Miracle-dz/UniFAR-FTUs huggingface dataset:
MINT: Mutual Information Based Transductive Feature Selection for Genetic Trait Prediction

Whole genome prediction of complex phenotypic traits using high-density genotyping arrays has attracted a lot of attention, as it is relevant to the fields of plant and animal breeding and genetic epidemiology. Since the number of genotypes is generally much bigger than the number of samples, predictive models suffer from the curse of dimensionality. The curse of dimensionality problem not only affects the computational efficiency of a particular genomic selection method, but can also lead to a poor performance, mainly due to possible overfitting, or un-informative features. In this work, we propose a novel transductive feature selection method, called MINT, which is based on the MRMR (Max-Relevance and Min-Redundancy) criterion. We apply MINT on genetic trait prediction problems and show that, in general, MINT is a better feature selection method than the state-of-the-art inductive method MRMR.
Predictors of oral health-related quality of life in patients following stroke.

Objectives: To explore the influence of socio-demographic and clinical oral health factors on oral health-related quality of life (OHRQoL) in patients after stroke, and to monitor OHRQoL outcomes following the provision of an in-hospital oral health intervention programme. Design: OHRQoL was measured before and after randomization and provision of oral health promotion interventions in a prospective clinical trial. Subjects: Eighty-one patients admitted to a stroke rehabilitation ward. Methods: OHRQoL was assessed using the Oral Health Impact Profile-14 (OHIP-14) and Oral Health Transition Scale upon admission and 3 weeks later following provision of an oral health promotion programme. Potential factors were examined for their association with OHRQoL outcomes. Results: Lack of a regular daily brushing habit was significantly associated with 6 of 8 transition scale items (p < 0.01) at baseline, while significant improvements in OHRQoL were observed over the course of the clinical trial for all patients as a whole (p < 0.05). Conclusion: OHRQoL is compromised following stroke and may be influenced by the lack of a regular daily brushing habit during hospitalization. The early re-establishment of an oral hygiene protocol is a priority in stroke rehabilitation wards in order to improve clinical oral health and OHRQoL.
PRIS at Knowledge Base Population 2013

Our method to Knowledge Base Population 2013 is described in this paper. An pattern bootstrapping system with automatic pattern evaluation is mainly utilized in the Slot Filling task. For the Entity Linking task, query expansion method and entity similarity ranking strategy are mainly considered. And for sentiment holder and target detection in the Sentiment Slot Filling task, two CRF models are primarily trained.
Stability Analysis of Inexact Solves in Moment Matching based Model Reduction

Recently a new algorithm for model reduction of second order linear dynamical systems with proportional damping, the Adaptive Iterative Rational Global Arnoldi (AIRGA) algorithm (Bonin et. al., 2016), has been proposed. The main computational cost of the AIRGA algorithm is solving a sequence of linear systems. Usually, direct methods (e.g., LU) are used for solving these systems. As model sizes grow, direct methods become prohibitively expensive. Iterative methods (e.g., Krylov) scale well with size, and hence, are a good choice with an appropriate preconditioner. Preconditioned iterative methods introduce errors in linear solves because they are not exact. They solve linear systems up to a certain tolerance. We prove that, under mild conditions, the AIRGA algorithm is backward stable with respect to the errors introduced by these inexact linear solves. Our first assumption is use of a Ritz-Galerkin based solver that satisfies few extra orthogonality conditions. Since Conjugate Gradient (CG) is the most popular method based upon the Ritz-Galerkin theory, we use it. We show how to modify CG to achieve these extra orthogonalities. Modifying CG with the suggested changes is non-trivial. Hence, we demonstrate that using Recycling CG (RCG) helps us achieve these orthogonalities with no code changes. The extra cost of orthogonalizations is often offset by savings because of recycling. Our second and third assumptions involve existence, invertibility and boundedness of two matrices, which are easy to satisfy. While satisfying the backward stability assumptions, by numerical experiments we show that as we iteratively solve the linear systems arising in the AIRGA algorithm more accurately, we obtain a more accurate reduced system. We also show that recycling Krylov subspaces helps satisfy the backward stability assumptions (extra-orthogonalities) at almost no extra cost.
Evaluation of Ductile Damage Progress of Aluminum Single Crystal with Prior Activity of Single Slip System under Tensile Loading by Using Synchrotron White X-Ray

