Miracle-dz/UniFAR-FTUs huggingface dataset:
Microarray and ChIP-seq data analysis revealed changes in p53-mediated transcriptional regulation in Nutlin-3-treated U2OS cells

Integrative analysis of chromatin immunoprecipitation-sequencing (ChIP-seq) data and microarray data was performed to illustrate the effect of Nutlin-3 on promoter selectivity and transcriptional regulation by the tumor suppressor p53 in U2OS human osteosarcoma cells. Raw data (accession number, GSE46642) were downloaded from Gene Expression Omnibus. Differential analyses were performed using package limma of R software. Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed for the differentially expressed genes (DEGs) using the Database for Annotation, Visualization and Integration Discovery. Integrative analysis of ChIP-seq data and microarray data were confirmed with ChIP-Array. A total of 565 DEGs were identified, including 373 upregulated genes and 192 downregulated genes. Genes involved in the p53 signaling pathway, cell cycle, DNA replication, cytokine-cytokine receptor interaction and melanoma were markedly over-represented in the DEGs. A total of 39 DEGs were directly regulated by p53 and two were the transcription factors (TFs), E2F2 and HOXA1. E2F2 regulated 25 DEGs, while HOXA1 regulated one DEG. The cell cycle, p53 signaling pathway, melanoma and pathways involved in cancer were enriched in the direct and indirect target genes. Changes in the p53-binding pattern induced by Nutlin-3 were described in the present study, which may advance the understanding of the regulatory network of p53 in osteosarcoma and aid in the development of novel therapies.
Current mode elementary motion perception neural cell

The paper proposes biologically inspired NN architecture that employs neural correlation of motion detection via a two-channel mechanism similar to the visual system of invertebrates that is capable of detecting the direction of motion. The correlation-based scheme with mutual lateral inhibition is adopted to implement current mode VLSI neuromorphic cells with the dynamics characterized by a first order nonlinear differential equation. Such cells act as elementary motion detectors (EMDs) sensitive to the direction of motion and can be implemented as a front-end section of a sophisticated object tracking system. Spatio-temporal responses of the VLSI model are investigated and simulation results are given.
Collaborative Filtering with Multi-component Rating for Recommender Systems

The dependency structure among the component ratings is discovered and incorporated into a mixture model. The parameters of the model were estimated using the Expectation Maximization algorithm. The algorithm was evaluated using data collected from Yahoo Movies. It was found that using multiple components leads to improved recommendations over using only one component when small amount of training data is used. However, when we have enough training data no gain from using additional components of the ratings was observed.
An asymptotic decider for robust and topologically correct triangulation of isosurfaces: topologically correct isosurfaces

A set of rules to generate a topologically correct and robust triangulation of isosurfaces across cells borders is presented. Ambiguous cases at cell faces are resolved with the asymptotic decider. The intersection of the isosurface with a face is a hyperbola. If the isovalue equals the asymptotic decider, the hyperbola at the face degenerates into two straight lines intersecting at the hyperbola's center. The center of the hyperbola is in this case a saddle point of the surface. A modified asymptotic decider is proposed to correctly handles this singular case. The method presented solves consistency problems of previously presented algorithms and resolves ambiguous cases efficiently without lookup tables.
Hydrocarbons in the upper troposphere and lower stratosphere observed from ACE‐FTS and comparisons with WACCM

Satellite measurements from the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE‐FTS) are used to examine the global, seasonal variations of several hydrocarbons, including carbon monoxide (CO), ethane (C2H6), acetylene (C2H2), and hydrogen cyanide (HCN). We focus on quantifying large‐scale seasonal behavior from the middle troposphere to the stratosphere, particularly in the tropics, and furthermore make detailed comparisons with the Whole Atmosphere Community Climate Model (WACCM) chemistry climate model (incorporating tropospheric photochemistry, time‐varying hydrocarbon emissions, and meteorological fields nudged from reanalysis). Comparisons with Microwave Limb Sounder (MLS) measurements of CO are also included to understand sampling limitations of the ACE‐FTS data and biases among observational data sets. Results show similar overall variability for CO, C2H6, and C2H2, with a semiannual cycle in the tropical upper troposphere related to seasonallyvarying sources and deep tropical convection, plus a maximum during Northern Hemisphere summer tied to the Asian monsoon anticyclone. These species also reveal a strong annual cycle above the tropical tropopause, tied to annual variations in the upward branch of Brewer‐Dobson circulation. HCN reveals substantial differences from the other species, due to a longer photochemical lifetime and a chemical sink associated with ocean surface contact, which produces a minimum in the tropical upper troposphere not observed in the other species. For HCN, transport to the stratosphere occurs primarily through the Asian summer monsoon anticyclone. Overall, the WACCM simulation is able to reproduce most of the large‐scale features observed in the ACE‐FTS data, suggesting a reasonable simulation of sources and large‐scale transport. The model is too low in the Southern Hemisphere subtropics during Austral spring, which indicates underestimate of biomass burning emissions and/or insufficient vertical transport in the model.
Logic-based Web services composition: from service description to process model

