Miracle-dz/UniFAR-FTUs huggingface dataset:
Sources of Signal in 62 Protein-Coding Nuclear Genes for Higher-Level Phylogenetics of Arthropods

Background This study aims to investigate the strength of various sources of phylogenetic information that led to recent seemingly robust conclusions about higher-level arthropod phylogeny and to assess the role of excluding or downweighting synonymous change for arriving at those conclusions. Methodology/Principal Findings The current study analyzes DNA sequences from 68 gene segments of 62 distinct protein-coding nuclear genes for 80 species. Gene segments analyzed individually support numerous nodes recovered in combined-gene analyses, but few of the higher-level nodes of greatest current interest. However, neither is there support for conflicting alternatives to these higher-level nodes. Gene segments with higher rates of nonsynonymous change tend to be more informative overall, but those with lower rates tend to provide stronger support for deeper nodes. Higher-level nodes with bootstrap values in the 80% – 99% range for the complete data matrix are markedly more sensitive to substantial drops in their bootstrap percentages after character subsampling than those with 100% bootstrap, suggesting that these nodes are likely not to have been strongly supported with many fewer data than in the full matrix. Data set partitioning of total data by (mostly) synonymous and (mostly) nonsynonymous change improves overall node support, but the result remains much inferior to analysis of (unpartitioned) nonsynonymous change alone. Clusters of genes with similar nonsynonymous rate properties (e.g., faster vs. slower) show some distinct patterns of node support but few conflicts. Synonymous change is shown to contribute little, if any, phylogenetic signal to the support of higher-level nodes, but it does contribute nonphylogenetic signal, probably through its underlying heterogeneous nucleotide composition. Analysis of seemingly conservative indels does not prove useful. Conclusions Generating a robust molecular higher-level phylogeny of Arthropoda is currently possible with large amounts of data and an exclusive reliance on nonsynonymous change.
Effect of wheat bran on glycemic control and risk factors for cardiovascular disease in type 2 diabetes.

OBJECTIVE Cohort studies indicate that cereal fiber reduces the risk of diabetes and coronary heart disease (CHD). Therefore, we assessed the effect of wheat bran on glycemic control and CHD risk factors in type 2 diabetes. RESEARCH DESIGN AND METHODS A total of 23 subjects with type 2 diabetes (16 men and 7 postmenopausal women) completed two 3-month phases of a randomized crossover study. In the test phase, bread and breakfast cereals were provided as products high in cereal fiber (19 g/day additional cereal fiber). In the control phase, supplements were low in fiber (4 g/day additional cereal fiber). RESULTS Between the test and control treatments, no differences were seen in body weight, fasting blood glucose, HbA(1c), serum lipids, apolipoproteins, blood pressure, serum uric acid, clotting factors, homocysteine, C-reactive protein, magnesium, calcium, iron, or ferritin. LDL oxidation in the test phase was higher than that seen in the control phase (12.1 +/- 5.4%, P < 0.034). Of the subjects originally recruited, more dropped out of the study for health and food preference reasons from the control phase (16 subjects) than the test phase (11 subjects). CONCLUSIONS High-fiber cereal foods did not improve conventional markers of glycemic control or risk factors for CHD in type 2 diabetes over 3 months. Possibly longer studies are required to demonstrate the benefits of cereal fiber. Alternatively, cereal fiber in the diet may be a marker for another component of whole grains that imparts health advantages or a healthy lifestyle.
Toward a Hybrid Recommender System for E-Learning Personalization Based on Web Usage Mining Techniques and Information Retrieval

The last decade has witnessed a great interest in e-learning and Web based education areas. Unfortunately, most of the e-learning environments used in the educational field today are still delivering the same educational resources and services in the same way to different learners. Hence, observing the increasing need for personalization in e-learning systems, we aim to make these systems deliver the most appropriate content to learners according to their interests and needs. This paper outlines the use of on-line automatic recommendations in e-learning systems based on learners’ access history. First we start by mining learner profiles using usage Web mining techniques and content-based profiles using information retrieval techniques. Then, we use these profiles to compute relevant links to recommend for an active learner by applying a number of recommendation strategies.
Boilerplate and Economic Power in Auto Manufacturing Contracts

This article studies the standard form contracts used by automobile manufacturers to purchase auto parts. It explores how the contracts reflect divisions of bargaining power, asymmetric information, problems of hold-up and renegotiation, and market competition. Based on interviews with representatives of buyers and suppliers, the article also describes the process of drafting the forms, the negotiation over price and other terms in the shadow of these forms, and the opportunities for non-drafters to extract improved terms. Some of the main lessons are: (i) The terms of the contracts and the bidding process prevent ex-post hold-up by suppliers (in contrast to the claims made by Benjamin Klein and others based on the GM/Fisher Body contract); (ii) There is surprisingly little ad-hoc tailoring of terms, even when such tailoring can increase the surplus from the deal; (iii) Internal organization structures are harnessed effectively to secure favorable bargaining outcomes; (iv) There is a significant variation between the standard forms utilized by the big automakers, in some of the most important aspects of the deals. This variation suggests that some of the terms are inefficient.
Commutative Families of the Elliptic Macdonald Operator

