Miracle-dz/UniFAR-FTUs huggingface dataset:
An Invariant Large Margin Nearest Neighbour Classifier

The k-nearest neighbour (kNN) rule is a simple and effective method for multi-way classification that is much used in Computer Vision. However, its performance depends heavily on the distance metric being employed. The recently proposed large margin nearest neighbour (LMNN) classifier [21] learns a distance metric for kNN classification and thereby improves its accuracy. Learning involves optimizing a convex problem using semidefinite programming (SDP). We extend the LMNN framework to incorporate knowledge about invariance of the data. The main contributions of our work are three fold: (i) Invariances to multivariate polynomial transformations are incorporated without explicitly adding more training data during learning - these can approximate common transformations such as rotations and affinities; (ii) the incorporation of different regularizes on the parameters being learnt; and (Hi) for all these variations, we show that the distance metric can still be obtained by solving a convex SDP problem. We call the resulting formulation invariant LMNN (lLMNN) classifier. We test our approach to learn a metric for matching (i) feature vectors from the standard Iris dataset; and (ii) faces obtained from TV video (an episode of 'Buffy the Vampire Slayer'). We compare our method with the state of the art classifiers and demonstrate improvements.
Correlation among Quasi-Periodic Oscillation Frequencies and Quiescent-State Duration in Black Hole Candidate GRS 1915+105

We discover a definite correlation between the frequency of the quasi-periodic oscillations (QPOs) in quiescent states and the duration of the quiescent state of the transient X-ray source GRS 1915+105. We find that while the QPO frequency can be explained by the oscillation of shocks in accretion flows, the switching of burst to quiescent states (and vice versa) and their duration can be explained by assuming an outflow from the postshock region. The duration of the quiescent state is inversely related to the QPO frequency. We derive this relation. We also find the correlation between the observed low (~0.001-0.01 Hz) and the intermediate (1-10 Hz) QPO frequencies. Our analytical solutions are verified by analyzing several days of public domain data from the Rossi X-Ray Timing Explorer.
The use of radial basis functions for the solution of a partial differential equation with an unknown time-dependent coefficient

In this paper, a numerical technique is presented for the solution of a parabolic partial differential equation with a time-dependent coefficient subject to an extra measurement. For solving the discussed inverse problem, at first we transform it into a nonlinear direct problem and then use the proposed method. This method is a combination of collocation method and radial basis functions. The radial basis functions (RBFs) method is an efficient meshfree technique for the numerical solution of partial differential equations. The main advantage of numerical methods which use radial basis functions over traditional techniques is the meshless property of these methods. The accuracy of the method is tested in terms of maximum and RMS errors. Illustrative examples are included to demonstrate the validity and applicability of the technique.
A novel optical network on chip design for future generation of multiprocessors system on chip

The paper presents a novel Optical Network on Chip (ONoC) relying on the multi-level optical layer design paradigm and called “OMNoC”. The proposed ONoC relies on multi-level microring resonator allowing efficient light coupling between superposed waveguides. Such microring resonator avoids using waveguide crossing, which contribute to reduce propagation losses. Preliminary experimental results demonstrate the potential of multi-level optical layer for reducing power consumption and increasing scalability in the proposed ONoC.
Parabolic Adjustment of Image Clearness Algorithm Based on Retinex Theory

If the histogram equalization on the basis of Retinex theory is used to an image, an excessive enhancement or darkening of brightness may arise. Aimed at these problems, this paper presents a parabolic adjustment of image clearness algorithm, which is mainly based on Retinex theory, equalizing histogram with the aid of parabolic transfer function, while stretching the contrast of image. Experimental results show that the proposed algorithm can make image more detailed, contour smoother, the whole image clearer and the visual effects more optimized.
The Genetic Architecture of Adaptations to High Altitude in Ethiopia

