Miracle-dz/UniFAR-FTUs huggingface dataset:
Ellipse-based modelling of hysteresis in a smart actuator

This work investigates the elliptical modelling of hysteresis in a smart actuator. The actuator in question is a rolled dielectric elastomer (DE) tubular actuator. The actuator actually demonstrates asymmetric hysteresis behaviour due to an inherent nonlinear voltage-strain characteristic. In this contribution the dynamic asymmetric hysteretic characteristics of the voltage driven tubular actuator are initially decomposed into the nonlinear static voltage-strain characteristic in series with a symmetric hysteretic characteristic. A gain scheduling term is introduced to compensate for the nonlinear voltage-strain behaviour of the actuator thereby producing the symmetric hysteretic characteristic of the actuator. The symmetric hysteresis characteristic seems to be elliptical in nature. In this contribution the modelling of this ‘decomposed’ symmetric hysteresis characteristic is investigated using an ellipse-based modeling approach.
Genetic dissection of two Pakistani families with consanguineous localized autosomal recessive hypotrichosis (LAH)

Objective(s): Genetic analysis of two consanguineous Pakistani families with localized autosomal recessive hypotrichosis was performed with the goal to establish genotype-phenotype correlation. Materials and Methods: Genomic DNA extraction had been done from peripheral blood samples. Extracted DNA was then subjected to PCR (polymerase chain reaction) for amplification. Linkage analysis was performed using 8% polyacrylamide gel. Candidate gene was sequenced after gene linkage supported at highly polymorphic microsatellite markers of the diseased region. Results: Both families were initially tested for linkage to known genes, which were involved in human hereditary hypotrichosis, by genotyping Highly polymorphic microsatellite markers. Family B showed partial linkage at P2RY5 gene on chromosome 13q14.11-q21.32; hence, all exonic regions and their introns boundaries were subjected to DNA sequencing for any pathogenic mutation. Conclusion: Both families were tested for linkage by genotyping polymorphic microsatellite markers linked to known alopecia loci. Family A excluded all known diseased regions that is suggestive of some novel chromosomal disorder. However, sequencing of P2RY5 gene in family B showed no pathogenic mutation.
Cassandra: flexible trust management, applied to electronic health records

We study the specification of access control policy in large-scale distributed systems. We present Cassandra, a language and system for expressing policy, and the results of a substantial case study, a security policy for a national electronic health record system, based on the requirements for the ongoing UK National Health Service procurement exercise. Cassandra policies are expressed in a language based on Datalog with constraints. The expressiveness of the language (and its computational complexity) can be tuned by choosing an appropriate constraint domain. Cassandra is role-based; it supports credential-based access control (e.g. between administrative domains); and rules can refer to remote policies (for automatic credential retrieval and trust negotiation). Moreover, the policy language is small, and it has a formal semantics for query evaluation and for the access control engine. For the case study we choose a constraint domain C/sub 0/ that is sufficiently expressive to encode many policy idioms. The case study turns out to require many subtle variants of these; it is important to express this variety smoothly, rather than add them as ad hoc features. By ensuring only a constraint compact fragment of C/sub 0/ is used, we guarantee a finite and computable fixed-point model. We use a top-down evaluation algorithm, for efficiency and to guarantee termination. The case study (with some 310 rules and 58 roles) demonstrates that this language is expressive enough for a real-world application; preliminary results suggest that the performance should be acceptable.
Statistical models for haplotype sharing in case-parent trio data.

