Miracle-dz/UniFAR-FTUs huggingface dataset:
A Semantic Infrastructure for the Integration of Bioinformatics Services

Web services integration has been a vigorous research area for the last years. With the introduction of the Semantic Web the publication of expressive metadata in a shared knowledge framework enables the deployment of services that can intelligently use web resources. Syntactic and semantic interoperability of services is crucial for services integration and complex scientific workflows creation. In this paper we propose a semantic based infrastructure for bioinformatics services integration that is designed and implemented in the context of the ACGT European project. This infrastructure features the integration of many different service registries in unified "meta-repository" and provides a knowledge based querying facility.
Practical aspects of monochromators developed for transmission electron microscopy

A few practical aspects of monochromators recently developed for transmission electron microscopy are briefly reviewed. The basic structures and properties of four monochromators, a single Wien filter monochromator, a double Wien filter monochromator, an omega-shaped electrostatic monochromator and an alpha-shaped magnetic monochromator, are outlined. The advantages and side effects of these monochromators in spectroscopy and imaging are pointed out. A few properties of the monochromators in imaging, such as spatial or angular chromaticity, are also discussed.
Event-Based Tone Mapping for Asynchronous Time-Based Image Sensor

The asynchronous time-based neuromorphic image sensor ATIS is an array of autonomously operating pixels able to encode luminance information with an exceptionally high dynamic range (>143 dB). This paper introduces an event-based methodology to display data from this type of event-based imagers, taking into account the large dynamic range and high temporal accuracy that go beyond available mainstream display technologies. We introduce an event-based tone mapping methodology for asynchronously acquired time encoded gray-level data. A global and a local tone mapping operator are proposed. Both are designed to operate on a stream of incoming events rather than on time frame windows. Experimental results on real outdoor scenes are presented to evaluate the performance of the tone mapping operators in terms of quality, temporal stability, adaptation capability, and computational time.
ORFEL: super-fast detection of defamation and illegitimate promotion in online recommendation

What if a successful company starts to receive a torrent of low-valued (one or two stars) recommendations in its mobile apps from multiple users within a short (say one month) period? Is it legitimate evidence that the apps have lost quality, or an intentional plan (via lockstep behavior) to steal market share through defamation? In case of a systematic attack to one's reputation, it might not be possible to manually discern between legitimate and fraudulent interaction in the immense universe of possibilities of user-product recommendation. Previous works have focused on this issue, but none of them has considered the context, modeling, and scale that we work with in this paper. We propose one novel method named Online-Recommendation Fraud ExcLuder (\ORFEL) to detect defamation and/or illegitimate promotion of online products using vertex-centric asynchronous parallel processing of bipartite (users-products) graphs. With an innovative algorithm, our results demonstrate efficacy -- detecting over $95\%$ of potential attacks; and efficiency -- at least two orders of magnitude faster than the state-of-the-art. Over our new methodology, we introduce three contributions: (1) a new algorithmic solution; (2) a scalable approach; and (3) a novel context and modeling of the problem, which now addresses both defamation and illegitimate promotion. Our work deals with relevant issues of the Web 2.0, potentially augmenting the credibility of online recommendation to prevent losses to both customers and vendors.
Alternations of phospholipid profile in placenta of streptozotocin‐induced diabetic rat

Phospholipids have important roles in many biological processes, but their role in fetal malformation in pregnancy in diabetes is unclear. Metabolic fingerprinting of placental phospholipids in pregnant streptozotocin‐induced type 1 diabetic rats was performed using Fourier transform‐ion cyclotron resonance mass spectrometry. Some of the fetuses from the pregnant diabetic rats exhibited ventricular septal defects. Alterations of phospholipid compositions in the diabetic rat placenta were detected. We suggest that these changes in phospholipids in the diabetic placenta might be involved in development of fetal malformation in a type 1 diabetic pregnancy.
From pre-recorded prompts to corporate voices: on the migration of interactive voice response applications

This paper describes our efforts towards the creation of corporate synthetic voices from low quality speech data, as it can typically be found on many Interactive Voice Response (IVR) units. In doing so, we first touch on several normalization techniques that aim on a better support of a highly automated voice construction process. Subsequently, we describe methods for the creation of enriched corporate voices which integrate speech recordings from different speakers in order to overcome problems arising from limited domain training data. Experiments are described which demonstrate the feasibility of the approach by comparing it to a less flexible solution that uses pre-recorded prompts in combination with a large footprint standard concatenative synthesizer. Results show that the enriched voices clearly outperform those voices build solely from IVR data, while achieving almost the same overall rating as the pre-recorded prompts solution.
GLOBAL REFORM OF PERSONAL INCOME TAXATION, 1981-2005: EVIDENCE FROM 189 COUNTRIES

