Miracle-dz/UniFAR-FTUs huggingface dataset:
Hypoxia-inducible Factor (HIF) Asparagine Hydroxylase Is Identical to Factor Inhibiting HIF (FIH) and Is Related to the Cupin Structural Family*

Activity of the hypoxia-inducible factor (HIF) complex is controlled by oxygen-dependent hydroxylation of prolyl and asparaginyl residues. Hydroxylation of specific prolyl residues by 2-oxoglutarate (2-OG)-dependent oxygenases mediates ubiquitinylation and proteasomal destruction of HIF-α. Hydroxylation of an asparagine residue in the C-terminal transactivation domain (CAD) of HIF-α abrogates interaction with p300, preventing transcriptional activation. Yeast two-hybrid assays recently identified factor inhibiting HIF (FIH) as a protein that associates with the CAD region of HIF-α. Since FIH contains certain motifs present in iron- and 2-OG-dependent oxygenases we investigated whether FIH was the HIF asparaginyl hydroxylase. Assays using recombinant FIH and HIF-α fragments revealed that FIH is the enzyme that hydroxylates the CAD asparagine residue, that the activity is directly inhibited by cobalt(II) and limited by hypoxia, and that the oxygen in the alcohol of the hydroxyasparagine residue is directly derived from dioxygen. Sequence analyses involving FIH link the 2-OG oxygenases with members of the cupin superfamily, including Zn(II)-utilizing phosphomannose isomerase, revealing structural and evolutionary links between these metal-binding proteins that share common motifs.
Distinctions between spatial and verbal working memory: a study using event-related potentials.

BACKGROUND The main manifestation of dementia is a defect in working memory. N-back tasks are frequently used in research on working memory. Researchers can study differences between different loadings by controlling N factors. Furthermore, the interface of N-back tasks can be verbal or visual-spatial. METHODS Event-related potentials under verbal and spatial tasks and different loadings were recorded using a digital electroencephalogram, and analyzed together with behavior results. RESULTS The differences between spatial and verbal processing were found mainly inter-component, where P3 was enhanced in verbal tasks and P2a was enhanced in spatial tasks. Furthermore, P3 was only enhanced in the left hemisphere in the target stimulus. N2 was enhanced by verbal non-target with similar amplitudes. The lateralization was not significant between spatial and verbal tasks. CONCLUSION The difference between spatial and verbal N-back tasks is not only lateralization but also more complex presentations, including P2a (for spatial tasks),P3 (for verbal tasks), and N2 (for non-target detection in verbal tasks).
Fabrication of Micro and Diffractive Optical Devices by Use of Slow Tool Servo Diamond Turning Process

In recent years it has become possible to fabricate freeform optics using multi-axes ultraprecision machines. Unlike conventional process where a single diamond tool is used to machine each individual lens one at a time, this research demonstrates the development of an innovative diamond tool trajectory which allows the entire microlens array or diffractive lens to be machined in a single operation. As compared to the conventional approach where indexing of the workpiece is difficult and unreliable, this process can be used to produce microlenses and diffractive lenses with accurate geometry and optical surface finish. Moreover, the possibility of fabricating any arbitrary shape using the same approach is also demonstrated in this research.
Natural gas properties and flow computation

