Miracle-dz/UniFAR-FTUs huggingface dataset:
The Production Logic Programs Approach , in a Nutshell : Foundations for Semantically Interoperable Web Rules

We overview our foundational work on a knowledge representation (KR) approach of web rules that are semantically interoperable between all four of the currently most commercially important families of rule systems, including production rules, relational database management systems, event-condition-action rules, and Prolog. Called here Production Logic Programs (PLP), the approach combines high degrees of expressiveness, scaleability, and incremental/modular implementability. Its KR is based on declarative logic programs, extending Datalog with several major web-izing and expressive features. These include, notably, a new approach to actions and tests via procedural attachments – in the manner of production rules but with declarative semantics. The PLP approach includes smoothly and powerfully combining rules with ontologies drawn from the currently most commercially important kinds of web-shared semantic ontologies. The PLP approach has been piloted and evolved in a number of important rule formats, tools, and efforts – including RuleML, SWRL, SWSL/SWSF, WSML/WRL, and SweetRules. An advanced set of PLP capabilities have already been implemented in open source and used to prototype a variety of e-business application scenarios.
Detection and defense mechanisms against DDoS attacks: A review

Distributed Denial of Service (DDoS) attacks is the most challenging problems for network security. The attacker uses large number of compromised hosts to launch attack on victim. Various DDoS defense mechanisms aim at detecting and preventing the attack traffic. The effectiveness depends on the point of deployment. The purpose of this paper is to study various detection and defense mechanisms, their performance and deployment characteristics. This helps in understanding which defense should be deployed under what circumstances and at what locations.
A STUDY ON CONTRACTUAL INFORMATION SHARING SYSTEM

Traditionally, the contractually required data are delivered with paper format, which could cause many problems such as waste of papers, difficulties in managing documents, error-prone in data processing, etc. If the owner and contractors in a construction project do not share the information specified in their contract efficiently and consistently, their communication cannot be effective and correct. Such problems can be improved by using advanced information technologies. This paper presents the concept of a model-based CITIS system for establishing a contractual sharing information system. By making use of Object-Oriented techniques, this research then proposes Contractual Document Information Model (CDIM).
NIST/Sandia/ICDD Electron Diffraction Database: A Database for Phase Identification by Electron Diffraction

A new database containing crystallographic and chemical information designed especially for application to electron diffraction search/match and related problems has been developed. The new database was derived from two well-established x-ray diffraction databases, the JCPDS Powder Diffraction File and NBS CRYSTAL DATA, and incorporates 2 years of experience with an earlier version. It contains 71,142 entries, with space group and unit cell data for 59,612 of those. Unit cell and space group information were used, where available, to calculate patterns consisting of all allowed reflections with d-spacings greater than 0.8 A for ~ 59,000 of the entries. Calculated patterns are used in the database in preference to experimental x-ray data when both are available, since experimental x-ray data sometimes omits high d-spacing data which falls at low diffraction angles. Intensity data are not given when calculated spacings are used. A search scheme using chemistry and r-spacing (reciprocal d-spacing) has been developed. Other potentially searchable data in this new database include space group, Pearson symbol, unit cell edge lengths, reduced cell edge length, and reduced cell volume. Compound and/or mineral names, formulas, and journal references are included in the output, as well as pointers to corresponding entries in NBS CRYSTAL DATA and the Powder Diffraction File where more complete information may be obtained. Atom positions are not given. Rudimentary search software has been written to implement a chemistry and r-spacing bit map search. With typical data, a full search through ~ 71,000 compounds takes 10~20 seconds on a PDP 11/23-RL02 system.
Emerging Roles of Human Prostatic Acid Phosphatase

