Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast and Accurate Estimates of Divergence Times from Big Data

Ongoing advances in sequencing technology have led to an explosive expansion in the molecular data available for building increasingly larger and more comprehensive timetrees. However, Bayesian relaxed-clock approaches frequently used to infer these timetrees impose a large computational burden and discourage critical assessment of the robustness of inferred times to model assumptions, influence of calibrations, and selection of optimal data subsets. We analyzed eight large, recently published, empirical datasets to compare time estimates produced by RelTime (a non-Bayesian method) with those reported by using Bayesian approaches. We find that RelTime estimates are very similar to Bayesian approaches, yet RelTime requires orders of magnitude less computational time. This means that the use of RelTime will enable greater rigor in molecular dating, because faster computational speeds encourage more extensive testing of the robustness of inferred timetrees to prior assumptions (models and calibrations) and data subsets. Thus, RelTime provides a reliable and computationally thrifty approach for dating the tree of life using large-scale molecular datasets.
Development of Image Processing Tools for Analysis of Laser Deposition Experiments

Abstract Microscopical metallography is a well established field with a long history of techniques for measuring features. Modern computational power allows much more rigorous investigation than simple area fractions and intercept measurements. This paper details the development of image processing tools using GNU Octave, a free, open source numerical computation package. Proposed in the paper is a method for characterizing features within a digital microscope image.
Study and Comparison of Rule-Based and Statistical Catalan-Spanish Machine Translation Systems

Machine translation systems can be classified into rule-based and corpus-based approaches, in terms of their core methodology. Since both paradigms have been largely used during the last years, one of the aims in the research community is to know how these systems differ in terms of translation quality. To this end, this paper reports a study and comparison of several specific Catalan-Spanish machine translation systems: two rule-based and two corpus-based (particularly, statistical-based) systems, all of them freely available on the web. The translation quality analysis is performed under two different domains: journalistic and medical. The systems are evaluated by using standard automatic measures, as well as by native human evaluators. In addition to these traditional evaluation procedures, this paper reports a novel linguistic evaluation, which provides information about the errors encountered at the orthographic, morphological, lexical, semantic and syntactic levels. Results show that while rule-based systems provide a better performance at orthographic and morphological levels, statistical systems tend to commit less semantic errors. Furthermore, results show all the evaluations performed are characterised by some degree of correlation, and human evaluators tend to be specially critical with semantic and syntactic errors.
Three-dimensional robotic-assisted endomicroscopy with a force adaptive robotic arm

Effective in situ, in vivo tumour margin assessment is an important, yet unmet, clinical demand in surgical oncology. Recent advances in probe-based optical imaging tools such as confocal endomicroscopy is making inroads in clinical applications. In practice, maintaining consistent tissue contact whilst ensuring large area surveillance is crucial for its practical adoption and for this reason there is a great demand for robotic assistance so that high-speed endomicroscopes can be combined with autonomous scanning, thus simphfying its incorporation in routine surgical workflows. In this paper, a cooperatively controlled robotic manipulator is developed, which provides a stable mechatronicaUy-enhanced platform for micro-scanning tools to perform local high resolution mosaics over 3D undulating moving surfaces. Detailed kinematic and overall system performance analyses are provided and the results demonstrate the adaptabUity in terms of both contact force and orientation control of the system, and thus its simplicity in practical deployment and value for clinical adoption.
LQ Control without Riccati Equations: Stochastic Systems

We study stochastic linear--quadratic (LQ) optimal control problems over an infinite horizon, allowing the cost matrices to be indefinite. We develop a systematic approach based on semidefinite programming (SDP). A central issue is the stability of the feedback control; and we show this can be effectively examined through the complementary duality of the SDP. Furthermore, we establish several implication relations among the SDP complementary duality, the (generalized) Riccati equation, and the optimality of the LQ control problem. Based on these relations, we propose a numerical procedure that provides a thorough treatment of the LQ control problem via SDP: it identifies a stabilizing feedback control that is optimal or determines that the problem possesses no optimal solution. For the latter case, we develop an e-approximation scheme that is asymptotically optimal.
Effect of Silhouette Color on Trap Catches of Dendroctonus frontalis (Coleoptera: Scolytidae)

