Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-layered Representation for Cell Signaling Pathways*

To understand complex signaling pathways and networks, it is necessary to develop a formal and structured representation of the available information in a format suitable for analysis by software tools. Due to the complexity and incompleteness of the current biological knowledge about cell signaling, such a device must be able to represent cellular pathways at differing levels of details, one level of information abstract enough to convey an essential signaling flow while hiding its details and another level of information detailed enough to explain the underlying mechanisms that account for the signaling flow described at a more abstract level. We have defined a formal ontology for cell-signaling events that allows us to describe these cellular pathways at various levels of abstraction. Using this formal representation, ROSPath (reactive oxygen species-mediated signaling pathway) database system has been implemented and made available on the web (rospath.ewha.ac.kr). ROSPath is a database system for reactive oxygen species (ROS)-mediated cell signaling pathways and signaling processes in molecular detail, which facilitates a comprehensive understanding of the regulatory mechanisms in signaling pathways. ROSPath includes growth factor-, stress-, and cytokine-induced signaling pathways containing about 500 unique proteins (mostly mammalian) and their related protein states, protein complexes, protein complex states, signaling interactions, signaling steps, and pathways. It is a web-based structured repository of information on the signaling pathways of interest and provides a means for managing data produced by large-scale and high-throughput techniques such as proteomics. Also, software tools are provided for querying, displaying, and analyzing pathways, thus furnishing an integrated web environment for visualizing and manipulating ROS-mediated cell-signaling events.
An Adaptive Algorithm Switching System for Image Based Object Registration

Most modern day image based object registration systems typically rely on one or two algorithms to perform registration across the entire spectrum of operating conditions. While such systems may perform well in one constrained environment, such as an indoor laboratory, they fail when used in varying conditions, such as outdoors. This paper proposes an adaptive system for image based object registration in unconstrained environments. There are two main components in this system. The first is a set of image metrics such as light levels and frequency as found in a fourier transform from a scene. The second is adaptive relationships between the metrics and a set of algorithms used for object registration, such as hue thresholding, Scale Invariant Feature Transforms and Edge Detection and Segmentation algorithms.
Topological Field Theories and formulae of Casson and Meng{Taubes

The goal of this paper is to give a new proof of a theorem of Meng and Taubes (9) that identies the Seiberg{Witten invariants of 3{manifolds with Milnor torsion. The point of view here will be that of topological quantum eld theory. In particular, we relate the Seiberg- Witten equations on a 3{manifold with the Abelian vortex equations on a Riemann surface. These techniques also give a new proof of the surgery formula for the Casson invariant, interpreted as an invariant of a homology S 2 S 1 . AMS Classication 57R57; 57M25, 57N10, 58D29
Officer strategies for managing interactions during police stops

ABSTRACT This paper draws on ethnographic research carried out in England and Wales soon after the Lawrence Inquiry to present an historical analysis of the strategies used by officers to manage interactions with suspects during police stops. The paper uses Goffman’s conceptual apparatus to explore how officers established order during interactions, monitored suspects’ demeanour closely to decide what was going on and how to proceed, and carefully controlled information to stage-manage encounters. By way of comparison, the paper describes interactions with known offenders who were stopped more regularly. The conclusions emphasise how officers exerted control during interactions through subtle uses of power, and discusses the policy implications.
New visco-elastic mechanism design for flexible joint manipulator

We describe a space-efficient visco-elastic mechanism design for a small lightweight flexible joint of a human-symbiotic robot arm. Human-symbiotic robots that can provide daily life support will be required in houses, offices, facilities, and other places. Since they will often make physical contact with humans, their arms should have mechanical flexible joints to absorb the contact force and follow the humanpsilas motion. Our design has two coaxial rotary elements: a torsion bar made from GUMMETAL and a rotary disk damper with the output hole at its center. These two elements are combined in parallel and coaxially, making our design highly space-efficient. This paper presents the specifications of the shear elastic characteristics of GUMMETAL measured in experiments using 1DOF (degree-of-freedom) test equipment. The results confirm that its shear elastic modulus is linear and has a small elastic hysteresis loop and our mechanism can provide the advantage for the robot servo control. Compared with the conventional design, our design can make a smaller lighter flexible joint.
A Network Gene-Based Framework for Detecting Advanced Persistent Threats

