Miracle-dz/UniFAR-FTUs huggingface dataset:
ILI: an adaptive infrastructure for dynamic interactive distributed applications

Addresses the middleware that is necessary to realize the construction of distributed laboratories in which scientists can construct and use complex computations and then analyze and share their results across geographically separated collaborations. We present a model of such middleware for heterogeneous distributed computing platforms and also show how middleware can dynamically adapt to changes in the behavior of instruments and end users. To address the demands of applications executing in a distributed laboratory, we have developed an infrastructure, called ILI (Interactivity Layer Infrastructure), that can dynamically adapt to changes in the behavior of the computational instruments and end users across a shared and dynamically changing set of computational nodes and networks.
Web user profiling using data redundancy

The study of Web user profiling can be traced back to 30 years ago, with the goal of extracting “semantic”-based user profile attributes from the unstructured Web. Despite slight differences, the general method is to first identify relevant pages of a specific user and then use machine learning models (e.g., CRFs) to extract the profile attributes from the page. However, with the rapid growth of the Web volume, such a method suffers from data redundancy and error propagation between the two steps. In this paper, we revisit the problem of Web user profiling in the big data era, trying to deal with the new challenges. We propose a simple but very effective approach for extracting user profile attributes from the Web using big data. To avoid error propagation, the approach processes all the extraction subtasks in one unified model. To further incorporate human knowledge to improve the extraction performance, we propose a Markov logic factor graph (MagicFG) model. The MagicFG model describes human knowledge as first-order logics and combines the logics into the extraction model. Our experiments on a real data set show that the proposed method significantly improves (+4-6%; p ≪ 0.01, t-test) the extraction performance in comparison with several baseline methods.
Empowering Business Users to Explore Visual Data Through Boundary Objects and Storytelling

This research is inspired by two important industry trends: (i) a growing demand for visual analytic (VA) across all industry sectors, and ii) serious shortage of VA skills on the market, especially among business professionals. This project focuses on the following practice-inspired research question: "How to empower business users to develop visual data exploration skills? " This paper describes a VA pilot project conducted at an industry, rather than organizational level. We focused on a challenge of gradual development of VA skills among industry professionals from the Australian Cooperative and Mutual Enterprises (CMEs) sector, which is considered to be of national importance for the Australian economy and society. The CME sector also plays significant economic and social roles in the lives of over one billion members worldwide. Following the principles of action design research, the paper describes a method of gradual development of VA skills using visual stories as boundary objects.
Magnitude Processing in the Brain: An fMRI Study of Time, Space, and Numerosity as a Shared Cortical System

Continuous dimensions, such as time, space, and numerosity, have been suggested to be subserved by common neurocognitive mechanisms. Neuroimaging studies that have investigated either one or two dimensions simultaneously have consistently identified neural correlates in the parietal cortex of the brain. However, studies investigating the degree of neural overlap across several dimensions are inconclusive, and it remains an open question whether a potential overlap can be conceptualized as a neurocognitive magnitude processing system. The current functional magnetic resonance imaging study investigated the potential neurocognitive overlap across three dimensions. A sample of adults (N = 24) performed three different magnitude processing tasks: a temporal discrimination task, a number discrimination task, and a line length discrimination task. A conjunction analysis revealed several overlapping neural substrates across multiple magnitude dimensions, and we argue that these cortical nodes comprise a distributed magnitude processing system. Key components of this predominantly right-lateralized system include the intraparietal sulcus, insula, premotor cortex/SMA, and inferior frontal gyrus. Together with previous research highlighting intraparietal sulcus, our results suggest that the insula also is a core component of the magnitude processing system. We discuss the functional role of each of these components in the magnitude processing system and suggest that further research of this system may provide insight into the etiology of neurodevelopmental disorders where cognitive deficits in magnitude processing are manifest.
Aerobic hydrogen production and dinitrogen fixation in the marine cyanobacterium Trichodesmium erythraeum IMS101

Rates of hydrogen production and acetylene reduction were measured in aerobic cultures of the marine cyanobacterium Trichodesmium erythraeum IMS101 grown in a supplemented seawater medium low in combined inorganic nitrogen. Both hydrogen production and acetylene reduction conformed to a circadian pattern with maximum activity in the afternoon. Normalized hydrogen production rates ranged from 0.06 to 0.71 nmol H2 [g chlorophyll a (Chl a)‐1 h‐1, while nitrogen fixation rates, calculated using an assumed ratio of 4 mol acetylene to 1 mol dinitrogen, ranged from 0.12 to 4.71 nmol N2 Chl a−1 h−1. Yields of hydrogen from nitrogen fixation were in the range 0.15–0.48 mol H2 evolved per mol N2 reduced. A comparatively low net rate of H2 uptake was observed in one culture during the dark period (20.01 nmol H2 [g Chl a−1 h−1). These measurements suggest that T. erythraeum is potentially a net source of hydrogen to the low‐latitude surface ocean.
A multi-agent model for provider centered trust in Service Oriented Architectures

