Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncertainty Explicit Assessment of Off-the-Shelf Software: Selection of an Optimal Diverse Pair

Assessment of software COTS components is an essential part of component-based software development. Sub-optimal selection of components may lead to solutions with low quality. The assessment is based on incomplete knowledge about the COTS components themselves and other aspects, which may affect the choice such as the vendor's credentials, etc. We argue in favor of assessment methods in which uncertainty is explicitly represented (`uncertainty explicit' methods) using probability distributions. We have adapted a model (developed elsewhere by Littlewood, B. et al. (2000)) for assessment of a pair of COTS components to take account of the fault (bug) logs that might be available for the COTS components being assessed. We also provide empirical data from a study we have conducted with off-the-shelf database servers, which illustrate the use of the method
Caenorhabditis elegans: nature and nurture gift to nematode parasitologists

Abstract The free-living nematode Caenorhabditis elegans is the simplest animal model organism to work with. Substantial knowledge and tools have accumulated over 50 years of C. elegans research. The use of C. elegans relating to parasitic nematodes from a basic biology standpoint or an applied perspective has increased in recent years. The wealth of information gained on the model organism, the use of the powerful approaches and technologies that have advanced C. elegans research to parasitic nematodes and the enormous success of the omics fields have contributed to bridge the divide between C. elegans and parasite nematode researchers. We review key fields, such as genomics, drug discovery and genetics, where C. elegans and nematode parasite research have convened. We advocate the use of C. elegans as a model to study helminth metabolism, a neglected area ready to advance. How emerging technologies being used in C. elegans can pave the way for parasitic nematode research is discussed.
Frondose Fossil from the Conasauga Formation (Cambrian: Drumian Stage) of Georgia, USA

The distal tip of a frondose fossil, similar in general morphology to some Ediacaran fronds, is reported from the Conasauga Formation (Cambrian Series 3: Drumian Stage) of Floyd County, Georgia. The new specimen is preserved in a siliceous concretion. Retention of its original convexity implies that it was rapidly silicified. Silicification associated with concretion formation is inferred to have been mediated by the activities of a microbial biofilm formed around the dead host. Sources of colloidal silica in the Conasauga Formation include the spicules of co-occurring Brooksella sponges and chancelloriids.
Memory-Based Dependency Parsing

This paper reports the results of experiments using memory-based learning to guide a deterministic dependency parser for unrestricted natural language text. Using data from a small treebank of Swedish, memory-based classifiers for predicting the next action of the parser are constructed. The accuracy of a classifier as such is evaluated on held-out data derived from the treebank, and its performance as a parser guide is evaluated by parsing the held-out portion of the treebank. The evaluation shows that memory-based learning gives a significant improvement over a previous probabilistic model based on maximum conditional likelihood estimation and that the inclusion of lexical features improves the accuracy even further.
On the evolution of virulence and the relationship between various measures of mortality

Smallpox causes roughly 20% mortality whereas chickenpox causes less than 0.1%. Most ‘verbal’ (i.e. non–mathematical) discussions using a mortality definition of virulence would therefore label smallpox as more virulent. Indeed, the virulence of many diseases is measured using such case mortalities, &b.chi;, or related measures such as expected host lifespan, T, or lethal dose, LDx. But &b.chi;, T and LDx are only indirectly related to parasite–induced instantaneous mortality rate, α, which is the mortality measure used in much of the theory developed to explain virulence evolution. Here I point out that relatively deadly pathogens can actually have lower values of α than benign pathogens, demonstrating that α does not, by itself, reflect the extent to which a parasite causes host mortality. I present mathematical relationships between α and &b.chi;, T and LDx, and use these to demonstrate that predictions about virulence evolution can be qualitatively altered depending upon which measure is used as the definition of virulence. Two simple examples are presented to illustrate this point, one of which demonstrates that the well–cited prediction that virulence should evolve to be higher when disease–independent host mortality increases need not hold. This prediction has been made in terms of parasite–induced instantaneous mortality, α, but if virulence is measured using case mortality (or T or LDx) then this prediction can easily be reversed. Theoretical and empirical researchers must use compatible mortality measures before a productive exchange between the two can take place, and it is suggested that case mortality (or lethal dose) is best suited as a single (mortality) measure of parasite virulence.
Fitness Landscapes and Memetic Algorithm Design 3.1 Introduction 3.2 Fitness Landscapes of Combinatorial Problems

