Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantum Chemical Studies of Structures and Binding in Noncanonical RNA Base pairs: The Trans Watson-Crick:Watson-Crick Family

Abstract The trans Watson-Crick/Watson-Crick family of base pairs represent a geometric class that play important structural and possible functional roles in the ribosome, tRNA, and other functional RNA molecules. They nucleate base triplets and quartets, participate as loop closing terminal base pairs in hair pin motifs and are also responsible for several tertiary interactions that enable sequentially distant regions to interact with each other in RNA molecules. Eleven representative examples spanning nine systems belonging to this geometric family of RNA base pairs, having widely different occurrence statistics in the PDB database, were studied at the HF/6–31G (d, p) level using Morokuma decomposition, Atoms in Molecules as well as Natural Bond Orbital methods in the optimized gas phase geometries and in their crystal structure geometries, respectively. The BSSE and deformation energy corrected interaction energy values for the optimized geometries are compared with the corresponding values in the crystal geometries of the base pairs. For non protonated base pairs in their optimized geometry, these values ranged from −8.19 kcal/mol to −21.84 kcal/mol and compared favorably with those of canonical base pairs. The interaction energies of these base pairs, in their respective crystal geometries, were, however, lesser to varying extents and in one case, that of A:A W:W trans, it was actually found to be positive. The variation in RMSD between the two geometries was also large and ranged from 0.32–2.19 Å. Our analysis shows that the hydrogen bonding characteristics and interaction energies obtained, correlated with the nature and type of hydrogen bonds between base pairs; but the occurrence frequencies, interaction energies, and geometric variabilities were conspicuous by the absence of any apparent correlation. Instead, the nature of local interaction energy hyperspace of different base pairs as inferred from the degree of their respective geometric variability could be correlated with the identities of free and bound hydrogen bond donor/acceptor groups present in interacting bases in conjunction with their tertiary and neighboring group interaction potentials in the global context. It also suggests that the concept of isostericity alone may not always determine covariation potentials for base pairs, particularly for those which may be important for RNA dynamics. These considerations are more important than the absolute values of the interaction energies in their respective optimized geometries in rationalizing their occurrences in functional RNAs. They highlight the importance of revising some of the existing DNA based structure analysis approaches and may have significant implications for RNA structure and dynamics, especially in the context of structure prediction algorithms.
On the inscrutable role of Inscuteable: structural basis and functional implications for the competitive binding of NuMA and Inscuteable to LGN

Alignment of the mitotic spindle to the cellular polarity axis is a prerequisite for asymmetric cell divisions. The protein network coordinating the spindle position with cortical polarity includes the molecular machinery pulling on astral microtubules, which is assembled on conserved NuMA:LGN:Gαi complexes, the polarity proteins Par3:Par6:aPKC and an adaptor molecule known as Inscuteable (Insc). To date, all these components were assumed to enter a macromolecular complex localized at polarity sites in mitosis. However, recent structural studies revealed the Insc and NuMA are mutually exclusive interactors of LGN, implying that the molecular mechanism of spindle coupling to polarity is more sophisticated than has been believed to date.
Expression and localization of the inwardly rectifying potassium channel Kir7.1 in native bovine retinal pigment epithelium.