This paper introduces a method for automatic composition of semantic Web services using Linear Logic (LL) theorem proving. The method uses semantic Web service language (DAML-S) for external presentation of Web services, while, internally, the services are presented by extralogical axioms and proofs in LL. We use a process calculus to present the composite service formally. The process calculus is attached to the LL inference rules in the style of type theory. Thus the process model for a composite service can be generated directly from the proof. The subtyping rules that are used for semantic reasoning are presented with LL inference figures. We propose a system architecture where the DAML-S translator, the LL theorem prover and the semantic reasoner can operate together to fulfill the task. This architecture has been implemented in Java.
Design considerations for digital circuits using organic thin film transistors on a flexible substrate

Organic thin film transistor (OTFT) is the basic device for building analog and digital circuits and systems on a flexible substrate. Our studies show that, complementary design logic (CMOS), which is most common in MOSFET circuit design, is not suitable for OTFT circuits. In this work, we propose a new design logic that fits the characteristics of OTFT devices. Considering the fact that the mobility of the p-type OTFT is much better than the n-type OTFT, the proposed design logic uses mostly p-type OTFTs to implement logic functions. Circuit simulations have been done to compare the proposed design logic with other existing ones. The results show that the proposed design logic can improve the performance of the circuit by 2~4times, lower the energy dissipation by 2~6times, and reduce the circuit area by 2~10times
In-Vehicle Virtual Traffic Lights: A graphical user interface

Traffic control through an adequate location of devices can improve traffic flow and reduce collisions. Today's technology is capable of virtually conveying to the driver information that is traditionally displayed through traffic signs on the road. Relying on this technology we propose a novel approach to regulate traffic through the ubiquitous optimized management of individual intersections replacing the physical devices by Virtual Traffic Lights. We virtually prompt the driver with information related to traffic control and evaluate the user interface system with respect to safety and user acceptance to identify possible negative effects on the primary driving task. Results are promising since the driving performance using Virtual Traffic Lights did not significantly differ from the performance using conventional devices.
An integrated language modeling with n-gram model and WA model for speech recognition

As to traditional n-gram model, smaller n value is an inherent defect for estimating language probabilities in speech recognition, simply because that estimation could not be executed over farther word association but by means of short sequential word correlated information. This has an strong effect on the performance of speech recognition. This paper introduces an integrated language modeling with ngram model and word association model (abbreviated as WA model). This model integrated two kind of joint probabilities, traditional n-gram probability and word association probability, to estimate actual output probability. WA model are based on a combined probability estimation of orderly word association without distant and strict sequential limitation. In addition, two kinds of local linguistic constraints have also been incorporated into n-gram estimation for smoothing date sparse and adjusting special language unit score locally. A substantial improvement for the performance of Chinese phonetic-to-text transcription in speech recognition has been obtained.
A Quality Assessment Method of Single-Lead ECG Signal Based on Spectral Analysis

There are various disturbances in the acquisition of ECG signals. Signal quality assessment can evaluate the noise level and signal quality. Traditional ECG quality assessment methods are not suitable for single-lead ECG signal. In this paper, first, simulated ECG signals with simulated powerline and EMG interferences were used to analyze the spectrum distribution of ECG signal and the effects of the noise, after that, the single-lead ECG signal quality assessment method was proposed based on the preceding analysis, and then the method was tested with simulated and real ECG signals. Results showed that the method is suitable for single-lead ECG signal quality assessment, and it is simple and effective, can assess the signal quality roughly, meanwhile, the index QI (quality index) can quantitatively assess the signal quality.
Sample-Driven Inspections

The main objective of software inspections is to find faults in software artefacts. The benefits of inspections are reported from researchers as well as software organizations. In some studies, the fault detection in inspections has shown to be more efficient than other validation and verification activities. A problem, however, is that inspections sometimes are not as efficient and effective as expected. The reason may be that the software artefact inspected contains few faults. In addition, when a software project runs late, inspections are often not properly conducted. This leads to that many faults are not detected, valuable time is lost and people’s trust in inspections is affected negatively. SampleDriven Inspections (SDI) provides a solution to these problems. The concept of SDI uses sampling, inspection and resource scheduling to increase the efficiency of an inspection session. SDI uses a pre-inspection phase in order to determine which artefacts need more inspection time, i.e. which artefacts contain most faults. The second phase of SDI is a main inspection with a special attention on the artefacts with most faults. In this paper, the SDI method is described and empirical evidence is provided, which indicates that the method is appropriate to use. A Monte Carlo simulation is used to evaluate the proposed method. Furthermore, the paper discusses the results and important future research in
Towards Faster Response Time Models for Vertical Elasticity