Although hypoxia is a major stress on physiological processes, several human populations have survived for millennia at high altitudes, suggesting that they have adapted to hypoxic conditions. This hypothesis was recently corroborated by studies of Tibetan highlanders, which showed that polymorphisms in candidate genes show signatures of natural selection as well as well-replicated association signals for variation in hemoglobin levels. We extended genomic analysis to two Ethiopian ethnic groups: Amhara and Oromo. For each ethnic group, we sampled low and high altitude residents, thus allowing genetic and phenotypic comparisons across altitudes and across ethnic groups. Genome-wide SNP genotype data were collected in these samples by using Illumina arrays. We find that variants associated with hemoglobin variation among Tibetans or other variants at the same loci do not influence the trait in Ethiopians. However, in the Amhara, SNP rs10803083 is associated with hemoglobin levels at genome-wide levels of significance. No significant genotype association was observed for oxygen saturation levels in either ethnic group. Approaches based on allele frequency divergence did not detect outliers in candidate hypoxia genes, but the most differentiated variants between high- and lowlanders have a clear role in pathogen defense. Interestingly, a significant excess of allele frequency divergence was consistently detected for genes involved in cell cycle control and DNA damage and repair, thus pointing to new pathways for high altitude adaptations. Finally, a comparison of CpG methylation levels between high- and lowlanders found several significant signals at individual genes in the Oromo.
Sirtuins: Molecular Traffic Lights in the Crossroad of Oxidative Stress, Chromatin Remodeling, and Transcription

Transcription is regulated by acetylation/deacetylation reactions of histone and nonhistone proteins mediated by enzymes called KATs and HDACs, respectively. As a major mechanism of transcriptional regulation, protein acetylation is a key controller of physiological processes such as cell cycle, DNA damage response, metabolism, apoptosis, and autophagy. The deacetylase activity of class III histone deacetylases or sirtuins depends on the presence of NAD+ (nicotinamide adenine dinucleotide), and therefore, their function is closely linked to cellular energy consumption. This activity of sirtuins connects the modulation of chromatin dynamics and transcriptional regulation under oxidative stress to cellular lifespan, glucose homeostasis, inflammation, and multiple aging-related diseases including cancer. Here we provide an overview of the recent developments in relation to the diverse biological activities associated with sirtuin enzymes and stress responsive transcription factors, DNA damage, and oxidative stress and relate the involvement of sirtuins in the regulation of these processes to oncogenesis. Since the majority of the molecular mechanisms implicated in these pathways have been described for Sirt1, this sirtuin family member is more extensively presented in this paper.
Visualization in the Earth Sciences: A Discussion on Various Visualization Methods using amira

It is widely acknowledged that an important aspect in Earth Science research is the ability to visualize huge amounts of data resulting from numerical simulations or data acquisition. Whether the data is a simple two-dimensional plot or a three-dimensional multivariate grid, the ability to visualize the data is imperative for researchers to properly demonstrate results. This poster will examine various visualization techniques of the software package, amira® (www.amiravis.com) with respect to three research projects. These projects are: a mantle convection simulation run on the Earth Simulator; a spherical harmonic model computed at the University of Minnesota's Supercomputing Institute; an upper mantle study of earthquake-generated shear waves down to 660 km obtained through computed tomography using seismogram data from the Incorporated Research Institutions for Seismology (IRIS). The data resulting from the mantle convection study is in the form of a regular cartesian grid consisting of various field parameters such as temperature, velocity and viscosity. Techniques employed to view these fields include but are not limited to volume rendering, illuminated streamlines and oblique slices. The spherical harmonics model is rendered as a volume and is also explored using an isosurface module. The upper mantle study is visualized using an oblique slice technique and also isosurfaces. An analysis of the benefits and drawbacks of various amira® modules in regard to the above projects will not only result in a better understanding of the data, but will also demonstrate the unique capabilities of the different techniques and how they can be best applied to specific problems in the Earth Sciences.
Linkage and Allostery in snRNP Protein/RNA Complexes

