Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficient Feature Selection and Multiclass Classification with Integrated Instance and Model Based Learning

Multiclass classification and feature (variable) selections are commonly encountered in many biological and medical applications. However, extending binary classification approaches to multiclass problems is not trivial. Instance-based methods such as the K nearest neighbor (KNN) can naturally extend to multiclass problems and usually perform well with unbalanced data, but suffer from the curse of dimensionality. Their performance is degraded when applied to high dimensional data. On the other hand, model-based methods such as logistic regression require the decomposition of the multiclass problem into several binary problems with one-vs.-one or one-vs.-rest schemes. Even though they can be applied to high dimensional data with L1 or L p penalized methods, such approaches can only select independent features and the features selected with different binary problems are usually different. They also produce unbalanced classification problems with one vs. the rest scheme even if the original multiclass problem is balanced. By combining instance-based and model-based learning, we propose an efficient learning method with integrated KNN and constrained logistic regression (KNNLog) for simultaneous multiclass classification and feature selection. Our proposed method simultaneously minimizes the intra-class distance and maximizes the interclass distance with fewer estimated parameters. It is very efficient for problems with small sample size and unbalanced classes, a case common in many real applications. In addition, our model-based feature selection methods can identify highly correlated features simultaneously avoiding the multiplicity problem due to multiple tests. The proposed method is evaluated with simulation and real data including one unbalanced microRNA dataset for leukemia and one multi-class metagenomic dataset from the Human Microbiome Project (HMP). It performs well with limited computational experiments.
Are granules good tracers of solar surface velocity fields

Using a numerical simulation of compressible convection with radiative transfer mimicking the solar photosphere, we compare the velocity eld derived from granule motions to the actual velocity eld of the plasma. We thus test the idea that granules may be used to trace large-scale velocity elds at the sun's surface. Our results show that this is indeed the case provided the scale separation is sucient. We thus estimate that neither velocity elds at scales less than 2500 km nor time evolution at scales shorter than 0.5 hr can be faithfully described by granules. At larger scales the granular motions correlate linearly with the underlying fluid motions with a slope of 2 reaching correlation coecients up to0.9.
Subgroup Visualization: A Method and Application in Population Screening

This paper presents a method for the visualisation of subgroups, detected by a subgroup discovery algorithm. The main advantage and novelty of the method is that the visualized models can be used to illustrate the distributions of detected groups in terms of the percentages of true positive and false positive cases covered by the model. Subgroup visualization is illustrated by graphs obtained for risk groups discovered in the problem of early detection of patient groups with risk for atherosclerotic coronary heart disease.
Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database

We report on the original integration of an automatic text categorization pipeline, so-called ToxiCat (Toxicogenomic Categorizer), that we developed to perform biomedical documents classification and prioritization in order to speed up the curation of the Comparative Toxicogenomics Database (CTD). The task can be basically described as a binary classification task, where a scoring function is used to rank a selected set of articles. Then components of a question-answering system are used to extract CTD-specific annotations from the ranked list of articles. The ranking function is generated using a Support Vector Machine, which combines three main modules: an information retrieval engine for MEDLINE (EAGLi), a gene normalization service (NormaGene) developed for a previous BioCreative campaign and finally, a set of answering components and entity recognizer for diseases and chemicals. The main components of the pipeline are publicly available both as web application and web services. The specific integration performed for the BioCreative competition is available via a web user interface at http://pingu.unige. ch:8080/Toxicat.
An investigation into the influence of stent strut thickness on in-stent restenosis using the finite element method

