a dynamic network. In the static environment the connectivity is perturbed only by fading between two fixed points, the performance of these protocols depends on how steady a route is. Thus these protocols have the following advantages: ability to interoperate with wired protocols, to ensure that the ad hoc network can communicate with the legacy wired infrastructure, it works in a low mobility environment, and it should be implemented using relatively simple off-the-shelf components
Detecting significant alarms using outlier detection algorithms

Although alarms in plants are designed to notify any anomaly or faults in order to prevent accidents or to improve process, it is very difficult for the operators to identify meaningful alarms, since there are large volumes of false and nuisance alarms. Outlier detection algorithms are used to identify anomaly in data, and thus they can be used to suggest abnormal alarms. In this research, we analysed real world alarm data collected from an iron processing company and constructed data features for algorithmic outlier detection. With the data we identified outlier alarms and compared their run length with nonoutlier alarms. Our results demonstrated that outlier alarms detected by the algorithms have significantly difference patterns in average run length compared to the normal alarms.
Toxicity of Tungsten Carbide and Cobalt-Doped Tungsten Carbide Nanoparticles in Mammalian Cells in Vitro

Background Tungsten carbide nanoparticles are being explored for their use in the manufacture of hard metals. To develop nanoparticles for broad applications, potential risks to human health and the environment should be evaluated and taken into consideration. Objective We aimed to assess the toxicity of well-characterized tungsten carbide (WC) and cobaltdoped tungsten carbide (WC-Co) nanoparticle suspensions in an array of mammalian cells. Methods We examined acute toxicity of WC and of WC-Co (10% weight content Co) nanoparticles in different human cell lines (lung, skin, and colon) as well as in rat neuronal and glial cells (i.e., primary neuronal and astroglial cultures and the oligodendro cyte precursor cell line OLN-93). Furthermore, using electron microscopy, we assessed whether nanoparticles can be taken up by living cells. We chose these in vitro systems in order to evaluate for potential toxicity of the nanoparticles in different mammalian organs (i.e., lung, skin, intestine, and brain). Results Chemical–physical characterization confirmed that WC as well as WC-Co nanoparticles with a mean particle size of 145 nm form stable suspensions in serum-containing cell culture media. WC nanoparticles were not acutely toxic to the studied cell lines. However, cytotoxicity became apparent when particles were doped with Co. The most sensitive were astrocytes and colon epithelial cells. Cytotoxicity of WC-Co nanoparticles was higher than expected based on the ionic Co content of the particles. Analysis by electron microscopy demonstrated presence of WC nanoparticles within mammalian cells. Conclusions Our findings demonstrate that doping of WC nanoparticles with Co markedly increases their cytotoxic effect and that the presence of WC-Co in particulate form is essential to elicit this combinatorial effect.
Reinforcement Learning, Conflict Monitoring, and Cognitive Control: An Integrative Model of Cingulate-Striatal Interactions and the ERN

Fortune favors those who are able to align their plans and goals to accord with the constraints imposed on them by an intricate and dynamic world. However, this presents an exceedingly difficult assignment, since the constraints pressed on an organism are typically complex, uncertain, and even paradoxical. When foodstuffs run low in the fall, should a hungry forager explore new and unfamiliar territory, or should it conserve energy and wait for something to turn up? The situation may appear dire and warrant the hazards of straying from routine, yet knowledge built up over years of experience may suggest that patience will be rewarded. Flexible goal-directed behavior demands an adaptive system capable of selecting behavior appropriate for a given context. Evidence spanning a range of methodologies suggests that the anterior cingulate cortex (ACC) and the basal ganglia (BG) are two of the core brain structures involved in cognitive control, both contributing to pathways critical for learning and decision making (see also chapters 2, 9, 17, and 18, this volume). At an abstract level of description, the ACC is generally thought to be involved in monitoring performance and instigating rapid behavioral adjustments when required, whereas the BG is thought to facilitate and suppress behavior based on more stable environmental statistics. Both of these functions have been simulated in separate computational models of the ACC and BG. Although considerable debate still surrounds the unique function each system serves, here we take the approach that a better understanding may also emerge from considering the interaction between the ACC and the BG. We propose a model in which ACC activity is modulated in part by reinforcement learning processes in the BG. In particular, we focus on how this relationship between the ACC and the BG may help clarify our understanding of the errorrelated negativity (ERN), a component of the event-related potential (ERP) thought to be generated in the ACC. We begin with a brief overview of the two dominant theories explaining the ERN: the reinforcement learning hypothesis advanced by Holroyd, Coles, and colleagues, and the conflict monitoring hypothesis advocated by Botvinick, Yeung, and colleagues. This overview is followed by a sketch of the 17
Microseismicity and stress in the vicinity of the Alpine Fault, central Southern Alps, New Zealand