BACKGROUND Haplotype sharing statistics have been introduced in an ad-hoc way, often relying heavily on permutation testing. As a result, applying these approaches to whole genome association studies or to evaluate their properties in extensive simulation experiments is problematic. Further, permutation testing may be inappropriate in the presence of phase ambiguity and population stratification. AIMS To present a simple framework for a class of haplotype sharing statistics useful for association mapping in case-parent trio data. This framework allows derivation of novel haplotype sharing tests as well as simple variance estimators and asymptotic distributions for haplotype sharing tests. RESULTS AND CONCLUSIONS We validated that our approach is appropriately sized using simulated data, and illustrate the methodology by analyzing a Crohn's disease dataset. We find that haplotype-based analyses are much more powerful than single-locus analyses for these data.
Locally-Transferred Fisher Vectors for Texture Classification

Texture classification has been extensively studied in computer vision. Recent research shows that the combination of Fisher vector (FV) encoding and convolutional neural network (CNN) provides significant improvement in texture classification over the previous feature representation methods. However, by truncating the CNN model at the last convolutional layer, the CNN-based FV descriptors would not incorporate the full capability of neural networks in feature learning. In this study, we propose that we can further transform the CNN-based FV descriptors in a neural network model to obtain more discriminative feature representations. In particular, we design a locally-transferred Fisher vector (LFV) method, which involves a multi-layer neural network model containing locally connected layers to transform the input FV descriptors with filters of locally shared weights. The network is optimized based on the hinge loss of classification, and transferred FV descriptors are then used for image classification. Our results on three challenging texture image datasets show improved performance over the state-of-the-art approaches.
ESPLA: A Catalog of Extractive SPL Adoption Case Studies

Building Software Product Lines (SPLs) from existing artefacts is known as the extractive approach for SPL adoption. The traditional case is that variants are created with ad-hoc reuse (e.g., copy-paste-modify to quickly respond to different customer needs) and practitioners want to reengineer them to an SPL. Several industrial cases have been presented in the literature to motivate the interest of the extraction and many case studies are used to validate methods and techniques for different activities during this adoption process. However, there is no catalog or repository that gather together case studies and artefacts related to extractive SPL adoption. In this paper we present ESPLA, a catalog of Extractive SPL Adoption case studies that aims to foster the advance of this field by providing comprehensive information about case studies that will be otherwise scattered in the literature. Researchers, practitioners and educators can use this catalog to find the case studies that better fit to their particular needs. Currently, ESPLA contains information about 123 case studies and it is intended to be a catalog that can be updated and extended by the community.
Comparison of the peptide binding preferences of three closely related TRAF paralogs: TRAF2, TRAF3, and TRAF5

Tumor necrosis factor receptor‐associated factors (TRAFs) constitute a family of adapter proteins that act in numerous signaling pathways important in human biology and disease. The MATH domain of TRAF proteins binds peptides found in the cytoplasmic domains of signaling receptors, thereby connecting extracellular signals to downstream effectors. Beyond several very general motifs, the peptide binding preferences of TRAFs have not been extensively characterized, and differences between the binding preferences of TRAF paralogs are poorly understood. Here we report a screening system that we established to explore TRAF peptide‐binding specificity using deep mutational scanning of TRAF‐peptide ligands. We displayed single‐ and double‐mutant peptide libraries based on the TRAF‐binding sites of CD40 or TANK on the surface of Escherichia coli and screened them for binding to TRAF2, TRAF3, and TRAF5. Enrichment analysis of the library sequencing results showed differences in the permitted substitution patterns in the TANK versus CD40 backgrounds. The three TRAF proteins also demonstrated different preferences for binding to members of the CD40 library, and three peptides from that library that were analyzed individually showed striking differences in affinity for the three TRAFs. These results illustrate a previously unappreciated level of binding specificity between these close paralogs and demonstrate that established motifs are overly simplistic. The results from this work begin to outline differences between TRAF family members, and the experimental approach established herein will enable future efforts to investigate and redesign TRAF peptide‐binding specificity.
Novel Regulator MphX Represses Activation of Phenol Hydroxylase Genes Caused by a XylR/DmpR-Type Regulator MphR in Acinetobacter calcoaceticus