PURPOSE The purpose of this study was to identify the molecular basis of the apical membrane K(+) conductance in native bovine retinal pigment epithelium (RPE). METHODS RT-PCR, Northern blot, and Western blot analyses were used to detect the expression of the inwardly rectifying K(+) (Kir) channel subunits Kir7.1 and Kir4.1 in native bovine RPE and neural retina. The distribution of Kir7.1 protein was determined in frozen sections of bovine retina-RPE-choroid by indirect immunofluorescence analysis. RESULTS RT-PCR analysis revealed Kir7.1 transcript in both RPE and neural retina, but Kir4.1 transcript only in the neural retina. In Northern blot analysis, Kir4.1 probe hybridized to an appropriately sized-transcript in neural retina but not in RPE. Kir7.1 probe hybridized to a major transcript of approximately 1.5 kb in both RPE and neural retina, but with greater expression in RPE. In Western blot analysis, Kir7.1 antibody recognized a major monomer of approximately 53 kDa in RPE, whereas Kir4.1 antibody recognized a monomer of approximately 60 kDa in neural retina but not in RPE. Intense Kir7.1 immunolabeling was present on the apical surface of all RPE cells and appeared to extend over the length of the apical processes. Na(+),K(+)-ATPase expression varied among RPE cells, but in highly expressing cells, it colocalized with Kir7.1. CONCLUSIONS These results indicate that the Kir7.1 channel subunit, but not Kir4.1, is a major component of the apical K(+) conductance in bovine RPE. Kir7.1 is distributed over the length of apical processes, where it probably functions in the regulation of K(+) transport and the electrical response of the RPE to light-evoked changes in subretinal K(+) concentration.
Sparse matrix-vector multiply on the HICAMP architecture

Sparse matrix-vector multiply (SpMV) is a critical task in the inner loop of modern iterative linear system solvers and exhibits very little data reuse. This low reuse means that its performance is bounded by main-memory bandwidth. Moreover, the random patterns of indirection make it difficult to achieve this bound. We present sparse matrix storage formats based on deduplicated memory. These formats reduce memory traffic during SpMV and thus show significantly improved performance bounds: 90x better in the best case. Additionally, we introduce a matrix format that inherently exploits any amount of matrix symmetry and is at the same time fully compatible with non-symmetric matrix code. Because of this, our method can concurrently operate on a symmetric matrix without complicated work partitioning schemes and without any thread synchronization or locking. This approach takes advantage of growing processor caches, but incurs an instruction count overhead. It is feasible to overcome this issue by using specialized hardware as shown by the recently proposed Hierarchical Immutable Content-Addressable Memory Processor, or HICAMP architecture.
Estimation and optimization of potentiometric sensor response parameters from surfactant titration data using Microsoft Excel Solver and Mathematica

Estimation and Optimization of Potentiometric Sensor Response Parameters from Surfactant Titration Data Using Microsoft Excel Solver and Mathematica Milan Sak-Bosnar1 ∗, Dubravka Madunic-Cacic2, Nikola Sakac1, Mirela Samardžic1, and Želimir Kurtanjek3 1Department of Chemistry, Josip Juraj Strossmayer University of Osijek, F. Kuhaea 20, HR-31000 Osijek, Croatia 2Saponia, Chemical, Pharmaceutical and Foodstuff Industry, M. Gupca 2, HR-31000 Osijek, Croatia 3Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, HR-10000 Zagreb, Croatia
A Turnout Switch for a Superconductively Levitated Linear Transport System

Within the SupraTrans project, a joint venture between research institutes, universities and industrial companies, a full working prototype of a superconductively levitated transport system has been constructed and developed. The levitation and guidance system is based on flux pinning in melt-textured bulk YBa2Cu3O7-delta (YBCO) that stabilizes the vertical and lateral position of the vehicle above the magnetic track. In contrast to conventional electromagnetic Maglev systems, track and vehicle do not mechanically envelop each other in the superconducting Maglev. It is therefore possible, to construct a non-mechanical turnout switch using electromagnets. Such fast working turnout switches are essential to establish a highly branched transportation network. An experimental set-up for an electromagnetic turnout switch has been created for a toy sized model train. Investigations regarding levitation force and stiffness of the vehicle during several crossings have been performed. Thereby the ideal line across the switch has been used to measure vertical and lateral forces in every step of the movement. The evaluation shows a small delay but appropriate levitation and guidance behavior.
Randomized Evaluation of Peer Support Arrangements to Support the Inclusion of High School Students With Severe Disabilities

