Miracle-dz/UniFAR-FTUs huggingface dataset:
The tRNA recognition mechanism of the minimalist SPOUT methyltransferase, TrmL

Unlike other transfer RNAs (tRNA)-modifying enzymes from the SPOUT methyltransferase superfamily, the tRNA (Um34/Cm34) methyltransferase TrmL lacks the usual extension domain for tRNA binding and consists only of a SPOUT domain. Both the catalytic and tRNA recognition mechanisms of this enzyme remain elusive. By using tRNAs purified from an Escherichia coli strain with the TrmL gene deleted, we found that TrmL can independently catalyze the methyl transfer from S-adenosyl-L-methionine to and isoacceptors without the involvement of other tRNA-binding proteins. We have solved the crystal structures of TrmL in apo form and in complex with S-adenosyl-homocysteine and identified the cofactor binding site and a possible active site. Methyltransferase activity and tRNA-binding affinity of TrmL mutants were measured to identify residues important for tRNA binding of TrmL. Our results suggest that TrmL functions as a homodimer by using the conserved C-terminal half of the SPOUT domain for catalysis, whereas residues from the less-conserved N-terminal half of the other subunit participate in tRNA recognition.
Trade castles and forts of West Africa

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MayoClinicNLP–CORE: Semantic representations for textual similarity

The Semantic Textual Similarity (STS) task examines semantic similarity at a sentencelevel. We explored three representations of semantics (implicit or explicit): named entities, semantic vectors, and structured vectorial semantics. From a DKPro baseline, we also performed feature selection and used sourcespecific linear regression models to combine our features. Our systems placed 5th, 6th, and 8th among 90 submitted systems.
Two-View Camera Housing Parameters Calibration for Multi-layer Flat Refractive Interface

In this paper, we present a novel refractive calibration method for an underwater stereo camera system where both cameras are looking through multiple parallel flat refractive interfaces. At the heart of our method is an important finding that the thickness of the interface can be estimated from a set of pixel correspondences in the stereo images when the refractive axis is given. To our best knowledge, such a finding has not been studied or reported. Moreover, by exploring the search space for the refractive axis and using reprojection error as a measure, both the refractive axis and the thickness of the interface can be recovered simultaneously. Our method does not require any calibration target such as a checkerboard pattern which may be difficult to manipulate when the cameras are deployed deep undersea. The implementation of our method is simple. In particular, it only requires solving a set of linear equations of the form Ax = b and applies sparse bundle adjustment to refine the initial estimated results. Extensive experiments have been carried out which include simulations with and without outliers to verify the correctness of our method as well as to test its robustness to noise and outliers. The results of real experiments are also provided. The accuracy of our results is comparable to that of a state-of-the-art method that requires known 3D geometry of a scene.
A hydrogen-bonded dimer of 13-hydroxy-13-[(triisopropylsilyl)ethynyl]pentacen-6(13H)-one.

The title compound, C33H34O2Si, has been obtained as a product in the synthesis of 6,13-bis[(triisopropylsilyl)ethynyl]-6,13-dihydropentacene-6,13-diol. The solid-state structure reveals a dimer, with strong hydrogen bonds holding the two molecules in a face-to-face arrangement [O.O = 2.746 (2) A and O-H.O = 173 (2) degrees ]. Within each dimer, the pentacene units are pi-stacked (the distance between the mean least-squares planes of 22 C atoms is 3.60 A).
The Role of Angiogenesis in Cancer Treatment

A number of anti-angiogenesis drugs have been FDA-approved and are being used in cancer treatment, and a number of other agents are in different stages of clinical development or in preclinical evaluation. However, pharmacologic anti-angiogenesis strategies that arrest tumor progression might not be enough to eradicate tumors. Decreased anti-angiogenesis activity in single mechanism-based anti-angiogenic strategies is due to the redundancy, multiplicity, and development of compensatory mechanism by which blood vessels are remodeled. Improving anti-angiogenesis drug efficacy will require identification of broad-spectrum anti-angiogenesis targets. These strategies may have novel features, such as increased porosity, and are the result of complex interactions among endothelial cells, extracellular matrix proteins, growth factors, pericyte, and smooth muscle cells. Thus, combinations of anti-angiogenic drugs and other anticancer strategies such as chemotherapy appear essential for optimal outcome in cancer patients. This review will focus on the role of anti-angiogenesis strategies in cancer treatment.
Performance limits of massive MIMO systems based on Bayes-optimal inference

