Miracle-dz/UniFAR-FTUs huggingface dataset:
Feature Mining and Integration for Improving the Prediction Accuracy of Translation Initiation Sites in Eukaryotic mRNAs

Accurate prediction of translation initiation sites (TISs) is important for the annotation of genomes. Although many methods have been proposed to solve this problem, the prediction accuracy is still limited. In this paper, the features that have been widely used for predicting TISs are further analyzed, and it is found that some features of TISs and non-TISs are heavily dependent on the C+G content of sequences around AUG codons, and some features are quite different for non-TISs located in untranslated regions and coding regions considering different reading frames. Further, the strategy of using multiple support vector machines to fully make use of the information is proposed, and a new program TISKey for the prediction of TISs is developed. Testing results on widely used dataset demonstrate that TISKey could get better prediction accuracy. TISKey can be accessed at http://infosci.hust. edu.cn
Infrared helium–hydrogen line ratios as a measure of stellar effective temperature

We have observed a large sample of compact planetary nebulae in the near-infrared to determine how the 21P–21S He i line at 2.058 μm varies as a function of stellar effective temperature, Teff. The ratio of this line with H i Brγ at 2.166 μm has often been used as a measure of the highest Teff present in a stellar cluster, and hence of whether there is a cut-off in the stellar initial mass function at high masses. However, recent photoionization modelling has revealed that the behaviour of this line is more complex than previously anticipated. Our work shows that in most aspects the photoionization models are correct. In particular, we confirm the weakening of the 21P–21S line as Teff increases beyond 40 000 K. However, in many cases the model underpredicts the observed ratio when we consider the detailed physical conditions in the individual planetary nebulae. Furthermore, there is evidence that there is still significant 21P–21S He i line emission even in the planetary nebulae with very hot central stars. It is clear from our work that this ratio cannot be considered as a reliable measure of effective temperature on its own.
Opening Up the Participation Laboratory

How to embed reflexivity in public participation in techno-science and to open it up to the agency of publics are key concerns in current debates. There is a risk that engagements become limited to “laboratory experiments,” highly controlled and foreclosed by participation experts, particularly in upstream techno-sciences. In this paper, we propose a way to open up the “participation laboratory” by engaging localized, self-assembling publics in ways that respect and mobilize their ecologies of participation. Our innovative reflexive methodology introduced participatory methods to public engagement with upstream techno-science, with the public contributing to both the content and format of the project. Reflecting on the project, we draw attention to the largely overlooked issue of temporalities of participation, and the co-production of futures and publics in participation methodologies. We argue that many public participation methodologies are underpinned by the open futures model, which imagines the future as a space of unrestrained creativity. We contrast that model with the lived futures model typical of localized publics, which respects latency of materials and processes but imposes limits on creativity. We argue that to continue being societally relevant and scientifically important, public participation methods should reconcile the open future of research with the lived futures of localized publics.
Design of Obstacle Avoidance System for Mobile Robot using Fuzzy Logic Systems

There were many reports about an obstacle avoidance of a mobile robot. In this paper, we design a fuzzy logic system and propose an obstacle avoidance algorithm for a path planning in unknown environment for a mobile robot. The ultrasonic sensors are employed for detecting the distance to obstacles and their positions. An angular velocity control for left and right wheels is implemented by a fuzzy logic system. We here propose another new rule table that is induced from the consideration of the distance to obstacles and the angle between the robot and the goal. Some simulation results show that the proposed method generates a good path with avoiding obstacles and has faster travelling time.
Design, implementation and validation of a simulation tool for Networked Virtual Environments

The popularisation of Networked Virtual Environment (NVE) applications in several context, including social interaction and e-Health fields, makes them an interesting subject of study. The proper estimation of their network requirements are key to ensure a good user experience, an important factor that determines the acceptance and success of the applications. The studies focused on NVE with an important social component are relatively scarce. This paper presents the design, implementation and validation of a simulation tool to assist in the study of the requirements of a NVE application, Open Wonderland. This tool will facilitate the study of several parameters that define the user experience. The study describes the overall structure, development framework and models that define the traffic generation patterns and validates the simulation results by comparing its traces with real traffic from previous studies.
Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin

Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments.
Counter-Based Cache Replacement and Bypassing Algorithms