We investigate present-day microseismicity associated with the central Alpine Fault and the zone of active deformation and uplift in the central Southern Alps. Using 14 months of data, robust hypocenter locations have been obtained for ∼1800 earthquakes of magnitudes between -0.3 and 4.2. We derived a magnitude scale with a frequency-dependent attenuation factor, γ(f) = γ0f, where γ0 = 1.89 ± 0.02 × 10-3 s/km, that enables magnitudes to be calculated consistently for earthquakes of different sizes and frequency contents. The maximum depth of the seismicity varies systematically with distance from the Alpine Fault, from 10 ± 2 km near the fault to 8 ± 2 km within 20 km and 15 ± 2 km further southeast. This distribution correlates with lateral variations in crustal resistivity: earthquake hypocenters are concentrated in areas of strong resistivity gradients and restricted to depths of resistivities >100 Ωm. Rocks at greater depth are too hot, too fluid-saturated, or too weak to produce detectable earthquakes. Focal mechanism solutions computed for 211 earthquakes (ML > 0.44) exhibit predominantly strike-slip mechanisms. We obtain a maximum horizontal compressive stress direction of 115 ± 10° from focal mechanism inversion. This azimuth is consistent with findings from elsewhere in the central and northern South Island, and indicates a uniform crustal stress field despite pronounced variations in crustal structure and topographic relief. Our stress estimates suggest that the Alpine Fault (with a mean strike of 055°) is poorly oriented in an Andersonian sense but that individual thrust and strike-slip segments of the fault's surface trace have close to optimal orientations. Copyright 2012 by the American Geophysical Union.
Diagonal Ordering: A New Approach to High-Dimensional KNN Processing

In this paper, we propose Diagonal Ordering, a new technique for K-Nearest-Neighbor (KNN) search in a high-dimensional space. Our solution is based on data clustering and a particular sort order of the data points, which is obtained by "slicing" each cluster along the diagonal direction. In this way, we are able to transform the high-dimensional data points into one-dimensional space and index them using a B+-tree structure. KNN search is then performed as a sequence of one-dimensional range searches. Advantages of our approach include: (1) irrelevant data points are eliminated quickly without extensive distance computations; (2) the index structure can effectively adapt to different data distributions; (3) on-line query answering is supported, which is a natural byproduct of the iterative searching algorithm. We conduct extensive experiments to evaluate the Diagonal Ordering technique and demonstrate its effectiveness.
Seamless BGP Migration with Router Grafting

Network operators are under tremendous pressure to make their networks highly reliable to avoid service disruptions. Yet, operators often need to change the network to upgrade faulty equipment, deploy new services, and install new routers. Unfortunately, changes cause disruptions, forcing a trade-off between the benefit of the change and the disruption it will cause. In this paper we present router grafting, where parts of a router are seamlessly removed from one router and merged into another. We focus on grafting a BGP session and the underlying link-from one router to another, or between blades in a cluster-based router. Router grafting allows an operator to rehome a customer with no disruption, compared to downtimes today measured in minutes. In addition, grafting a BGP session can help in balancing load between routers or blades, planned maintenance, and even traffic management. We show that grafting a BGP session is practical even with today's monolithic router software. Our prototype implementation uses and extends Click, the Linux kernel, and Quagga, and introduces a daemon that automates the migration process.