Advanced Persistent Threat (APT) poses a serious threat to cyber security, and its unique high unpredictability, deep concealment and grave harmfulness make the traditional network monitoring technology facing unprecedented challenges in the background of massive and complicated network traffic. This paper aimed for the urgent demand of APT network monitoring. Relying on the rapid development of big data analysis and cloud computing technology, to draw lessons from biology gene concept, we put forward a new connotation of the network gene to depict the semantic-rich behavior characteristics pattern of network applications. Through the organic combination of network protocol reverse analysis and the network data stream processing technology, we established a set of basic theories and technical architecture of network gene construction and calculation, forming a new detection framework for APTs to support the construction of intrusion-tolerant network ecological environment.
Very late activation antigens (VLA) are human leukocyte-neuronal crossreactive cell surface antigens

The antigenic relationship between human neuronal and lymphocyte cell surface antigens has been analyzed using heteroantisera raised against human peripheral blood mononuclear cells (PBMC). The specificities of the crossreactive antigens were examined by immunoprecipitation of 125I- labeled SK-N-SH cultured neuronal cells using rabbit anti-PBMC (RAPBMC) sera and compared to known specificities using mAb. The predominant reactivity of each rabbit antiserum tested against SK-N-SH cells was with three molecules of 130,000, 160,000, and 180,000 Mr. These three chains comigrated with three molecules precipitated with the very late activation antigen (VLA)-specific mAb A-1A5. Sequential precipitations with mAb A-1A5 established that the three RAPBMC-precipitated bands were members of the VLA complex. This was confirmed by two-dimensional PAGE of the RAPBMC and A-1A5 immunoprecipitates, which were indistinguishable from one another. The two-dimensional pattern was more complex than was anticipated from the heterodimeric model of VLA chain association, and suggests an additional 130,000 Mr component of VLA. The three chains of the VLA complex precipitated by RAPBMC or mAb A-1A5 from SK-N-SH neurons closely resembled the VLA pattern present on activated T cells, including the 180,000 Mr activation-specific alpha 1 chain recognized by mAb TS2/7. Normal brain cell membranes also contain VLA molecules that are precipitated by RAPBMC and mAb A-1A5. Thus the VLA complex provides potentially important shared immunogens on human neurons and T cells.
Code for prompt numerical computation of the leading order GPD evolution

This paper describes the design and work of a set of computer routines capable for numerical computation of generalized parton distributions (GPDs) evolution at the leading order. The main intention of this work is to present a fast-working computer code making possible fitting of GPDs parameters to the data on hard electron-nucleon scattering.
Automated Coverage-Driven Test Data Generation Using Dynamic Symbolic Execution

Recently code transformations or tailored fitness functions are adopted to achieve coverage (structural or logical criterion) driven testing to ensure software reliability. However, some internal threats like negative impacts on underlying search strategies or local maximum exist. So we propose a dynamic symbolic execution (DSE) based framework combined with a path filtering algorithm and a new heuristic path search strategy, i.e., predictive path search, to achieve faster coverage-driven testing with lower testing cost. The empirical experiments (three open source projects and two industrial projects) show that our approach is effective and efficient. For the open source projects w.r. t branch coverage, our approach in average reduces 25.5% generated test cases and 36.3% solved constraints than the traditional DSE-based approach without path filtering. And the presented heuristic strategy, on the same testing budget, improves the branch coverage by 26.4% and 35.4% than some novel search strategies adopted in KLEE and CREST.
Slip Model for the 25 November 2016 Mw 6.6 Aketao Earthquake, Western China, Revealed by Sentinel-1 and ALOS-2 Observations

