Miracle-dz/UniFAR-FTUs huggingface dataset:
NMF-Based LncRNA-Disease Association Inference and Bi-Clustering

Long non-coding RNAs (lncRNAs) have been implicated in various biological processes, and are linked in many dysregulations. Researchers have reported large number of lncRNA associated human diseases over the past decade. In this article we employed the Non-negative Matrix Factorization method to develop a low-dimensional computational model that can describe the existing knowledge about lncRNA-disease associations represented in a two dimensional association matrix. The non-negativity constraints of the matrix and its corresponding factors ensure that each lncRNA's disease profile can be represented as an additive linear combination of the latent coordinates. To learn such a constrained model from an incomplete association matrix, several NMF formulations were developed. Based on our experiments, we found that the Sparse NMF obtained the best model among all the other models. Moreover, by exploiting the inherent bi-clustering ability of the NMF models, we extracted several lncRNA groups and disease groups that possess biological significance.
Art to Engineering: Curved Folding and Developable Surfaces in Mechanism and Deployable Structure Design

Art to Engineering: Curved Folding and Developable Surfaces in Mechanism and Deployable Structure Design Todd G Nelson Department of Mechanical Engineering, BYU Doctor of Philosophy This work investigates how curved-crease origami and the developable surfaces which compose it can be transitioned to engineering design. Methods for creating flexible, tailorableproperty surfaces that function as thick panels in place of paper are presented. Concepts from curved-crease origami and developable surfaces that can describe and extend engineering applications are discussed and demonstrated. These concepts are particularly beneficial to applications where curved surfaces are integral to the function, deployability is desired, and planar manufacturing could be beneficial. The first part of this work uses arrays of compliant elements to create flexible-tailorable property surfaces. The key feature to these arrays is the alignment of the most flexible bending axis of the individual elements to the ruling line arrangement of a developable surface. This alignment can enable bending of thick panels while maintaining lower stresses, a quality necessary for the transitioning of curved-crease origami into thick materials. The stiffness and stress of these arrays is modeled and physical prototypes are demonstrated. Additionally, shape factors are developed for these compliant arrays (CAs) to facilitate material selection for the panels and understand how the geometry of the array changes the effective properties of the panel. The second part of this work describes and demonstrates several concepts of curved-crease origami and developable surfaces that can benefit mechanism and structure design, particularly in the context of rolling-contact mechanisms. The design of a rolling-contact joint connected by flexible bands similar to a Jacob’s Ladder toy is extended through incorporating curved creases into the design. The resulting design is deployable from a compact state to a functional state and can be manufactured from a single plane and folded into shape. Mathematical formulations are presented to describe the classes of developable surfaces in terms of properties which are frequently important in mechanism design. These natural equations for a single class of developable surface are conducive to modeling the folding motion of rigid-ruling developables, developables whose ruling lines do change location in a surface during folding. These formulations are used to generalize the design of rolling-contact joints to a family of joints capable of single degree of freedom spatial motions, being manufactured from a plane, and exhibiting a tailorable force response. Finally practical design suggestions for the implementation of rolling-contact joints is given. These include methodology to create sunken flexures which serve to increase the normal force between rolling bodies to prevent slip.
From Editors’ Desk

Treatment of respiratory ailments is important part of health care system. Though we have good international data on various respiratory problems yet simple extrapolation may fail to solve the problems related to Indian conditions. Therefore, we need to have Indian research data to draw appropriate inferences. During past few years respiratory physicians in India have collected good respiratory data.
Laser-based joining of three-dimensional thermoplastic parts and thermoplastic aluminum hybrids

In near future the use of plastics in the automotive industry will continue to grow strongly because of the increasing use of lightweight construction. The range of applications of plastics already extends from smallest electronics to large structure components. The rising use of plastic parts causes a high demand for efficient technologies to join thermoplastics as well as hybrid structures made out of dissimilar lightweight materials. Therefore laser-based joining technologies are becoming increasingly important. In this paper, two approaches for the laser-based joining of large thermoplastic parts with three-dimensional weld contours and for the production of thermoplastic aluminum hybrids are presented. Both technologies are considered suitable for flexible and easy automation. However a big issue is still their small gap bridging capability. A promising approach to improve the gap bridging capability is a highly dynamic laser beam oscillation leading to quasi-simultaneous intensity distributions. In this paper a system technology designed for laser-based joining of three-dimensional parts performing such laser beam oscillation is introduced. Further experimental results of polyamide welding and polyamide aluminum hybrids are discussed.In near future the use of plastics in the automotive industry will continue to grow strongly because of the increasing use of lightweight construction. The range of applications of plastics already extends from smallest electronics to large structure components. The rising use of plastic parts causes a high demand for efficient technologies to join thermoplastics as well as hybrid structures made out of dissimilar lightweight materials. Therefore laser-based joining technologies are becoming increasingly important. In this paper, two approaches for the laser-based joining of large thermoplastic parts with three-dimensional weld contours and for the production of thermoplastic aluminum hybrids are presented. Both technologies are considered suitable for flexible and easy automation. However a big issue is still their small gap bridging capability. A promising approach to improve the gap bridging capability is a highly dynamic laser beam oscillation leading to quasi-simultaneous intensity distributions. In .
Building Chemical Information Systems - the ViFaChem II Project