We use a panel of 189 countries to describe trends in national personal income tax systems between the years 1981 and 2005. Using complete national income tax schedules, we show that tax rates at higher income levels, structural progressivity and the complexity of national tax systems have declined significantly; however, the degree of these changes varies considerably across countries. We also find that the relationship between tax rates and revenue is positive for high income countries but declines with weaker institutions and lower levels of economic development.
Cortical dysarthria and dysprosody of speech

The natuLre and indeed the existence of a syndrome of cortical dysarthria has been the subject of considerable argument in the past 50 years: some of it acri-monious, and much of it dissolving into semantic discussion. The matter has been concisely reviewed by Critchley (1952) in considering articulatory defects in aphasia. There is no doubt that whatever the descriptive term used occasional cases occur in which
Integrated single-arm assembly and manipulation planning using dynamic regrasp graphs

This paper presents an integrated single-arm assembly and motion planning algorithm to recursively find how to assemble two objects with the help of a plenary surface as the supporting fixture. The algorithm is done in both assembly level and motion level. In the assembly level, the algorithm checks all combinations of the assembly and gets a set of candidate assembly orders. For each assembly order, it performs motion planning to pick-and-place the base object and assemble the other object to the base. In the motion level, the algorithm integrates the orders computed in the assembly level incrementally and recursively with graph searching and motion planning, and finds a motion sequence to finish assembly tasks. The proposed algorithm can find a feasible solution to assemble two objects with completeness. It is practical and is ready to be integrated with force control to perform real-world assembly tasks.
Activity put in context: identifying implicit task context within the user's document interaction

Modern desktop search is ill-fitted to our personal document workspace. On one hand, many of the methods which render web search effective cannot be applied on the desktop. On the other, desktop search does not take full advantage of attributes that are unique to our personal documents. In this work, we present Confluence, a desktop search system that addresses this problem by capturing the task context within which a user interacts with their documents. This context is then integrated with traditional desktop search techniques to enable task-based document retrieval. Building upon Connections, a system that identifies task context by passively monitoring the user's interaction with their documents within the file system. Confluence also traces user activity within the user interface and incorporates methods to analyze and integrate this new stream of information. We show that this approach significantly improves the accuracy of task identification, achieving 25% to 30% better recall.
Layered elaboration: a new technique for co-design with children

As technology for children becomes more mobile, social, and distributed, our design methods and techniques must evolve to better explore these new directions. This paper reports on "Layered Elaboration," a co-design technique created to support these evolving needs. Layered Elaboration allows design teams to generate ideas through an iterative process in which each version leaves prior ideas intact while extending concepts. Layered Elaboration is a useful technique as it enables co-design to take place asynchronously and does not require much space or many resources. Our intergenerational team, including adults and children ages 7 -- 11 years old, used the technique to design both a game about history and a prototype of an instructional game about energy conservation.
A Cross Cultural Study of Online Shoppers in London and Bangkok

This paper reflects upon the qualitative data collected from cultural research evaluating the attitudes of online shoppers living in Bangkok and London. The study identified two negative aspects identified by both groups in respect of home delivery; having to make arrangements to wait for delivery (inconvenience), and returning unwanted products (time-consuming). Whilst a positive experience is reported by consumers up to the point of transaction, the research indicates that they will have a negative experience resulting from late or inconvenient delivery or issues related to the return of unwanted goods. Generally the positive features of online shopping (“usefulness”, “ease of use”, and “enjoyment”) appear to be more important to consumers than the negative features (“Internet security”, “privacy of personal information” and “post purchase fulfilment”). The online retailer would benefit from making the experience of shopping online more accommodating and more user-friendly, to encourage the high street shopper onto their site, and meet their expectations.
In-situ optical monitoring of silicon membrane etching

We present a simple yet efficient technique to obtain membrane with precise thickness by the etching of silicon in anisotropic etchant. This technique uses a mechanical holder to protect the front side of the wafer and a light signal to monitor from a distance the thickness of a reference hole in the etched wafer. The original feature in our set-up is that we measure the absorption of the light in two different bands of wavelength, one where the silicon is highly absorbant and the other where it is not, to improve the robustness of the measurement. This principle allows for effectively compensating for the fluctuation in the light source intensity, and provide real-time information on the membrane thickness, removing the incertitude inherent in the usual timed etch. We present the application of this technique to the manufacturing of thick single-crystal stiffener used to prevent the warp of stacked thin films presenting a gradient of stress.
Investigation of the Mechanism of Alloy Dendrite Deflection due to Flowing Melt by Phase-Field Simulation

