Miracle-dz/UniFAR-FTUs huggingface dataset:
The Ngram Statistics Package (Text::NSP) : A Flexible Tool for Identifying Ngrams, Collocations, and Word Associations

The Ngram Statistics Package (Text::NSP) is freely available open-source software that identifies ngrams, collocations and word associations in text. It is implemented in Perl and takes advantage of regular expressions to provide very flexible tokenization and to allow for the identification of non-adjacent ngrams. It includes a wide range of measures of association that can be used to identify collocations.
Lysine120 Interactions with p53 Response Elements can Allosterically Direct p53 Organization

p53 can serve as a paradigm in studies aiming to figure out how allosteric perturbations in transcription factors (TFs) triggered by small changes in DNA response element (RE) sequences, can spell selectivity in co-factor recruitment. p53-REs are 20-base pair (bp) DNA segments specifying diverse functions. They may be located near the transcription start sites or thousands of bps away in the genome. Their number has been estimated to be in the thousands, and they all share a common motif. A key question is then how does the p53 protein recognize a particular p53-RE sequence among all the similar ones? Here, representative p53-REs regulating diverse functions including cell cycle arrest, DNA repair, and apoptosis were simulated in explicit solvent. Among the major interactions between p53 and its REs involving Lys120, Arg280 and Arg248, the bps interacting with Lys120 vary while the interacting partners of other residues are less so. We observe that each p53-RE quarter site sequence has a unique pattern of interactions with p53 Lys120. The allosteric, DNA sequence-induced conformational and dynamic changes of the altered Lys120 interactions are amplified by the perturbation of other p53-DNA interactions. The combined subtle RE sequence-specific allosteric effects propagate in the p53 and in the DNA. The resulting amplified allosteric effects far away are reflected in changes in the overall p53 organization and in the p53 surface topology and residue fluctuations which play key roles in selective co-factor recruitment. As such, these observations suggest how similar p53-RE sequences can spell the preferred co-factor binding, which is the key to the selective gene transactivation and consequently different functional effects.
Under-expression of the Auxin Response Factor Sl-ARF4 improves post-harvest behavior of tomato fruits

Auxin is one of the most prominent phytohormones regulating many aspects of fleshy fruit development including fruit set, fruit size through the control of cell division and cell expansion, and fruit ripening. To shed light on the role of auxin fruit ripening, we have previously shown that Sl-ARF4 is a major player in mediating the auxin control of sugar metabolism in tomato fruit (cv MicroTom). Further extending this study, we show here that down-regulation of Sl-ARF4 in tomato alters some ripening-related fruit quality traits including enhanced fruit density at mature stage, increased firmness, prolonged shelf-life and reduced water (weight) loss at red ripe stage. These findings suggest that Sl-ARF4 plays a role in determining fruit cell wall architecture and thus providing a potential genetic marker for improving post-harvest handling and shelf life of tomato fruits.
Two algorithms for network size estimation for master/slave ad hoc networks

This paper proposes an adaptation of two network size estimation methods: random tour and gossip-based aggregation to suit master/slave mobile ad hoc networks. We show that it is feasible to accurately estimate the size of ad hoc networks when topology changes due to mobility using both methods. The algorithms were modified to account for the specific constraints of master/slave ad hoc networks and the results show that the proposed modifications perform better on these networks than the original protocols. Each of the two algorithms presents strengths and weaknesses and these are outlined in this paper.
A volume image foreground identification method by dual multi-scale morphological operations

A simple and regular foreground identification (FGID) method is proposed for image indexing. The gray-level morphological open/close by reconstruction (MOR/MCR) is operated on one image in a dual and multi-scale approach to construct a background gray-level mesh to distinguish foregrounds (FGs). The highly regular MOR/MCR operations make it feasible to deal with FG segmentation of volume images. The FGID efficiency is verified by the image retrieval performance, i.e., recall, precision and rank.With precisely identified FGs, MPEG-7 shape descriptors, in additional to color ones, can be used to improve the image retrieval performance. For the retrieval unit, a greedy boosting retrieval method is used to perform shape-based multiinstance query in considering the feature element dependency. To perform multi-instance query with multiple features, the retrieval unit integrates the similarity ranks of different feature types according to the feature saliency among query samples to yield the final similarity rank. The normalized correlation coefficient of features among query samples is computed to provide weighting factors for integrating ranks. Experiments show that the FGID unit helps much in improving the retrieval performances, i.e., 7% improvement for the precision-recall (PR) and 20% improvement for the averaged normalized modified retrieval rank (ANMRR), as compared to non-FGID ones.
Estimators for Time-Variant Channels Applied to UMTS-HSDPA