Acinetobacter calcoaceticus PHEA-2 utilizes phenol as its sole carbon and energy source and has a multi-component phenol hydroxylase-encoding gene operon (mphKLMNOP) for phenol degradation. Two additional genes, mphR and mphX, were found upstream and downstream of mphKLMNOP, respectively. The mphR gene encodes a XylR/DmpR-type regulator-like protein and is transcribed in the opposite direction to mphKLMNOP. The mphX gene is transcribed in the same direction as mphKLMNOP and encodes a protein with 293 amino acid residues showing weak identity with some unknown proteins encoded in the meta-cleavage pathway gene clusters for aromatic compound degradation. Disruption of mphR by homologous recombination resulted in the loss of phenol degradation while disruption of mphX caused significantly faster phenol degradation than in the wild type strain. Transcriptional assays for mphK, mphR, and mphX revealed that mphR activated mphKLMNOP transcription in the presence of phenol, but mphX partially repressed this activation. Gel mobility-shift assay demonstrated a direct interaction of MphR with the mphK promoter region. These results indicate the involvement of a novel repressor protein MphX in transcriptional regulation of phenol hydroxylase genes caused by a XylR/DmpR-type regulator MphR.
Abnormalities on MRI of the subscapularis tendon in the presence of a full-thickness supraspinatus tendon tear.

OBJECTIVE Our objective was to determine the association between size and chronicity of full-thickness supraspinatus tendon tears with subscapularis tendon abnormalities on MRI. MATERIALS AND METHODS One hundred forty-two MRI examinations with full-thickness supraspinatus tendon tears were categorized on the basis of the supraspinatus muscle (SS): normal muscle (SS(normal)), suggesting a recent or small tear; reduced muscle bulk without fatty atrophy (SS(volume loss)); and those with fatty atrophy, suggesting a large or chronic tear (SS(fatty atrophy)). Subscapularis tendon abnormalities, the subcoracoid interval, and subcortical bone marrow edema in the lesser tuberosity and coracoid process were recorded. RESULTS The mean size of supraspinatus tendon tears in the SS(normal) (n = 45) group was 8.5 mm, 16.6 mm in SS(volume loss) (n = 53), and 29 mm in the SS(fatty atrophy) group (n = 44). Subscapularis tendon abnormality was identified in 22% of SS(normal) patients, 61% of SS(volume loss), and 86% of the SS(fatty atrophy) group (p < 0.001). There was moderate correlation between chronicity of supraspinatus tendon tears and subscapularis tendon abnormality (r = 0.47; p < 0.0001), with no correlation between the subcoracoid interval and abnormalities of the subscapularis tendon. There was moderate correlation between chronicity of supraspinatus tendon tears and bone marrow changes in the lesser tuberosity (r = 0.44; p < 0.0001). CONCLUSION Subscapularis tendon abnormality is related to chronicity of supraspinatus tendon tears. Bone marrow edema in the lesser tuberosity with a subscapularis tendon abnormality suggests increased stress at the subscapularis tendon insertion with chronicity of full-thickness supraspinatus tendon tears. Lack of correlation with the subcoracoid interval indicates that anterior instability may be a more important contributing factor to subscapularis tendon abnormalities than static subcoracoid impingement in the setting of a full-thickness supraspinatus tendon tear.
Performance optimization of sequential circuits by eliminating retiming bottlenecks

A method to improve the effectiveness of retiming by transforming the sequential circuit is proposed. Bottlenecks which prevent retiming to achieve a desired clock period are identified. Conditions to eliminate the retiming bottlenecks are derived. These conditions are satisfied by a process of identifying subcircuits and satisfying a set of timing constraints on the subcircuits. The transformed circuit, which satisfies the timing constraints, can be retimed to achieve the desired clock period. If the original circuit has its initial state specified, the method always generates the final circuit with an equivalent initial state. Experimental results on a variety of sequential benchmark circuits demonstrate significant performance improvement. <<ETX>>
WeDo: End-To-End Computer Supported Collective Action