On 25 November 2016 (UTC 14:24:30), an Mw 6.6 dextral strike-slip earthquake ruptured Aketao county in the northwestern portion of the Kongur Shan extensional system, western China. We extracted surface deformation maps and investigated the distribution of the coseismic slip of the 2016 Aketao earthquake by exploiting the Interferometric Synthetic Aperture Radar data imaged by the Sentinel-1 satellites of the European Space Agency and the ALOS-2 satellite of the Japanese Aerospace Exploration Agency. Assuming the crust of the earth is an elastic half-space homogeneous medium, the best fitting slip model suggests a dip angle of 78° for the seismogenic fault. The rupture of the 2016 Aketao earthquake may have consisted of two sub-events that occurred in rapid succession within a few seconds, resulting in two large discrete asperities with maximum slip of ~0.85 m, which were separated by a ~6 km-wide small slip gap. The maximum slip for the sub-event near the epicenter was mainly concentrated at a depth of ~10 km and that of the other at a depth of ~5 km. The estimated total seismic moment from the optimal slip model is 1.58 × 1019 N•m, corresponding to an event with a moment magnitude of 6.74. More than 65% of the aftershocks occurred in the areas of increased Coulomb failure stress, in which the stress was estimated to have been increased by at least 0.1 bar. Matching the potential barrier on the fault with the depth distribution of aftershocks implies that friction on the causative fault was heterogeneous, which may play a primary role in controlling the active behavior of the Muji fault.
Prosthetic groups of the NADH-dependent nitrite reductase from Escherichia coli K12.

A substantially improved purification of Escherichia coli NADH-dependent nitrite reductase was obtained by purifying it in presence of 1 mM-NO2- and 10 microM-FAD. The enzyme was obtained in 20% yield with a maximum specific activity of 1.04 kat . kg-1: more than 95% of this sample subjected to sodium dodecyl sulphate/polyacrylamide-gel electrophoresis migrated as a single band of protein. This highly active enzyme contained one non-covalently bound FAD molecule, and, probably, 5 Fe atoms and 4 acid-labile S atoms per subunit. No FMN, covalently bound flavin or Mo was detected. The spectrum of the enzyme shows absorption maxima at 386, 455, 530 and about 575 nm with a shoulder at 480--490 nm. The Soret-band/alpha-band absorbance ratio is about 4:1. These spectral features are characteristic of sirohaem, apart from the maximum at 455nm, which is attributed to flavin. The enzyme also catalyses the NADH-dependent reduction of horse heart cytochrome c, 2,6-dichlorophenol-indophenol and K3Fe(CN)6. The presence of sirohaem in E. coli nitrite reductase explains the apparent identity of the cysG and nirB gene of E. coli and inability of hemA mutants to reduce nitrite.
Combining Erasure-Code and Replication Redundancy Schemes for Increased Storage and Repair Efficiency in P 2 P Storage Systems

This paper introduces a new family of redundancy schemes called replicated erasure codes (REC), which combine the storage-space efficiency of erasure codes and the repairtraffic efficiency of replications. A formal model for analyzing the storage and repair-traffic costs under availability and persistency constraints is also developed. It is shown that under parameters that characterize common P2P environments, REC generally achieves better results than each of the two methods separately.
Academic development to support the internationalization of the curriculum (IoC): a qualitative research synthesis

ABSTRACT While the literature acknowledges the central role of academics in internationalization of the curriculum (IoC), little has been published regarding training of academic developers themselves to support IoC initiatives. However, higher education institutions around the globe are responding to strategic demands for IoC that prepare students as global citizens. We employed qualitative research synthesis to identify journal articles that consider academic development to support IoC. Despite their diversity, we found common themes in the five selected studies. We weave these themes with Betty Leask’s five-stage model of the IoC process, and Cynthia Joseph’s call for a pedagogy of social justice.
A Research in Performances of Non-normal ARCH Type Models and of VaR Measure

