Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics of an immune response in house sparrows Passer domesticus in relation to time of day, body condition and blood parasite infection

in relation to time of day,body condition and blood parasite infection. – Oikos 101: 291–298.The T-cell mediated response to a challenge of the immune system with phytohemag-glutinin (PHA) is a common measure used in ecological studies of host-parasiteinteractions or parasite-mediated selection. We investigated the temporal dynamics ofthis response in house sparrows
IgG subclass, IgE, and IgA anti-trinitrophenyl antibody production within trinitrophenyl-Ficoll-responsive B cell clones. Evidence in support of three distinct switching pathways

The IgM, IgG subclass, IgE, and IgA anti-trinitrophenyl (TNP) antibody (Ab) response of B cells to the type 2 antigen TNP-Ficoll was studied in athymic nude mice and in the in vitro splenic focus assay. Results from the splenic focus assay in which purified B lymphocyte preparations had been transferred to irradiated nu/nu recipients indicate that many TNP-Ficoll stimulated B cell clones secrete multiple isotypes and hence appear to be undergoing intraclonal isotype switching. Although the frequency of clones secreting each of the IgG subclasses was found to correlate with 5' to 3' Igh-gamma gene order, the frequency of IgE and IgA-secreting clones did not appear to be influenced by the respective position of Igh-epsilon and Igh-alpha on the chromosome. Unlike clones that secreted anti-TNP Ab of the IgG subclasses, IgE and IgA anti-TNP Ab-secreting clones did not have a high propensity for coexpression of isotypes encoded by 5' Igh-C genes. These data suggest that three distinct switching pathways may be employed by B cells responding to TNP-Ficoll: a common IgG pathway, an IgE pathway, and an IgA pathway. The presence of T cells resulted in a preferential enhancement of the production of anti-TNP Ab of those IgG subclasses which were least represented in the absence of T cells, i.e., IgG2b and IgG2a. No significant enhancement of IgE anti-TNP clonal frequency was found in the presence of T lymphocytes, but T cells were found to significantly enhance the clonal expression of IgA anti-TNP Ab. Although a relatively large number of B cell clones were found to synthesize IgE and IgA anti-TNP Ab in the splenic focus assay, relatively little or no secretion of these isotypes was detected in immune mice. Possible explanations for this apparent discrepancy are discussed.
Multimedia Content Segmentation Based on Speaker Recognition

Many recent works attempt to index multimedia data based on characteristics such as speaker identity and emotional content. In this work, speaker segmentation is performed on movies to extract the shots in which the target actor is speaking. A case of speaker identification on conversational speech under noisy conditions-this work is organized into two phases; an audio classification phase, for the removal of non-speech content, followed by a speaker recognition phase. Along with the speaker models, Gaussian mixture models are constructed for sound effects like fight sequences and drum beats to refine the removal of non-speech sounds. Results prove the effectiveness of this deviation from the conventional methods
SOX2 haploinsufficiency is associated with slow progressing hypothalamo-pituitary tumours

SOX2 is an early developmental transcription factor and marker of stem cells that has recently been implicated in the development of the pituitary gland. Heterozygous SOX2 mutations have been described in patients with hypopituitarism and severe ocular abnormalities. In the majority of published cases, the pituitary gland is either small or normal in size. Here, we report two unrelated patients with SOX2 haploinsufficiency (a heterozygous gene deletion and a novel c.143TC>AA/p.F48X mutation) who developed nonprogressive pituitary tumors of early onset, suggesting a congenital etiology. The truncating mutation resulted in significant loss of function and impaired nuclear localization of the mutant protein, in addition to a failure to repress β‐catenin transcriptional activity in vitro. This is the first indication that SOX2 haploinsufficiency is implicated in the generation of pituitary tumors with distinct clinical characteristics, possibly mediated via its effects on the Wnt signaling pathway. 32:1376–1380, 2011. ©2011 Wiley Periodicals, Inc.
RSS-based indoor positioning utilizing Firefly algorithm in Wireless Sensor networks