In the paper (J. Math. Phys. 50 (2009), 095215, 42 pages), Feigin, Hashizume, Hoshino, Shiraishi, and Yanagida constructed two families of commuting operators which contain the Macdonald operator (commutative families of the Macdonald operator). They used the Ding{Iohara{Miki algebra and the trigonometric Feigin{Odesskii algebra. In the previous paper (arXiv:1301.4912), the present author constructed the elliptic Ding{Iohara{ Miki algebra and the free field realization of the elliptic Macdonald operator. In this paper, we show that by using the elliptic Ding{Iohara{Miki algebra and the elliptic Feigin{Odesskii algebra, we can construct commutative families of the elliptic Macdonald operator. In Appendix, we will show a relation between the elliptic Macdonald operator and its kernel function by the free field realization.
Detection and classification of PQ disturbances in the supply to induction motor using wavelet transform and feedforward neural network

In real world applications, induction motors are normally operated on load. Any variation in the supply voltage, would adversely affect its normal operation. Hence it is important to detect any power quality disturbance and identify the nature of the disturbance. A major issue is to find the motor parameter which can satisfactorily identify and classify the disturbance. This paper proposes a novel method for the detection and classification of PQ disturbances in the supply to induction motor using the signature of the stator current. The tools used for the analysis are wavelet transforms and neural network. In the first stage the stator current is sampled and DWT is applied to it to capture the feature of the disturbance. The DWT co-efficients so obtained are used as input to a feed forward neural network, in the second stage, to classify the disturbance. This method has been tested for different PQ disturbances such as balanced voltage sag, balanced voltage swell, unbalanced voltage sag and unbalanced voltage swell (or simply called as unbalance in the magnitude of the supply). The method has been found to be effective for varying degrees of disturbance. It is observed that the proposed network has performance efficiency greater than 97%.
A versatile paradigm for scan chain diagnosis of complex faults using signal processing techniques

Scan chains are popularly used as the channels for silicon testing and debugging. However, they have also been identified as one of the culprits of silicon failure more recently. To cope with this problem, several scan chain diagnosis approaches have been proposed in the past. The existing methods, however, suffer from one common drawback—that is, they rely on fault models and matching heuristics to locate the faults. Such a paradigm may run into difficulty when the fault under diagnosis does not match the fault model exactly, for example, when there is a bridging between a flip-flop and a logic cell, or the fault is temporal and only manifests itself intermittently. In light of this, we propose in this article a more versatile model-free paradigm for locating the faulty flip-flops in a scan chain, incorporating a number of signal processing techniques, such as filtering and edge detection. These techniques performed on the test responses of the failing chip under diagnosis directly can effectively reveal the fault location(s) in a scan chain. As compared to the previous works, our approach is better capable of handling intermittent faults and bridging faults, even under nonideal conditions, for example, when the core logic is also faulty. Experimental results on several real designs indicate that this approach can indeed catch some nasty faults that previous methods could not catch.
Suppression of F1 Male-Specific Lethality in Caenorhabditis Hybrids by cbr-him-8

Haldane’s Rule and Darwin’s Corollary to Haldane’s Rule are the observations that heterogametic F1 hybrids are frequently less fit than their homogametic siblings, and that asymmetric results are often obtained from reciprocal hybrid crosses. In Caenorhabditis, Haldane’s Rule and Darwin’s Corollary have been observed in several hybrid crosses, including crosses of Caenorhabditis briggsae and C. nigoni. Fertile F1 females are obtained from reciprocal crosses. However, F1 males obtained from C. nigoni mothers are sterile and F1 males obtained from C. briggsae die during embryogenesis. We have identified cbr-him-8 as a recessive maternal-effect suppressor of F1 hybrid male-specific lethality in this combination of species. This result implicates epigenetic meiotic silencing in the suppression of F1 male-specific lethality. It is also shown that F1 males bearing a C. briggsae X chromosome are fertile. When crossed to C. briggsae hermaphrodites or F1 females derived from C. briggsae hermaphrodites, viable F2 and backcross (B2) progeny were obtained. Sibling males that possessed a C. nigoni X chromosome were sterile. Therefore, the sterility of F1 males bearing a C. nigoni X chromosome must result from dysgenic interactions between the X chromosome of C. nigoni and the autosomes of C. briggsae. The fertility of F1 males bearing a C. briggsae X chromosome provides an opportunity to identify C. nigoni loci that prevent spermatogenesis, and hence hermaphroditic reproduction, in diplo-X hybrids.
Gaia-ESO Survey: Analysis of pre-main sequence stellar spectra

