Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptive Evolution of Recently Duplicated Accessory Gland Protein Genes in Desert Drosophila

The relationship between animal mating system variation and patterns of protein polymorphism and divergence is poorly understood. Drosophila provides an excellent system for addressing this issue, as there is abundant interspecific mating system variation. For example, compared to D. melanogaster subgroup species, repleta group species have higher remating rates, delayed sexual maturity, and several other interesting differences. We previously showed that accessory gland protein genes (Acp's) of Drosophila mojavensis and D. arizonae evolve more rapidly than Acp's in the D. melanogaster subgroup and that adaptive Acp protein evolution is likely more common in D. mojavensis/D. arizonae than in D. melanogaster/D. simulans. These findings are consistent with the idea that greater postcopulatory selection results in more adaptive evolution of seminal fluid proteins in the repleta group flies. Here we report another interesting evolutionary difference between the repleta group and the D. melanogaster subgroup Acp's. Acp gene duplications are present in D. melanogaster, but their high sequence divergence indicates that the fixation rate of duplicated Acp's has been low in this lineage. Here we report that D. mojavensis and D. arizonae genomes contain several very young duplicated Acp's and that these Acp's have experienced very rapid, adaptive protein divergence. We propose that rapid remating of female desert Drosophila generates selection for continuous diversification of the male Acp complement to improve male fertilization potential. Thus, mating system variation may be associated with adaptive protein divergence as well as with duplication of Acp's in Drosophila.
Dose Finding for Continuous and Ordinal Outcomes with a Monotone Objective Function: A Unified Approach

Summary In many phase I trials, the design goal is to find the dose associated with a certain target toxicity rate. In some trials, the goal can be to find the dose with a certain weighted sum of rates of various toxicity grades. For others, the goal is to find the dose with a certain mean value of a continuous response. In this article, we describe a dose‐finding design that can be used in any of the dose‐finding trials described above, trials where the target dose is defined as the dose at which a certain monotone function of the dose is a prespecified value. At each step of the proposed design, the normalized difference between the current dose and the target is computed. If that difference is close to zero, the dose is repeated. Otherwise, the dose is increased or decreased, depending on the sign of the difference.
Legion: flexible support for wide-area computing

1 The Oppor tun i t y Recent technological changes have made the realization of nationwide, and indeed worldwide, virtual computers possible. A nationwide virtual computer would consist of workstations, personal computers, graphics rendering engines, supercomputers, and possibly non-traditional computing and rendering devices such as TV's, all connected via the Nil and an integrated software infrastructure. Such a system, if constructed, may well revolutionize how we work, how we play, and in general, how we interact with one another. The staggering success of the World Wide Web only hints at the potential of such a system. The technological changes that enable the realization of a worldwide virtual computer are (1) the introduction of gigabit/second fiber-optic backbones, which effectively "shrink" the distance between geographically separate computers, (2) the maturation of parallel compilers that support parallel execution on distributed memory machines, (3) advances in distributed systems software over twenty years which have increased our understanding of how to manage complex distributed environments, (4) the widespread acceptance in industry of the object-oriented paradigm, and (5) advances in cryptography and authentication protocols. These changes challenge the computer science community to provide a solid integrated software foundation on which to build applications, and with which to unleash the potential of so many diverse, powerful resources. The foundation must at least hide the underlying physical infrastructure from users and from the vast majority of programmers, support access, location, and fault transparency, enable inter-operability of components, support construction of larger integrated components using existing components, and provide a secure environment for both resource owners and users. Further, the services must be provided in the context of tens of thousands to millions of autonomous hosts; thus, the software infrastructure must be scalable or it will fail to meet users' performance expectations. It is this software foundation that will make the collection of hosts and fiber connections a virtual computer. We call such software metasystems software. Whether or not metasystems software is explicitly designed, the nation (and the world) will eventually end up with a metasystem. The reason is simple--both individual and organizational users will be required to deal with increasingly obvious shortcomings of the nationwide computer system. The World Wide Web and gopher show that tools will be developed in an ad hoc fashion to paper over the gaps between local systems. The issue is not whether metasystems will be developed; clearly they will. It is, rather, whether they will come about by design in a coherent, seamless system, or painfully and in an ad hoc manner by patching together independently developed systems, each with different objectives, design philosophies, and computation models.
Targeting Nuclear Hormone Receptors: PPARα Agonists as Potential Disease-Modifying Drugs for Rheumatoid Arthritis

