Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic changes in the mobility of LAT in aggregated lipid rafts upon T cell activation

Lipid rafts are known to aggregate in response to various stimuli. By way of raft aggregation after stimulation, signaling molecules in rafts accumulate and interact so that the signal received at a given membrane receptor is amplified efficiently from the site of aggregation. To elucidate the process of lipid raft aggregation during T cell activation, we analyzed the dynamic changes of a raft-associated protein, linker for activation of T cells (LAT), on T cell receptor stimulation using LAT fused to GFP (LAT-GFP). When transfectants expressing LAT-GFP were stimulated with anti-CD3–coated beads, LAT-GFP aggregated and formed patches at the area of bead contact. Photobleaching experiments using live cells revealed that LAT-GFP in patches was markedly less mobile than that in nonpatched regions. The decreased mobility in patches was dependent on raft organization supported by membrane cholesterol and signaling molecule binding sites, especially the phospholipase Cγ1 binding site in the cytoplasmic domain of LAT. Thus, although LAT normally moves rapidly at the plasma membrane, it loses its mobility and becomes stably associated with aggregated rafts to ensure organized and sustained signal transduction required for T cell activation.
Discrete optimization via simulation using Gaussian Markov random fields

We construct a discrete optimization via simulation (DOvS) procedure using discrete Gaussian Markov random fields (GMRFs). Gaussian random fields (GRFs) are used in DOvS to balance exploration and exploitation. They enable computation of the expected improvement (EI) due to running the simulation to evaluate a feasible point of the optimization problem. Existing methods use GRFs with a continuous domain, which leads to dense covariance matrices, and therefore can be ill-suited for large-scale problems due to slow and ill-conditioned numerical computations. The use of GMRFs leads to sparse precision matrices, on which several sparse matrix techniques can be applied. To allocate the simulation effort throughout the procedure, we introduce a new EI criterion that incorporates the uncertainty in stochastic simulation by treating the value at the current optimal point as a random variable.
Computational Complexity of Network Reliability Analysis: An Overview

This paper presents an overview of results related to the computational complexity of network reliability analysis problems. Network reliability analysis problems deal with the determination of reliability measures for stochastic networks. We show how these problems are related to the more familiar computational network problems of recognizing certain subnetworks, finding optimal subnetworks, and counting certain subnetworks. We use these relationships to show that the k-terminal, the 2-terminal, and the all-terminal network reliability analysis problems are at least as hard as the renowned set of computationally difficult problems, NP-Complete. Finally, we discuss the impact of these results on how one should approach problem solving in this area.
Semantic media application with user created content to enhance enjoying cultural heritage

There are two important trends bringing changes and new opportunities into media consumption: the emergence of user-created content and Semantic Web technologies. In this paper we present an application that shows how these technologies can be combined to create an enjoyable media consumption experience. The application development work served also as a feasibility test of the maturity of Semantic Web technologies for media sector applications. The application contains material to the historical Ox road of Häme, and this way it also supports enjoying cultural heritage. The results indicated that users enjoyed using the application. Several ontologies were utilised, most of which were based on existing ontologies or taxonomies. With their help, it was possible to offer multiple views and exploratory routes into the available content. Further development can, among other things, be made in improving search strategies and in utilising user-created metadata for both for enriching ontologies and as an indication of user interests.
Exploring OLAP aggregates with hierarchical visualization techniques

This paper presents an approach to exploring multidimensional data cubes with hierarchical visualization techniques. Analysts interact with data in a predominantly "drill-down" fashion, i.e. from coarse grained aggregates towards the desired level of detail. We suggest that visual hierarchies are adequate for mapping the multiscale nature of decomposition as they preserve the results of the entire interaction. We introduce a class of visual structures called Enhanced Decomposition Tree. Every tree level is created by a disaggregation step along a chosen dimension, the nodes contain the corresponding sub-aggregates arranged into a chart and the edges are labeled with their dimensional values. Various layouts are proposed to account for different analysis tasks. Data cubes are queried using a schema-based browser which presents dimensions by the hierarchies of their granularity levels, thus offering an efficient way of generating hierarchical visualizations. Multiple data cubes may be explored in parallel along their shared dimensions. The power of our approach is exemplified using a real-world study from the domain of academic administration.
Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families