Abstract With the exception of responses to semiochemicals, host selection behaviors of D. frontalis are largely unstudied. To better understand the host finding behavior of D. frontalis, and to identify potential visual disruptants, we evaluated the response of D. frontalis to multiple-funnel traps of eight different colors. Multiple-funnel traps provide an attractive vertical silhouette, similar to a host stem, that aids in capturing bark beetles and allows for controlled evaluation of visual cues. Evaluation of mean trap catch of each color by analysis of variance (ANOVA) produced two separate groups: white and yellow traps caught significantly fewer D. frontalis than the other six colors tested (black, blue, brown, gray, green, red). Examination of spectral reflectance curves showed that the eight colors could be naturally placed into two groups, those with high peak reflectance (white and yellow) and those with low peak reflectance (black, blue, brown, gray, green, red). When high and low peak reflectance were substituted for color in a separate ANOVA, reflectance group was as good as color at explaining the variability in trap catch (r2 = 0.88 versus 0.92). Therefore, hue (dominant wavelength) was unimportant in affecting D. frontalis host finding behavior at the reflectance levels we tested and, thus, we found no strong evidence that differential wavelength sensitivity affected the response of D. frontalis. These results show that dark colored silhouettes (those with low reflectance values), regardless of hue, are best for capturing D. frontalis, while white or yellow are the best candidate colors for disrupting host finding.
The Role of the Immune System in Obesity and Insulin Resistance

The innate immune system provides organisms with rapid and well-coordinated protection from foreign pathogens. However, under certain conditions of metabolic dysfunction, components of the innate immune system may be activated in the absence of external pathogens, leading to pathologic consequences. Indeed, there appears to be an intimate relationship between metabolic diseases and immune dysfunction; for example, macrophages are prime players in the initiation of a chronic inflammatory state in obesity which leads to insulin resistance. In response to increases in free fatty acid release from obese adipose depots, M1-polarized macrophages infiltrate adipose tissues. These M1 macrophages trigger inflammatory signaling and stress responses within cells that signal through JNK or IKKβ pathways, leading to insulin resistance. If overnutrition persists, mechanisms that counteract inflammation (such as M2 macrophages and PPAR signaling) are suppressed, and the inflammation becomes chronic. Although macrophages are a principal constituent of obese adipose tissue inflammation, other components of the immune system such as lymphocytes and mast cells also contribute to the inflammatory cascade. Thus it is not merely an increased mass of adipose tissue that directly leads to attenuation of insulin action, but rather adipose tissue inflammation activated by the immune system in obese individuals that leads to insulin resistance.
Immunoneutralization of Agmatine Sensitizes Mice to μ-Opioid Receptor Tolerance

Systemically or centrally administered agmatine (decarboxylated arginine) prevents, moderates, or reverses opioid-induced tolerance and self-administration, inflammatory and neuropathic pain, and sequelae associated with ischemia and spinal cord injury in rodents. These behavioral models invoke the N-methyl-d-aspartate (NMDA) receptor/nitric-oxide synthase cascade. Agmatine (AG) antagonizes the NMDA receptor and inhibits nitric-oxide synthase in vitro and in vivo, which may explain its effect in models of neural plasticity. Agmatine has been detected biochemically and immunohistochemically in the central nervous system. Consequently, it is conceivable that agmatine operates in an anti-glutamatergic manner in vivo; the role of endogenous agmatine in the central nervous system remains minimally defined. The current study used an immunoneutralization strategy to evaluate the effect of sequestration of endogenous agmatine in acute opioid analgesic tolerance in mice. First, intrathecal pretreatment with an anti-AG IgG (but not normal IgG) reversed an established pharmacological effect of intrathecal agmatine: antagonism of NMDA-evoked behavior. This result justified the use of anti-AG IgG to sequester endogenous agmatine in vivo. Second, intrathecal pretreatment with the anti-AG IgG sensitized mice to induction of acute spinal tolerance of two μ-opioid receptor-selective agonists, [d-Ala2,N-Me-Phe4,Gly5-ol]-enkephalin and endomorphin-2. A lower dose of either agonist that, under normal conditions, produces moderate or no tolerance was tolerance-inducing after intrathecal pretreatment of anti-AG IgG (but not normal IgG). The effect of the anti-AG IgG lasted for at least 24 h in both NMDA-evoked behavior and the acute opioid tolerance. These results suggest that endogenous spinal agmatine may moderate glutamate-dependent neuroplasticity.
Heart Rate Variability in Insomniacs and Matched Normal Sleepers

Objective It was hypothesized that psychophysiological insomniacs, who have been shown to have elevated heart rate, body temperature, and whole body metabolic rate, would also have increased low frequency and decreased high frequency power in the spectral analysis of their heart period data. Method Groups of 12 objectively defined insomniacs and age-, sex-, and weight-matched controls with normal sleep were evaluated on sleep and EKG measures over a 36-hour sleep laboratory stay. Results Heart period was decreased (ie, heart rate was increased) and its SD was decreased in all stages of sleep in the insomniacs compared with the controls. Spectral analysis revealed significantly increased low frequency power and decreased high frequency power in insomniacs compared with controls across all stages of sleep. Conclusions Because increased low frequency spectral power is an indicator of increased sympathetic nervous system activity, these data imply that chronic insomniacs could be at increased risk for the development of disorders, such as coronary artery disease, that are related to increased sympathetic nervous system activity.
Gene 19 of plasmid R1 is required for both efficient conjugative DNA transfer and bacteriophage R17 infection