In recent years, peroxisome proliferator-activated receptors (PPARs) have received growing interest due to the broad spectrum of their biological activities. PPARα, an isoform of PPAR, plays an important role in lipid homeostasis and inflammation, which makes it a potential target for the treatment of chronic inflammatory disorders, including RA. This paper reviews studies on the properties of PPARα agonists which may be pertinent to the treatment of RA. These properties include effects on lipid metabolism, inflammation, and angiogenesis, as well as interference with glucocorticoid effects, and a potential role in gender dimorphism of autoimmune disorders. However, current clinical experience with this class of drugs in RA is limited. New studies are needed to elucidate whether PPARα agonism may be an effective treatment strategy for RA patients.
REVERSION-TO-ETHYLENE SENSITIVITY1, a conserved gene that regulates ethylene receptor function in Arabidopsis

Arabidopsis thaliana has five ethylene hormone receptors, which bind ethylene and elicit responses critical for plant growth and development. Here we describe a negative regulator of ethylene responses, REVERSION-TO-ETHYLENE SENSITIVITY1 (RTE1), which regulates the function of at least one of the receptors, ETR1, in Arabidopsis. RTE1 was identified based on the ability of rte1 mutations to suppress ethylene insensitivity of the dominant gain-of-function allele etr1-2. rte1 loss-of-function mutants have an enhanced ethylene response that closely resembles the etr1 null phenotype. The etr1 rte1 double null mutant is identical to the etr1 and rte1 single null mutants, suggesting that the two genes act in the same pathway. rte1 is unable to suppress the etr1-1 gain-of-function allele, placing RTE1 at or upstream of ETR1. rte1 also fails to suppress gain-of-function mutations in each of the four other ethylene receptor genes. RTE1 encodes a previously undescribed predicted membrane protein, which is highly conserved in plants and protists but absent in fungi and prokaryotes. Ethylene treatment induces RTE1 expression, and overexpression of RTE1 confers reduced ethylene sensitivity that partially depends on ETR1. These findings demonstrate that RTE1 is a negative regulator of ethylene signaling and suggest that RTE1 plays an important role in ETR1 function.
Evaluation of CYP2D6 phenotype in the Yoruba Nigerian population

ABSTRACT Background: There is a lack of information on CYP2D6, a major metabolizing enzyme, in Africa ethnic nationalities. The objective was to determine CYP2D6 phenotype in Yoruba Nigerians using dextromethorphan (DEX). Method: A total of 89 healthy volunteers received 30 mg of DEX orally followed by blood and urine sample collection at 3-hour and over 8 h post-dose, respectively. DEX and dextrorphan (DOR) concentrations were determined using High Performance Liquid Chromatography (HPLC). The metabolic ratio (MR, DEX/DOR) were plotted for the phenotype determination. Results: The log MR that separated poor (PMs) from normal metabolizers (NMs) was 0.28 and 0.75 for urine and plasma, respectively. Two subjects (2.3%) identified as PMs had a mean MR of 17 and 3.2 in plasma and urine, significantly higher than that of NMs (p < .0001). A positive correlation between urine and plasma MR was noted. Conclusion: The prevalence of PMs in the Yoruba Nigerians was similar to that reported among blacks.
Hemophagocytic syndrome associated with retinoic acid syndrome in acute promyelocytic leukemia

A 56‐year‐old woman with an acute promyelocytic leukemia (APL) developed a severe all‐trans‐retinoic (ATRA) syndrome on day 17 of treatment. Shortly after, she presented a picture of pancytopenia, hepatosplenomegaly, increased triglycerides, ferritin, and liver enzymes. A bone marrow biopsy showed abundant macrophages and no evidence of leukemia. Tests for secondary hemophagocytic syndrome (HPS) were negative. A diagnosis of HPS was made. Treatment with dexamethasone and high‐dose immunoglobulins was unsuccessful. Consolidation chemotherapy with idarubicin and ATRA rapidly reversed the HPS. The HPS in this patient could be related to the release of macrophage‐stimulating cytokines by APL cells during ATRA syndrome. Am. J. Hematol. 76:172–175, 2004. © 2004 Wiley‐Liss, Inc.
Delay Differential Analysis of Time Series