The notion of tness landscapes has been introduced to describe the dynamics of evolutionary adaptation in nature 40] and has become a powerful concept in evolutionary theory. Fitness landscapes are equally well suited to describe the behavior of heuristic search methods in optimization, since the process of evolution can be thought of as searching a collection of genotypes in order to nd the genotype of an organism with highest tness and thus highest chance of survival. Thinking of a heuristic search method as a strategy to \navigate" in the tness landscape of a given optimization problem may help in predicting the performance of a heuristic search algorithm if the structure of the landscape is known in advance. Furthermore, the analysis of tness landscapes may help in designing highly eeective search algorithms. In the following we show how the analysis of tness landscapes of combinatorial optimization problems can aid in designing the components of memetic algorithms. However, some of the presented concepts can also be utilized for the development of other search algorithms , including genetic algorithms and neighborhood search algorithms (e.g. simulated annealing and tabu search). In combinatorial optimization, the number of (candidate) solutions of a given problem is nite. Due to the fact that the complete enumeration of the search space is in many cases impractical (many combinatorial optimization problems are known to be NP-hard 12]), only a small fraction of all solutions can be evaluated and thus the structure of the problem must be exploited to nd optimum or near optimum solutions. To identify the structure of a given problem, the idea of tness landscape analysis appears to be a promising approach.
MGluR5 Mediates the Interaction between Late-LTP, Network Activity, and Learning

Hippocampal synaptic plasticity and learning are strongly regulated by metabotropic glutamate receptors (mGluRs) and particularly by mGluR5. Here, we investigated the mechanisms underlying mGluR5-modulation of these phenomena. Prolonged pharmacological blockade of mGluR5 with MPEP produced a profound impairment of spatial memory. Effects were associated with 1) a reduction of mGluR1a-expression in the dentate gyrus; 2) impaired dentate gyrus LTP; 3) enhanced CA1-LTP and 4) suppressed theta (5–10 Hz) and gamma (30–100 Hz) oscillations in the dentate gyrus. Allosteric potentiation of mGluR1 after mGluR5 blockade significantly ameliorated dentate gyrus LTP, as well as suppression of gamma oscillatory activity. CA3-lesioning prevented MPEP effects on CA1-LTP, suggesting that plasticity levels in CA1 are driven by mGluR5-dependent synaptic and network activity in the dentate gyrus. These data support the hypothesis that prolonged mGluR5-inactivation causes altered hippocampal LTP levels and network activity, which is mediated in part by impaired mGluR1-expression in the dentate gyrus. The consequence is impairment of long-term learning.
Pain Modulation by Nitric Oxide in the Spinal Cord

Nitric oxide (NO) is a versatile messenger molecule first associated with endothelial relaxing effects. In the central nervous system (CNS), NO synthesis is primarily triggered by activation of N-methyl-D-aspartate (NMDA) receptors and has a Janus face, with both beneficial and harmful properties. There are three isoforms of the NO synthesizing enzyme nitric oxide synthase (NOS): neuronal (nNOS), endothelial (eNOS), and inducible nitric oxide synthase (iNOS), each one involved with specific events in the brain. In the CNS, nNOS is involved with modulation of synaptic transmission through long-term potentiation in several regions, including nociceptive circuits in the spinal cord. Here, we review the role played by NO on central pain sensitization.
Remote sensing tools for snow and avalanche research

Since the first images acquired from airplanes (1915) and satellites (1960), remote sensing has had a great impact in diverse number of fields such as meteorology, military, topographic mapping, archaeology and forestry. Today remote sensing has even become a common tool for the general public, with location searches using high spatial resolution (< 1m) imagery on GoogleEarth or Bing Maps. The advantages are clear, remote sensing instruments can cover large spatially continuous areas without touching the ground. This is especially important for high-alpine terrain due to restricted accessibility. However, the application of remote sensing instruments in snow and avalanche research is limited. Important reasons for this might have been the low spatial and temporal resolution of past technology as well as the high costs for satellite imagery, which may have hindered successful and economic applications. However, with advancing sensor technology capable of acquiring data with 12bit radiometric resolution and very high spatial resolution, such limitations are being addressed. Today, more than a dozen civil satellite sensors are operational, which are capable of acquiring data with a spatial resolution better than 5m as well as many airborne sensors with comparable characteristics. This paper presents an overview of the promising remote sensing applications for snow and avalanche research which apply the currentsensor technology. We discuss potential applications such as digital elevation model DEM generation, avalanche detection, snow depth and snow type mapping, give a short overview past research in this field and show preliminary results from current projects at the SLF.
Equivalent circuits for unidirectional SAW-IDTs based on the coupling-of-modes theory

A three-port distributed-parameter equivalent circuit representing the whole structure of a unidirectional interdigital transducer (IDT) is derived from generalized coupling-of-modes (COM) equations with complex parameters. The circuit has a simple form similar to that of a bidirectional IDT, but involves two additional impedance elements of opposite signs. It is shown that the two additional elements express well the behaviors of unidirectional IDTs and the directivity can easily be derived from the equivalent circuit. Some examples of calculations of device characteristics using the circuit are also presented.
The journey of resveratrol from yeast to human