Emerging high‐throughput technologies have led to a deluge of putative non‐coding RNA (ncRNA) sequences identified in a wide variety of organisms. Systematic characterization of these transcripts will be a tremendous challenge. Homology detection is critical to making maximal use of functional information gathered about ncRNAs: identifying homologous sequence allows us to transfer information gathered in one organism to another quickly and with a high degree of confidence. ncRNA presents a challenge for homology detection, as the primary sequence is often poorly conserved and de novo secondary structure prediction and search remain difficult. This unit introduces methods developed by the Rfam database for identifying “families” of homologous ncRNAs starting from single “seed” sequences, using manually curated sequence alignments to build powerful statistical models of sequence and structure conservation known as covariance models (CMs), implemented in the Infernal software package. We provide a step‐by‐step iterative protocol for identifying ncRNA homologs and then constructing an alignment and corresponding CM. We also work through an example for the bacterial small RNA MicA, discovering a previously unreported family of divergent MicA homologs in genus Xenorhabdus in the process. © 2016 by John Wiley & Sons, Inc.
Crystal Structure and Functional Insights of Hemopexin Fold Protein from Grass Pea1[W][OA]

A regulatory protein from grass pea (Lathyrus sativus), LS-24, a close homolog of albumin 2 from garden pea (Pisum sativum) that is associated with polyamine biosynthesis, was characterized and the structure of a hemopexin-type fold among plant proteins illustrated. Crystal structure of LS-24 determined at 2.2 Å resolution by multiple isomorphous replacement phasing showed four-bladed β-propeller structure having a pseudo 4-fold molecular symmetry along a metal ion-binding central channel. The structure represents typical mammalian hemopexin fold with discernible features correlated with the possible functional variations. The protein was found to exist in the dimeric state. While LS-24 dimer binds to spermine in the crystal structure as well as in solution, binding of heme in solution resulted in the dissociation of the dimer into monomers with concomitant release of bound spermine. Interactions of heme and spermine with LS-24 bear physiological implications. While binding of spermine to LS-24 can be linked with polyamine biosynthesis that of heme correlates with oxidative stress. Mutually exclusive binding of heme and spermine in different oligomeric states suggest a role for LS-24 in sensing oxidative stress through a ligand-regulated monomer-dimer transition switch.
2-aminoethoxydiphenyl borate provides an anti-oxidative effect and mediates cardioprotection during ischemia reperfusion in mice

Excessive levels of reactive oxygen species (ROS) and impaired Ca2+ homeostasis play central roles in the development of multiple cardiac pathologies, including cell death during ischemia-reperfusion (I/R) injury. In several organs, treatment with 2-aminoethoxydiphenyl borate (2-APB) was shown to have protective effects, generally believed to be due to Ca2+ channel inhibition. However, the mechanism of 2-APB-induced cardioprotection has not been fully investigated. Herein we investigated the protective effects of 2-APB treatment against cardiac pathogenesis and deciphered the underlying mechanisms. In neonatal rat cardiomyocytes, treatment with 2-APB was shown to prevent hydrogen peroxide (H2O2) -induced cell death by inhibiting the increase in intracellular Ca2+ levels. However, no 2-APB-sensitive channel blocker inhibited H2O2-induced cell death and a direct reaction between 2-APB and H2O2 was detected by 1H-NMR, suggesting that 2-APB chemically scavenges extracellular ROS and provides cytoprotection. In a mouse I/R model, treatment with 2-APB led to a considerable reduction in the infarct size after I/R, which was accompanied by the reduction in ROS levels and neutrophil infiltration, indicating that the anti-oxidative properties of 2-APB plays an important role in the prevention of I/R injury in vivo as well. Taken together, present results indicate that 2-APB treatment induces cardioprotection and prevents ROS-induced cardiomyocyte death, at least partially, by the direct scavenging of extracellular ROS. Therefore, administration of 2-APB may represent a promising therapeutic strategy for the treatment of ROS-related cardiac pathology including I/R injury.
Reducing Energy of DRAM/Flash Memory System by OS-controlled Data Refresh

This paper presents a new approach to reduce energy consumption of DRAM/flash memory system by lowering the frequency of DRAM refreshes. The approach is based on two ideas: (1) a DRAM based swap-cache that reduces the number of writes to the flash memory by keeping dirty pages as long as possible; and (2) OS-controlled page allocation/aging policy that stops refreshing for banks, whose pages are clean and not accessed for a long time. Simulations show that the approach can reduce the DRAM refresh energy by 59-74% and the overall energy of DRAM/flash memory system by 8-24% without increase in the execution.
High speed position control of a swinging load

This paper presents the control design and test results of the high speed position control of a spherical pendulum system. Altogether three oscillatory modes are considered: two swing modes and a torsion mode. A sequence of input shapers including the Zero Vibration and Zero Vibration-Derivative shapers are implemented in the robot controller to minimize command induced cable swing. Experiment data confirms that the proposed sequential input shaper method minimizes oscillations as well as settling times of the test trajectory execution.
Increasing the accuracy of a spam-detecting artificial immune system

