Miracle-dz/UniFAR-FTUs huggingface dataset:
The Stanford RNA Mapping Database for sharing and visualizing RNA structure mapping experiments

We have established an RNA Mapping Database (RMDB) to enable a new generation of structural, thermodynamic, and kinetic studies from quantitative single-nucleotide-resolution RNA structure mapping (freely available at this http URL). Chemical and enzymatic mapping is a rapid, robust, and widespread approach to RNA characterization. Since its recent coupling with high-throughput sequencing techniques, accelerated software pipelines, and large-scale mutagenesis, the volume of mapping data has greatly increased, and there is a critical need for a database to enable sharing, visualization, and meta-analyses of these data. Through its on-line front-end, the RMDB allows users to explore single-nucleotide-resolution chemical accessibility data in heat-map, bar-graph, and colored secondary structure graphics; to leverage these data to generate secondary structure hypotheses; and to download the data in standardized and computer-friendly files, including the RDAT and community-consensus SNRNASM formats. At the time of writing, the database houses 38 entries, describing 2659 RNA sequences and comprising 355,084 data points, and is growing rapidly.
Carbonylation Modification Regulates Na/K-ATPase Signaling and Salt Sensitivity: A Review and a Hypothesis

Na/K-ATPase signaling has been implicated in different physiological and pathophysiological conditions. Accumulating evidence indicates that oxidative stress not only regulates the Na/K-ATPase enzymatic activity, but also regulates its signaling and other functions. While cardiotonic steroids (CTS)-induced increase in reactive oxygen species (ROS) generation is an intermediate step in CTS-mediated Na/K-ATPase signaling, increase in ROS alone also stimulates Na/K-ATPase signaling. Based on literature and our observations, we hypothesize that ROS have biphasic effects on Na/K-ATPase signaling, transcellular sodium transport, and urinary sodium excretion. Oxidative modulation, in particular site specific carbonylation of the Na/K-ATPase α1 subunit, is a critical step in proximal tubular Na/K-ATPase signaling and decreased transcellular sodium transport leading to increases in urinary sodium excretion. However, once this system is overstimulated, the signaling, and associated changes in sodium excretion are blunted. This review aims to evaluate ROS-mediated carbonylation of the Na/K-ATPase, and its potential role in the regulation of pump signaling and sodium reabsorption in the renal proximal tubule (RPT).
A Comprehensive Availability Modeling and Analysis of a Virtualized Servers System Using Stochastic Reward Nets

It is important to assess availability of virtualized systems in IT business infrastructures. Previous work on availability modeling and analysis of the virtualized systems used a simplified configuration and assumption in which only one virtual machine (VM) runs on a virtual machine monitor (VMM) hosted on a physical server. In this paper, we show a comprehensive availability model using stochastic reward nets (SRN). The model takes into account (i) the detailed failures and recovery behaviors of multiple VMs, (ii) various other failure modes and corresponding recovery behaviors (e.g., hardware faults, failure and recovery due to Mandelbugs and aging-related bugs), and (iii) dependency between different subcomponents (e.g., between physical host failure and VMM, etc.) in a virtualized servers system. We also show numerical analysis on steady state availability, downtime in hours per year, transaction loss, and sensitivity analysis. This model provides a new finding on how to increase system availability by combining both software rejuvenations at VM and VMM in a wise manner.
A stepped-wedge cluster randomised controlled trial for evaluating rates of falls among inpatients in aged care rehabilitation units receiving tailored multimedia education in addition to usual care: a trial protocol

Introduction Falls are the most frequent adverse event reported in hospitals. Approximately 30% of in-hospital falls lead to an injury and up to 2% result in a fracture. A large randomised trial found that a trained health professional providing individualised falls prevention education to older inpatients reduced falls in a cognitively intact subgroup. This study aims to investigate whether this efficacious intervention can reduce falls and be clinically useful and cost-effective when delivered in the real-life clinical environment. Methods A stepped-wedge cluster randomised trial will be used across eight subacute units (clusters) which will be randomised to one of four dates to start the intervention. Usual care on these units includes patient's screening, assessment and implementation of individualised falls prevention strategies, ongoing staff training and environmental strategies. Patients with better levels of cognition (Mini-Mental State Examination >23/30) will receive the individualised education from a trained health professional in addition to usual care while patient's feedback received during education sessions will be provided to unit staff. Unit staff will receive training to assist in intervention delivery and to enhance uptake of strategies by patients. Falls data will be collected by two methods: case note audit by research assistants and the hospital falls reporting system. Cluster-level data including patient's admissions, length of stay and diagnosis will be collected from hospital systems. Data will be analysed allowing for correlation of outcomes (clustering) within units. An economic analysis will be undertaken which includes an incremental cost-effectiveness analysis. Ethics and dissemination The study was approved by The University of Notre Dame Australia Human Research Ethics Committee and local hospital ethics committees. Results The results will be disseminated through local site networks, and future funding and delivery of falls prevention programmes within WA Health will be informed. Results will also be disseminated through peer-reviewed publications and medical conferences. Trial registration The study is registered with the Australian New Zealand Clinical Trials registry (ACTRN12612000877886).
Configuration Provider: A Pattern for Configuring Threaded Applications

