Miracle-dz/UniFAR-FTUs huggingface dataset:
AcconPred: Predicting Solvent Accessibility and Contact Number Simultaneously by a Multitask Learning Framework under the Conditional Neural Fields Model

Motivation. The solvent accessibility of protein residues is one of the driving forces of protein folding, while the contact number of protein residues limits the possibilities of protein conformations. The de novo prediction of these properties from protein sequence is important for the study of protein structure and function. Although these two properties are certainly related with each other, it is challenging to exploit this dependency for the prediction. Method. We present a method AcconPred for predicting solvent accessibility and contact number simultaneously, which is based on a shared weight multitask learning framework under the CNF (conditional neural fields) model. The multitask learning framework on a collection of related tasks provides more accurate prediction than the framework trained only on a single task. The CNF method not only models the complex relationship between the input features and the predicted labels, but also exploits the interdependency among adjacent labels. Results. Trained on 5729 monomeric soluble globular protein datasets, AcconPred could reach 0.68 three-state accuracy for solvent accessibility and 0.75 correlation for contact number. Tested on the 105 CASP11 domain datasets for solvent accessibility, AcconPred could reach 0.64 accuracy, which outperforms existing methods.
Higher Levels of Immersion Improve Procedure Memorization Performance

Researchers have proposed that immersion could have advantages for tasks involving abstract mental activities, such as conceptual learning; however, there are few empirical results that support this idea. We hypothesized that higher levels of immersion would benefit such tasks if the mental activity can be mapped to objects or locations in a 3D environment. To investigate this hypothesis, we performed an experiment in which participants memorized procedures in a virtual environment and then attempted to recall those procedures. We aimed to understand the effects of three components of immersion on performance. Results demonstrate that a matched software field of view (SFOV), a higher physical FOV, and a higher field of regard (FOR) all contributed to more effective memorization. The best performance was achieved with a matched SFOV and either a high FOV or a high FOR, or both. In addition, our experiment demonstrated that memorization in a virtual environment could be transferred to the real world. The results suggest that, for procedure memorization tasks, increasing the level of immersion even to moderate levels, such as those found in head-mounted displays (HMDs) and display walls, can improve performance significantly compared to lower levels of immersion.
The Use of Labanotation for Choreographing a Noh-Play

This paper aims at description and reproduction of the body motion of stylized traditional dances by using fundamental elements of Labanotation while keeping the quality of body movement of CG character animation. We propose and implement a dynamic template technique enabling users to notate stylized traditional dances and reproducing it in 3D CG animation from a Labanotation score.
Interpreting noun compounds using paraphrases

Noun compounds are abundant in English and their interpretation is crucial for many natural language processing tasks. We propose a method for automatic two-noun noun compound interpretation that searches for suitable paraphrases in static corpora and then issues Web search engine queries to validate them. Native speakers were recruited to evaluate the returned paraphrases for noun compounds: those ranked first, second and third received an average score of 3.1842, 2.7687 and 2.5583 (on a scale of 1 to 5), respectively, which is considered promising given the difficulty of the task.
Optimal control for Wheeled Mobile Vehicles based on Cell Mapping techniques

The aim of this paper has been to integrate the kinematics and dynamic spaces in only one mathematical model, suitable to employ the cell-mapping technique in order to obtain the minimum-time solution to the optimal motion planning of a wheeled mobile vehicle. Through transformation of the cell-to-cell transitions the time spent in the knowledge of the vehicle dynamics and environment has been notably reduced. Four state variables have been considered: the velocity of the vehicle, X and Y Cartesian coordinates and the orientation of the vehicle. Also, two different control actions can act on the vehicle: the traction torque used for speeding up/braking the vehicle and the steering angle. The results show the applicability of the proposed algorithm in environments with presence of obstacles.
Population genetics of Galápagos land iguana (genus Conolophus) remnant populations

The Galápagos land iguanas (genus Conolophus) have faced significant anthropogenic disturbances since the 17th century, leading to severe reduction of some populations and the extinction of others. Conservation activities, including the repatriation of captive‐bred animals to depleted areas, have been ongoing since the late 1970s, but genetic information has not been extensively incorporated. Here we use nine species‐specific microsatellite loci of 703 land iguanas from the six islands where the species occur today to characterize the genetic diversity within, and the levels of genetic differentiation among, current populations as well as test previous hypotheses about accidental translocations associated with early conservation efforts. Our analyses indicate that (i) five populations of iguanas represent distinct conservation units (one of them being the recently discovered rosada form) and could warrant species status, (ii) some individuals from North Seymour previously assumed to be from the natural Baltra population appear related to both Isabela and Santa Cruz populations, and (iii) the five different management units exhibit considerably different levels of intrapopulation genetic diversity, with the Plaza Sur and Santa Fe populations particularly low. Although the initial captive breeding programmes, coupled with intensive efforts to eradicate introduced species, saved several land iguana populations from extinction, our molecular results provide objective data for improving continuing in situ species survival plans and population management for this spectacular and emblematic reptile.
Nucleation Control for Large, Single Crystalline Domains of Monolayer Hexagonal Boron Nitride via Si-Doped Fe Catalysts