The ongoing decrease in the cost of handheld wireless devices, coupled with the growing demand for these, has increased the demand for localization applications. Consequently, position estimation is a problem that has been addressed using a variety of technologies. Owing to the simplicity of radio signal strength (RSS) methods, the most recent research on localization using wireless sensor networks uses RSS-based algorithms. Our present study comes up with a novel positioning technique utilizing RSS method and a meta-heuristic optimization, namely, Firefly algorithm (FFA). Meta-heuristic algorithms are proven to outperform the traditional gradient based algorithms for optimization problems. The first contribution of this work is involving FFA in RSS-based positioning. Secondly, involve Kalman Filtering in position prediction, and for barometer sensor measurements for attitude estimation. The experimental results show that the proposed algorithm can accurately determine the position with error distance less than two and half meters.
A biologically inspired immune system for computers

Computer viruses are the rst and only form of arti cial life to have had a measurable impact on society Cur rently they are a relatively manageable nuisance How ever two alarming trends are likely to make computer viruses a much greater threat First the rate at which new viruses are being written is high and accelerating Second the trend towards increasing interconnectivity and interoperability among computers will enable com puter viruses and worms to spread much more rapidly
Using high-frequency ultrasound statistical scattering model to assess Nonalcoholic Fatty Liver Disease (NAFLD) in mice

In non-invasive ultrasound (US) imaging, diagnosis of Nonalcoholic Fatty Liver Disease (NAFLD) often depends on the subjective judgment of the image brightness and speckle uniformity. In order to assist the differentiation between the NAFLD and the normal liver in US diagnoses, quantitative tissue characterization based on acoustic backscattering behaviors are performed using high-frequency US system in mice. Two statistical models of acoustic scattering, Nakagami and Acoustic Structure Quantification (ASQ), are compared in this study. Simulations of random Rayleigh amplitudes indicate an reciprocal relation between the scattering parameters of the two models. In animal experiments, mice were fed with high-fat diet for 12 weeks to induce NAFLD. Experimental results demonstrated that, though both models can distinguish normal liver and NAFLD liver with statistical conference, ASQ appears to be more stable and provides higher sensitivity.
The Advanced Radiometric Ray-Tracer: ARARAT for plant canopy reflectance simulation

A Monte Carlo ray tracing system, known as 'the Advanced RAdiometric RAy Tracer' (ARARAT) has been developed as a tool for simulating radiance as measured by remote sensing instruments. The system takes 3-D geometric models of vegetation and/or surfac~ topographic data (Digital Elevation ModelDEM) with associated radiometric attributes, and renders a scene for given illumination conditions for a given set of sensor characteristics. ARARAT has been designed primarily for use with plant geometric data generated with the UCL Botanical Plant Modelling System to provide a simulation system capable of realistically simulating directional radiance and reflectance to allow investigations of the dependence of the signal received at a remote sensing instrument on the complex radiometric and geometric properties of plant canopies. The design philosophy and implementation of ARARAT are discussed in this paper, with reference to Monte Carlo methods of estimating the integral of the radiance rendering equation. Results of simulated maize (Zea mais) canopy reflectance are presented for the simple rendering case of singly-scattered directional radiance, and compared with values measured in the field.
Nonparametric Simulation of Signal Transduction Networks with Semi-Synchronized Update

Simulating signal transduction in cellular signaling networks provides predictions of network dynamics by quantifying the changes in concentration and activity-level of the individual proteins. Since numerical values of kinetic parameters might be difficult to obtain, it is imperative to develop non-parametric approaches that combine the connectivity of a network with the response of individual proteins to signals which travel through the network. The activity levels of signaling proteins computed through existing non-parametric modeling tools do not show significant correlations with the observed values in experimental results. In this work we developed a non-parametric computational framework to describe the profile of the evolving process and the time course of the proportion of active form of molecules in the signal transduction networks. The model is also capable of incorporating perturbations. The model was validated on four signaling networks showing that it can effectively uncover the activity levels and trends of response during signal transduction process.
Semiparametric Mean Field Variational Bayes: General Principles and Numerical Issues