The detailed procedure for the calculation of thermodynamic properties based on formulations explicit in Helmholtz energy (Lemmon & Starling, 2003) and on AGA-8 detail characterization equation (Starling & Savidge, 1992) is given in (ISO-207651-1, 2005). Here we elaborate an alternative procedure for the calculation of properties of a natural gas that was originally published in the Journal Flow Measurement and Instrumentation (Maric, 2005 & 2007). The procedure is derived using fundamental thermodynamic equations (Olander, 2007), DIPPR AIChE (DIPPR® Project 801, 2005) generic ideal heat capacity equations, and AGA-8 (Starling & Savidge, 1992) extended virial-type equations of state. The procedure specifies the calculation of specific heat capacities at a constant pressure cp and at a constant volume cv, the JT coefficient μJT, and the isentropic exponent κ of a natural gas. The effect of a JT expansion on the accuracy of natural gas flow rate measurements will be pointed out. The possibilities of using the computational intelligence methods - Artificial Neural Networks - ANNs (Ferrari & Stengel, 2005, Wilamowski et al., 2008) and machine learning tools - Group Method of Data Handling - GMDH (Ivakhnenko, 1971, Nikolaev & Iba, 2003) for meta-modeling the effects of natural gas properties in flow rate measurements (Maric & Ivek, 2010) will be illustrated. The practical examples of ANN and GMDH surrogate models for the compensation of natural gas flow rate measurement error caused by the thermodynamic effects, with the corresponding accuracies and execution times will be given. The models are particularly suitable for implementation in low computing power embedded systems.
Parameterization of neutron-induced SER in bulk SRAMs from reverse Monte Carlo Simulations

We used a reverse Monte Carlo method for calculating SEU cross section within the RPP approximation. The method allows reducing calculation times and accounting for long range particles which may be involved in a failure even if produced far from the sensitive volume. A global parameterization of the Soft Error Rate is given as a function of the sensitive volume size and the critical charge. This parameterization allows obtaining quickly the SER of a generic structure, which may be used as a useful guideline.
CONVOLUTIONAL NEURAL NETWORK FOR SPEAKER CHANGE DETECTION IN

The aim of this paper is to propose a speaker change detection technique based on Convolutional Neural Netvork (CNN) and evaluate its contribution to the performance of a speaker diarization system for telephone conversations. For the comparison we used an i-vector based speaker diarization system. The baseline speaker change detection uses Generalized Likelihood Ratio (GLR) metric. Experiments were conducted on the English part of the CallHome corpus. Our proposed CNN speaker change detection outperformed the GLR approach, reducing the Equal Error Rate relatively by 46 %. The final results on speaker diarization system indicate that the use of speaker change detection based on CNN is beneficial with relative improvement of diarization error rate by 28 %.
Online generation and use of macro-actions in forward-chaining planning

This thesis presents a technique for online learning and management of macroactions in forward chaining planning. Macro-actions are learnt on plateaux, areas of the search landscape where the heuristic cannot offer good search guidance, and are reused when future plateaux are encountered. Libraries of macro-actions are generated, storing macro-actions for use on future problems. Several strategies for the management and pruning of such libraries are considered allowing the planner to maintain a smaller collection of macro-actions to minimise potential negative effects on performance. The work is extended to investigate the potential for the simulation of macroactions without increasing the branching factor during search. Actions are reordered during enforced hill-climbing (EHC) search, and best-first search, based on the number of times they have followed the action currently at the tail of the plan in past solutions. In EHC this is equivalent to suggesting two-step macroactions without increasing the branching factor. The techniques are evaluated across a wide range of domains with differing properties under the relaxed planning graph heuristic. The results show that a library of plateau-escaping macro-actions can improve planner performance using only online learning techniques to select the best macro-actions to keep. Search time pruning is shown to be very effective; whilst pruning the library of macro-actions based on the number of times each action is used can offer further improvements. Action reordering has been shown to offer performance improvements, albeit not as great as those produced by using macro-actions, but without the occasional degradation in performance on some problems that is often associated with macro-actions.
Interferon alfa-2b combined with cytarabine versus interferon alone in chronic myelogenous leukemia. French Chronic Myeloid Leukemia Study Group.

