Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring phylogenomic relationships within Myriapoda: should high matrix occupancy be the goal?

Myriapods are one of the dominant terrestrial arthropod groups including the diverse and familiar centipedes and millipedes. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes in many species) or on maximizing matrix occupancy (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed forty Illumina transcriptomes representing three myriapod classes (Diplopoda, Chilopoda and Symphyla); twenty-five transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Eight supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at three levels of mean gene occupancy per taxon (50%, 75% and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in two alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but two nodes remained in conflict in the different analyses despite dense taxon sampling at the family level, situating the order Scolopendromorpha as sister group to a morphologically-anomalous grouping of Lithobiomorpha + Geophilomorpha in a subset of analyses. Interestingly, this anomalous result was obtained for all analyses conducted with the most complete matrix (90% of occupancy), being at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) or with the matrices optimizing phylogenegic informativeness and the most conserved genes, but also with previous hypotheses based on morphology, development or other molecular data sets. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies. [Chilopoda; Diplopoda; Symphyla: gene tree; species tree; node calibration; missing data. ]
Towards a theory of quark masses, mixings and CP violation

We discuss the structure of Yukawa couplings in D-brane models in which the SM fermion spectrum appears at the intersections of D-branes wrapping a compact space. In simple toroidal realistic examples one can explicitly compute the Yukawa couplings as a function of the geometrical data summing over world-sheet instanton contributions. A particular simple model with a N = 1 SUSY spectrum and three quark-lepton generations is studied in some detail. Remarkably, one can reproduce the observed spectrum of quark masses and mixings for particular choices of the compact radii and brane locations. In order to reproduce the smallness of up- and down-quark masses branes should be located in simple geometric configurations leading to some accidental global symmetries. We also find that the brane configurations able to reproduce the observed data may be considered as a deformation (by brane translation) of a configuration with Pati-Salam gauge symmetry. The origin of CP-violation in this formalism is quite elegant. It appears as a consequence of the generic presence of U(1) Wilson line backgrounds in the compact dimensions. One can reproduce the observed results for the CP-violation Jarlskog invariant J as long as the compact radii are of order of the string scale. DISCLAIMER: This paper is going to be substantially revised. Althought the physics and general concepts are still valid, the Yukawa couplings of the particular model presented in this paper have a simpler form than discussed here, as we recently pointed out in hep-th/0302105. A properly revised version will be eventually sent as the paper is appropriately corrected.
Decentralized intercell interference coordination for fair resource allocation in large-scale networks

Cellular networks with a dense reuse of spectrum strongly suffer from intercell interference (ICI). By coordinating the resource allocations (RA) of the individual base stations (BS) the ICI can be effectively mitigated. Since centralized ICI coordination schemes become prohibitive in large-scale networks, we propose a decentralized RA procedure that coordinates the local RA steps among the BSs. Our scheme efficiently suppresses the so-called domino effect where a RA step of a single BS may impact the entire network by causing a large number of subsequent RA adaptations at remote BSs. The objective of our proposed RA procedure is to provide high degrees of fairness among the users. Since such an objective usually results in poor overall system performance (e.g. high blocking rates) we extended the RA procedure for a cooperative user detection scheme that employs an ICI cancellation. The results indicate significant gains in user fairness for both cases, ICI coordination based on short-term as well as long-term channel statistics.
Stepped and Standard Care for Childhood Trauma

Objective: This study explored the feasibility of stepped care trauma-focused cognitive behavioral therapy (SC-TF-CBT) relative to TF-CBT with children (aged 8–12). Method: Children (N = 33) with post-traumatic stress symptoms (PTSS) were randomly assigned (2:1) to SC-TF-CBT or TF-CBT. SC-TF-CBT consisted of Step 1, parent-led therapist-assisted treatment, and Step 2 (nine TF-CBT sessions). TF-CBT consisted of 12 therapist-directed sessions. Baseline, post-Step 1, posttreatment, and 3-month follow-up assessments occurred. Cost-related data were collected throughout the treatment. Results: In all, 64% (intent-to-treat) to 82% (completers) responded to Step 1. Group × Time interactions were not statistically significant for PTSS (p = .888), severity (p = .576), and internalizing (p = .862)/externalizing (p = .974) symptoms, indicating comparable improvements in outcomes across both conditions. There were no significant differences in parental treatment credibility (p = .440), expectations (p = .664), and satisfaction (p = .768). SC-TF-CBT total costs were significantly lower than TF-CBT (Effect Size [ES] = 1.61, confidence interval [CI] = [0.65, 2.59], p < .0001). Conclusion: Step 1 may be a viable service delivery approach although further research is needed.
Effects of Late Administration of Pentoxifylline and Tocotrienols in an Image-Guided Rat Model of Localized Heart Irradiation