Prostate cancer is one of the most prevalent non-skin related cancers. It is the second leading cause of cancer deaths among males in most Western countries. If prostate cancer is diagnosed in its early stages, there is a higher probability that it will be completely cured. Prostatic acid phosphatase (PAP) is a non-specific phosphomonoesterase synthesized in prostate epithelial cells and its level proportionally increases with prostate cancer progression. PAP was the biochemical diagnostic mainstay for prostate cancer until the introduction of prostate-specific antigen (PSA) which improved the detection of early-stage prostate cancer and largely displaced PAP. Recently, however, there is a renewed interest in PAP because of its usefulness in prognosticating intermediate to high-risk prostate cancers and its success in the immunotherapy of prostate cancer. Although PAP is believed to be a key regulator of prostate cell growth, its exact role in normal prostate as well as detailed molecular mechanism of PAP regulation is still unclear. Here, many different aspects of PAP in prostate cancer are revisited and its emerging roles in other environment are discussed.
Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm

This article describes the PROSPECTOR_3 threading algorithm, which combines various scoring functions designed to match structurally related target/template pairs. Each variant described was found to have a Z‐score above which most identified templates have good structural (threading) alignments, Zstruct (Zgood). ‘Easy’ targets with accurate threading alignments are identified as single templates with Z > Zgood or two templates, each with Z > Zstruct, having a good consensus structure in mutually aligned regions. ‘Medium’ targets have a pair of templates lacking a consensus structure, or a single template for which Zstruct < Z < Zgood. PROSPECTOR_3 was applied to a comprehensive Protein Data Bank (PDB) benchmark composed of 1491 single domain proteins, 41–200 residues long and no more than 30% identical to any threading template. Of the proteins, 878 were found to be easy targets, with 761 having a root mean square deviation (RMSD) from native of less than 6.5 Å. The average contact prediction accuracy was 46%, and on average 17.6 residue continuous fragments were predicted with RMSD values of 2.0 Å. There were 606 medium targets identified, 87% (31%) of which had good structural (threading) alignments. On average, 9.1 residue, continuous fragments with RMSD of 2.5 Å were predicted. Combining easy and medium sets, 63% (91%) of the targets had good threading (structural) alignments compared to native; the average target/template sequence identity was 22%. Only nine targets lacked matched templates. Moreover, PROSPECTOR_3 consistently outperforms PSIBLAST. Similar results were predicted for open reading frames (ORFS) ≤200 residues in the M. genitalium, E. coli and S. cerevisiae genomes. Thus, progress has been made in identification of weakly homologous/analogous proteins, with very high alignment coverage, both in a comprehensive PDB benchmark as well as in genomes. Proteins 2004;55:000–000. © 2004 Wiley‐Liss, Inc.
Diversity of the Germination Apparatus in Clostridium botulinum Groups I, II, III, and IV

Clostridium botulinum is a highly dangerous pathogen that forms very resistant endospores that are ubiquitous in the environment, and which, under favorable conditions germinate to produce vegetative cells that multiply and form the exceptionally potent botulinum neurotoxin. To improve the control of botulinum neurotoxin-forming clostridia, it is important to understand the mechanisms involved in spore germination. Here we present models for spore germination in C. botulinum based on comparative genomics analyses, with C. botulinum Groups I and III sharing similar pathways, which differ from those proposed for C. botulinum Groups II and IV. All spores germinate in response to amino acids interacting with a germinant receptor, with four types of germinant receptor identified [encoded by various combinations of gerA, gerB, and gerC genes (gerX)]. There are three gene clusters with an ABC-like configuration; ABC [gerX1], ABABCB [gerX2] and ACxBBB [gerX4], and a single CA-B [gerX3] gene cluster. Subtypes have been identified for most germinant receptor types, and the individual GerX subunits of each cluster show similar grouping in phylogenetic trees. C. botulinum Group I contained the largest variety of gerX subtypes, with three gerX1, three gerX2, and one gerX3 subtypes, while C. botulinum Group III contained two gerX1 types and one gerX4. C. botulinum Groups II and IV contained a single germinant receptor, gerX3 and gerX1, respectively. It is likely that all four C. botulinum Groups include a SpoVA channel involved in dipicolinic acid release. The cortex-lytic enzymes present in C. botulinum Groups I and III appear to be CwlJ and SleB, while in C. botulinum Groups II and IV, SleC appears to be important.
Test Generation for Asynchronous Sequential Digital Circuits