In this work we analyze the mean-square error (MSE) of two correlative channel estimators in time-variant channels. Both estimators make use of orthogonal basis functions that approximate the time-variant channel. The first approximation is based on a set of time shifted rectangular basis (RB) functions. The second approximation makes use of Slepian basis (SB) functions. We calculate the number of basis functions that minimize the MSE for the RB-and the SB-approach. Both estimators are designed for the full velocity range using the maximum velocity as design parameter only. Further, we apply the two estimators to the high-speed downlink packet access (HSDPA) mode of UMTS and illustrate the impact of the MSE on the throughput. With the SB-approach we observe a gain of roughly 0.4 dB over the RB-functions in case of an i.i. d. Rayleigh multipath channel with five taps
Introduction. Ecological immunology

An organism's fitness is critically reliant on its immune system to provide protection against parasites and pathogens. The structure of even simple immune systems is surprisingly complex and clearly will have been moulded by the organism's ecology. The aim of this review and the theme issue is to examine the role of different ecological factors on the evolution of immunity. Here, we will provide a general framework of the field by contextualizing the main ecological factors, including interactions with parasites, other types of biotic as well as abiotic interactions, intraspecific selective constraints (life-history trade-offs, sexual selection) and population genetic processes. We then elaborate the resulting immunological consequences such as the diversity of defence mechanisms (e.g. avoidance behaviour, resistance, tolerance), redundancy and protection against immunopathology, life-history integration of the immune response and shared immunity within a community (e.g. social immunity and microbiota-mediated protection). Our review summarizes the concepts of current importance and directs the reader to promising future research avenues that will deepen our understanding of the defence against parasites and pathogens.
Survey of Tools for Collaborative Knowledge Construction and Sharing

The fast growth and spread of Web 2.0 environments have demonstrated the great willingness of general Web users to contribute and share various type of content and information. Many very successful web sites currently exist which thrive on the wisdom of the crowd, where web users in general are the sole data providers and curators. The Semantic Web calls for knowledge to be semantically represented using ontologies to allow for better access and sharing of data. However, constructing ontologies collaboratively is not well supported by most existing ontology and knowledge-base editing tools. This has resulted in the recent emergence of a new range of collaborative ontology construction tools with the aim of integrating some Web 2.0 features into the process of structured knowledge construction. This paper provides a survey of the start of the art of these tools, and highlights their significant features and capabilities.
Locating and quantifying greenhouse gas emissions at a geological CO2 storage site using atmospheric modeling and measurements

The Cooperative Research Centre for Greenhouse Gas Technologies (CO2CRC) Otway Project is Australia's first demonstration of the geological storage of carbon dioxide (CO2), where about 65,000 metric tons of fluid consisting of 92% CO2 and 8% methane (CH4) by mass have been injected underground. As part of the project objective of developing methodologies to detect, locate, and quantify potential leakage of the stored fluid into the atmosphere, we formulate an inverse atmospheric model based on a Bayesian probabilistic framework coupled to a state‐of‐the‐art backward Lagrangian particle dispersion model. A Markov chain Monte Carlo method is used for efficiently sampling the posterior probability distribution of the source parameters. Controlled experiments used to test the model involved releases of the injected fluid from one of the nearby wells and were staggered over 1 month. Atmospheric measurements of CO2 and CH4 concentrations were taken at two stations installed in an upwind‐downwind configuration. Modeling both the emission rate and the source location using the concentration measurements from only two stations is difficult, but the fact that the emission rate was constant, which is not an unrealistic scenario for potential geological leakage, allows us to compute both parameters. The modeled source parameters compare reasonably well with the actual values, with the CH4 tracer constraining the source better than CO2, largely as a result of its 6 times higher signal‐to‐noise ratio. The results lend confidence in the ability of atmospheric techniques to quantify potential leakage from CO2 storage as well as other source types.
Structural and Functional Impact of the Transgenic Expression of Cytokines in the CNS a

