Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptive evolution to novel predators facilitates the evolution of damselfly species range shifts

Most species have evolved adaptations to reduce the chances of predation. In many cases, adaptations to coexist with one predator generate tradeoffs in the ability to live with other predators. Consequently, the ability to live with one predator may limit the geographic distributions of species, such that adaptive evolution to coexist with novel predators may facilitate range shifts. In a case study with Enallagma damselflies, we used a comparative phylogenetic approach to test the hypothesis that adaptive evolution to live with a novel predator facilitates range size shifts. Our results suggest that the evolution of Enallagma shifting from living in ancestral lakes with fish as top predators, to living in lakes with dragonflies as predators, may have facilitated an increase in their range sizes. This increased range size likely arose because lakes with dragonflies were widespread, but unavailable as a habitat throughout much of the evolutionary history of Enallagma because they were historically maladapted to coexist with dragonfly predators. Additionally, the traits that have evolved as defenses against dragonflies also likely enhanced damselfly dispersal abilities. While many factors underlie the evolutionary history of species ranges, these results suggest a role for the evolution of predator‐prey interactions.
Aerobic Mineralization of Trichloroethylene, Vinyl Chloride, and Aromatic Compounds by Rhodococcus Species

Two Rhodococcus strains which were isolated from a trichloroethylene (TCE)-degrading bacterial mixture and Rhodococcus rhodochrous ATCC 21197 mineralized vinyl chloride (VC) and TCE. Greater than 99.9% of a 1-mg/liter concentration of VC was degraded by cell suspensions. [1,2-14C]VC was degraded by cell suspensions, with the production of greater than 66% 14CO2 and 20% 14C-aqueous phase products and incorporation of 10% of the 14C into the biomass. Cultures that utilized propane as a substrate were able to mineralize greater than 28% of [1,2-14C]TCE to 14CO2, with approximately 40% appearing in 14C-aqueous phase products and another 10% of 14C incorporated into the biomass. VC degradation was oxygen dependent and occurred at a pH range of 5 to 10 and temperatures of 4 to 35°C. Cell suspensions degraded up to 5 mg of TCE per liter and up to 40 mg of VC per liter. Propane competitively inhibited TCE degradation. Resting cell suspensions also degraded other chlorinated aliphatic hydrocarbons, such as chloroform, 1,1-dichloroethylene, and 1,1,1-trichloroethane. The isolates degraded a mixture of aromatic and chlorinated aliphatic solvents and utilized benzene, toluene, sodium benzoate, naphthalene, biphenyl, and n-alkanes ranging in size from propane to hexadecane as carbon and energy sources. The environmental isolates appeared more catabolically versatile than R. rhodochrous ATCC 21197. The data report that environmental isolates of Rhodococcus species and R. rhodochrous ATCC 21197 have the potential to degrade TCE and VC in addition to a variety of aromatic and chlorinated aliphatic compounds either individually or in mixtures.
Gaussian Processes for POMDP-Based Dialogue Manager Optimization

A partially observable Markov decision process (POMDP) has been proposed as a dialog model that enables automatic optimization of the dialog policy and provides robustness to speech understanding errors. Various approximations allow such a model to be used for building real-world dialog systems. However, they require a large number of dialogs to train the dialog policy and hence they typically rely on the availability of a user simulator. They also require significant designer effort to hand-craft the policy representation. We investigate the use of Gaussian processes (GPs) in policy modeling to overcome these problems. We show that GP policy optimization can be implemented for a real world POMDP dialog manager, and in particular: 1) we examine different formulations of a GP policy to minimize variability in the learning process; 2) we find that the use of GP increases the learning rate by an order of magnitude thereby allowing learning by direct interaction with human users; and 3) we demonstrate that designer effort can be substantially reduced by basing the policy directly on the full belief space thereby avoiding ad hoc feature space modeling. Overall, the GP approach represents an important step forward towards fully automatic dialog policy optimization in real world systems.
Approximate reflection coefficients for a thin VTI layer

ABSTRACTWe have developed an approximate method to derive simple expressions for the reflection coefficients of P- and SV-waves for a thin transversely isotropic layer with a vertical symmetry axis (VTI) embedded in a homogeneous VTI background. The layer thickness is assumed to be much smaller than the wavelengths of P- and SV-waves inside. The exact reflection and transmission coefficients are derived by the propagator matrix method. In the case of normal incidence, the exact reflection and transmission coefficients are expressed in terms of the impedances of vertically propagating P- and S-waves. For subcritical incidence, the approximate reflection coefficients are expressed in terms of the contrast in the VTI parameters between the layer and the background. Numerical examples are designed to analyze the reflection coefficients at normal and oblique incidence and investigate the influence of transverse isotropy on the reflection coefficients. Despite giving numerical errors, the approximate formulas a.
Whole-Exome Sequencing Suggests LAMB3 as a Susceptibility Gene for Morbid Obesity

