Miracle-dz/UniFAR-FTUs huggingface dataset:
A genetic fuzzy system for large-scale regression

In genetic fuzzy systems (GFS) the size of the problem has a huge influence in the performance of the obtained models, since i) the fuzzy rule bases learned suffer from exponential rule explosion when the number of variables increases, and ii) the convergence time increments with the number of examples. In this paper we present S-FRULER, a scalable distributed version of FRULER which is a GFS that learns simple and linguistic TSK-1 knowledge bases for regression problems. S-FRULER obtains models with high accuracy and low complexity, whilst reducing the algorithm runtime. S-FRULER focuses on splitting the problem into smaller partitions and incorporates a feature selection process for reducing the number of variables used in each partition. Each partition is then solved independently using the FRULER algorithm. The Reduce function obtains linguistic TSK fuzzy rule bases from the information generated in each partition. S-FRULER has been validated in terms of scalability, precision and complexity using 10 large-scale datasets and has been compared with three state of the art GFSs. Experimental results show that S-FRULER scales well while achieving simple models with a linguistic approach and a precision comparable with approximative models.
β‐Catenin and p53 analyses of a breast carcinoma tissue microarray

Aberrant activation of the β‐catenin signaling pathway has been implicated in several malignancies, including breast carcinoma. Recently, it was shown that p53 down‐regulated β‐catenin in a complex fashion. The authors examined the expression of β‐catenin, key members of its signaling pathway, and p53 in a large cohort of breast tumors.
Inactivation of Sonic Hedgehog Signaling and Polydactyly in Limbs of Hereditary Multiple Malformation, a Novel Type of Talpid Mutant

Hereditary Multiple Malformation (HMM) is a naturally occurring, autosomal recessive, homozygous lethal mutation found in Japanese quail. Homozygote embryos (hmm−/−) show polydactyly similar to talpid2 and talpid3 mutants. Here we characterize the molecular profile of the hmm−/− limb bud and identify the cellular mechanisms that cause its polydactyly. The hmm−/− limb bud shows a severe lack of sonic hedgehog (SHH) signaling, and the autopod has 4 to 11 unidentifiable digits with syn-, poly-, and brachydactyly. The Zone of Polarizing Activity (ZPA) of the hmm−/− limb bud does not show polarizing activity regardless of the presence of SHH protein, indicating that either the secretion pathway of SHH is defective or the SHH protein is dysfunctional. Furthermore, mesenchymal cells in the hmm−/− limb bud do not respond to ZPA transplanted from the normal limb bud, suggesting that signal transduction downstream of SHH is also defective. Since primary cilia are present in the hmm−/− limb bud, the causal gene must be different from talpid2 and talpid3. In the hmm−/− limb bud, a high amount of GLI3A protein is expressed and GLI3 protein is localized to the nucleus. Our results suggest that the regulatory mechanism of GLI3 is disorganized in the hmm−/− limb bud.
Selective inhibition of ASIC1a confers functional and morphological neuroprotection following traumatic spinal cord injury

Tissue loss after spinal trauma is biphasic, with initial mechanical/haemorrhagic damage at the time of impact being followed by gradual secondary expansion into adjacent, previously unaffected tissue. Limiting the extent of this secondary expansion of tissue damage has the potential to preserve greater residual spinal cord function in patients. The acute tissue hypoxia resulting from spinal cord injury (SCI) activates acid-sensing ion channel 1a (ASIC1a). We surmised that antagonism of this channel should provide neuroprotection and functional preservation after SCI. We show that systemic administration of the spider-venom peptide PcTx1, a selective inhibitor of ASIC1a, improves locomotor function in adult Sprague Dawley rats after thoracic SCI. The degree of functional improvement correlated with the degree of tissue preservation in descending white matter tracts involved in hind limb locomotor function. Transcriptomic analysis suggests that PcTx1-induced preservation of spinal cord tissue does not result from a reduction in apoptosis, with no evidence of down-regulation of key genes involved in either the intrinsic or extrinsic apoptotic pathways. We also demonstrate that trauma-induced disruption of blood-spinal cord barrier function persists for at least 4 days post-injury for compounds up to 10 kDa in size, whereas barrier function is restored for larger molecules within a few hours. This temporary loss of barrier function provides a “ treatment window” through which systemically administered drugs have unrestricted access to spinal tissue in and around the sites of trauma. Taken together, our data provide evidence to support the use of ASIC1a inhibitors as a therapeutic treatment for SCI. This study also emphasizes the importance of objectively grading the functional severity of initial injuries (even when using standardized impacts) and we describe a simple scoring system based on hind limb function that could be adopted in future studies.
Bacille Calmette-Guérin Lymphadenitis and Recurrent Oral Candidiasis in an Infant With a New Mutation Leading to Interleukin-12 Receptor ß-1 Defi ciency