Enhancing the social and learning experiences of students with severe disabilities in inclusive classrooms has been a long-standing focus of research, legislative, and advocacy efforts. The authors used a randomized controlled experimental design to examine the efficacy of peer support arrangements to improve academic and social outcomes for 51 students with severe disabilities in high school general education classrooms. Paraprofessionals or special educators recruited, trained, and supported 106 peers to provide individualized academic and social assistance to students with severe disabilities throughout one semester. Compared to students exclusively receiving adult-delivered support (n = 48), students participating in peer support arrangements experienced increased interactions with peers, increased academic engagement, more progress on individualized social goals, increased social participation, and a greater number of new friendships. Moreover, an appreciable proportion of relationships lasted one and two semesters later after the intervention had concluded. These findings challenge prevailing practices for supporting inclusive education and establish the efficacy and social validity of peer support arrangements as a promising alternative to individually assigned paraprofessional support.
Thiazolidinones : a novel class of hepatitis C virus NS 5 B polymerase inhibitors

1. Abstract 2. Introduction 3. Materials and Methods 3.1. Synthesis of inhibitors 3.2. Purification of recombinant replicase proteins 3.3. RNA-dependent RNA polymerase (RdRp) assay 3.4. Cross-linking of NS5B to TP 3.5. Determination of the Ki and mode of inhibition 3.6. Molecular modeling 4. Results 4.1. Expression and purification of recombinant replicase proteins 4.2. Identification of 4-Thiazolidinones as inhibitors of HCV NS5B RdRp activity 4.3. Mechanism of inhibition 4.4. Molecular docking and analysis of the binding mode of compound 6 5. Discussion 6. Acknowledgement 7. References
Easy As CBA: A Simple Probabilistic Model for Tagging Music

Many songs in large music databases are not labeled with semantic tags that could help users sort out the songs they want to listen to from those they do not. If the words that apply to a song can be predicted from audio, then those predictions can be used both to automatically annotate a song with tags, allowing users to get a sense of what qualities characterize a song at a glance. Automatic tag prediction can also drive retrieval by allowing users to search for the songs most strongly characterized by a particular word. We present a probabilistic model that learns to predict the probability that a word applies to a song from audio. Our model is simple to implement, fast to train, predicts tags for new songs quickly, and achieves state-of-the-art performance on annotation and retrieval tasks.
Transform based approaches for Palmprint Identification

In this paper, identification of a person is carried out using Discrete Cosine Transform (DCT) and Discrete Wavelet Transform (DWT) coefficients as palmprint features. Dimensionality reduction was carried out using Principal Component Analysis (PCA) and the reduced features were classified using Support Vector Machine (SVM). The segmented palmprint images used in this study are from the IITD palmprint database. Here, we describe the palmprint identification methodology, which can be summarized in a number of distinct steps: (1) preprocessing, (2) feature extraction, and (3) classification. Experiments were developed on a database of 100 images from 20 individuals. This study shows that DCT is better for palmprint identification with an accuracy of 99% compared to DWT which gives 96.66% accuracy.
Why do nurses migrate? - a review of recent literature.

AIM To identify the reasons why nurses continue migrating across international borders. BACKGROUND International nurse recruitment and migration have been increasing in the last decade and recent trends show an increase in the movement of nurses between developing and developed countries, resulting in a worldwide shortage of nurses. METHODS A manual and electronic database literature search was conducted from January 2004 to May 2010. Qualitative content analysis was completed for the final 17 articles that satisfied the inclusion criteria. RESULTS Motivators to nurse migration were linked to financial, professional, political, social and personal factors. Although economic factors were the most commonly reported, they were not the only reason for migration. This was especially evident among nurses migrating between developed countries. CONCLUSION Nurses migrate for a wide variety of reasons as they respond to push and pull factors. IMPLICATIONS FOR NURSING MANAGEMENT It is important for nurse managers in the source countries to advocate incentives to retain nurses. In the recipient countries the number of international nurses continues to increase implying the need for more innovative ways to mentor and orientate these nurses.
The effects of changes in internal ionic concentrations on the electrical properties of perfused giant axons