This paper gives a replica analysis for the minimum mean square error (MSE) of a massive multiple-input multipleoutput (MIMO) system by using Bayesian inference. The Bayesoptimal estimator is adopted to estimate the data symbols and the channels from a block of received signals in the spatial-temporal domain. We show that using the Bayes-optimal estimator, the interfering signals from adjacent cells can be separated from the received signals without pilot information of the interfering signals. In addition, the MSEs with respect to the data symbols and the channels of the desired users decrease with the number of receive antennas and the number of data symbols, respectively. There are no residual interference terms that remain bounded away from zero as the numbers of receive antennas and data symbols approach infinity.
An Event System Architecture for Scaling Scale-Resistant Services

Large organizations are deploying ever-increasing numbers of networked compute devices, from utilities installing smart controllers on electricity distribution cables, to the military giving PDAs to soldiers, to corporations putting PCs on the desks of employees. These computers are often far more capable than is needed to accomplish their primary task, whether it be guarding a circuit breaker, displaying a map, or running a word processor. These devices would be far more useful if they had some awareness of the world around them: a controller that resists tripping a switch, knowing that it would set off a cascade failure, a PDA that warns its owner of imminent danger, a PC that exchanges reports of suspicious network activity to its peers to identify stealthy computer crackers. In order to provide these higher-level services, the devices need a modelof their environment. The controller needs a model of the distribution grid, the PDA needs a model of the battlespace, and the PC needs a model of the network and of normal network and user behavior. Unfortunately, not only might models such as these require substantial computational resources, but generating and updating them is even more demanding. Modelbuilding algorithms tend to be bad in three ways: requiring large amounts of CPU and memory to run, needing large amounts of data from the outside to stay up to date, and running so slowly that can’t keep up with any fast changes in the environment that might occur. We can solve these problems by reducing the scope of the model to the immediate locale of the device, since reducing the size of the model makes the problem of model generation much more tractable. But such models are also much less useful, having no knowledge of the wider system. This thesis proposes a better solution to this problem called Level of Detail , after the computer graphics technique of the same name. Instead of simplifying the representation of distant objects, however, we simplify less-important data. Compute devices in the system receive streams of data that is a mixture of detailed data from devices that directly affect them and data summaries ( aggregateddata) from less directly influential devices. The degree to which the data is aggregated (i.e., how much it is reduced) is determined by calculating aninfluence metricbetween the target device and the remote device. The smart controller thus receives a continuous stream of raw data from the adjacent transformer, but only an occasional small status report summarizing all the equipment in a neighborhood in another part of the city. This thesis describes the data distribution system, the aggregation functions, and the influence metrics that can be used to implement such a system. I also describe my current towards establishing a test environment and validating the concepts, and describe the next steps in the research plan.
CIGAR: Application Partitioning for a CPU/Coprocessor Architecture

We present CIGAR, a methodology and development platform that facilitates the use of data-parallel coprocessors. With CIGAR, application developers use profiling tools to identify parts of the application for data-parallel execution, determine the application data structures to be hosted by the coprocessor, prototype coprocessor execution of these parts, and debug correctness of partitioned execution of the application using emulation. The CIGAR methodology is complemented by a CPU/FPGA prototyping platform that runs a fully functional version of the Linux operating system and associated development tools and libraries. To guide the development of our work and to evaluate its utility, we have instrumented SPECint2006 applications to utilize coprocessors emulated by softcore processors embedded in our prototyping platform. Examples of how a developer would use CIGAR to partition an application for a heterogeneous CPU/coprocessor environment are demonstrated.
Evaluation and modelling of the size fractionated aerosol particle number concentration measurements nearby a major road in Helsinki – Part I: Modelling results within the LIPIKA project

A field measurement campaign was conducted near a major road "Itavayla" in an urban area in Helsinki in 17–20 February 2003. Aerosol measurements were conducted using a mobile laboratory "Sniffer" at various distances from the road, and at an urban background location. Measurements included particle size distribution in the size range of 7 nm–10 μm (aerodynamic diameter) by the Electrical Low Pressure Impactor (ELPI) and in the size range of 3–50 nm (mobility diameter) by Scanning Mobility Particle Sizer (SMPS), total number concentration of particles larger than 3 nm detected by an ultrafine condensation particle counter (UCPC), temperature, relative humidity, wind speed and direction, driving route of the mobile laboratory, and traffic density on the studied road. In this study, we have compared measured concentration data with the predictions of the road network dispersion model CAR-FMI used in combination with an aerosol process model MONO32. For model comparison purposes, one of the cases was additionally computed using the aerosol process model UHMA, combined with the CAR-FMI model. The vehicular exhaust emissions, and atmospheric dispersion and transformation of fine and ultrafine particles was evaluated within the distance scale of 200 m (corresponding to a time scale of a couple of minutes). We computed the temporal evolution of the number concentrations, size distributions and chemical compositions of various particle size classes. The atmospheric dilution rate of particles is obtained from the roadside dispersion model CAR-FMI. Considering the evolution of total number concentration, dilution was shown to be the most important process. The influence of coagulation and condensation on the number concentrations of particle size modes was found to be negligible on this distance scale. Condensation was found to affect the evolution of particle diameter in the two smallest particle modes. The assumed value of the concentration of condensable organic vapour of 10 12 molecules cm −3 was shown to be in a disagreement with the measured particle size evolution, while the modelling runs with the concentration of condensable organic vapour of 10 9 –10 10 molecules cm −3 resulted in particle sizes that were closest to the measured values.
Development of a compact and low cost axial flux machine using soft magnetic composite and hard ferrite