Abstract: Cytokines are powerfu1 mediators of biologic responses in the CNS and may contribute to cellular injury in pathophysiologic states. In order to better understand the actions of cytokines in the intact mammalian CNS, a transgenic approach was employed that targeted the expression of different cytokines to astrocytes in mice. Fusion gene constructs consisting of a GFAP expression vector into which was inserted the DNA encoding the cytokines interleukin‐6 (IL‐6), IL‐3, or TNF‐α were used to generate transgenic mice. Expression of the transgene‐encoded cytokines in astrocytes was confirmed at both the RNA and protein levels. Transgenic mice were subject to multilevel analysis to determine the extent of structural and functional CNS alterations. Transgenic mice exhibited distinct adult‐onset, chronic‐progressive neurological disorders that correlated with the level and anatomic distribution of transgene‐encoded cytokine expression. The principal findings were neurodegeneration and cognitive decline due to IL‐6 expression, macrophage/microglial‐mediated primary demyelination with motor disease resulting from IL‐3 expression, and lymphocytic meningoencephalomyelitis with paralysis induced by TNF‐α expression. These transgenic models (1) indicate that expression of cytokines per se in the intact CNS is pathogenic, with cytokine‐specific neural cell injury leading to unique functional deficits; (2) recapitulate many of the structural and functional changes seen in human inflammatory neurological disorders; (3) provide a valuable tool for advancing our understanding of the CNS pathobiology of cytokines; and (4) offer a unique resource for the development and testing of therapies aimed at abrogating the harmful actions of these important mediators.
Physical Implementation of the DSPIN Network-on-Chip in the FAUST Architecture

This paper presents a physical implementation of the DSPIN network-on-chip in the FAUST architecture. FAUST is a stream-oriented multi- application SoC platform for telecommunications addressing IEEE 802.11a and MC-CDMA standards. The original asynchronous network-on-chip (ANOC) of FAUST has been replaced by the multi-synchronous DSPIN network-on-chip. In this paper, we analyze how the DSPIN network-on-chip, originally designed to support shared memory and multi-processors architectures, can support stream-oriented architectures. The physical implementation of both ANOC and DSPIN are presented. Finally, a comparison between ANOC and DSPIN designs in a 130 nm technology is carried out in terms of area, throughput, packet latency, and power consumption.
Wireless Information and Power Transfer: Energy Efficiency Optimization in OFDMA Systems

This paper considers orthogonal frequency division multiple access (OFDMA) systems with simultaneous wireless information and power transfer. We study the resource allocation algorithm design for maximization of the energy efficiency of data transmission (bits/Joule delivered to the receivers). In particular, we focus on power splitting hybrid receivers which are able to split the received signals into two power streams for concurrent information decoding and energy harvesting. Two scenarios are investigated considering different power splitting abilities of the receivers. In the first scenario, we assume receivers which can split the received power into a continuous set of power streams with arbitrary power splitting ratios. In the second scenario, we examine receivers which can split the received power only into a discrete set of power streams with fixed power splitting ratios. For both scenarios, we formulate the corresponding algorithm design as a non-convex optimization problem which takes into account the circuit power consumption, the minimum data rate requirements of delay constrained services, the minimum required system data rate, and the minimum amount of power that has to be delivered to the receivers. By exploiting fractional programming and dual decomposition, suboptimal iterative resource allocation algorithms are developed to solve the non-convex problems. Simulation results illustrate that the proposed iterative resource allocation algorithms approach the optimal solution within a small number of iterations and unveil the trade-off between energy efficiency, system capacity, and wireless power transfer: (1) wireless power transfer enhances the system energy efficiency by harvesting energy in the radio frequency, especially in the interference limited regime; (2) the presence of multiple receivers is beneficial for the system capacity, but not necessarily for the system energy efficiency.
Multiview Stereo and Silhouette Consistency via Convex Functionals over Convex Domains

We propose a convex formulation for silhouette and stereo fusion in 3D reconstruction from multiple images. The key idea is to show that the reconstruction problem can be cast as one of minimizing a convex functional, where the exact silhouette consistency is imposed as convex constraints that restrict the domain of feasible functions. As a consequence, we can retain the original stereo-weighted surface area as a cost functional without heuristic modifications of this energy by balloon terms or other strategies, yet still obtain meaningful (nonempty) reconstructions which are guaranteed to be silhouette-consistent. We prove that the proposed convex relaxation approach provides solutions that lie within a bound of the optimal solution. Compared to existing alternatives, the proposed method does not depend on initialization and leads to a simpler and more robust numerical scheme for imposing silhouette consistency obtained by projection onto convex sets. We show that this projection can be solved exactly using an efficient algorithm. We propose a parallel implementation of the resulting convex optimization problem on a graphics card. Given a photoconsistency map and a set of image silhouettes, we are able to compute highly accurate and silhouette-consistent reconstructions for challenging real-world data sets. In particular, experimental results demonstrate that the proposed silhouette constraints help to preserve fine-scale details of the reconstructed shape. Computation times depend on the resolution of the input imagery and vary between a few seconds and a couple of minutes for all experiments in this paper.
Controlling factors and the paleoenvironmental significance of chemical elements in Holocene calcareous root tubes in the Alashan Desert, Northwest China