A ductile damage progress of an aluminum single crystal with the prior activity of the single slip system under tensile loading was verified by a profile analysis using white X-ray obtained in BL28B2 beam line of SPring-8. In this study, the aluminum single crystal of the purity 6N was used as a specimen prepared in I-type geometry for tensile test. A notch was introduced into one side of the center of a parallel part of the specimen by the wire electric discharge machining. White X-ray beam, which has 50 μm in both height and width, was incident into the specimen on the Bragg angle θ of 3 degrees using energy dispersive X-ray diffraction technique. The specimen was deformed by elongation in the direction of 45°to [11 and [11 crystal orientations, respectively, and a diffraction profile of the white X-ray from Al220 plane was analyzed. In profile analysis, an instrumental function was defined in consideration both of a divergence by a slit and a response function peculiar to the energy dispersive method. The Gauss component of integral breadth related to non-uniform strain and the Cauchy component of integral breadth related to crystallite size were determined by eliminating the broadening by the instrumental function from the diffraction profile of white X-ray. As a result, the characteristics of ductile damage progress near the notch of the aluminum single crystal were inspected from the distribution of both non-uniform strain and dislocation density.
Characterisation and functional mapping of surface potentials in the rat dorsal column nuclei

The brainstem dorsal column nuclei (DCN) process sensory information arising from the body before it reaches the brain and becomes conscious. Despite significant investigations into sensory coding in peripheral nerves and the somatosensory cortex, little is known about how sensory information arising from the periphery is represented in the DCN. Following stimulation of hind‐limb nerves, we mapped and characterised the evoked electrical signatures across the DCN surface. We show that evoked responses recorded from the DCN surface are highly reproducible and are unique to nerves carrying specific sensory information.
SoK: Deep Packer Inspection: A Longitudinal Study of the Complexity of Run-Time Packers

Run-time packers are often used by malware-writers to obfuscate their code and hinder static analysis. The packer problem has been widely studied, and several solutions have been proposed in order to generically unpack protected binaries. Nevertheless, these solutions commonly rely on a number of assumptions that may not necessarily reflect the reality of the packers used in the wild. Moreover, previous solutions fail to provide useful information about the structure of the packer or its complexity. In this paper, we describe a framework for packer analysis and we propose a taxonomy to measure the runtime complexity of packers. We evaluated our dynamic analysis system on two datasets, composed of both off-the-shelf packers and custom packed binaries. Based on the results of our experiments, we present several statistics about the packers complexity and their evolution over time.
LSD1 activates a lethal prostate cancer gene network independently of its demethylase function

Significance Medical castration or interference with androgen receptor (AR) function is the principal treatment for advanced prostate cancer. However, progression is universal, and therapies following the emergence of castration resistance do not offer durable control of the disease. Lysine-specific demethylase 1 (LSD1) is an important regulator of gene expression, including in cancer. Here, we show that LSD1 is highly expressed in tumors of patients with lethal castration-resistant prostate cancer (CRPC) and that LSD1 promotes AR-independent survival in CRPC cells in a noncanonical, demethylase-independent manner. We determined that the drug SP-2509 acts as an allosteric inhibitor of LSD1–blocking demethylase-independent functions. Our demonstration of tumor suppression with this inhibitor in CRPC preclinical models provides the rationale for clinical trials with LSD1 inhibitors. Medical castration that interferes with androgen receptor (AR) function is the principal treatment for advanced prostate cancer. However, clinical progression is universal, and tumors with AR-independent resistance mechanisms appear to be increasing in frequency. Consequently, there is an urgent need to develop new treatments targeting molecular pathways enriched in lethal prostate cancer. Lysine-specific demethylase 1 (LSD1) is a histone demethylase and an important regulator of gene expression. Here, we show that LSD1 promotes the survival of prostate cancer cells, including those that are castration-resistant, independently of its demethylase function and of the AR. Importantly, this effect is explained in part by activation of a lethal prostate cancer gene network in collaboration with LSD1’s binding protein, ZNF217. Finally, that a small-molecule LSD1 inhibitor―SP-2509―blocks important demethylase-independent functions and suppresses castration-resistant prostate cancer cell viability demonstrates the potential of LSD1 inhibition in this disease.
VEGF released from a fibrin biomatrix increases VEGFR‐2 expression and improves early outcome after ischaemia–reperfusion injury