In-stent restenosis represents the major limitation for stenting procedures. In-stent restenosis is the renarrowing o f the artery lumen within a stent predominantly due to excessive growth of neointimal hyperplasia. Clinical studies have found that stent design is a key determinant in the propensity o f stents to cause restenosis, indicating a vital link between the biomechanics o f stents and the development of the disease. The ISAR-STEREO Trial specifically assessed the effect o f strut thickness on restenosis outcome and found that for the same stent design, a thinner strut stent was associated with a significant reduction o f angiographic and clinical restenosis compared to the same stent with a thicker strut. The main objective o f this study is to use the finite element method to simulate these stenting procedures, and to examine the stresses induced within the stented arterial vessel walls by the stents, thus enabling the mechanical stimuli for in-stent restenosis to be identified. Finite element models o f thin and thick strut stents were developed and the stents were deployed in various stenosed vessel geometries such that the stresses induced within the stented vessels by the two stents could be compared. The stresses were examined at the end o f stent deployment, to determine the mechanical stimuli for acute damage, and again at stent unloading, to determine the long term stimuli for in-stent restenosis. The stress analyses were used to determine the level of vascular injury caused to the artery by different strut thickness stents. The finite element studies successfully identified differences between the mechanical loading of the arterial tissue in the vessels stented with the two different stents. The higher restenosis rate of the thicker strut stent, reported in the ISAR-STEREO clinical study, was found to be the result of the higher luminal gain achieved by the thicker strut stent, due to the lower recoil of the stent structure when both stents were expanded to the same initial lumen diameter. Further stenting analyses, however, found that the thicker strut stent resulted in a lower percentage of volume stressed at high levels compared with the thinner strut stent when it was expanded to the same final lumen diameter. This suggests that a thicker strut stent may in fact have the potential to be expanded to an optimal diameter whereby the in-stent restenosis is minimised. Therefore, it is proposed that the use of preclinical testing tools, such as finite element modelling, could be used to predetermine the deployment protocol and optimum luminal gain of a particular stent design in order to minimise the mechanical stimuli for in-stent restenosis.
CREWS Validation Frames: Patterns for Validating Systems Requirements

This paper proposes a pattern language for socio-technical system design to inform validation of system requirements. The development of this language takes inspiration from Alexander’s pattern language for building design in architecture. It identifies different types of patterns which fulfil different roles in the requirements engineering process. This pattern-based validation approach has been operationalised in the CREWS-SAVRE software prototype. CREWS-SAVRE applies patterns to both scenarios and requirements documents to detect missing and incorrect system requirements, as well as to recommend new requirements which can improve the design of the socio-technical system. 1 Patterns in Requirements Engineering Patterns are a novel alternative technique to help us better acquire, model and validate system requirements. In simple terms, patterns enable people to reuse knowledge about old solutions to solve similar new problems. However, there is little reported research into patterns for requirements engineering, in spite of the considerable current interest in software patterns for system design and implementation (e.g. Gamma et al. 1995). Indeed, each existing requirements engineering research initiative still tends to have a singular focus on process, domain or language. In contrast, patterns for requirements engineering, as we shall see, cuts across the divisions between process, domain and language. After all, experienced engineers do not separate them when acquiring, modelling and validating system requirements. Patterns which describe the common elements of complex structures were first documented in the field of building architecture. Christopher Alexander, in his book "The Timeless Way of Building" (Alexander 1979), argues that "Beyond its elements, each building is defined by certain patterns of relationships amongst its elements. " Patterns can be used to abstract away from the details of particular buildings and 1 This research has been funded by the European Commission ESPRIT 21903 ‘CREWS’ (Co-operative Requirements Engineering With Scenarios) long-term research project.
Chiral Anomalies in the Spectral Action 1