This paper, taking the Shanghai Stock Exchange (SSE) Composite Index as the sample, constructs ARCH models under the assumptions of normal residuals and non-normal residuals and compares the forecast performances of volatility of normal and non-normal ARCH models and the performance of VaR measure to demonstrate the effects of the distribution assumptions on GARCH model's forecasting ability and risk measure.
Numerical Modeling and Experimental Validation by Calorimetric Detection of Energetic Materials Using Thermal Bimorph Microcantilever Array: A Case Study on Sensing Vapors of Volatile Organic Compounds (VOCs)

Bi-layer (Au-Si3N4) microcantilevers fabricated in an array were used to detect vapors of energetic materials such as explosives under ambient conditions. The changes in the bending response of each thermal bimorph (i.e., microcantilever) with changes in actuation currents were experimentally monitored by measuring the angle of the reflected ray from a laser source used to illuminate the gold nanocoating on the surface of silicon nitride microcantilevers in the absence and presence of a designated combustible species. Experiments were performed to determine the signature response of this nano-calorimeter platform for each explosive material considered for this study. Numerical modeling was performed to predict the bending response of the microcantilevers for various explosive materials, species concentrations, and actuation currents. The experimental validation of the numerical predictions demonstrated that in the presence of different explosive or combustible materials, the microcantilevers exhibited unique trends in their bending responses with increasing values of the actuation current.
Estimation of Land Surface Temperature under Cloudy Skies Using Combined Diurnal Solar Radiation and Surface Temperature Evolution

Land surface temperature (LST) is a key parameter in the interaction of the land-atmosphere system. However, clouds affect the retrieval of LST data from thermal-infrared remote sensing data. Thus, it is important to determine a method for estimating LSTs at times when the sky is overcast. Based on a one-dimensional heat transfer equation and on the evolution of daily temperatures and net shortwave solar radiation (NSSR), a new method for estimating LSTs under cloudy skies (Tcloud) from diurnal NSSR and surface temperatures is proposed. Validation is performed against in situ measurements that were obtained at the ChangWu ecosystem experimental station in China. The results show that the root-mean-square error (RMSE) between the actual and estimated LSTs is as large as 1.23 K for cloudy data. A sensitivity analysis to the errors in the estimated LST under clear skies (Tclear) and in the estimated NSSR reveals that the RMSE of the obtained Tcloud is less than 1.5 K after adding a 0.5 K bias to the actual Tclear and 10 percent NSSR errors to the actual NSSR. Tcloud is estimated by the proposed method using Tclear and NSSR products of MSG-SEVIRI for southern Europe. The results indicate that the new algorithm is practical for retrieving the LST under cloudy sky conditions, although some uncertainty exists. Notably, the approach can only be used during the daytime due to the assumption of the variation in LST caused by variations in insolation. Further, if there are less than six Tclear observations on any given day, the method cannot be used.
Pna Probability, Networks and Algorithms Probability, Networks and Algorithms Inter-cell Scheduling in Wireless Data Networks Inter-cell Scheduling in Wireless Data Networks Inter-cell Scheduling in Wireless Data Networks