The interdisciplinary ViFaChem II project aims at providing a chemical digital library infrastructure for creating personalized information spaces. The value added services and scientific Web 2.0 techniques actively support chemical scientists and researchers in retrieval tasks as well as in deriving new knowledge from the collected information in a highly personalized fashion. The complex requirements of a digital library for chemists are described and an overall architecture tackling these requirements is presented. Also preliminary results regarding chemical entity recognition and automatic dynamic generated document facets are presented and discussed.
Optimal Active Control and Optimization of a Wave Energy Converter

This paper investigates optimal active control schemes applied to a point absorber wave energy converter within a receding horizon fashion. A variational formulation of the power maximization problem is adapted to solve the optimal control problem. The optimal control method is shown to be of a bang-bang type for a power takeoff mechanism that incorporates both linear dampers and active control elements. We also consider a direct transcription of the optimal control problem as a general nonlinear program. A variation of the projected gradient optimization scheme is formulated and shown to be feasible and computationally inexpensive compared to a standard NLP solver. Since the system model is bilinear and the cost function is not convex quadratic, the resulting optimization problem is not a quadratic program. Results will be compared with an optimal command latching method to demonstrate the improvement in absorbed power. All time domain simulations are generated under irregular sea conditions.
NEUDM: A System for Topic-Based Message Polarity Classification

In this paper, we describe our system for the topic-based Chinese message polarity classification in SIGHAN 8 Task 2. Our system integrates two SVM classifiers which consist of LinearSVC and LibSVM to train the classification model and predict the results of Chinese message polarity in the restricted resource and the unrestricted resource, respectively. In order to assure our feature engineering effort on the task, we use some feature selection methods, such as LDA, word2vec, and sentiment lexicons including DLUT emotion ontology and NTUSD. Our system achieves the overall F1 score of 74.88% in the restricted evaluation and 74.43% in the unrestricted evaluation.
Listeria monocytogenes-Induced Cell Death Inhibits the Generation of Cell-Mediated Immunity

ABSTRACT The influence of cell death on adaptive immunity has been studied for decades. Despite these efforts, the intricacies of how various cell death pathways shape immune responses in the context of infection remain unclear, particularly with regard to more recently discovered pathways such as pyroptosis. The emergence of Listeria monocytogenes as a promising immunotherapeutic platform demands a thorough understanding of how cell death induced in the context of infection influences the generation of CD8+ T-cell-mediated immune responses. To begin to address this question, we designed strains of L. monocytogenes that robustly activate necrosis, apoptosis, or pyroptosis. We hypothesized that proinflammatory cell death such as necrosis would be proimmunogenic while apoptosis would be detrimental, as has previously been reported in the context of sterile cell death. Surprisingly, we found that the activation of any host cell death in the context of L. monocytogenes infection inhibited the generation of protective immunity and specifically the activation of antigen-specific CD8+ T cells. Importantly, the mechanism of attenuation was unique for each type of cell death, ranging from deficits in costimulation in the context of necrosis to a suboptimal inflammatory milieu in the case of pyroptosis. Our results suggest that cell death in the context of infection is different from sterile-environment-induced cell death and that inhibition of cell death or its downstream consequences is necessary for developing effective cell-mediated immune responses using L. monocytogenes-based immunotherapeutic platforms.
A Functional Hitchhiker's Guide to Hereditarily Finite Sets, Ackermann Encodings and Pairing Functions

The paper is organized as a self-contained literate Haskell program that implements elements of an executable finite set theory with focus on combinatorial generation and arithmetic encodings. The code, tested under GHC 6.6. 1, is available at this http URL . We introduce ranking and unranking functions generalizing Ackermann's encoding to the universe of Hereditarily Finite Sets with Urelements. Then we build a lazy enumerator for Hereditarily Finite Sets with Urelements that matches the unranking function provided by the inverse of Ackermann's encoding and we describe functors between them resulting in arithmetic encodings for powersets, hypergraphs, ordinals and choice functions. After implementing a digraph representation of Hereditarily Finite Sets we define {\em decoration functions} that can recover well-founded sets from encodings of their associated acyclic digraphs. We conclude with an encoding of arbitrary digraphs and discuss a concept of duality induced by the set membership relation. Keywords: hereditarily finite sets, ranking and unranking functions, executable set theory, arithmetic encodings, Haskell data representations, functional programming and computational mathematics
Multicultural competence: Criteria and case examples.