You have an application that reads in configuration data at start-up. Your program consists of multiple threads with similar functionality. Some of the configuration data applies to all threads; the other part of the data applies to individual threads only. The configuration data should be read-only after it has been provided at start-up. This paper introduces the pattern Configuration Provider as an implementation suggestion for this context.
On topological conditions to maintain leader-follower connectivity in double-integrator multi-agent systems

In this work, a set of sufficient conditions that guarantee consensus towards a pre-specified target state in double-integrator leader-follower proximity-based networks are derived. Since only the leader agents are aware of the global objective and proximity-based communication between agents is considered, the follower agents must not lose contact to the leaders. We establish a connectivity analysis framework which is used to show that the initial network topology is maintained if the ratio of leaders-to-followers and the magnitude of the goal attraction force experienced by the leaders are below certain bounds. Various network topologies are examined, starting from a complete graph and extending to incomplete graphs. The theoretical results are illustrated by simulations.
Communication energy oriented scheduling optimization for network on chip

It is difficult to improve the performance for the traditional processor architecture. The power consumption and the temperature of the processors are the main bottlenecks for CPU with single core. Chip multiprocessor is proposed to solve such problems. In order to solve the communication problem between the on chip components, network on chip is taken as the promising diagram. The on-chip cores are connected by lines. However, the communication is now the core of the on-chip network and the power consumed is more than before. This paper aims at the energy consumption problem in communication. The tasks will be mapped to the cores according to the communication density to reduce the power consumption and improve the performance. The experimental results show that our algorithm can achieve its target.
Observer-based finite-time control for discrete fuzzy jump nonlinear systems with time delays

This paper investigates the problem of observer-based finite-time H∞ control for a family of discrete jump nonlinear systems with time delays represented by Takagi-Sugeno (T-S) model. The main contribution of this paper is to design an observer-based finite-time H∞ controller such that the resulting closed-loop system is stochastic finite-time bounded and satisfies a prescribed H∞ disturbance attenuation level over the given finite-time interval. Sufficient criteria on stochastic finite-time H∞ stabilization via observer-based fuzzy state feedback are provided for the solvability of the problem, which can be tackled by a feasibility problem in terms of linear matrix inequalities. A simulation example is presented to illustrate the validity of our contributions.
Microstructure of martensite : why it forms and how it gives rise to the shape-memory effect

1. Introduction 2. Review of Continuum Mechanics 3. Continuum Theory of Crystalline Solids 4. Martensitic Phase Transformation 5. Twinning in Martensite 6. Origin of Microstructure 7. Special Microstructures 8. Analysis of Microstructure 9. The Shape-Memory Effect 10. Thin Films 11. Geometrically Linear Theory 12. Piece-wise Linear Elasticity 13. Polycrystals
A technique for positioning nanoparticles using an atomic force microscope

In this paper we present a method for manipulating nanometer-sized particles on surfaces using a commercial atomic force microscope (AFM). A PC-mouse-based `click and move' manipulation scheme was implemented without the need for additional software or hardware development. The success of the scheme depends mostly on the choice of tip and cantilever which should be able to operate in both the contact mode and vibrating cantilever mode. Four different tip/cantilever combinations were tested and suitable types were found among those commercially available. The necessary properties are defined. The technique enables the fabrication of various kinds of two-dimensional structures of nanoparticles but may have relevance also to other areas of nanoscience, e.g. biotechnology. We developed the technique in order to study the magnetization of single nanoparticles using a very sensitive Hall micromagnetometer. The AFM is used as a tool to select and position a specific particle in the active region of the magnetometer.
Psychosomatic Medicine in Germany: More Timely than Ever

a Department of Psychosomatic Medicine and Psychotherapy, University Medical Hospital Tübingen, Tübingen , b Department of General Internal Medicine and Psychosomatics, Heidelberg University Hospital, Heidelberg , c Department of Psychosomatic Medicine and Psychotherapy, University Hospital Giessen and Marburg, Giessen and Marburg , and d Department of Psychosomatic Medicine and Psychotherapy, Klinikum rechts der Isar, Technical University of Munich, Munich , Germany
Web Search Clustering and Labeling with Hidden Topics