CWI's research has a theme-oriented structure and is grouped into four clusters. Listed below are the names of the clusters and in parentheses their acronyms. ABSTRACT Over the past few years, the design and performance of channel-aware scheduling strategies have attracted huge interest. In the present paper we examine a somewhat different notion of scheduling, namely coordination of transmissions among base stations, which has received little attention so far. The inter-cell coordination comprises two key elements: (i) interference avoidance; and (ii) load balancing. The interference avoidance involves coordinating the activity phases of interfering base stations so as to increase transmission rates. The load balancing aims at diverting traffic from heavily-loaded cells to lightly-loaded cells. We consider a dynamic scenario where users come and go over time as governed by the arrival and completion of random data transfers, and evaluate the potential capacity gains from inter-cell coordination in terms of the maximum amount of traffic that can be supported for a given spatial traffic pattern. We also show that simple adaptive strategies achieve the maximum capacity without the need for any explicit knowledge of the traffic characteristics. Numerical experiments demonstrate that inter-cell scheduling may provide significant capacity gains, the relative contribution from interference avoidance vs. load balancing depending on the configuration and the degree of load imbalance in the network. Abstract— Over the past few years, the design and performance of channel-aware scheduling strategies have attracted huge interest. In the present paper we examine a somewhat different notion of scheduling, namely coordination of transmissions among base stations, which has received little attention so far. The inter-cell coordination comprises two key elements: (i) interference avoidance; and (ii) load balancing. The interference avoidance involves coordinating the activity phases of interfering base stations so as to increase transmission rates. The load balancing aims at diverting traffic from heavily-loaded cells to lightly-loaded cells. We consider a dynamic scenario where users come and go over time as governed by the arrival and completion of random data transfers, and evaluate the potential capacity gains from inter-cell coordination in terms of the maximum amount of traffic that can be supported for a given spatial traffic pattern. We also show that simple adaptive strategies achieve the maximum capacity without the need for any explicit knowledge of the traffic characteristics. Numerical experiments demonstrate that inter-cell scheduling may provide significant capacity gains, the relative contribution from interference avoidance vs. load balancing …
On the Security of Iterated Hashing based on Forgery-resistant Compression Functions

In this paper we re-examine the security notions suggested for hash functions, with an emphasis on the delicate notion of second preimage resistance. We start by showing that, in the random oracle model, both Merkle-Damgard and Haifa achieve second preimage resistance beyond the birthday bound, and actually up to the level of known generic attacks, hence demonstrating the optimality of Haifa in this respect. We then try to distill a more elementary requirement out of the compression function to get some insight on the properties it should have to guarantee the second preimage resistance of its iteration. We show that if the (keyed) compression function is a secure FIL-MAC then the Merkle-Damgard mode of iteration (or Haifa) still maintains the same level of second preimage resistance. We conclude by showing that this “new” assumption (or security notion) implies the recently introduced Preimage-Awareness while ensuring all other classical security notions for hash functions.
Alignment-free sequence comparison with vector quantization and hidden Markov models

We introduce the concept of multiresolutions using vector quantization and hidden Markov models as a basis for alignment-free comparison of sequences. Different similarity measures can be discovered at different resolutions of the two sequences. The proposed approach provides a new aspect for studying the complexity of biological data and is effective for real-time processing.
Adding a conscience to competitive learning

There are a number of neural networks that self-organize on the basis of what has come to be known as Kohonen learning. The author introduces a modification of Kohonen learning that provides rapid convergence and improved representation of the input data. In many areas of pattern recognition, statistical analysis, and control, it is essential to form a nonparametric model of a probability density function p(x). The purpose of the improvement to Kohonen learning presented is to form a better approximation of p(x). Simulation results are presented to illustrate the operation of this competitive learning algorithm. <<ETX>>
Decision fusion for frontal face verification

It has been established that the combination of a set of classifiers designed for a given pattern recognition problem may achieve higher recognition/classification rates than any of the classifiers taken individually. One of the contributing factor for the improvement is the rule applied to get a unified decision and the diversity of the classifiers. Principal Components Analysis (PCA) and Linear Discriminant Analysis (LDA) are two popular approaches in face recognition and verification. The authors will demonstrate a verification performance in which the fusion of both methods produces an improved rate compared to individual performance. Tests are carried out on FERET (Facial Recognition Technology) database using a modified protocol. A major drawback in applying LDA is that it requires a large set of individual face images sample to extract the intra-class variation. Performance is presented as the rate of verification when false acceptance rate is zero, in other words, no impostors allowed. Results using fusion of three verification experts show improvement compared with the best individual expert.