Drosophila SNF is a member of the U1A/U2B″/SNF protein family that is found in U1 and U2 snRNPs, where it binds to Stemloop II and Stemloop IV of U1 and U2 snRNA, respectively. SNF also binds to the U2A′ protein, but only in the U2 snRNP. Although previous reports have implicated U2A′ as a necessary auxiliary protein for the binding of SNF to Stemloop IV, there are no mechanisms that explain the partitioning of U2A′ to the U2 snRNP and its absence from the U1 snRNP. Using in vitro RNA binding isotherms and isothermal titration calorimetry, the thermodynamics of SNF/RNA/U2A′ ternary complex formation have now been characterized. There is a very large binding cooperativity unique to Stemloop IV that favors formation of the SLIV/SNF/U2A′ complex. The binding cooperativity, or heterotropic linkage, is interpreted with respect to linked conformational equilibria of both SNF and its RNA ligand and so represents an example of protein–RNA allostery.
PREFER: Using a Graph-Based Approach to Generate Paraphrases for Language Learning

Paraphrasing is an important aspect of language competence; however, EFL learners have long had difficulty paraphrasing in their writing owing to their limited language proficiency. Therefore, automatic paraphrase suggestion systems can be useful for writers. In this paper, we present PREFER, a paraphrase reference tool for helping language learners improve their writing skills. In this paper, we attempt to transform the paraphrase generation problem into a graphical problem in which the phrases are treated as nodes and translation similarities as edges. We adopt the PageRank algorithm to rank and filter the paraphrases generated by the pivot-based paraphrase generation method. We manually evaluate the performance of our method and assess the effectiveness of PREFER in language learning. The results show that our method successfully preserves both the semantic meaning and syntactic structure of the query phrase. Moreover, the students' writing performance improve most with the assistance of PREFER.
Solving large sparse eigenvalue problems on supercomputers

An important problem in scientific computing consists in finding a few eigenvalues and corresponding eigenvectors of a very large and sparse matrix. The most popular methods to solve these problems are based on projection techniques on appropriate subspaces. The main attraction of these methods is that they only require the use of the matrix in the form of matrix by vector multiplications. The implementations on supercomputers of two such methods for symmetric matrices, namely Lanczos' method and Davidson's method are compared. Since one of the most important operations in these two methods is the multiplication of vectors by the sparse matrix, methods of performing this operation efficiently are discussed. The advantages and the disadvantages of each method are compared and implementation aspects are discussed. Numerical experiments on a one processor CRAY 2 and CRAY X-MP are reported. Possible parallel implementations are also discussed.
RNA Binding Protein/RNA Element Interactions and the Control of Translation

A growing body of work demonstrates the importance of post-transcriptional control, in particular translation initiation, in the overall regulation of gene expression. Here we focus on the contribution of regulatory elements within the 5’ and 3’ untranslated regions of mRNA to gene expression in eukaryotic cells including terminal oligopyrimidine tracts, internal ribosome entry segments, upstream open reading frames and cytoplasmic polyadenylation elements. These mRNA regulatory elements may adopt complex secondary structures and/or contain sequence motifs that allow their interaction with a variety of regulatory proteins, RNAs and RNA binding proteins, particularly hnRNPs. The resulting interactions are context-sensitive, and provide cells with a sensitive and fast response to cellular signals such as hormone exposure or cytotoxic stress. Importantly, an increasing number of diseases have been identified, particularly cancers and those associated with neurodegeneration, which originate either from mutation of these regulatory motifs, or from deregulation of their cognate binding partners.
Prolonged islet allograft survival by adenovirus-mediated transfer of sICAM-1/Ig immunoadhesin gene.