Abstract Nonlinear dynamical system analysis based on embedding theory has been used for modeling and prediction, but it also has applications to signal detection and classification of time series. An embedding creates a multidimensional geometrical object from a single time series. Traditionally either delay or derivative embeddings have been used. The delay embedding is composed of delayed versions of the signal, and the derivative embedding is composed of successive derivatives of the signal. The delay embedding has been extended to nonuniform embeddings to take multiple timescales into account. Both embeddings provide information on the underlying dynamical system without having direct access to all the system variables. Delay differential analysis is based on functional embeddings, a combination of the derivative embedding with nonuniform delay embeddings. Small delay differential equation (DDE) models that best represent relevant dynamic features of time series data are selected from a pool of candidate models for detection or classification. We show that the properties of DDEs support spectral analysis in the time domain where nonlinear correlation functions are used to detect frequencies, frequency and phase couplings, and bispectra. These can be efficiently computed with short time windows and are robust to noise. For frequency analysis, this framework is a multivariate extension of discrete Fourier transform (DFT), and for higher-order spectra, it is a linear and multivariate alternative to multidimensional fast Fourier transform of multidimensional correlations. This method can be applied to short or sparse time series and can be extended to cross-trial and cross-channel spectra if multiple short data segments of the same experiment are available. Together, this time-domain toolbox provides higher temporal resolution, increased frequency and phase coupling information, and it allows an easy and straightforward implementation of higher-order spectra across time compared with frequency-based methods such as the DFT and cross-spectral analysis.
Semi-Random Projection for Dimensionality Reduction and Extreme Learning Machine in High-Dimensional Space

Random Projection (RP) is a popular technique for dimensionality reduction because of its high computational efficiency. However, RP may not yield highly discriminative low-dimensional space to produce best pattern classification performance since the random transformation matrix of RP is independent of data. In this paper, we propose a Semi-Random Projection (SRP) framework, which takes the merit of random feature sampling of RP, but employs learning mechanism in the determination of the transformation matrix. One advantage of SRP is that it achieves a good balance between computational complexity and classification accuracy. Another advantage of SRP is that multiple SRP modules can be stacked to form a deep learning architecture for compact and robust feature learning. In addition, based on the insight on the relationship between RP and Extreme Learning Machine (ELM), the SRP is applied to ELM to derive Partially Connected ELM (PC-ELM). The hidden nodes of PC-ELM are more discriminative and hence a smaller number of nodes are needed. Experiments on two real-world text corpus, i.e., 20 Newsgroups and Farms Ads. , verify the effectiveness and efficiency of the proposed SRP. Experimental results also show that PC-ELM outperforms ELM for high-dimensional data.
Longitudinal patterns of language use, diversity, support, and competence

Children’s acquisition of speech and language is a major area of focus in childhood. Speech and language competence enables positive educational and social outcomes in childhood and occupational outcomes in adulthood (McCormack, McLeod, McAllister, & Harrison, 2009). Cultural beliefs, practices, and identity are transmitted through language. Children’s language and culture are inextricably linked with the development of their personal identity and sense of belonging. For example, the Early Years Learning Framework for Australia states
Erythropoietin improves cardiac contractility in post‐hypoxic mice

Summary. Mice myocardia, in which plasma erythropoietin (EPO) concentrations were modified in response to different experimental conditions, were studied to evaluate contractility (dF/dt). CF1 mice were randomly separated into four main groups: group I, normocythaemic normoxic; group II‐a, normocythaemic intermittently exposed to hypobaria for 72 h; group II‐b, normocythaemic intermittently exposed to hypobaria for 3 weeks; group III, hypertransfused polycythaemic exposed to 72 h hypobaria; and group IV, hypertransfused polycythaemic maintained in normobaric air. Plasma EPO, contractile studies and binding assays were performed. The dF/dt was significantly higher in group II‐a than in group I and group II‐b; but in groups III and IV, the dF/dt was reduced. The toxic action of ouabain was reduced and delayed in its onset, accompanied by increased numbers of 3H‐ouabain binding sites in group II‐a. Contractility was positively correlated with plasma EPO (pEPO) in the different groups. Treating group I with recombinant human (rHu)‐EPO enhanced contractility while treating group II‐a with a monoclonal anti‐EPO decreased the dF/dt. The inhibition of enzymatic pathway(s) known to participate in the cytokines signal transduction, decreased the basal dF/dt values on atria from group II‐a and on group I atria treated with rHu‐EPO. The results demonstrated: (1) a cardiac non‐haematopoietic effect of EPO; (2) that mice in which the pEPO concentration increased showed improvement in contractility and in the therapeutic action of ouabain; and (3) it is possible that EPO may act as a cardioprotective agent by modulating the cardiac Na+–K+ pump.
Driver's situation awareness during supervision of automated control - comparison between SART and SAGAT measurement techniques

Systems enabling to drive automatically are being introduced on the market. When using this technology, drivers are in need for interfaces which support them with supervision of the automated control. Assessment of Situation Awareness (SA) which drivers are able to gain while using such interfaces, is important. Based on comparison between SART and SAGAT measurement techniques within a simulator study, the test set-up presented in this paper suggests to be successful in providing a coherent test-bed with relevant situations to assess the level of SA drivers gain when involved in supervision of automated control and while using different types of feedback.
Questions Feature Extraction and Semi-supervised Classification Based on Terms Relevance