■ Abstract Mendelian susceptibility to mycobacterial diseases (MSMD) is a rare syndrome characterized by predisposition to infections caused by weakly virulent mycobacteria, such as those in bacille Calmette-Guerin (BCG) vaccine and environmental mycobacteria. Salmonellosis has been reported in almost half of affected patients. Patients are also vulnerable to Mycobacterium tuberculosis infection. Several other infectious diseases may occur, albeit rarely. Mucocutaneous candidiasis is more common. Interleukin-12 receptor s1 (IL-12Rs1) defi ciency is the most frequent genetic cause of MSMD. Here, we describe an infant with a single episode of BCG lymphadenitis who also suffered from recurrent oral candidiasis. Genetic analysis revealed a new homozygous mutation (64+1G>T) in the IL12RB1 gene that caused complete IL-12Rs1 defi ciency. IL-12Rs1 defi ciency should be considered in patients with BCG infection, even in those who experience a single episode of BCG lymphadenitis or recurrent mucocutaneous candidiasis. Every attempt should be made to heighten awareness in countries where BCG vaccination is performed.
A1: end-user programming for web-based system administration

System administrators work with many different tools to manage and fix complex hardware and software infrastructure in a rapidly paced work environment. Through extensive field studies, we observed that they often build and share custom tools for specific tasks that are not supported by vendor tools. Recent trends toward web-based management consoles offer many advantages but put an extra burden on system administrators, as customization requires web programming, which is beyond the skills of many system administrators. To meet their needs, we developed A1, a spreadsheet-based environment with a task-specific system-administration language for quickly creating small tools or migrating existing scripts to run as web portlets. Using A1, system administrators can build spreadsheets to access remote and heterogeneous systems, gather and integrate status data, and orchestrate control of disparate systems in a uniform way. A preliminary user study showed that in just a few hours, system administrators can learn to use A1 to build relatively complex tools from scratch.
Green wireless video sensor networks using FM radio system as control channel

The rise of the Internet of Things and the growth of the IP cameras market are making Wireless Video Sensor Networks (WVSNs) popular. In turn, Wi-Fi is becoming the enabling technology for WVSNs due to its flexibility, high bitrates provided and low cost; however, these networks suffer from three major problems: bad performance, throughput unfairness, and energy inefficiency. In order to address the lack of holistic solutions to solve these problems, we propose the FM-WiFIX+ solution. This solution uses FM radio as an out-of-band control channel to signal when a video sensor should turn its IEEE 802.11 interface OFF, thus saving energy. The results obtained with a proof-of-concept prototype show that for a network with 7 nodes the proposed solution can achieve gains of energy up to 48 %, while maintaining good levels of performance and throughput fairness.
UvA-DARE ( Digital Academic Repository ) Towards Task-Based Temporal Extraction and Recognition

We seek to improve the robustness and portability of temporal information extraction systems by incorporating data-driven techniques. We present two sets of experiments pointing us in this direction. The first shows that machine-learning-based recognition of temporal expressions not only achieves high accuracy on its own but can also improve rule-based normalization. The second makes use of a staged normalization architecture to experiment with machine learned classifiers for certain disambiguation sub-tasks within the normalization task.
Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks

SUMMARY The Boolean network (BN) can be used to create discrete mathematical models of gene regulatory networks. In this paper, we consider three problems on BNs that are known to be NP-hard: detection of a singleton attractor, finding a control strategy that shifts a BN from a given initial state to the desired state, and control of attractors. We propose integer programming-based methods which solve these problems in a unified manner. Then, we present results of computational experiments which suggest that the proposed methods are useful for solving moderate size instances of these problems. We also show that control of attractors is Σ p hard, which suggests that control of attractors is harder than the other two problems.
Development of apparent viscosity test for hot-poured crack sealants.

Current crack sealant specifications focus on utilizing simple empirical tests such as penetration, resilience, flow, and bonding to cement concrete briquettes (ASTM D3405) to measure the ability of the material to resist cohesive and adhesion failures. There is, however, no indication of the pertinence of these standard tests to predict the success of field installation and sealant performance. In an effort to bridge the gap between sealant fundamental properties and field performance, performance-based guidelines for selection of hot-poured crack sealants are currently being developed. This report focuses on the development of the apparent viscosity test method. This test uses a modified version of the Brookfield rotational viscometer. Based on the results of this study, the measured apparent viscosity of hot-poured crack sealant using SC4-27 spindle at 60rpm (20.4s-1) at the recommended installation temperature was determined to be reasonably representative of sealant viscosity at shear rates resembling field application. To ensure measurement consistency and stability, a 20min melting time and a 30-s waiting time prior to data collection are recommended. To establish precision and bias for the test, a round robin testing was conducted among seven laboratories. Average coefficient of variation within and between laboratories was found to be 2% and 6%, respectively. Using the data from the round robin testing, and based on ASTM precision and bias standard (ASTM practices C802 and C670), maximum permissible differences within a laboratory and between laboratories were found to be 4.6% and 16.9%. Considering the high polymer or crumb rubber content in crack sealants and sealant temperature sensitivity, the repeatability and reproducibility of the developed test is within an acceptable range. These values are comparable to those of asphalt binder: 3.5% and 14.5% based on ASTM D4402-02 and 3.5% and 12.1% based on AASHTO 2006 T316.
A reduced order sampled-data dynamic model for a series-parallel resonant converter

A novel reduced fifth-order sampled data dynamic model for the self-sustained series-parallel resonant converter with inductive output filter is described in this paper. A generalized sampled data algorithm suitable for any switched converter is given with a step-by-step procedure. Based on this algorithm, accurate simple state-space large signal and small signal dynamic models are derived. The main advantage of the sampled data technique is its systematic procedure, high accuracy, and less mathematical effort. The proposed dynamic models are verified by the analytical, simulation, and experimental results.
The modifying influence of country development on the effect of individual educational attainment on self-rated health.

OBJECTIVES We investigated how much the Human Development Index (HDI), a global measure of development, modifies the effect of education on self-reported health. METHODS We analyzed cross-sectional World Health Survey data on 217,642 individuals from 49 countries, collected in 2002 to 2005, with random-intercept multilevel linear regression models. RESULTS We observed greater positive associations between educational levels and self-reported good health with increasing HDI. The magnitude of this effect modification of the education-health relation tended to increase with educational attainment. For example, before adjustment for effect modification, at comparable HDI, on average, finishing primary school was associated with better general health (b = 1.49; 95% confidence interval [CI] = 1.18, 1.80). With adjustment for effect modification by HDI, the impact became 4.63 (95% CI = 3.63, 5.62) for every 0.1 increase in HDI. Among those who completed high school, these associations were, respectively, 5.59 (95% CI = 5.20, 5.98) and 9.95 (95% CI = 8.89, 11.00). CONCLUSIONS The health benefits of educational attainment are greater in countries with greater human development. Health inequalities attributable to education are, therefore, larger in more developed countries.
The sigma profile: A formal tool to study organization and its evolution at multiple scales