In current SOAs, the selection is mainly performed by the client, who creates a workflow adapted to his needs and then selects the providers she feels the most adapted to complete her overall goal. In this approach, service providers are assumed to be passive and thus cannot decide who they collaborate with. This can cause several problems such as forced collaboration with concurrents, disparity of quality for the composite service and unwanted sharing of private data. This problem is different from automated web service composition since we assume that the client already has her workflow structure and just search for providers to fill the functions needed to achieve her service. SOAs, as distributed systems are closely related to Multi-Agent Systems. We argue that finding suitable partners for an abstract workflow is not that different from forming a coalition of agents endowed with specific skills working together to solve a set of tasks. Furthermore, we think that the best criterion, beside the payoff, to select a potential partner is trust. This study is based on the Language Grid project [4], an infrastructure for sharing language resources. We identified the current drawbacks in term of provider involvement and tried to design an architecture to take providers’ collaboration expectations into account.
An active noise control system based on simultaneous equations method without auxiliary filters

A simultaneous equations method gives an active noise control algorithm without estimating an error path. This algorithm requires the identification of a transfer function from a reference microphone to an error microphone containing the effect of a noise control filter. It is achieved by the system identification of an auxiliary filter. As a result, the amount of computation is increased. A new simultaneous equations method without the identification of the auxiliary filter is proposed. By storing a small part of an input signal and an error signal, we avoid this identification. Therefore, the amount of computation can be reduced by approximately 25% and the same noise reduction performance as with an ordinary method is obtained. From simulation examples, it is verified that the merits of the ordinary method are retained in the proposed method.
CCR New Strategies New Strategies in Diffuse Large B-cell Lymphoma : Translating Findings from Gene Expression Analyses into Clinical Practice

Gene expression profiling has had amajor impact on our understanding of the biology and heterogeneity of diffuse large B-cell lymphoma (DLBCL). Using this technology, investigators can identify biologic subgroups of DLBCL that provide unique targets for rational therapeutic intervention. This review summarizes these potential targets and updates the progress of clinical development of exciting novel agents for the treatment of DLBCL. Results of ongoing studies suggest that in the near future, we will be able to use gene expression profiling, or an accurate surrogate, to define the best therapeutic approach for individual patients with DLBCL. Clin Cancer Res; 17(19); 6112–7. 2011 AACR.
Efficient Topological Localization Using Orientation Adjacency Coherence Histograms

This paper describes an efficient vision-based global topological localization approach that uses a coarse-to-fine strategy. Orientation adjacency coherence histogram (OACH), a novel image feature, is proposed to improve the coarse localization. The coarse localization results are taken as inputs for the fine localization which is carried out by matching Harris-Laplace interest points characterized by the SIFT descriptor. Computation of OACHs and interest points is efficient due to the fact that these features are computed in an integrated process. We have implemented and tested the localization system in real environments. The experimental results demonstrate that our approach is efficient and reliable in both indoor and outdoor environments
Search for Protein Sequence Homologues that Display Considerable Domain Length Variations

Independent folding units which have the capability of carrying out biological functions have been classified as â€œprotein domainsâ€ . These minimal structural units lead not only to considerable sequence changes of protein domains of similar folds and functions, but also gives rise to remarkable length variations under evolutionary pressure. Rapid and heuristic sequence search algorithms are generally sensitive and effective in recognizing protein domains that are distantly related within large sequence databases, but are not well-suited to identify remote homologues of varying lengths. An even more challenging aspect is introduced to distinguish reliable hits from a vast number of putative false positives that could have suboptimal sequence similarities. Here, the authors present a data-mining approach that provides stage-specific filters in sequence searches to reliably accumulate remote homologues, which encourages sampling of length variations albeit with a low false positive rate. Realization of such remote homologues with vivid length variations could contribute to better understanding of functional variety within protein domain superfamilies.
Fully-functional succinct trees