Especially for automotive applications, the request for small, lightweight, powerful and cheap electrical machines is tremendous - not only for the drivetrain in electrical vehicles but also for ancillary components like air conditioning compressors, starters/generators or pumps. In terms of small size and high power to weight ratio, the use of permanent magnets, especially rare earth magnets is essential. However, rare earth permanent magnets(PM's) have several concerns caused by a very concentrated resource market, which has already caused unpredictable price increase or export restrictions. Therefore, it is the goal to avoid rare earth magnets on the one hand but, on the other hand, keep the characteristics of a machine for the automotive industry. The combination of hard-ferrite magnets and soft magnetic composites, combined in an axial flux motor topology is a promising approach to fulfill the requirements of a high power density, low-cost and rare earth magnet-free machine. The designed motor structure with ferrite PMs replacing the rare earth PMs and the results of three-dimensional finite element analyses are introduced in detail in this paper. Moreover, a prototype with 600W nominal output power was produced and tested.
Measuring Similarity from Word Pair Matrices with Syntagmatic and Paradigmatic Associations

Two types of semantic similarity are usually distinguished: attributional and relational similarities. These similarities measure the degree between words or word pairs. Attributional similarities are bidrectional, while relational similarities are one-directional. It is possible to compute such similarities based on the occurrences of words in actual sentences. Inside sentences, syntagmatic associations and paradigmatic associations can be used to characterize the relations between words or word pairs. In this paper, we propose a vector space model built from syntagmatic and paradigmatic associations to measure relational similarity between word pairs from the sentences contained in a small corpus. We conduct two experiments with different datasets: SemEval-2012 task 2, and 400 word analogy quizzes. The experimental results show that our proposed method is effective when using a small corpus.
The CMOS carry-forward adders

The ripple-carry adder (RCA) has the simplest circuit structure but the longest delay among all adders. Thus, it is often realized with the dynamic circuits when speed is the major concern. In this paper, we propose circuit-level and architecture-level innovations over the dynamic RCA (DRCA) that lead to high operation speed and low hardware overhead. Circuit-wise, we propose a cost-effective way to eliminate the race problem of DRCA. Architecture-wise, we propose a new carry-forwarding scheme that combines a diagonal forwarding with the multilevel folding for dramatic speed improvement of the DRCA. Finally, a new multilevel carry-forwarding scheme is proposed to reduce the circuit complexity while keeping the speed. Based on all the proposed techniques, a 32-bit dynamic carry-forward adder (CFA32) with two-level carry forwarding is designed and fabricated with the 0.25-/spl mu/m CMOS technology. The CFA32 consists of 1202 MOS transistors, and occupies only 0.017-mm/sup 2/ silicon area after layout. The measurement result, which agrees with the simulation result, shows that the adder needs only 640 ps to perform an add operation under room temperature. Using the same techniques, a 64-bit carry-forward adder (CFA64) with two-level forwarding technique is also designed and simulated. The CFA64 consists of only 2502 MOS transistors, and the simulation result shows the evaluation time is only 780 ps.
Elucidating the mechanism of DNA-dependent ATP hydrolysis mediated by DNA-dependent ATPase A, a member of the SWI2/SNF2 protein family

The active DNA-dependent ATPase A domain (ADAAD), a member of the SWI2/SNF2 family, has been shown to bind DNA in a structure-specific manner, recognizing DNA molecules possessing double-stranded to single-stranded transition regions leading to ATP hydrolysis. Extending these studies we have delineated the structural requirements of the DNA effector for ADAAD and have shown that the single-stranded and double-stranded regions both contribute to binding affinity while the double-stranded region additionally plays a role in determining the rate of ATP hydrolysis. We have also investigated the mechanism of interaction of DNA and ATP with ADAAD and shown that each can interact independently with ADAAD in the absence of the other. Furthermore, the protein can bind to dsDNA as well as ssDNA molecules. However, the conformation change induced by the ssDNA is different from the conformational change induced by stem-loop DNA (slDNA), thereby providing an explanation for the observed ATP hydrolysis only in the presence of the double-stranded:single-stranded transition (i.e. slDNA).
Multiple Genome Rearrangement and Breakpoint Phylogeny