Skeletal ischaemia–reperfusion (I–R) injury may influence patient outcome after severe vascular trauma or clamping of major vessels. The aim of this study was to observe whether locally applied vascular endothelial growth factor (VEGF) in fibrin could induce the expression of VEGF‐receptor‐2 (VEGFR‐2) and improve the outcome after I–R injury. Transgenic mice expressing VEGFR‐2 promoter‐controlled luciferase were used for the assessment of VEGFR‐2 expression. Ischaemia was induced for 2 h by a tension‐controlled tourniquet to the hind limb, followed by 24 h of reperfusion. The animals were locally injected subcutaneously with fibrin sealant containing 20 or 200 ng VEGF; control animals received no treatment or fibrin sealant application. In vivo VEGFR‐2 expression was quantified upon administration of luciferin at several observation times. For oedema and inflammation quantification, wet:dry ratio measurements and a myeloperoxidase assay of the muscle tissue were performed. Laser Doppler imaging showed that ischaemia was present and that the blood flow had returned to baseline levels after 24 h of reperfusion. VEGFR‐2 expression levels in the fibrin + 200 ng VEGF were significantly higher than in all other groups. Granulocyte infiltration was reduced in both treatment groups, as well as reduced oedema formation. These results showed that VEGF released from fibrin had a positive effect on early I–R outcome in a mouse model, possibly via VEGFR‐2. Copyright © 2016 John Wiley & Sons, Ltd.
The Role of Epigenomics in Aquatic Toxicology

Over the past decade, the field of molecular biology has rapidly incorporated epigenetic studies to evaluate organism–environment interactions that can result in chronic effects. Such responses arise from early life stage stress, the utilization of genetic information over an individual's life time, and transgenerational inheritance. Knowledge of epigenetic mechanisms provides the potential for a comprehensive evaluation of multigenerational and heritable effects from environmental stressors, such as contaminants. Focused studies have provided a greater understanding of how many responses to environmental stressors are driven by epigenetic modifiers. We discuss the promise of epigenetics and suggest future research directions within the field of aquatic toxicology, with a particular focus on the potential for identifying key heritable marks with consequential impacts at the organism and population levels. Environ Toxicol Chem 2017;36:2565–2573. © 2017 SETAC
Expression of embryonal stem cell transcription factors in breast cancer: Oct4 as an indicator for poor clinical outcome and tamoxifen resistance