Question classification, an important component of question answering systems, has a direct impact on the answer extraction accuracy. In this paper, a question classification method is proposed by combined the question feature extracting of term relevance with semi-supervised classification. In detail, the method extracts structure terms in interrogative sentences as the feature space through statistical means, and calculates the relevance among terms by literal similarity method, besides, feature vectors of question classification are obtained by using term similarity relationship to build the questions’ feature value in feature space. And then, utilizing unlabeled samples classify questions with the help of Co-training style and semisupervised learning algorithm. Experimented on 20,000 questions in Yunnan tourism domain, the results show that more remarkable effects have been achieved by adopting the method above. The classification accuracy rate reaches 82.34%, which is higher than the TFIDF feature extraction methods and supervised learning methods by 15.4 percentage points and 1.4 percentage points separately.
Reliable NoC architecture utilizing a robust rerouting algorithm

Moving towards reconfigurability is an approach to increase fault tolerance on System-on-Chip design. In this paper, we propose a self-reconfigurable NoC architecture utilizing a robust rerouting method. At first, an offline test strategy for locating system-level faults in NoC switch ports is utilized. Using the information achieved in the test phase, every switch reconfigures itself to avoid routing packets through faulty links by utilizing our local rerouting method. The proposed rerouting method is evaluated using a Transaction-Level platform. Experimental results show that our proposed rerouting method delivers all the packets in a faulty NoC successfully and has a less communication overhead compared to a pure flooding method.
The trophy effect

By extending a typical endowment effect experiment with the possibility of winning the endowment in a real effort contest, we found two reinforcing effects that led to a complete market failure. Subjects who won the item in the effortful competition had a very high willingness to accept (trophy winner effect). By contrast, subjects who were not successful had an extremely low willingness to pay for the same item (trophy loser effect). We disentangle different components of these effects and investigate the underlying emotional responses. Further, we analyze the duration of the effects and discuss economic implications
Resolving the integrity/performance conflict

It is argued that future applications will require integrity of complex, persistent data in the face of hardware and program failures. We discuss Thor, a new object-oriented database, which offers a computational model that ensures data integrity in a distributed system without sacrificing expressiveness or performance. Perhaps surprisingly, compiler technology is important to make this work well. <<ETX>>
Improved Result Ranking in P2P File-Sharing Systems by Probing for Metadata

One of the reasons that search performance of peer-to-peer file-sharing systems is poor is that results are poorly described, hurting the client's ability to rank them. This is a consequence of the independent and distributed nature of servers in this architecture. We propose automatically probing the network for better descriptions to improve result ranking. Search performance improvements are demonstrated through extensive simulation results
A Variation Evolving Method for Optimal Control

A new method for the optimal solutions is proposed. Originating from the continuous-time dynamics stability theory in the control field, the optimal solution is anticipated to be obtained in an asymptotically evolving way. By introducing a virtual dimension, the variation time, a dynamic system that describes the variation motion is deduced from the Optimal Control Problem (OCP), and the optimal solution is its equilibrium point. Through this method, the intractable OCP is transformed to the Initial-value Problem (IVP) and it may be solved with mature Ordinary Differential Equation (ODE) numerical integration methods. Especially, the deduced dynamic system is globally stable, so any initial value will evolve to the extremal solution ultimately.
A new Advanced Traveler Advisory Tool based on personal user preferences

This paper focuses on an Advanced Traveler Advisory Tool (ATAT) aiming at supporting users travelling on multimodal networks and at suggesting the best path set according to user personal preferences. In order to find the best personal paths, the presented ATAT uses the Random Utility Theory framework to assign an estimation of the path utility perceived by the user for each path alternative. The first part of this paper illustrates the user needs and the ATAT logical architecture, and presents the modeling framework able to provide personalized pre-trip and en-route information. The second part reports the results of some test applications and the results of a benefit assessment of the ATAT use for transit travelers.
Cooperative Differential Space–Time Spreading for the Asynchronous Relay Aided CDMA Uplink Using Interference Rejection Spreading Code

This letter proposes a differential Space-Time Coding (STC) scheme designed for asynchronous cooperative networks, where neither channel estimation nor symbol-level synchronization is required at the cooperating nodes. More specifically, our system employs differential encoding during the broadcast phase and a Space-Time Spreading (STS)-based amplify-and-forward scheme during the cooperative phase in conjunction with interference rejection direct sequence spreading codes, namely Loosely Synchronized (LS) codes. Our simulation results demonstrate that the proposed Cooperative Differential STS (CDSTS) scheme is capable of combating the effects of asynchronous uplink transmissions without any channel state information.