Identification of rare sequencing variants with a larger functional impact has the potential to highlight new pathways contributing to obesity. Using whole-exome sequencing followed by genotyping, we have identified a low-frequency coding variant rs2076349 (V527M) in the laminin subunit β3 (LAMB3) gene showing strong association with morbid obesity and thereby risk of type 2 diabetes. We exome-sequenced 200 morbidly obese subjects and 100 control subjects with pooled DNA samples. After several filtering steps, we retained 439 obesity-enriched low-frequency coding variants. Associations between genetic variants and obesity were validated sequentially in two case-control cohorts. In the final analysis of 1,911 morbidly obese and 1,274 control subjects, rs2076349 showed strong association with obesity (P = 9.67 × 10−5; odds ratio 1.84). This variant was also associated with BMI and fasting serum leptin. Moreover, LAMB3 expression in adipose tissue was positively correlated with BMI and adipose morphology (few but large fat cells). LAMB3 knockdown by small interfering RNA in human adipocytes cultured in vitro inhibited adipogenesis. In conclusion, we identified a previously not reported low-frequency coding variant that was associated with morbid obesity in the LAMB3 gene. This gene may be involved in the development of excess body fat.
Optimally Relaxing Partial-Order Plans with MaxSAT

Partial-order plans (POPs) are attractive because of their least commitment nature, providing enhanced plan flexibility at execution time relative to sequential plans. Despite the appeal of POPs, most of the recent research on automated plan generation has focused on sequential plans. In this paper we examine the task of POP generation by relaxing or modifying the action orderings of a plan to optimize for plan criteria that promotes flexibility in the POP. Our approach relies on a novel partial weighted MaxSAT encoding of a plan that supports the minimization of deordering or reordering of actions. We further extend the classical least commitment criterion for a POP to consider the number of actions in a solution, and provide an encoding to achieve least commitment plans with respect to this criterion. We compare the effectiveness of our approach to a previous approach for POP generation via sequential-plan relaxation. Our results show that while the previous approach is proficient at heuristically finding the optimal deordering of a plan, our approach gains greater flexibility with the optimal reordering.
On the information storage of associative matrix memories

This paper aims at providing insights onto fundamental properties of two of the earlier models of matrix memories: nonlinear or Willshaw's matrix model, and the linear matrix memory. These are traditional models of artificial neural networks (ANNs) on which little has been done in recent years on themes such as retrieval and storage properties, which are studied in this paper. Equations for predicting network connectivity and storage capacity as a function of the activity levels at the input and output fields and network dimension are presented for Willshaw's model. For the linear model, an equation for relating input and output net work errors is presented. The theoretical results presented for both models fit very well with computer simulations.
Direct Energy Supply to the Reaction Mixture during Microwave-Assisted Hydrothermal and Combustion Synthesis of Inorganic Materials

The use of microwaves to perform inorganic synthesis allows the direct transfer of electromagnetic energy inside the reaction mixture, independently of the temperature manifested therein. The conversion of microwave (MW) radiation into heat is useful in overcoming the activation energy barriers associated with chemical transformations, but the use of microwaves can be further extended to higher temperatures, thus creating unusual high-energy environments. In devising synthetic methodologies to engineered nanomaterials, hydrothermal synthesis and solution combustion synthesis can be used as reference systems to illustrate effects related to microwave irradiation. In the first case, energy is transferred to the entire reaction volume, causing a homogeneous temperature rise within a closed vessel in a few minutes, hence assuring uniform crystal growth at the nanometer scale. In the second case, strong exothermic combustion syntheses can benefit from the application of microwaves to convey energy to the reaction not only during the ignition step, but also while it is occurring and even after its completion. In both approaches, however, the direct interaction of microwaves with the reaction mixture can lead to practically gradient-less heating profiles, on the basis of which the main observed characteristics and properties of the aforementioned reactions and products can be explained.
Channel selection through a recommender system

Spectrum sharing between a cognitive network and a coexisting interfering network is considered. Among a collection of channels, in each time slot, each node in the cognitive network selects one channel based upon partial knowledge of the interference levels over these channels. The process of channel selection is treated as a recommender system, due to the similarity of recommending multiple items for multiple buyers and selecting multiple channels for multiple nodes. A modified collaborative filtering algorithm is proposed to perform prediction for the interference levels which would be suffered at receive nodes. Numerical experiments are presented to reveal the behavior of the proposed algorithm.
On-chip cross talk noise model for deep-submicrometer ULSI interconnect