Radiation-induced heart disease (RIHD) is a long-term side effect of radiotherapy of intrathoracic, chest wall and breast tumors when radiation fields encompass all or part of the heart. Previous studies have shown that pentoxifylline (PTX) in combination with α-tocopherol reduced manifestations of RIHD in rat models of local heart irradiation. The relative contribution of PTX and α-tocopherol to these beneficial effects are not known. This study examined the effects of PTX alone or in combination with tocotrienols, forms of vitamin E with potential potent radiation mitigation properties. Rats received localized X-irradiation of the heart with an image-guided irradiation technique. At 3 months after irradiation rats received oral treatment with vehicle, PTX, or PTX in combination with a tocotrienol-enriched formulation. At 6 months after irradiation, PTX-treated rats showed arrhythmia in 5 out of 14 animals. PTX alone or in combination with tocotrienols did not alter cardiac radiation fibrosis, left ventricular protein expression of the endothelial markers von Willebrand factor and neuregulin-1, or phosphorylation of the signal mediators Akt, Erk1/2, or PKCα. On the other hand, tocotrienols reduced cardiac numbers of mast cells and macrophages, but enhanced the expression of tissue factor. While this new rat model of localized heart irradiation does not support the use of PTX alone, the effects of tocotrienols on chronic manifestations of RIHD deserve further investigation.
Searching Your Life on Web Maps

In recent years, GPS-enabled device, which facilitate people to record their outdoor movement with GPS logs, has become prevalent in our daily lives. In this paper, we build a platform, referred to as GeoLife, where people are enabled to visualize and manage their GPS logs as well as associated photos on Web maps for life-logging and life-sharing. The GPS logs from each person are not only used to exchange life experience among multiple users but also leveraged as a kind of cues to trigger the owner’s memory about past. Further, given the fact that people usually can roughly remember a past event rather than the exact time and location of the event, a spatio-temporal search function is proposed to support subjects’ recall of past experience. By performing a user study, we find evidences that the GPS log data do improve people’s memory about past beyond natural remembering, and search function is more effective than normal browsing method to help users connect to their past.
Recursive functional link polynomial filters: An introduction

In this paper, we first introduce a novel sub-class of recursive linear-in-the-parameters nonlinear filters, called recursive functional link polynomial filters, which are derived by using the constructive rule of Volterra filters. These filters are universal approximators, according to the Stone-Weierstrass theorem, and offer a remedy to the main drawback of their finite memory counterparts, that is the curse of dimensionality. Since recursive nonlinear filters become, in general, unstable for large input signals, we then consider a simple stabilization procedure by slightly modifying the input-output relationship of recursive functional link polynomial filters. The resulting filters are always stable and, even though no more universal approximators, still offer good modeling performance for nonlinear systems.
Experimenting with Multi-Class Semi-Supervised Support Vector Machines and High-Dimensional Datasets

In this paper we explore variations on semi-supervised multi-class support vector machines (SVMs), using the MNIST handwritten digit dataset as a benchmark for the algorithm. Support vector machines are well studied classiﬁers, however extending SVMs to a multi-class or a semi-supervised formulation is still an open research question. We will examine one of the most popular semi-supervised support vector machine approaches, called S 3 VM
On the locality of keywords in Twitter streams

The continuously increasing popularity of social media sites such as Twitter and Facebook has recently led to a number of approaches to detect and extract event information from social media streams. Such events play an important role, e.g., in supporting location-based services and improving situational awareness. Moreover, the introduction of GPS-equipped communication devises has led to an increase in the percentage of geo-tagged messages. These help to detect localized events, i.e., events occurring at a certain location, such as sport events or accidents. The main entities that indicate a localized event are local keywords that exhibit a surge in usage at the event location. In this paper, we propose an approach to extract local keywords from a Twitter stream by (1) identifying local keywords, and (2) estimating the central location of each keyword. This extraction process is performed in an online fashion using a sliding window on the Twitter stream. In addition, we address the problem of spatial outliers that adversely affect a proper identification of local keywords. Outliers occur when people far away from an event location use related keywords in their Tweets. We handle this problem by adjusting the spatial distribution of keywords based on their co-occurrence with place names that may refer to the location of an event. We evaluate the performance of our framework to reliably and efficiently extracting local keywords and estimating their central locations using a Twitter dataset.
Influence of Pre-Annotation on POS-Tagged Corpus Development