The transcription factors of embryonic stem cells, such as Oct4, Sox2, Nanog, Bmi1, and Klf4, are known to be associated with stemness, epithelial–mesenchymal transition and aggressive tumor behavior. This study was designed to evaluate the clinicopathological significance of their expression in breast cancer. Immunohistochemistry for Oct4, Sox2, Nanog, Bmi1, and Klf4 was performed in 319 cases of invasive breast cancer. The relationship between the expression of these markers and clinicopathologic features of the tumors, including breast cancer stem cell phenotype and epithelial–mesenchymal transition marker expression, and their prognostic value in breast cancer, were analyzed. Expression of Oct4 and Sox2 was commonly associated with high histologic grade and high Ki-67 index in the whole group and in the hormone receptor-positive subgroup. On the other hand, expression of Nanog, Bmi1, and Klf4 was inversely correlated with aggressive features of the breast cancer. Oct4 expression was associated with ALDH1 expression but not with epithelial–mesenchymal transition marker expression. In survival analysis, Oct4 expression was independently associated with poor prognosis in the whole group and in the hormone receptor-positive subgroup, but not in hormone receptor-negative subgroup. Particularly, Oct4 expression was associated with poor clinical outcome in patients with hormone receptor-positive breast cancer treated with tamoxifen. Our results indicate that Oct4 expression is associated with aggressive features, ALDH1 expression, tamoxifen resistance and poor clinical outcomes in hormone receptor-positive breast cancer, and thus may be useful as a predictive and prognostic marker in this subgroup of breast cancer.
Neural Mechanisms for Binocular Depth, Rivalry and Multistability

The purpose of this chapter is to present a review of recent functional neuroimaging (fMRI) studies of binocular vision, including binocular depth and rivalry, as well as a review of studies of perceptual multistability. As such, we will first emphasize the binocular aspects of binocular rivalry, while later emphasizing the rivalrous aspects. The interrelationship of binocular depth and rivalry, as well as multistability, will be described with reference to fMRI studies and single-unit recording studies in animals. These studies have provided provocative new evidence that the neural substrates for depth and rivalry, as well as other forms of multistability are remarkably similar. We will also describe our own research findings from two recent experiments, in which we performed (1) a direct comparison between binocular rivalry and depth, and (2) a direct comparison between binocular rivalry and monocular rivalry, a related form of bistability [1,2]. Our studies are unique in using both matched stimulation and comparable tasks, overcoming a limitation in the interpretation of many previous studies. As a result, these experiments are particularly relevant in delineating some of the global similarities and differences in the cortical networks activated in each of these different domains.
Symmetric Generative Methods and tSNE: A Short Survey

In data visualization, a family of methods is dedicated to the symmetric numerical matrices which contain the distances or similarities between high-dimensional data vectors. The method t-Distributed Stochastic Neighbor Embedding and its variants lead to competitive nonlinear embeddings which are able to reveal the natural classes. For comparisons, it is surveyed the recent probabilistic and model-based alternative methods from the literature (LargeVis, Glove, Latent Space Position Model, probabilistic Correspondence Analysis, Stochastic Block Model) for nonlinear embedding via low dimensional positions.
Real-time Human Pose Estimation with Convolutional Neural Networks

In this paper, we present a method for real-time multi-person human pose estimation from video by utilizing convolutional neural networks. Our method is aimed for use case specific applications, where good accuracy is essential and variation of the background and poses is limited. This enables us to use a generic network architecture, which is both accurate and fast. We divide the problem into two phases: (1) pre-training and (2) finetuning. In pre-training, the network is learned with highly diverse input data from publicly available datasets, while in finetuning we train with application specific data, which we record with Kinect. Our method differs from most of the state-of-the-art methods in that we consider the whole system, including person detector, pose estimator and an automatic way to record application specific training material for finetuning. Our method is considerably faster than many of the state-of-the-art methods. Our method can be thought of as a replacement for Kinect in restricted environments. It can be used for tasks, such as gesture control, games, person tracking, action recognition and action tracking. We achieved accuracy of 96.8% (PCK@0.2) with application specific data.
Soft magnetic composites in active magnetic bearings

Active magnetic bearings are being considered increasingly for high-speed electrical machines, since they eliminate frictional losses and are virtually maintenance-free. However, in addition to the copper loss in the coils, there may be a significant eddy current and hysteresis loss in the soft magnetic rotor. These can be minimised by an appropriate choice of rotor material and bearing topology, whilst the use of nonlinear control can also assist in reducing the total loss. The example of an energy storage flywheel using a PM motor/generator is discussed.
Automated Generation of Music Playlists: Survey and Experiments