This paper is concerned with the effects of altering the composition of the internal fluid on the electrical properties of giant axons from which the bulk of the axoplasm had been removed by extrusion (Baker, Hodgkin & Shaw, 1962). To begin with, we shall consider a series of experiments which show that the difference in potassium concentration between the internal and external fluid provides the main electromotive force for generating the resting potential. In order to reduce the error introduced by junction potentials and to avoid making uncertain estimates of the activity coefficient ofK+ in K2S04 it was simplest to work with an internal solution consisting of mixtures ofKCI and NaCl. The high concentration of chloride did not have any markedly deleterious effect, for fibres filled with isotonic KCI were usually excitable and had a resting potential only about 5 mV less than in those filled with isotonic potassium sulphate.
IEEE 802.11 rate adaptation: a practical approach

Today, three different physical (PHY) layers for the IEEE 802.11 WLAN are available (802.11a/b/g); they all provide multi-rate capabilities. To achieve a high performance under varying conditions, these devices need to adapt their transmission rate dynamically. While this rate adaptation algorithm is a critical component of their performance, only very few algorithms such as Auto Rate Fallback (ARF) or Receiver Based Auto Rate (RBAR) have been published and the implementation challenges associated with these mechanisms have never been publicly discussed. In this paper, we first present the important characteristics of the 802.11 systems that must be taken into account when such algorithms are designed. Specifically, we emphasize the contrast between low latency and high latency systems, and we give examples of actual chipsets that fall in either of the different categories. We propose an Adaptive ARF (AARF) algorithm for low latency systems that improves upon ARF to provide both short-term and long-term adaptation. The new algorithm has very low complexity while obtaining a performance similar to RBAR, which requires incompatible changes to the 802.11 MAC and PHY protocol. Finally, we present a new rate adaptation algorithm designed for high latency systems that has been implemented and evaluated on an AR5212-based device. Experimentation results show a clear performance improvement over the algorithm previously implemented in the AR5212 driver we used.
Methods for Activity Analysis of the Proteins that Regulate Histone Methylation

The enzymes that regulate histone methylation states and the protein domains that recognize methylated histone residues have been implicated in a number of human diseases, including cancer, as a result of their ability to affect transcriptional changes by altering chromatin structure. These proteins are recognized as potential therapeutic targets for the treatment of diseases associated with epigenetic disruption; however, few inhibitors of their activity have been identified. The majority of histone demethylase and methyltransferase enzyme inhibitors have been discovered on the basis of their structural similarity to substrates or known inhibitors of enzymes with analogous mechanisms. The general lack of potency and specificity of these compounds indicates that novel chemotypes are needed to address the large number of recently discovered histone-modifying enzymes. High-throughput screening (HTS) allows rapid testing of chemically diverse small molecule libraries, provided assays amenable to HTS exist. Here we review the biochemical and cellular assays available for testing the proteins and enzymes that regulate histone methylation. Progress in the development of high-throughput, sensitive, and robust assays will enable discovery of small molecules for epigenetic therapy.
Substrate Integrated Waveguide Cavity-Backed Wide Slot Antenna for 60-GHz Bands

A wide slot antenna backed by a substrate integrated waveguide (SIW) cavity is presented and investigated for the enhancement of operating bandwidth at 60-GHz band. The 10-dB return loss impedance bandwidth of the antenna increases from 3% to 11.6% with consistent radiation performance as the width to length ratio (WLR) of the rectangular slot cutting from the SIW increases from 0.12 to 0.71. Its dual-resonance operation mechanism is verified by a parametric study. Three 2 × 4 antenna arrays with different slot WLRs are designed and fabricated with a printed circuit board (PCB) process at the 60-GHz bands. The measured results show that the antenna array with slot WLR of 0.71 achieves the gain of 10-12 dBi and the cross-polarization levels of better than 25 dB in both E- and H-planes over the enhanced operating bandwidth of about 11.6%.
Transformation of Output Constraints in Optimal Control Applied to a Double Pendulum on a Cart