The natural polyphenolic compound resveratrol was first discovered in the 1940s. In the recent years, this compound received renewed interest as several findings implicated resveratrol as a potent SIRT1 activator capable of mimicking the effects of calorie restriction, and regulating longevity in lower organisms. Given the worldwide increase in age-related metabolic diseases the beneficial effects of resveratrol on metabolism and healthy aging in humans are currently a topic of intense investigation.
Intramolecular ex vivo Fluorescence Resonance Energy Transfer (FRET) of Dihydropyridine Receptor (DHPR) β1a Subunit Reveals Conformational Change Induced by RYR1 in Mouse Skeletal Myotubes

The dihydropyridine receptor (DHPR) β1a subunit is essential for skeletal muscle excitation-contraction coupling, but the structural organization of β1a as part of the macromolecular DHPR-ryanodine receptor type I (RyR1) complex is still debatable. We used fluorescence resonance energy transfer (FRET) to probe proximity relationships within the β1a subunit in cultured skeletal myotubes lacking or expressing RyR1. The fluorescein biarsenical reagent FlAsH was used as the FRET acceptor, which exhibits fluorescence upon binding to specific tetracysteine motifs, and enhanced cyan fluorescent protein (CFP) was used as the FRET donor. Ten β1a reporter constructs were generated by inserting the CCPGCC FlAsH binding motif into five positions probing the five domains of β1a with either carboxyl or amino terminal fused CFP. FRET efficiency was largest when CCPGCC was positioned next to CFP, and significant intramolecular FRET was observed for all constructs suggesting that in situ the β1a subunit has a relatively compact conformation in which the carboxyl and amino termini are not extended. Comparison of the FRET efficiency in wild type to that in dyspedic (lacking RyR1) myotubes revealed that in only one construct (H458 CCPGCC β1a -CFP) FRET efficiency was specifically altered by the presence of RyR1. The present study reveals that the C-terminal of the β1a subunit changes conformation in the presence of RyR1 consistent with an interaction between the C-terminal of β1a and RyR1 in resting myotubes.
Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential

Within the subarctic climate of Clinton Creek, Yukon, Canada, lies an abandoned and flooded open-pit asbestos mine that harbors rapidly growing microbialites. To understand their formation we completed a metagenomic community profile of the microbialites and their surrounding sediments. Assembled metagenomic data revealed that bacteria within the phylum Proteobacteria numerically dominated this system, although the relative abundances of taxa within the phylum varied among environments. Bacteria belonging to Alphaproteobacteria and Gammaproteobacteria were dominant in the microbialites and sediments, respectively. The microbialites were also home to many other groups associated with microbialite formation including filamentous cyanobacteria and dissimilatory sulfate-reducing Deltaproteobacteria, consistent with the idea of a shared global microbialite microbiome. Other members were present that are typically not associated with microbialites including Gemmatimonadetes and iron-oxidizing Betaproteobacteria, which participate in carbon metabolism and iron cycling. Compared to the sediments, the microbialite microbiome has significantly more genes associated with photosynthetic processes (e.g., photosystem II reaction centers, carotenoid, and chlorophyll biosynthesis) and carbon fixation (e.g., CO dehydrogenase). The Clinton Creek microbialite communities had strikingly similar functional potentials to non-lithifying microbial mats from the Canadian High Arctic and Antarctica, but are functionally distinct, from non-lithifying mats or biofilms from Yellowstone. Clinton Creek microbialites also share metabolic genes (R2 < 0.750) with freshwater microbial mats from Cuatro Ciénegas, Mexico, but are more similar to polar Arctic mats (R2 > 0.900). These metagenomic profiles from an anthropogenic microbialite-forming ecosystem provide context to microbialite formation on a human-relevant timescale.
Multiple error diagnosis based on Xlists

In this paper, we present multiple error diagnosis algorithms to overcome two significant problems associated with current error diagnosis techniques targeting large circuits: their use of limited error models and a lack of solutions that scale well for multiple errors. Our solution is based on a non-enumerative analysis technique, based on logic simulation (3-valued and symbolic), for simultaneously analyzing all possible errors at sets of nodes in the circuit. Error models are introduced in order to address the "locality" aspect of error location and to identify sets of nodes that are "local" with respect to each other. Theoretical results are provided to guarantee the diagnosis of modeled errors and robust diagnosis approaches are shown to address the cases when errors do not correspond to the modeled types. Experimental results on benchmark circuits demonstrate accurate and extremely rapid location of errors of large multiplicity.
Antithrombotic Therapy in Patients With Atrial Fibrillation Undergoing Coronary Stenting: A North American Perspective: Executive Summary