Recent studies have shown that, in highly associative caches, the performance gap between the least recently used (LRU) and the theoretical optimal replacement algorithms is large, motivating the design of alternative replacement algorithms to improve cache performance. In LRU replacement, a line, after its last use, remains in the cache for a long time until it becomes the LRU line. Such deadlines unnecessarily reduce the cache capacity available for other lines. In addition, in multilevel caches, temporal reuse patterns are often inverted, showing in the L1 cache but, due to the filtering effect of the L1 cache, not showing in the L2 cache. At the L2, these lines appear to be brought in the cache but are never reaccessed until they are replaced. These lines unnecessarily pollute the L2 cache. This paper proposes a new counter-based approach to deal with the above problems. For the former problem, we predict lines that have become dead and replace them early from the L2 cache. For the latter problem, we identify never-reaccessed lines, bypass the L2 cache, and place them directly in the L1 cache. Both techniques are achieved through a single counter-based mechanism. In our approach, each line in the L2 cache is augmented with an event counter that is incremented when an event of interest such as certain cache accesses occurs. When the counter reaches a threshold, the line ";expires"; and becomes replaceable. Each line's threshold is unique and is dynamically learned. We propose and evaluate two new replacement algorithms: Access interval predictor (AIP) and live-time predictor (LvP). AIP and LvP speed up 10 capacity-constrained SPEC2000 benchmarks by up to 48 percent and 15 percent on average (7 percent on average for the whole 21 Spec2000 benchmarks). Cache bypassing further reduces L2 cache pollution and improves the average speedups to 17 percent (8 percent for the whole 21 Spec2000 benchmarks).
Software Agents for Distributed Social Networking

Especially in the case of completely distributed or federated social networking platforms, multi-agent systems can play an important role. In particular, multi-agent systems have been used as (i) an underlying layer or a middleware for developing social networking platforms, (ii) a technology to increase the autonomous and intelligent behaviour of existing systems and (iii) a tool to develop simulation environments for studying both online and offline human social networks. In this paper we propose the integration of multi-agent technology into Blogracy, a novel peer-to-peer, anonymous and uncensurable social networking platform. The resulting system augments the platform with locality and proximity groups, making it fit for pervasive computing scenarios, exploiting the adaptivity, proactivity and negotiation ability of multi-agent systems. Distributed Micro-blogging, Peer-to-peer Computing, Social Networking, Multi-Agent Systems
Human hip joint center analysis for biomechanical design of a hip joint exoskeleton

We propose a new method for the customized design of hip exoskeletons based on the optimization of the humanmachine physical interface to improve user comfort. The approach is based on mechanisms designed to follow the natural trajectories of the human hip as the flexion angle varies during motion. The motions of the hip joint center with variation of the flexion angle were measured and the resulting trajectory was modeled. An exoskeleton mechanism capable to follow the hip center’s movement was designed to cover the full motion ranges of flexion and abduction angles, and was adopted in a lower extremity assistive exoskeleton. The resulting design can reduce human-machine interaction forces by 24.1% and 76.0% during hip flexion and abduction, respectively, leading to a more ergonomic and comfortable-to-wear exoskeleton system. The human-exoskeleton model was analyzed to further validate the decrease of the hip joint internal force during hip joint flexion or abduction by applying the resulting design.
Building bridges with words: an inferential account of ethical univocity

Abstract Explaining genuine moral disagreement is a challenge for metaethical theories. For expressivists, this challenge comes from the plausibility of agents making seemingly univocal claims while expressing incongruent conative attitudes. I argue that metaethical inferentialism – a deflationary cousin to expressivism, which locates meaning in the inferential import of our moral assertions rather than the attitudes they express – offers a unique solution to this problem. Because inferentialism doesn’t locate the source of moral disagreements in a clash between attitudes, but instead in conflicts between the inferential import of ethical assertions, the traditional problem for expressivism can be avoided. After considering two forms of inferentialism that lead to revenge versions of the problem, I conclude by recommending that we understand the semantics of moral disagreements pragmatically: the source of univocity does not come from moral or semantic facts waiting to be described, but instead from the needs that ethical and semantic discourses answer – a solution to the problems of what we are to do and how we are to talk about it.
Adiabatic Vacua and Hadamard States for Scalar Quantum Fields on Curved Spacetime

Quasifree states of a linear Klein-Gordon quantum field on globally hyperbolic spacetime man-ifolds are considered. Using techniques from the theory of pseudodifferential operators and wavefront sets on manifolds a criterion for a state to be an Hadamard state is developed. It is shown that ground-and KMS-states on certain static spacetimes and adiabatic vacuum states on Robertson-Walker spaces are Hadamard states. Finally, the problem of constructing Hadamard states on arbitrary curved spacetimes is solved in principle. Raumzeiten angegeben.
Evaluation of Versant Hepatitis C Virus Genotype Assay (LiPA) 2.0