The dissertation thesis is aimed at test generation for asynchronous sequential digital circuits, contributes to their timeand cost-effective testing, and indirectly supports their wider application, which improves the performance, the power consumption and the electromagnetic emission of future digital circuits. The main scientific contribution is design of the new test generator (optimized for test length and area overhead) for wide spectrum of asynchronous sequential digital circuits. The contributions are identification of unacceptable signal transitions before test generation, reduced number of generated test patterns for combinational representation, effective state justification on the gate level, fast (optimized for test length) sequential fault propagation to outputs and effective fault simulation. Experimental results confirmed the generation of optimal tests with good fault coverage and without application of any method for increasing the testability. The developed methods can be used with wider spectrum of circuits than other recently developed test generators, and at the same time their effectiveness ensures fast test generation.
Biexcitability and Bursting Mechanisms in Neural and Genetic Circuits

Abstract This paper compares mechanisms for generating repetitive spikes (bursts) in neural and transcriptional circuits. Neurons generate bursts followed by refractory periods controlled by ion channels in the membrane. In contrast, in gene transcription the bursts occur during a short time period followed by silent periods regulated by sis-regulatory elements. The role of excitability in producing different patterns of bursts is discussed by comparing the topology of a neural model with natural and synthetic transcriptional genetic circuits. In particular, a special bi-excitable architecture which embeds two excitable states are compared in these systems.
Sensor-based online hand gesture recognition on multi-core DSPs

In this paper we propose a novel approach for parallelized computation of sensor-based online hand gesture recognition on multi-core DSPs. To this end, we dispatch different windows of sensor data segments to different groups of cores. Within a group of cores, we distribute the template-based recognition on the basis of reference recordings. In order to model different configurations of our approach, we use extended data flow graphs. Our experiments show real time performance making our approach suitable for online hand gesture recognition.
Development of two degrees of freedom deterministic parallel robotic arm unit

This paper investigates the development of an exact constraint parallel robotic arm unit. In addition to the advantages of simple structure and compact size, the six points exactly constrained parallel robotic arm unit is both statically and kinematicaly deterministic, thus is more suitable for precision position application. Theoretical analysis based on the principle of exact constraint is given to explore the degree of freedom and constrain pattern of the parallel robotic arm unit. Furthermore, the orientation adjusting principles at various input statuses are presented to promote the orientation process. The performances of the fabricated parallel robotic arm unit are confirmed by experimental studies. As the parallel robotic arm unit has relatively small workspace, numerous parallel robotic arm units, with various sizes, should be cooperated to achieved the desired workspace.
A Configuration-Independent Score-Based Benchmark for Distributed Databases

The business potential of big data is leading to a data-driven economy, where low-cost and low-latency data analysis represents a major competitive advantage. The research community has proposed many technological solutions for big data, such as NoSQL databases, which are difficult to evaluate and compare via standard IT procurement procedures. In addition, lack of competences in big data domains make procurement of big data solutions a tedious and uncertain process, which might impair the success of a business. In this paper, we present a score-based benchmark for distributed databases, which supports adopters in selecting a solution that fits their needs. The proposed benchmark is independent from the configurations of the specific database and deployment environment, requires low effort on the part of end users, is extensible and can be applied to both SQL and NoSQL databases, can be used to evaluate databases according to different properties (e.g., performance, consistency), and can be integrated with existing benchmarks to reduce the burden of their execution. We experimentally evaluate our methodology to validate its effectiveness.
You See, the Ends Don’t Justify the Means