This article details a series of carefully designed experiments aiming at evaluating the influence of automatic pre-annotation on the manual part-of-speech annotation of a corpus, both from the quality and the time points of view, with a specific attention drawn to biases. For this purpose, we manually annotated parts of the Penn Treebank corpus (Marcus et al., 1993) under various experimental setups, either from scratch or using various pre-annotations. These experiments confirm and detail the gain in quality observed before (Marcus et al., 1993; Dandapat et al., 2009; Rehbein et al., 2009), while showing that biases do appear and should be taken into account. They finally demonstrate that even a not so accurate tagger can help improving annotation speed.
Specification and Informational Issues in Credit Scoring

Lenders use rating and scoring models to rank credit applicants on their expected performance. The models and approaches are numerous. We explore the possibility that estimates generated by models developed with data drawn solely from extended loans are less valuable than they should be because of selectivity bias. We investigate the value of "reject inference"--methods that use a rejected applicant's characteristics, rather than loan performance data, in scoring model development. In the course of making this investigation, we also discuss the advantages of using parametric as well as nonparametric modeling. These issues are discussed and illustrated in the context of a simple stylized model.
Learning latent friendship propagation networks with interest awareness for link prediction

It's well known that the transitivity of friendship is a popular sociological principle in social networks. However, it's still unknown that to what extent people's friend-making behaviors follow this principle and to what extent it can benefit the link prediction task. In this paper, we try to adopt this sociological principle to explain the evolution of networks and study the latent friendship propagation. Unlike traditional link prediction approaches, we model link formation as results of individuals' friend-making behaviors combined with personal interests. We propose the Latent Friendship Propagation Network (LFPN), which depicts the evolution progress of one's egocentric network and reveals future growth potentials driven by the transitivity of friendship based on personal interests. We model individuals' social behaviors using the Latent Friendship Propagation Model (LFPM), a probabilistic generative model from which the LFPN can be learned effectively. To evaluate the power of the friendship propagation in link prediction, we design LFPN-RW which models the friend-making behavior as a random walk upon the LFPN naturally and captures the co-influence effect of the friend circles as well as personal interests to provide more accurate prediction. Experimental results on real-world datasets show that LFPN-RW outperforms the state-of-the-art approaches. This convinces that the transitivity of friendship actually plays important roles in the evolution of social networks.
Ensembles of Classifiers Based on Approximate Reducts

The problem of improving rough set based expert systems by modifying a notion of reduct is discussed. The notion of approximate reduct is introduced, as well as some proposals of quality measure for such a reduct. The complete classifying system based on approximate reducts is presented and discussed. It is proved that the problem of finding optimal set of classifying agents based on approximate reducts is NP-hard; the genetic algorithm is applied to find the suboptimal set. Experimental results show that the classifying system is effective and relatively fast.
The Impact of SARS on the Mentality and Behavior of People

The research by questionnaire method surveyed 730 people in Ningbo to investigate Ningbo people's mentation and response to SARS. The results indicated that: 1) Some people feel stress and panic, but most people keep good mentation which helps to prevent and cure SARS. 2) People's familiarity with SARS ranged at 3.15 which means that people is not familiar enough with SARS and that affect the people's response to SARS. 3) There were significant difference in mentation and behavior response to SARS between sexes and among people with different vocations. 4) Some suggestions were put forwarded based on these results.
In the Era of Precision Medicine and Big Data, Who Is Normal?

The definition of “normal” values for common laboratory tests often governs the diagnosis, treatment, and overall management of tested individuals. Some test results may depend on demographic traits of the tested population including age, race, and sex. Ideally, laboratory test results should be interpreted in reference to a population of“similar” “healthy”individuals. In many settings, however, it is unclear exactly who these individual sare.How much population stratification and what criteria for healthy individuals are optimal? In particular, with the evolution of medicine into fully personalized or “precision” medicine and the availability of large-scale data sets, there may be interest in trying to match each person to an increasingly granular normal reference population. Is this precision feasible to obtain in reliable ways and will it improve practice? are analyses of baseline variation across demographically diverse population strata (including race/ancestry, gender/sex, age, and socioeconomic strata of the population) for even widespread clinical laboratory tests. after of routine use, be that reference standards should be reconsidered for some populations.For example, he 1c (HbA ) underestimate past glycemia in African American patients with the sickle cell trait. of and more granular stratification correlates with clinical studies that assess the outcomes of individuals with laboratory measurements classified as normal with one system vs abnormal with another. include both natural history and treatment benefits and harms. small laboratory incomplete capture of long-term this difficult to
The Chinese Version of Aspiration Index:Reliability and Validity