Most of the time when we listen to music on the radio or on our portable devices, the order in which the tracks are played is governed by so-called playlists. These playlists are basically sequences of tracks that traditionally are designed manually and whose organization is based on some underlying logic or theme. With the digitalization of music and the availability of various types of additional track-related information on the Web, new opportunities have emerged on how to automate the playlist creation process. Correspondingly, a number of proposals for automated playlist generation have been made in the literature during the past decade. These approaches vary both with respect to which kind of data they rely on and which types of algorithms they use. In this article, we review the literature on automated playlist generation and categorize the existing approaches. Furthermore, we discuss the evaluation designs that are used today in research to assess the quality of the generated playlists. Finally, we report the results of a comparative evaluation of typical playlist generation schemes based on historical data. Our results show that track and artist popularity can play a dominant role and that additional measures are required to better characterize and compare the quality of automatically generated playlists.
Distributed Fibre Optic Strain Sensing to Monitor Deterioration in Reinforced Concrete

Structural health monitoring (SHM) is an increasingly useful tool for life cycle management of deteriorating infrastructure. Rayleigh backscatter distributed fibre optic strain sensing (FOS) is a promising measurement technology that can provide relevant quantitative data across an entire structure as opposed to the single point data acquisition of conventional strain sensors. Utilizing this FOS technology, an experimental investigation to measure and better understand the effects of deterioration on reinforced concrete behaviour was undertaken. Reinforced concrete tension specimens were instrumented with optical fibres and tested in axial tension to determine if FOS is capable of measuring the effects of tension stiffening and to develop insights into the bond performance of reinforced concrete. It was found that FOS could be used to measure the distributed reinforcement strain, especially before cracking occurs, and these results illustrate how the bond deteriorates with increasing load. In addition, FOS can detect crack locations as well as when cracks develop on only one side of the specimen. The FOS technology was utilized to detect and quantify corrosion levels of the reinforcing steel and to determine how corrosion affects bond performance. An impressed current accelerated corrosion technique was used to corrode additional reinforced concrete tension specimens. Test results showed that reinforced concrete specimens that were corroded to 13% mass loss had a decrease in ultimate capacity of over 30%. This was due to pitting corrosion of the reinforcement that the FOS was able to detect. Additionally, the FOS results showed that as the corrosion levels increase, the bond performance continues to deteriorate. To explore the usefulness of FOS in assessing deteriorated reinforced concrete structures, beams instrumented with optical fibres had the bottom flexural reinforcement corroded and were tested in three point bending. The FOS system was capable of detecting both flexural and shear cracks in the concrete, early signs of corrosion, and bond loss. Test results also showed that just 4.0% mass loss of the bottom
An approach to correlate experimental and theoretical thermal conductivity of MWNT/PMMA polymer composites

In this paper an effort is made to correlate temperature dependent effective thermal conductivity measured by experimental method to theoretical results obtained from different models. MWNT/PMMA polymer nanocomposites were prepared by solution casting method, with different wt% of MWNT (0, 0.05, 0.1, 0.2, 0.3, 0.5, 1, 5, 10 wt%) dispersed in the PMMA matrix. The effective thermal conductivity from 30 °C to 110 °C is measured by Hot Disk Thermal Constant Analyser, based on transient plane source technique. Experimental study reveals that effective thermal conductivity increases with increasing concentration of MWNT in PMMA and increases exponentially at high temperatures for high (5, 10) wt% samples. This behavior of effective thermal conductivity is explained in terms of the interactions between polymer–MWNT and MWNT–MWNT. Consequently these results were found to be in agreement with theoretical models such as Series, Parallel, Lewis/Neilson and empirical formula. The discrepancy found in Lewis/Neilson model at high temperature for high wt% of MWNT in PMMA is due to some change in values of parameters incorporated in the model.