The definition of the spectral action involves the trace operator over states in the physical Hilbert space. We show that in the presence of chiral fermions there are consistency conditions on the fermionic representations. These conditions are identical to the conditions for absence of gauge and gravitational anomalies obtained in the path integral formalism. To appear in the book ”Quantum Groups and Fundamental Physical Interactions”, Editor: D. Kastler, Publisher: Nova Science Publishing Company. Email chams@aub.edu. lb , chams@itp.phys.ethz.ch Permanent address. 1 At present we have a great deal of information about the particle physics spectrum at low-energies. Using the tools of noncommutative geometry it is now possible to use the particle physics spectrum to study the geometry of space-time [1, 2, 3, 4, 5] . This program has been advocated in [6] where it is shown that a real spectral triple corresponding to a product of a continuous space by a discrete space serves as a good starting point. In [6] a new principle is proposed, the spectral action principle. This states that the action for the dynamical degrees of freedom contained in the metric is given by some function of the perturbed Dirac operator. The results do not depend crucially on the form of the function used in the spectral action, but mainly on the spectrum of the Dirac operator. In other words, the spectrum contains all the information about geometric invariants and should help in indicating the relevant geometry of space-time. It is well known that fermions in the standard model are chiral, and that masses are generated when the Higgs field acquires a vev so that the Higgs-fermi-fermi interaction produces a fermionic mass term. The trace operator is defined by summing over eigenstates of the Dirac operator. In the case of chiral fermions, the eigenvalue problem for the Dirac operator cannot be defined without adding fermions with opposite chirality. This is the familiar problem encountered in the path integral formalism, and there one assumes the spinors and their conjugates to be independent. The trace operator, unlike the fermionic kinetic energy, is not invariant under chiral rotations. The invariance is spoiled by the appearance of a phase factor which must be made to vanish for the action to be consistent. First, I shall briefly review the ingredients that enter the derivation of the spectral action for the standard model, and then show how this action transforms under chiral rotations. The subtleties involved in working with Euclidean signature, as well as with Minkowski signature, are also discussed [7, 8]. A noncommutative space is defined by a spectral triple (A,H, D) where A is an algebra of operators, H a Hilbert space of states, D an unbounded operator in H. The space is supplied with a real structure [9] J satisfying J = ǫ, JD = ǫ ′ DJ, Jγ = ǫ ′′ γJ ; (1) ǫ, ǫ ′ , ǫ ′′ ∈ {−1, 1} , where the value of ǫ, ǫ ′ , ǫ ′′ is determined by n modulo 8. The algebra A is taken to be A = C(M) ⊗AF , (2) where the algebra AF is finite dimensional AF = C ⊕H ⊕M3(C), (3) and H is the algebra of quaternions H = {(
Differentiation- and stress-dependent nuclear cytoplasmic redistribution of myopodin, a novel actin-bundling protein

We report the cloning and functional characterization of myopodin, the second member of the synaptopodin gene family. Myopodin shows no significant homology to any known protein except synaptopodin. Northern blot analysis resulted in a 3.6-kb transcript for mouse skeletal and heart muscle. Western blots showed an 80-kD signal for skeletal and a 95-kD signal for heart muscle. Myopodin contains one PPXY motif and multiple PXXP motifs. Myopodin colocalizes with α-actinin and is found at the Z-disc as shown by immunogold electron microscopy. In myoblasts, myopodin shows preferential nuclear localization. During myotube differentiation, myopodin binds to stress fibers in a punctuated pattern before incorporation into the Z-disc. Myopodin can directly bind to actin and contains a novel actin binding site in the center of the protein. Myopodin has actin-bundling activity as shown by formation of latrunculin-A–sensitive cytosolic actin bundles and nuclear actin loops in transfected cells expressing green fluorescent protein–myopodin. Under stress conditions, myopodin accumulates in the nucleus and is depleted from the cytoplasm. Nuclear export of myopodin is sensitive to leptomycin B, despite the absence of a classical nuclear export sequence. We propose a dual role for myopodin as a structural protein also participating in signaling pathways between the Z-disc and the nucleus.
A Molybdopterin Oxidoreductase Is Involved in H2 Oxidation in Desulfovibrio desulfuricans G20