Spam, the electronic equivalent of junk mail, affects over 600 million users worldwide. Even as anti-spam solutions change to limit the amount of spam sent to users, the senders adapt to make sure their messages are seen. This paper looks at application of the artificial immune system model to protect email users effectively from spam. In particular, it tests the spam immune system against the publicly available spam assassin corpus of spam and non-spam, and extends the original system by looking at several methods of classifying email messages with the detectors produced by the immune system. The resulting system classifies the messages with similar accuracy to other spam filters, but uses fewer detectors to do so, making it an attractive solution for circumstances where processing time is at a premium.
Revisiting Matrix Product on Master-Worker Platforms

This paper is aimed at designing efficient parallel matrix-product algorithms for homogeneous master-worker platforms. While matrix-product is well-understood for homogeneous 2D-arrays of processors (e.g., Cannon algorithm and ScaLAPACK outer product algorithm), there are two key hypotheses that render our work original and innovative: 1) centralized data: we assume that all matrix files originate from, and must be returned to, the master. The master distributes both data and computations to the workers (while in ScaLAPACK, input and output matrices are initially distributed among participating resources). Typically, our approach is useful in the context of speeding up MATLAB or SCILAB clients running on a server (which acts as the master and initial repository of files). 2) Limited memory: because we investigate the parallelization of large problems, we cannot assume that full matrix panels can be stored in the worker memories and re-used for subsequent updates (as in ScaLAPACK). The amount of memory available in each worker is expressed as a given number of buffers, where a buffer can store a square block of matrix elements. These square blocks are chosen so as to harness the power of level 3 BIAS routines; they are of size 80 or 100 on most platforms. We have devised efficient algorithms for resource selection (deciding which workers to enroll) and communication ordering (both for input and result messages), and we report a set of MPI experiments conducted on a platform at the University of Tennessee.
Detection of Neuroblastoma Cells in Bone Marrow and Peripheral Blood by Different Techniques

Purpose: Detection of metastatic tumor cells in bone marrow (BM) and peripheral blood (PB) of children with neuroblastoma is crucial for prognosis and planning of therapy. Aims of this large descriptive repeated survey were to evaluate the diagnostic accuracy of different techniques in diagnostic samples obtained at several disease course time points and to correlate positive results with patient clinical features and outcome. Experimental Design: BM aspirates, trephine biopsies, PB, and peripheral blood stem cell (PBSC) samples from Italian children with neuroblastoma were analyzed by morphological and histologic techniques, as well as by immunocytochemistry (IC) for disialoganglioside GD2 and reverse transcription-PCRs (RT-PCRs) for tyrosine hydroxylase (TH) and pgp9.5 genes. The diagnostic odd ratio (DOR) was used to measure the accuracy of the different techniques. Results: A total of 2,247 evaluations were done on 561 BM, 265 PB, and 69 PBSC samples from 247 patients. IC showed the best accuracy. Whereas TH RT-PCR accuracy was satisfactory, that of pgp9.5 was very low. Positive results obtained by IC in BM and PB samples at diagnosis from stage 1, 2, and 3 patients correlated with unfavourable outcome. No correlation was found between positive results obtained by IC or TH RT-PCR in BM, PB, and PBSC samples from stage 4 patients and their outcome. Conclusions: Because of its elevated diagnostic accuracy, IC may represent a useful adjunct to conventional morphological techniques, especially in view of its potential prognostic role in patients with localized disease. Longitudinal multicenter studies are warranted to definitely establish the clinical usefulness of TH RT-PCR.
ERMHAN: A Context-Aware Service Platform to Support Continuous Care Networks for Home-Based Assistance

Continuous care models for chronic diseases pose several technology-oriented challenges for home-based continuous care, where assistance services rely on a close collaboration among different stakeholders such as health operators, patient relatives, and social community members. Here we describe Emilia Romagna Mobile Health Assistance Network (ERMHAN) a multichannel context-aware service platform designed to support care networks in cooperating and sharing information with the goal of improving patient quality of life. In order to meet extensibility and flexibility requirements, this platform has been developed through ontology-based context-aware computing and a service oriented approach. We also provide some preliminary results of performance analysis and user survey activity.
Expanding the World of Marine Bacterial and Archaeal Clades