F-like plasmids require a number of genes for conjugation, including tra operon genes and genes traM and traJ, which lie outside the tra operon. We now establish that a gene in the "leading region," gene 19, provides an important function during conjugation and RNA phage infection. Mutational inactivation of gene 19 on plasmid R1-16 by introduction of two nonpolar stop codons results in a 10-fold decrease in the conjugation frequency. Furthermore, infection studies with the male-specific bacteriophage R17 revealed that the phage is not able to form clear plaques in Escherichia coli cells carrying an R1-16 plasmid with the defective copy of gene 19. The total number of cells infected by phage R17 is reduced by a factor of 10. Both the conjugation- and infection-attenuated phenotypes caused by the defective gene 19 can be complemented in trans by introducing gene 19 alleles encoding the wild-type protein. Restoration of the normal phenotypes is also possible by introduction of the pilT gene encoded by the unrelated IncI plasmid R64. Our functional studies and similarities of protein 19 to proteins encoded by other DNA transfer systems, as well as the presence of a conserved motif in all of these proteins (indicative for a putative muramidase activity) suggest that protein 19 of plasmid R1 facilitates the passage of DNA during conjugation and entry of RNA during phage infection.
Evaluation of the Quality of Coatings Deposited on AZ31 Magnesium Alloy Using the Anodising Method / Ocena Jakości Powłok Wykonanych Na Stopie Magnezu Az31 Metodą Anodowania

The paper presents results of a study on the quality of coatings deposited on surfaces of AZ31 magnesium alloy products. In order to obtain protective coatings (corrosion and erosive wear protection), the methods of anodising (specimens A, B and C) and, for comparison, electroless plating (specimen D) were applied. The assessment of coating quality was based on the scratch test results. The results were used for determination of critical loads resulting in coating rupture. The best result was obtained for the specimen B (sulphuric acid anodising in combination with sealing): the critical load was 7.5 N. The smallest value (5.5 N) was observed for the specimen D, i.e. the coating produced using the electroless plating method. Moreover, erosion resistance of the coatings was assessed. In this case, a depth of the wear trace due to an erodent agent (SiC powder) effects was investigated. The results are comparable to those obtained in the scratch test. The poorest erosion resistance is demonstrated by the coating D and the best resistance is observed for the coating B.
Maternal Drug Use and Infant Birthweight : Accounting for Measurement Error in Selected Data

This paper analyzes a sample selection model where a binary valued covariate is potentially misclassified. Although data with such features arise quite commonly in empirical research, the problem appears to have gone unnoticed in the literature. In keeping with an earlier tradition, we assume that two noisy reports of the true covariate are observed, and derive both bounds as well as point estimates of the parameter of interest. We also consider identification and estimation when only a single noisy report is available. Our analytical results are then applied to estimating the effects of maternal drug use on infant birthweight. Our empirical study shows large parameter biases that arise from ignoring either the measurement error in drug-use report, or selection of birthweight, or both.
Policy gradient approaches for multi-objective sequential decision making: A comparison

This paper investigates the use of policy gradient techniques to approximate the Pareto frontier in Multi-Objective Markov Decision Processes (MOMDPs). Despite the popularity of policy-gradient algorithms and the fact that gradient-ascent algorithms have been already proposed to numerically solve multi-objective optimization problems, especially in combination with multi-objective evolutionary algorithms, so far little attention has been paid to the use of gradient information to face multi-objective sequential decision problems. Three different Multi-Objective Reinforcement-Learning (MORL) approaches are here presented. The first two, called radial and Pareto following, start from an initial policy and perform gradient-based policy-search procedures aimed at finding a set of non-dominated policies. Differently, the third approach performs a single gradient-ascent run that, at each step, generates an improved continuous approximation of the Pareto frontier. The parameters of a function that defines a manifold in the policy parameter space are updated following the gradient of some performance criterion so that the sequence of candidate solutions gets as close as possible to the Pareto front. Besides reviewing the three different approaches and discussing their main properties, we empirically compare them with other MORL algorithms on two interesting MOMDPs.
Proteolytic processing of the Alzheimer's disease amyloid precursor protein in brain and platelets