ABSTRACT Three mutants deficient in hydrogen/formate uptake were obtained through screening of a transposon mutant library containing 5,760 mutants of Desulfovibrio desulfuricans G20. Mutations were in the genes encoding the type I tetraheme cytochrome c 3 (cycA), Fe hydrogenase (hydB), and molybdopterin oxidoreductase (mopB). Mutations did not decrease the ability of cells to produce H2 or formate during growth. Complementation of the cycA and mopB mutants with a plasmid carrying the intact cycA and/or mopB gene and the putative promoter from the parental strain allowed the recovery of H2 uptake ability, showing that these specific genes are involved in H2 oxidation. The mop operon encodes a periplasm-facing transmembrane protein complex which may shuttle electrons from periplasmic cytochrome c 3 to the menaquinone pool. Electrons can then be used for sulfate reduction in the cytoplasm.
The JULIE LAB MANTRA System for the CLEF-ER 2013 Challenge

We here describe the set-up for the system from the Jena Univer- sity Language & Information Engineering (JULIE) Lab which participated in the CLEF-ER 2013 Challenge. The task of this challenge was to identify hitherto unknown translation equivalents for biomedical terms from several parallel text corpora. The languages being covered are English, German, French, Spanish and Dutch. Our translation system enhanced, in a realistic scenario, the French, Ger- man, Spanish and Dutch parts of a UMLS-derived terminology with 4k to 15k new entries each. Based on expert assessment of the new German translations about 76% of these were judged as plausible term enhancements.
p-MANET: Efficient Power Saving Protocol for Multi-Hop Mobile Ad Hoc Networks

In this paper, we propose an efficient power saving protocol for multi-hop mobile ad hoc networks, called p-MANET. Our design is expected as a new foundation MAC layer power saving protocol. The main goals of p-MANET protocol are to reduce significant power consumption and transmission latency, and to achieve efficient power saving. Each mobile node in p-MANET only needs to become active during one beacon interval for every n interval where n is the size of a super frame. Thus, efficient power saving is expected. p-MANET also yields low transmission latency because that every mobile node is aware of the active beacon intervals of its neighbors such that it can easily choose a neighbor in active mode or with the least remaining time to wake up to forward packets. Simulations are also conducted to show the efficiency of the proposed p-MANET
Modifications of powders properties by dry-coating: some examples of processes and products characteristics

Dry-coating appears to be an interesting way to create new composite materials in various application areas, avoiding the use of solvents involved in traditional processes, like granulation. Moreover, dry coating processes can be performed on smaller particles sizes. Typical applications include, but are not limited to, altering flowability, solubility, dispersibility, wettability (hydrophilic/hydrophobic properties), electric, electrostatic, magnetic, optical, color, flavor, shape, etc. Particles with relatively large particle size (host particles, 1-500 µm) can be mechanically coated with fine particles (guest particles, 0,1-50 µm) in order to create new functionality or to improve their initial characteristics. In this study we present results obtained with various products and in particular more accurately in the case of silica host particles coated by magnesium stearate using two processes: the Hybridizer NSH0 of the Nara Machinery company and the Cyclomix of Hosokawa company. In this paper we describe the experimental investigation of an application of dry coating technique to change the surface properties of silica gel particles (d50 = 55 µm) coated with different mass ratio of magnesium stearate (MgSt; d50 = 4,6 µm): 1%, 5% and 15%. The products properties were characterised though different methods: particles size distribution (in order to examine the adhesion quality of the fine particles on host particles), flowability, wettability, Atomic Force Microscopy (AFM), and Electron Microscopy (ESEM). The flowability of the samples was characterized by measurements of the tapped and aerated densities. It has been shown in particular that the flowability of silica gel treated with and without MgSt in Hybridizer was not significantly affected and remained good. The wettability of silica gel was determined by measurements of the contact angle between the water drop and the powder bed prepared for each sample. The results obtained have shown that the coating of silica gel powder by hydrophobic magnesium stearate, can improve its hydrophobic properties.
Model-based animation of co-verbal gesture