Objective: To develop Chinese version of the thirty five-item Aspiration Index (AI-35) and examine its reliability and validity. Methods: A sample of 634 undergraduate students was tested. We examined the internal reliability and test-retest reliability of the Chinese version of the AI-35. Using confirmatory factor analysis,we tested the seven-factor model. Results: The Cronbach's coefficients of the AI-35 was 0.92,the test-retest reliability coefficient was 0.70. The inter item correlation coefficients ranged from 0.33 to 0.53,and the correlation coefficients among the seven factors ranging from 0.21 to 0.63. The factor loadings ranging from 0.53 to 0.86. The squared multiple correlations were 0.28~0.68. The χ2/df(4.17),NFI(0.97),CFI(0.98),TLI(0.97),REMEA(0.07) all met the criteria of psychometrics. Conclusion: The Chinese version of the AI-35 is a reliable and valid measure for aspiration orientation in Chinese-speaking sample.
Leaders Wanted! The Skills Expected and Needed for a Successful 21st Century Historically Black College and University Presidency

This study examines the 21st-century Historically Black College and University (HBCU) presidency. First, we gathered information on the skills needed for the 21st century HBCU president. Then, we examined the background of future HBCU presidents. Through an analysis and discussion of the responses of current HBCU presidents, trustees,1 and presidential search consultants, we determined what skills are pertinent for HBCU presidential hopefuls to attain. Lastly, we made recommendations, based on our findings, regarding the skills needed for HBCU presidential aspirants to not only reach the presidency but to perform well upon doing so.
A novel hypothesis for histone-to-protamine transition in Bos taurus spermatozoa

DNA compaction with protamines in sperm is essential for successful fertilization. However, a portion of sperm chromatin remains less tightly packed with histones, which genomic location and function remain unclear. We extracted and sequenced histone-associated DNA from sperm of nine ejaculates from three bulls. We found that the fraction of retained histones varied between samples, but the variance was similar between samples from the same and different individuals. The most conserved regions showed similar abundance across all samples, whereas in other regions, their presence correlated with the size of histone fraction. This may refer to gradual histone–protamine transition, where easily accessible genomic regions, followed by the less accessible regions are first substituted by protamines. Our results confirm those from previous studies that histones remain in repetitive genome elements, such as centromeres, and added new findings of histones in rRNA and SRP RNA gene clusters and indicated histone enrichment in some spermatogenesis-associated genes, but not in genes of early embryonic development. Our functional analysis revealed significant overrepresentation of cGMP-dependent protein kinase G (cGMP-PKG) pathway genes among histone-enriched genes. This pathway is known for its importance in pre-fertilization sperm events. In summary, a novel hypothesis for gradual histone-to-protamine transition in sperm maturation was proposed. We believe that histones may contribute structural information into early embryo by epigenetically modifying centromeric chromatin and other types of repetitive DNA. We also suggest that sperm histones are retained in genes needed for sperm development, maturation and fertilization, as these genes are transcriptionally active shortly prior to histone-to-protamine transition.
A benchmark image set for evaluating stylization

The non-photorealistic rendering community has had difficulty evaluating its research results. Other areas of computer graphics, and related disciplines such as computer vision, have made progress by comparing algorithms' performance on common datasets, or benchmarks. We argue for the benefits of establishing a benchmark image set to which image stylization methods can be applied, simplifying the comparison of methods, and broadening the testing to which a given method is subjected. We propose a preliminary set of benchmark images, representing a range of possible subject matter and image features of interest to researchers, and we describe the policies, tradeoffs, and reasoning that led us to the particular images in the set.
Hawkeye: Finding spamming accounts

Email spam is a critical problem to the Internet for a long time. The average amount of spam mail reached 72.1% of all email traffic in the world in 2012. The greatest threat to the email service providers was the spam mail sent from botnet, because the spam mail sent from botnet was accounting for more than 78% in 2011; therefore appeared many anti-spam solutions and techniques that were focus on the botnet. Owing to these anti-spam techniques, botnet spam is not effective as before. Spammers are finding new way to send the spam mail. One of the effective methods is using compromised accounts (or bot accounts) to send the spam mail because compromised accounts have good reputation IP addresses and compromised accounts send the spam mail with complete SMTP implemented server, such as Gmail, Yahoo! Mail, and Microsoft Live Mail. The spam mail send form compromised accounts are very difficult to be detected by any anti-spam techniques. Hence, we focus on the features spammers cannot easily hide. According to our research we find that normal users usually do not reply to the spam mail. Moreover, our empirical analysis reveals that the compromised account actually have low reply rate. We develop a system called “Hawkeye” that can find the compromised accounts effectively by checking the account's reply rate.