Multiple alignment of macromolecular sequences generalizes from N = 2 to N > or = 3 the comparison of N sequences which have diverged through the local processes of insertion, deletion and substitution. Gene-order sequences diverge through non-local genome rearrangement processes such as inversion (or reversal) and transposition. In this paper we show which formulations of multiple alignment have counterparts in multiple rearrangement. Based on difficulties inherent in rearrangement edit-distance calculation and interpretation, we argue for the simpler "breakpoint analysis. " Consensus-based multiple rearrangement of N > or = 3 orders can be solved exactly through reduction to instances of the Travelling Salesman Problem (TSP). We propose a branch-and-bound solution to TSP particularly suited to these instances. Simulations show how non-uniqueness of the solution is attenuated with increasing numbers of data genomes. Tree-based multiple alignment can be achieved to a great degree of accuracy by decomposing the tree into a number of overlapping 3-stars centered on the non-terminal nodes, and solving the consensus-based problem iteratively for these nodes until convergence. Accuracy improves with very careful initializations at the non-terminal nodes. The degree of non-uniqueness of solutions depends on the position of the node in the tree in terms of path length to the terminal vertices.
Cluster Randomized Trial of Text Message Reminders to Retail Staff in Tanzanian Drug Shops Dispensing Artemether-Lumefantrine: Effect on Dispenser Knowledge and Patient Adherence

Artemisinin combination therapies are available in private outlets, but patient adherence might be compromised by poor advice from dispensers. In this cluster randomized trial in drug shops in Tanzania, 42 of 82 selected shops were randomized to receive text message reminders about what advice to provide when dispensing artemether-lumefantrine (AL). Eligible patients purchasing AL at shops in both arms were followed up at home and questioned about each dose taken. Dispensers were interviewed regarding knowledge of AL dispensing practices and receipt of the malaria-related text messages. We interviewed 904 patients and 110 dispensers from 77 shops. Although there was some improvement in dispenser knowledge, there was no difference between arms in adherence measured as completion of all doses (intervention 68.3%, control 69.8%, p [adjusted] = 0.6), or as completion of each dose at the correct time (intervention 33.1%, control 32.6%, p [adjusted] = 0.9). Further studies on the potential of text messages to improve adherence are needed.
Data Stream Warehousing In Tidalrace

data is a ubiquitous feature of large modern en terprises. Many organizations generate huge amounts of on-line stre aming data - examples include network monitoring, Twitter feeds, financial data, and industrial application monitoring. Maki ng effective use of these data streams can be challenging. While Da ta Stream Management Systems can provide support for real-time alerting and data reduction, many applications require compl ex analytics on a data history to best make use of the streams. We have been developing technologies for data stream warehousing , starting with the DataDepot (14) system. A data stream warehouse continually ingests data streams, computes complex derived data products, and stores long term histories. To take advantage of new technologies, we have developed a next- generation data stream warehousing system. In this paper we describe the Tidalrace system, our motivations for developing it, and architectural features of Tidalrace that suppor t data stream warehousing.
Is software engineering as we know it over the hill?

Many of the best practices we follow today were originally proposed decades ago. For instance, Walker Royce first described the famous Waterfall lifecycle model in 1970.1 Michael Fagan first described his inspection method—arguably the most effective of all peer review methods—in the open literature in 1976.2 The insights and techniques that the leaders of the day contributed were welcome revelations. However, how well have these contributions withstood the last three decades? Is classical software engineering as we tend to think of it obsolete? Have these techniques run their course?
Detection of Human Factor B Biosynthesis in Culture Supernatants and Cell Lysates by ELISA

Abstract We report here on the development of a simple, sensitive, convenient, and quantitative enzyme-linked immunosorbent assay for human factor B, a protein of the alternative complement pathway, by the sandwich method using goat anti-human factor B antibody. The assay described herein is reproducible and highly specific for human factor B. The assay was used to determine biosynthesis (cell lysates or extracts) and secretion (supernatants) of human factor B using human monocyte cell line U937. Phorbol myristate acetate strongly enhanced (10- to 20-fold) biosynthesis of factor B by U937. The combination of a sensitive enzyme-linked immunosorbent assay and phorbol myristate acetate enabled us to use a microculture system.
Modeling Groundwater Flow and Contaminant Transport

Jacob Bear and Alexander H. -D. Cheng. Springer, 233 Spring St., New York, NY 10013. 2010. 834 pp. Hardcover $99.00. ISBN 978-1-4020-6681-8 Groundwater flow and contaminant transport models have been widely used to test hypotheses, interpret and analyze field experiment data, predict future