The scalable chemical vapor deposition of monolayer hexagonal boron nitride (h-BN) single crystals, with lateral dimensions of ∼0.3 mm, and of continuous h-BN monolayer films with large domain sizes (>25 μm) is demonstrated via an admixture of Si to Fe catalyst films. A simple thin-film Fe/SiO2/Si catalyst system is used to show that controlled Si diffusion into the Fe catalyst allows exclusive nucleation of monolayer h-BN with very low nucleation densities upon exposure to undiluted borazine. Our systematic in situ and ex situ characterization of this catalyst system establishes a basis for further rational catalyst design for compound 2D materials.
Design and Implementation of Adaptive Streaming Modules for Multipoint Video Communication

We've developed a middleware system for multipoint video communication on interconnected computer networks, which is able to use several audio video formats and transcode formats as necessary. The system is based on mobile agent technique and able to support multipoint video communication event with consideration of users' communication environments. In this paper, we describe design and implementation of adaptive streaming modules for multipoint video communication in our middleware system. By using the streaming modules in the middleware, it is able to use functions for processing WMV (Windows Media Video), DV (Digital Video) and HDV (High Definition Video) on multipoint video communication.
Validation of an Ion Torrent Sequencing Platform for the Detection of Gene Mutations in Biopsy Specimens from Patients with Non-Small-Cell Lung Cancer

Background Treatment for patients with advanced non-small cell lung cancer (NSCLC) is often determined by the presence of biomarkers that predict the response to agents targeting specific molecular pathways. Demands for multiplex analysis of the genes involved in the pathogenesis of NSCLC are increasing. Methods We validated the Ion Torrent Personal Genome Machine (PGM) system using the Ion AmpliSeq Cancer Hotspot Panel and compared the results with those obtained using the gold standard methods, conventional PCR and Sanger sequencing. The cycleave PCR method was used to verify the results. Results and Conclusion The Ion Torrent PGM resulted in a similar level of accuracy in identifying multiple genetic mutations in parallel, compared with conventional PCR and Sanger sequencing; however, the Ion Torrent PGM was superior to the other sequencing methods in terms of increased ease of use, even when taking into account the small amount of DNA that was obtained from formalin-fixed paraffin embedded (FFPE) biopsy specimens.
Models for an Energy-Efficient P2P Delivery Service

Data and service delivery have been historically based on a ''network centric'' model, with datacentres being the focal sources. The amount of energy consumed by these datacentres has become an emerging issue for the companies operating them. Thus, many contributions have proposed solutions to improve the energy efficiency of current datacentre architecture and deployments. A recently proposed approach argues for removing the datacentres from the delivery architecture. Their functionalities will instead be distributed at the edge of the network, directly within operator-managed home devices, such as Home Gateways, or Set-Top-Box (STB). This paper presents a study of the overall energy consumption required by such a community of STBs in order to provide the same services as datacentres. This paper also investigates a possible distributed algorithm to further reduce this overall energy consumption. This algorithm will be deployed over a managed peer-to-peer network of STBs. It will make optimized decisions and instruct unused STBs to switch Off to save energy without altering the general Service Level Agreement. We demonstrate the potential benefit of such an algorithm through an off-line scheduling. Finally, we propose a service-delivery model that allows us to integrate the service availability in the energy optimization problem. The combination of these two models is the first step in the development of our energy optimisation distributed algorithm.
Effect of pulmonary rehabilitation on muscle remodelling in cachectic patients with COPD