We conducted three experiments indicating that characteristically deontological judgments—here, disapproving of sacrificing one person for the greater good of others—are preferentially supported by visual imagery. Experiment 1 used two matched working memory tasks—one visual, one verbal—to identify individuals with relatively visual cognitive styles and individuals with relatively verbal cognitive styles. Individuals with more visual cognitive styles made more deontological judgments. Experiment 2 showed that visual interference, relative to verbal interference and no interference, decreases deontological judgment. Experiment 3 indicated that these effects are due to people’s tendency to visualize the harmful means (sacrificing one person) more than the beneficial end (saving others). These results suggest a specific role for visual imagery in moral judgment: When people consider sacrificing someone as a means to an end, visual imagery preferentially supports the judgment that the ends do not justify the means. These results suggest an integration of the dual-process theory of moral judgment with construal-level theory.
A multilevel adaptive sparse grid stochastic collocation approach to the non-smooth forward propagation of uncertainty in discretized problems

This work proposes a scheme for significantly reducing the computational complexity of discretized problems involving the non-smooth forward propagation of uncertainty by combining the adaptive hierarchical sparse grid stochastic collocation method (ALSGC) with a hierarchy of successively finer spatial discretizations (e.g. finite elements) of the underlying deterministic problem. To achieve this, we build strongly upon ideas from the Multilevel Monte Carlo method (MLMC), which represents a well-established technique for the reduction of computational complexity in problems affected by both deterministic and stochastic error contributions. The resulting approach is termed the Multilevel Adaptive Sparse Grid Collocation (MLASGC) method. Preliminary results for a low-dimensional, non-smooth parametric ODE problem are promising: the proposed MLASGC method exhibits an error/cost-relation of $\varepsilon \sim t^{-0.95}$ and therefore significantly outperforms the single-level ALSGC ($\varepsilon \sim t^{-0.65}$) and MLMC methods ($\varepsilon \lesssim t^{-0.5}$).
MCMC-based posterior independence approximation for RFS multitarget particle filters

The objective of this paper is to approximate the unlabelled posterior random finite set (RFS) density in multitarget tracking (MTT) using particle filters (PFs). The unlabelled posterior can be equivalently represented by any labelled density that belongs to the posterior RFS family. For the limited number of particles used in practice, PFs that assume posterior independence among target states outperform those without it. Consequently, we can improve the PF approximation by aiming at the labelled density within the posterior RFS family whose target states are as independent as possible. In this paper, we focus on the case of fixed and known number of targets and propose an algorithm based on Markov chain Monte Carlo (MCMC) that pursues this aim. This algorithm can be added to any PF with posterior independence assumption.
Absence of Protoheme IX Farnesyltransferase CtaB Causes Virulence Attenuation but Enhances Pigment Production and Persister Survival in MRSA

The membrane protein CtaB in S. aureus is a protoheme IX farnesyltransferase involved in the synthesis of the heme containing terminal oxidases of bacterial respiratory chain. In this study, to assess the role of CtaB in S. aureus virulence, pigment production, and persister formation, we constructed a ctaB mutant in the methicillin-resistant Staphylococcus aureus (MRSA) strain USA500. We found that deletion of ctaB attenuated growth and virulence in mice but enhanced pigment production and formation of quinolone tolerant persister cells in stationary phase. RNA-seq analysis showed that deletion of ctaB caused decreased transcription of several virulence genes including RNAIII which is consistent with its virulence attenuation. In addition, transcription of 20 ribosomal genes and 24 genes involved in amino acid biosynthesis was significantly down-regulated in the ctaB knockout mutant compared with the parent strain. These findings suggest the importance of heme biosynthesis in virulence and persister formation of S. aureus.
On meeting P2P streaming bandwidth demand with limited supplies

