Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Conservation and Diversification of the Translation Initiation Apparatus in Trypanosomatids

Trypanosomatids are ancient eukaryotic parasites that migrate between insect vectors and mammalian hosts, causing a range of diseases in humans and domestic animals. Trypanosomatids feature a multitude of unusual molecular features, including polycistronic transcription and subsequent processing by trans-splicing and polyadenylation. Regulation of protein coding genes is posttranscriptional and thus, translation regulation is fundamental for activating the developmental program of gene expression. The spliced-leader RNA is attached to all mRNAs. It contains an unusual hypermethylated cap-4 structure in its 5′ end. The cap-binding complex, eIF4F, has gone through evolutionary changes in accordance with the requirement to bind cap-4. The eIF4F components in trypanosomatids are highly diverged from their orthologs in higher eukaryotes, and their potential functions are discussed. The cap-binding activity in all eukaryotes is a target for regulation and plays a similar role in trypanosomatids. Recent studies revealed a novel eIF4E-interacting protein, involved in directing stage-specific and stress-induced translation pathways. Translation regulation during stress also follows unusual regulatory cues, as the increased translation of Hsp83 following heat stress is driven by a defined element in the 3′ UTR, unlike higher eukaryotes. Overall, the environmental switches experienced by trypanosomatids during their life cycle seem to affect their translational machinery in unique ways.
Interaction design at the Utrecht School of the Arts

The "Hogeschool voor de Kunsten Utrecht" (Utrecht School of the Arts, Utrecht, The Netherlands) offers a four-year curriculum in interaction design (roughly equivalent to an MA) and a one year master of arts degree in interactive multimedia. The material here presents our approach to interaction design as a discipline and the curriculum that embodies this approach. It features a collection of thoughts and snapshots-- we regard it as work in progress. Interaction design is a new field. It is growing fast, continuously adapting to new circumstances. We believe in our approach, but do not regard it as the final truth. There will be questions, as well as answers. Your comments, criticisms and suggestions are appreciated!
SPNP: stochastic Petri net package

SPNP, a powerful GSPN package that allows the modeling of complex system behaviors, is presented. Advanced constructs are available in SPNP such as marking-dependent arc multiplicities, enabling functions, arrays of places or transitions, and subnets; the full expressive power of the C programming language is also available to increase the flexibility of the net description. Sophisticated steady-state and transient solvers are available including cumulative and up-to-absorption measures. The user is not limited to a predefined set of measures; detailed expressions reflecting exactly the measures sought can be easily specified. The authors conclude by comparing SPNP with two other SPN-based packages, Great SPN and METASAN. <<ETX>>
Automated generation of hierarchic image database with hybrid method of ontology and GMM-based image clustering

In the field of computer vision, “generic object recognition” is one of the most important topics. Generic object recognition needs three types research: feature extraction, pattern recognition, and database preparation. This paper targets at database preparation, and proposes a method to automatically generate hierarchic image database. The proposed method considers both object semantic and visual features in images. In the proposed method, semantic is covered by ontology framework, and visual similarity is covered by images clustering based on Gaussian Mixture Model. The image databases generated by the proposed method covered over 4,800 concepts (where 152 concepts have more than 100 images) and its structure was hierarchic. Through the subjective evaluation experiments, whether images in the database were correctly mapped or not was examined. The results of the evaluation experiments showed over 84% precision in average. It is suggested that the generated image database was sufficiently practicable as learning database for generic object recognition.
Lightweight Operating-System support for a scalable and robust virtual network infrastructure

PlanetLab [3] is a platform for planetary-scale services that has been used very successfully by distributed systems researchers. Multiple simultaneous experiments are contained within separate “slices”, which on each machine is implemented as a lightweight, Linux-VServer based VM [4]. Linux-VServer isolates services with respect to the filesystem, memory, CPU and bandwidth. However, it does not provide complete virtualization of the network; rather, all slices on a node share the same IP address and port space.
Using Locality Surfaces to Determine Cache Miss Ratios