BACKGROUND Treatment with interferon prolongs survival in chronic myelogenous leukemia. We conducted a clinical trial to assess the efficacy of treatment with a combination of interferon and cytarabine. METHODS Previously untreated patients with chronic myelogenous leukemia were randomly assigned to receive either hydroxyurea (50 mg per kilogram of body weight per day) and interferon alfa-2b (5 million units per square meter of body-surface area per day), or hydroxyurea and interferon in the same dosages plus monthly courses of cytarabine (20 mg per square meter per day, for 10 days). The end points were overall survival, complete hematologic remission at 6 months, and major cytogenetic response (less than 35 percent Philadelphia chromosome-positive cells in the bone marrow) at 12 months. RESULTS The trial was stopped when a sequential analysis showed a benefit of interferon and cytarabine. A significant improvement in survival was observed in the interferon-cytarabine group (360 patients) as compared with the interferon group (361 patients) (P=0.02; relative risk of death, 0.64; 95 percent confidence interval, 0.44 to 0.93). After three years, the survival rate was 85.7 percent with interferon and cytarabine and 79.1 percent with interferon alone. The rate of hematologic response was higher in the interferon-cytarabine group than in the interferon group (P=0.003). Major cytogenetic responses were observed 12 months after randomization in 126 of 311 patients treated with interferon and cytarabine (41 percent) and in 75 of 314 patients treated with interferon only (24 percent, P<0.001). CONCLUSIONS The combination of interferon and cytarabine, as compared with interferon alone, increases the rate of major cytogenetic response and prolongs survival in patients with the chronic phase of chronic myelogenous leukemia.
Face verification using sparse representation techniques

We present a novel method of face verification which is based on the concept of sparse representation of signals. The sparse representation techniques are used in both feature extraction and classification steps. The proposed method is relatively invariant to changes in imaging conditions such as illumination variations. This is due to the characteristics of the sparse sampling method. Our experimental studies on the XM2VTS and XM2VTS-DARK datasets demonstrate that the proposed method improves the performance of the verification system.
Navigation via Pavlovian conditioning: a robotic bio-constrained model of autoshaping in rats

Within the autonomous robotics literature, bio-inspired models of navigation in organisms (e.g. rats) usually rely on instrumental conditioning processes based on the learning of associations between places in the environment and navigation actions leading to rewarded goal places. This paper presents a neural-network model capable of solving navigation tasks on the basis of Pavlovian conditioning processes (‘autoshaping’) which allow transferring innate approaching behaviours from biologically salient stimuli (e.g., food) to neutral stimuli (e.g., a landmark seen from far away and close to the food). The overall architecture and functioning of the model is biologically constrained on the basis of relevant neuroscientiﬁc anatomical and physiological knowledge on amygdala, nucleus accumbens, and ventral tegmental area. The model is tested with a simulated robotic rat engaged in autoshaping and devaluation experiments. The results show that, although the model allows solving only simple navigation tasks, it produces fast learning and a ﬂexible sensitivity of behaviour to internal states typical of Pavlovian processes. The model is also important for the investigation of adaptive behaviour in general as it clariﬁes the nature of some Pavlovian core mechanisms which play a key role in several forms of learning.
A review of the implication of hypoxanthine excess in the physiopathology of Lesch–Nyhan disease

ABSTRACT Lesch–Nyhan disease is caused by HGprt deficiency, however, the mechanism by which enzyme deficiency leads to the severe neurological manifestations is still unknown. We hypothesized that hypoxanthine excess leads, directly or indirectly, through its action in adenosine transport, to aberrations in neuronal development. We found that hypoxanthine diminishes adenosine transport and enhances stimulation of adenosine receptors. These effects cause an imbalance between adenosine, dopamine, and serotonin receptors in HGprt deficient cells, and cells differentiated with hypoxanthine showed an increase in dopamine, adenosine and serotonin receptors expression. Hypoxanthine deregulates early neuronal differentiation increasing WNT4 and EN1 gene expression.
Improving aggregate user utilities and providing fairness in multi-rate wireless LANs