Many celebrate the Internet’s ability to connect individuals and facilitate collective action toward a common goal. While numerous systems have been designed to support particular aspects of collective action, few systems support participatory, end-to-end collective action in which a crowd or community identifies opportunities, formulates goals, brainstorms ideas and develops plans, mobilizes, and takes action. To explore the possibilities and barriers in supporting such interactions, we introduce WeDo, a system aimed at promoting simple forms of participatory, end-to-end collective action. Pilot deployments of WeDo illustrate that sociotechnical systems can support automated transitions through different phases of end-to-end collective action, but that challenges, such as the elicitation of leadership and the accommodation of existing group norms, remain.
Supervised Anomaly Detection in Uncertain Pseudoperiodic Data Streams

Uncertain data streams have been widely generated in many Web applications. The uncertainty in data streams makes anomaly detection from sensor data streams far more challenging. In this article, we present a novel framework that supports anomaly detection in uncertain data streams. The proposed framework adopts the wavelet soft-thresholding method to remove the noises or errors in data streams. Based on the refined data streams, we develop effective period pattern recognition and feature extraction techniques to improve the computational efficiency. We use classification methods for anomaly detection in the corrected data stream. We also empirically show that the proposed approach shows a high accuracy of anomaly detection on several real datasets.
SemreX: Towards Large-Scale Literature Information Retrieval and Browsing with Semantic Association

Access to scientific literature information is a very important, as well as time-consuming daily work for scientific researchers. Current methods of retrieval are usually limited to keyword-based searching using information retrieval techniques. In this paper, we present SemreX which implements efficient large-scale literature retrieval and browsing with a single access point based on semantic Web technologies. The concept of semantic association is proposed to reveal explicit or implicit relationships between semantic entities, combining with the ontology-based information visualization technique so as to facilitate researchers retrieving semantically relevant information, as well as context relationships which can capture user's current search intentions while preserving an overall picture of scientific knowledge
Influence of alkali treatment on the mechanical properties of new cane fibre/polyester composites

In recent years, natural fibres have been experimented to replace glass fibres in reinforcing thermosetting polymer. Since the interfacial adhesion between the raw natural fibres and the polymer matrix are often not adapted to the intended applications, the fibre surface most often requires a preliminary chemical modification. The fibres which were extracted from the Arundo donax L. Plant (called cane fibres), are little studied in the literature of fibre/polymer composites. In the present work, the cane fibres have been treated at constant soaking time with 2–8% NaOH aqueous solutions for 24 h. The composite reinforced by 6% NaOH-treated cane fibres, exhibited maximum improvements in tensile and flexural strength by 57% and 45% respectively. A combination of Fourier transform infrared, scanning electron microscopy, X-ray diffraction and moisture absorption techniques has been used for material characterisation. The crystallinity index yields information about fibre modification by NaOH. Such cane fibre composites could become an alternative to existing materials, with interesting tensile and flexural strengths, low cost and less ecological impact.
Algorithm to Identify Frequent Coupled Modules from Two-Layered Network Series: Application to Study Transcription and Splicing Coupling

Current network analysis methods all focus on one or multiple networks of the same type. However, cells are organized by multi-layer networks (e.g., transcriptional regulatory networks, splicing regulatory networks, protein-protein interaction networks), which interact and influence each other. Elucidating the coupling mechanisms among those different types of networks is essential in understanding the functions and mechanisms of cellular activities. In this article, we developed the first computational method for pattern mining across many two-layered graphs, with the two layers representing different types yet coupled biological networks. We formulated the problem of identifying frequent coupled clusters between the two layers of networks into a tensor-based computation problem, and proposed an efficient solution to solve the problem. We applied the method to 38 two-layered co-transcription and co-splicing networks, derived from 38 RNA-seq datasets. With the identified atlas of coupled transcription-splicing modules, we explored to what extent, for which cellular functions, and by what mechanisms transcription-splicing coupling takes place.
Improved Bagging Algorithm for Pattern Recognition in UHF Signals of Partial Discharges