Context. The Gaia-ESO Public Spectroscopic Survey is obtaining high-quality spectroscopy of some 100 000 Milky Way stars using the FLAMES spectrograph at the VLT, down to V = 19 mag, systematically covering all the main components of the Milky Way and providing the first homogeneous overview of the distributions of kinematics and chemical element abundances in the Galaxy. Observations of young open clusters, in particular, are giving new insights into their initial structure, kinematics, and their subsequent evolution. Aims. This paper describes the analysis of UVES and GIRAFFE spectra acquired in the fields of young clusters whose population includes pre-main sequence (PMS) stars. The analysis is applied to all stars in such fields, regardless of any prior information on membership, and provides fundamental stellar atmospheric parameters, elemental abundances, and PMS-specific parameters such as veiling, accretion, and chromospheric activity. Methods. When feasible,different methods were used to derive raw parameters (e. g. line equivalent widths) fundamental atmospheric parameters and derived parameters (e. g. abundances). To derive some of these parameters, we used methods that have been extensively used in the past and new ones developed in the context of the Gaia-ESO survey enterprise. The internal precision of these quantities was estimated by inter-comparing the results obtained by these different methods, while the accuracy was estimated by comparison with independent external data, such as effective temperature and surface gravity derived from angular diameter measurements, on a sample of benchmarks stars. A validation procedure based on these comparisons was applied to discard spurious or doubtful results and produce recommended parameters. Specific strategies were implemented to resolve problems of fast rotation, accretion signatures, chromospheric activity, and veiling. Results. The analysis carried out on spectra acquired in young cluster fields during the first 18 months of observations, up to June 2013, is presented in preparation of the first release of advanced data products. These include targets in the fields of the rho Oph, Cha I, NGC2264, gamma Vel, and NGC 2547 clusters. Stellar parameters obtained with the higher resolution and larger wavelength coverage from UVES are reproduced with comparable accuracy and precision using the smaller wavelength range and lower resolution of the GIRAFFE setup adopted for young stars, which allows us to provide stellar parameters with confidence for the much larger GIRAFFE sample. Precisions are estimated to be approximate to 120 K rms in T-eff, approximate to 0.3 dex rms in log g, and approximate to 0.15 dex rms in [Fe/H] for the UVES and GIRAFFE setups.
Speech production assessment of mouth breathing children with hypertrophy of palatines and/or pharyngeal tonsils

ABSTRACT Objective: to evaluate the speech sound production of children diagnosed with a palatine mouth breathing and / or hypertrophic pharyngeal tonsil and compare it to that of a group of children that do not show any respiratory alterations, besides associating with age and sex. Methods: a quantitative, cross-sectional, analytical and observational research. Children from five to twelve years old have took part of the study, 50 of them diagnosed as mouth breathers (research group - RG) and 50 with no respiratory alteration (control group - CG). Anamnesis and evaluation based on MBGR protocol was performed, focusing on the speech, supported by figures and with samples of automatic and spontaneous speech. Results: there were no differences between the groups, taking into account the parents' complaint. Speech alterations, such as phonetic deflection, lingual interposition and distortions, and occlusion alterations were more frequent in RG. Speech alterations prevailed for males in 83% and the average age related to speech did not show any significance. Conclusion: mouth breathing children present more alterations of speech sounds than those presented with no respiratory alteration, regardless of the age group, being more common in male children.
The Moral Hazard of Terrorism Prevention

How does a policy of reacting to terrorist attacks with restrictions on free speech protections affect the likelihood of terrorism in the first place? In this article, I develop a dynamic model of an interaction between a security agency and a terrorist organization to study the dynamic consequences of adopting policies that curtail free speech protections and other rights when terror strikes. The article shows that in a world in which democratic governments respond to major terrorist attacks with restrictions on freedom of expression and other rights and liberties, such policies have perverse effects on the pre-attack incentives of terrorism prevention/occurrence, which can make a terrorist attack more likely. The analysis suggests that a commitment to respecting fundamental rights and liberties in times of duress can be security-beneficial: if liberal societies were to remain faithful to their fundamental values in the aftermath of terrorist attacks, such a strategy can decrease the probability of a terrorist attack in the first place.
When Weather Forecasters Are Wrong: Image Repair and Public Rhetoric After Severe Weather