The σ profile is presented as a tool to analyze the organization of systems at different scales, and how this organization changes in time. Describing structures at different scales as goal-oriented agents, one can define σ ∈ [0,1] (satisfaction) as the degree to which the goals of each agent at each scale have been met. σ reflects the organization degree at that scale. The σ profile of a system shows the satisfaction at different scales, with the possibility to study their dependencies and evolution. It can also be used to extend game theoretic models. The description of a general tendency on the evolution of complexity and cooperation naturally follows from the σ profile. Experiments on a virtual ecosystem are used as illustration. © 2011 Wiley Periodicals, Inc.
Virtual screening of chemical libraries for drug discovery

Background: Virtual screening has become an established tool for lead generation. In recent years, the computational science behind these tools has evolved to become ever more sophisticated and diverse, whilst the quantity of published successes has continued to increase. Objective: By understanding the origins of virtual screening, the theoretical limitations behind it, and the published examples of success, to understand the current and potential value of these techniques to drug discovery. Method: By reviewing the underlying science and current practice of virtual screening, this article demonstrates the ability of the methods to generate lead molecules. Conclusion: Based on current literature and comparison with ‘wet’ screening techniques such as high-throughput screening and fragment screening, the author suggests areas that need to be addressed if the science of virtual screening is to fulfil its potential.
Increased Plasma Levels of Asymmetric Dimethylarginine in Nonalcoholic Fatty Liver Disease

Background and Aim Cardiovascular disease (CVD) is the most frequent cause of death in nonalcoholic fatty liver disease (NAFLD). Insulin resistance, hepatic dysfunction, and chronic inflammation are factors interacting in explaining the increased CVD incidence in NAFLD. We aimed to evaluate the effects of insulin resistance and inflammatory biomarkers on asymmetric dimethylarginine (ADMA) levels, a predictor of CVD. We also investigated relationship between these markers and histological findings in patients with NAFLD. Patients and Methods Plasma ADMA, high-sensitivity C-reactive protein (hs-CRP), interleukin 6 (IL-6), and homeostasis model assessment of insulin resistance (HOMA-IR) were measured in 70 patients with histologically verified NAFLD (53 with nonalcoholic steatohepatitis [NASH], 17 with non-NASH) and 12 controls. Results The HOMA-IR (5.3 [3.9] vs 1.9 [1], P < 0.001), hs-CRP (5.6 [4.2] vs 2.2 [2.3] mg/L, P < 0.001), ADMA (0.81 [0.25] vs 0.48 [0.24] μmol/L, P = 0.005), and IL-6 (4.1 [1.2] vs 1.0 [0.4] pg/mL, P < 0.001) levels were all found higher in the NAFLD group than the control group. The ADMA levels were significantly higher in patients with NAFLD independent from HOMA-IR and body composition (P = 0.02). The IL-6 and HOMA-IR levels of the NASH group were found significantly higher than those of the non-NASH group. The only determinant significantly correlated to ADMA was HOMA-IR. Conclusions Our data suggested that although ADMA levels are independently higher in NAFLD, the only determinant correlated to ADMA is HOMA-IR and not inflammatory biomarkers (hs-CRP, IL-6) or presence/absence of NASH.
Adaptive reconstruction method of missing textures based on kernel canonical correlation analysis

This paper presents an adaptive reconstruction method of missing textures based on kernel canonical correlation analysis (CCA). The proposed method calculates the correlation between two areas, which respectively correspond to a missing area and its neighbor area, from known parts within the target image and realizes the estimation of the missing textures. In order to obtain this correlation, the kernel CCA is applied to each set containing the same kind of textures, and the optimal result is selected for the target missing area. Specifically, a new approach monitoring errors caused in the above estimation process enables the selection of the optimal result. This approach provides a solution to the problem in traditional methods of not being able to perform adaptive reconstruction of the target textures due to the missing intensities. Experimental results show subjective and quantitative improvement of the proposed reconstruction technique over previously reported reconstruction techniques.
A Haptic Parameter Exploration Method for Force Feedback Devices