Phase-field simulation of the dendrite growth of an Fe-0.15 mass%C binary alloy with fluid flow was carried out, and the mechanism of deflection of dendrites in the alloy system was examined. In the simulation, the primary arms growing in a flowing melt inclined toward the upstream direction, and the deflection angle increased with increase in flow velocity. Decrease in deflection angle with increase in growth velocity of the dendrite tip and accelerated growth of side branches were also observed in the simulation. These results of simulation were in good agreement with experimental results. The simulation showed that the change in the thermal field has little effect on the deflection and that the change in the solutal field is the main factor responsible for the deflection of a dendrite in an alloy system. The maximum deflection angle of a single dendrite in the simulation was less than 15°. The large deflection angles of grains (more than 20°-30°) in the experiments were thought to have been caused by nucleation in front of the dendrites and the subsequent competitive growth.
Universal Prediction with Other Losses

Thus far, in our discussion of universal prediction and related ideas, we have focused (essentially) exclusively on making predictions with the logarithmic loss, so that we play a full distribution over the set X as our prediction at each time step in the procedure. This is natural in settings, such as coding (recall examples 7.5 and 9.1), in which the log loss corresponds to a quantity we directly care about, or when we do not necessarily know much about the task at hand but rather wish to simply model a process. (We will see this more shortly.) In many cases, however, we have a natural task-specific loss. The natural question that follows, then, is to what extent it is possible to extend the results of Chapter 9 to different settings in which we do not necessarily care about prediction of an entire distribution. (Relevant references include the paper of Cesa-Bianchi and Lugosi [3], which shows how complexity measures known as Rademacher complexity govern the regret in online prediction games; the book by the same authors [4], which gives results covering a wide variety of online learning, prediction, and other games; the survey by Merhav and Feder [12]; and the study of consequences of the choice of loss for universal prediction problems by Haussler et al. [7].) 10.1 Redudancy and expected regret We begin by considering a generalization of the redundancy (9.1.3) to the case in which we do not use the log loss. In particular, we have as usual a space X and a loss function ℓ : X × X → R, where ℓ(x, x) is the penalty we suffer for playing x when the instantaneous data is x. (In somewhat more generality, we may allow the loss to act on X × X , where the prediction space X may be different from X .) As a simple example, consider a weather prediction problem, where X i ∈ {0, 1} indicates whether it rained on day i and X i denotes our prediction of whether it will rain. Then a natural loss includes ℓ(x, x) = 1 { x · x ≤ 0}, which simply counts the number of mistaken predictions.
Spatially mapping the elastic properties of the lens using bubble-based acoustic radiation force

Bubble-based acoustic radiation force has been used to measure highly localized tissue viscoelastic properties. In the current study, we use acoustic radiation force applied to laser- induced bubbles to measure the spatial distribution of elastic properties in explanted porcine lenses. A potential in vivo technique to map lens elasticity is crucial to understanding the onset of presbyopia and guiding surgical procedures to restore accommodation. Current techniques to measure lens stiffness are primarily ex vivo procedures requiring lens sectioning to achieve spatial localization. Bubble-based acoustic radiation force can measure the spatial elasticity distribution without disrupting the lens capsule or significantly altering intervening tissue. Microbubbles were generated using laser-induced optical breakdown (LIOB) laterally along the equator of explanted porcine lenses with 1 mm spacing. Optical breakdown occurs when sufficiently high threshold fluence is attained at the focus of femtosecond pulsed lasers, inducing plasma formation and bubble generation. 18 uJ laser pulses from a 800 fs Nd:glass laser generated microbubbles. Optical microscopy provided feedback on bubble size, shape, and lifetime. A two-element confocal ultrasonic transducer applied 6.7 ms acoustic radiation force- tone bursts with the 1.5 MHz outer element while monitoring bubble displacement within the lens using the 7.44 MHz inner element. Bubble displacements found in the lens nucleus were larger than those in the lens cortex, suggesting that the nucleus is stiffer than the cortex. Bubble lifetime, the duration from creation until collapse, also correlated with local lens stiffness. LIOB bubbles not exposed to acoustic radiation force excitation demonstrate much longer lifetimes in the lens nucleus in the lens cortex. This result is consistent with previous findings that longer bubble lifetimes occur in stiffer materials. Both bubble displacements and lifetimes are symmetric about the lens center, as expected, and predict that the porcine lens nucleus is several times stiffer than the lens cortex. Bubble-based acoustic radiation force appears well-suited as a potential in vivo technique to spatially map the elastic properties of the lens.
Performance of Gene Name Recognition Tools on Patents