1 Introduction Caches are and will continue to be important computer components that help alleviate the disparity between processor speeds and main memory speeds. To enable the performance of computer systems to continue to increase, it is important to study and improve the performance of caches. Caches operate on the principle of memory reference locality, namely that programs tend to use a small section of memory most of the time. Hennessy and Patterson [1] define two kinds of locality: temporal and spatial. Temporal locality is when items referenced tend to be referenced again soon. Spatial locality is when items close together in memory tend to be referenced close together in time. Caches utilize both aspects of locality by storing items in faster memory that were either recently referenced or close to something recently referenced. The more locality exhibited by a workload, the better the cache performance. Thus, the ability to accurately measure locality can facilitate accurate predictions about cache performance. John and Maynard discuss the importance of studying locality in [2]. They claim that " it should be possible to arrive at a locality index or locality function for every application. This locality function should be useful in predicting cache performance without detailed simulations. " However, there is no standard for locality measurement. Nor is there a locality function that can directly predict cache performance. Traditional methods for studying locality are often limited to qualitative measures. After defining locality, researchers may simply look at the cache miss rates for a given workload [3,4]. Low miss rates denotes a Agood amount of locality@ for that workload; high miss rates denote Alittle@ locality. Attempts to quantify locality are generally limited to a series of two dimensional graphs [5]. One graph usually contains only the temporal locality, defined by the distribution of the number of items between successive references to the same item. Another graph may contain limited information about spatial locality, perhaps looking only at items that are followed by the next item in memory. In [6], Conte and Hwu improve the evaluation of temporal locality by using the number of unique items between successive references. Jacob et. al. call this measure the stack distance in [7]. However, all of these methods involve multiple graphs and ignore many aspects of spatial locality. In [8,9], Grimsrud et al. present a unique approach to quantifying locality by uniting temporal and spatial locality and plotting …
Role of Omega-3 Polyunsaturated Fatty Acids in the Production of Prostaglandin E2 and Nitric Oxide during Experimental Murine Paracoccidioidomycosis

There has recently been increased interest in the potential health effects of omega-3 polyunsaturated fatty acids on the immune system. Paracoccidioidomycosis is the most important endemic mycosis in Latin America. Macrophages have a fundamental role and act as first line of organism defense. The purpose of this study was to analyze the effect of n-3 fatty acids on the production of PGE2 and NO by mice infected with Pb18 and fed a diet enriched with LNA for 8 weeks. To study the effect of omega-3 fatty acids on macrophage activity during experimental paracoccidioidomycosis, mice were infected with Pb18 and fed a diet supplemented with LNA. PGE2 in the serum of animals was analyzed and NO in the supernatants of macrophages cultured and challenged in vitro with Pb18 was measured. Omega-3 fatty acids seemed to decrease the production of PGE2 in vivo in the infected group fed an LNA-supplemented diet during the 4th and 8th weeks of the experiment. At the same time, we observed an increase in synthesis of NO by peritoneal macrophages in this group. Omega-3 fatty acids thus appear to have an immunomodulatory effect in paracoccidioidomycosis.
Temporal decrease in upper atmospheric chlorine

We report a steady decrease in the upper stratospheric and lower mesospheric abundances of hydrogen chloride (HCl) from August 2004 through January 2006, as measured by the Microwave Limb Sounder (MLS) aboard the Aura satellite. For 60°S to 60°N zonal means, the average yearly change in the 0.7 to 0.1 hPa (∼50 to 65 km) region is −27 ± 3 pptv/year, or −0.78 ± 0.08 percent/year. This is consistent with surface abundance decrease rates (about 6 to 7 years earlier) in chlorine source gases. The MLS data confirm that international agreements to reduce global emissions of ozone‐depleting industrial gases are leading to global decreases in the total gaseous chlorine burden. Tracking stratospheric HCl variations on a seasonal basis is now possible with MLS data. Inferred stratospheric total chlorine (ClTOT) has a value of 3.60 ppbv at the beginning of 2006, with a (2‐sigma) accuracy estimate of 7%; the stratospheric chlorine loading has decreased by about 43 pptv in the 18‐month period studied here. We discuss the MLS HCl measurements in the context of other satellite‐based HCl data, as well as expectations from surface chlorine data. A mean age of air of ∼ 5.5 years and an age spectrum width of 2 years or less provide a fairly good fit to the ensemble of measurements.
DHFS: A High-Throughput Heterogeneous File System Based on Mainframe for Cloud Storage

The file system for the Cloud Storage usually use the distributed structure which store the metadata and the user data respectively. The I/O nodes get the management information of file from the specific metadata server through the networks. Under this mode, the metadata server should be the performance bottleneck of the whole system when huge number nodes or the heavy workloads in Cloud Storage. Therefore, the capability of the metadata server become one of the key aspect for the whole system. In this paper, we present DHFS(Distribute Heterogeneous File System), a high throughput system for Cloud Storage, building metadata server on the high performance mainframe. For the different organization of the file system between mainframe and open system(Unix, Solaris, Windows, Linux, etc.), we implement the user-level library for the heterogeneous share of data which allow application in open system accessing files of mainframe. We also employ a series of strategies for the performance optimization.
A spatiotemporal nonparametric Bayesian model of multi-subject fMRI data