It is known that non-cachectic patients with chronic obstructive pulmonary disease (COPD) respond well to pulmonary rehabilitation, but whether cachectic COPD patients are capable of adaptive responses is both important and unknown. 10 cachectic and 19 non-cachectic COPD patients undertook high-intensity cycling training, at the same relative intensity, for 45 min·day−1, 3 days·week−1 for 10 weeks. Before and after rehabilitation vastus lateralis muscle biopsies were analysed morphologically and for the expression of muscle remodelling factors (insulin-like growth factor (IGF)-I, myogenic differentiation factor D (MyoD), tumour necrosis factor (TNF)-α, nuclear factor (NF)-&kgr;B and myostatin) and key components of ubiquitin-mediated proteolytic systems (muscle ring finger protein (MURF)-1 and Atrogin-1). Rehabilitation improved peak work-rate and the 6-min walk distance similarly in non-cachectic (18±3% and 42±13 m, respectively) and cachectic (16±2% and 53±16 m, respectively) patients, but quality of life only improved in non-cachectic COPD. Mean muscle fibre cross-sectional area increased in both groups, but significantly less in cachectic (7±2%) than in non-cachectic (11±2%) patients. Both groups equally decreased the proportion of type IIb fibres and increased muscle capillary/fibre ratio. IGF-I mRNA expression increased in both groups, but IGF-I protein levels increased more in non-cachectic COPD. MyoD was upregulated, whereas myostatin was downregulated at the mRNA and protein level only in non-cachectic patients. Whilst rehabilitation had no effect on TNF-α expression, it decreased the activation of the transcription factor NF-&kgr;B in both groups by the same amount. Atrogin-1 and MURF-1 expression were increased in cachectic COPD, but it was decreased in non-cachectic patients. Cachectic COPD patients partially retain the capacity for peripheral muscle remodelling in response to rehabilitation and are able to increase exercise capacity as much as those without cachexia, even if they exhibit both quantitative and qualitative differences in the type of muscle fibre remodelling in response to exercise training.
2-Phase 2-stage capacitor-less gate driver for Gallium Nitride Gate Injection Transistor for reduced gate ringing

Increasingly stringent requirements for higher power density and efficiency have driven development for lower on-resistance (Ron) and gate charge (Qg) power transistors. Gallium Nitride (GaN) and Silicon Carbide (SiC) are good contenders for replacing conventional Si power transistors. This work attempts to develop a driver IC to fulfil specific needs of Gallium Nitride Gate Injection Transistor (GIT), which is a non-insulated gate enhancement mode GaN power transistor. In order to supply a forward gate current, a two stage driver is a strong contender to resolve this issue. The application of GaN GITs typically target applications where the slew rates are required to be high. High slew rate results in ringing and current clamping at the gate. This project proposes a 2-phase circuit to reduce the gate ringing. Simulation is conducted to verify the design and the proposed design demonstrates reduction in gate ringing.
Visual primes and EU identity: designing experimental research

There has been considerable attention paid to the role of symbols in forging identification with and support for the European Union (Bruter 2003, 2009; Laffan 1996; Manners 2011; Mclaren 2006; Shore 2000). Detailed empirical analysis is still, however, required of the following: i) the extent to which such symbols carry implicit messages about European Union identity; ii) the type of messages that different symbols convey; iii) the effect that exposure to these symbols in different contexts might have on political preferences. The authors employed an experimental approach to establish the extent to which implicit visual reminders of EU membership, from images of ceremonial flags to more mundane, functional symbols (like passports and driving licences), prime particular - affective or instrumental - associations, and how these associations may shape EU-related attitudes. Our motivation came from Billig’s (1995: 59) observation that: 'no one asks how many stars and stripes the average American is likely to encounter in the course of the day. Nor what is the effect of all this flagging. ' Our analysis sought to measure the effect of visual cues that prime the EU on attitudes to the European Union. This chapter discusses the theoretical puzzle addressed, the details of the research design, the contribution of this approach to our understanding of the nature and consequences of EU identity and potential further applications of this type of experimental approach in the field of EU studies.
INCAS: A Computation Model for Dynamic Workflows in Autonomous Distributed Environments

Awork ow is a long-durationmulti-step activity. The task of the work owmanager is to automate the execution and the control of the work ow activities. In this paper we are interested in work ows that execute under the control of various processing stations that may be located at di erent nodes of a distributed system. The stations may be autonomous and only partially automated. We present the design and a proposed implementation of a new model for work ow management. The model presented is modular in the sense that modi cation of a subactivities of the work ow does not necessarily require changes to the work ow speci cation. Furthermore, the model preserves the autonomy of the individual o ce environments and does not require them to modify the means they use to process the individual steps of the activity.
A novel ultrasonic image zooming algorithm based on sparse representation

In ultrasound imaging, it is usually needed to zoom in the B-mode image with high resolution. Therefore, a novel ultrasound image super-resolution zooming algorithm based on sparse representation was introduced in this paper. Sparse representation can achieve super-resolution reconstruction as long as the signal is sparse in certain dictionary. Simulation results show that our method outperforms the other methods not only on visual perception but also on edge protection.
The Angular dependence of the three point correlation function of the cosmic microwave background radiation as predicted by inflationary cosmologies

Inflationary models predict a definite, model-independent, angular dependence for the three-point correlation function of ΔT/T at large angles (≥1°) which we calculate. The overall amplitude is model dependent and generically unobservably small, but may be large in some specific models. We compare our results with other models of non-Gaussian fluctuations
Isolation and characterization of Clostridium difficile associated with beef cattle and commercially produced ground beef.