How do you as a professional psychologist know if you are competent to treat clients whose cultural origins and values differ from your own? What awareness, knowledge, and skills do you need? With whom should you consult? When should you refer? Adopting an idiographic, inclusive approach, the authors identify 12 minimal multicultural competencies for practice and illustrate their usefulness through 3 case examples. Suggestions for how professional psychologists can augment and evaluate their own multicultural competencies are offered as well as implications for professional psychology educators. Consider the following scenario: Dr. Mary Ann Smith is a European American licensed clinical psychologist trying to build her private practice in a medium-sized town in the upper Midwest. She has worked to become listed on provider panels and realizes how important self-referred individuals with good insurance are to her livelihood. In 1 week, she receives three new clients: a recently fired Native American male nurse filing a discrimination lawsuit against the school district; a Spanish-speaking Mexican American lesbian fighting a custody battle with her ex-husband; and a blind, indigent, 70-year-old Irish American man with depression. "Am I competent to treat these clients? " wonder^ Dr. Smith, "and if not, to whom do I refer? " For professional psychologists like Dr. Smith, working with diverse clients will soon become the norm rather than the exception. Shortly after the year 2050, racial and ethnic minorities will become a numerical majority in the United States (U.S. Bureau of the Census, 1995). Nearly 75% of the current entering labor force are racial and ethnic minorities or women, and when "baby
A large-scale study of link spam detection by graph algorithms

Link spam refers to attempts to promote the ranking of spammers' web sites by deceiving link-based ranking algorithms in search engines. Spammers often create densely connected link structure of sites so called "link farm". In this paper, we study the overall structure and distribution of link farms in a large-scale graph of the Japanese Web with 5.8 million sites and 283 million links. To examine the spam structure, we apply three graph algorithms to the web graph. First, the web graph is decomposed into strongly connected components (SCC). Beside the largest SCC (core) in the center of the web, we have observed that most of large components consist of link farms. Next, to extract spam sites in the core, we enumerate maximal cliques as seeds of link farms. Finally, we expand these link farms as a reliable spam seed set by a minimum cut technique that separates links among spam and non-spam sites. We found about 0.6 million spam sites in SCCs around the core, and extracted additional 8 thousand and 49 thousand sites as spams with high precision in the core by the maximal clique enumeration and by the minimum cut technique, respectively.
Entrainment to Natural Oscillations via Uncoupled Central Pattern Generators

Mechanical systems can often be controlled efficiently by exploiting a resonance. An optimal trajectory minimizing an energy cost function is found at (or near) a natural mode of oscillation. Motivated by this fact, we consider the natural entrainment problem: the design of nonlinear feedback controllers for linear mechanical systems to achieve a prescribed mode of natural oscillation for the closed-loop system. We adopt a set of distributed central pattern generators (CPGs) as the basic control architecture, inspired by biological observations. The method of multivariable harmonic balance (MHB) is employed to characterize the condition, approximately, for the closed-loop system to have a natural oscillation as its trajectory. Necessary and sufficient conditions for satisfaction of the MHB equation are derived in the forms useful for control design. It is shown that the essential design freedom can be captured by two parameters, and the design parameter plane can be partitioned into regions, in each of which approximate entrainment to one of the natural modes, with an error bound, is predicted by the MHB analysis. Control mechanisms underlying natural entrainment, as well as limitations and extensions of our results, are discussed.
Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors

G protein-coupled receptors for dopamine and serotonin control signaling pathways targeted by many psychoactive drugs. A puzzle is how receptors with similar functions and nearly identical binding site structures, such as D2 dopamine receptors and 5-HT2A serotonin receptors, could evolve a mechanism that discriminates stringently in their cellular responses between endogenous neurotransmitters. We used the Difference Evolutionary Trace (Difference-ET) and residue-swapping to uncover two distinct sets of specificity-determining sequence positions. One at the ligand-binding pocket determines the relative affinities for these two ligands, and a distinct, surprising set of positions outside the binding site determines whether a bound ligand can trigger the conformational rearrangement leading to G protein activation. Thus one site specifies affinity while the other encodes a filter for efficacy. These findings demonstrate that allosteric pathways linking distant interactions via alternate conformational states enforce specificity independently of the ligand-binding site, such that either one may be rationally rekeyed to different ligands. The conversion of a dopamine receptor effectively into a serotonin receptor illustrates the plasticity of GPCR signaling during evolution, or in pathological states, and suggests new approaches to drug discovery, targeting both classes of sites.
Performance tests of a novel coaxial tube catheter in an in vitro model of intracranial cell delivery