The accurate identification of gene and protein names in patents is an essential step in many commercially highly relevant applications, such as patent retrieval, prior art search, or patent classification. Since patents exhibit a number of properties that make them quite different from scientific articles, it is questionable whether tools developed for the latter sort of texts will work equally well for the former. Answering this question is aggravated by the fact that only few annotated patent corpora exist which makes training hard. In this paper, we report on a comparative evaluation of four existing gene/protein named entity recognition and normalization tools trained on scientific articles regarding their performance on the two patent corpora. We analyze the tools with respect to different evaluation metrics to highlight their respective strengths and limitations. Our results reveal that the performances of these tools over patents are generally lower than for scientific articles. Exemplified by one of the four tools, we also show that training on annotated patents considerably improves performance on patent corpora. We conclude that more efforts must be taken to produce adequate training data for working with patents. keywords: Patent Mining, Named Entity Recognition, Named Entity Normalization, Gene and Protein Entities, Performance Measurements.
Positive Mode LC-MS/MS Analysis of Chondroitin Sulfate Modified Glycopeptides Derived from Light and Heavy Chains of The Human Inter-α-Trypsin Inhibitor Complex*

The inter-α-trypsin inhibitor complex is a macromolecular arrangement of structurally related heavy chain proteins covalently cross-linked to the chondroitin sulfate (CS) chain of the proteoglycan bikunin. The inter-α-trypsin inhibitor complex is abundant in plasma and associated with inflammation, kidney diseases, cancer and diabetes. Bikunin is modified at Ser-10 by a single low-sulfated CS chain of 23–55 monosaccharides with 4–9 sulfate groups. The innermost four monosaccharides (GlcAβ3Galβ3Galβ4Xylβ-O-) compose the linkage region, believed to be uniform with a 4-O-sulfation to the outer Gal. The cross-linkage region of the bikunin CS chain is located in the nonsulfated nonreducing end, (GalNAcβ4GlcAβ3)n, to which heavy chains (H1-H3) may be bound in GalNAc to Asp ester linkages. In this study we employed a glycoproteomics protocol to enrich and analyze light and heavy chain linkage and cross-linkage region CS glycopeptides derived from the IαI complex of human plasma, urine and cerebrospinal fluid samples. The samples were trypsinized, enriched by strong anion exchange chromatography, partially depolymerized with chondroitinase ABC and analyzed by LC-MS/MS using higher-energy collisional dissociation. The analyses demonstrated that the CS linkage region of bikunin is highly heterogeneous. In addition to sulfation of the Gal residue, Xyl phosphorylation was observed although exclusively in urinary samples. We also identified novel Neu5Ac and Fuc modifications of the linkage region as well as the presence of mono- and disialylated core 1 O-linked glycans on Thr-17. Heavy chains H1 and H2 were identified cross-linked to GalNAc residues one or two GlcA residues apart and H1 was found linked to either the terminal or subterminal GalNAc residues. The fragmentation behavior of CS glycopeptides under variable higher-energy collisional dissociation conditions displays an energy dependence that may be used to obtain complementary structural details. Finally, we show that the analysis of sodium adducts provides confirmatory information about the positions of glycan substituents.
Tetraarsenictetrasulfide and Arsenic Trioxide Exert Synergistic Effects on Induction of Apoptosis and Differentiation in Acute Promyelocytic Leukemia Cells

Since arsenic trioxide (As3+) has been successfully used in the treatment of acute promyelocytic leukemia (APL), its adverse effects on patients have been problematic and required a solution. Considering the good therapeutic potency and low toxicity of tetraarsenictetrasulfide (As4S4) in the treatment of APL, we investigated the effects of combining As4S4 and As3+ on the apoptosis and differentiation of NB4 and primary APL cells. As4S4, acting similarly to As3+, arrested the G1/S transition, induced the accumulation of cellular reactive oxygen species, and promoted apoptosis. Additionally, low concentrations of As4S4 (0.1–0.4 μM) induced differentiation of NB4 and primary APL cells. Compared with the As4S4- or As3+-treated groups, the combination of As4S4 and As3+ obviously promoted apoptosis and differentiation of NB4 and primary APL cells. Mechanistic studies suggested that As4S4 acted synergistically with As3+ to down-regulate Bcl-2 and nuclear factor-κB expression, up-regulate Bax and p53 expression, and induce activation of caspase-12 and caspase-3. Moreover, the combination of low concentrations of As4S4 and As3+ enhanced degradation of the promyelocytic leukemia-retinoic acid receptor α oncoprotein. In summary, As4S4 and As3+ synergistically induce the apoptosis and differentiation of NB4 and primary APL cells.
Graph Storage : How good is CSR really ?

In the last decade, the data size is growing exponentially and processing those data is becoming a difficult problem. Nowadays researchers and industry have been interested in the analysis of the graph to get deep understanding of social networks. Many of these graphs used in industry have become very large, containing hundreds of millions of nodes and edges. In this paper, I compare Compressed Sparse Row(CSR) as a fast graph container to Adjacency List(AL) in terms of latency and memory consumption. My CSR implementation also supports updates on graph. On a static graph, CSR gives up to 3x better performance over AL Implementation on Depth-First-Search(DFS) and Breadth-First-Search(BFS) and sometimes better performance on Dijkstra algorithm(Shortest path).