The incidence of Clostridium difficile infection has recently increased in North American and European countries. This pathogen has been isolated from retail pork, turkey, and beef products and reported associated with human illness. This increase in infections has been attributed to the emergence of a toxigenic strain designated North America pulsed-field gel electrophoresis type 1 (NAP1). The NAP1 strain has been isolated from calves as well as ground meat products, leading to speculation of illness from consumption of contaminated meat products. However, information on C. difficile associated with beef cattle during processing and commercially produced ground beef is limited. To address this data gap, samples from various steps during beef production were collected. Samples from hides (n = 525), preevisceration carcasses (n = 475), postintervention carcasses (n = 471), and 956 commercial ground beef samples were collected from across the United States. The prevalence of C. difficile spores on hides was 3.2%. C. difficile spores were not detected on preevisceration and postintervention carcasses or in commercially produced ground beef. Phenotypic and genetic characterizations were carried out for all 18 isolates collected from hide samples. Twenty-two percent of the isolates were nontoxigenic strains, while 78% of the isolates were toxigenic. Toxinotyping and PCR ribotyping patterns revealed that 6 and 33% of the isolates were identified as NAP1 and NAP7 strains, respectively. This article evidences that the prevalence of C. difficile, specifically pathogenic strains, in the U.S. beef production chain is low.
Questioning the Use of Outcome Measures to Evaluate Principal Preparation Programs

ABSTRACT Policymakers are proposing the use of outcome measures as indicators of effective principal preparation programs. The three most common metrics recommended are: (1) graduates’ effectiveness in improving student achievement test scores, (2) graduate job placement rates, and (3) principal job retention once employed. This article explores the use of these three measures as indicators of program effectiveness by reviewing existing empirical research, employing program evaluation methodology to review potential approaches, and applying program evaluation standards to the evaluation effort. We conclude that the effort to evaluate principal preparation programs using these outcome measures is far less accurate than policymakers assume.
THE ABDUS SALAM INTERNATIONAL CENTRE FOR THEORETICAL PHYSICS A SYMPLECTIC GENERALIZATION OF THE PERADZYŃSKI HELICITY THEOREM AND SOME APPLICATIONS

Symplectic and symmetry analysis for studying MHD superfluid flows is devised, a new version of the Z. Peradzyński [8] helicity theorem based on differential–geometric and group-theoretical methods is derived. Having reanalyzed the Peradzyński helicity theorem within the modern symplectic theory of differential–geometric structures on manifolds, a new unified proof and a new generalization of this theorem for the case of compressible MHD superfluid flow are proposed. As a by–product, a sequence of nontrivial helicity type local and global conservation laws for the case of incompressible superfluid flow, playing a crucial role for studying the stability problem under suitable boundary conditions, is constructed. MIRAMARE – TRIESTE December 2007 pryk.anat@ua.fm, prykanat@cybergal.com nikolai bogolubov@hotmail.com goljols@tlen.pl
Performance Analysis of Forward ErrorCorrection Codes used for Transmission of dataconsidering Failures in Coder/Decoder Circuits

Reliable and efficient transmission of data over a wireless network has been an increasing demand for the past few years. Whereas, major concern is the control of errors and to obtain reliable reproduction of data . This is achieved by using a variety of error control codes which improves BER performance in digital communication systems and are important in wireless information networks. Performance of Error correcting codes for a complete system analysis includes finding the reliability of coding and decoding circuits as this plays a significant role in undetected errors. Error Control Codes used in this paper evaluate their performance by computing the probability of not correcting an error. In general, the fact that the coder and decoder circuitry can also fail is neglected. This paper explains that under certain circumstances [e.g., low bit error rate and low data transmission rates (bits/sec), variable message bits] the chip failure probabilities can actually dominate and eliminate the gains achieved with coding. Some of the Error correcting codes like parity bit code, Hamming code and Reed Solomon code for various message lengths and different code rates including the effect of coding & decoding circuits is analysed. Finally the improvement ratio is calculated between probability of not correcting error without coding and with coding for 3 codes. Results reveal that for lengthy messages & at low data rates reliability of coding circuitry is of major importance in determining overall system performance. Comparison curves for the 3 codes with respect to different Baud rate is also established for system design
A method for testing the cosmic homogeneity with Shannon entropy

We propose a method for testing Cosmic homogeneity based on the Shannon entropy in Information theory and test the potentials and limitations of the method on Monte Carlo simulations of some homogeneous and inhomogeneous 3D point process in a finite region of space. We analyze a set of N-body simulations to investigate the prospect of determining the scale of homogeneity with the proposed method and show that the method could serve as an efficient tool for the study of homogeneity.