Abstract In the hinterland of the desert, valuable archives of paleoenvironmental evolution are scarce. Calcareous root tubes (CRTs) have a strong potential for reconstructing paleoenvironmental conditions. It is still unclear, however, whether chemical elements in the CRTs can provide insights into paleoenvironmental conditions. In this study, the major- and trace-element composition of 32 CRT samples from the Alashan Desert were analyzed by X-ray fluorescence spectrometry. Results showed that the elemental composition and content change were controlled by the parent material and climatic conditions at the time of CRT formation. Ca, Mg, and Sr were significantly affected by climate, whereas the enrichment of P is likely related to the growth of plants. Higher (lower) Mg/Ca and Sr/Ca ratios corresponded to higher (lower) effective moisture and a higher (lower) Mg/Sr ratio indicated a higher (lower) temperature during the middle Holocene (8–5 cal ka BP). The reconstruction results for effective moisture were consistent with those in the Asian monsoon margin of northwestern China, which were caused by higher monsoon precipitation and lower evaporation. Therefore, chemical elements in the CRTs can reflect changes in paleo-effective moisture and paleotemperature at a millennial resolution in this area.
Boundedness of Synchronverters using bounded integral control

Synchronverters are grid-friendly inverters that mimic the operation of conventional synchronous generators. In this paper, the non-linear stability of the synchronverter in the sense of boundedness is investigated and proven for the first time. To this end, initially, the complete non-linear model of the synchronverter is obtained and then the field-excitation current loop of the synchronverter is implemented using a bounded integral control (BIC) structure, as proposed by the authors in the literature. While maintaining the original synchronverter operation near the rated value, the BIC additionally guarantees that the field-excitation current will remain bounded in a given range. Using non-linear analysis and input-to-state stability theory, it is proven that the frequency dynamics will remain bounded which leads to a bounded synchronverter voltage and finally results in the stability of the closed-loop system in the sense of boundedness. Extensive simulation results verify that the proposed synchronverter with the BIC approximates the behavior of the original synchronverter near the rated value with a guaranteed bounded performance.
Toward Instrumenting Network Warfare Competitions to Generate Labeled Datasets

Unlabeled network traffic data is readily available to the security research community, but there is a severe shortage of labeled datasets that allow validation of experimental results. The labeled DARPA datasets of 1998 and 1999, while innovative at the time, are of only marginal utility in today's threat environment. In this paper we demonstrate that network warfare competitions can be instrumented to generate modern labeled datasets. Our contributions include design parameters for competitions as well as results and analysis from a test implementation of our techniques. Our results indicate that network warfare competitions can be used to generate scientifically valuable labeled datasets and such games can thus be used as engines to produce future datasets on a routine basis.
An Adaptive Mechanism for Fair Sharing of Storage Resources

To ensure Quality of Service (QoS) for data centers, it is critical to enforce a fair share of storage resources between competing users. Interposed schedulers are one of the most practical methods for performance isolation. Most fair queuing-based proportional sharing algorithms for existing interposed scheduler are variants of counterparts designed for network routers and may result in breaking the fairness of proportional sharing required by Service Level Agreements for storage systems. This paper presents a novel algorithm to address this problem. As an extension of the fair queuingbased algorithm, it can dynamically adapt to the performance variation of storage systems and guarantee a fair sharing of resources as well as satisfying the minimal performance requirements for different clients. The design and performance evaluation are presented.
Model Selection in Estimating Equations

Summary. Model selection is a necessary step in many practical regression analyses. But for methods based on estimating equations, such as the quasi‐likelihood and generalized estimating equation (GEE) approaches, there seem to be few well‐studied model selection techniques. In this article, we propose a new model selection criterion that minimizes the expected predictive bias (EPB) of estimating equations. A bootstrap smoothed cross‐validation (BCV) estimate of EPB is presented and its performance is assessed via simulation for overdispersed generalized linear models. For illustration, the method is applied to a real data set taken from a study of the development of ewe embryos.
An AIG-based QBF-solver using SAT for preprocessing

In this paper we present a solver for Quantified Boolean Formulas (QBFs) which is based on And-Inverter Graphs (AIGs). We use a new quantifier elimination method for AIGs, which heuristically combines cofactor-based quantifier elimination with quantification using BDDs and thus benefits from the strengths of both data structures. Moreover, we present a novel SAT-based method for preprocessing QBFs that is able to efficiently detect variables with forced truth assignments, allowing for an elimination of these variables from the input formula. We describe the used algorithm which heavily relies on the incremental features of modern SATsolvers. Experimental results demonstrate that our preprocessing method can significantly improve the performance of QBF preprocessing and thus is able to accelerate the overall solving process when used in combination with state-of-the-art QBF-solvers. In particular, we integrated the preprocessing technique as well as the quantifier elimination method into the QBF-solver AIGSolve, allowing it to outperform state-of-the-art solvers.