Touch sensation called “haptic” interface attracts increasing attentions from many researchers as a way for providing a new interaction modality. Integrating the haptic interface with traditional audio-visual communication channels has a potential ability to create more sophisticated human computer interaction (HCI) method and application systems. One big hurdle for utilizing the haptic interface is to design appropriate touch feelings presented in the system. It requires the optimization of various parameter values for presenting the realistic touch feelings through the specific devices. We designed and implemented a device independent method enabling users to easily design various haptic effects (touch feelings) without any special knowledge and technical skills. We implemented a haptic effect design system targeted at using the PHANTOM TM force feedback device based on the method. We also conducted an experiment to verify the effectiveness of the implemented system.
A Unique and Conserved Neutralization Epitope in H5N1 Influenza Viruses Identified by an Antibody against the A/Goose/Guangdong/1/96 Hemagglutinin

ABSTRACT Despite substantial efforts to control and contain H5N1 influenza viruses, bird flu viruses continue to spread and evolve. Neutralizing antibodies against conserved epitopes on the viral hemagglutinin (HA) could confer immunity to the diverse H5N1 virus strains and provide information for effective vaccine design. Here, we report the characterization of a broadly neutralizing murine monoclonal antibody, H5M9, to most H5N1 clades and subclades that was elicited by immunization with viral HA of A/Goose/Guangdong/1/96 (H5N1), the immediate precursor of the current dominant strains of H5N1 viruses. The crystal structures of the Fab′ fragment of H5M9 in complexes with H5 HAs of A/Vietnam/1203/2004 and A/Goose/Guangdong/1/96 reveal a conserved epitope in the HA1 vestigial esterase subdomain that is some distance from the receptor binding site and partially overlaps antigenic site C of H3 HA. Further epitope characterization by selection of escape mutants and epitope mapping by flow cytometry analysis of site-directed mutagenesis of HA with a yeast cell surface display identified four residues that are critical for H5M9 binding. D53, Y274, E83a, and N276 are all conserved in H5N1 HAs and are not in H5 epitopes identified by other mouse or human antibodies. Antibody H5M9 is effective in protection of H5N1 virus both prophylactically and therapeutically and appears to neutralize by blocking both virus receptor binding and postattachment steps. Thus, the H5M9 epitope identified here should provide valuable insights into H5N1 vaccine design and improvement, as well as antibody-based therapies for treatment of H5N1 infection.
Patients With Chronic Pancreatitis Have Islet Progenitor Cells in Their Ducts, but Reversal of Overt Diabetes in NOD Mice by Anti-CD3 Shows No Evidence for Islet Regeneration

Monoclonal antibodies to T-cell coreceptors have been shown to tolerise autoreactive T-cells and prevent or even reverse autoimmune pathology. In type 1 diabetes, there is a loss of insulin-secreting β-cells, and a cure for type 1 diabetes would require not only tolerance induction but also recovery of the functional β-cell mass. Although we have previously shown that diabetic mice have increased numbers of ductal progenitors in the pancreas, there is no evidence of any increase of insulin-secreting cells in the ducts. In contrast, in the adult human pancreas of patients with chronic pancreatitis, we can demonstrate, in the ducts, increased numbers of insulin-containing cells, as well as cells containing other endocrine and exocrine markers. There are also significantly increased numbers of cells expressing the homeodomain protein, pancreatic duodenal homeobox-1. Anti-CD3 has been shown to reverse overt diabetes in NOD mice; thus, we have used this model to ask whether monoclonal antibody–mediated inhibition of ongoing β-cell destruction enables islet regeneration to occur. We find no evidence that such monoclonal antibody therapy results in either regeneration of insulin-secreting β-cells or of increased proliferation of islet β-cells.