The optimal regimen of the anticoagulant and antiplatelet therapies in patients with atrial fibrillation who have had a coronary stent is unclear. It is well recognized that “triple therapy” with aspirin, clopidogrel, and warfarin is associated with an increased risk of bleeding. National guidelines have not made specific recommendations, given the lack of adequate data. In choosing the best antithrombotic options for a patient, consideration needs to be given to the risks of stroke, stent thrombosis, and major bleeding. This executive summary describes these risks, provides specific recommendations concerning vascular access, stent choice, concomitant use of proton pump inhibitors, and the use and duration of triple therapy after stent placement, based on the risk assessment.
Exospheric Neutral Hydrogen Density at the Nominal 10 RE Subsolar Point Deduced From XMM‐Newton X‐Ray Observations

We investigate the exospheric neutral density near the subsolar magnetopause, assuming Xgse = 10 RE as its typical location, to support the upcoming Solar wind‐Magnetosphere‐Ionosphere Link Explorer that will visualize the Earth's magnetosheath and cusps in soft X‐rays. Neutral hydrogen density is a key parameter that controls soft X‐ray emission and can be inversely extracted from the soft X‐ray observations. We introduce a unique method to estimate the dayside neutral density by using X‐ray Multi‐Mirror Mission (XMM)‐Newton astrophysics X‐ray observations and Open Geospace Global Circulation Model (OpenGGCM) global magnetosphere‐ionosphere magnetohydrodynamics (MHD) model. On 4 May 2003 and 16 October 2001, the XMM‐Newton line of sight traversed the dayside of the Earth's magnetosheath and observed strong near‐Earth soft X‐ray emission. We simulate these two events using the OpenGGCM model. Although the model tends to produce a spatially thicker magnetosheath than measured, modeled magnetosheath plasma fluxes match well with the in situ observations of Cluster and Geotail. We calculate the neutral densities every thousand seconds by comparing the modeled count rates with the XMM‐Newton rates. The densities are averaged at 39.9 ± 8.0 and 57.6 ± 8.0 cm−3 for the 4 May 2003 and 16 October 2001 events, respectively. Since our MHD tends to underestimate neutral densities due to its thicker magnetosheath, the true neutral density is likely to lie within the upper half of these error bars.
Genome Sequence of the Mesophilic Thermotogales Bacterium Mesotoga prima MesG1.Ag.4.2 Reveals the Largest Thermotogales Genome To Date

Here we describe the genome of Mesotoga prima MesG1.Ag4. 2, the first genome of a mesophilic Thermotogales bacterium. Mesotoga prima was isolated from a polychlorinated biphenyl (PCB)-dechlorinating enrichment culture from Baltimore Harbor sediments. Its 2.97 Mb genome is considerably larger than any previously sequenced Thermotogales genomes, which range between 1.86 and 2.30 Mb. This larger size is due to both higher numbers of protein-coding genes and larger intergenic regions. In particular, the M. prima genome contains more genes for proteins involved in regulatory functions, for instance those involved in regulation of transcription. Together with its closest relative, Kosmotoga olearia, it also encodes different types of proteins involved in environmental and cell–cell interactions as compared with other Thermotogales bacteria. Amino acid composition analysis of M. prima proteins implies that this lineage has inhabited low-temperature environments for a long time. A large fraction of the M. prima genome has been acquired by lateral gene transfer (LGT): a DarkHorse analysis suggests that 766 (32%) of predicted protein-coding genes have been involved in LGT after Mesotoga diverged from the other Thermotogales lineages. A notable example of a lineage-specific LGT event is a reductive dehalogenase gene—a key enzyme in dehalorespiration, indicating M. prima may have a more active role in PCB dechlorination than was previously assumed.
Fully Automatic Semantic MT Evaluation

We introduce the first fully automatic, fully semantic frame based MT evaluation metric, MEANT, that outperforms all other commonly used automatic metrics in correlating with human judgment on translation adequacy. Recent work on HMEANT, which is a human metric, indicates that machine translation can be better evaluated via semantic frames than other evaluation paradigms, requiring only minimal effort from monolingual humans to annotate and align semantic frames in the reference and machine translations. We propose a surprisingly effective Occam's razor automation of HMEANT that combines standard shallow semantic parsing with a simple maximum weighted bipartite matching algorithm for aligning semantic frames. The matching criterion is based on lexical similarity scoring of the semantic role fillers through a simple context vector model which can readily be trained using any publicly available large monolingual corpus. Sentence level correlation analysis, following standard NIST MetricsMATR protocol, shows that this fully automated version of HMEANT achieves significantly higher Kendall correlation with human adequacy judgments than BLEU, NIST, METEOR, PER, CDER, WER, or TER. Furthermore, we demonstrate that performing the semantic frame alignment automatically actually tends to be just as good as performing it manually. Despite its high performance, fully automated MEANT is still able to preserve HMEANT's virtues of simplicity, representational transparency, and inexpensiveness.