As a basic requirement of live peer-to-peer multimedia streaming sessions, the streaming playback rate needs to be strictly enforced at each of the peers. In real-world peer-to-peer streaming sessions with very large scales, the number of streaming servers for each session may not be easily increased, leading to a limited supply of bandwidth. To scale to a large number of peers, one prefers to regulate the bandwidth usage on each of the overlay links in an optimal fashion, such that limited supplies of bandwidth may be maximally utilized. In this paper, we propose a decentralized bandwidth allocation algorithm that can be practically implemented in peer-to-peer streaming sessions. Given a mesh P2P topology, our algorithm explicitly reorganizes the bandwidth of data transmission on each overlay link, such that the streaming bandwidth demand is always guaranteed to be met at any peer in the session, without depending on any a priori knowledge of available peer upload or overlay link bandwidth. Our algorithm is especially useful when there exists no or little surplus bandwidth supply from servers or other peers. It adapts well to time-varying availability of bandwidth, and guarantees bandwidth supply for the existing peers during volatile peer dynamics. We demonstrate the effectiveness of our algorithm with in-depth simulation studies.
Promoting Interactions in Preschoolers with Autism Spectrum Disorder via Peer-mediated Intervention.

The purpose of this dissertation is to develop and examine the efficacy of a social skills intervention program that was delivered to preschoolers with Autism Spectrum Disorder (ASD) via typically-developing peers. According to the Diagnostic and Statistical Manual of Mental Disorders (5 th ed.; DSM 5; American Psychiatric Association, 2013), one of the defining characteristics of ASD is a marked impairment in social interaction. Children with ASD often lack the ability to use social cues and frequently fail to develop peer relationships that are appropriate to their developmental level. In this model, a speech language pathologist and three early childhood educators trained typicallydeveloping peers to engage children with ASD in play. Three preschool children with ASD and six peers participated in five social skills training sessions followed by 12 implementation sessions (six sessions for each peer). The peer intervention took place in early childhood classrooms during play sessions with blocks and play dough. A single-subject multiple baseline design across subjects was used to determine the effects of the intervention. All three children
Implementation and Performance Evaluation of a Safe Runtime System in Cyclone

In this paper we outline the implementation of a simple Scheme interpreter and a copying garbage collector that manages the memory allocated by the interpreter. The entire system including the garbage collector is implemented in Cyclone [11], a safe dialect of C, which supports safe and explicit memory management. We describe the high-level design of the system, report preliminary benchmarks, and compare our approach to other Scheme systems. Our preliminary benchmarks demonstrate that one can build a system with reasonable performance when compared to other approaches that guarantee safety. More importantly we can signican tly reduce the amount of unsafe code needed to implement the system. Our benchmarks also identify some key algorithmic bottlenecks related to our approach that we hope to address in the future. Although most of the theoretical ideas in this work are not by themselves novel, there are a few interesting variations and combinations of the existing literature we will discuss. However, the primary motivation and goal is to build a realistic working system that puts all the existing theory to test against existing systems which rely on larger amounts of unsafe code in their implementation.
PKA Inhibitor H89 (N-[2-p-bromocinnamylamino-ethyl]-5-isoquinolinesulfonamide) Attenuates Synaptic Dysfunction and Neuronal Cell Death following Ischemic Injury

The cyclic AMP-dependent protein kinase (PKA), which activates prosurvival signaling proteins, has been implicated in the expression of long-term potentiation and hippocampal long-term memory. It has come to light that H89 commonly known as the PKA inhibitor have diverse roles in the nervous system that are unrelated to its role as a PKA inhibitor. We have investigated the role of H89 in ischemic and reperfusion injury. First, we examined the expression of postsynaptic density protein 95 (PSD95), microtubule-associated protein 2 (MAP2), and synaptophysin in mouse brain after middle cerebral artery occlusion injury. Next, we examined the role of H89 pretreatment on the expression of brain-derived neurotrophic factor (BDNF), PSD95, MAP2, and the apoptosis regulators Bcl2 and cleaved caspase-3 in cultured neuroblastoma cells exposed to hypoxia and reperfusion injury. In addition, we investigated the alteration of AKT activation in H89 pretreated neuroblastoma cells under hypoxia and reperfusion injury. The data suggest that H89 may contribute to brain recovery after ischemic stroke by regulating neuronal death and proteins related to synaptic plasticity.