Proteolytic processing of the amyloid precursor protein by β ‐and γ‐secretases results in the production of Alzheimer's disease (AD) Aβ amyloid peptides. Modulation of secretase activity is being investigated as a potential therapeutic approach. Recent studies with human brain have revealed that the β‐secretase protein, BACE, is increased in cortex of AD patients. Analysis of βCTF (or C99), the amyloid precursor protein (APP) product of BACE cleavage that is the direct precursor to Aβ, shows it is also elevated in AD, underlying the importance of β‐secretase cleavage in AD pathogenesis. The C‐terminal product of γ‐secretase cleavage of APP, ϵCTF (or AICD), is enriched in human brain cortical nuclear fractions, a subcellular distribution appropriate for a putative involvement of APP cytosolic domain in signal transduction. Analysis of AD cortex samples, particularly that of a carrier of a familial APP mutation, suggests that processing of APP transmembrane domain generates an alternative CTF product. All these particularities observed in the AD brain demonstrate that APP processing is altered in AD. The transgenic mouse model Tg2576 seems to be a promising laboratory tool to test potential modulators of Aβ formation. Indeed, C‐terminal products of α‐, β‐, and γ‐secretase cleavage are readily detectable in the brain of these transgenic mice. Finally, the finding of the same secretase products in platelets and neurons make platelets a potentially useful and easily accessible clinical tool to monitor effects of novel therapies based on inhibition of β‐ or γ‐secretase. © 2003 Wiley‐Liss, Inc.
ABDTR: Approximation-Based Dynamic Traffic Regulation for Networks-on-Chip Systems

Traffic regulation is an essential technology of networks-on-chip (NoC) to achieve communication performance guarantees with effective use of the system interconnect and low traffic delay. This paper presents approximation-based dynamic traffic regulation (ABDTR), which approximates part of traffic data instead of network transmission for mitigating network congestion based on the inherent error resilience of some applications. ABDTR drops a fraction of safe-to-approximate packet data that may aggravate network congestion before they are injected into network, and predicts the lost data in packet after being received in destination node. Traffic drop rate is fully adaptive to the traffic and network states. The regulation range of drop rate is a knob to control the trade-off between performance/energy efficiency and output quality. The proposed method is effective and can be implemented in hardware with small area. Experimental results have confirmed that the ABDTR can help reduce up to 44.4 percent average network delay with less than 10% loss in quality. The results also show ABDTR yields significant application speedup and NoC energy reduction for a wide range of quality-loss levels.
Semantic Web Annotation and Representation of Cloud APIs

In this paper we present an analysis of existing annotation techniques for semantic description of Application Programming Interfaces exposed as web services through SOAP or REST based protocol. We propose an original methodology and technique for semantic annotation of web APIs particularly taylored to Cloud APIs. In cloud scenario particularly important for the characterization of cloud services are the non functional requirements, such as the service level requests, offers to be matched for reach a Service Level Agreement (SLA) and offers. The technique we illustrate in this paper includes semantic description of such non functional requirement in addition to functional ones. Two case studies on semantically describing IBM and Amazon cloud APIs are provided, in the context of the Semantic Engine development for the mosaic European project.
Human Action Recognition Using Improved Salient Dense Trajectories

Human action recognition in videos is a topic of active research in computer vision. Dense trajectory (DT) features were shown to be efficient for representing videos in state-of-the-art approaches. In this paper, we present a more effective approach of video representation using improved salient dense trajectories: first, detecting the motion salient region and extracting the dense trajectories by tracking interest points in each spatial scale separately and then refining the dense trajectories via the analysis of the motion saliency. Then, we compute several descriptors (i.e., trajectory displacement, HOG, HOF, and MBH) in the spatiotemporal volume aligned with the trajectories. Finally, in order to represent the videos better, we optimize the framework of bag-of-words according to the motion salient intensity distribution and the idea of sparse coefficient reconstruction. Our architecture is trained and evaluated on the four standard video actions datasets of KTH, UCF sports, HMDB51, and UCF50, and the experimental results show that our approach performs competitively comparing with the state-of-the-art results.
Link-Based Ranking of the Web with Source-Centric Collaboration

Web ranking is one of the most successful and widely used collaborative computing applications, in which Web pages collaborate in the form of varying degree of relationships to assess their relative quality. Though many observe that links display strong source-centric locality, for example, in terms of administrative domains and hosts, most Web ranking analysis to date has focused on the flat page-level Web linkage structure. In this paper we develop a framework for link-based collaborative ranking of the Web by utilizing the strong Web link structure. We argue that this source-centric link analysis is promising since it captures the natural link-locality structure of the Web, can provide more appealing and efficient Web applications, and reflects many natural types of structured human collaborations. Concretely, we propose a generic framework for source-centric collaborative ranking of the Web. This paper makes two unique contributions. First, we provide a rigorous study of the set of critical parameters that can impact source-centric link analysis, such as source size, the presence of self-links, and different source-citation link weighting schemes (e.g., uniform, link count, source consensus). Second, we conduct a large-scale experimental study to understand how different parameter settings may impact the time complexity, stability, and spam-resilience of Web ranking. We find that careful tuning of these parameters is vital to ensure success over each objective and to balance the performance across all objectives