In this paper we propose a uniﬁed, probabilistically coherent framework for the analysis of task-related brain activity in multi-subject fMRI experiments. This is distinct from two-stage “group analysis” approaches traditionally considered in the fMRI literature, which separate the inference on the individual fMRI time courses from the inference at the population level. In our modeling approach we consider a spatiotemporal linear regression model and speciﬁcally account for the between-subjects heterogeneity in neuronal activity via a spatially informed multi-subject nonparametric variable selection prior. For posterior inference, in addition to Markov chain Monte Carlo sampling algorithms, we develop suitable variational Bayes algorithms. We show on simulated data that variational Bayes inference achieves satisfactory results at more reduced computational costs than using MCMC, allowing scalability of our methods. In an application to data collected to assess brain responses to emotional stimuli our method correctly detects activation in visual areas when visual stimuli are presented.
Accountability and deterrence in online life

The standard technical approach to privacy and security in online life is preventive: Before someone can access confidential data or take any other action that implicates privacy or security, he should be required to prove that he is authorized to do so. As the scale and complexity of online activity has grown, it has become apparent that the preventive approach is inadequate; thus, a growing set of information-security researchers has embraced greater reliance on accountability mechanisms to complement preventive measures. Despite widespread agreement that "accountability" is important in online life, the term has no standard definition. We make three contributions to the study of accountability: (1) We flesh out with realistic examples our claim that a purely preventive approach to security is inadequate; (2) We present, compare, and contrast some existing formal frameworks for accountability; (3) We explore the question of whether "deterrence" may be a better general term in this context than "accountability. "
Ex situ conservation of Ruscus aculeatus L. – ruscogenin biosynthesis, genome-size stability and propagation traits of tissue-cultured clones

Ruscus aculeatus L. is a perennial semi-shrub with distinctive leaf-like branches (cladodes). Rhizomes and roots contain steroidal saponins (ruscogenins) that are used in medicine and cosmetics for their anti-inflammatory, venotonic and antihaemorroidal activity. Problematic cultivation of the species causes in many countries unsustainable over-collection from the wild. Tissue culture propagation of R. aculeatus was carried out for conservation and propagation purposes. The impact of the clonal origin (genotype) on the ruscogenin biosynthesis, genome-size stability and propagation traits and morpho-physiological response to long-term cultivation in vitro was studied. Production of ruscogenins in fully developed regenerants was quantified by high-performance liquid chromatography (HPLC). Genome-size stability of the clones was assessed by flow cytometry. Slow growth and prolonged lag-phase were characteristic for the whole propagation cycle. Produced plantlets with well-defined organs were suitable for direct ex vitro planting. Genome DNA content of all clones was stable and comparable to native plants. Ruscogenin biosynthesis was clone-specific, presenting distinctive profiles of the cultures. Our results imply that clone origin and culture type might influence saponin biosynthesis in Ruscus. These traits should be considered in the ex situ conservation of the genetic diversity of this species and by production of planting material as well.
FRICTIONS AND THE CONTRIBUTION OF INVENTORY TO SHAREHOLDER WEALTH

type="main" xml:lang="en"> Shareholder wealth effects associated with inventory are examined. Initial results indicate a positive and significant relation between shareholder wealth and inventory. Additional findings suggest that operating conditions, financial constraints, and working capital behavior influence the value of inventory. These findings are consistent with tactical and strategic decisions influencing managers to hold inventory. Overall, the results suggest that shareholders price the strategic advantages accompanying inventory.
A survey of extensions to APL

A survey of proposed extensions to the APL language is made with emphasis placed on the motivations for various proposals, the differences between them and the consequences of their adoption. Some issues of a more general nature concerning the purpose, process and direction of language extension are also discussed. An extensive bibliography is provided with annotations concerning the nature, development and influence of various authors' works. Areas of extension encompassed by the survey include nested arrays, complex numbers, uniform application of functions, laminar extension, primitive functions, control structures, direct definition, operators, system functions and variables, name scope control and event trapping.
Using video-oriented instructions to speed up sequence comparison

MOTIVATION This document presents an implementation of the well-known Smith-Waterman algorithm for comparison of proteic and nucleic sequences, using specialized video instructions. These instructions, SIMD-like in their design, make possible parallelization of the algorithm at the instruction level. RESULTS Benchmarks on an ULTRA SPARC running at 167 MHz show a speed-up factor of two compared to the same algorithm implemented with integer instructions on the same machine. Performance reaches over 18 million matrix cells per second on a single processor, giving to our knowledge the fastest implementation of the Smith-Waterman algorithm on a workstation. The accelerated procedure was introduced in LASSAP--a LArge Scale Sequence compArison Package software developed at INRIA--which handles parallelism at higher level. On a SUN Enterprise 6000 server with 12 processors, a speed of nearly 200 million matrix cells per second has been obtained. A sequence of length 300 amino acids is scanned against SWISSPROT R33 (1,8531,385 residues) in 29 s. This procedure is not restricted to databank scanning. It applies to all cases handled by LASSAP (intra- and inter-bank comparisons, Z-score computation, etc.
TOUCHSTONE: An ab initio protein structure prediction method that uses threading-based tertiary restraints