Weather forecasts are a unique type of prediction rhetoric—science communication with inherent uncertainty and multiple potential interpretations from diverse audiences. When forecasts are wrong, audiences often turn their ire toward the weather forecaster. This rhetorical analysis considers image repair efforts of a meteorologist following a botched winter storm forecast. Implications for communication efforts of weather forecasters are offered, in addition to consideration of insight into the larger realm of the rhetoric of science.
“My French is rusty”: Proficiency and bilingual gesture use in a majority English community

Gestures serve many functions, including aiding language access and message construction, particularly in spatial tasks. Some researchers have argued that gesture frequency is linked to proficiency in bilinguals, although results have been inconsistent. We tested Nicoladis’ (2007) proposal that bilinguals’ proficiency interacts with task: namely, more spatial tasks elicit greater proficiency effects. French–English bilinguals completed a cartoon-retell task (high spatial) and an interview task (low spatial) in both languages. We measured bilingual proficiency categorically by first language (L1) and continuously by assessing receptive vocabulary, oral fluency, and word types. Participants gestured more in the cartoon-retell task, but there were minimal proficiency effects and no interactions between proficiency and task. Interestingly, only participants with English as their L1 gestured more in their second language (L2), potentially due to ‘rustiness’, or lexical access difficulties in French from low usage in the majority English community.
Virality overYouTube : an Empirical Analysis

Purpose: The purpose of this research is to seek reasons for some videos going viral over YouTube (a type of social media platform). Methodology:Using YouTube APIs (Application Programming Interface) and Webometrics analyst tool, we collected data on about 100 all-time-most-viewed YouTube videos and information about the users associated with the videos. We constructed and tested an empirical model to understand the relationship among users‘ social and non-social capital—user age, gender, view count, subscriber, join date, total videos posted, video characteristics—postdate, duration, and video category, external network capital— in-links and hit counts, and Virality—likes, dislikes, favorite count, view count, and comment count. Partial Least Square (PLS) and Webometric analysis was used to explore the association among the constructs. Main findings: Among other findings, our results showed that popularity of the videos was not only the function of YouTube system per se, but that network dynamics (e.g., in-links and hits counts) and offline social capital (e.g., fan base and fame) play crucial roles in the viral phenomenon, particularly view count. Originality: We for the first time constructed and tested an empirical model to find out the determinants of viral phenomenon over YouTube.
A novel image classifier based on Gaussian mixture language model

In this paper, we propose a novel Gaussian Mixture Language Model to address the issues of the traditional bag of visual words (BoVW) based model. We firstly take full advantage of image semantic information to learn a new distance metric which can achieve the minimal loss of image information, and then we train Gaussian Mixture Models (GMM) using this distance metric. Given a test image, a visual document is firstly constructed using this codebook, and then its category is determined by estimating the maximum probability using the language model under a specific category. Experiments show that the codebook generated by our method can effectively reflect the image semantic information and highly suitable the language model, and confirm that the proposed method is satisfactory and competitive in comparison with the traditional BoVW based method as well as other state of the art methods.
Resource Allocation and Cross-Layer Control in Wireless Networks

Information flow in a telecommunication network is accomplished through the interaction of mechanisms at various design layers with the end goal of supporting the information exchange needs of the applications. In wireless networks in particular, the different layers interact in a nontrivial manner in order to support information transfer. In this text we will present abstract models that capture the cross-layer interaction from the physical to transport layer in wireless network architectures including cellular, ad-hoc and sensor networks as well as hybrid wireless-wireline. The model allows for arbitrary network topologies as well as traffic forwarding modes, including datagrams and virtual circuits. Furthermore the time varying nature of a wireless network, due either to fading channels or to changing connectivity due to mobility, is adequately captured in our model to allow for state dependent network control policies. Quantitative performance measures that capture the quality of service requirements in these systems depending on the supported applications are discussed, including throughput maximization, energy consumption minimization, rate utility function maximization as well as general performance functionals. Cross-layer control algorithms with optimal or suboptimal performance with respect to the above measures are presented and analyzed. A detailed exposition of the related analysis and design techniques is provided.
STUDIES ON STREPTOCOCCAL BACTERIOPHAGES

Evidence has been presented that the burst size in the Group A and Group C streptococcal phage-host systems are in general similar producing approximately 13 phage particles per infected coccus. The exception was the C1 phage which produced 10 times more virus particles than all the other phages tested. The eclipse period for the A25 phage-host system was found to extend for 34 min, while the C1 phage were found as early as 10 min after infection. Conclusive evidence has been presented indicating that mercuric ions at 2.5 x 10–6 M concentration have the ability to halt intracellular phage production at any point during the infective cycle of A25 bacteriophages. This blocking action can then be quickly reversed with the addition of reduced glutathione with subsequent completion of the viral cycle.