We propose new succinct representations of ordinal trees, which have been studied extensively. It is known that any n-node static tree can be represented in 2n + o(n) bits and a large number of operations on the tree can be supported in constant time under the word-RAM model. However existing data structures are not satisfactory in both theory and practice because (1) the lower-order term is Ω(n log log n/ log n), which cannot be neglected in practice, (2) the hidden constant is also large, (3) the data structures are complicated and difficult to implement, and (4) the techniques do not extend to dynamic trees supporting insertions and deletions of nodes. We propose a simple and flexible data structure, called the range min-max tree, that reduces the large number of relevant tree operations considered in the literature to a few primitives, which are carried out in constant time on sufficiently small trees. The result is then extended to trees of arbitrary size, achieving 2n + O(n/polylog(n)) bits of space. The redundancy is significantly lower than in any previous proposal, and the data structure is easily implemented. Furthermore, using the same framework, we derive the first fully-functional dynamic succinct trees.
ATP6V0C Knockdown in Neuroblastoma Cells Alters Autophagy-Lysosome Pathway Function and Metabolism of Proteins that Accumulate in Neurodegenerative Disease

ATP6V0C is the bafilomycin A1-binding subunit of vacuolar ATPase, an enzyme complex that critically regulates vesicular acidification. We and others have shown previously that bafilomycin A1 regulates cell viability, autophagic flux and metabolism of proteins that accumulate in neurodegenerative disease. To determine the importance of ATP6V0C for autophagy-lysosome pathway function, SH-SY5Y human neuroblastoma cells differentiated to a neuronal phenotype were nucleofected with non-target or ATP6V0C siRNA and following recovery were treated with either vehicle or bafilomycin A1 (0.3–100 nM) for 48 h. ATP6V0C knockdown was validated by quantitative RT-PCR and by a significant decrease in Lysostracker Red staining. ATP6V0C knockdown significantly increased basal levels of microtubule-associated protein light chain 3-II (LC3-II), α-synuclein high molecular weight species and APP C-terminal fragments, and inhibited autophagic flux. Enhanced LC3 and LAMP-1 co-localization following knockdown suggests that autophagic flux was inhibited in part due to lysosomal degradation and not by a block in vesicular fusion. Knockdown of ATP6V0C also sensitized cells to the accumulation of autophagy substrates and a reduction in neurite length following treatment with 1 nM bafilomycin A1, a concentration that did not produce such alterations in non-target control cells. Reduced neurite length and the percentage of propidium iodide-positive dead cells were also significantly greater following treatment with 3 nM bafilomycin A1. Together these results indicate a role for ATP6V0C in maintaining constitutive and stress-induced ALP function, in particular the metabolism of substrates that accumulate in age-related neurodegenerative disease and may contribute to disease pathogenesis.
Mycobacterium tuberculosis belonging to family LAM and sublineage RDRio: common strains in Southern Brazil for over 10 years

A sublineage of Mycobacterium tuberculosis called RDRio was described in 2007. Although only recently described, this strain may have been present previously in the population, and its identification in clinical isolates will elucidate bacterial transmission dynamics and host-pathogen interactions. This study evaluated the clonal diversity of the RDRio sublineage in clinical isolates from Rio Grande-RS obtained between 1998 and 2001. Among the 45 samples analyzed by the MIRU-VNTR method, there were six clusters with two samples each and 33 orphan strains with unique pattern. The strains were distributed across several different lineages including LAM (34.04%), × (14.89%), Haarlem (12.77%), UgandaI (10.64%), S (4.26%), NEW-1 (2.13%) and Cameroon (2.13%); 14.89% of the strains matched to multiple lineages. RDRio strains were present in 28.9% of the samples and 81.25% of the identified strains belonged to the LAM family. The high clonal diversity observed in this study is a constant feature in this region. The RDRio sublineage has been in Rio Grande-RS since 1998. The continued monitoring of RDRio in clinical isolates will enhance the understanding of its epidemiological significance.
How Does It Fold? Searching for Folding Pathways using A Motion Planning Approach

In this paper, we present a framework for studying folding problems from a motion planning perspective. The version of the motion planning problem we consider is that of determining a sequence of motions to transform an extended, or flat, configuration of a foldable object (the start) into a known folded configuration (the goal). Modeling foldable objects as tree-like multi-link objects allows us to apply recent techniques developed in the robotics motion planning community for articulated objects with many degrees of freedom (many links) to folding problems. An important feature of this approach is that it not only allows us to study foldability questions, such as, can one object be folded (or unfolded) into another object, but most importantly, provides us with another tool for investigating the dynamic folding process itself. For example, the folding sequences, or pathways, found might provide insight about how a protein folds in nature. Or, the inability to generate a folding sequence could offer insight regarding the foldability of a paper or box folding problem. The framework proposed here has application to traditional motion planning areas such as automation, teaching through demonstration, and animation, and most interesting to us, presents a novel approach for studying folding pathways for proteins. We hope our approach, which constructs a folding sequence to the known native fold, will prove complementary to other methods and might offer additional insight into the larger question of protein structure prediction.
Pulmonary and Cerebral Fat Embolism Syndrome After Total Knee Replacement