The successful prediction of protein structure from amino acid sequence requires two features: an efficient conformational search algorithm and an energy function with a global minimum in the native state. As a step toward addressing both issues, a threading-based method of secondary and tertiary restraint prediction has been developed and applied to ab initio folding. Such restraints are derived by extracting consensus contacts and local secondary structure from at least weakly scoring structures that, in some cases, can lack any global similarity to the sequence of interest. Furthermore, to generate representative protein structures, a reduced lattice-based protein model is used with replica exchange Monte Carlo to explore conformational space. We report results on the application of this methodology, termed TOUCHSTONE, to 65 proteins whose lengths range from 39 to 146 residues. For 47 (40) proteins, a cluster centroid whose rms deviation from native is below 6.5 (5) Å is found in one of the five lowest energy centroids. The number of correctly predicted proteins increases to 50 when atomic detail is added and a knowledge-based atomic potential is combined with clustered and nonclustered structures for candidate selection. The combination of the ratio of the relative number of contacts to the protein length and the number of clusters generated by the folding algorithm is a reliable indicator of the likelihood of successful fold prediction, thereby opening the way for genome-scale ab initio folding.
Graph-Based Reasoning and Reinforcement Learning for Improving Q/A Performance in Large Knowledge-Based Systems

Learning to plausibly reason with minimal user intervention could significantly improve knowledge acquisition. We describe how to integrate graph-based heuristic generalization, higher-order knowledge, and reinforcement learning to learn to produce plausible inferences with only small amounts of user training. Experiments on ResearchCyc KB contents show significant improvement in Q/A performance with high accuracy.
Do Security-differentiated Water Rights Improve Efficiency?

Most existing water markets combine water rights trading and water allocation trading. Offering different levels of security for rights can make the market more sophisticated and allow water users to manage the risks of supply uncertainty better. We compare results from a laboratory experiment with two water right designs, one with a unique security level and another with two security levels. We find that a two security levels system improves both allocative eciency and risk management, but only when transactions costs are higher in the market for water allocation than in the market for water rights.
Preesm: A dataflow-based rapid prototyping framework for simplifying multicore DSP programming

The high performance Digital Signal Processors (DSPs) currently manufactured by Texas Instruments are heterogeneous multiprocessor architectures. Programming these architectures is a complex task often reserved to specialized engineers because the bottlenecks of both the algorithm and the architecture need to be deeply understood in order to obtain a fairly parallel execution. The PREESM framework objective is to simplify the programming of multicore DSP systems by building on dataflow programming methods. The current functionalities of this scalable framework cover memory and time analysis, as well as automatic deadlock-free code generation. Several tutorials are provided with the tool for fast initiation of C programmers to multicore DSP programming. This paper demonstrates PREESM capabilities by comparing simulation and execution performances on a stereo matching algorithm prototyped on the TMS320C6678 8-core DSP device.
Deciphering the Enigma of Human Creativity: Can a Digital Computer Think?

The objective of the present article is a) to explain humans’ high creativity in non-mystic and unambiguous terms, b) to evaluate the performance of problem-solving computer programs and c) to make suggestions about future designs of heuristics. Unlike many previous attempts in the past century, we sought inspiration from two sources that had been neglected or excluded from considerations by experts: artificial intelligence and introspections of a number of highly creative individuals, who confessed that they had a penchant for visual thinking. Simonton’s chance-configuration model was refurbished accordingly. It is now possible for the refurbished model to explain a number of outstanding puzzles that had eluded our predecessors: a) what intuition is, b) why creators had no idea about their source of inspiration even after the fact, c) a peculiar event happening at the discovery time, known as the “aha” phenomenon, d) a type of accidental discoveries known as serendipity. Moreover, the elusive concept of abduction advanced by philosopher Charles Peirce is actually visual thinking in disguise. Blessed with this new understanding, we could evaluate the performance of a number of problem-solving computer programs from a cognitive point of view. It turned out that the common thread that links human creativity and computer-based creative problem solving is heuristic searching. Recognizing that a digital computer must perform heuristic searching in a digital environment, which is not the most user-friendly environment to do so, we made suggestions about how to circumvent the restrictions without sacrificing the principles in future designs of heuristics.