Interconnect geometry in deep-submicrometer integrated circuit technologies is being aggressively scaled down for wiring density, leading to high aspect ratios in metal lines.1-3 For example, according to the Semiconductor Industries Association roadmap, metal aspect ratio is expected to reach 2:1 in the 0.25m technology generation and 3:1 by the year 2004. As a result of the increasing metal aspect ratio, capacitive coupling between neighboring signal lines increases and more cross talk noise is generated. With increasing edge rates and ground bounce in advanced technologies, cross talk will become a pervasive signal integrity issue.
Anomaly Detection by Naive Bayes & RBF Network

Intrusion detection by automated means is gaining widespread interest due to the serious impact of Intrusions on computer system or network. Several techniques have been introduced in an effort to minimize up to some extent the risk associated with Intrusion attack. In this respect, we have used a novel Machine learning technique which comprises of Naive Bayes approach and weighted radial basis function Network approach. The proposed scheme exhibits very promising results in comparison with many earlier techniques while experimenting on KDDCup’99 data set in detecting Intrusions.
STAMP2 increases oxidative stress and is critical for prostate cancer

The six transmembrane protein of prostate 2 (STAMP2) is an androgen‐regulated gene whose mRNA expression is increased in prostate cancer (PCa). Here, we show that STAMP2 protein expression is increased in human PCa compared with benign prostate that is also correlated with tumor grade and treatment response. We also show that STAMP2 significantly increased reactive oxygen species (ROS) in PCa cells through its iron reductase activity which also depleted NADPH levels. Knockdown of STAMP2 expression in PCa cells inhibited proliferation, colony formation, and anchorage‐independent growth, and significantly increased apoptosis. Furthermore, STAMP2 effects were, at least in part, mediated by activating transcription factor 4 (ATF4), whose expression is regulated by ROS. Consistent with in vitro findings, silencing STAMP2 significantly inhibited PCa xenograft growth in mice. Finally, therapeutic silencing of STAMP2 by systemically administered nanoliposomal siRNA profoundly inhibited tumor growth in two established preclinical PCa models in mice. These data suggest that STAMP2 is required for PCa progression and thus may serve as a novel therapeutic target.
Design & implementation of IEEE 802.11s mesh nodes with enhanced features

This paper describes the implementation of wireless mesh nodes based on the IEEE 802.11s draft where the motivation is to build a real life mesh network. The mesh nodes developed have mesh, mesh access point and mesh portal functionalities simultaneously. The mesh nodes use different radios for mesh and access point functionalities, thus giving better service to client stations. Both reactive and proactive modes of HWMP are supported. The paper also suggests some measures to enhance the performance of the overall network by reducing the number of PREQs.
Research article BIOSYNTHESIS AND CHARACTERIZATION OF KERATINOLYTIC PROTEASE FROM ACTINOBACTERIUM SP. IN SOLID STATE CULTURE

The aim of this study was to use agro-industrial residues for the production of a halotolerant keratinolytic- protease by Actinobacterium sp. in solid-state fermentation. Among various agro-industrial residues that were evaluated, apple pomace supported maximum protease production (8400 U/g material). The optimum conditions required for enzyme production were a fermentation period of 72 h, 10% (w/v) NaCl, pH 7.0, 120% (v/w) moisture and 10% (v/w) inoculum. The enzyme exhibited activity to a range of pH (7.0-9.0) and temperature (30-45°C), with optima at 8.0 and 40 °C, respectively. Most of the divalent ions tested stimulated the protease activity and Ca 2+ ion was required for its activity and stability. The enzyme was widely active at the range of NaCl concentration (5%-15%, w/v) and effectively degraded chicken feather. This protease could be useful in fish sauce fermentation and also in feed industry.
Hormonal pleiotropy and the juvenile hormone regulation of Drosophila development and life history

Understanding how traits are integrated at the organismal level remains a fundamental problem at the interface of developmental and evolutionary biology. Hormones, regulatory signaling molecules that coordinate multiple developmental and physiological processes, are major determinants underlying phenotypic integration. The probably best example for this is the lipid‐like juvenile hormone (JH) in insects. Here we review the manifold effects of JH, the most versatile animal hormone, with an emphasis on the fruit fly Drosophila melanogaster, an organism amenable to both genetics and endocrinology. JH affects a remarkable number of processes and traits in Drosophila development and life history, including metamorphosis, behavior, reproduction, diapause, stress resistance and aging. While many molecular details underlying JH signaling remain unknown, we argue that studying “hormonal pleiotropy” offers intriguing insights into phenotypic integration and the mechanisms underlying life history evolution. In particular, we illustrate the role of JH as a key mediator of life history trade‐offs. BioEssays 27:999–1010, 2005. © 2005 Wiley Periodicals, Inc.
EdgeMiner: Automatically Detecting Implicit Control Flow Transitions through the Android Framework