Web search clustering is a solution to reorganize search results (also called “snippets”) in a more convenient way for browsing. There are three key requirements for such post-retrieval clustering systems: (1) the clustering algorithm should group similar documents together; (2) clusters should be labeled with descriptive phrases; and (3) the clustering system should provide high-quality clustering without downloading the whole Web page. This article introduces a novel framework for clustering Web search results in Vietnamese which targets the three above issues. The main motivation is that by enriching short snippets with hidden topics from huge resources of documents on the Internet, it is able to cluster and label such snippets effectively in a topic-oriented manner without concerning whole Web pages. Our approach is based on recent successful topic analysis models, such as Probabilistic-Latent Semantic Analysis, or Latent Dirichlet Allocation. The underlying idea of the framework is that we collect a very large external data collection called “universal dataset,” and then build a clustering system on both the original snippets and a rich set of hidden topics discovered from the universal data collection. This can be seen as a richer representation of snippets to be clustered. We carry out careful evaluation of our method and show that our method can yield impressive clustering quality.
Unconstrained human identification using comparative facial soft biometrics

Soft biometrics are attracting a lot of interest with the spread of surveillance systems, and the need to identify humans at distance and under adverse visual conditions. Comparative soft biometrics have shown a significantly better impact on identification performance compared to traditional categorical soft biometrics. However, existing work that has studied comparative soft biometrics was based on small datasets with samples taken under constrained visual conditions. In this paper, we investigate human identification using comparative facial soft biometrics on a larger and more realistic scale using 4038 subjects from the View 1 subset of the LFW database. Furthermore, we introduce a new set of comparative facial soft biometrics and investigate the effect of these on identification and verification performance. Our experiments show that by using only 24 features and 10 comparisons, a rank-10 identification rate of 96.98% and a verification accuracy of 93.66% can be achieved.
Hierarchical Tracking Control of Car-Like Mobile Robots

A hierarchical tracking controller for a car-like mobile robot subject to nonholonomic constraints is designed in this paper. The special structure of the derived equations of motion makes it possible to separate the design into three levels: motion planning, kinematic, and dynamic. In the proposed scheme, a fuzzy inference engine in the kinematic level is used to change the desired trajectory computed from the motion planning level. A sliding mode controller is adopted to track the new reference values of privileged coordinates in the dynamic level, which subsequently drives the non-privileged coordinates to the desired values. From the simulation results, it is shown that such hierarchical tracking control which simultaneously takes kinematics and dynamics into consideration indeed effectively solve the tracking problem. All the variables can be steered to their desired values asymptotically, which is assured by the skew-symmetric property of the reduced Appell equation.
Rigid and Conductive Dual Nanoprobe for Single Cell Analysis

Electrical property characterization of a single cell can be used to infer about its physiological condition, e.g. cell viability. Due to that, a dual nanoprobe-microfluidic system for electrical properties measurement of single cells has been proposed. This paper is concerned about the mechanical and electrical characterizations of the dual nanoprobe. Electrical and mechanical characterizations were conducted to measure the resistance and the strength of the dual nanoprobe for five different metals i.e. Aluminium, Copper, Silver, Tungsten, and Zinc using finite element approach. From the findings, Tungsten’s nanoprobe has the highest strength while the resistance values for the five materials are not significantly different. Therefore, Tungsten is selected as the most recommended metal for the dual nanoprobe. We also performed single cell electrical measurement to test the functionality of the sensor. This work provides general information of the nanoprobe which can be used as a framework in other applications involving Nano devices i.e. cell surgery and drug delivery.
In vivo evaluation of a novel ‘diastole-patching’ algorithm for the estimation of pulse transit time: advancing the precision in pulse wave velocity measurement

Carotid-to-femoral pulse wave velocity (PWV) is the gold standard for the assessment of aortic stiffness. It is calculated by the ratio of pulse transit time (PTT) between two arterial sites and the distance between them. The precision of PTT estimation depends upon the algorithm that determines characteristic points at the foot of the pulse waveforms. Different algorithms yield variable PTT values thus affecting the precision of PWV and subsequently its diagnostic and prognostic accuracy. Our aim was to apply in vivo a new ‘diastole-patching’ algorithm and investigate whether it improves the precision of PWV measurement. Two repeated PWV measurements were performed in a general population (340 subjects) by a reference apparatus (SphygmoCor) which uses the tangential method for PTT estimation. PTT was re-estimated by the ‘diastole-patching’ algorithm. We computed statistical parameters of agreement, consistency, precision and variability between the two PWV measurements. The ‘diastole-patching’ method yielded more precise and reproducible measurements of PWV compared to the tangential method at the total population. In those cases where the reference method provided PWV measurements with difference >1 m s−1, the ‘diastole-patching’ algorithm further improved the precision of PWV. These findings may have direct implications concerning the enhancement of the diagnostic and prognostic value of PWV.
Health Benefits of Whole Grain Phytochemicals