We introduce the term semiparametric mean field variational Bayes to describe the relaxation of mean field variational Bayes in which some density functions in the product density restriction are pre-specified to be members of convenient parametric families. This notion has appeared in various guises in the mean field variational Bayes literature during its history and we endeavor to unify this important topic. We lay down a general framework and explain how previous relevant methodologies fall within this framework. A major contribution is elucidation of numerical issues that impact semiparametric mean field variational Bayes in practice.
The R ⊕-tree : Incorporating Object Partitioning into the R 0-tree

During the past three decades, researchers devoted much effort to developing efficient techniques to index spatial data. Of those proposed, the R-tree[1] is perhaps the most important. R-trees are ubiquitous in commercial database management systems, and they find myriad applications in other disciplines as well. In this paper, we seek to improve the state-of-the-art R-tree[2] by introducing spatial extent based partitioning of the indexed objects. We define the distention and fragmentation bound metrics and we develop three partitioning schemes, one of which employs unconditional partitioning and two that employ conditional partitioning. We evaluate the performance of each partitioning scheme for various threshold values of the metrics. Our results show that partitioning objects based on spatial extent is useful when indexing spatial data, improving query performance on average by five percent and in some cases by as much as ten percent.
Cluster-based data oriented hashing

Many multidimensional hashing schemes have been actively studied in recent years, providing efficient nearest neighbor search. Generally, we can distinguish several hashing families, such as learning based hashing, which provides better hash function selectivity by learning the dataset distribution. The spacial hashing family proposes a suitable partition of the multidimensional space, more adapted to data points distribution. In spite of the efficiency of multidimensional hashing techniques to solve the nearest neighbor search problem, these techniques suffer from scalabity issues. In this paper, we propose a novel hashing algorithm, named Cluster Based Data Oriented Hashing, that combines space hashing and learning based hashing techniques. The proposed approach applies first a clustering algorithm for structuring the multidimensional space into clusters. Then, in each cluster, a learning based hashing algorithm is applied by selecting an appropriate hash function that fits the data distribution. Experimental comparisons with standard Euclidean Locality Sensitive Hashing demonstrate the effectiveness of the proposed method for large datasets.
VARIATIONAL ASSIMILATION OF TAO AND XBT DATA IN THE HOPE OGCM, ADJUSTING THE SURFACE FLUXES IN THE TROPICAL OCEAN

A four-dimensional variational method has been developed that assimilates XBT and TAO sub-surface temperature data into the Hamburg Ocean Primitive Equation model. The method decreases the misfit between model and observed ocean temperatures by adjusting the surface forcing. The main goal of the assimilation scheme is to improve ocean analyses in the tropical Pacific. As a first study, only wind stress is adjusted in the assimilation. In two identical-twin experiments it is demonstrated that the scheme works well in the equatorial Pacific. The scheme is capable to reduce errors in the ocean analysis which originate either from the wind-stress forcing or the initial state. The impact of model errors on the data assimilation is investigated in an experiment with real observations. In this experiment, the temperature innovations near the equator are comparable to those of an Optimal Interpolation data-assimilation scheme.
Codification and Collaboration: Information Quality in Social Media

This paper argues that social media combines the codification and collaboration features of earlier generations of knowledge management systems. This combination potentially changes the way knowledge is created, potentially requiring new theories and methods for understanding these processes. We forward the specialized social network method of two-mode networks as one such approach. We examine the information quality of 16,244 articles built through 2,677,397 revisions by 147,362 distinct contributors to Wikipedia’s Medicine Wikiproject. We find that the structure of the contributor-artifact network is associated with information quality in these networks. Our findings have implications for managers seeking to cultivate effective knowledge creation environments using social media and to identify valuable knowledge created external to the firm.
Eotaxin-2 Th 2 Cytokines , Th 17 Cytokines , and ofInflammation Associated with Suppression Alendronate Attenuates Eosinophilic Airway Yamamoto