Administration of monoclonal antibodies directed against the leukocyte function-associated antigen 1 (LFA-1)-intercellular adhesion molecule 1 (ICAM-1) pathway showed that these costimulatory molecules play a key role in allograft rejection. Here, adenoviral gene transfer of an immunoadhesin, sICAM-1/Ig, was used to prolong islet allograft survival in a mouse model, and was compared with anti-LFA-1 antibody administration. A replication-deficient recombinant adenoviral vector encoding a chimeric protein, in which the extracellular domain of ICAM-1 is covalently linked to the C(H)2-C(H)3 domains of an IgG1, was used for gene transfer. C3H murine islets were transplanted under the kidney capsule of streptozotocin-induced diabetic BALB/c mice. Experimental groups underwent adenovirus vector administration either in vivo (intravenous injection) or ex vivo (gene transfer to the graft), and control groups received either an empty vector (Ad.null) or an anti-LFA-1 monoclonal antibody. Graft survival was significantly prolonged by in vivo sICAM-1/Ig gene transfer as compared with both Ad.null and anti-LFA-1 groups, but not by ex vivo gene transfer. Histological examination of the grafts showed the presence of a mononuclear infiltrate within functioning grafts, suggesting that the homing of alloreactive T cells was not altered. In vitro T cell proliferation experiments indicated that sICAM-1/Ig exerted agonist effects on both CD4(+) and CD8(+) T cells.
TGF-β1 genotype and accelerated decline in lung function of patients with cystic fibrosis

BACKGROUND Polymorphisms in transforming growth factor (TGF)-β1 associated with variations in cytokine levels are linked to fibrosis in a number of tissues. However, the contribution of this cytokine to organ fibrosis in patients with cystic fibrosis is presently unclear. This study was undertaken to examine the association between TGF-β1 gene polymorphisms and the development of pulmonary dysfunction in patients with cystic fibrosis. METHODS Polymorphisms in the TGF-β1 gene defining amino acids of codons 10 and 25 were determined by ARMS-PCR using DNA stored on 171 Caucasian patients who were homozygous for the ΔF508 mutation of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Clinical information on the patients was obtained from medical records. RESULTS Patients with cystic fibrosis of a TGF-β1 high producer genotype for codon 10 had more rapid deterioration in lung function than those with a TGF-β1 low producer genotype. The relative risk of accelerated decline in forced expiratory volume in one second (FEV1) to 50% predicted and forced vital capacity (FVC) to 70% predicted of patients with a high producer genotype was 1.74 (95% CI 1.11 to 2.73) compared with 1.95 (95% CI 1.24 to 3.06) for those with a low producer genotype. DISCUSSION TGF-β1genotypes may have a role in mediating pulmonary dysfunction in patients with cystic fibrosis. Further work is required to determine whether inhibition of TGF-β1 activity in these patients may slow disease progression.
Hair Cells and Supporting Cells Share a Common Progenitor in the Avian Inner Ear

Sensory organs of the vertebrate inner ear contain two major cell types: hair cells (HCs) and supporting cells (SCs). To study the lineage relationships between these two populations, replication-defective retroviral vectors encoding marker genes were delivered to the otic vesicle of the chicken embryo. The resulting labeled clones were analyzed in the hearing organ of the chicken, called the basilar papilla (BP), after cellular differentiation. BPs were allowed to develop for 2 weeks after delivery of the retrovirus, were removed, and were processed histochemically as whole mounts to identify clones of cells. Clusters of labeled cells were evident in the sensory epithelium, the nonsensory epithelium, and in adjacent tissues. Labeled cell types included HCs, two morphologically distinct types of SCs, homogene cells, border cells, hyaline cells, ganglion cells, and connective tissue cells. Each clone was sectioned and cell-type identification was performed on sensory clones expressing retrovirally transduced β-galactosidase. Cell composition was determined for 41 sensory clones, most of which contained both HCs and SCs. Clones containing one HC and one SC were observed, suggesting that a common progenitor exists that can remain bipotential up to its final mitotic division. The possibility that these two cell types may also arise from a mitotic precursor during HC regeneration in the mature basilar papilla is consistent with their developmental history.
Effects of electrochemical hydrogen charging on lead-based relaxor ferroelectric multilayer ceramic capacitors