Fat embolism occurs after long bone fracture or orthopedic surgery and usually shows mild symptom. But it rarely results in fat embolism syndrome, presenting as multiorgan dysfunction such as lung, brain and skin. Although the diagnosis of fat embolism syndrome is mostly based on clinical features, we experienced fat embolism syndrome involving lung and brain, showing typical imaging findings in pulmonary computed tomography and brain magnetic resonance image. So we present interesting case about fat embolism syndrome after total knee replacement with reviewing associated literatures including imaging findings.
Rapid analysis of Δ-9-tetrahydrocannabinol in hair using direct analysis in real time ambient ionization orbitrap mass spectrometry.

RATIONALE Forensic hair analysis methods are laborious, time-consuming and provide only a rough retrospective estimate of the time of drug intake. Recently, hair imaging methods using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) were reported, but these methods require the application of MALDI matrix and are performed under vacuum. Direct analysis of entire locks of hair without any sample pretreatment and with improved spatial resolution would thus address a need. METHODS Hair samples were attached to stainless steel mesh screens and scanned in the X-direction using direct analysis in real time (DART) ambient ionization orbitrap MS. The DART gas temperature and the accuracy of the probed hair zone were optimized using Δ-9-tetrahydrocannabinol (THC) as a model compound. Since external contamination is a major issue in forensic hair analysis, sub-samples were measured before and after dichloromethane decontamination. RESULTS The relative intensity of the THC signal in spiked blank hair versus that of quinine as the internal standard showed good reproducibility (26% RSD) and linearity of the method (R(2) = 0.991). With the DART hair scan THC could be detected in hair samples from different chronic cannabis users. The presence of THC was confirmed by quantitative liquid chromatography/tandem mass spectrometry. Zones with different THC content could be clearly distinguished, indicating that the method might be used for retrospective timeline assessments. Detection of THC in decontaminated drug user hair showed that the DART hair scan not only probes THC on the surface of hair, but penetrates deeply enough to measure incorporated THC. CONCLUSIONS A new approach in forensic hair analysis has been developed by probing complete locks of hair using DART-MS. Longitudinal scanning enables detection of incorporated compounds and can be used as pre-screening for THC without sample preparation. The method could also be adjusted for the analysis of other drugs of abuse.
Effect of high-pressure processing and thermal treatment on quality attributes and nutritional compounds of "Songold" plum purée.

UNLABELLED The application of hydrostatic high pressure on a "Songold" plum purée was assessed in comparison with heat pasteurization. To simulate industrial conditions, one-half of the total purée was manufactured with a pretreatment of thermal blanching (TB) and the other half without it (nonthermally blanched, NTB). Changes after thermal treatment and high-pressure processing (HPP: 400, 600 MPa) and after 20 d of refrigerated storage were evaluated. HPP maintained the microbial stability of the purées until the end of the storage period. Polyphenol oxidase activity was lower in TB purées than NTB purées. No treatment was completely effective to stop the enzyme activity, although a significant reduction was reached. Thermally treated purées showed more intense color changes after processing and storage than HP-treated purées. After processing, high-pressure (HP) purées treated at 600 MPa (TB and NTB) increased the extractability of carotenoids compared with initial untreated purée. Nevertheless, at the end of the storage, the highest carotenoid content was found in the TB purée treated at 400 MPa. After processing, total polyphenol levels were similar in all purées. TB and 600 MPa processing was more effective in the maintenance of the polyphenols than the other purées. TB increased the level of antioxidants after storage, compared to NTB purées. A previous TB step is necessary to inactivate browning enzymes before HPP to maintain the levels of bioactive compounds. HPP of plum purée could be a suitable alternative to traditional thermal processing, but more studies are necessary to ensure a major inactivation of polyphenol oxidase. PRACTICAL APPLICATION High-pressure processing is one of the most successful technologies to obtain high-quality fruit purées without appreciable losses in taste, flavor, color, and nutritive value. However, for the introduction of a new technology, some advantages compared to the traditional thermal treatment need to be emphasized. The application of this technology could be reduced due to resistance of certain enzymes to pressurization. For this reason, in some cases the application of a previous thermal blanching can be necessary at industrial level. However, this can reduce the advantages of HPP application. This paper provides interesting information about the storage stability of plum purées after high-pressure treatments and assesses the need for applying heat pretreatments.