Virtual conversational agents are supposed to combine speech with non-verbal modalities for intelligible and believable utterances. However, the automatic synthesis of co-verbal gestures is still struggling with several problems like naturalness in procedurally generated animations, flexibility in pre-defined movements, and synchronization with speech. In this paper we focus on generating complex multimodal utterances including gesture and speech from XML-based descriptions of their overt form. We describe a coordination model that reproduces coarticulation and transition effects in both modalities. In particular, an efficient kinematic approach to creating gesture animations from shape specifications is presented, which provides fine adaptation to temporal constraints that are imposed by cross-modal synchrony.
Effect of lysosomotropic amines on the secretory pathway and on the recycling of the asialoglycoprotein receptor in human hepatoma cells

We studied the intracellular transport of secretory and membrane proteins in the human hepatoma cell line HepG-2 infected with vesicular stomatitis virus. Cells were pulse-labeled in the presence of [35S]methionine and chased in the presence of the lysosomotropic agent primaquine. At a concentration of 0.3 mM primaquine effectively inhibited the secretion of albumin and, to a lesser extent, that of orosomucoid and transferrin. The drug also prevented the budding of virus particles at the cell surface. The intracellular transport to the Golgi complex of the membrane protein VSV-G was not affected by primaquine as it acquires resistance to endo-beta-N- acetylglucosaminidase H at the same rate as in control cells. Addition of primaquine at various times after the initiation of the chase period indicates that the effect of primaquine occurs just before secretion. In confirmation of the biochemical data, immunocytochemical localization of albumin in cells treated with NH4Cl demonstrated that albumin accumulated in vesicles at the trans side of the Golgi complex. The effect of primaquine on secretion was also compared with its effect on receptor recycling. The dose-response characteristics of the effect of primaquine on receptor recycling are identical to those of the effects on protein secretion and virus budding. These results indicate that both processes involve the same transport mechanism, and/or that they occur via at least one identical intracellular compartment.
Evaluation of mechanical, thermal, electrical, and transport properties of MWCNT‐filled NR/NBR blend composites

Carbon nanotube based polymer nanocomposites found versatile applications and hence studying its reinforcing effect on NR/NBR blend system is a promising step in developing flexible elastomer gadgets. In this study, attempts have been made to prepare multi-walled carbon nanotube (MWCNT)-filled nanocomposites of NR/NBR blends. Raman spectra and transmission electron microscopic analysis indicate that there has been a finer and uniform dispersion of carbon nanotubes within the polymer matrix. Mechanical properties like tensile strength, tear resistance, abrasion loss and compression set of pure and blend samples showed an improvement with the increase in the dosage of MWCNT from 0.5 to 4 phr. 70/30 NR/NBR blend with 4 phr of MWCNT showed an improvement of 83% in tensile strength and 72% in tear strength compared to pure NBR. This is attributed to the uniform dispersion, high surface area, nano level interaction, and compatibility of MWCNT with the polymeric molecular chains. MWCNT is acting as a compatibilizing agent as is manifest from the increased negative values of free energy. Electrical conduction and thermal stability of the mixes were increased with the concentration of MWCNT due to the increase in the interfacial interaction resulting from the pi-pi interaction with the nanotubes. POLYM. ENG. SCI., 2017. © 2017 Society of Plastics Engineers
Improving Chinese Parsing with Special-Case Probability Re-estimation

Syntactic patterns which are hard to be expressed by binary dependent relations need special treatments, since structure evaluations of such constructions are different from general parsing framework. Moreover, these different syntactic patterns (special cases) should be handled with distinct estimated model other than the general one. In this paper, we present a special-case probability re-estimation model (SCM), integrating the general model with an adoptable estimated model in special cases. The SCM model can estimate evaluation scores in specific syntactic constructions more accurately, and is able for adopting different features in different cases. Experiment results show that our proposed model has better performance than the state-of-the-art parser in Chinese.