Bisphosphonates (BPs) have been widely used to treat osteoporosis. They act by inhibiting farnesyl diphosphate synthase in the mevalonate pathway. This resembles the action of statins, whose immune-modulating effect has recently been highlighted. In contrast , the effect of BPs on immune responses has not been elucidated well. In this study, we examined the effect of alendronate (ALN), a nitrogen-containing BP, on allergic airway inflammation in a mouse model. BALB/c mice were sensitized twice with OVA and challenged three times with nebulized OVA to induce eosinophilic airway inflammation. ALN was administered by an intragastric tube before each inhalation. ALN strongly suppressed airway eosinophilia and Th2, as well as Th17 cytokine production in the lung. ALN also attenuated eotaxin-2 production in the lung. Immunohistochemistry demonstrated that the major cell source of eotaxin-2 was peribronchial/perivascular macrophages, and flow cytometrical studies confirmed that ALN decreased eotaxin-2 expression in these macrophages. Furthermore, ALN attenuated eotaxin-2 production from mouse pleural macrophages and human monocyte/ macrophage-like THP-1 cells in vitro. These results suggest that ALN suppressed Ag-induced airway responses in the mouse model. The suppression of eotaxin-2 production from macrophages appears to be one of ALN's immunomodulatory effects, whereas the mechanism by which ALN suppressed Th2 and Th17 responses could not be fully elucidated in this study. Although a clinical study should be conducted, ALN could be a novel therapeutic option for asthma. B isphosphonates (BPs) are widely used for the treatment of osteoporosis in the elderly and for other bone diseases such as bone cancer. Second-generation " nitrogen-containing BPs (N-BPs), such as alendronate (ALN) and risedronate, inhibit farnesyl pyrophosphate synthase in the mevalonate pathway. The mechanism of their action is similar to that of statins, the inhibition of HMG-CoA reductase. The immune-modulating effect of statins has recently been elucidated (1). The suppressive effects of statins have been reported in many animal models of immune-mediated disorders (2–6). For example , several studies have been conducted using simvastatin (7, 8) or pravastatin (9) in models of allergic airway inflammation. We also showed that pravastatin suppressed allergic airway inflammation partly by suppressing the Ag-presenting capacity of dendritic cells (10). Based on their similar mechanism of action to statins, N-BPs may affect allergic airway inflammation; however, this possibility has not yet been examined. N-BPs are mainly distributed in the bones. Few reports have examined the tissue distribution of BPs in the respiratory system. Hisaka and coworkers (11) reported that …
A study of BPR based iris recognition method

Biomimetic pattern recognition (BPR) has been proposed for several years, but it has never been applied to iris recognition yet. In this paper, a new iris recognition method combined with BPR was proposed here. Experiments on the CASIA iris image database show that the iris recognition method based on BPR is reliable and efficient.
An Anti-Interleukin-2 Receptor Drug Attenuates T- Helper 1 Lymphocytes-Mediated Inflammation in an Acute Model of Endotoxin-Induced Uveitis