ABSTRACT Hepatitis C virus (HCV) genotyping is a tool used to optimize antiviral treatment regimens. The newly developed Versant HCV genotype assay (LiPA) 2.0 uses sequence information from both the 5′ untranslated region and the core region, allowing distinction between HCV genotype 1 and subtypes c to l of genotype 6 and between subtypes a and b of genotype 1. HCV-positive samples were genotyped manually using the Versant HCV genotype assay (LiPA) 2.0 system according to the manufacturer's instructions. For the comparison study, Versant HCV genotype assay (LiPA) 1.0 was used. In this study, 99.7% of the samples could be amplified, the genotype of 96.0% of samples could be determined, and the agreement with the reference method was 99.4% when a genotype was determined. The reproducibility study showed no significant differences in performance across sites (P = 0.43) or across lots (P = 0.88). In the comparison study, 13 samples that were uninterpretable or incorrectly genotyped with Versant HCV genotype assay (LiPA) 1.0 were correctly genotyped by Versant HCV genotype assay (LiPA) 2.0. Versant HCV genotype assay (LiPA) 2.0 is a sensitive, accurate, and reliable assay for HCV genotyping. The inclusion of the core region probes in Versant HCV genotype assay (LiPA) 2.0 results in a genotyping success rate higher than that of the current Versant HCV genotype assay (LiPA) 1.0.
Continuous visual speech recognition for multimodal fusion

It is admitted that human speech perception is a multimodal process that combines both visual and acoustic informations. In automatic speech perception, visual analysis is also crucial as it provides a complementary information in order to enhance the performances of audio systems especially in highly noisy environments. In this paper, we propose a unified probabilistic framework for speech unit recognition that combines both visual and audio informations. The method is based on the optimization of a criterion that achieves continuous speech unit segmentation and decoding using a learned (joint) phonetic-visemic model. Experiments conducted on the standard LIPS2008 dataset, show a clear and a consistent gain of our multimodal approach compared to others.
Application of a Nonlinear Dynamic Method in the Analysis of the HRV (Heart Rate Variability) Towards Clinical Application: Tiresome Diagnosis

Heart rate variability (HRV) or the study of cardiac rhythm fluctuations has attracted the interest Of many physicists in the recent years for its potential predictive value. The extracted and analyzed heart rate variability signal parameters, are highly useful in diagnostics. The HRV analysis is based on the concept that fast fluctuations may specifically reflect changes of sympathetic and vagal activity and may contain indicators Of current behavior, or even warnings about impending diseases. This work deals with the study of the ECG (electrocardiogram) and the application of a nonlinear dynamic method in the analysis of the HRV (heart rate variability) towards clinical application: Tiresome diagnosis. The analysis method adopted for this purpose: the DFA (detrended fluctuation analysis) which is a nonlinear dynamic method based on the quantification of fractal like correlation properties of the data, shows through the obtained results, its efficiency in the prediction field of the current and the future health behavior. The study is made by analyzing a group of 10 healthy cases practicing several activities. For each one 24 hours ECG (RR intervals) was recorded. Statistical analysis was performed by means of non parametric Mann-Whitney test. The analysis show plots shape depends on the current behavior and the toughness of the activity. Our study reveals that by using DFA method, we could quantitatively and qualitatively study the heart rate variability towards tiresome diagnosis
Mini-Column for Cytoadherence: A New Method for Measuring the Relative Size of Binding Subpopulations in Plasmodium falciparum Isolates

Background Cytoadherence of Plasmodium falciparum- infected red blood cells to endothelial cells is an important mechanism for parasite survival and a major trigger for diseases pathology. Here, we describe a new adhesion assay in which different cell types (CHO, CHO/CD36 and CHO/ICAM-1) are attached to Cytodex beads in a mini-column format to measure the relative sizes of various binding subpopulations as a percentage of the total population. Methods Relative size of CD36 and ICAM-1-binding subpopulations of erythrocytes infected with P. falciparum were measured by amount of parasitemia before and after passing the infected erythrocytes through a particular column. Results The mini-column adhesion assay was a suitable method as parasitemia always reduced after passing through a particular column in independent experiments. For example, in a typical experiment using P. falciparum ITG line, 75% of the parasites are retained on a CHO/ICAM-1 while 0% of clone 3D7 is retained. Conclusion This work introduced and validated a method for measuring the relative size of parasite binding subpopulations and the selection of them. Also, the mini-column method is of value for assessments of cytoadherence and can be used as tool for different applications.
Ovine clone ST1464: a predominant genotype of Staphylococcus aureus subsp. anaerobius isolated from sheep in Sudan.