This paper presents an Improved Bagging Algorithm (IBA) to recognize ultra-high-frequency (UHF) signals of partial discharges (PDs). This approach establishes the sample information entropy for each sample and the re-sampling process of the traditional Bagging algorithm is optimized. Four typical discharge models were designed in the laboratory to simulate the internal insulation faults of power transformers. The optimized third order Peano fractal antenna was applied to capture the PD UHF signals. Multi-scale fractal dimensions as well as energy parameters extracted from the decomposed signals by wavelet packet transform were used as the characteristic parameters for pattern recognition. In order to verify the effectiveness of the proposed algorithm, the back propagation neural network (BPNN) and the support vector machine (SVM) based on the IBA were adopted in this paper to carry out the pattern recognition for PD UHF signals. Experimental results show that the proposed approach of IBA can effectively enhance the generalization capability and also improve the accuracy of the recognition for PD UHF signals.
Transmembrane Helix 11 Is a Genuine Regulator of the Endoplasmic Reticulum Ca2+ Pump and Acts as a Functional Parallel of β-Subunit on α-Na+,K+-ATPase*

Background: The ubiquitous sarco/endoplasmic reticulum Ca2+ ATPase SERCA2b has a C-terminal extension that increases the Ca2+ affinity. It consists of a transmembrane helix (TM11) and a luminal extension. Results: Both parts control Ca2+ affinity independently. Conclusion: TM11 is an independent and highly conserved functional region of SERCA2b. Significance: This study shows that TM11 acts as a genuine regulator of the Ca2+ pump. The housekeeping sarco(endo)plasmic reticulum Ca2+ ATPase SERCA2b transports Ca2+ across the endoplasmic reticulum membrane maintaining a vital Ca2+ gradient. Compared with the muscle-specific isoforms SERCA2a and SERCA1a, SERCA2b houses an 11th transmembrane segment (TM11) and a short luminal extension (LE) at its C terminus (2b-tail). The 2b-tail imposes a 2-fold higher apparent Ca2+ affinity and lower Vmax. Previously, we assumed that LE is the sole functional region of the 2b-tail and that TM11 is a passive element providing an additional membrane passage. However, here we show that peptides corresponding to the TM11 region specifically modulate the activity of the homologous SERCA1a in co-reconstituted proteoliposomes and mimic the 2b-tail effect (i.e. lower Vmax and higher Ca2+ affinity). Using truncated 2b-tail variants we document that TM11 regulates SERCA1a independently from LE, confirming that TM11 is a second, previously unrecognized functional region of the 2b-tail. A phylogenetic analysis further indicates that TM11 is the oldest and most conserved feature of the 2b-tail, found in the SERCA pump of all Bilateria, whereas LE is only present in Nematoda and vertebrates. Considering remarkable similarities with the Na+,K+-ATPase α-β interaction, we now propose a model for interaction of TM11 with TM7 and TM10 in the anchoring subdomain of the Ca2+ pump. This model involves a TM11-induced helix bending of TM7. In conclusion, more than just a passive structural feature, TM11 acts as a genuine regulator of Ca2+ transport through interaction with the pump.
Semantic rules representation in controlled natural language in FluentEditor

This paper presents a way of representation of semantic rules (SWRL) in controlled English in order to facilitate understanding the rules by humans interacting with a machine. This approach (implemented in FluentEditor) may be applied in many domains, where the understandability of the rules used to support a decision process is of great importance.
A New Payment Rule for Core-Selecting Package Auctions

We propose a new, easy-to-implement class of payment rules, "Reference Rules" to make core-selecting package auctions more robust. Small, almost-riskless, profitable deviations from "truthful bidding" are often easy for bidders to find under currently used payment rules. Reference Rules perform better than existing rules on our marginal-incentive-to-deviate criterion, and are as robust as existing rules to large deviations. Other considerations, including fairness and comprehensibility, also support the use of Reference Rules. (JEL: D44, C71) (c) 2010 by the European Economic Association.