Resource provisioning in cloud computing is typically coarse-grained. For example, entire CPU cores may be allocated for periods of up to an hour. The Resource-as-a-Service cloud concept has been introduced to improve the efficiency of resource utilization in clouds. In this concept, resources are allocated in terms of CPU core fractions, with granularities of seconds. Such infrastructures could be created using existing technologies such as lightweight virtualization using LXC or by exploiting the Xen hyper visor's capacity for vertical elasticity. However, performance models for determining how much capacity to allocate to each application are currently lacking. To address this deficit, we evaluate two performance models for predicting mean response times: the previously proposed queue length model and the novel inverse model. The models are evaluated using 3 applications under both open and closed system models. The inverse model reacted rapidly and remained stable even with targets as low as 0.5 seconds.
Applying process programming to the spiral model

The Spiral Model [Boehm,19S6; Belz,19S6] provides a candidate approach to determining the requirements, architecture, and design of a software process. The Spiral Model activity of determining mission objectives and constraints addresses the requirements for the process: the nature of the product required; budget and schedule constraints; organizational and procedural (e.g. contracting) constraints, etc. The Spiral Model "alternatives" activity addresses process architecture and design considerations: the use of prototypes, simulations and competitive concept definition phases; the choice of incremental products, cutover strategies, and integration strategies; the use of design-to-cost, independent V & V contractors, etc. The choice of process architecture is obtained in the Spiral Model by determining which alternative process architecture minimizes the risk of not meeting the system objectives within the system constraints.
Sedimentation of generalized systems of interacting particles. I. Solution of systems of complete Lamm equations

A very general approach to the chemical equilibria between many interacting molecules during sedimentation (boundary, band, or active enzyme) taking into account boundary conditions, cell geometry, equilibrium constants, diffusion, enzyme kinetics, etc., is presented. Through a Fortran program, the method has been applied to two very simple but typical cases. With only minor adjustments, the method presented here for sedimentation studies can be extended to all sorts of problems in which “pools” of various species are interacting with each other.
Towards From Manual to Automatic Semantic Annotation: Based on Ontology Elements and Relationships

Automatic annotation is offering a standards base for retrieving information from web services. It has been observed that many existing protocol e.g. Annotea did not support the fully automatic annotation directly or the process to be carried out needs pr ofessional developers (i.e. non-trivial protocol) such as KIM. In this paper a description of the architecture of the proposed system is given and a figurative structure is supplied. The diagrams that represent the structure will be described along with the main resources usage.
ROLE OF GALAXY MERGERS IN COSMIC STAR FORMATION HISTORY

We present a morphology study of intermediate-redshift (0.2 < z<1.2) luminous infrared galaxies (LIRGs) and general field galaxies in the GOODS fields using a revised asymmetry measurement method optimized for deep fields. By taking careful account of the importance of the underlying sky-background structures, our new method does not suffer from systematic bias and offers small uncertainties. By redshifting local LIRGs and low-redshift GOODS galaxies to different higher redshifts, we have found that the redshift dependence of the galaxy asymmetry due to surface-brightness dimming is a function of the asymmetry itself, with larger corrections for more asymmetric objects. By applying redshift-, infrared (IR)-luminosity- and optical-brightness-dependent asymmetry corrections, we have found that intermediate-redshift LIRGs generally show highly asymmetric morphologies, with implied merger fractions ∼50% up to z = 1.2, although they are slightly more symmetric than local LIRGs. For general field galaxies, we find an almost constant relatively high merger fraction (20%–30%). The B-band luminosity functions (LFs) of galaxy mergers are derived at different redshifts up to z = 1.2 and confirm the weak evolution of the merger fraction after breaking the luminosity–density degeneracy. The IR LFs of galaxy mergers are also derived, indicating a larger merger fraction at higher IR luminosity. The integral of the merger IR LFs indicates a dramatic evolution of the merger-induced IR energy density [(1 + z)∼(5−6)], and that galaxy mergers start to dominate the cosmic IR energy density at z ≳ 1.
Aspects of "Too" and "Enough" Constructions

Karttunen (1971) first pointed out that T&E can sometimes have ‘implicative’ readings, implying that their complement holds (in the case of enough)—or fails to hold (in the case of too)—in the actual world, instead of merely holding in some possible world(s). In uttering (2) for example, the speaker seems to imply that Jean actually left early (contrast this inference to the (lack of) inference that Mary actually drives in (1a)):
ProTherm and ProNIT: thermodynamic databases for proteins and protein–nucleic acid interactions