BACKGROUND The aim of the present study was to examine the phenotypic and genotypic relatedness of 17 Staphylococcus aureus subsp. anaerobius isolates recovered from sheep abscesses in Khartoum state, Sudan, during the period 2007-2008. METHODOLOGY This sample was characterised using antibiogram typing, biochemical typing with the commercial PhenePlate system (PhP-CS) and multilocus sequence typing (MLST). RESULTS Low levels of resistance were noted to the 11 antimicrobial agents tested. All the isolates corresponded to a single PhP type, and to a single, novel, multilocus sequence type, designated ST1464. CONCLUSION These results demonstrate that the vast majority of cases of sheep abscess disease in Khartoum state are caused by a single novel clone of S. aureus subsp. anaerobius.
The effect of stellar activity on the Li I 6708, Na I 5896 and K I 7699 Ålines - A comparison with the Pleiades, field stars and the Sun

An analytical model has been developed to empirically study the eects of stellar spots and faculae on the observed equivalent widths of Li i 6708, Na i 5896 and K i 7699 A lines (and abundances in the case of lithium) in late-type stars, taking into account the changes in the observed magnitudes and colors. Solar spectra corresponding to dierent active regions are used as input data and a range of lling factors are applied to simulate the surfaces of stars with dierent levels of activity. Detailed comparisons between predicted and observed photometric colors and equivalent widths are made for late-type stars of the Pleiades and the eld. The observed dispersions in K i and Li i equivalent widths for Pleiades stars can be partially accounted by the simultaneous eects of activity on colors and the line formation, indicating that the lithium-rotation connection suggested for0:7 0:9 M Pleiades stars could be due in part to the stellar activity. However, under realistic values for the lling factors, only a small portion of the observed spread could be explained by these eects.
Modeling and Scheduling of Transactional Work ows

The transactional workkows (TWF) model can be regarded as a merging point of extended transaction models and general workkow model, it emphasizes both transactional aspect and business process aspect. In this report, we present a hierarchical approach for representing transactional workkows and discuss both transactional and business process aspects that a TWF should capture. We also introduce an execution model which allows us to reason about the correctness of a TWF, and to generate and execute TWF schedules.
A Simulation Times Model of Multi-core Simulation

Chip multi-processor (CMP) increases processor throughput by duplicating resources for many threads. Due to the main frequency of a single processor approaching to limit, CMP is becoming more and more popular. However, it is not well studied how to evaluate a new CMP design by simulation. This paper analyzes the possible organizations of cores on a CMP and then presents a mathematical model for the simulation times. It also provides a sampling policy used to reduce the simulation times. The sampling experiments show that the simulation time is 7.5 days under condition that the required confidence level is 95% and confidence interval is 4 when the benchmarks in SPEC CPU2000 are used. As for the simulation of CMPs, the simulation time is very short.
Syntactico Semantic Word Representations in Multiple Languages

Our project is an extension of the project “Syntactico Semantic Word Representations in Multiple Languages”[1]. The previous project aims to improve the semantical representation of English vocabulary via incorporating the local context with global context and supplying homonymy and polysemy for multiple embeddings per word. It also introduces a new neural network architecture that learns the word embeddings from both local and global context and multiple embeddings of each word with homonymy and polysemy. Based on this neural network learning model, our project learns the embeddings for German words and improves the semantical representation of German vocabulary. After the learning procedure, we produce a new dataset of German word embeddings and visualize them in t-SNE figures.
NoC Interconnect Yield Improvement Using Crosspoint Redundancy

Systems-on-chip integrate increasingly larger numbers of pre-designed cores interconnected through complex communication fabrics. For nanometer-scale VLSI processes (45 nm and below), it is difficult to guarantee correct fabrication with an acceptable yield without employing design techniques that take into account the intrinsic existence of manufacturing defects. In order to improve the yield and reliability of multi-core SoCs, their interconnect infrastructures must be designed such that fabrication and life-time faults can be tolerated. In this work we present a self-repair method for the interconnect fabrics of integrated multi-core systems. Our method is based on the use of redundant links and crosspoints, and improves both post-manufacturing yield and life-time reliability of on-chip communication fabrics. Our method can provide a significant interconnect yield improvement (up to 72% in our experiments), and allows fine-tuning of yield versus redundant components