A distributed medium access control (MAC) protocol is responsible for allocating the shared spectrum efficiently and fairly among competing devices using a wireless local area network. Unfortunately, existing MAC protocols, including 802.11's DCF, achieve neither efficiency nor fairness under many realistic conditions. In this dissertation, we show that both bit and frame-based fairness, the most widely used notions, lead to drastically reduced aggregate throughput and increased average delay in typical environments, in which competing nodes transmit at different data transmission rates. We demonstrate the advantages of time-based fairness, in which each competing node receives an equal share of the wireless channel occupancy time. Through analysis, experiments on a Linux test bed, and simulation, we demonstrate that time-based fairness can lead to significant improvements in aggregate throughput and average delay. Through a game theoretic analysis and simulation, we also show that existing MAC protocols encourage non-cooperative nodes to employ globally inefficient transmission strategies that lead to low aggregate throughput. We show that providing long-term time share guarantees among competing nodes leads rational nodes to employ efficient transmission strategies at equilibriums. We describe two novel solutions, TES (Time-fair Efficient and Scalable MAC protocol) and TBR (Time-based Regulator) that provide time-based fairness and long-term time share guarantees among competing nodes. TBR is a backward-compatible centralized solution that runs at the AP, works in conjunction with DCF, and requires no modifications to clients nor to DCF. TBR is appropriate for existing access point based networks, but not effective when nearby non-cooperative nodes fall under different administrative domains. Our evaluation of TBR on an 802.11b/Linux test bed shows that TBR can improve aggregate TCP throughput by as much as 105% in rate diverse environments. TES is a non-backward compatible distributed contention-based MAC protocol that is effective in any environment, including non-cooperative environments. Furthermore, the aggregate throughputs sustained with increased loads. Through extensive simulation experiments, we demonstrate that TES is significantly more efficient (as much as 140% improvement in aggregate TCP throughput) and fairer than existing MAC protocols including DCF. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.) (Abstract shortened by UMI.)
Analytical Perspective of Interfering Resonances in High-Index-Contrast Periodic Photonic Structures

We investigate the extraordinary behavior of periodic photonic structures within radiation continuum from the perspective of interfering resonance. The coupled-channel equations of both TE-like and TM-like polarizations are reformulated into the similar forms of the quantum-defect theory that describes the interference of resonances belonging to different Coulombic quantum channels. The concepts of closed-channel, open-channel, coupling potential, and eigenvalues are well interpreted. Some iteration techniques, i.e., field-iteration and k-iteration, are proposed to obtain self-consistent solution of the coupled-channel equations. The iterations are important to guarantee quantitative accuracy for high-index-contrast structure, in which the strength of wave interactions is significantly enhanced compared with its low-index-contrast counterpart. The semianalytical results of resonance wavelength, transmissivity/reflectivity spectrum, and band structure agree well with the rigorous coupled-wave analysis (RCWA) and finite-difference time-domain (FDTD) simulation, confirming the accuracy of the iterations. The interfering resonance provides a clear and consistent picture to understand the periodic photonic structure within radiation continuum, and also reveals the intrinsic similarities between the photonic and quantum systems.
Efficiency of gene frequency estimates for the ABO system.

SINCE THE MAXIMUM LELIHOOD gene frequency estimates for the ABO blood group system are efficient, explicit algebraic expressions for their covariance matrix may be useful in simplifying many statistical problems. One such problem is the evaluation of the efficiencies of alternative estimation procedures. We will derive concise expressions for the maximum likelihood variances and covariances and carry out a quantitative comparison of the efficiencies of two simpler estimation schemes, namely those of Bernstein (1925) and Wiener et al. (1929). The following notation is employed throughout the paper. We denote the total number of observations in the sample by N and the observed proportions of individuals of each type by 0, A, B, and AB. Estimates of the gene frequencies, p, q, and r, are denoted by p', q', and r'. The letter V signifies the variance of an estimate, and the subscript B, W, or ML on V denotes the particular estimation procedure under consideration; e.g., VB(p') is the variance of the Bernstein estimate of p. We denote by CV(p', q'), with appropriate subscript, the covariance of p' and q'. All of the variances and covariances considered are understood to be large sample results. Boyd (1956) discusses the accuracy of these results for the sample sizes usually encountered in practice. It is also assumed throughout that neither p, q, nor r is zero; thus, these quantities are used freely as divisors. The special cases in which one of them is zero may be easily treated separately.
Separation of chlorophylls and carotenoids from marine phytoplankton: a new HPLC method using a reversed phase C8 column and pyridine-containing mobile phases