This paper describes a constraint transformation technique for optimal control problems (OCP) with nonlinear single-input single-output (SISO) systems subject to output constraints. An input-output transformation and saturation functions are used to transform the system dynamics into a new unconstrained representation. This method allows to reformulate the original OCP into an unconstrained counterpart. The transformation technique is applied to a double pendulum on a cart in order to compute optimal trajectories for a multi-stage transition scenario. Simulation as well as experimental results with an additional feedback control demonstrate the applicability of the presented method.
Exact optimization for a class of second order Markov random field via graph cuts

Optimization for the maximum a posterior (MAP) estimation of a Markov random field often comes down to a large combinational optimization problem, and the general purpose optimization technology such as simulated annealing requires exponential time in theory and is very slow in practice. In recent years a new method based on graph cuts has been developed to solve this problem. But right now it is restricted to the first order MRF. In this paper we have developed an exact optimization method for a class of second order MRF, which are wildly used in many applications. We consider each term in the posterior energy function separately and then merge them together. We give a detailed construction of the graph in the paper.
Consistency of Learning Bayesian Network Structures with Continuous Variables: An Information Theoretic Approach

We consider the problem of learning a Bayesian network structure given n examples and the prior probability based on maximizing the posterior probability. We propose an algorithm that runs in O(n log n) time and that addresses continuous variables and discrete variables without assuming any class of distribution. We prove that the decision is strongly consistent, i.e., correct with probability one as n ! 1. To date, consistency has only been obtained for discrete variables for this class of problem, and many authors have attempted to prove consistency when continuous variables are present. Furthermore, we prove that the “log n” term that appears in the penalty term of the description length can be replaced by 2(1+e) log log n to obtain strong consistency, where e > 0 is arbitrary, which implies that the Hannan–Quinn proposition holds.
A Novel Robust Modified Support Vector Machines

In this paper, a novel general robust SVM approach for classification is proposed which can better characterize the distribution of the data compared with the traditional SVM. The classical Support Vector Machines is heavily relied on the Support Vector which has neglected the holistic distribution of the data that sometimes will lead to gross errors. We first take use of the majority of the data distribution. Then we apply the distance between the two classes and modify the original SVM objective function. In the last step we search the best weights to make a balance between the distance and the maximum margin. We developed an improved method for optimizing over the SVM algorithm. Experiments on 10 famous data sets clearly demonstrate improved performance and this method is also readily applicable for data sets with different distribution.
Echovirus 30 Induced Neuronal Cell Death through TRIO-RhoA Signaling Activation

Background Echovirus 30 (Echo30) is one of the most frequently identified human enteroviruses (EVs) causing aseptic meningitis and encephalitis. However the mechanism underlying the pathogenesis of Echo30 infection with significant clinical outcomes is not completely understood. The aim of this investigation is to illustrate molecular pathologic alteration in neuronal cells induced by Echo30 infection using clinical isolate from young patient with neurologic involvement. Methodology/Principal Findings To characterize the neuronal cellular response to Echo30 infection, we performed a proteomic analysis based on two-dimensional gel electrophoresis (2-DE) and MALDI-TOF/TOF Mass Spectrophotometric (MS) analysis. We identified significant alteration of several protein expression levels in Echo30-infected SK-N-SH cells. Among these proteins, we focused on an outstanding up-regulation of Triple functional domain (TRIO) in Echo30-infected SK-N-SH cells. Generally, TRIO acts as a key component in the regulation of axon guidance and cell migration. In this study, we determined that TRIO plays a role in the novel pathways in Echo30 induced neuronal cell death. Conclusions/Significance Our finding shows that TRIO plays a critical role in neuronal cell death by Echo30 infection. Echo30 infection activates TRIO-guanine nucleotide exchange factor (GEF) domains (GEFD2) and RhoA signaling in turn. These results suggest that Echo30 infection induced neuronal cell death by activation of the TRIO-RhoA signaling. We expect the regulation of TRIO-RhoA signaling may represent a new therapeutic approach in treating aseptic meningitis and encephalitis induced by Echo30.