Lead-based relaxor ferroelectric multilayer ceramic capacitors (MLC’s) were placed in 0.05 M NaOH solution to evolve hydrogen on their silver termination electrode by electrolysis of water. After this treatment, the MLC’s failed as their insulation resistance was greatly decreased, their dielectric loss was considerably increased, and their capacitance was obviously decreased. By annealing in air at 650 °C for 30 min, the properties of the MLC’s were restored. It is proposed that electrochemically generated hydrogen atoms can diffuse into the ceramic body of MLC’s and undergo reduction to it, which may be one of the reasons for the negative influence of electroplating on lead-based relaxor ferroelectric MLC’s.
Natural killer (NKH-1+) cell number and activity in health and disease.

The proportion of lymphocytes bearing the NKH-1 membrane marker (a natural killer-cell marker) was determined by flow cytometric analysis of the peripheral blood of 40 healthy individuals, 45 patients with multiple sclerosis and 19 with other neurological diseases. Natural killer (NK) cell activity was determined in parallel. It was shown that NKH-1-positive cells were more abundant in the lymphocytic than the mononuclear cell window on the flow-cytometric granularity versus cell size two-parameter display. NK-cell concentration did not correlate with NK-activity in any of the three groups of individuals studied. However, when the data for the three groups were compounded (i.e. when the number of samples analysed exceeded 100) significant correlations were disclosed. No correlation was found between age and NKH-1-positive cell number or activity in any of the three groups of subjects. High variability of the number and activity of natural killer cells in different individuals, and imprecision of phenotyping of the entire pool of NK-cells by means of a single marker, appeared to be responsible for poor correlations of NK-cell number and activity as observed in the study.
Male reproductive fitness and queen polyandry are linked to variation in the supergene Gp-9 in the fire ant Solenopsis invicta

Supergenes are clusters of tightly linked loci maintained in specific allelic combinations to facilitate co-segregation of genes governing adaptive phenotypes. In species where strong selection potentially operates at different levels (e.g. eusocial Hymenoptera), positive selection acting within a population to maintain specific allelic combinations in supergenes may have unexpected consequences for some individuals, including the preservation of disadvantageous traits. The nuclear gene Gp-9 in the invasive fire ant Solenopsis invicta is part of a non-recombining, polymorphic supergene region associated with polymorphism in social organization as well as traits affecting physiology, fecundity and behaviour. We show that both male reproductive success and facultative polyandry in queens have a simple genetic basis and are dependent on male Gp-9 genotype. Gp-9b males are unable to maintain exclusive reproductive control over their mates such that queens mated to Gp-9b males remain highly receptive to remating. Queens mated to multiple Gp-9B males are rare. This difference appears to be independent of mating plug production in fertile males of each Gp-9 genotype. However, Gp-9b males have significantly lower sperm counts than Gp-9B males, which could be a cue to females to seek additional mates. Despite the reduced fitness of Gp-9b males, polygyne worker-induced selective mortality of sexuals lacking b-like alleles coupled with the overall success of the polygyne social form act to maintain the Gp-9b allele within nature. Our findings highlight how strong worker-induced selection acting to maintain the Gp-9b allele in the polygyne social form may simultaneously result in reduced reproductive fitness for individual sexual offspring.
3-D FEM simulation of piezoelectric boundary acoustic wave resonator

In this paper, a 3D finite element method (FEM) is performed to accurately investigate the propagation characteristics of PBAW in SiO<sub>2</sub>/metal grating/rotated YX-LiNbO<sub>3</sub> substrate structure by the commercial software of COMSOL Multiphysics. The simulated results show a SH-type PBAW with large K<sup>2</sup> in SiO<sub>2</sub>/Cu grating/0° or 15° YX-LiNbO<sub>3</sub> substrate structure. The optimized structure has been obtained which could suppress spurious signals providing not seriously reducing K<sup>2</sup> of the main mode. It's proved that the analysis is very helpful for understanding and design of such layered SAW devices.