ProTherm and ProNIT are two thermodynamic databases that contain experimentally determined thermodynamic parameters of protein stability and protein–nucleic acid interactions, respectively. The current versions of both the databases have considerably increased the total number of entries and enhanced search interface with added new fields, improved search, display and sorting options. As on September 2005, ProTherm release 5.0 contains 17 113 entries from 771 proteins, retrieved from 1497 scientific articles (∼20% increase in data from the previous version). ProNIT release 2.0 contains 4900 entries from 273 research articles, representing 158 proteins. Both databases can be queried using WWW interfaces. Both quick search and advanced search are provided on this web page to facilitate easy retrieval and display of the data from these databases. ProTherm is freely available online at and ProNIT at .
Qualitative Spatial Reasoning about Sketch Maps

Sketch maps are an important spatial representation used in many geospatial-reasoning tasks. This article describes techniques we have developed that enable software to perform humanlike reasoning about sketch maps. We illustrate the utility of these techniques in the context of nuSketch Battlespace, a research system that has been successfully used in a variety of experiments. After an overview of the nuSketch approach and nuSketch Battlespace, we outline the representations of glyphs and sketches and the nuSketch spatial reasoning architecture. We describe the use of qualitative topology and Voronoi diagrams to construct spatial representations, and explain how these facilities are combined with analogical reasoning to provide a simple form of enemy intent hypothesis generation.
Reverse-engineering distributed applications to understand their behaviour

Understanding the behaviour of distributed applications is a very challenging task, due to their complexity. To manage this complexity, the top-down use of suitable abstraction hierarchies is frequently proposed. Given the size of distributed applications, manually deriving such abstraction hierarchies seems not realistic. This paper discusses tools that automate the derivation of suitable abstraction hierarchies and reports on initial experience with these tools. These abstraction hierarchies enable a top{down approach to the behaviour understanding task, keeping the overall amount of information manageable. We modiied an existing prototype visualization tool to provide abstract visualizations of an execution. A user can navigate through the abstraction hierarchies derived with our tools, displaying an execution at various levels of abstraction. Examples of such abstract visualizations for the execution of one speciic distributed application are given. In general , the abstractions derived represent meaningful parts of the application: they can be interpreted in terms of the application domain.
Quasistatic rheology of foams: I. Low strain response

A quasistatic simulation is used to study the mechanical response of a disordered, bidimensional aqueous foam submitted to an oscillating shear strain. The application of shear appears to progressively extend the elastic domain, i.e. the strain range within which no plastic process occurs. It is associated with the development of an irreversible normal stress difference, and a decrease in the shear modulus, which both are signatures of the appearance of anisotropy in the film network. Beyond this mechanical measurement, the evolution of the structural properties of the foam is investigated. We focus in particular on the structural energy defined as the minimum line-length energy under zero shear stress. For strain amplitude less than 0.5, this quantity is found to decay with the number of applied cycles as a result of the curing of topological defects. However, for higher strain amplitude, plastic events appear to increase the structural disorder and tend to gather near the shearing walls. This process is a precursor of the shear-banding transition observed in fully developed flows, which will be studied in the companion paper.
The perception of quinine taste intensity is associated with common genetic variants in a bitter receptor cluster on chromosome 12

The perceived taste intensities of quinine HCl, caffeine, sucrose octaacetate (SOA) and propylthiouracil (PROP) solutions were examined in 1457 twins and their siblings. Previous heritability modeling of these bitter stimuli indicated a common genetic factor for quinine, caffeine and SOA (22–28%), as well as separate specific genetic factors for PROP (72%) and quinine (15%). To identify the genes involved, we performed a genome-wide association study with the same sample as the modeling analysis, genotyped for approximately 610 000 single-nucleotide polymorphisms (SNPs). For caffeine and SOA, no SNP association reached a genome-wide statistical criterion. For PROP, the peak association was within TAS2R38 (rs713598, A49P, P = 1.6 × 10−104), which accounted for 45.9% of the trait variance. For quinine, the peak association was centered in a region that contains bitter receptor as well as salivary protein genes and explained 5.8% of the trait variance (TAS2R19, rs10772420, R299C, P = 1.8 × 10−15). We confirmed this association in a replication sample of twins of similar ancestry (P = 0.00001). The specific genetic factor for the perceived intensity of PROP was identified as the gene previously implicated in this trait (TAS2R38). For quinine, one or more bitter receptor or salivary proline-rich protein genes on chromosome 12 have alleles which affect its perception but tight linkage among very similar genes precludes the identification of a single causal genetic variant.