Android users can choose from over one million applications (apps) offered through the official Google Play marketplace. Furthermore, a wealth of alternative sources for Android applications is available for users to choose from. These range from curated stores, such as Amazon’s Appstore to less legitimate sources that offer pirated content. The sheer number of mobile applications prompted researchers from academia and industry to develop static analysis techniques that scrutinize these applications for vulnerabilities and malicious functionality. Android applications always execute in the context of the Android framework — a comprehensive collection of functionality that developers can conveniently use from their applications. The prolific use of the framework poses unique challenges for the analysis of Android applications.
Modeling T-cell activation using gene expression profiling and state-space models

MOTIVATION We have used state-space models to reverse engineer transcriptional networks from highly replicated gene expression profiling time series data obtained from a well-established model of T-cell activation. State space models are a class of dynamic Bayesian networks that assume that the observed measurements depend on some hidden state variables that evolve according to Markovian dynamics. These hidden variables can capture effects that cannot be measured in a gene expression profiling experiment, e.g. genes that have not been included in the microarray, levels of regulatory proteins, the effects of messenger RNA and protein degradation, etc. RESULTS Bootstrap confidence intervals are developed for parameters representing 'gene-gene' interactions over time. Our models represent the dynamics of T-cell activation and provide a methodology for the development of rational and experimentally testable hypotheses. AVAILABILITY Supplementary data and Matlab computer source code will be made available on the web at the URL given below. SUPPLEMENTARY INFORMATION http://public.kgi. edu/~wild/LDS/index.htm
Building Large Scale Relation KB from Text

Recently more and more structured data in form of RDF triples have been published and integrated into Linked Open Data (LOD). While the current LOD contains hundreds of data sources with billions of triples, it has a small number of distinct relations compared with the large number of entities. On the other hand, Web pages are growing rapidly, which results in much larger number of textual contents to be exploited. With the popularity and wide adoption of open information extraction technology, extracting entities and relations among them from text at the Web scale is possible. In this paper, we present an approach to extract the subject individuals and the object counterparts for the relations from text and determine the most appropriate domain and range as well as the most confident dependency path patterns for the given relation based on the EM algorithm. As a preliminary results, we built a knowledge base for relations extracted from Chinese encyclopedias. The experimental results show the effectiveness of our approach to extract relations with reasonable domain, range and path pattern restrictions as well as high-quality triples.
Defects of Vps15 in skeletal muscles lead to autophagic vacuolar myopathy and lysosomal disease

The complex of Vacuolar Protein Sorting 34 and 15 (Vps34 and Vps15) has Class III phosphatidylinositol 3‐kinase activity and putative roles in nutrient sensing, mammalian Target Of Rapamycin (mTOR) activation by amino acids, cell growth, vesicular trafficking and autophagy. Contrary to expectations, here we show that Vps15‐deficient mouse tissues are competent for LC3‐positive autophagosome formation and maintain mTOR activation. However, an impaired lysosomal function in mutant cells is traced by accumulation of adaptor protein p62, LC3 and Lamp2 positive vesicles, which can be reverted to normal levels after ectopic overexpression of Vps15. Mice lacking Vps15 in skeletal muscles, develop a severe myopathy. Distinct from the autophagy deficient Atg7−/− mutants, pathognomonic morphological hallmarks of autophagic vacuolar myopathy (AVM) are observed in Vps15−/− mutants, including elevated creatine kinase plasma levels, accumulation of autophagosomes, glycogen and sarcolemmal features within the fibres. Importantly, Vps34/Vps15 overexpression in myoblasts of Danon AVM disease patients alleviates the glycogen accumulation. Thus, the activity of the Vps34/Vps15 complex is critical in disease conditions such as AVMs, and possibly a variety of other lysosomal storage diseases.
Glacial Modulation of Rapid Climate Change During the Last 0.5 Million Years

viding evidence for additional environmental fl uctuations not seen in this part of the ice-core record. From this correlation with GISP2, as well as from correlations with high resolution ocean records such as that from DSDP–609, it is concluded that the Monticchio record clearly demonstrates a link between the closely coupled ocean–atmosphere system of the North Atlantic region and environmental changes in the Mediterranean region.
AnswerFinder at TREC 2005

AnswerFinder has been completely redesigned for TREC 2005. The new architecture allows a fast development of question-answering systems for their deployment in the TREC tasks and other applications. The AnswerFinder modules use XML to express the services they provide, and they can be queried with XML for their services. The QA method now incorporates graphbased methods to compute the answerhood of a sentence and pin-point the answer. The system uses a set of graph-based rules that are learnt automatically. Unfortunately the system could not be completed and debugged before the TREC deadline and the runs did not fare well. Currently we are debugging and evaluating the system.