The aim of the present study was to evaluate the anti-inflammatory efficacy of Daclizumab, an anti-interleukin-2 receptor drug, in an experimental uveitis model upon a subcutaneous injection of lipopolysaccharide into Lewis rats, a valuable model for ocular acute inflammatory processes. The integrity of the blood-aqueous barrier was assessed 24 h after endotoxin-induced uveitis by evaluating two parameters: cell count and protein concentration in aqueous humors. The histopathology of all the ocular structures (cornea, lens, sclera, choroid, retina, uvea, and anterior and posterior chambers) was also considered. Enzyme-linked immunosorbent assays of the aqueous humor samples were performed to quantify the levels of the different chemokine and cytokine proteins. Similarly, a biochemical analysis of oxidative stress-related markers was also assessed. The inflammation observed in the anterior chamber of the eyes when Daclizumab was administered with endotoxin was largely prevented since the aqueous humor protein concentration substantially lowered concomitantly with a significant reduction in the uveal and vitreous histopathological grading. Th1 lymphocytes-related cytokines, such as Interleukin-2 and Interferon-γ, also significantly reduced with related anti-oxidant systems recovery. Daclizumab treatment in endotoxin-induced uveitis reduced Th1 lymphocytes-related cytokines, such as Interleukin-2 and Interferon gamma, by about 60–70% and presented a preventive role in endotoxin-induced oxidative stress. This antioxidant protective effect of Daclizumab may be related to several of the observed Daclizumab effects in our study, including IL-6 cytokine regulatory properties and a substantial concomitant drop in INFγ. Concurrently, Daclizumab treatment triggered a significant reduction in both the uveal histopathological grading and protein concentration in aqueous humors, but not in cellular infiltration.
60 Extending UML for Modelling Geographical Information Systems

On this work we present a Unified Modelling Language profile for representing Geographic Information Systems, given the problems faced in this area in the modelling of some specific concepts associated to the field such as: geospatial information modelling, geographic class interaction and specific hardware devices. We describe some examples using class diagrams and deployment diagrams through the Software Development Process of one case of study. This is a part of one more general profile that should include specifications for some other kinds of Unified Modelling Language diagrams required for Geographic Information Systems modelling. The proposed profile helps on direct modelling over software development standard methodologies and besides using conceptual modelling. Based on the presented sample diagrams, it can be used on GIS modelling and also extended for other diagrams beyond class and deployment diagrams, given that most of the target UML classes (mapped classes) are the commonly used when modelling using UML. The proposal also respects existing specific variants commonly used when developing this kind of applications in Web environment.
Impact of Drug Abuse on Face Recognition Systems: A Preliminary Study

Drug abuse leads to high degree of the change in the facial structure of a person due to multiple factors which include loss of fat in face, change of facial structure due to changes in facial muscles and change of skin texture due to appearance of acnes. The combination of such effects lead to completely deformed face which presents a complex challenge to face based authentication systems. To study the impact of the drug-abuse on face recognition systems, in this work, we create a new face database collected before and after the drug-abuse. The newly collected database which is referred as Drug Abuse Database (DAD) consists of images obtained from 101 subjects. Further, the collected database is analysed using various state-of-art face recognition algorithms along with a widely used commercial-off-the-shelf (COTS) system. The obtained performance of GMR = 12.90% at FMR = 0.01% indicates the challenge presented by such face images and underlines the importance of newer algorithms to handle such challenge.
Evaluating Retail Recommender Systems via Retrospective Data: Lessons Learnt from a Live-Intervention Study

Performance evaluation via retrospective data is essential to the development of recommender systems. However, it is necessary to ensure that the evaluation results are representative of live, interactive behaviour. We present a case study of several common evaluation strategies applied to data from a live intervention. The intervention is designed as a case-control experiment applied to two cohorts of consumers (active and non-active) from an online retailer. This results in four binary hit rate indicators of live performance to compare with evaluation strategies applied to the same basket data as was available immediately prior to the recommendations being made, treating them as historical data. It was found that in this case none of the standard evaluation strategies predicted comparable binary hit rates to those observed during the live intervention. We argue that they may not sufficiently represent live, interactive behaviour to usefully guide system development with retrospective data. We present a novel evaluation strategy that consistently provides binary hit rates comparable to the live results, which seems to mirror the actual operation of the recommender more closely, paying particular attention to the principles and constraints that are expected to apply. Key Words—Recommender Systems, Performance Evaluation, Model Selection & Comparison, Business Applications, Lessons Learnt