Determining which microbial taxa are out there, where they live, and what they are doing is a driving approach in marine microbial ecology. The importance of these questions is underlined by concerted, large-scale, and global ocean sampling initiatives, for example the International Census of Marine Microbes, Ocean Sampling Day, or Tara Oceans. Given decades of effort, we know that the large majority of marine Bacteria and Archaea belong to about a dozen phyla. In addition to the classically culturable Bacteria and Archaea, at least 50 “clades,” at different taxonomic depths, exist. These account for the majority of marine microbial diversity, but there is still an underexplored and less abundant portion remaining. We refer to these hitherto unrecognized clades as unknown, as their boundaries, names, and classifications are not available. In this work, we were able to characterize up to 92 of these unknown clades found within the bacterial and archaeal phylogenetic diversity currently reported for marine water column environments. We mined the SILVA 16S rRNA gene datasets for sequences originating from the marine water column. Instead of the usual subjective taxa delineation and nomenclature methods, we applied the candidate taxonomic unit (CTU) circumscription system, along with a standardized nomenclature to the sequences in newly constructed phylogenetic trees. With this new phylogenetic and taxonomic framework, we performed an analysis of ICoMM rRNA gene amplicon datasets to gain insights into the global distribution of the new marine clades, their ecology, biogeography, and interaction with oceanographic variables. Most of the new clades we identified were interspersed by known taxa with cultivated members, whose genome sequences are available. This result encouraged us to perform metabolic predictions for the novel marine clades using the PICRUSt approach. Our work also provides an update on the taxonomy of several phyla and widely known marine clades as our CTU approach breaks down these randomly lumped clades into smaller objectively calculated subgroups. Finally, all taxa were classified and named following standards compatible with the Bacteriological Code rules, enhancing their digitization, and comparability with future microbial ecological and taxonomy studies.
Microstructure-property development in linear friction welding of nickel-based superalloys

Linear friction welding (LFW) is known as an advanced technique to substitute fusion welding of joining Ni-based superalloys. However, due to the complex microstructural development caused by LFW, some unexplained issues still need to be solved, such as: influence of weld parameters (weld pressure, amplitude of oscillation, and frequency of oscillation) on the development of microstructural, microhardness, texture and residual stresses in LFWed IN718-IN713LC; impact of post-weld heat treatment (PWHT) on the microstructural and microhardness development; influence of rapid thermal cycle on the precipitate dissolution of IN718 and IN713LC; formation mechanisms of alumina inclusions (Al-oxides) on the weld interface. The present work aims to investigate these issues.
A gesture-based american sign language game for deaf children

We present a system designed to facilitate language development in deaf children. The children interact with a computer game using American Sign Language (ASL). The system consists of three parts: an ASL (gesture) recognition engine; an interactive, game-based interface; and an evaluation system. Using interactive, user-centered design and the results of two Wizard-of-Oz studies at Atlanta Area School for the Deaf, we present some unique insights into the spatial organization of interfaces for deaf children.
KMnO4 pre-treatment of linen

Currently, for the textile industry, the economical considerations are of great importance. The concept of eco-friendliness is of greater concern for textile processing, as the chemical wet treatment has a major role in effluent generation. Thus, research activities these days are oriented towards the alternative ways of chemical processing. Potassium permanganate, a strong oxidising agent can be employed for the pre-treatment of grey linen. The experimental investigation reveals that the KMnO4 concentration, temperature and treatment time have noticeable impact on quality of bleached linen. The results are evaluated in terms of whiteness index and strength of fabric and the treatment factors are optimised using design of experiment. The results demonstrate that the KMnO4 can be employed for simultaneous desizing and bleaching of grey linen.
Compensatory Movement Detection through Inertial Sensor Positioning for Post-stroke Rehabilitation

An increasing ageing society and consequently rising number of post-stroke related neurological dysfunction patients are forcing the rehabilitation field to adapt to ever-growing demands. In parallel, an unprecedented number of research efforts and technological solutions meant for human monitoring are continuously influencing traditional methodologies, causing paradigm shifts; extending the therapist patient dynamics. Compensatory movements can be observed in post-stroke patient when performing functional tasks. Although some controversy remains regarding the functional benefits of compensatory movement as a way of accomplish a given task, even in the presence of a motor deficit; studies suggest that such maladaptive strategies may limit the plasticity of the nervous system to enhance neuro-motor recovery. This preliminary study intends to aid in the development of a system for compensatory movement detection in stroke patients through the use of accelerometry data. A post-stroke patients group is presented and discussed, instructed to perform reach and press movements while sensors were positioned at different location on the arm, forearm and trunk, in order to assess sensor positioning influence. Results suggest that P1 is advantageous for compensatory elevation movement detection at the shoulder; P4 seems the most appropriate for detecting the abduction; and P5 presents a reasonable sensitivity for detection of anteriorization and rotation of the trunk.
The treatment of pharyngeal gonorrhoea with a single oral dose of cefixime

An audit of the efficacy treatment of pharyngeal gonorrhoea with a single oral dose of 400 mg of cefixime was undertaken; 83% of patients also received a single oral dose of azithromycin to treat possible concurrent anogenital chlamydial infection. Of the 54 patients studied, only one of 45 patients who attended for at least one test of cure had a positive culture seven days after treatment; the possibility of reinfection could not have been excluded. Two tests of cure were obtained from 18 patients. Cefixime, therefore, seems to be effective in the treatment of pharyngeal gonorrhoea.