A whole grain consists of the intact, ground, cracked, or flaked caryopsis, whose principal anatomical components—the starchy endosperm, germ, and bran—are present in the same relative proportions as they exist in the intact caryopsis. Whole grain food products can be intact, consisting of the original composition of bran, germ, and endosperm, throughout the entire lifetime of the product, or reconstituted, in which one or more of the original components of a whole grain is recombined to the relative proportion naturally occurring in the grain kernel. Increased consumption of whole grains has been associated with reduced risk of major chronic diseases including cardiovascular disease, type II diabetes, and some cancers. Whole grain foods offer a wide range of phytochemicals with health benefits that are only recently becoming recognized. The unique phytochemicals in whole grains are proposed to be responsible for the health benefits of whole grain consumption. In this paper, whole grain phytochemicals and the health benefits associated with their consumption are reviewed.
Infrared spectra of methanol, ethanol, and n-propanol

The infrared absorption spectra of methanol, ethanol, and n-propanol have been measured with prism instruments. Studies have been made of the vapors and of several dilute solutions. The methanol spectra, between 2 to 15 microns, prpvided a direct comparison with the other two alcohols and confirmed earlier work on the existence of a number of lowintensity bands. The two other alcohols were studied from 2 to 36 microns. The bands have been classified in relation to the O —H, C —H, C —O, and C —C vibrations within the molecules. The long-wave absorption, in the region beyond 30 microns, for each alcohol, is attributed to the hindered rotation of OH. The object of the present study was to confirm the assignments for methanol and to study and assign the vibrational spectra of ethanol and n-propanol.
Inhibition of CDKs: A Strategy for Preventing Kainic Acid‐Induced Apoptosis in Neurons

Abstract: Stimulation of ionotropic glutamate receptors are implicated in neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Recently this has been demonstrated in the expression of cell cycle proteins in vulnerable neurons in Alzheimer's disease. Thus, the aim of the present study was to evaluate the expression of cell cycle proteins in cerebellar granule cells after stimulation of AMPA/KA receptors and likewise to study the neuroprotective effects of CDK inhibitors. Our results demonstrated that after a treatment with CDK inhibitors, a significant decrease in apoptotic nuclei induced by kainic acid was found in the presence of flavopiridol and 3‐ATA. We concluded that CDK activation is involved, at least, in part, in the pro‐apoptotic effects of kainic acid.
Explanation-Based Approximate Weighted Model Counting for Probabilistic Logics

Probabilistic inference can be realized using weighted model counting. Despite a lot of progress, computing weighted model counts exactly is still infeasible for many problems of interest, and one typically has to resort to approximation methods. We contribute a new bounded approximation method for weighted model counting based on probabilistic logic programming principles. Our bounded approximation algorithm is an anytime algorithm that provides lower and upper bounds on the weighted model count. An empirical evaluation on probabilistic logic programs shows that our approach is effective in many cases that are currently beyond the reach of exact methods.
Multiscale Reaction-Diffusion Algorithms: PDE-Assisted Brownian Dynamics

Two algorithms that combine Brownian dynamics (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the domain, whilst making use of a mean-field reaction-diffusion PDE description elsewhere. The first PBD algorithm couples BD simulations with PDEs by randomly creating new particles close to the interface, which partitions the domain, and by reincorporating particles into the continuum PDE-description when they cross the interface. The second PBD algorithm introduces an overlap region, where both descriptions exist in parallel. It is shown that the overlap region is required to accurately compute variances using PBD simulations. Advantages of both PBD approaches are discussed and illustrative numerical examples are presented.
Separating Operational and Control Behaviors: A New Approach to Web Services Modeling

The ability to develop flexible business applications is one of the ultimate objectives behind the use of Web services. Before taking part in such applications, each Web service should be modeled so that service engineers can monitor its execution and identify and address design problems early on. The authors propose a novel approach for modeling Web services that distinguishes operational behavior, which defines the business logic underpinning the Web service's functioning, and control behavior, which guides the operational behavior's execution progress by identifying the actions to take and the constraints to satisfy. The authors' prototype system assists service engineers in specifying, enforcing, and monitoring these behaviors, thereby achieving a better design.