A high-performance liquid chromatographic (HPLC) method based on a reversed-phase C8 column and pyridine-containing mobile phases was developed for the simultaneous separation of chlorophylls and carotenoids. The method is selective enough to resolve monovinyl (MV) and divinyl (DV) pairs of polar chlorophylls and DV chlorophyll a (chl a ) (the marker pigment for the prokaryote Prochlorococcus marinus) from chl a (the MV analogue). Only the pair DV chl alchl b was not resolved. This resolution capability for chlorophylls was only prev~ously achieved using polymeric C),, columns in combination with ammonium acetate or pyridine-containing mobile phases. The proposed method also allows the separation of taxon-specific carotenoids belonging to 8 algal classes, including some critical pigment pairs for previous HPLC methods using C,, columns. The method employs a binary gradient, so it can be used with both low-pressure and high-pressure mixing instruments. Method transferability was tested using 3 HPLC systems. Only a slight adjustment of gradient profile was required to obtain similar results with HPLC equipment having different dwell volumes. The selectivity of the method towards some recently discovered chlorophyll and carotenoid pigments makes it especially suitable for studying not only fleld samples, but also for re-examining the pigment composition of different algal classes.
HEPATOPROTECTIVE ACTIVITY OF LEAF OF METHANOL EXTRACT OF LAURUS NOBILIS.L AGAINST PARACETAMOL INDUCED HEPATOTOXICITY IN RATS

Objective: The present study was conducted to evaluate the hepatoprotective activity of methanol extract of Laurus nobilis against paracetamol induced liver damage in rats. Materials and Methods: The methanol extract of Laurus nobilis (200 mg/kg & 400 mg/kg) was administered orally to the animals with hepatotoxicity induced by paracetamol (400 mg/kg). Silymarin (25mg/kg) was given as reference standard. All the test drugs were administered orally by suspending in 0.5% Carboxy methyl cellulose solution. Results: Paracetamol has enhanced the levels of ALT, AST, ALP and bilirubin, whereas the group receiving high dose (400 mg/kg body weight) methanol extract of Laurus nobilis was effective in protecting the liver against the injury induced by paracetamol in rats than that of low dose (200mg/kg body weight) treated group. This was evident from a significant reduction in serum enzymes alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP) and bilirubin. Conclusion: It was concluded from the result that the methanol extract of Laurus nobilis acts on the liver as a potent scavenger of free radicals to prevent the toxic effects of paracetamol induced hepatotoxicity in rats. Keywords: Laurus nobilis, ALT, AST, ALP, hepatotoxicity.
Comparing Different Classifiers in Sensory Motor Brain Computer Interfaces

A problem that impedes the progress in Brain-Computer Interface (BCI) research is the difficulty in reproducing the results of different papers. Comparing different algorithms at present is very difficult. Some improvements have been made by the use of standard datasets to evaluate different algorithms. However, the lack of a comparison framework still exists. In this paper, we construct a new general comparison framework to compare different algorithms on several standard datasets. All these datasets correspond to sensory motor BCIs, and are obtained from 21 subjects during their operation of synchronous BCIs and 8 subjects using self-paced BCIs. Other researchers can use our framework to compare their own algorithms on their own datasets. We have compared the performance of different popular classification algorithms over these 29 subjects and performed statistical tests to validate our results. Our findings suggest that, for a given subject, the choice of the classifier for a BCI system depends on the feature extraction method used in that BCI system. This is in contrary to most of publications in the field that have used Linear Discriminant Analysis (LDA) as the classifier of choice for BCI systems.