We have tested prototypes of a novel coaxial tube catheter in an in vitro gel model of cell delivery into the brain. Devices 1.6 and 2.0 mm outer diameter were used to deliver PC 12 cells (concentration = 106 cells ml−1) at 1 μl min−1 into a 5 ml sandwich of collagen and 0.1% agarose, with and without follow-on infusions of nerve growth factor (NGF). Post-infusion microscopic imaging (40X) at the infusion sites was then carried out over 7-day periods. The results showed that under these experimental conditions, it was possible to use these catheters to deliver cells without either leakage of trapped air into the gel or reflux of the cell suspension along the catheter insertion track. Differentiation of the NGF-treated cells was observed.
Hidden Markov models for detecting remote protein homologies

MOTIVATION A new hidden Markov model method (SAM-T98) for finding remote homologs of protein sequences is described and evaluated. The method begins with a single target sequence and iteratively builds a hidden Markov model (HMM) from the sequence and homologs found using the HMM for database search. SAM-T98 is also used to construct model libraries automatically from sequences in structural databases. METHODS We evaluate the SAM-T98 method with four datasets. Three of the test sets are fold-recognition tests, where the correct answers are determined by structural similarity. The fourth uses a curated database. The method is compared against WU-BLASTP and against DOUBLE-BLAST, a two-step method similar to ISS, but using BLAST instead of FASTA. RESULTS SAM-T98 had the fewest errors in all tests-dramatically so for the fold-recognition tests. At the minimum-error point on the SCOP (Structural Classification of Proteins)-domains test, SAM-T98 got 880 true positives and 68 false positives, DOUBLE-BLAST got 533 true positives with 71 false positives, and WU-BLASTP got 353 true positives with 24 false positives. The method is optimized to recognize superfamilies, and would require parameter adjustment to be used to find family or fold relationships. One key to the performance of the HMM method is a new score-normalization technique that compares the score to the score with a reversed model rather than to a uniform null model. AVAILABILITY A World Wide Web server, as well as information on obtaining the Sequence Alignment and Modeling (SAM) software suite, can be found at http://www.cse.ucsc.edu/research/compbi o/ CONTACT karplus@cse.ucsc.edu; http://www.cse.ucsc.edu/karplus
A robust video encoding scheme to enhance error concealment of intra frames

In this paper a robust encoding scheme is proposed to improve the visual quality of HEVC decoded video when intra frames are lost along the streaming path. For this purpose, the encoding process includes frame loss simulation and subsequent error concealment, to find the most efficient method that should be used by a decoder to recover lost intra frames. In this novel scheme, each image is divided into partitions, which are associated with the error concealment method that achieves the lowest distortion. Then this information is signalled to the decoder through SEI messages in the coded stream. In order to efficiently use the signalling overhead, rate-distortion optimisation is used to achieve the best trade-off between the number of transmitted symbols and distortion of reconstructed frames. Experimental results show the effectiveness of the proposed method to enhance the quality of reconstructed intra frames under different packet loss ratios (PLR). For PLR=10%, the robust coding scheme is able to improve the average PSNR of all frames affected by errors, up to 1.50 dB and 3.44 dB in Low-Delay and Random-Access configurations respectively, at a maximum overhead cost of 0.24%.
Hyperspectral superpixel extraction using boundary updates based on optimal spectral similarity metric

The high spectral resolution of hyperspectral images (HSI) requires a heavy processing load. Assigning each pixel to a group in the image, which is called superpixel, and processing the superpixels instead of the pixels is resorted as a means to overcome this challenge in the hyperspectral literature. In this paper, we propose an algorithm to segment a hyperspectral image into superpixels by means of iteratively updating the boundary pixels of superpixels. We first explore the optimal similarity metric for the boundary pixel updates with the contraint of keeping the superpixel boundaries aligned with the object boundaries in the image. We investigate two approaches for similarity detection between pixels during this update, first comparing the hyperspectral pixels individually, and second, comparing the pixels by using also their neigborhood. The spectral similarity metrics used for investigation are selected as spectral angle mapping (SAM) [1], spectral information divergence (SID) [2] and spatial coherence distance [3] due to their common usage. The proposed approach is compared with a pioneer state-of-the-art superpixel algorithm, SLIC [4], and its superiority is verified in terms of the superpixelization performance metrics, namely boundary recall and undersegmentation error [5].